|
| Status |
Public on Jun 22, 2021 |
| Title |
Histone-Kcr_Crotonate_E13.5_NSPCs_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Neural stem/progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E13.5 forebrain derived neural stem/progenitor cells (NSPCs)
passages: P1-P3
strain: C57BL/6
|
| Treatment protocol |
Briefly, NSPCs (passage 2–3) were grown to 50–60% confluence in 10-cm plates, and were treated with DMSO (control group), 10 mM crotonate (crotonate group), or 1 μM MS-275 (MS-275 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 |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA library prep kit for Illumina® (NEB) was used with 2 ug of total RNA for the construction of sequencing libraries.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v. 2.3.5.1) with default parameters. MACS (v. 2.2.5) was used to call peaks (-q 0.05) relative to the IgG sample.
Genome_build: GRCm38
|
| |
|
| Submission date |
Jan 02, 2019 |
| Last update date |
Jun 22, 2021 |
| Contact name |
Dai Shang Kun |
| E-mail(s) |
daisk@sdut.edu.cn
|
| Organization name |
Shandong University of Technology
|
| Department |
School of Life Sciences and Medicine
|
| Lab |
Laboratory of Developmental and Evolutionary Biology
|
| Street address |
266 Xincun West Road
|
| City |
Zibo |
| State/province |
Shandong |
| ZIP/Postal code |
255000 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE124540 |
ChIP-seq and RNA-seq analysis of histone Kcr in the embryonic forebrain and neural stem/progenitor cells. |
|
| Relations |
| BioSample |
SAMN10678412 |
| SRA |
SRX5192762 |
