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| Status |
Public on Mar 03, 2023 |
| Title |
Control_6_4 |
| Sample type |
SRA |
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| Source name |
male liver
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| Organism |
Pimephales promelas |
| Characteristics |
tissue: liver
developmental stage: adult
Sex: male
treatment: Control group at 6h
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| 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
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| Submission date |
Mar 07, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Weichun Huang |
| Organization name |
US EPA
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| Department |
ORD
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| Street address |
109 TW Alexander Dr
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27711 |
| Country |
USA |
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| Platform ID |
GPL25572 |
| Series (1) |
| GSE198081 |
Effects of metformin and its metabolite guanylurea on fathead minnow (Pimephales promelas) reproduction |
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| Relations |
| BioSample |
SAMN26510603 |
| SRA |
SRX14401046 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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