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Sample GSM2361921 Query DataSets for GSM2361921
Status Public on Nov 15, 2016
Title CB pre-cDC_S263
Sample type SRA
 
Source name Cord Blood pre-cDCs
Organism Homo sapiens
Characteristics cell type: CB pre-cDC
cell type: cord blood pre-conventional dendritic cells (cDCs)
Extracted molecule polyA RNA
Extraction protocol cDNA from each sample was prepared using the SMART-Seq 2 protocol (Picelli et al., 2013).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description CB pre-cDC_S263
Data processing Raw sequencing data were processed as previously described (Shalek et al., 2014). Briefly, short sequencing reads were aligned to the UCSC hg19 transcriptome and were also used as input in RSEM v 1.2.1 to quantify gene expression levels (transcripts per million; TPM) for all UCSC hg19 genes in all samples.
We filtered out cells from our dataset where we detected less than 1,000 unique genes per cell. All genes that were not detected in at least 1% of all our single cells were discarded, leaving 20,869 genes for all further analyses. Data were log transformed (log TPM+1) for all downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: matrix of gene expression estimates across good quality samples
 
Submission date Oct 27, 2016
Last update date May 15, 2019
Contact name Thiago Y Oliveira
E-mail(s) toliveira@rockefeller.edu
Organization name The Rockefeller University
Department Immunology, Virology and Microbiology
Lab Laboratory of Molecular Immunology
Street address 1230 YORK AVE
City NEW YORK
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL16791
Series (1)
GSE89232 Single-cell RNA-seq reveals heterogeneity within human pre-cDCs
Relations
BioSample SAMN05946584
SRA SRX2272067

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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