|
| Status |
Public on Jun 25, 2021 |
| Title |
RNA-Seq Control1 |
| Sample type |
SRA |
| |
|
| Source name |
cultured fetal lung fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblast
cell culture: WI-38
treatment: control miR
|
| Treatment protocol |
Cells were transfected with 50 nM control miRNA or pre-miR-340-5p and cultured for an additional four days, changing media every 48h (DMEM with 20% FBS).
|
| Growth protocol |
WI-38 fibroblasts were plated in a six-well plate at a density of 1 x 10^5 cells for 24h in DMEM + 20% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells using the TriPure isolation reagent (Roche) and the Direct-zol Mini Kit (Zymo) following the manufacturers’ protocols.
Samples were quantified on a NanoDrop ND-1000 instrument. Agarose electrophoresis was used to check the integrality of total RNA samples. 1 ∼ 2 µg total RNA of each sample was taken for RNA-seq library preparation. Briefly, rRNA is removed from the total RNA with a RiboZero Magnetic Gold Kit; The enriched rRNA depleted RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The library preparation procedure included: 1) Fragmentation of the RNA molecules; 2) Reverse transcription to synthesis first strand cDNA; 3) Second strand cDNA synthesis incorporating dUTP; 4) End-repair and A-tailing of the double stranded cDNA; 5) Illumina compatible adapter ligation; 6) PCR amplification and purification for the final RNA-seq library. The completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400 ∼ 600 bp, and adapter dimer contamination. The amount was determined by absolute quantification qPCR method. The barcoded libraries were mixed in equal amounts and used for sequencing on the instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Control1
|
| Data processing |
The RNA-seq reads were aligned to human genome hg19 using Spliced Transcripts Alignment to a Reference (STAR) software version 2.4.0j
featureCounts (v1.4.6-p5) were used to create gene counts
Differential expression analysis of gene counts was performed using the DESeq2 version 1.26.0
Genome_build: human genome hg19
Supplementary_files_format_and_content: text file
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jun 25, 2021 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE165468 |
Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis (RNA-Seq 2) |
| GSE165469 |
Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis |
|
| Relations |
| BioSample |
SAMN17530757 |
| SRA |
SRX9933127 |
