|
| Status |
Public on Apr 17, 2024 |
| Title |
HCT116_RNA_Nut0h_BR2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
treatment: DMSO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 200,000 frozen cell pellets using the RNAeasy Mini Kit (Qiagen #74104) following the manufacturer’s instructions. otal RNA’s integrity and concentration was assessed using RNA ScreenTape Analysis (Agilent #5067-5576) on an Agilent 2200 Tapestation
Samples were sequenced to reach a minimum number of 30M unique valid paired reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
ENCODE standards were followed to process paired-end reads. Sequencing adapters were trimmed using Trim Galore! (0.6.6).
Reads were then mapped to the reference genome (GRCh37.p13) using STAR (2.7.0f) with parameters recommended by ENCODE. Read counts were quantified using featureCounts from subread (2.0.0)
Normalization and differential analysis were performed using R package DESeq2 (1.36.0)
Library statistics were assessed using FastQC and MultiQC
Assembly: hg19
Supplementary files format and content: raw count, DESeq2 output
|
| |
|
| Submission date |
Jun 27, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Biola M Javierre |
| E-mail(s) |
bmjavierre@carrerasresearch.org
|
| Organization name |
Josep Carreras Leukaemia Research Institute
|
| Lab |
3D Chromatin Organization
|
| Street address |
Ctra de Can Ruti, Camí de les Escoles , s/n
|
| City |
Badalona |
| State/province |
Barcelona |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE235946 |
p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response [RNA-seq] |
| GSE235947 |
p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response |
|
| Relations |
| BioSample |
SAMN36001983 |
| SRA |
SRX20793719 |
