|
| Status |
Public on Mar 18, 2023 |
| Title |
Smarce1-MD09_240min_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
strain: 129S5/SvEvBrd
treatment: cells were released from mitosis for 240 min
|
| 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 |
total RNA |
| Extraction protocol |
Click-iT® Nascent RNA Capture Kit (https://www.thermofisher.com/order/catalog/product/C10365)
KAPA Hyper Prep Kit (KK8504)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
nascent RNA
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Total stranded RNA sequencing data were mapped to mouse genome assembly mm10 using an internal AutoMapper pipeline. Briefly, the raw reads were trimmed with trim galore (V0.60) and mapped to mouse genome mm10 using STAR V2.7.1a.
Then the read counts were computed using RSEM(V1.3.0) based on GENCODE vM23.
RPM (Reads Per Million) was applied to normalize read counts in bigwig tracks
Genome_build: mm10
Supplementary_files_format_and_content: read counts from RSEM
|
| |
|
| 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) |
| GSE189559 |
The study of nascent RNA transcripts in asynchronous cells and cells released from mitosis at the indicated timepoints between Smarce1- MD (R42A) and Smarce1- MD mESCs. |
| GSE189563 |
Mitotic bookmarking by SWI/SNF subunits |
|
| Relations |
| BioSample |
SAMN23440403 |
| SRA |
SRX13228018 |
