|
| Status |
Public on Mar 02, 2021 |
| Title |
shTRIM28-1% O2-#2 [SUM159-shTRIM28-1pct-2] |
| Sample type |
SRA |
| |
|
| Source name |
SUM159_TRIM28 knockdown_1% O2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159
cell type: breast cancer cell line
genotype: TRIM28 knockdown
treatment: 1% O2
|
| Treatment protocol |
SUM159 subclones were seeded into 6-well plates in three biological replicates and exposed to 20% or 1% O2 for 24 hours.
|
| Growth protocol |
SUM159 cells were maintained DMEM/F12 (50:50) medium. The culture media were supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin-streptomycin. Cells were cultured at 37°C in a 5% CO2, 95% air incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) and treated with DNase (Qiagen).
Library preparation and sequencing using the Illumina NovaSeq 6000 were performed by Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SUM159-shTRIM28-1pct-2_S26_L001
|
| Data processing |
The Fastq files were subjected to quality check and analyzed by Genialis (https://www.genialis.com/)
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming. Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
astQC reports, alignment statistics and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
The dataset is normalised within DESEq2, and fold change and log2(FC) are reported/computed from that.
The Fastq files were subjected to quality check and analyzed by Genialis (https://www.genialis.com/)
Genome_build: Homo sapiens_GRCh38_ens92
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 01, 2021 |
| Last update date |
Mar 02, 2021 |
| Contact name |
Gregg Leonard Semenza |
| E-mail(s) |
gsemenza@jhmi.edu
|
| Organization name |
Johns Hopkins University
|
| Street address |
733 North Broadway
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE167956 |
HIF-1 Recruits TRIM28 and DNA-PK to Release Paused RNA Polymerase II and Activate Target Gene Transcription in Response to Hypoxia |
|
| Relations |
| BioSample |
SAMN18095142 |
| SRA |
SRX10196161 |
