|
| Status |
Public on Jun 27, 2023 |
| Title |
H3K27Ac, ab4729, E14CTX, KCl, BioRep 1 |
| 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 |
SAMN30169819 |
| SRA |
SRX16890549 |
