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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 06, 2013 |
| Title |
Taf4 loxp/- (ctrl), replicate 2 |
| Sample type |
SRA |
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| Source name |
Taf4 wild type cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: MEF cells
genotype/variation: Taf4 wild type
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| Growth protocol |
The MEF cells were maintained in DMEM (Invitrogen, CA) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 100 μg/ml streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to a version of Illumina's mRNA-Seq protocol (Illumina, CA)
Libraries were prepared using the Illumina RNA-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
mRNA isolated from mouse taf4loxp/- MEF cells
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| Data processing |
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long reads were mapped to the reference mouse genome sequence, mm9, using Tophat aligner (Trapnell et al, Bioinformatics 2009, 25 (9): 1105-1111) with the default parameters. The mRNA expression level for each gene was represented as FPKM (fragments per kilobase of transcript per million fragments mapped), called by Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515), and differential expression between control vs. knockout, wild type vs. knockout, and deletion vs. knockout were called by Cuffdiff in Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515).
Genome_build: mm9
Supplementary_files_format_and_content: wiggle track raw reads
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| Submission date |
May 09, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Huimin Geng |
| E-mail(s) |
[email protected]
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| Organization name |
UCSF
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| Department |
Department of Laboratory Medicine
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| Street address |
513 Parnassus Ave., MSB S-1480
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE46807 |
A TAF4 coactivator function for E proteins that involves enhanced TFIID binding |
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| Relations |
| BioSample |
SAMN02141752 |
| SRA |
SRX276758 |
| Named Annotation |
GSM1138583_Taf4-ctrl-2.mm9.bigWIG |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1138583_Taf4-ctrl-2.mm9.bigWIG |
84.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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