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Sample GSM4128763 Query DataSets for GSM4128763
Status Public on May 04, 2020
Title HeLa cells, YTHDC1_SCR_B
Sample type SRA
 
Source name adenocarcinoma of the cervix
Organism Homo sapiens
Characteristics cell line: HeLa
sirna used: Control YTHDC1 [Catalog No. 1022076] (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 SAMN13054591
SRA SRX7018706

Supplementary file Size Download File type/resource
GSM4128763_YTHDC1_SCR_B_CIRI2.txt.gz 363.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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