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| Status |
Public on Nov 17, 2017 |
| Title |
RNA_D0_shCon_C2C12 |
| Sample type |
SRA |
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| Source name |
C2C12 myoblast cell
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| Organism |
Mus musculus |
| Characteristics |
cell type: C2C12 myoblast cell line
stage of adipogenesis or myogenesis: Undifferentiated myoblasts
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| Treatment protocol |
Cells were infected with lentiviral shRNA to generate control or Brd4 knockdown cells
For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.
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| Growth protocol |
Primary brown preadipocytes were isolated from interscapular BAT of newborn Brd4f/f mice and immortalized with SV40T-expressing retroviruses generated from the pBabepuro-large T plasmid
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent. mRNA was further purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit (Cat. 610-11).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
Sequencing reads were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
For ChIP-seq, peaks were called using SICER with following configuration: Windows (50), Gaps (50), FDR (1e-10 for Brd4 ChIP-Seq in MLL3 KO and MLL3/MLL4 KO cells, 1e-3 for all the other ChIP-Seq)
For RNA-seq, RPKM (Reads per kilobase per million) values were calculated to measure gene (RefSeq) expression levels using in-house script.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.
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| Submission date |
May 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kai Ge |
| E-mail(s) |
kai.ge@nih.gov
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| Phone |
301-451-1998
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| Organization name |
NIH
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| Department |
NIDDK
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| Street address |
50 South Dr Rm 4154
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE99101 |
Enhancer-binding of Brd4 controls cell differentiation |
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| Relations |
| BioSample |
SAMN07146652 |
| SRA |
SRX2836980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2633468_RNA_C2C12_shCon_D0_RPKM.txt.gz |
277.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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