|
| Status |
Public on Jun 14, 2021 |
| Title |
ChIP-seq_Crotonate-H3K27me3 |
| Sample type |
SRA |
| |
|
| Source name |
E13.5 Forebrain
|
| Organism |
Mus musculus |
| Characteristics |
age: E13.5
cell type: Embryonic Neural Stem/Progenitor Cells (eNSPCs)
treatment: Crotonate
chip antibody: H3K27me3
chip antibody vendor: PTM Biolab, Hangzhou, China
chip antibody catalog#: 39157
|
| Treatment protocol |
Briefly, NSPCs (passage 2–3) were grown to 50–60% confluence in 10-cm plates, and were treated with water (control group) and 10 mM crotonate (crotonate group) for 24 h.
|
| Growth protocol |
NSPCs isolated from the E13.5 mice forebrain were cultured with DMEM/F12 medium (Invitrogen) supplemented with 20 ng/ml epidermal growth factor and 20 ng/ml fibroblast growth factor (EGF/FGF, PeproTech), 1% penicillin/streptomycin (Invitrogen), 0.5× B27 (Invitrogen), and 0.5× N2 (Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 4’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with default parameters. MACS (v.2.2.7.1) was used to call peaks (-q 0.05) relative to the input sample.
Genome_build: GRCm38
Supplementary_files_format_and_content: bw, Peaks.txt
|
| |
|
| Submission date |
Apr 19, 2021 |
| Last update date |
Jun 14, 2021 |
| Contact name |
Peipei liu |
| E-mail(s) |
strawberrylpp@163.com
|
| Phone |
13041069075
|
| Organization name |
institute of zoology,Chinese academy of sciences
|
| Department |
State Key Laboratory of Stem cells and Reproductive Biology
|
| Lab |
Group of Stem Cell and Neurological Diseases
|
| Street address |
No. 25-1 West Beisihuan Rd, Haidian District, Beijing
|
| City |
beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE172310 |
ChIP-seq analysis of H3K4me3, H3K27ac and H3K27me3 in the neural stem/progenitor cells under crotonate treatment |
|
| Relations |
| BioSample |
SAMN18795673 |
| SRA |
SRX10633830 |
