|
| Status |
Public on Jun 01, 2023 |
| Title |
Ch12 treated with TGFb for 6 hours |
| Sample type |
SRA |
| |
|
| Source name |
Ch12 cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Ch12 cell line
treatment: treated with TGFb for 6 hours
experimental type: mRNA-Seq
|
| Treatment protocol |
Cultured CH12 B cells were treated with TGFb (5 ng/ml; 240-B R&D systems) for a period of 6 h or 24 h before harvesting.
|
| Growth protocol |
CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA-seq: Total RNA was extracted from 0.5 million cultured cells using RNAqueous™ Total RNA Isolation Kit (AM1912). mRNA was then isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
library: RNAch126hTGFb
|
| Data processing |
Base calling: Illumina CASAVA 1.8.2
mRNA-Seq: Align raw reads to the reference genome with STAR.
mRNA-Seq: Quantify transcript and gene abundances with RSEM.
mRNA-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
Genome_build: mm10
|
| |
|
| Submission date |
Jan 22, 2021 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Yongbing Zhao |
| Phone |
3014805852
|
| Organization name |
National Institutes of Health
|
| Department |
NIAMS
|
| Lab |
Casellas Lab
|
| Street address |
10 Center Drive RooM 13C101A
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE165331 |
Genome-wide binding profile of Smad3 and Smad7 in mouse Ch12 cell line (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN17496758 |
| SRA |
SRX9920307 |
