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Sample GSM1112586 Query DataSets for GSM1112586
Status Public on Jan 10, 2014
Title BXC_1ng_liver_RNA_0
Sample type SRA
Source name Liver
Organism Mus musculus
Characteristics strain: C57BL/6J(mother) x CAST/EiJ(father)
cross: first generation cross
developmental stage: adult
tissue: liver (pooled)
Extracted molecule polyA RNA
Extraction protocol We used Trizol (Ambion catalog number 15596-026)
We used the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description 1 ng total RNA, from pool of liver RNA, technical replicate
Data processing For expression values, we aligned reads using bowtie 0.12.7, option --best, against the genome and transcriptome (Ensembl, version 16 May 2011) with the genotype of both strains, in mm9 coordinates
Non-uniquely mapped reads were removed
Rpkmforgenes (available at, 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.
For allelic ratios, we aligned using gsnap version 2012-07-20, with tolerance for known SNP positions
We used samtools mpileup to extract allelic counts
Genome_build: mm9
Supplementary_files_format_and_content: gene expression values (tab-delimited text)
Submission date Apr 02, 2013
Last update date May 15, 2019
Contact name Daniel Ramsköld
Organization name Karolinska Institutet
Lab Rickard Sandberg's group ( (2008-2014, 2018-); Rheumatology unit (2014-2018)
Street address Nobels väg 3
City Stockholm
ZIP/Postal code 17177
Country Sweden
Platform ID GPL13112
Series (1)
GSE45719 Single-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells
SRA SRX259201
BioSample SAMN01997378

Supplementary file Size Download File type/resource
GSM1112586_BXC_1ng_liver_RNA_0r_expression.txt.gz 374.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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