|
| Status |
Public on May 07, 2016 |
| Title |
PacBio_enhancer-Barcodes |
| Sample type |
SRA |
| |
|
| Source name |
MCF7, input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
capturing system: MYbaits custom capturing system
|
| Treatment protocol |
p53 stimulation with Nutlin-3a or stable knockdown of p53.
|
| Growth protocol |
Cells were grown at 37°C to 85% confluency before harvest. Medium used was Ham's F-10 nutrient mix supplemented with FBS and l-alanyl-glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with a plasmid extraction protocol from Qiagen; RNA was extracted using the RNeasy protocol from Qiagen.
Custom library prep.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
| |
|
| Description |
Plasmid DNA library input.
PacBio long-read sequencing of the plasmid library (i.e., the 2-3kb length fragment spanning the cloned enhancer, the reporter and the barcode in the plasmid).
|
| Data processing |
Library strategy: CHEQ-Seq
Files were cleaned and trimmed where needed.
Reads were mapped to the hg19 genome using STAR.
The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read, resulting in the removal of the first five base pairs for each read.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *counts.txt: Counts are raw and were generated using HTseq counts.
|
| |
|
| Submission date |
Jan 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zeynep Kalender Atak |
| Organization name |
KULeuven
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21311 |
| Series (2) |
| GSE76653 |
Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic [CHEQ-seq] |
| GSE76657 |
Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic |
|
| Relations |
| BioSample |
SAMN04388603 |
| SRA |
SRX1522020 |
