|
| Status |
Public on Feb 03, 2017 |
| Title |
Pool3_Plasmid |
| Sample type |
SRA |
| |
|
| Source name |
plasmid DNA
|
| Organism |
synthetic construct |
| Characteristics |
cell line: Plasmid DNA
molecule subtype: plasmid DNA
|
| 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 |
genomic DNA |
| 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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
fastq of 3' UTR barcode and residual 5' flanking sequencing
|
| Data processing |
Perfect UTR barcode matches were assigned to their respective oligo. Counts for all barcodes assigned to an oligo were summed.
Read counts corresponding to each barcode for each oligo
Genome_build: mm9
|
| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sharon R Grossman |
| E-mail(s) |
grossman@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL15228 |
| Series (1) |
| GSE84888 |
Distinct roles for motif affinity, chromatin state, and co-regulatory motifs in PPARĪ³ binding and enhancer activity |
|
| Relations |
| BioSample |
SAMN05447733 |
| SRA |
SRX1979649 |
