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| Status |
Public on Feb 14, 2019 |
| Title |
HFL4 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Haemulon flavolineatum |
| Characteristics |
tissue: liver
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| Growth protocol |
Wild samples
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAqueous Kit (Life Technologies)
The preparation of normalized cDNA libraries for transcriptome sequencing followed the protocol of Meyer et al., (2009), with modifications for Illumina sequencing. First-strand cDNA synthesis was prepared with 500ng of RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Removal of low-quality reads and PCR duplicates was done with fastq_quality_filter and fastx_clipper, part of the FastX Tool Kit
Adaptor trimming for the TagSeq reads was done with the script rnaseq_clipper.pl (https://github.com/z0on/tag-based_RNAseq).
Mapping to reference transcriptome done with Bowtie2
Scripts used to extract the number of reads that mapped to a particular transcript are available at https://github.com/z0on/tag-based_RNAseq
Differentially Expressed Genes (DEGs) were identified with DESeq2
Genome_build: Trinity-forblast-hmacro.fasta
Supplementary_files_format_and_content: SAM files resulting from assembly to reference transcriptome using Bowtie2
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| Submission date |
Dec 19, 2018 |
| Last update date |
Feb 14, 2019 |
| Contact name |
Moises A Bernal |
| E-mail(s) |
bernal.moises@gmail.com
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| Phone |
7162819985
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| Organization name |
SUNY Buffalo
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| Department |
Biological Sciences
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| Street address |
109 Cooke Hall
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14260 |
| Country |
USA |
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| Platform ID |
GPL25959 |
| Series (1) |
| GSE124093 |
Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon) |
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| Relations |
| BioSample |
SAMN10614717 |
| SRA |
SRX5163594 |
| 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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