|
| Status |
Public on Mar 18, 2023 |
| Title |
E14T_mit_input_2381321_rep1 |
| 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: NA
|
| 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.
|
| 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 |
truChIP® Chromatin Shearing Kit (https://www.covaris.com/products-services/kits-reagents/truchip)
KAPA Hyper Prep Kit (KK8504)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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.
Uniquely mapped reads for ChIP-seq were obtained using samtools (V1,10), with parameter “-q 10 -F1024".
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using Input (for ChIP-seq) as control and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
RPM was applied to the normalized read counts to generate bigwig tracks
Assembly: mm10
Supplementary files format and content: bigwig files of normalized read counts and subtracted by input
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 |
| GSE216663 |
The study of SOX2 deposition in asynchronous and mitotic E14TG2a cells |
|
| Relations |
| BioSample |
SAMN31468264 |
| SRA |
SRX18040245 |
