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Sample GSM831875 Query DataSets for GSM831875
Status Public on Jun 04, 2013
Title MelJuSo doxorubicin H3K4me3 ChIP-seq
Sample type SRA
Source name MelJuSo cells
Organism Homo sapiens
Characteristics cell type: Human skin melanoma cell line
treatment: Doxorubicin 9uM 2 hours
time point: 24 hours post drug removal
cell line: MelJuSo
chip antibody: H3K4me3
chip antibody manufacturer: Abcam
chip antibody catalog #: ab1012
chip antibody lot #: 814968
Treatment protocol Cells were treated with indicated drugs for 2 hours and followed by extensive washing . Cells were further cultured for another 24 hours before cells were fixed and subjected for ChIP procedures.
Growth protocol Cells were grown in 15cm dishes around 80% confluency.
Extracted molecule genomic DNA
Extraction protocol After fixation, lysates were cleared from sonicated nuclei and antibodies against H3K4me3 were used to IP the histone-DNA complexes. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against H3K4me3
Data processing Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm with default parameter.
Submission date Nov 11, 2011
Last update date May 15, 2019
Contact name Baoxu Pang
Organization name Stanford University
Department Genetics
Lab Michael Snyder
Street address 3165 Porter Drive
City Palo Alto
State/province CALIFORNIA
ZIP/Postal code 94304
Country USA
Platform ID GPL10999
Series (2)
GSE33633 Epigenetic changes due to histone eviction induced by anthracycline doxorubicin and aclarubicin
GSE33634 Topoisomerase II inhibitors and histone eviction
SRA SRX105598
BioSample SAMN00754063

Supplementary file Size Download File type/resource
GSM831875_MJ_ChIP_H3K4trimet_Doxo_macspeaks.bed.gz 284.4 Kb (ftp)(http) BED
GSM831875_MJ_ChIP_H3K4trimet_Doxo_uniq-q37.bam 532.2 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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