|
| Status |
Public on Jul 20, 2020 |
| Title |
NS_Dex Rep1 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL cell line
|
| Organism |
Mus musculus |
| Characteristics |
background strain: FVBN
genotype: Tal1/Lmo2
tissue: Thymic tumor
cell type: T-ALL cell line
RNAi knockdown: non-targeting shRNA
|
| Growth protocol |
6 hours with 100 nM dexamethasone
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purelink RNA mini kit
BGI-Seq500 Library prep method; MultiPLEX single End
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
4_FPKM
T-ALL cell line (1390) derived in this lab from a thymic tumor that arose in a Tal1/Lmo2 transgenic mouse
Tal1/Lmo2 transgenic mice contain transgenes Tal1 and Lmo2 under the LCK promoter, which result in transformation of the thymocytes
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Clean reads are mapped to reference using HISAT/Bowtie2
Gene expression level quantified by RSEM
Differential genes screened by EBseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the annotation of the genes and the FPKM values from RSEM for each sample
|
| |
|
| Submission date |
Jun 05, 2018 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Julie Zhu |
| E-mail(s) |
julie.zhu@umassmed.edu
|
| Phone |
5088565377
|
| Organization name |
UMass Medical School
|
| Department |
Molecular Cellular and Cancer Biology
|
| Street address |
364 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE115363 |
ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN09370645 |
| SRA |
SRX4169234 |
