|
| Status |
Public on Mar 18, 2023 |
| Title |
NS_Smarce1-MD30_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
neural cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESCs derived neural cells
strain: 129S5/SvEvBrd
treatment: RHB-A (TAKARA#Y40001)
genotype: Smarce1-MD
|
| Treatment protocol |
For direct neural differentiation, mESCs were cultured in RHA-B media for 6 days.
|
| 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. For direct neural differentiation, mESCs were cultured in RHA-B media for 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol (https://www.thermofisher.com/order/catalog/product/15596026)
KAPA Hyper Prep Kit (KK8504)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
NS_Smarce1-MD30_2177396
|
| 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
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) |
| GSE189557 |
Transcription profiling of Smarce1- MD (R42A) and Smarce1- MD mESCs, and their derived cell cultures at day 06 after neural induction. |
| GSE189563 |
Mitotic bookmarking by SWI/SNF subunits |
|
| Relations |
| BioSample |
SAMN23440282 |
| SRA |
SRX13228052 |
