|
| Status |
Public on May 13, 2021 |
| Title |
SUM-159 control replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
cultured SUM-159 cells
|
| Organism |
Homo sapiens |
| Characteristics |
transfection treatment: control
fusion buffer: none
|
| Treatment protocol |
Cells were transfected with VSV-G using Lipofectamine 3000 (Thermo) according to manufacturer's instructions.
|
| Growth protocol |
SUM-159 cells were grown in a 37C, 5% CO2 tissue culture incubator on tissue culture treated dishes. Cells were cultured in DMEM + 10% FBS, L-glutamine, and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Media was removed and cells were lysed with Trizol (Thermo) according to manufacturer's instructions. A second CHCl3 extraction was performed to increase purity. Total RNA was quantified by Nanodrop.
RNA-seq libraries were made from 5 ng total RNA spiked with 1e-5 final dilution of ERCC Mix 1 (Thermo) using Ovation RNA-seq v2 kit (NuGEN) to make cDNA and Ovation Rapid DR Multiplex System (NuGEN) to make libraries according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequencing reads were trimmed to remove TruSeq adapters using Cutadapt v1.16, then were aligned to the human genome (Hg38) using STAR v2.5.3a.
Gene expression estimates were made using the built-in htseq-count feature in STAR.
Differential expression analysis was performed using edgeR v3.6 with FDR = 0.05. Gene enrichment analyses were performed using DAVID Bioinformatics Resources.
We used ToppCluster and Cytoscape to construct the subcategory network.
Genome_build: Hg38
Supplementary_files_format_and_content: gene_counts_matrix.txt = text file containing un-normalized htseq counts
|
| |
|
| Submission date |
Mar 03, 2021 |
| Last update date |
May 13, 2021 |
| Contact name |
Daniel Feliciano |
| E-mail(s) |
[email protected]
|
| Organization name |
Janelia, HHMI
|
| Street address |
19700 Helix Dr
|
| City |
Ashburn |
| State/province |
VA |
| ZIP/Postal code |
20147 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE168125 |
YAP1 nuclear efflux and transcriptional reprograming is triggered by membrane diminution upon VSV-G-induced cell fusion |
|
| Relations |
| BioSample |
SAMN18121056 |
| SRA |
SRX10218234 |
