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| Status |
Public on Jun 30, 2015 |
| Title |
post-spawning matured eel |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Anguilla anguilla |
| Characteristics |
tissue: ovary
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were taken from anterior, posterior and middle parts of gonad from each individual, and stored in RNAlater (Ambion) at -80ºC till RNA extraction. The different parts of gonad tissue of each individual were pooled. Total RNA was isolated from the pooled samples using the Qiagen miRNeasy kit according to the manufacturer’s instructions (Qiagen), and analyzed with an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent). A transcriptome library for each individual was prepared from 10 microgram total RNA, using the Illumina mRNAseq Sample Preparation Kit following the manufacturer’s instructions (Illumina Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Origin of specimen: Lake Veerse, The Netherlands, 26 May 2010
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| Data processing |
Illumina Casava software used for basecalling: SCS2.7/RTA1.7
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (Anders et al., 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: Gene Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component; Transcripts; Longest transcript length; Total length; yellow_gonads_fulllength_unique_reads; yellow_gonads_fulllength_corrected_total_reads; yellow_gonads_fulllength_RPKM; silver_gonads_fulllength_unique_reads; silver_gonads_fulllength_corrected_total_reads; silver_gonads_fulllength_RPKM; spawned_gonads_fulllength_unique_reads; spawned_gonads_fulllength_corrected_total_reads; spawned_gonads_fulllength_RPKM; gonads_yellow_vs_silver_foldChange; gonads_yellow_vs_silver_adjlog2FC; gonads_yellow_vs_silver_pval; gonads_yellow_vs_silver_padj; gonads_silver_vs_spawned_foldChange; gonads_silver_vs_spawned_adjlog2FC; gonads_silver_vs_spawned_pval; gonads_silver_vs_spawned_padj; gonads_yellow_vs_spawned_foldChange; gonads_yellow_vs_spawned_adjlog2FC; gonads_yellow_vs_spawned_pval; gonads_yellow_vs_spawned_padj
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| Submission date |
Jun 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ron P Dirks |
| E-mail(s) |
[email protected]
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| Phone |
+31-71-2074610
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| Organization name |
Future Genomics Technologies BV
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| Street address |
Sylviusweg 74
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| City |
Leiden |
| ZIP/Postal code |
2333 BE |
| Country |
Netherlands |
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| Platform ID |
GPL20639 |
| Series (1) |
| GSE70381 |
Changes in ovarian gene expression profiles in maturing European eel (Anguilla anguilla) |
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| Relations |
| BioSample |
SAMN03800398 |
| SRA |
SRX1075739 |
| 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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