|
| Status |
Public on Jan 22, 2013 |
| Title |
ChIP_STHdhQ7_JUND_reps1and2 |
| Sample type |
SRA |
| |
|
| Source name |
STHdhQ7
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129SvEv/CD1
cell type: Embyronic E14 striatal derived
genotype: HdhQ7/Q7
passages: less than 15
chip antibody: Jund (Santa Cruz, sc-74x, lot B0111)
|
| Growth protocol |
STHdhQ7 and STHdhQ111 cell lines were cultured according as described previously (Trettel et al, Hum Mol Genet, 2000). In order to stop cell division and mitigate cell cycle differences, the culture is maintained at 33oC and raised to 39oC for two days prior to each experiment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-seq
processed data file: ChIP_STHdhQ7_STHdhQ111_JUND_GPS_significant.txt
|
| Data processing |
ChIP-Seq reads were aligned to the reference mouse genome (mm9) using Bowtie (v0.12.7).
The enrichment of genomic regions for protein binding was assessed relative to a set of control reads obtained by sequencing unenriched IgG bound DNA.
Binding events were identified using the GPS algorithm(v1.1) with a calculated alignable genome size of 2.107 Gbp, a standard expected ChIP-Seq read distribution, a multiple hypothesis corrected enrichment q-value cutoff of 1e-2, and an alpha value of 20.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab delimited file contains GPS output with the following columns: Location (the genome coordinate), IP binding strength (the number of IP reads associated with the event), Control binding strength (the number of control reads in corresponding region), Fold enrichment (IP/Control), -log10(Q-value), -log10(P-value), IPvsEMP [KL divergence from the empirical read distribution (log10(KL))], IPvsCTR [KL divergence from the read density in the corresponding control region (log10(KL))]
|
| |
|
| Submission date |
Jan 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Ng |
| Organization name |
Massachusetts Institute of Technology
|
| Street address |
77 Massachusetts Ave.
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE43429 |
Extensive changes in DNA methylation are associated with expression of mutant huntingtin [ChIP-seq] |
| GSE43433 |
Extensive changes in DNA methylation are associated with expression of mutant huntingtin |
|
| Relations |
| SRA |
SRX216286 |
| BioSample |
SAMN01885655 |
