|
| 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 |
| 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) |
| 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 |
|
| Relations |
| BioSample |
SAMN06350706 |
| SRA |
SRX2578763 |
