|
Status |
Public on Jan 09, 2014 |
Title |
KYSE150_shCtrl_H3K9me3 |
Sample type |
SRA |
|
|
Source name |
KYSE150_shCtrl_H3K9me3
|
Organism |
Homo sapiens |
Characteristics |
cell line: KYSE150 treatment: shCtrl chip antibody: H3K9me3
|
Treatment protocol |
KYSE150 cells were transfected with the indicated pRetrosuper shRNA constructs using Fugene 6 (Roche Diagnostics) according to manufacturer's instructions and selected 24h after transfection with 2 μg/ml puromycin for 72 h prior to harvesting.
|
Growth protocol |
KYSE150 cells were cultured in D-MEM/F-12 1:1 (Invitrogen) supplemented with 10% FBS (Hyclone).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed using formaldehyde crosslinked chromatin sonicated to an average size of 200-600 bp and the indicated antibodies. 5-10 ng of DNA was processed using NEBNext and Illumina ChIP seq kits according to the manufacturer's instructions. In brief, DNA was adaptor-ligated, subjected to gel size selection, amplified and analyzed by Solexa/Illumina high-throughput sequencing.
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Data processing |
No filtering of the raw reads were performed prior to alignment. Raw sequence reads were mapped to the human genome using the the BOWTIE tool (version 0.12.7) with default parameters except: “-S -m 1” OR “-S -m 1 –solexa1.3-quals” BedGraph files were generated by extending each aligned read to 250 bp in the 3' direction & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount” Genome_build: hg18 Supplementary_files_format_and_content: bedgraph: BedGraph files were generated by extending each aligned read in the 3' direction to 250 bp & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”
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|
|
Submission date |
Jan 09, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Marianne Terndrup Pedersen |
E-mail(s) |
marianne.pedersen@bric.ku.dk
|
Organization name |
BRIC
|
Department |
University of Copenhagen
|
Lab |
Kim B. Jensen
|
Street address |
Ole Maaloes Vej 5
|
City |
Copenhagen N |
ZIP/Postal code |
2200 |
Country |
Denmark |
|
|
Platform ID |
GPL10999 |
Series (2) |
GSE28332 |
The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites |
GSE53938 |
The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq KYSE150 cell line) |
|
Relations |
BioSample |
SAMN02580204 |
SRA |
SRX424015 |