|
| Status |
Public on Jun 07, 2023 |
| Title |
AV HCT116 miRTar3p-1 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial provider: Korean Collection for Type Cultures (KCTC)
cell line: HCT116
treatment: Transfected with 10 nM miR-TAR-3p for 24hrs
genotype: wt
|
| Treatment protocol |
HCT116 cells were plated in 6-well plates and transfected with 10nM of miRNA mimic using RNAiMax. Total RNA was isolated after 24 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
RNA-Seq; sequenced on an NovaSeq SP PE150 using Illumina provided reagents and protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads were mapped to hg38 human genome using Tophat and bowtie2
raw counts were calculated by HTSeq
Assembly: hg38
Supplementary files format and content: Excel sheet with normalized read counts for each sample comparison of interest, along with log2FoldChange values, p-values and adjusted p-values.
|
| |
|
| Submission date |
Nov 17, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Marcus Peter |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Street address |
303 East Superior Street, Lurie 6-123
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE218194 |
Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity (DISE-69) |
| GSE218195 |
Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity |
|
| Relations |
| BioSample |
SAMN31771194 |
| SRA |
SRX18293345 |
