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Sample GSM2496434 Query DataSets for GSM2496434
Status Public on Dec 03, 2017
Title shU_CTCF_ChIPSeq_rep1
Sample type SRA
Source name AML12
Organism Mus musculus
Characteristics tissue: AML12 cells
chip antibody: CTCF
Treatment protocol The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.
Growth protocol AML12 cell were kept in complete growth medium:a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed with 1X10e7 AML12 cells as previously described (Wen et al., 2008).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
Data processing Basecalls performed using CASAVA version 1.4.
Samples were aligned to the mm9 genome using bowtie1.1.2 (-m 1 -n 2 -e 70 -k 1 --best -l 75).
sam files were converted to bam with the samtools version 1.2 and low quailty reads were filtered (MAPQ < 10).
PCR duplicates were removed using Picard.
peaks were called for each samples using MACS2 callpeak with the default parameters except q = 0.01.
we also remove the peaks if they are discordant between biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: bw files were generated using bedtools genomecov: reads were extended to 300bp and coverage were scaled to RPM.
Submission date Feb 21, 2017
Last update date May 15, 2019
Contact name Bo Wen
Organization name Fudan University
Department Institutes of Biomedical Sciences
Street address 130 DongAn Road
City Shanghai
ZIP/Postal code 200032
Country China
Platform ID GPL16417
Series (2)
GSE95113 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 1]
GSE95116 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture
BioSample SAMN06350706
SRA SRX2578763

Supplementary file Size Download File type/resource 192.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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