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| Status |
Public on Sep 25, 2021 |
| Title |
sorted CD45+ VDJ batch1 (020218_6_TEL) |
| Sample type |
SRA |
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| Source name |
frozen PBMC
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| 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: 007-001 Day28
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| Treatment protocol |
Cells were thawed into X-vivo media, counted and sorted for CD45+/live dead
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| Growth protocol |
N/A
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| 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
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Jun 27, 2021 |
| Last update date |
Sep 25, 2021 |
| Contact name |
Jeffrey A Bluestone |
| E-mail(s) |
Jeff.Bluestone@ucsf.edu
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| Phone |
415-514-0417
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| Organization name |
UCSF
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| Lab |
Bluestone Lab, HSW 1112
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| Street address |
513 Parnassus Ave
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| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN19904424 |
| SRA |
SRX11238240 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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