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| Status |
Public on Jan 10, 2014 |
| Title |
fibroblast_22_BxC |
| Sample type |
SRA |
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| Source name |
fibroblast (primary culture from tail)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J(mother) x CAST/EiJ(father)
cross: first generation cross
developmental stage: fibroblast (primary culture from tail)
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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 Smart-seq2, as described by Picelli et al. Nature methods 2013 (PMID 24056875)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
fibroblast 22 genotype CASTxC57
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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 (but for Smart-seq2 samples we used rna-star against the genome)
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 (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)
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| Submission date |
Dec 03, 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 |
| BioSample |
SAMN02429294 |
| SRA |
SRX386097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1278044_fibroblast_22_BxC_expression.txt.gz |
342.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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