|
| Status |
Public on May 24, 2023 |
| Title |
HEK293 T-Rex Flp-In cells, BRD4-NUT, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
kidney; embryo
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney; embryo
cell line: HEK293
cell type: epithelial
genotype: BRD4-NUT
treatment: 2h 5ng/mL doxycycline + 4h washout
|
| Treatment protocol |
Induction of protein expression was performed by treating cells with 5ng/mL doxycycline for 2h, followed by 4h washout with medium with no added antibiotics.
|
| Growth protocol |
The cells were grown in DMEM medium with addition of 10% heat-inactivated Fetal Bovine Serum, 1% penicillin – streptomycin, 15μg/mL blasticidin and either 100μg/mL zeocin (control cell line) or 100μg/mL hygromycin B (developed stable cell lines).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BNFL_2
|
| Data processing |
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Fastq files were mapped to human genome using STAR (v2.5.3a)
Read counts were generated using featureCounts (subread) for coding genes from igenomes
Differential expression results were generated using edgeR
Assembly: hg19
Supplementary files format and content: tab delimited txt files that includes normalized read counts for each sample per gene
|
| |
|
| Submission date |
May 24, 2023 |
| Last update date |
May 24, 2023 |
| Contact name |
Michael K Rosen |
| E-mail(s) |
michael.rosen@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Biophysics
|
| Lab |
Michael Rosen Laboratory
|
| Street address |
6001 Forest Park Rd., ND8.124
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75235 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE233302 |
Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct [RNA-seq] |
| GSE233303 |
Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct |
|
| Relations |
| BioSample |
SAMN35346250 |
| SRA |
SRX20503064 |
