|
| Status |
Public on Apr 14, 2021 |
| Title |
Sample 34_VC_DMSO_B_Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
TK6_VC_DMSO_B
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TK6
cell type: Human lymphoblastoid cell line
chemical: DMSO
concentration: 1% (v/v)
|
| Treatment protocol |
Prior to exposure, cells were plated in 6-well plates with 5 mL of 3x10^5 cells/mL suspension in each well. Cells were exposed to each chemical prepared in their respective vehicle solvent (1% v/v). After 4 hours, cells were rinsed once with PBS and lysed in TempO-Seq lysis buffer. RNA was extracted using a Qiagen RNeasy Mini kit. The exposure was performed on three separate occasions to produce three replicates of each sample.
|
| Growth protocol |
TK6 cells were cultured in suspension in a T75 flask in RPMI1640 medium supplemented with 10% v/v heat-inactivated horse serum, 2 mM L-glutamine, and 1 mM sodium pyruvate at 37ºC in 5% CO2. The cell density was maintained between 1x10^5 cells/mL and 1x10^6 cells/mL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Qiagen RNeasy Mini kit. Quality was assessed using High Sensitiy RNA ScreenTapes on an Agilent TapeStation. RNA integrity number (RIN) of all samples was above 7.5.
The Templated Oligo-Sequencing (TempO-Seq) Human Whole Transcriptome Assay kit (BioSpyder, Carlsbad, CA) was used to generate sequencing libraries using total RNA from TK6 cells following the manufacturer's protocol. An input of 100ng was used from each RNA sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HDACi_DMSO_D0_368_S80
|
| Data processing |
library strategy: TempO-Seq
Initial quality assessment was performed using negative controls (water only) and reference standards (human universal reference RNA and human brain total RNA) included on every TempO-Seq plate. We confirmed very little signal (< 0.3%) from samples with no cells/RNA. The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.42. The FASTQ files were processed using the “pete. star. Script_v3.0” (BioSpyder). The script uses star v.2.5 and the qCount function from QuasR to align the reads and to extract the feature counts specified in a Gene Transfer Format (GTF) file from the aligned reads, respectively.
Using R 3.4.1, the read counts of all samples were normalized as counts per million (CPM) (Law et al. 2014).
Supplementary_files_format_and_content: Text file with counts per million (CPM) for each gene
|
| |
|
| Submission date |
Jan 08, 2021 |
| Last update date |
Apr 14, 2021 |
| Contact name |
Matthew Meier |
| E-mail(s) |
matthew.meier@hc-sc.gc.ca, lauren.bradford@hc-sc.gc.ca
|
| Phone |
613-447-6705
|
| Organization name |
Government of Canada
|
| Department |
Health Canada
|
| Lab |
Mechanistic Studies Division Genomics Laboratory
|
| Street address |
251 Sir Frederick Banting Driveway
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0K9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE164478 |
Development of a transcriptomic biomarker to detect histone deacetylase inhibitors (HDACi) in TK6 cells |
|
| Relations |
| BioSample |
SAMN17265021 |
| SRA |
SRX9808376 |
