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Sample GSM3520373 Query DataSets for GSM3520373
Status Public on Feb 14, 2019
Title HCAR1
Sample type SRA
 
Source name liver
Organism Haemulon carbonarium
Characteristics tissue: liver
Growth protocol Wild samples
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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
 
Submission date Dec 19, 2018
Last update date Feb 14, 2019
Contact name Moises A Bernal
E-mail(s) bernal.moises@gmail.com
Phone 7162819985
Organization name SUNY Buffalo
Department Biological Sciences
Street address 109 Cooke Hall
City Buffalo
State/province NY
ZIP/Postal code 14260
Country USA
 
Platform ID GPL25958
Series (1)
GSE124093 Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)
Relations
BioSample SAMN10614727
SRA SRX5163584

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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