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Sample GSM4332394 Query DataSets for GSM4332394
Status Public on Mar 16, 2020
Title D1_100_8hr_Rep1
Sample type SRA
 
Source name kidney
Organism Rousettus aegyptiacus
Characteristics cell type: kidney fibroblasts
cell line: RoNi/7.1 cells
tissue: kidney
treatment: recombinant D1 peptide 100ng/mL for 8 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 SAMN14167061
SRA SRX7784785

Supplementary file Size Download File type/resource
GSM4332394_D1_1_8hr_p2.txt.gz 83.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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