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| Status |
Public on Feb 03, 2017 |
| Title |
Pool5_barcodes |
| Sample type |
SRA |
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| Source name |
plasmid DNA
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| Organism |
synthetic construct |
| Characteristics |
cell line: Plasmid DNA
molecule subtype: plasmid DNA
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| Treatment protocol |
none
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Barcode/oligo libraries were prepared as described by Tewkey et al. (Cell 2016 Jun 2;165(6):1519-29. PMID: 27259153)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
fastq of the barcode linked to oligo
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| Data processing |
Paired-end reads were aligned to the oligonucleotide pool using Bowtie2 2.1.0 (Langmead and Salzberg, 2012), trimming the tag sequence and adapters. Read pairs that were not aligned in proper pairs, had mapping scores less than 25, or edit distance greater than 5 were discarded. Remaining oligo/barcode pairs were merged. Barcodes that were observed in only 1 read or that matched multiple test sequences were removed from further analysis.
Tab file linking barcodes and oligos
Genome_build: mm9
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| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sharon R Grossman |
| E-mail(s) |
grossman@broadinstitute.org
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| Organization name |
Broad Institute
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL17769 |
| Series (1) |
| GSE84888 |
Distinct roles for motif affinity, chromatin state, and co-regulatory motifs in PPARĪ³ binding and enhancer activity |
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| Relations |
| BioSample |
SAMN05447724 |
| SRA |
SRX1979658 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2253165_Pool5.barcodes.txt.gz |
5.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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