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Sample GSM1481573 Query DataSets for GSM1481573
Status Public on Dec 31, 2015
Title H3K27ac LTED
Sample type SRA
Source name LTED
Organism Homo sapiens
Characteristics cell line: LTED
chip antibody: H3K27ac (ab4729 abcam lot GR132150)
protocol: DMEM without phenol + 10% DCS-FBS and1% Pen-Sprep-Glutamine
Growth protocol Cells were cultured in DMEM containing 10%FCS or DCFCS (plus drugs, see Shaw et al 2006 for conditions).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and H3K27ac--DNA complexes were isolated with antibody.
Libraries were prepared according to NEB DNA UltraKit's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated using Ampure SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the H-Seq2000 following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description H3K27ac LTED
Data processing Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 300 bp to create summary windows. Alignments were done using Bowtie 1.0.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm ( using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files
Submission date Aug 19, 2014
Last update date May 15, 2019
Contact name Luca Magnani
Organization name Imperial College London
Department Surgery and Cancer
Lab Magnani's Lab
Street address DuCane road
City London
ZIP/Postal code W120NN
Country United Kingdom
Platform ID GPL11154
Series (1)
GSE60517 Drug specific epigenetic reprogramming leads to increased cellular invasion in ERα positive breast cancer via de novo cholesterol biosynthesis.
BioSample SAMN03002681
SRA SRX685194

Supplementary file Size Download File type/resource
GSM1481573_H3K27ac_Darbre_LTED_treat_afterfiting_all.wig.gz 344.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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