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Sample GSM3140412 Query DataSets for GSM3140412
Status Public on Feb 13, 2019
Title KS1-S1
Sample type SRA
 
Source name Pooled, whole zebrafish embryos
Organism Danio rerio
Characteristics strain: AB
developmental stage: 96 hpf
# embryos pooled per sample: 15
exposure: Control (0.01% DMSO)
Treatment protocol Embryos were manually dechorionated at 24 hpf. Exposures were renewed every 24 hours.
Growth protocol Embryos were maintained in 100 mm petri dishes at 37 degrees Celsius throughout the study.
Extracted molecule polyA RNA
Extraction protocol Samples collected at 4 dpf into FastPrep homogenization tubes containing TRIzol Reagent (Invitrogen, Carlsbad, CA) and 0.1 mm RNase-free glass beads (Next Advance Inc., Troy, NY). All contents were vortexed for 15 s and homogenized in a FastPrep-24 5G benchtop homogenizer equipped with the QuickPrep adapter (MP Biomedicals, Santa Ana, CA). The supernatant was transferred to a sterile tube, and total RNA was purified using the Direct-zol RNA MicroPrep kit with in-column DNase-I treatment following manufacturer instructions (Zymo Research, Irvine, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols. PolyA capture, paired ends. Total RNA (input of 1 microgram) was used to isolate poly(A) mRNA and prepare stranded libraries using the NEBNext Ultra-II Directional RNA Library Prep Kit for Illumina following manufacturer instructions (New England Biolabs, Ipswich, MA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina BaseSpace Sequence Hub platform
annotated and assessed using the Illumina RNA-Seq Alignment (v1.1.1) and Cufflinks Assembly & DE (v2.1.0) apps
Data provided as FRKM
Genome_build: Danio rerio UCSC danRer7 (RefSeq gene annotation)
Supplementary_files_format_and_content: Processed data files are given as .csv. Log2 FPKM values are presented, as well as q-values.
 
Submission date May 11, 2018
Last update date Feb 13, 2019
Contact name Karilyn Sant
E-mail(s) ksant@sdsu.edu
Organization name San Diego State University
Department School of Public Health
Lab Sant
Street address 5500 Campanille Dr., Hardy Tower 119
City San Diego
State/province CA
ZIP/Postal code 92182
Country USA
 
Platform ID GPL14875
Series (1)
GSE114356 This study examined gene expression in zebrafish embryos exposed to 0 (0.01% DMSO), 16 µM, or 32 µM perfluorobutane sulfonate.
Relations
BioSample SAMN09198492
SRA SRX4073781

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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