|
| Status |
Public on Mar 18, 2023 |
| Title |
Smarce1-AID_3day_r1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
strain: 129S5/SvEvBrd
treatment: Treated with IAA for 3days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
KAPA Hyper Prep Kit (KK8504)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
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.
Counts were further normalized and differentially expressed genes were calculated using DESeq2
Assembly: mm10
Supplementary files format and content: read counts from RSEM
|
| |
|
| 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 |
| GSE216653 |
Transcription profiling of Smarce1- AID mESCs , cultured the cells with IAA treatment from 0min to 7 days. |
|
| Relations |
| BioSample |
SAMN31468181 |
| SRA |
SRX18040347 |
