Showing posts with label scRNAseq. Show all posts

Monday, March 24, 2025

Asian Immune Diversity Atlas (AIDA) CZI Cell Science

https://cellxgene.cziscience.com/collections/ced320a1-29f3-47c1-a735-513c7084d508

Asian Immune Diversity Atlas (AIDA)

CZI Cell Science

The relationships of human diversity with biomedical phenotypes are pervasive, yet remain understudied, particularly in a single-cell genomics context. Here we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA-sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 donors, spanning 7 population groups across 5 Asian countries, and 6 controls. Though population groups are frequently compared at the continental level, we found that sub-continental diversity, age, and sex pervasively impacted cellular and molecular properties of immune cells. These included differential abundance of cell neighbourhoods, as well as cell populations and genes relevant to disease risk, pathogenesis, and diagnostics. We discovered functional genetic variants influencing cell type-specific gene expression which were under-represented in non-Asian populations, and helped contextualise disease-associated variants. AIDA enables analyses of multi-ancestry disease datasets and facilitates the development of precision medicine efforts in Asia and beyond. Please note that the AIDA Phase 1 Data Freeze v1 object comprises 1,058,909 peripheral blood mononuclear cells from 503 healthy donors from Japan, Singapore, and South Korea alongside common controls. This first AIDA data freeze was released to the research community pre-publication, and was also part of the first CZ CELLxGENE Census assembled in May 2023. Going from Data Freeze v1 to Data Freeze v2, we added additional healthy Asian donor samples and control samples - please see our publications for further details.

Friday, March 14, 2025

AD Knowledge portal

https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyDetails?Study=syn18485175

study

The Single-cell transcriptomic analysis of Alzheimers disease (snRNAseqPFC_BA10) Study

Harvard University, Massachusetts Institute of Technology, Rush University

This study provides single-cell transcriptomic data from the prefrontal cortex from individuals sleceted from the Religious Orders Study and Memory and Aging Project (ROSMAP).

Data Types	Gene Expression
Study Focus	Alzheimer Disease
Specimen Type	Brain
Species	Human
Program	CDCP
Grant	RF1AG054321

from bulk sequence to scRNA

bulk RNAseq is cheap and easy to geneerate. scRNA is expensive but more inforamtive.

https://github.com/AI-in-Biomedical-Science/scaden

Friday, January 10, 2025

Profiling the transcriptomic age of single-cells in humans

https://zenodo.org/records/10405106

Data for "Profiling the transcriptomic age of single-cells in humans"

Wednesday, August 30, 2023

workflow for Seurat and Velocity

#workflow for Seurat and Velocity

#open Rstudio on VNC desktop

rstudio

library(Seurat)

#load in 10x data

sample1=Read10X(data.dir = 'path1')

sample2=Read10X(data.dir = 'path2')

#convert 10xdata into Seurat object

sample1.seurat=CreateSeuratObject(sample1, project = 'ID1')

sample2.seurat=CreateSeuratObject(sample2, project = 'ID2')

#calculate percent mito content

sample1.seurat[['percent.mt']]=PercentageFeatureSet(male5mo.seurat, pattern = 'mt-')

sample2.seurat[['percent.mt']]=PercentageFeatureSet(female5mo.seurat, pattern = 'mt-')

#show basic QC parameters for samples

VlnPlot(sample1.seurat, c('nCount_RNA','nFeature_RNA','percent.mt'), pt.size=0)

VlnPlot(sample2.seurat, c('nCount_RNA','nFeature_RNA','percent.mt'), pt.size=0)

#can filter based on top/bottoms of violins to remove outliers e.g.

sample1.seurat=subset(sample1.seurat, subset = nFeature_RNA > 200 & nCount_RNA <20000 & percent.mt <5)

sample2.seurat=subset(sample2.seurat, subset = nFeature_RNA > 500 & nCount_RNA <20000 & percent.mt <5)

#remake vlnplots to compare vs before

VlnPlot(male5mo.seurat, c('nCount_RNA','nFeature_RNA','percent.mt'), pt.size=0)

VlnPlot(female5mo.seurat, c('nCount_RNA','nFeature_RNA','percent.mt'), pt.size=0)

VlnPlot(male22mo.seurat, c('nCount_RNA','nFeature_RNA','percent.mt'), pt.size=0)

VlnPlot(female22mo.seurat, c('nCount_RNA','nFeature_RNA','percent.mt'), pt.size=0)

#normalise data

sample1.seurat <- NormalizeData(sample1.seurat, verbose = FALSE)

sample2.seurat <- NormalizeData(sample2.seurat, verbose = FALSE)

sample1.seurat <- FindVariableFeatures(sample1.seurat)

sample2mo.seurat <- FindVariableFeatures(sample2.seurat)

integ.anchors <- FindIntegrationAnchors(object.list = list(sample1.seurat, sample2.seurat))

combo.seurat <- IntegrateData(anchorset = integ.anchors)

# Run the standard workflow for visualization and clustering

combo.seurat <- ScaleData(combo.seurat, verbose = FALSE, vars.to.regress=c('nCount_RNA', 'nFeature_RNA', 'percent.mt'))

combo.seurat <- RunPCA(combo.seurat, verbose = FALSE)

# UMAP and Clustering

combo.seurat <- RunUMAP(combo.seurat, dims = 1:10)

combo.seurat <- FindNeighbors(combo.seurat)

combo.seurat <- FindClusters(combo.seurat)

combo.seurat$cluster_by_genotype = paste(Idents(combo.seurat), sep='_', combo.seurat$orig.ident)

DefaultAssay(combo.seurat)='RNA'

combo.seurat=CellCycleScoring(combo.seurat, s.features = stringr::str_to_title(cc.genes.updated.2019$s.genes), g2m.features = stringr::str_to_title(cc.genes.updated.2019$g2m.genes))

#command to find top enriched genes in each cluster vs all other cells is FindAllMarkers()

FindAllMarkers(combo.seurat, assay='RNA', only.pos=T)

#output is pasted in terminal, either save it to an object e.g. x=FindAllMarkers() or write it out into a text file

write.csv(FindAllMarkers(combo.seurat, assay='RNA', only.pos=T), file='combo_allmarkers.csv')

#command to compare two specific clusters is FindMarkers()

write.csv(FindMarkers(combo.seurat, group.by = 'cluster_by_genotype', ident.1 = '16_UOmet', ident.2 = '16_UOcont'), file='combo_cluster16_UOmet_v_UOcont_DEG.csv')

#group.by can be column name in combo.seurat$

#ident.1 and ident.2 must be set, if only ident.1 set then it compares against all other cells

#calculate Otsu threshold for gene, autothresholdr must use integers so multiple out all decimal places then divide back down

OtsuThresh = function(seurat_object, gene_name) {

library(autothresholdr)

array=as.integer(seurat_object@assays$RNA@data[gene_name,]*10000000)

auto_thresh(array, method='Otsu')[1]/10000000

}

Wednesday, June 15, 2022

genome wide pertub-seq

CRISPi + scRNA

https://gwps.wi.mit.edu/

matrix file in H5AD format

https://doi.org/10.25452/figshare.plus.20029387

Genome wide screen targeted n=9867 genes.

Essential-wide screen targeted n=2285 essential genes.

Growth phenotypes were measured log2-guide enrichment per cell doubling (gamma)

"The relative homogeneity of CRISPRi reduces selection for unperturbed cells, especially when studying essential genes. Unlike CRISPR knockout, CRISPRi does not lead to activation of the DNA damage response which can alter transcriptional signatures (Haapaniemi et al., 2018)."

"We use a compact, multiplexed CRISPR interference (CRISPRi) library to assay thousands of loss-of-function genetic perturbations with single-cell RNA sequencing (scRNA-seq) in chronic myeloid leukemia (CML) (K562) and retinal pigment epithelial (RPE1) cell lines."

There are four datasets on SRA:

K562 day 8 Perturb-seq (KD8): targeting all expressed genes at day 8 after transduction
RPE1 day 7 Perturb-seq (RD7): targeting DepMap essential genes at day 7 after transduction
K562 day 6 Perturb-seq (KD7): targeting DepMap essential genes at day 6 after transduction
K562 day 8 Perturb-seq (KD8_ultima): scRNA-seq libraries from the KD8 experiment sequenced on the Ultima sequencing platform rather than the Illumina sequencing platform

Potential problem: essential gene cannot be deleted?

This is good data set for graph controllability, graph neural network analysis.

Wednesday, April 27, 2022

Seurat scRNA normalisation

The default normalisation in Seurat is pretty simple - it simply scales the counts by the total counts in each cell, multiplies by 10,000 and then log transforms.

https://www.bioinformatics.babraham.ac.uk/training/10XRNASeq/seurat_workflow.html#Normalisation,_Selection_and_Scaling

Saturday, September 18, 2021

single cell RNA, human aging

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138544

It contained seq counts in a matrix.

reconstruct boolean networks

https://www.sciencedirect.com/science/article/pii/S2001037021003974?via%3Dihub

Friday, July 23, 2021

single cell transcriptomics with tidyverse

https://github.com/stemangiola/bioc_2020_tidytranscriptomics

https://github.com/stemangiola/tidySingleCellExperiment

Monday, May 24, 2021

FFQ

Python download meta information of SRA

https://github.com/pachterlab/ffq

Friday, April 2, 2021

Partek single cell analysis

https://www.partek.com/webinar-registration-follow-up/

Sunday, March 7, 2021

Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms

https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(21)00051-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1934590921000515%3Fshowall%3Dtrue

Single-cell transcriptome and whole-genome sequencing of HSPCs from individuals with MPNs

This paper use scRNA to detect somatic mutations. It showed tumor mutaiton occured dacades ago. The tumor cells have a selective growth advantage.

Thursday, February 25, 2021

single gene co-expression, scLink

using mixture Gamma + Normal to model single gene expression: Gamma is the noise and Normal is the signal!!

co-expression network were constrcuted using Gaussian method.

Reference:

https://www.biorxiv.org/content/10.1101/2020.09.19.304956v1.full.pdf

Tuesday, February 23, 2021

Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (ChIP-seq)

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104404

*** Ageing affects DNA methylation and transcriptional cell-to-cell variability in muscle stem cells [scRNA-seq]

Ageing affects DNA methylation and transcriptional cell-to-cell variability in muscle stem cells [scRNA-seq]

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121364

5 young and 3 old mice.

Hernando-Herraez I, Evano B, Stubbs T, Commere PH et al. Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells. Nat Commun 2019 Sep 25;10(1):4361. PMID: 31554804

Supplementary file	Size	Download	File type/resource
GSE121364_Table_raw_counts_RNA_QSC.txt.gz	2.0 Mb	(ftp)(http)	TXT
SRA Run Selector https://pubmed.ncbi.nlm.nih.gov/31554804/ This dataset provided a matrix, rows start with gene names eneName chr start lane3_Tom_Y4_TA_Hi_11_CTATCATG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam lane3_Tom_Y4_TA_Hi_12_TCTCAGTG_L003_22540_7$ Xkr4 1 3205901 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 $ Gm1992 1 3466587 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 $ Rp1 1 4343507 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0$ Sox17 1 4490928 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0$ Mrpl15 1 4773206 0 0 121 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 109 0 140 0 0 0 0 0 0 0 86 0 0 0 0 190 0 0 0 49 0 0 0 0 109 0 0 4 0 1 $ Lypla1 1 4807788 0 0 0 0 407 0 1 136 0 0 0 0 4 0 0 0 0 0 0 6 0 0 0 60 0 0 0 0 0 0 138 0 0 1 319 0 0 0 0 0 0 146 0 6 1 0 3 0 0 0 9 0 0$ Tcea1 1 4857814 69 0 0 0 290 3 5 0 0 0 0 0 18 0 0 6 86 0 0 237 0 72 0 0 0 0 0 0 0 0 73 0 0 3 2 0 0 120 0 0 0 6 0 20 147 0 126 0 0 6 2$ Gm6104 1 4879202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 $ Rgs20 1 4

The columns of these data sets are:

lanlane3_Tom_Y4_TA_Hi_11_CTATCATG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_12_TCTCAGTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_13_GCCTGCCC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_1_TTCCTGCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_23_CGCCTGAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_25_TTCCATTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_27_CTAGATAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_28_CCCATAGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_29_CGAGATCC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_30_GTATAGGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_31_TAAGGGTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_34_GAGCCAAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_35_CCGACAAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_36_GCTGTGAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_37_GCGCTGAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_38_AGTCCGAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_39_CCGTTAGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_43_CATAGGTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_44_ACAAAGCC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_45_GAGGGCAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_47_CCTACCCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_48_CATTTTGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_49_TCTCACGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_4_AATGAATT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_50_GTTGTCGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_51_CGCTAAGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_52_GCTGGACA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_53_GAGATGCC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_54_GTGTCTGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_55_TATACATC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_56_AGCAACGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_57_TAAGTTCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_58_GATAGAGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_59_CAGCTGAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_61_GCATCCGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_63_GAAGCGCA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_64_CGACCCTT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_68_TGCTCTAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_69_GAGGTCGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_71_GATTGCGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_72_GAGCGCAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_74_GCCTGTTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_75_CGTTACTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_77_TTTTACGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_79_ATCGTCCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_7_GGGTCCAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_80_CCGATGTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_81_TCAGATTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_82_GCTAACTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_83_CTCTCTCA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_84_ACTCTTTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_85_AGTGTAGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_87_CGCACCTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_88_CAAGGAGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_90_GTCTTGGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_91_CCTGAGCA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_92_TAAACATA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_93_AAATACTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_94_ATGCGTCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y4_TA_Hi_95_CGAATCGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_10_TCGTTAGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_12_AGGCAGCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_13_TGTCATCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_17_GCCAATGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_19_GGCACAAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_1_CGATGTTT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_20_AACGTGTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_21_AGTCCAAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_26_TTGCGTAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_27_GTGCAGTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_29_TCTGACGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_2_TATGTGGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_33_TAGCTTGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_34_TGACAGAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_36_ATCAACCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_37_GTCACGTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_41_CTTGTACT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_42_TCATCCTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_43_GTAACCGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_44_ACTGTTAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_45_GAGACATA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_49_TCTCGGTT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_4_CGGAGGAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_50_TAGACGGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_52_ATTCGGAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_57_TCCGTCTT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_5_TACCGCAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_60_ACAAGTGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_61_ACGGCAGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_65_TTCTGTGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_66_TGAAGCCA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_67_CGTTCGGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_68_AGAGGACC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_69_CGCCTTTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_73_TTGGAGGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_74_TGCGTGAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_75_CTGCGAGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_82_GATCTCTT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_83_CGCTTCCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_84_AGGATTCA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_91_CACACACT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_92_ACAACGCA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_93_TAGTCGGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y5_TA_Hi_9_TGACCACT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_10_GTACATCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_11_CTATCATG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_12_TCTCAGTG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_13_GCCTGCCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_14_TGGGTTGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_15_AATAGAGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_17_TGTGGTTG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_19_CCACTTGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_21_CTTGACCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_22_GACCGGAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_23_CGCCTGAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_26_GTCGCTAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_27_CTAGATAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_29_CGAGATCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_2_GGTCGTGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_30_GTATAGGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_31_TAAGGGTG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_34_GAGCCAAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_35_CCGACAAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_36_GCTGTGAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_37_GCGCTGAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_38_AGTCCGAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_39_CCGTTAGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_41_TGAACTGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_42_GTAAGGTG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_43_CATAGGTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_44_ACAAAGCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_45_GAGGGCAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_47_CCTACCCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_49_TCTCACGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_4_AATGAATT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_50_GTTGTCGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_51_CGCTAAGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_52_GCTGGACA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_53_GAGATGCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_54_GTGTCTGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_55_TATACATC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_57_TAAGTTCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_58_GATAGAGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_59_CAGCTGAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_5_ACGTACTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_60_CATCCGTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_61_GCATCCGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_62_CCGCATGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_63_GAAGCGCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_65_TGTATGCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_66_GCAATCCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_67_CGTGTCAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_68_TGCTCTAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_69_GAGGTCGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_6_TCTGGCGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_70_GTGGTACT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_71_GATTGCGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_73_TGGCTCAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_74_GCCTGTTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_75_CGTTACTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_77_TTTTACGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_78_TTACCTTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_79_ATCGTCCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_7_GGGTCCAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_81_TCAGATTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_82_GCTAACTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_83_CTCTCTCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_84_ACTCTTTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_85_AGTGTAGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_86_CTACGTAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_87_CGCACCTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_89_TTCAGCTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_91_CCTGAGCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_92_TAAACATA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_93_AAATACTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_94_ATGCGTCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_95_CGAATCGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_Y7_TA_Hi_9_TACAGGAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_10_GAATCTGT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_11_CTTCACAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_12_TAGGACCC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_13_AGCGCCAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_14_AATTTGCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_15_ATAACTAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_16_AGCGATGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_17_TCCTCAAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_19_CATGAATG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_20_CATGGGAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_23_TCACCATT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_25_TAGTCTTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_26_GTTAGCCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_27_CTGTACGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_28_CTCAGATA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_29_AGGTCTAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_2_GCAACATT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_30_GATCGAAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_33_TCGAAGTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_34_GGAATGAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_35_CACTCGAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_36_GCTATGAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_38_GGTAAGAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_39_GGTGTCGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_3_CCTAGTAT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_41_TTGGTATG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_42_GCTCCTTG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_43_CTTGCTTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_44_ACCTTCAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_45_TGCTGAAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_46_ATACAGGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_47_TGGCAAAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_48_GTACGGAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_49_TACTTCGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_4_CGGAAACA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_51_CACATTGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_53_GTTTTCAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_54_ACTCAGGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_55_AACAGCGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_56_TCCTCTCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_57_TCAGGAGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_58_GGATTAGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_59_CAACCTCC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_5_CGCACGAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_60_AAGTCGTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_61_TTGAGAAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_62_CTTGAATC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_63_AAGCGACT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_65_TCCAGTCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_66_GTGTGTCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_67_CTCAAGAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_68_TTGTGTCT_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_69_GTCACCAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_6_GTCTGAGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_71_ACCTCTAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_73_TCATTGAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_74_GACCTTAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_75_CCATGCAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_77_AAGGGGTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_78_AGCTGTGC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_80_AACTTATC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_81_TATGCCAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_82_GCACTGTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_83_CAAGTAGA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_84_GTTCCACG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_85_TTCCTACA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_86_TCCGGGTA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_87_GGACACGG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_89_TACTAGTC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_90_GATTCATC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_91_CGACTGCA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_92_TATTGGAG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_93_GTGGCCAA_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_94_TCGGACCG_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane3_Tom_Y8_TA_Hi_96_TGGTTGAC_L003_22540_7_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_11_GCGATTAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_12_AGGCAGCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_13_TGTCATCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_16_AGGACACT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_17_GCCAATGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_21_AGTCCAAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_22_CTCGTCGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_23_AGCCGTGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_26_TTGCGTAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_27_GTGCAGTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_29_TCTGACGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_31_AGGTATCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_34_TGACAGAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_35_GCTATGGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_36_ATCAACCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_38_ATAAGACT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_39_CTGTTTGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_3_GATGGTCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_40_CATACTAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_42_TCATCCTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_43_GTAACCGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_44_ACTGTTAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_47_TTGGAGCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_4_CGGAGGAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_50_TAGACGGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_51_GCCTTACA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_52_ATTCGGAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_53_AGCAAGTT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_54_AAGCCGAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_56_GCGTAGGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_57_TCCGTCTT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_58_TCTCTTCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_59_GCAGGTAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_5_TACCGCAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_60_ACAAGTGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_61_ACGGCAGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_62_ATTGCACA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_63_AGGTAGAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_66_TGAAGCCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_67_CGTTCGGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_68_AGAGGACC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_69_CGCCTTTG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_6_TCGTGGTT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_70_TAGCGAGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_72_AACTTTTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_73_TTGGAGGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_7_TGAGTAAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_81_TGATACGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_82_GATCTCTT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_84_AGGATTCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_86_GCGGGTCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_87_CGGTTGGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_8_AGCTCTTT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_92_ACAACGCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_94_ATGCAAAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O1_TA_Hi_95_GCCGAACC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_10_GAATCTGT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_11_CTTCACAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_12_TAGGACCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_14_AATTTGCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_15_ATAACTAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_19_CATGAATG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_20_CATGGGAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_21_AGGACGAT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_22_AGTTGAAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_23_TCACCATT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_26_GTTAGCCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_27_CTGTACGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_28_CTCAGATA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_29_AGGTCTAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_30_GATCGAAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_31_GCGTGAAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_32_GCTTAAAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_35_CACTCGAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_36_GCTATGAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_37_ATTAGCGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_38_GGTAAGAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_39_GGTGTCGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_41_TTGGTATG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_43_CTTGCTTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_44_ACCTTCAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_45_TGCTGAAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_46_ATACAGGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_47_TGGCAAAA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_48_GTACGGAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_50_GAGGATGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_51_CACATTGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_52_CAAAACCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_53_GTTTTCAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_55_AACAGCGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_56_TCCTCTCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_57_TCAGGAGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_59_CAACCTCC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_60_AAGTCGTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_61_TTGAGAAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_62_CTTGAATC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_63_AAGCGACT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_64_ACAGAAGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_65_TCCAGTCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_66_GTGTGTCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_67_CTCAAGAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_68_TTGTGTCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_69_GTCACCAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_70_AAGTAACA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_71_ACCTCTAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_73_TCATTGAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_74_GACCTTAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_75_CCATGCAC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_77_AAGGGGTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_78_AGCTGTGC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_79_GCTGGTTG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_7_ACTTTACT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_82_GCACTGTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_83_CAAGTAGA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_84_GTTCCACG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_85_TTCCTACA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_86_TCCGGGTA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_87_GGACACGG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_89_TACTAGTC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_90_GATTCATC_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_91_CGACTGCA_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_92_TATTGGAG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_94_TCGGACCG_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

lane2_Tom_O5_TA_Hi_95_CTTCGGCT_L002_22540_5_R1_val_1_GRCm38_hisat2.bam

So, there are these Tom entries:

(base) CS313BQin:Downloads hqin$ head -n 1 GSE121364_Table_raw_counts_RNA_QSC.txt | fmt -1| cut -c 7-13 | sort | uniq

Tom_O1_

Tom_O5_

Tom_Y4_

Tom_Y5_

Tom_Y7_

Tom_Y8_

The mouse id are explained on NCBI

For Y8_TA_Hi_9, see https://www.ncbi.nlm.nih.gov/biosample/SAMN10249737

age 2 months, mouse id Y8

It seems O1 are old mouse

O1_TA_Hi_11 [scRNA-seq]
Sample type	SRA

Source name	Tibialis anterior muscles
Organism	Mus musculus
Characteristics	strain: MGI: 5308730 cell type: Muscle stem cells age: 24 months mouse id: O1