|
| Status |
Public on Mar 27, 2017 |
| Title |
psop2 |
| Sample type |
SRA |
| |
|
| Source name |
Opercular, lateral line organ-enriched
|
| Organism |
Polyodon spathula |
| Characteristics |
tissue: Opercular
developmental stage: Stage 46 yolk-sac larvae
|
| Treatment protocol |
Stage 46 yolk-sac larvae were preserved in RNALater (Ambion, Thermo Fisher Scientific Inc., Waltham, MA) overnight at 4oC. Excess solution was removed and sample were stored at -80oC until processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Opercular (lateral line organ-enriched) and fin (no lateral line organs) tissues were manually dissected and pooled from different sets of 6-7 specimens each, to form three biological replicates. RNA was extracted using Trizol reagent (Ambion), as per manufacturer's protocol. RNA concentration was assessed using a Nanodrop N1000 spectophotometer and integrity using an Agilent 2100 Bioanalyzer (Cambridge Genomic Services). Only samples with a RNA integrity number (RIN) greater than 9 were used for next-generation sequencing.
Libraries were prepared following the standard Illumina RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Opercular paired end data biological replicate 2
|
| Data processing |
High-quality reads were filtered based on the score value given in fastq files (FastQC vers. 0.10.1)
Read lengths were trimmed and reads with primer/adaptor sequences removed using Trimmomatic-0.30)
Reads were de novo assembled using Velvet (ver. 1.2.10) and OASES (ver. 0.2.08). Velvet and OASIS were run using different k-mer lengths k27-k77 in k10 increments along with other default parameters. Results of these assemblies were merged using Velvet and OASES k-mer of K27.
Reads were mapped back to the transcriptome using Bowtie2 (vers. 2-2.1.0).
SAM files were cleaned to remove PCR duplicates and long-stretch (>85%) poly-A sequences.
Transcript counts for each sample were obtained with HTseq-count (vers. 0.5.4p3). A locus-to-transcript mapping file was used to collapse related transcripts and obtain locus-level counts.
The BioConductor package DESeq was used for differential expression analysis. A p-value of <0.1 was considered significant after adjustment (multiple testing using Benjamini-Hochberg)
Enrichment Analysis: Gene ontology (GO) and protein domain annotations were extracted from relevant UniProt records. Enrichment analysis was performed using hypergeometric mean and Bonferonni multiple testing correction. Enriched genes were classified using GO terms according to molecular function using the web-based resource PANTHER (Mi et al., 2016 Nucl. Acids Res. (2016) doi: 10.1093/nar/gkv1194).
Supplementary_files_format_and_content: Modrell_Suppl_File_1.xlsx: File contains protein uniprot id; Gene symbol; Gene description; Locus id; log2Fold and Fold change from the differential expression analysis; Padj value (p-value adjusted for multiple testing with Benjamini-Hochberg); Enriched protein domains and Enriched gene ontology terms
Supplementary_files_format_and_content: countTable_gt2_v3.txt: Raw count data for each loci for each biological replicate
Supplementary_files_format_and_content: pfish_v3_chordates.blast2.txt: Top blast results for all transcripts against chordates. These are in compact format with no alignments. There can be multiple hits per transcript.
Supplementary_files_format_and_content: pfish_v3_drerio.blast2.txt: Top blast results for all transcripts against zebrafish. These are in compact format with no alignments. There can be multiple hits per transcript.
Supplementary_files_format_and_content: pfish_v3_chordates_func.txt: Extracted functional mapping of top blast hits against chordates for the highest scoring transcript in each locus (where the blast score is <= 10e-5). Loci with no matches will not be represented in this file. The file also contains extracted GO terms and PFAM terms, where present.
Supplementary_files_format_and_content: pfish_v3_zfish_func.txt: Extracted functional mapping of top blast hits against zebrafish for the highest scoring transcript in each locus (where the blast score is <= 10e-5). Loci with no matches will not be represented in this file. The file also contains extracted GO terms and PFAM terms, where present.
|
| |
|
| Submission date |
Dec 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Clare Baker |
| E-mail(s) |
cvhb1@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
PDN
|
| Street address |
Anatomy Building, Downing Street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 3DY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22801 |
| Series (1) |
| GSE92470 |
Insights into electrosensory organ development, physiology and evolution from a lateral line organ-enriched transcriptome |
|
| Relations |
| BioSample |
SAMN06146131 |
| SRA |
SRX2426798 |
