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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 26, 2016 |
| Title |
fibroblast.60.cl6 |
| Sample type |
SRA |
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| Source name |
single.fibroblast
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| Organism |
Mus musculus |
| Characteristics |
age: E15
Sex: male
strain: C57BL/6J (mother) x CAST/EiJ (father)
cell type: single fibroblast
clone.info: fibroblast.cl6
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| Extracted molecule |
total RNA |
| Extraction protocol |
SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed 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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| 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.
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| Submission date |
Dec 03, 2015 |
| 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) |
| GSE75659 |
Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq |
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| Relations |
| BioSample |
SAMN04312247 |
| SRA |
SRX1460916 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1961810_fibroblast.60.cl6_expression.txt.gz |
804.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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