|
| Status |
Public on Nov 02, 2023 |
| Title |
A549 12 h 0.05% DMSO rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
A549
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: non small cell lung cancer cell line
genotype: wt
treatment: 12 h, 0.5% DMSO
|
| Treatment protocol |
Cells were treated with 5uM BRM014 or 0.05% DMSO for 12 hours
|
| Growth protocol |
Cell were grown in F12-K + L-glutamine (Gibco 21127-022, lot 2517130) with 10% Fetal Bovine Serum (Thermo Fisher #1600044) and 1X Penicillin-Streptomycin (Thermo Fisher #10378016)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in Trizol and ERCC92 spike-ins were added by cell number. Total RNA was extracted with chloroform precipitation and Dnase treated. Samples were run on the tapestation to confirm RNA integrity scores > 8.5
Sequencing libraries were prepared from 500 ng of RNA using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion using 9 cycles of PCR amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed for a minimum quality score of 20 Using a custom script (https://github.com/AdelmanLab/NIH_scripts/tree/main/trim_and_filter_PE) reads were trimmed for a minimum quality score of 20 prior to trimming adapater sequences using cutadapt (v1.14). Reads were then first mapped to ERCC92 spike-ins using bowtie (v1.2.2), before aligning to hg38 using STAR (v2.7.3a). Mapped reads were deduplicated using STAR.
GetGeneAnnotations (GGA) scripts (https://github.com/AdelmanLab/GetGeneAnnotation_GGA) were used to annotate dominant active TSS and TES positions from RNA-seq data in H1299 and A549 cells. Gene counts were generated using featurecounts function of the Rsubread package (v2.0.1), and log2 fold change following BRM011 treatment calculated with DESeq2 version (v1.26.0). As the ERCC92 spike-ins did not show a statistically significant difference between DMSO and BRM014 conditions, RNA-seq was normalized using the DESeq2 generated size factors.
Assembly: hg38
Supplementary files format and content: A549_RNAseq_raw_gene_counts.tsv - A549 RNA-seq raw gene counts generated by featureCounts
Supplementary files format and content: H1299_RNAseq_raw_gene_counts.tsv - H1299 RNA-seq raw gene counts generated by featureCounts
|
| |
|
| Submission date |
Oct 06, 2022 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Karen Adelman |
| E-mail(s) |
karen_adelman@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE198517 |
Inhibition of SWI/SNF broadly disrupts enhancers and reveals remodeler redundancy at promoters |
|
| Relations |
| BioSample |
SAMN31185189 |
| SRA |
SRX17820225 |
