|
| Status |
Public on Apr 01, 2020 |
| Title |
RNAseq on EPZ-6438 treated siMCRS1 replicate A |
| Sample type |
SRA |
| |
|
| Source name |
HepG2_EPZ-6438 treated siMCRS1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: liver cancer cell line
sirna: MCRS1 (s20435 Life Tech)
treated with: 1uM EPZ-6438
|
| Treatment protocol |
siRNA experiments were conducted by adding 50nM siRNA in optimem using RNAimax transfection reagent per manufacturers instructions. Cells were harvested at 72 hours post transfection for processing. For drug treatment experiments. 1uM EPZ-6438 or 1uM DMSO were added 3 days prior to transfections with siRNA as previously described.
|
| Growth protocol |
Cells were grown in DMEM + 10% FBS + P +S and maintained for less than 10 passages.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using trizol and Direct-zol kit (Zymo Research) per manufacturers instructions
Libraries were constructed using Kapa stranded mRNA sequencing kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
EPZ_MCRS1_A
processed data file:
drug_norm_counts.csv
|
| Data processing |
Kallisto was used to quantitate transcript expression levels using GRCh38 reference with the following paramters --single -l 200 -s 50 -b 50
tximport was used to aggregate count data per gene using Kallisto output.
DESeq2 was used for differential expression analysis with an FDR of 0.5 and no explicit fold change cut off
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files of count data for each sample
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Jesse Raab |
| E-mail(s) |
jesse.r.raab@gmail.com
|
| Organization name |
University of North Carolina Chapel Hill
|
| Department |
Genetics
|
| Street address |
120 Mason Farm Rd
|
| City |
Chapel Hill |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE97412 |
Expression analysis of INO80 complex in HepG2 liver cancer cells [RNA-seq] |
| GSE97413 |
INO80 complex assembly is antagonized by PRC2. |
|
| Relations |
| BioSample |
SAMN06688201 |
| SRA |
SRX2708852 |
