|
| Status |
Public on Feb 03, 2017 |
| Title |
Pool7_RNA |
| Sample type |
SRA |
| |
|
| Source name |
3T3-L1 cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3-L1
molecule subtype: total RNA
|
| Treatment protocol |
none
|
| Growth protocol |
3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days after confluence, the cells were induced with DMEM supplemented with 10% FBS, 1uM dexamethasone, 1.7uM insulin, and 0.5mM 3-isobutyl-1-methylxanthine (IBMX). 48h later, the medium was replaced with DMEM supplemented with 10% FBS and the cells were fed every two days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MPRA libraries were prepared as described by Melnikov et al. (Nat Biotechnol 2012 Feb 26;30(3):271-7. PMID: 22371084)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
fastq of 3' UTR barcode and residual 5' flanking sequencing
processed data file: Pool7_MPRA.txt
|
| Data processing |
Perfect UTR barcode matches were assigned to their respective oligo. Counts for all barcodes assigned to an oligo were summed.
Read counts in RNA and Plasmid libraries summed across all barcodes corresponding to each oligo
Genome_build: mm9
|
| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sharon R Grossman |
| E-mail(s) |
[email protected]
|
| Organization name |
Broad Institute
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE84888 |
Distinct roles for motif affinity, chromatin state, and co-regulatory motifs in PPARĪ³ binding and enhancer activity |
|
| Relations |
| BioSample |
SAMN05447726 |
| SRA |
SRX1979656 |
