|
| Status |
Public on Sep 26, 2016 |
| Title |
fibroblast.split.E.297 |
| Sample type |
SRA |
| |
|
| Source name |
splitted.fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
age: adult
Sex: female
strain: C57BL/6J (mother) x CAST/EiJ (father)
cell type: splitted fibroblast
clone.info: non.clonal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
genome build: mm9
Aligned reads with rna-star
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track
Supplementary_files_format_and_content: Tab-delimited text files report RPKMs and read counts.
|
| |
|
| Submission date |
Dec 03, 2015 |
| 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) |
| GSE75659 |
Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq |
|
| Relations |
| BioSample |
SAMN04312496 |
| SRA |
SRX1461153 |
