|
| Status |
Public on Nov 10, 2012 |
| Title |
R53-L6-Input-Sequences |
| Sample type |
SRA |
| |
|
| Source name |
Human neonatal epidermis_input
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human differentited primary keratinocytes (NHEK)
|
| Treatment protocol |
Medium containing high calcium levels (1.8mM) was used to induce differentiation in NHEK cells. Cells were collected 24 hours after the switch to high calcium medium
|
| Growth protocol |
NHEK cells were grown in DermaLife medium (LifeLine Cell Technologies) at 37C, 5%CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 24 ug of sonicated chromatin was used for each IP. The following antibodies were used : Grhl3 (Andersen Lab), WDR5 (AbCam cat#ab56919)
Sequencing libraries were generated for the GRHL3, WDR5, and Input samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [PMID 19275939]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calls were made using RTA version 1.12.4.2.
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using macs14, with input aligned sequences as the control file, m fold of 8,30, and p-value 1e-7
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: Human hg19
Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations
|
| |
|
| Submission date |
Nov 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Amelia Soto Hopkin |
| E-mail(s) |
sotoa@uci.edu
|
| Phone |
9498249372
|
| Organization name |
University of California Irvine
|
| Department |
Biological Chemistry & Medicine
|
| Lab |
Bogi Andersen
|
| Street address |
250 Sprague Hall
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92617 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE42180 |
Genome-wide binding of WDR5 and GRHL3 |
|
| Relations |
| SRA |
SRX204108 |
| BioSample |
SAMN01805314 |
