|
Status |
Public on Nov 15, 2016 |
Title |
CB pre-cDC_S90 |
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_S90
|
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 |
SAMN05946340 |
SRA |
SRX2271894 |