|
| Status |
Public on Jul 28, 2023 |
| Title |
RNA-seq siNIPBL 72h replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
RPE cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: RPE
control sample: Control_1
treatment: NIPBL siRNA#1
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 |
SAMN25817305 |
| SRA |
SRX14121449 |
