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| Status |
Public on Jan 07, 2022 |
| Title |
Av-RNA-Rep2 |
| Sample type |
SRA |
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| Source name |
whole animal
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| Organism |
Adineta vaga |
| Characteristics |
strain: MBL
tissue: whole animal
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. PolyA selection.
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 NextSeq 500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (cutadapt v1.9.2), and masked for short sequences (<15nt) or low-quality scores (<20), then mapped to reference genome using TopHat v2.1.1, with default parameters and --max-intron-length 100
Prediction of protein-coding genes in AvL1 strain: BRAKER, a combination of GeneMark-ET and AUGUSTUS, was used to predict protein-coding genes in the AvL1 genome using aligned RNA-Seq data. TopHat aligments were used to generate UTR training examples for AUGUSTUS to train UTR parameters and predict genes. This procedure was done with --softmasking enabled, after masking the genome with RepeatMasker. Total predictions comprised 74,569 gene models, saved as fasta and GFF-format.
Prediction of protein-coding genes in Av reference genome (MBL) was taken from Flot et al. Nature 2013.
Aligned sequence reads were counted by genomic feature with HTSeq-count, using Tophat RNA-seq alignment output bam file and gene annotation gff file.
Supplementary_files_format_and_content: read counts
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| Submission date |
Nov 06, 2019 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Irina Arkhipova |
| E-mail(s) |
iarkhipova@mbl.edu
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| Organization name |
Marine Biological Laboratory
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| Department |
Josephine Bay Paul Center
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| Lab |
Arkhipova Lab
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| Street address |
7 MBL St
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| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
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| Platform ID |
GPL27727 |
| Series (2) |
| GSE140051 |
Non-canonical base modifications of bacterial origin in a eukaryotic genome [RNA-seq] |
| GSE140052 |
Non-canonical base modifications of bacterial origin in a eukaryotic genome |
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| Relations |
| BioSample |
SAMN13226617 |
| SRA |
SRX7107237 |
| 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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