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Sample GSM3374613 Query DataSets for GSM3374613
Status Public on Sep 04, 2018
Title lna_cell_pbmc_original
Sample type SRA
Source name Human PBMCs
Organism Homo sapiens
Characteristics sample type: Human PBMCs
Extracted molecule total RNA
Extraction protocol PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell R-seq platform
10x genomics 3' end single cell RNA-seq kit. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Original single cell RNA-seq library from the 10x genomics 3' end library prep. PBMCs were isolated from a health human donor.
Data processing Data analysis pipeline and custom scripts are provided in a github repository ( Single cell RNA-Seq libraries were preprocessed to append the read 1 sequence to the paired read 2 read id (append_read_name) followed by quality trimming and poly(A) tail removal from read 2 using cutadapt (v. 1.8.3 -a 'A{{100}}' -O 6 -m 20 -q 10) (Martin 2011). Reads were next aligned with STAR (Dobin et al. 2013) to either the human genome assembly (hg38) for the PBMC experiments or a genome with both human (hg38) and mouse (mm38) sequences for all other experiments. Sequence headers in the human/mouse combined genome were prefixed with either an “H_” or “M_” to designate human or mouse references respectively. Following alignment, BAM files were processed to extract the cell barcode and UMI sequences into tags (CN and BX) within the BAM file (barcode_tag_bam). The cell barcode was error corrected against a list of cell barcodes, either as known well barcodes (Wafergen experiments), or generated from the original 10x genomics single cell libraries processed with the 10x genomics software cellranger (v. 2.1.1). Cell barcodes within edit distance of 1 of the known barcodes were considered valid cell barcodes and corrected to the known barcode. Alignments not designated as multi-mapping that overlapped distinct exonic features were tagged in the BAM file (subread v. 1.6.0) (Liao et al. 2014). Gencode v25 annotations was used for human data, and a union reference containing Gencode v25 and mouse v11 was used for human/mouse datasets. UMIs per gene were enumerated per cell using umi-tools (v 0.5.3) (Smith et al. 2017) using the directional method to disambiguate similar UMI sequences.
Genome_build: mm38, hg38
Supplementary_files_format_and_content: Text files containing cell barcode sequences, count matrices of UMIs per gene per cell are provided. For the TCR single cell libraries JSON files are provided with detailed annotations for each assembled contig per cell.
Submission date Sep 04, 2018
Last update date Sep 05, 2018
Contact name Kent Augustus Riemondy
Organization name University of Colorado School of Medicine
Department Biochemistry and Molecular Genetics
Street address 12801 E 17th Ave
City Aurora
State/province Colorado
ZIP/Postal code 80045
Country USA
Platform ID GPL24676
Series (1)
GSE119428 Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries
BioSample SAMN09951389
SRA SRX4637903

Supplementary file Size Download File type/resource
GSM3374613_kirkpatrick_umis.tsv.gz 3.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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