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Sample GSM3504943 Query DataSets for GSM3504943
Status Public on Jun 19, 2020
Title PDP-0-RNA rep1
Sample type SRA
 
Source name 293T_PDP-0-RNA
Organism Homo sapiens
Characteristics cell line: 293T
cell type: human embryonic kidney cell line
treatment: PDP 0 μM + 500 μM s4U
Growth protocol HEK293T cells were grown at 37 °C in DMEM containing 10% FBS and 1% P/S.
Extracted molecule polyA RNA
Extraction protocol 3×10^6 HEK293T cells were seeded per 10-cm cell dish and grown for 24 h. For T > C conversion identification, 0 or 50 μM s4U was added to the medium and grown for another 24 h; For mRNA half-life calculation, 500 μM s4U was added to the medium and grown for 1 h; For PDP-mediated RNA dynamic analysis, PDP (0 or 4 or 8 μM) was added to the medium for 20 min prior to 1 h 500 μM s4U incubation. After that, RNA samples for library construction were prepared by total RNA extraction, polyadenylated RNA isolation, gDNA removal, RNA fragmentation and acrylonitrile treatment. For T > C conversion identification, we named the RNA samples as Con-RNA (no s4U treatment, no acrylonitrile treatment), s4U-RNA (s4U treatment, no acrylonitrile treatment), Con-acrylonitrile-RNA (no s4U treatment, acrylonitrile treatment) and s4U-acrylonitrile-RNA (s4U treatment, acrylonitrile treatment), respectively. For mRNA half-life calculation, we named the RNA samples as halflife-RNA. For PDP-mediated RNA dynamic analysis, we named the RNA samples as PDP-0-RNA (no PDP treatment), PDP-4-RNA (4 μM PDP treatment) and PDP-8-RNA (8 μM PDP treatment), respectively.
Standard RNA seq libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB) according to manufacturer’s instructions. Sequencing was performed on Illumina Illumina HiSeq X Ten.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Basecalls performed using Illumina version 1.9
Reads were removed adapter sequences using cutadapt version 1.18 and deduplicated using FastUniq
RNA-seq reads were aligned to the hg19 genome assembly using hisat2 version 2.1.0 with parameter --mp 4,2
Alignments with mismatch (not induced by SNPs) were extract by python scripts.
Any other results were analysed by python scripts.
Genome_build: hg19
Supplementary_files_format_and_content: csv file contains fragment count, FPM and half-life; mismatch count of fragment csv file contains "mismatch count" and "fragment count" columns; gene level mismatch count of fragment csv files contain the combine of mismatch count and fragment count at the last column.
 
Submission date Dec 07, 2018
Last update date Jun 19, 2020
Contact name Zonggui Chen
E-mail(s) chenzonggui@outlook.com
Organization name Peking University
Department Academy for Advanced Interdisciplinary Studies
Lab Fuchou Tang
Street address No.5 Yiheyuan Road Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL20795
Series (1)
GSE123483 Acrylonitrile-mediated nascent RNA sequencing for transcriptome-wide profiling of RNA dynamics
Relations
BioSample SAMN10532533
SRA SRX5105340

Supplementary file Size Download File type/resource
GSM3504943_FPM_PDP-0-Rep1.csv.gz 2.2 Mb (ftp)(http) CSV
GSM3504943_half-life_1.csv.gz 2.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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