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| Status |
Public on Jan 15, 2021 |
| Title |
PBMC ECCITE-seq RNA_5P |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
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| Extracted molecule |
total RNA |
| Extraction protocol |
For the CITE/ECCITE-seq experiment: a panel of antibodies (ADTs) was used to stain the cells according to the CITE/ECCITE-seq protocol. To identify cell doublets. and keep track of patients identity and their vaccination time points, we split cells into aliquots and stained each aliquot with a unique hashing (HTOs) antibody. Samples were washed and recombined and loaded on a 10X genomics chip. 5prime 10X genomics was ran and the manufacturers protocols was followed for cDNA library generation. To recover HTOs, ADTs and TCR/BCRs we followed the CITE/ECCITE-seq protocol found here: https://cite-seq.com/protocol/.
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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: ECCITE-seq
CITE-seq and ECCITE-seq RNA reads were mapped to the human genome (hg38). Transcripts were quanitfied using CellRanger v3.1.0
ADT, HTO counts were quantified using Alevin (https://salmon.readthedocs.io/en/latest/alevin.html#)
Cells were demultiplexed into their experimental conditions after normalization (centered log ratio transformation, margin = 2) using the HTOdemux function in Seurat.
TCR and BCR clonotypes were identified using the 10x Genomics cellranger vdj pipeline (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/vdj)
Genome_build: hg38
Supplementary_files_format_and_content: Processed data contains 3P and 5P single cell expression matrices where the rows correspond to features (genes, or protein) and the columns to single cells, their corresponding meta data tables, and 5P BCR, TCR analysis results.
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| Submission date |
Jan 07, 2021 |
| Last update date |
Jan 15, 2021 |
| Contact name |
Yuhan Hao |
| E-mail(s) |
yhao@nygenome.org
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| Organization name |
New York Genome Center
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| Street address |
101 6th Ave
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| City |
New York |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE164378 |
Integrated analysis of multimodal single-cell data |
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| Relations |
| BioSample |
SAMN17248722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5008740_RNA_5P-barcodes.tsv.gz |
235.8 Kb |
(ftp)(http) |
TSV |
| GSM5008740_RNA_5P-features.tsv.gz |
227.9 Kb |
(ftp)(http) |
TSV |
| GSM5008740_RNA_5P-matrix.mtx.gz |
207.8 Mb |
(ftp)(http) |
MTX |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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