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Status |
Public on Jun 19, 2020 |
Title |
PDP-0-RNA rep1 |
Sample type |
SRA |
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Source name |
293T_PDP-0-RNA
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Organism |
Homo sapiens |
Characteristics |
cell line: 293T cell type: human embryonic kidney cell line treatment: PDP 0 μM + 500 μM s4U
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Growth protocol |
HEK293T cells were grown at 37 °C in DMEM containing 10% FBS and 1% P/S.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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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.
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Submission date |
Dec 07, 2018 |
Last update date |
Jun 19, 2020 |
Contact name |
Zonggui Chen |
E-mail(s) |
chenzonggui@outlook.com
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Organization name |
Peking University
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Department |
Academy for Advanced Interdisciplinary Studies
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Lab |
Fuchou Tang
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Street address |
No.5 Yiheyuan Road Haidian District
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City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100871 |
Country |
China |
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Platform ID |
GPL20795 |
Series (1) |
GSE123483 |
Acrylonitrile-mediated nascent RNA sequencing for transcriptome-wide profiling of RNA dynamics |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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