|
| Status |
Public on Mar 20, 2015 |
| Title |
snoG:dox#2 |
| Sample type |
SRA |
| |
|
| Source name |
H9c2 cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: cardiac ventricular myoblast
|
| Treatment protocol |
Cells were seeded in 10cm plates 24h prior to treatment; treatment was 1h with water, DPI (500nM), dox (20uM), or both DPI and dox.
|
| Growth protocol |
H9c2 cells (ATCC: CRL-1446) were maintained in DMEM/10% FBS at subconfluent density and low passage (<20)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected by trypsinization and washed in PBS. Cytosol was isolated by plasma membrane permeabilization and differential centrifugation. Cytosolic RNA was isolated using Trizol LS.
Indexed RNA-seq libraries were made using the Illumina TruSeq Small RNA kit. Libraries were amplified with 14 cycles of PCR, pooled, and separated by PAGE. Products from small RNA with input sizes of 35 to 350 nucleotides were excised, collected, and sequenced using an Illumina HiSeq 2500.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cytoplasmic RNA
size 35-350nt
|
| Data processing |
Demultiplexed data was uploaded to Galaxy for manipulation. FASTQ Groomer and Quality trimmer were applied and FASTQC was used to review raw data quality. 3' adapter sequences were removed using Clip.
Reads were mapped to rat genome (rn4) using Bowtie. Resulting SAM files were converted to BAM format.
BAM files were imported to Partek Genomics Suite (6.6) for read annotation and quantification.
Read frequencies were normalized as RpM (reads per million) based on the total number of reads obtained per indexed sample (deposited as matrix_table.csv).
Genome_build: rn4 (Ensembl e69, RGSC3.4.69)
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Mar 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher L Holley |
| Organization name |
Duke University
|
| Street address |
2301 Erwin Rd
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27705 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE67050 |
Cytosolic Accumulation of Small Nucleolar RNAs (snoRNAs) is Dynamically Regulated by NADPH Oxidase |
|
| Relations |
| BioSample |
SAMN03433289 |
| SRA |
SRX961264 |
