 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 15, 2020 |
| Title |
Treat 3- Co |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow-derived cell line SK-N-SH
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
cell type: Neuroblastoma
treatment: Treated (simultaneously exposed to H2O2 and ATRA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed directly in the culture plates by the addition of 1ml Trizol reagent. Lysate was transferred to microcentrifuge tubes and 200ml of chloroform was added before centrifugation at 13000g at 4°C for 10 minutes in accordance with the manufacturer’s instructions (ThermoFisher). The resultant aqueous phase, containing total RNA, was separated from organic phase and mixed with 80μg glycogen and 500μL isopropanol, and incubated at -20°C overnight for RNA to precipitate. After centrifuge at 9000g at 4°C for 30 minutes, the supernatant was discarded, and the pellet was washed with 75% cold ethanol twice. Finally, the RNA pellet was re-suspended in nuclease-free water and stored at -80°C.
Briefly, 350 ng of total RNA (RNA integrity number (RIN) ≥ 8.5) was DNAse I treated (1U/μg RNA, Thermo Scientific, Waltham, MA, USA), before ribosomal RNA depletion using the Ribo-Zero kit (Illumina, San Diego, CA, USA). The Illumina TruSeq Stranded Total RNA Library Prep Kit was applied to construct sequencing libraries according to the manufacturer’s protocol. In order to determine the quality and concentrations of libraries, High Sensitivity DNA Bioanalyzer chip was used,
Total RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Co_treatment-differential.expression.results.txt
|
| Data processing |
Reads Quality Control; Fastqc (v0.11.8)
Reads Trimming; Cutadapt (v2.10)
Reads Alignment to the Reference Genome; HISAT2 (v2.1.0)
Reads Quantification (Counting); htseq-count (v0.7.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing read counts for individual samples, generated by htseq-count
Space-delimited (Co-treatment) and tab-delimited (Pre-treatment) text files containing differential expression and FDR data
|
| |
|
| Submission date |
Nov 20, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Behnaz Khavari |
| E-mail(s) |
behnaz.khavari@uon.edu.au
|
| Organization name |
University of Newcastle
|
| Department |
School of Biomedical Sciences and Pharmacy
|
| Lab |
Murray Cairns Lab
|
| Street address |
1 University Dr Callaghan
|
| City |
Newcastle |
| State/province |
NSW |
| ZIP/Postal code |
2308 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE161860 |
Oxidative Stress Impact on the Transcriptome of Differentiating Neuroblastoma Cells |
|
| Relations |
| BioSample |
SAMN16844653 |
| SRA |
SRX9536223 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4916141_AH3-counts.txt.gz |
213.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
