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Sample GSM1062365 Query DataSets for GSM1062365
Status Public on Jan 22, 2013
Title ChIP_STHdhQ111_JUND_reps1and2
Sample type SRA
 
Source name STHdhQ111
Organism Mus musculus
Characteristics strain: 129SvEv/CD1
cell type: Embyronic E14 striatal derived
genotype: HdhQ111/Q111
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 SRX216287
BioSample SAMN01885656

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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