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Sample GSM5402868 Query DataSets for GSM5402868
Status Public on Sep 25, 2021
Title sorted CD45+ VDJ batch1 (020218_7_TEL)
Sample type SRA
 
Source name frozen PBMC
Organism Homo sapiens
Characteristics cell type: PBMC
sequencing kit: 10X genomics VDJ 5'
number of samples that has been pooled: 1
patient id, time point: 002-009 Day28
Treatment protocol Cells were thawed into X-vivo media, counted and sorted for CD45+/live dead
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Chromium Single Cell V(D)J Enriched and 5' Gene Expression libraries generation and sequencing under the guidance of the official instruction manual
illumina Novaseq sequencing
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Library strategy: VDJ-seq
Cell Ranger Single-Cell Software Suite (version 3.1.0, 10x Genomics)
VCF genotype files and scRNAseq BAM files were used to run Demuxlet with default parameters. Demultiplexing results were largely concordant with freemuxlet (https://github.com/statgen/popscle/). Subsequently, the multiplexed single cell RNAseq and single cell TCRseq data were filtered according to a singlet whitelist extracted from the demuxlet.best output file.
Using Scanpy (Wolf et al., 2018), we performed BBKNN batch correction after poolong all the demuxletted samples, PCA on the gene expression matrix and we then build a nearest neighbor graph to calculate a UMAP and find clusters via the louvain algorithm
Supplementary_files_format_and_content: 20201228_adata.h5ad is the combination of all the h5 files (cell ranger output), demuxleted and annotated for TCRs, patients ID, timepoints
 
Submission date Jun 27, 2021
Last update date Sep 25, 2021
Contact name Jeffrey A Bluestone
E-mail(s) Jeff.Bluestone@ucsf.edu
Phone 415-514-0417
Organization name UCSF
Lab Bluestone Lab, HSW 1112
Street address 513 Parnassus Ave
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platform ID GPL24676
Series (1)
GSE178991 10X genomics single cell GEX and VDJ 5' sequencing of PBMC from Type 1 Diabetes patients treated with Treg therapy alone or plus low dose IL-2
Relations
BioSample SAMN19904422
SRA SRX11238242

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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