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| Status |
Public on Apr 05, 2018 |
| Title |
st3_rep2 |
| Sample type |
SRA |
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| Source name |
spider embryos
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| Organism |
Parasteatoda tepidariorum |
| Characteristics |
isolate: Osaka
tissue: whole embryo
developmental stage: stage 3 (20-21 h AEL)
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| Growth protocol |
Embryos were incubated at 25˚C until they reached the appropriate stages.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Poly(A) mRNA was extracted using the Dynabeads mRNA DIRECT Kit (Ambion) from 10-100 embryos of each successive developmental stage.
mRNA was fragmented using the NEBNext Rnase III RNA Fragmentation Module (New England BioLabs). Sequencing libraries were constructed from fragmented RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England BioLabs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
devRNAseq_aug3_RPKM.txt
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| Data processing |
Base call and quality scoring were performed by the Real Time Analysis software application during Illumina's sequencing runs.
Sequence reads were trimmed for adaptor and primer sequences and low-quality sequences using the CLC Genomics Workbench 7.0.3 (Qiagen) with the following parameter settings: trim using quality scores, limit=0.05; trim ambiguous nucleotides, maximum number of ambiguities=2; filter on length, discard reads below length=30. Trimmed reads were then aligned to Ptep_1.0 genome assembly using the BLAT algorithm version 34 in the DDBJ Read Annotation Pipeline with default settings.
The output alignments were filtered based on quality, coverage, and uniqueness using a perl script filterPSL.pl available from the AUGUSTUS 3.0.1 scripts folder. The parameter settings were as follows: minimum coverage, 60%; minimum percent identity, 90%; unique threshold, 0.96. The filtered alignments were converted into sam files with a custom perl script.
Using the sam files, abundance of mRNAs against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62) was calculated with htseq-count v. 0.6.1p1 in -s reverse, -m union settings and was normalized in Reads Per Kilobase of exon per Million reads (RPKM).
The alignments were converted into wig files using a script aln2wig available from the AUGUSTUS 3.0.1 scripts folder.
Genome_build: Ptep_1.0
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for gene models and the features of the gene models.
Supplementary_files_format_and_content: wig files ; Scores represent normalized read coverage (per 10 million reads).
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| Submission date |
Apr 04, 2018 |
| Last update date |
Apr 05, 2018 |
| Contact name |
Hiroki Oda |
| E-mail(s) |
hoda@brh.co.jp
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| Organization name |
JT Biohistory Research Hall
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| Lab |
Laboratory of Evolutionary Cell and Developmental Biology
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| Street address |
1-1 Murasaki-cho
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| City |
Takatsuki |
| State/province |
Osaka |
| ZIP/Postal code |
569-1125 |
| Country |
Japan |
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| Platform ID |
GPL24841 |
| Series (1) |
| GSE112712 |
Developmental profiling of gene expression in embryos of the spider Parasteatoda tepidariorum |
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| Relations |
| BioSample |
SAMN08865684 |
| SRA |
SRX3885538 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3081869_NN741_st3.wig.gz |
119.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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