|
| Status |
Public on Mar 16, 2020 |
| Title |
W4_1_4hr_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Rousettus aegyptiacus |
| Characteristics |
cell type: kidney fibroblasts
cell line: RoNi/7.1 cells
tissue: kidney
treatment: recombinant interferon omega4 1ng/mL for 4 hrs
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested in RNAzol RT and frozen at -80°C prior to extraction by pelleting out of DNA and proteins and then precipitation with isopropanol.
RNA libraries were prepared with the Illumina TruSeq® Stranded mRNA Library Prep kit. Pooled libraries underwent pippin size selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing, base-calling, and de-multiplexing was done by Tufts Genomics Center
5’ adapter sequences were trimmed using cutadapt v1.5. Reads shorter than 50 bp were discarded
Trimmed reads were mapped to the Raegyp2.0 genome with hisat2 v2.1.0
Count tables of uniquely mapped reads were tabulated with HTSeq v0.6.1p1
Count tables were used for pairwise differential expression analysis with edgeR (v3.20.9) within the R environment (R version 3.4.3)
Genome_build: Raegyp2.0 genome (RefSeq accession: GCF_001466805.2)
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene
|
| |
|
| Submission date |
Feb 23, 2020 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Stephanie Sarah Pavlovich |
| E-mail(s) |
sdsouza@bu.edu
|
| Organization name |
Boston University School of Medicine
|
| Department |
Microbiology
|
| Lab |
Kepler Lab
|
| Street address |
700 Albany St, W508D
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL24487 |
| Series (1) |
| GSE145761 |
Different Egyptian rousette interferon omega proteins elicit an overlapping but not identical transcriptional response in bat cells. |
|
| Relations |
| BioSample |
SAMN14167083 |
| SRA |
SRX7784796 |
