|
| Status |
Public on Aug 01, 2017 |
| Title |
R2-INT_S7 |
| Sample type |
SRA |
| |
|
| Source name |
viral contents: both FL and DVG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
|
| Treatment protocol |
A549 were either mock infected with, PBS or infected with SeV HD at MOI 1.5 for 24 hrs. cells were trypsinized, resuspended in 1% FBS in PBS, fixed and permeabilized in 100% methanol for at least 15min on ice. Hybridization was performed in100μl hybridization buffer in presence of 1.25μM RNA FISH probes for 16 h in a humidified chamber at 37°C. Cells were resuspended in GLOX anti-fade media for sorting based on different accumulaiton of viral contants
|
| Growth protocol |
3x10^6 A549 cells were plated in 100mm culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples from FISH-FACS-sorted cells were prepared as follows: RNA extracted from TRIzol reagents was re-purified by PicoPureTM RNA isolation kit (Thermo Fisher Scientific).
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Replicate pool 2
Sample 7
|
| Data processing |
fastq files were aligned to Release 79 of human reference All cDNA GRCh38 using Kallisto.
Transcript-level count data were importd into R using the Tximport package
Expression data was normalized using the VOOM function from the Limma package in R, and batch effects were corrected with the ComBat function of the SVA package in R.
Differentially expressed genes (2-fold and ≤ 1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: human transcriptome, build 38 (Homo_sapiens.GRCh38.cdna.all.fa)
Supplementary_files_format_and_content: TxiCounts.txt: raw gene counts
Supplementary_files_format_and_content: TxiAbundance.txt: non-normalized transcripts per million (TPM), summarized to the gene level
Supplementary_files_format_and_content: normData_batchCorrect.txt: transcripts per million (TPM), normalized using Limma VOOM, and summarized to the gene level
|
| |
|
| Submission date |
Mar 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Carolina B Lopez |
| E-mail(s) |
clopezzalaquett@wustl.edu
|
| Phone |
3142737026
|
| Organization name |
Washington University in St. Louis
|
| Street address |
425 S Euclid Ave
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE96774 |
Replication defective viral products exploit a cellular pro-survival mechanism to establish persistent infections |
|
| Relations |
| BioSample |
SAMN06614853 |
| SRA |
SRX2649470 |
