NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM791710 Query DataSets for GSM791710
Status Public on Sep 08, 2011
Title 0hrKCl-Input-sampleB1
Sample type SRA
 
Source name cultured cortical neurons E16+7DIV
Organism Mus musculus
Characteristics strain: C57BL6
sample: B1
ip antibody: NA
condition: Unstimulated
fragmentation method: sonication+Mnase digestion
Treatment protocol neuronal cultures were pre-treated with 1 µM tetrodotoxin (TTX) and 100 µM D-APV (Tocris Bioscience) overnight to reduce endogenous neuronal activity prior to stimulation and then left unstimulated or membrane depolarized for 2hrs with 55 mM extracellular KCl by addition of 0.5 volumes of prewarmed depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES pH7.5)
Growth protocol Dissociated cortical cultures (E16+7DIV) grown in neurobasal media supplemented with B27, glutamine, and pen/strep.
Extracted molecule genomic DNA
Extraction protocol Samples were crosslinked, chromatin was fragmented and immunoprecipitation was performed using the indicated antibodies. IP'd DNA was decrosslinked and purified. qPCR was used to validate successful IP before proceeding with library preparation. Input samples were taken after fragmentation, but before IP. Sequencing libraries were constructed by cloning fragments of ~125-175bp using the SOLiD Fragment Library Adaptor kit Module 1-16 (PN4444836)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB SOLiD 4 System
 
Data processing Reads were mapped to mm9 using the large genomes matching pipeline from Life Technolofies with parameters -e 3 -t 35 -z 10. BigWig files were generated for uniquely mapped reads of IP samples; reads were extended to 150 bps, corresponding to the estimated fragmen length of the DNA. If multiple reads were mapped to the same starting base and strand, only one of those reads was retained.
 
Submission date Sep 07, 2011
Last update date May 15, 2019
Contact name Harrison Wren Gabel
E-mail(s) harrison_gabel@hms.harvard.edu
Phone 617-512-0289
Organization name Harvard Medical School
Department Neurobiology
Lab Michael Greenberg
Street address 7 Linden St Apt 3
City Brookline
State/province MA
ZIP/Postal code 02445
Country USA
 
Platform ID GPL14602
Series (2)
GSE31851 Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function
GSE31951 Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [ChIP-Seq]
Relations
SRA SRX096334
BioSample SAMN00716110

Supplementary data files not provided
SRA Run SelectorHelp
Processed data not applicable for this record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap