|
| Status |
Public on Mar 18, 2023 |
| Title |
Smarce1-MD #09 BRM014_BAF57_2433156 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
strain: 129S5/SvEvBrd
treatment: BRM014 + MD
antibody: SMARCE1 (Bethyl, A300-810A)
|
| Treatment protocol |
For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off. For mitotic release, mitotic cells were washed out three times by fresh mESC culture medium to remove residual nocodazole and then cultured in mESC medium for the indicated time.
|
| Growth protocol |
mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
https://doi.org/10.1038/nprot.2018.015
KAPA Hyper Prep Kit (KK8504)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Properly paired uniquely mapped reads were obtained using samtools (V1.10, with parameters “-q 10 -F 1804”)
We only kept CUT&RUN fragments with length shorter than 2000 bp for further analysis.
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using IgG (for CUT&RUN) and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
Assembly: mm10
Supplementary files format and content: bigwig files of normalized read counts subtracted by IgG.
Supplementary files format and content: narrowPeak from MACS2
|
| |
|
| Submission date |
Oct 26, 2022 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Zhexin Zhu |
| E-mail(s) |
zhexin.zhu@gmail.com
|
| Organization name |
St Jude Children's Research Hospital
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE189563 |
Mitotic bookmarking by SWI/SNF subunits |
| GSE216657 |
The study of SMARCE1 and SOX2 deposition in DMSO or BRM014 treated Smarce1-MD(R42A) and Smarce1-MD cells at 90 min after releasing from mitosis. |
|
| Relations |
| BioSample |
SAMN31468211 |
| SRA |
SRX18040209 |
