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Status |
Public on Jul 28, 2023 |
Title |
RNA-seq siPDS5B replicate2 |
Sample type |
SRA |
|
|
Source name |
RPE cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: RPE control sample: Control_2 treatment: PDS5B siRNA 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.
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|
|
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".
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|
|
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 |
SAMN25817290 |
SRA |
SRX14121464 |