|
| Status |
Public on Jun 26, 2024 |
| Title |
293_ML60218_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: HEK293T
cell type: epithelial
treatment: ML60218
|
| Treatment protocol |
siRNA is transfected using Lipofectamine® RNAiMax (cat # 13778150) with standard protocol
|
| Growth protocol |
HEK293Tcells were obtained from ATCC (CRL-3216, Batch#70049877) and grown in 10 cm BioLite™ Cell Culture Treated Dishes (Catalog# 12-556-002 Thermo Scientific) in Dulbecco’s Modified Eagle Medium, high glucose (Catalog# 11965092, Gibco). HEK293T experiments were conducted on cells between passage 10-25.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E.Z.N.A.® Total RNA Kit I (Catalog# R6834-01, Omega), with 100% ethanol instead of 70% at the binding step to enrich small RNA.
Kapa Hyper Stranded mRNA library kit (Roche)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Data processing |
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina
Reads were first trimmed using TrimGalore
mapped to the hg38 transcriptome and quantified with Salmon43 Differentially expressed genes were determined using DESeq2
Assembly: hg38
Supplementary files format and content: raw counts, and Transcribe per milion in CSV format
|
| |
|
| Submission date |
May 28, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Ruiying Cheng |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
2178983908
|
| Organization name |
The University of Illinois Urbana-Champaign
|
| Department |
School of Molecular & Cellular Biology
|
| Lab |
Van Bortle Lab
|
| Street address |
B520 Chemical & Life Sciences Laboratory
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE268457 |
mRNAseq: Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters |
|
| Relations |
| BioSample |
SAMN41568268 |
| SRA |
SRX24723240 |
