|
| Status |
Public on Feb 18, 2014 |
| Title |
Input_DNA |
| Sample type |
SRA |
| |
|
| Source name |
HT1080_Input_DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT1080
cell type: Fibrosarcoma cells
chip antibody: none
|
| Growth protocol |
HT1080 cells were cultured in Minimum Essential Medium Eagle, Alpha Modification (MEM-alpha) supplemented with 5% FBS, penicillin, and streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei crosslinked with 5% formaldehyde were sonicated and precleared with crosslinked Staph A cells. ChIPs were performed with a 1:200 dilution of mouse monoclonal 1B1 directed against the N-terminus of CSB (Hua-Ying Fan, University of Pennsylvania) precipitated using Protein G Dynabeads (Invitrogen). The input sample was digested with RNase, protease, and decrosslinked without enrichment by ChIP. The input sample was digested with RNase, protease, and decrosslinked without enrichment by ChIP. The ends of the ChIP and input samples were repaired using End-It (Epicentre), A-tailed using Taq polymerase (Invitrogen), and Illumina paired-end sequencing adapters were ligated using Quick T4 DNA Ligase (NEB). DNA fragments ranging from 400 to 700 bp were selected and purified by PAGE, then preamplified for 9 (input) or 12 cycles (ChIP) using Illumina paired-end preamplification primers and BioRad iTaq supermix. The preamplified samples were purified using a Qiagen PCR Cleanup kit and sequenced on the Genome Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3
|
| Data processing |
Base calls were made using Illumina RTA 1.5
Raw reads were trimmed to 60 bp and filtered to remove pairs of reads in which either mate contained 3 or more base calls with a PHRED score below 20. Trimmed, filtered reads were aligned to the hg19 human genome using Bowtie v0.12.7 with settings -n 0 -m 1 --chumkmbs=256 -S to SAM format
A fragment map in bedGraph format was generated using a Perl script that treated paired end reads as the boundaries of IPed fragments. For Input controls, an equal number of fragments from the Input pool were randomly selected to match the number of enriched fragments for XPB or XPD. This fragment map was converted to binary bigWig format using the UCSC bedGraphtobigWig tool.
Peaks were called using MACS v1.4 with a p-value < 1e-15
Summits were located in peaks using a Perl script that searched for the highest point of fragment overlap in each peak.
Genome_build: hg19
Supplementary_files_format_and_content: A fragment map in bedGraph format was generated using a Perl script that treated paired end reads as the boundaries of IPed fragments. This fragment map was converted to binary bigWig format using the UCSC bedGraphtobigWig tool. Scores represent the number of fragments overlapping each genomic position.
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lucas T Gray |
| E-mail(s) |
lucasg@alleninstitute.org
|
| Organization name |
Allen Institute for Brain Science
|
| Department |
Molecular Genetics
|
| Lab |
Tasic
|
| Street address |
615 Westlake Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44849 |
Genome binding profile of TFIIH helicases XPB and XPD in HT1080 cells |
|
| Relations |
| SRA |
SRX246955 |
| BioSample |
SAMN01939160 |
| Named Annotation |
GSM1092546_xpb_input_fragments.bigWig |
| Named Annotation |
GSM1092546_xpd_input_fragments.bigWig |
