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Sample GSM1278020 Query DataSets for GSM1278020
Status Public on Jan 10, 2014
Title 8cell_12-4_smartseq2
Sample type SRA
Source name 8-cell stage blastomere
Organism Mus musculus
Characteristics strain: CAST/EiJ(mother) x C57BL/6J(father)
cross: first generation cross
developmental stage: 8-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 Smart-seq2, as described by Picelli et al. Nature methods 2013 (PMID 24056875)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description 8-cell stage embryo 12 cell 4
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 (but for Smart-seq2 samples we used rna-star against the genome)
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 (but for Smart-seq2 samples we used rna-star)
We used samtools mpileup to extract allelic counts
Genome_build: mm9
Supplementary_files_format_and_content: gene expression values (tab-delimited text)
Submission date Dec 03, 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
BioSample SAMN02429272
SRA SRX386073

Supplementary file Size Download File type/resource
GSM1278020_8cell_12-4_smartseq2_expression.txt.gz 307.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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