|
| Status |
Public on May 27, 2024 |
| Title |
HEK293 cells, ENL-T1, DMSO, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
treatment: DMSO
|
| Treatment protocol |
Cells were treated with DMSO or TDI-11055 (10 μM) for 24 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy UCP Micro kit (Qiagen, #73934) was used to extract total RNA and remove genomic DNA.
500ng total RNA was used for library preparation using polyA mRNA magnetic Isolation module (NEB, #E7490) and RNA library prep kit (NEB, #7770) following manufacturer’s instructions. The library quality was assessed on an Agilent Bioanalyzer DNA chip (Agilent, #5067-1504).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
RNA-seq samples were sequenced using Illumina NextSeq 550.
Raw reads were mapped to the mouse reference genome (hg19) and transcriptome using HISAT2 v 2.2.1 with default parameters.
The raw counts for gene were calculated by featureCounts v2.0.2.
Differentially expressed genes between conditions were statistically determined using R package DESeq2 v1.40.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene raw count number for each sample
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
May 27, 2024 |
| Contact name |
Liling Wan |
| E-mail(s) |
wanlabepigenetics@gmail.com
|
| Organization name |
University of Pennsylvania
|
| Department |
Cancer Biology
|
| Lab |
Wanlab
|
| Street address |
421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE243867 |
Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (RNA-Seq) |
| GSE243871 |
Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney |
|
| Relations |
| BioSample |
SAMN37519109 |
| SRA |
SRX21865384 |
