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Sample GSM7421858 Query DataSets for GSM7421858
Status Public on May 24, 2023
Title HEK293 T-Rex Flp-In cells, BRD4-p300(I), biol rep 1
Sample type SRA
 
Source name kidney; embryo
Organism Homo sapiens
Characteristics tissue: kidney; embryo
cell line: HEK293
cell type: epithelial
genotype: BRD4-p300(I)
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 Q1
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 SAMN35346241
SRA SRX20503073

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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