|
| Status |
Public on Jun 19, 2012 |
| Title |
HSF1 STHdhQ7/Q7 Heat Shock ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
STHdhQ7/Q7 striatal cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: striatal cells derived from wild type HdhQ7/Q7 embryonic mice
genotype: HdhQ7/Q7
treatment: cells were heat-shocked at 42°C for six hours
chip antibody catalog #: sc-9144
chip antibody: HSF-1
chip antibody manufacturer: Santa Cruz
|
| Treatment protocol |
cells were heat-shocked at 42°C for six hours
|
| Growth protocol |
STHdhQ7/Q7 and STHdhQ111/Q111 striatal cells derived from wild type HdhQ7/Q7 and HdhQ111/Q111 knock-in embryonic mice were used in this study. Cells were grown at 5% CO2 at 33°C in Dulbecco’s modified Eagle’s medium (DMEM, from CellGro, Manassas, VA) with 10% fetal bovine serum (HyClone, Logan, UT), Pen/Strep/Glutamine and 400 μg/ml G418 (both from CellGro). The cells were only used up to passage 15.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cells were crosslinked with 1% formaldehyde and immunoprecipitated using antibody sc-9144 (Santa Cruz Biotech) for HSF-1. Library preparation for sequencing was performed according to the standard Illumina protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments around 200-300bp were cut from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Samples were sequenced on the Illumina Genome Analyzer II following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against HSF1
|
| Data processing |
Alignment: sequence reads were mapped to the mouse genome (UCSC, mm9) using eland extended with the default parameters.
Only ChIP-Seq reads that aligned to exactly one location in the reference mouse genome were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) to identify bound regions by comparing the enrichment of the IP sample against a control IgG IP for background correction. MACS version 1.4.0rc2 was run with all parameters at their default settings and with an enrichment p-value cutoff of 1e-9
Genome_build: mm9
Supplementary_files_format_and_content: peak files, that are bed files, were generated using MACS version 1.4.0rc2.
|
| |
|
| Submission date |
May 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Laura Riva |
| E-mail(s) |
lriva@mit.edu
|
| Organization name |
MIT
|
| Department |
Biological Engineering
|
| Lab |
Fraenkel Lab
|
| Street address |
77 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE38000 |
Polyglutamine expanded huntingtin dramatically alters the genome-wide binding of HSF1 (ChIP-Seq) |
| GSE38002 |
Polyglutamine expanded huntingtin dramatically alters the genome-wide binding of HSF1 |
|
| Relations |
| SRA |
SRX148354 |
| BioSample |
SAMN00996413 |
