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| Status |
Public on Jun 01, 2013 |
| Title |
C4 ChIP-Seq |
| Sample type |
SRA |
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| Source name |
Blood lymphocytes
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| Organism |
Homo sapiens |
| Characteristics |
individual type: control
gender: male
mutation type: N/A
cell type: blood lymphocyte
phenotype: control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lymphocytes were isolated from 10 ml Heparin blood using a swelling buffer (155 mM NH4CL2, 10 mM KHCO3, 0,01 mM EDTA) to disrupt erythrocytes.
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature. Chromatin was sonicated using a Bioruptor sonicator (Diagenode, Liège, Belgium) for 28 minutes at high power, 30 s ON, 30 s OFF, and ChIP was performed using a CTCF antibody (Millipore, Billerica, MA, USA; 07-729). 7 ng of DNA as measured by Qubit (Life Technologies) was prepared for sequencing. A barcoded NEXTflex adaptor was ligated to the DNA fragments, and fragments with adaptors were amplified by a pre-size selection PCR of 4 cycles, followed by size selection (∼300 bp) and further amplification by 14 PCR cycles. Three barcoded samples were sequenced in one lane on a HiSeq 2000 (Illumina, San Diego, CA, USA). The reads were demultiplexed using CASAVA 1.8.2 (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were mapped to the human GRCh37 genome (hg19; assembly February 2009) using BWA 0.6.1 with standard parameters.
All duplicate reads and reads mapping to repeat regions were removed.
Peaks were called using MACS 1.4.2 with default settings, with the ENCODE UW Gm12878 lymphoblastoid cell line ChIP-seq input track used as background control.
Gm12878 control input track is a publicly available data set generated at the University of Washington as part of the international ENCODE project (http://www.genome.gov/10005107).
Genome_build: hg19
Supplementary_files_format_and_content: MACS output files; an .txt file with peak data and a .bed file with peak scores
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| Submission date |
May 10, 2013 |
| Last update date |
Jun 14, 2022 |
| Contact name |
Jo Huiqing Zhou |
| E-mail(s) |
jo.zhou@radboudumc.nl
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| Organization name |
Radboud University
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| Street address |
Geert Grooteplein 26/18
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| City |
Nijmegen |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE46832 |
De novo mutations in the genome organizer CTCF cause Intellectual Disability (ChIP-Seq) |
| GSE46833 |
De novo mutations in the genome organizer CTCF cause Intellectual Disability |
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| Relations |
| BioSample |
SAMN02142013 |
| SRA |
SRX277081 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1138985_macspeaks_vsinput_ctcf_1e5_C4_peaks.bed.gz |
372.3 Kb |
(ftp)(http) |
BED |
| GSM1138985_macspeaks_vsinput_ctcf_1e5_C4_peaks.xls.gz |
509.0 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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