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Sample GSM4647555 Query DataSets for GSM4647555
Status Public on Apr 29, 2021
Title SETX-KO_MeDIP-Seq
Sample type SRA
 
Source name HAP1 SETX Knockout Cells
Organism Homo sapiens
Characteristics cell type: HAP1 cells derived from male CML cell line KBM7
morphology: Fibroblast-like
genotype: SETX Knockout
chip antibody: anti-5meC clone 33D3
Treatment protocol Cells were harvested by trypsinization followed by two washes with ice-cold PBS.
Growth protocol Human HAP1 WT and DSETX cells were cultured in IMDM (ThermoFisher) supplemented with 10% FBS (Sigma-Aldrich) and 1% Penicillin/Streptomycin (Sigma-Aldrich). Cells were grown at 37°C and in a humidified atmosphere containing 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted and sonicated to ~150-300 bp using a Misonix Sonicator 300 equipped with a microtop. Illumina adaptors were added to the sonicated DNA and immunoprecipitated using a mouse monoclonal antibody against 5-methylcytosine (5meC; Clone 33D3, Active Motif) following the protocol described in the Active Motif MeDIP kit (Active Motif, Catalog No. 55009).
Libraries were prepared according to Illumina's instructions. Deep sequencing libraries were generated from the DNA immunoprecipitates and input DNA by the standard consecutive enzymatic steps of end-polishing, dA-addition and adaptor ligation. After a final PCR amplification step using barcoded primers, the resulting DNA libraries were quantified and sequenced.
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina NextSeq 500
 
Description MeDIP-Seq
Data processing Sequenced reads were aligned to the human hg19 genome assembly using Burrows Wheeler Aligner (BWA, RRID:SCR_010910) with default settings.
Only reads that aligned with no more than 2 mismatches and mapped uniquely to the genome were used for subsequent analyses. PCR duplicate reads were removed.
The sequence reads represented the 5’-ends of the IP-fragments, hence the reads were extended in silico using proprietary software from Active Motif at their 3’-ends to a length of 150 bp to match the fragment length of the library. To identify the density of fragments, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. The resulting metric (“fragment density”) was used for the peak metrics in further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files representing normalised coverage, created using the standard Active Motif MeDIP-seq pipeline.
 
Submission date Jun 30, 2020
Last update date Apr 29, 2021
Contact name Steve West
E-mail(s) stephen.west@crick.ac.uk
Organization name The Francis Crick Institute
Street address 1 Midland Road
City London
ZIP/Postal code NW1 1AT
Country United Kingdom
 
Platform ID GPL18573
Series (2)
GSE143574 Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2
GSE153577 Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 [MeDIP-Seq]
Relations
BioSample SAMN15408009
SRA SRX8642913

Supplementary file Size Download File type/resource
GSM4647555_2_2995Crick_HAP1-SETX-KO_MeDIP_i6_uniqnorm_signal.bw 74.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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