|
| Status |
Public on Mar 18, 2023 |
| Title |
mitotic mESCs_IgG_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
strain: 129S5/SvEvBrd
treatment: nocodazole synchronization
antibody: Rabbit (DA1E) mAb IgG XP® Isotype Control (CST#3900S)
|
| 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 |
| |
|
| Description |
mitotic mESCs_CUT&RUN_IgG_2041757
mitotic mESCs_CUT&RUN_IgG_2041757
|
| Data processing |
Library strategy: CUT&RUN-seq
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.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of normalized read counts.
Supplementary_files_format_and_content: narrowPeak from MACS2
|
| |
|
| Submission date |
Nov 25, 2021 |
| 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) |
| GSE189560 |
The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis |
| GSE189563 |
Mitotic bookmarking by SWI/SNF subunits |
|
| Relations |
| BioSample |
SAMN23440349 |
| SRA |
SRX13228242 |
