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| Status |
Public on Sep 29, 2014 |
| Title |
muh11ESC_ev_fj209 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells, TC11, empty vector
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| Organism |
Mus musculus |
| Characteristics |
strain/background: 129/Ola
transchromosomic: hsa11
plasmid: empty vector
nickname: TC11+EV r2 RNA
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| Growth protocol |
MEF feeders + W8 (fj074, fj095, fj096), feeder-free GMEM+Lif (dg011, fj208-211), MEF feeders + KSR15 (fj078. fj113).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol + RNeasy cleanup, followed by ribozero rRNA depletion.
Strand-specific dUTP followed by TruSeq DNA library prep kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
fj209
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| Data processing |
Samples were mapped with Tophat2 using Bowtie2 as the underlying alignment tool. Sample dg011 was trimmed to 80x80bp from the 3' end. Others were not trimmed prior to mapping. The target assemblies were hg19 (human samples) and mm9+hg19chr11 (transchromosomic samples). Tophat was supplied with a gene model using the --GTF option. The gene model was UCSC KnownGenes.
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtool rmdup.
The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
The coverage summed over all exonic positions of a gene was divided by 200 to determine the read per gene for a sample. This was done for all hg19 UCSC KnownGenes.
For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
Genome_build: mm9 (MGSCv37) + hg19 (GRCh37) chr11
Supplementary_files_format_and_content: Excel workbook with DESeq results.
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| Submission date |
Aug 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sofie Salama |
| E-mail(s) |
[email protected]
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| Phone |
8314592814
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| Organization name |
Univerity of California, Santa Cruz
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| Department |
Center for Biomolecular Science and Engineering
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| Lab |
Haussler
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| Street address |
MS: CBSE, 1156 High St
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| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95060 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE60178 |
Human embryonic stem cell, rhesus embryonic stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) RNA-seq |
| GSE60211 |
An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons |
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| Relations |
| BioSample |
SAMN02953921 |
| SRA |
SRX671548 |
| 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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