|
| Status |
Public on May 02, 2019 |
| Title |
NMuMG RNA-seq PBKD replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
NMuMG cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Lentiviral transfection of shPBRM1
|
| Treatment protocol |
Stress treatments were performed immediately prior to RNA extraction. For peroxide stress, cells were treated with media containing 200 µM H2O2 for two hours. For low-glucose stress, cell media was replaced with glucose-free media for six hours.
|
| Growth protocol |
HK-2 cells were cultured in RPMI supplemented with 10% FBS and 1% L -glutamine. NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10 µM/mL insulin, 1% L -glutamine, and 1% sodium pyruvate. All cell lines were grown at 37°C in a humidified atmosphere in a 5% CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA). Genomic DNA for ATAC-seq was obtained according to the ENCODE ATAC-seq pipeline.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were trimmed using Trimmomatic and aligned to the appropriate reference genome using HISAT2 in paired-end mode. ATAC-seq reads were trimmed using Trimmomatic and mapped to the appropriate reference genome using Bowtie2 in very sensitive end-to-end mode.
For RNA-seq, gene expression levels were computed using htseq-count using default parameters. For ATAC-seq, BAM files were converted to BED files using BEDtools.
For RNA-seq, differential expression analysis was performed using edgeR with a FDR threshold of 0.05. For ATAC-seq, peaks of differential enrichment were identified using SICER-df with a false discovery rate threshold of 0.05. The annotatePeaks utility of HOMER was used to annotate statistically significant peaks.
Genome_build: hg19 for HK2. mm10 for NmuMG.
Supplementary_files_format_and_content: For RNA-seq, the raw counts matrix is provided as a tab-delimted text file. For ATAC-seq, files are tab-delimited text containing the annotated peaks obtained from HOMER.
|
| |
|
| Submission date |
May 01, 2019 |
| Last update date |
May 02, 2019 |
| Contact name |
Benjamin Carter |
| E-mail(s) |
beccarte@gmail.com
|
| Organization name |
National Institutes of Health
|
| Department |
NHLBI
|
| Lab |
Keji Zhao
|
| Street address |
10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE113606 |
RNA-seq and ATAC-seq analysis of the role of PBRM1 under stress conditions |
|
| Relations |
| BioSample |
SAMN11549454 |
| SRA |
SRX5774884 |
