NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6434455 Query DataSets for GSM6434455
Status Public on Jun 27, 2023
Title H3K27Ac, ab4729, MGE, KCl, BioRep 2
Sample type SRA
 
Source name E16 mouse embryos
Organism Mus musculus
Characteristics tissue: E16 mouse embryos
cell type: Primary cortical neurons
genotype: C57/BL6
treatment: 2hr KCl stimulation
chip antibody: H3K27Ac (Abcam, #ab4729)
Treatment protocol Neurons at DIV6 were silenced with 1µM TTX and 100µM D-AP5 overnight. At DIV7 neurons were either stimulated for 2hrs with 55mM KCl or left untreated.
Growth protocol Neurobasal, 2% B27 (Invitrogen), 1mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Forty million cortical neurons were fixed with 1% formaldehyde for 10 minutes at RT followed by quenching and nuclei isolation. The chromatin was then sonicated using Misonix 3000 (Misonix) to obtain fragments of 200 bp to 2 kb and incubated with the H3K27Ac antibody (Abcam, #ab4729) for immunoprecipitation.
Purified immunoprecipitated DNA was sent to BGI China for library construction and sequencing.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description 50bp reads
Data processing Demultiplexed raw fastq files were obtained from BGI China
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Cutadapt v1.18, discarding reads left with < 36 bp.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.3.3 with default settings.
Broad peaks were called uing MACS3 v3.0.0a7 with the significance cut-off q-value <=0.05.
Assembly: bigWig files were generated from BAM files using bamCoverage from deepTools v3.4.3 with a binsize of 3 and smoothing 20. Score represents the raw read coverage of DNA fragments at a given genomic coordinate. broadPeak files were generated using MACS3 v3.0.0a7 with the significance cut-off q-value <=0.05.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, broadPeak
 
Submission date Aug 05, 2022
Last update date Jul 28, 2023
Contact name Ivo Spiegel
E-mail(s) ivo.spiegel@weizmann.ac.il
Organization name Weizmann Institute of Science
Street address 234 Herzl St
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL13112
Series (2)
GSE210656 Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex (ChIP-Seq)
GSE210658 Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex
Relations
BioSample SAMN30169814
SRA SRX16890554

Supplementary file Size Download File type/resource
GSM6434455_H3K27Ac_ab4729_MGE_KCl_B2.broadPeak.gz 1.3 Mb (ftp)(http) BROADPEAK
GSM6434455_H3K27Ac_ab4729_MGE_KCl_B2.bw 725.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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