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Status |
Public on Jan 10, 2014 |
Title |
earlyblast_2-1 |
Sample type |
SRA |
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Source name |
Early blastocyst cell (86-88h post-fertilization)
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Organism |
Mus musculus |
Characteristics |
strain: CAST/EiJ(mother) x C57BL/6J(father) cross: first generation cross developmental stage: Early blastocyst cell (86-88h post-fertilization)
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
Early blastocyst 2 cell 1
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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)
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Submission date |
Apr 02, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Daniel Ramsköld |
E-mail(s) |
daniel.ramskold@ki.se
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Organization name |
Karolinska Institutet
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Lab |
Rickard Sandberg's group (rickard.sandberg@ki.se) (2008-2014, 2018-); Rheumatology unit (2014-2018)
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Street address |
Nobels väg 3
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City |
Stockholm |
ZIP/Postal code |
17177 |
Country |
Sweden |
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Platform ID |
GPL13112 |
Series (1) |
GSE45719 |
Single-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells |
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Relations |
SRA |
SRX259226 |
BioSample |
SAMN01997403 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1112611_earlyblast_2-1_expression.txt.gz |
319.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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