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Sample GSM1810583 Query DataSets for GSM1810583
Status Public on Jan 27, 2016
Title T74_P4_H8_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 SAMN03841730
SRA SRX1082117

Supplementary file Size Download File type/resource
GSM1810583_T74_P4_H8_ILC3_expression.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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