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Sample GSM5938517 Query DataSets for GSM5938517
Status Public on Mar 03, 2023
Title MET41_GU100_24_12
Sample type SRA
 
Source name male liver
Organism Pimephales promelas
Characteristics tissue: liver
developmental stage: adult
Sex: male
treatment: Group exposed to a mixture (41 ug/Lmetformin + 100 ug/Lguanylurea) at 24h
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Tri-Reagent (Molecular Research Center, Inc.) following manufacturer’s protocol and quantified using a Nanodrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE). RNA quality was checked using RNA ScreenTape Analysis on an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep for 48 samples (Illumina, San Diego, CA) according to the manufacturer’s protocol with an epMotion 5075 automated liquid handling platform
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Base calling was done with Illumina Real Time Analysis software v1.17.21.3 and output was converted to FASTQ format with Illumina Bcl2fastq v1.8.4.
Bowtie2 (ver. 2.3.5) was used to map RNA-seq sequencing reads to the full transcriptome of the fathead minnow genome.. RSEM (ver. 1.3.1) was employed to obtain estimated read count matrices for all samples
Genome_build: FHM2.0 EPA internal version with the same genome sequences of GCF_016745375.1. Annotations are publicly available through the UCSC browser hub track data at https://data.cyverse.org/dav-anon/iplant/home/myepa/FHM/FHM2assembly_hub.txt
Supplementary_files_format_and_content: Matrix table with estimated raw gene counts by RSEM for every transcript and every sample
 
Submission date Mar 07, 2022
Last update date Mar 03, 2023
Contact name Weichun Huang
Organization name US EPA
Department ORD
Street address 109 TW Alexander Dr
City Durham
State/province NC
ZIP/Postal code 27711
Country USA
 
Platform ID GPL25572
Series (1)
GSE198081 Effects of metformin and its metabolite guanylurea on fathead minnow (Pimephales promelas) reproduction
Relations
BioSample SAMN26510440
SRA SRX14401104

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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