|
| Status |
Public on May 04, 2020 |
| Title |
HeLa cells, YTHDC1_KD_B |
| Sample type |
SRA |
| |
|
| Source name |
adenocarcinoma of the cervix
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
sirna used: YTHDC1 siRNA [Catalog No. SI00882161] (Qiagen)
sirna pulse: single
|
| Treatment protocol |
Hela cells (150000) were plated in 35mm plates and transfected 12 hrs later with the siRNA indicated (30 nM) using Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific) according to the manufacturer's instructions. After 48hrs from the first siRNA pulse, cells were harvested (single pulse) or treated with a second 48h hrs siRNA pulse (double pulse).
|
| Growth protocol |
HeLa cells were cultured in DMEM with 10% FBS, L-Glutamine 2 mM and Penicillin/Streptomycin 1X.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA in this study was extracted with TRIazol reagent and the direct-zol RNA Miniprep kit according to the manufacturer’s specifications (ZYMO RESEARCH).
Truseq Stranded Total RNA Prep kit with Ribo-Zero H/M/R treatment (Illumina) was used for the library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bcl2fastq2 (Version 2.20) was used for base calling.
Trimmomatic was used to remove adapter sequences; minimum read length after trimming was set to 20.
Reads were then aligned to the human reference genome (GRCh38) using BWA-MEM with -T 19 option.
CircRNA detection in each sample was then carried out using CIRI2 software with -0 option. To identify circRNA host genes, the program was provided with Ensembl 90 gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Sample-specific CIRI2 output files containing, for each circRNA, its genomic coordinates, the number of supporting reads, the host gene and other information.
|
| |
|
| Submission date |
Oct 18, 2019 |
| Last update date |
May 05, 2020 |
| Contact name |
Gaia Di Timoteo |
| Organization name |
University of Rome "La Sapienza"
|
| Street address |
piazza Aldo Moro 5
|
| City |
Rome |
| State/province |
RM |
| ZIP/Postal code |
00185 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE139076 |
circRNA expression in METTL3 and YTHDC1 KNOCK-DOWN conditions |
|
| Relations |
| BioSample |
SAMN13054589 |
| SRA |
SRX7018708 |
