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Sample GSM2789724 Query DataSets for GSM2789724
Status Public on Dec 03, 2017
Title BirA-HNRNPU_ChIPSeq_rep2
Sample type SRA
 
Source name BirA-HNRNPU_ChIPSeq
Organism Mus musculus
Characteristics cell line: AML12
genotype/variation: BirA HNRNPU
chip antibody: Biotin
Treatment protocol The BirA HNRNPU stable cell line was obtained through 1μg/ml puromycin, and then the protein was induced for three days with 0.5μg/ml DOX, and 50μM Biotin treated the cells for one day.
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 BirA-ChIP seq experiments were performed as described (PMID: 22412018). Briefly, 1*10^7 cells were fixed with 4% formaldehyde for 10min at RT, and then the cells were divided into six part equally. Cells were lysed at 25°C in 200ul lysis buffer for 5 min.After cell lysis, the chromatin was sonicated by the Bioruptor sonicator. The cell lysate was centrifuged at 17,000g for 15min at 4°C. Supernatants were incubated with 30 μl High Capacity Streptavidin Agarose (Thermo Fisher Scientific) overnight. Beads were washed twice for 5 min with buffer 1 (2% SDS) at 25°C,once with buffer 2,once with buffer 3 and twice with buffer 4. Lastly, adding 60μl Elution buffer to the beads, and then placed in a 70°C water bath overnight with shaking.
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 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, --broad, --broad-cutoff 0.01.
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 Sep 21, 2017
Last update date May 15, 2019
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
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)
GSE95116 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture
GSE104098 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]
Relations
BioSample SAMN07680671
SRA SRX3203546

Supplementary file Size Download File type/resource
GSM2789724_BirA-HNRNPU_rep2.bw 135.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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