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Sample GSM1416435 Query DataSets for GSM1416435
Status Public on Jul 14, 2014
Title P1_3
Sample type SRA
 
Source name P1_3
Organism Mus musculus
Characteristics cell type: MEF
Extracted molecule total RNA
Extraction protocol cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera-Zymo-IlluminaPCRmix
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.
 
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) or mouse (mm10) 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 (Feb 2013).
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: RPKM gene expression values (tab-delimited text)
 
Submission date Jun 19, 2014
Last update date May 15, 2019
Contact name Rickard Sandberg
E-mail(s) Rickard.Sandberg@ki.se
Organization name Karolinska Institutet
Department Department of Cell and Molecular Biology
Street address Berzelius vag 35
City Stockholm
ZIP/Postal code 17177
Country Sweden
 
Platform ID GPL13112
Series (1)
GSE58652 Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
Relations
BioSample SAMN02867387
SRA SRX611272

Supplementary file Size Download File type/resource
GSM1416435_P1_3_expression.txt.gz 328.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table

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