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Sample GSM5884401 Query DataSets for GSM5884401
Status Public on Jul 28, 2023
Title RNA-seq siNIPBL si8 replicate2
Sample type SRA
 
Source name RPE cells
Organism Homo sapiens
Characteristics cell type: RPE
control sample: Control_1
treatment: NIPBL siRNA#2
treatment time: 72h
Treatment protocol RNAi transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in accordance with the manufacturer's protocol, using final RNA duplex concentration of 50 nM.
Growth protocol RPE cells were routinely cultured in DMEM supplemented with penicilline-streptomycin-L-glutamine solution (Wako) and 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Thermo Fisher Scientific) and Nucleospin RNA kit (Macherey-Nagel) following the manufacturer's instructions. Removal of rRNA was performed by using Ribo-Zero Gold rRNA Removal Kit (Illumina.)
Sequencing library preparation by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing BAM-formatted map files were generated using STAR version 2.7.3a with default parameters. "Allsamples.GRCh38.xlsx" is the expression matrix.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: The expression values were estimated by RSEM v1.3.1 with the option "--estimate-rspd --strandedness reverse".
 
Submission date Feb 09, 2022
Last update date Jul 28, 2023
Contact name Ryuichiro Nakato
E-mail(s) rnakato@iqb.u-tokyo.ac.jp
Phone +81-3-5841-1471
Organization name The University of Tokyo
Department Institute for Quantitative Biosciences
Lab Laboratory of Computational Genomics
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
 
Platform ID GPL16791
Series (2)
GSE196449 Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [RNA-seq]
GSE196450 Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
Relations
BioSample SAMN25817302
SRA SRX14121452

Supplementary file Size Download File type/resource
GSM5884401_2017_034B_si8_d3_rep2.GRCh38.genes.results.txt.gz 1.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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