 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 17, 2021 |
| Title |
miRNA-TiBP-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish whole embryos
|
| Organism |
Danio rerio |
| Characteristics |
strain: 5D
developmental stage: 48 h post fertilization
treatment: TiBP
|
| Treatment protocol |
Embryos were treated with EC80 or limit concentrations of FRCs from 6 to 48 hpf.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FRC-exposed embryos were homogenzied in RNAzol (4 replicates per treatment) and total RNA was extracted using the Direct-zol MiniPrep kit. Total RNA was then processed for library preparation
mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively.
Illumina HiSeq 3000, single end, 100 bp for mRNA and 50 bp for small RNA
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
miRNA Sample 49
|
| Data processing |
For mRNA seq, reads were evaluated by FastQC v0.11.3 to detect major sequencing problems, and then trimmed for quality control with Skewer v0.2.2 to remove ends of reads with low mean Phred quality score. RNA-seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 (GRCz10) genome
For mRNA seq, the Bioconductor package, edgeR v3.26.0, was used to normalize gene counts and determine differential expression
For miRNA, reads were evaluated by FastQC v0.11.3 to detect major sequencing problems, and then trimmed for quality control with Skewer v0.2.2 to remove ends of reads with low mean Phred quality score. RNA-seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 (GRCz10) genome
For miRNA, the Bioconductor package, edgeR v3.26.0, was used to normalize miRNA gene counts and determine expression
Genome_build: GRz10 for mRNA
Supplementary_files_format_and_content: DGE_rlog_TMM_normalized_counts_FRC_mRNA.tab is a tab-delimited text files include TMM-normalized values for each Sample
Supplementary_files_format_and_content: Combined_HTSeq-count_table_FRC_mRNA.tab is a tab-delimited text files contain raw gene counts for every gene and every sample
Supplementary_files_format_and_content: DGE_rlog_transformed_counts_FRC_miRNA.tab is a tab-delimited text file with transformed miRNA counts for each sample
Supplementary_files_format_and_content: Count_matrix_FRC_miRNA.tab is a tab-delimited text file with miRNA counts for each sample
|
| |
|
| Submission date |
Mar 16, 2021 |
| Last update date |
Mar 17, 2021 |
| Contact name |
Christopher Michael Sullivan |
| Organization name |
Oregon State University
|
| Department |
Environmental & Molecular Toxicology
|
| Lab |
Robert L. Tanguay
|
| Street address |
Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97333 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE169013 |
Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks |
|
| Relations |
| BioSample |
SAMN18321092 |
| SRA |
SRX10356670 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
