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| Status |
Public on Aug 19, 2019 |
| Title |
Nipbl_dCas9Control_rep1 |
| Sample type |
SRA |
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| Source name |
v-Abl transformed pro-B cell line
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| Organism |
Mus musculus |
| Characteristics |
cell type: v-Abl transformed pro-B cell line
genotype: JH-del, dCas9 expressing, Emu-Bcl2, RAG2 deficient
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| Treatment protocol |
3 uM STI-571 treated for 4 days
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| Growth protocol |
RPMI1640+15% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 20 million cells were crosslinked in 37oC prewarmed culture medium with 1% formaldehyde for 10 min at RT. Cells were then treated with cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50 mM TrisCl pH 8.1, 10 mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4oC to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin was then precleared with Dynabeads Protein A at 4oC for 2 hours. 1/30 lysates were kept as input and the rest were incubated with 5 ug NIPBL antibody (Bethyl Laboratories, A301-779A) overnight at 4oC. IP samples were then captured by Dynabeads Protein A at 4oC for at least 2 hours, followed by bead washing and elution. IP and Input DNA were de-crosslinked at 65oC overnight and purified via Qiagen PCR purification columns. Purified DNA was subjected to ChIP-Seq library preparation with Illumina Truseq ChIP Sample Preparation Kit (Illumina, IP-202-1012).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
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| Description |
aligned to mm9 genome
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| Data processing |
Library strategy: ChIP-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Unmapped reads were filtered using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Peak calling was performed using MACS2 with the following commands:
macs2 callpeak -t IP.bam -c Input.bam -n Result_directory --nomodel --extsize 51 --nolambda -B --SPMR -g mm --verbose 0 --broad
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples, bed files contain peak calling information.
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| Submission date |
Apr 23, 2019 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Frederick W Alt |
| E-mail(s) |
jianqiao.hu@childrens.harvard.edu
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| Organization name |
Boston Children's Hospital
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| Department |
PCMM
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| Lab |
Alt
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE130213 |
The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [ChIP-Seq] |
| GSE130224 |
The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination |
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| Relations |
| BioSample |
SAMN11484049 |
| SRA |
SRX5726852 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3733939_Nipbl_dCas9Control_rep1.broadPeak.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
| GSM3733939_Nipbl_dCas9Control_rep1.bw |
639.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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