|
| Status |
Public on Jun 30, 2020 |
| Title |
RNASEQ001_G9a_inhibitor_2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116, Treated with G9a inhibitor
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colon cancer
|
| Treatment protocol |
HCT 116 cells and the foreskin fibroblast cells were grown on Lab-Tek II Chamber Slide system with low density and treated with 0.5 μM BIX 01294 trihydrochloride hydrate (B9311, Sigma-Aldrich) for 72 hrs. 10 nM of G9a siRNA (sc-43777, Santa Cruz) was transfected in HCT 116 using LipofectamineTM RNAiMAX Transfection Reagent (13778-075, Invitrogen) and maintained for 72 hrs according to the provided protocol on both 6-well plates and Lab-Tek II Chamber Slide.
|
| Growth protocol |
Human colon cancer cells (HCT116) and the foreskin fibroblast cells (CRL2429,ATCC) were seeded for 48hrs on an 8 well Lab-Tek II Chamber slides (154534, Lab Tek), fixed with 3% monomeric formaldehyde for 15 minutes at room temperature1 and then stored in 70% ethanol at -20°C until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA-Seq library was prepared under the instruction of TruSeq Stranded Total RNA Sample Prep Kit (illumine, RS-122-2201), and the sequencing was done on HiSeq-2000 in SciLife (Stockholm, Sweden)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Treated with G9a inhibitor
|
| Data processing |
map with STAR v2.3.0e aligner
Convert to sorted/index bam files with Samtools v0.1.19
Run cufflinks with --library-type fr-firststrand
Genome_build: HG19
Supplementary_files_format_and_content: Cufflinks FPKM gene counts (no normalization)
|
| |
|
| Submission date |
Jun 16, 2014 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Anita Göndör |
| Organization name |
Karolinska Institutet
|
| Department |
MTC
|
| Lab |
Anita Göndör group
|
| Street address |
Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280
|
| City |
Stockholm |
| ZIP/Postal code |
171 77 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE58535 |
H3K9 methylation fine-tunes coordination of transcription by regulating the conformational plasticity of chromosomal folding [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN02863397 |
| SRA |
SRX603428 |
