|
| Status |
Public on Nov 01, 2023 |
| Title |
HEK293 cells with negative control mimics, sample on 9/18 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
treatment: co-transfection of negative control mimics and Flag-Ago2, followed by Flag-IP
|
| Treatment protocol |
HEK293 cells were cotransfected of Flag-Ago2 with negative control or mir-219 mimics. The cells were lysed and RNA-induced silencing complexes (RISC) were precipitated with anti-flag agarose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA samples from the RISC-IP products were extracted with miVANA miRNA Isolation kit (Thermo Fisher Scientific, Carlsbad, CA)
The library was prepared with NEBnext Ultra II RNA library Prep Kit for Illumina folllowing the manufacturer's mannual.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data mapping with STAR v2.5.
Quantification with HTSeq v0.6.1 to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of he gene and reads count mapped to this gene.
Differential Analysis with DESeq2 R package v2_1.6.3, padj<0.05
Assembly: Hg19
Supplementary files format and content: Raw read counts only
Supplementary files format and content: Raw counts, FPKM values, log2 fold change, P value
|
| |
|
| Submission date |
Jun 26, 2023 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Qingqing Wei |
| E-mail(s) |
QWEI@AUGUSTA.EDU
|
| Phone |
7067213551
|
| Organization name |
Augusta University
|
| Department |
Cellular Biology & Anatomy
|
| Lab |
CB1124
|
| Street address |
1460 Laney Walker Blvd.
|
| City |
AUGUSTA |
| State/province |
Georgia |
| ZIP/Postal code |
30912 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE235842 |
Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis [RIP-Seq] |
| GSE236019 |
Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis |
|
| Relations |
| BioSample |
SAMN35991770 |
| SRA |
SRX20785449 |
