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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
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]
BioSample SAMN07680671
SRA SRX3203546

Supplementary file Size Download File type/resource 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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