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| Status |
Public on Jan 27, 2016 |
| Title |
T75_P1_B1_ILC3 |
| Sample type |
SRA |
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| Source name |
cDNA
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| Organism |
Homo sapiens |
| Characteristics |
tonsil donor: Donor T75
facs gating: ILC3
cell type: tonsil Innate lymphoid cells
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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)
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| Submission date |
Jul 07, 2015 |
| Last update date |
May 07, 2020 |
| Contact name |
Asa Kristina Bjorklund |
| E-mail(s) |
[email protected]
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| Organization name |
Uppsala University
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| Department |
Cell and Molecular Biology
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| Street address |
Box 596
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| City |
Uppsala |
| ZIP/Postal code |
75124 |
| Country |
Sweden |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE70580 |
Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs) |
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| Relations |
| Reanalyzed by |
GSM4521380 |
| BioSample |
SAMN03841742 |
| SRA |
SRX1082128 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1810594_T75_P1_B1_ILC3_expression.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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