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Status |
Public on Dec 03, 2017 |
Title |
BirA-HNRNPU_ChIPSeq_rep1 |
Sample type |
SRA |
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Source name |
BirA-HNRNPU_ChIPSeq
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Organism |
Mus musculus |
Characteristics |
cell line: AML12 genotype/variation: BirA HNRNPU chip antibody: Biotin
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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.
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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%.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina MiSeq |
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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.
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Submission date |
Sep 21, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Bo Wen |
E-mail(s) |
bowen75@fudan.edu.cn
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Organization name |
Fudan University
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Department |
Institutes of Biomedical Sciences
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Street address |
130 DongAn Road
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City |
Shanghai |
ZIP/Postal code |
200032 |
Country |
China |
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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] |
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Relations |
BioSample |
SAMN07680672 |
SRA |
SRX3203545 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2789723_BirA-HNRNPU_rep1.bw |
138.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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