single cell aging mouse brain （error）

 37069 cells

https://singlecell.broadinstitute.org/single_cell/study/SCP263/aging-mouse-brain

455M is too big to download by browser. 

Tring to get certificate at local server

openssl s_client -showcerts -servername singlecell.broadinstitute.org/single_cell/api/v1 -connect server:443 > cacert.pem

https://singlecell.broadinstitute.org/

singlecell.broadinstitute.org/single_cell/api/v1

(base) hqin@CS313BQin q-sandbox % which openssl

/Users/hqin/opt/anaconda3/bin/openssl

(base) hqin@CS313BQin q-sandbox % openssl s_client -showcerts -servername https://singlecell.broadinstitute.org -connect server:443 > cacert.pem

4504972800:error:2008F002:BIO routines:BIO_lookup_ex:system lib:crypto/bio/b_addr.c:730:nodename nor servname provided, or not known

connect:errno=0

CURL download error

curl: (60) SSL certificate problem: unable to get local issuer certificate

More details here: https://curl.haxx.se/docs/sslcerts.html

single cell multiplexed and image and proteomic data

Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data

Geuenich Michael; Hou Jinyu; Lee Sunyun; Ayub Shanza;  Jackson Hartland;  Campbell Kieran 

https://zenodo.org/record/5156049#.YUjywGZKjzc

biohub, single cell data

 

single cell gene-networks, topological robustness of gene networks, cellular life in different tissues, blood versus neurons

https://tabula-microcebus-cellxgene.ds.czbiohub.org/all/

Yu Welch 2021 disentangled features of single cell expression

 https://github.com/welch-lab/MichiGAN 

https://www.biorxiv.org/content/10.1101/2021.01.15.426872v1 

single cell portal at Broad

 

https://singlecell.broadinstitute.org/single_cell

Aging keyword return several single cell study project, aging mouse brain, aging haematopoietic stem cells

scDNA-seq and LOH monitoring in yeast aging

 single cell DNA seq

Natural communication, 2019, Luquette, .. Peter Park, Identification of somatic mutations in single cell DNA-seq using  a spatial model of allelic imbalance. 

somatic SNV (single nucleotide variation). 

variant allele fraction (VAF), the fraction of sequencing reads supporting allele a heterozygous variant. 

Qin: VAF on loss of heterozygosity during aging can be done with young cells as the background. The young cells provide a reference distribution of VAF at allelic positions genome-wide. Comparison between VAF of aging cells and young cells. If loss of heterozygocity occurs a loci, VAF at a loci can only be caused by amplification artifacts, which are expect to be 'random' and has a very small probability to overlap with the natural variations. S288c and RM is 0.5-1%. 

Luquette19 proposed a genome-location spatial model for Amplification Balance to evaluate VAF.  Luquette used nearby known SNP VAF to show the allele imbalance.  Luquette19 used a 'smooth curve' to model the spatial distribution of allele imbalance on chromosomes. 

single cell DNA sequencing (genome sequencing)

 

=>QIAGEN single cell DNA library prep

https://www.qiagen.com/us/products/next-generation-sequencing/library-preparation/qiaseq-fx-single-cell-dna-library-kit/?cmpid=PC_GEN_single-cell-analysis-sales_0620_SEA_GA&clear=true#orderinginformation

The QIAseq FX Single Cell DNA Library kit provides a complete solution for whole genome sequencing from isolated single animal or bacterial cells or low amounts of genomic DNA. The kit includes all reagents required for cell lysis, whole genome amplification, enzymatic DNA fragmentation and PCR-free NGS library preparation. The kit provides comprehensive genome coverage and exceptional sequence fidelity, reducing false positives and minimizing drop-outs. The kit is ideally suited to the analysis of aneuploidy and copy number variation and sequence variation in single cells of for whole genome sequencing from rare samples

single cell genomics pseduotime

https://github.com/hongqin/single-cell-pseudotime


https://www.sciencedirect.com/science/article/pii/S0959437X17300084

Single-cell transcriptomic profiling of the aging mouse brain

https://www.nature.com/articles/s41593-019-0491-3?fbclid=IwAR1AZtVaFSyd_cNpzWpLoRjVUhYiu5WvTuYVR5Wz_DlUWRaePByTC5svsbA

single cell sequencing

https://www.the-scientist.com/techedge/techedge-single-cell-sequence-analysis-64770?utm_medium=email&_hsenc=p2ANqtz-_PorJTkgpFB1mdlAjg2EILqZpveTA3x8mDsMhMQlf29xCT6O-FqLeD7WRSnuACVXq8Eei9P8YqlooX_MlK1FIRabG5PA&_hsmi=68520001&utm_content=68519999&utm_source=hs_email&hsCtaTracking=7b7ef6f3-21a3-4b9a-b000-31b73e7703e6%7C0da0b3d2-be3d-4a34-8adc-2837179ba724

Tapestri, Mission BIO


Miko, single cell western platform

BD Rhapsody single cell analysis
https://www.the-scientist.com/sponsored-videos/bd--rhapsody-single-cell-analysis-system-65030


Single cell RNS Seq
https://www.the-scientist.com/daily-news/single-cell-rna-sequencing-reveals-neuronal-diversity-33313

single cell transcriptome analysis

single cell transcriptiome in aging mouse brain
https://www.nature.com/articles/s41593-019-0491-3?fbclid=IwAR1AZtVaFSyd_cNpzWpLoRjVUhYiu5WvTuYVR5Wz_DlUWRaePByTC5svsbA

single cell gene expression analysis
http://cole-trapnell-lab.github.io/monocle-release/docs/#installing-monocle