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Sample GSM1112502 Query DataSets for GSM1112502
Status Public on Jan 10, 2014
Title 16cell_1-8
Sample type SRA
 
Source name 16-cell stage blastomere
Organism Mus musculus
Characteristics strain: CAST/EiJ(mother) x C57BL/6J(father)
cross: first generation cross
developmental stage: 16-cell stage blastomere
Extracted molecule polyA RNA
Extraction protocol We used lysis buffer of the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech
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 16-cell stage embryo 1 cell 8
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 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.
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
E-mail(s) daniel.ramskold@ki.se
Organization name Karolinska Institutet
Lab Rickard Sandberg's group (rickard.sandberg@ki.se) (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
Relations
SRA SRX259117
BioSample SAMN01997294

Supplementary file Size Download File type/resource
GSM1112502_16cell_1-8_expression.txt.gz 311.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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