|
| Status |
Public on Jan 27, 2016 |
| Title |
T74_P4_A8_ILC3 |
| Sample type |
SRA |
| |
|
| Source name |
cDNA
|
| Organism |
Homo sapiens |
| Characteristics |
tonsil donor: Donor T74
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 |
GSM4521379 |
| BioSample |
SAMN03841582 |
| SRA |
SRX1082102 |
