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Sample GSM2033059 Query DataSets for GSM2033059
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
BioSample SAMN04388603
SRA SRX1522020

Supplementary file Size Download File type/resource
GSM2033059_PacBio_enhancer-Barcodes.txt.gz 1.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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