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| Status |
Public on Dec 31, 2014 |
| Title |
DAOY_ZFX_ChIPseq |
| Sample type |
SRA |
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| Source name |
DAOY cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: medulloblastoma cell line
cell line: DAOY
chip antibody: ZFX
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| Growth protocol |
Cells were maintained in high glucose 1x DMEM (Gibco) with 10% heat-inactivated FBS and supplemented to 1x for: non-essential amino acids, sodium pyruvate, L-Gln, and pen/strep. Media was also made with 4 uL/L betamercaptoethanol.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonication-sheared nuclear lysate from DAOY human MB cells was obtained using Covaris sonicator and truChIP High Cell Chromatin Shearing Kit with SDS Shearing Buffer, as per manufacturer's specifications. For ZFX ChIP-seq, ZFX-DNA complexes were isolated using a rabbit polyclonal antibody against Zfx and via IP with Protein A Dynabeads (invitrogen). Sonication-sheared chromatin not subjected to IP was used as the Input control.
Library construction and sequencing were performed at the Yale Center for Genome Analysis. Briefly, magnetic AMPure XP beads (Beckman Coulter) are used to purify the user-sheared DNA samples and remain with the sample throughout library construction. Following each process step, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution. Following fragmentation, T4 DNA polymerase and T4 polynucleotide kinase blunt end and phosphorylate the fragments. The large Klenow fragment then adds a single adenine residue to the 3' end of each fragment and custom adapters (IDT) are ligated using T4 DNA ligase. The inserts are size-selected in-solution and adapter-ligated DNA fragments are then PCR amplified using custom-made primers (IDT). During PCR, a unique 6 base index is inserted at one end of each DNA fragment. Samples were sequenced on a single-end version 3 Illumina flow cell on a HiSeq 2000
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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 |
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were aligned to the human hg19 genome using the short read aligner Bowtie (2.0.0)
Significantly enriched ChIP regions were identified using the Model-based analysis of ChIP-Seq (MACS) (1.4.0) using data from sonication-sheared Input chromatin as control
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated by MACS. The 5th column of MACS-generated bed files is the -10*log10pvalue of peak region.
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| Submission date |
Mar 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Colin Palmer |
| E-mail(s) |
cjp2123@columbia.edu
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| Organization name |
Columbia University
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| Department |
Microbiology & Immunology
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| Lab |
Reizis Lab
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| Street address |
701 W. 168th Street
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE45394 |
Anti-ZFX ChIP-seq in a human medulloblastoma cell line |
| GSE45396 |
Transcription factor ZFX |
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| Relations |
| SRA |
SRX253212 |
| BioSample |
SAMN01985563 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1103555_DAOY_peaks.txt.gz |
205.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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