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| Status |
Public on Jun 20, 2017 |
| Title |
wt_tp1.1 |
| Sample type |
SRA |
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| Source name |
WT MEFs d33
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| Organism |
Mus musculus |
| Characteristics |
strain: C57B1/6
genotype: WT
cell type: primary mouse embryonic fibroblast
passages: 11
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from bulk MEF populations was extracted using the RNeasy mini kit (Qiagen). 1.5 and 3 ug of total RNA was used for the preparation of the library using the TruSeq mRNA stranded LT (Illumina kit)
TruSeq mRNA stranded LT (Illumina kit), with qubit quantification and QC with tapestation 4200 and Fragment analyzer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
WT MEFs d33 rep1
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| Data processing |
Mapping: software Bowtie2 v.2.2.1, assembly: mm10
web-based HTSstation was used to process the data (David, et al. 2014)
RNA counter: HTSstation
Differential expression analysis: Bioconductor limma (v. 3.18.13)
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each sample.
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| Submission date |
Jun 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Selene Glück |
| E-mail(s) |
selene.glueck@epfl.ch
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| Organization name |
EPFL
|
| Department |
SV-GHI
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| Lab |
Ablasser
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| Street address |
Station 19
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE100102 |
Innate immune sensing of cytosolic chromatin fragments through cGAS promotes senescence |
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| Relations |
| BioSample |
SAMN07249208 |
| SRA |
SRX2924814 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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