|
Status |
Public on Jan 27, 2016 |
Title |
T75_P2_H9_ILC3 |
Sample type |
SRA |
|
|
Source name |
cDNA
|
Organism |
Homo sapiens |
Characteristics |
tonsil donor: Donor T75 facs gating: ILC3 cell type: tonsil Innate lymphoid cells
|
Extracted molecule |
polyA RNA |
Extraction protocol |
cDNA was generated from FACS sorted cells using to Smart-seq2 (Picelli et al. Nature Methods 2013) Nextera XT DNA Sample Preparation Index Kit (24 index primers, Illumina)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
All reads were aligned to the human (hg19) genomes using STAR (Dobin et al. 2013) Non-uniquely mapped reads were removed Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq and Ensembl (Feb 2013) and ERCC-spike in annotations. Genome_build: hg19 Supplementary_files_format_and_content: gene expression values (tab-delimited text)
|
|
|
Submission date |
Jul 07, 2015 |
Last update date |
May 07, 2020 |
Contact name |
Asa Kristina Bjorklund |
E-mail(s) |
asa.bjorklund@scilifelab.se
|
Organization name |
Uppsala University
|
Department |
Cell and Molecular Biology
|
Street address |
Box 596
|
City |
Uppsala |
ZIP/Postal code |
75124 |
Country |
Sweden |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE70580 |
Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs) |
|
Relations |
Reanalyzed by |
GSM4521381 |
BioSample |
SAMN03841475 |
SRA |
SRX1082257 |