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| Status |
Public on Apr 21, 2015 |
| Title |
yak.U.2 |
| Sample type |
SRA |
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| Source name |
D. yakuba_Whole embryo
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| Organism |
Drosophila yakuba |
| Characteristics |
tissue: unfertilized egg
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| Growth protocol |
Egg laying and development at room temperature, until embryos have reached the blastoderm stage, according to morphological criteria.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction (Invitrogen), according to the manufacturer's instructions.
Liraries were made using the standard Illumina Truseq protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
We used the annotation version 5.39 for D. melanogaster and the annotation previously published for D. yakuba, D. pseudoobscura, and D. virilis described in Paris et al. (2013), PLoS Genetics (10.1371/journal.pgen.1003748)
We trimmed all sequenced tags so that their average quality was above 30 and mapped the tags to the transcripts using Bowtie2 [19] with command-line options ‘-a -N 1‘, thereby allowing all possible mappings. We then estimated transcript levels using eXpress [20]. Gene levels were obtained by summing levels over all transcripts of a gene. Gene levels were then normalized to the 95th percentile, log transformed and averaged over replicates. Orthology was assessed from Paris et al. (2013), PLoS Genetics (10.1371/journal.pgen.1003748.
Supplementary_files_format_and_content: six tab-delimited summary tablesincluding normalized and log-transformed FPKM values for all samples. The table is organized as follows: each line corresponds to a particular gene. The corresponding gene ID in the four species and the usual name in D. melanogaster, as well as their genomic localization, and the abundance measurements in all 31 samples. 6 normalizations have been done: simple FPKM (as from eXpress), FPKM+additional median normalization, FPKM + additional 75th percentile normalization, FPKM + additional 95th percentile normalization, FPKM + additional TMM percentile normalization and FPKM + additional quantile normalization.
Supplementary_files_format_and_content: tab table summarizing the maternal/zygotic/maternal-zygotic origin of each gene in each species, according to an SVM classifier. Associated probabilities are indicated.
Gene_abundances_after_p75_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM 75th percentile normalization)
Gene_CLASS_after_p75_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + 75th percentile normalization)
Gene_CLASS_after_FPKM_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM normalization)
Gene_abundances_after_FPKM_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM normalization)
Gene_abundances_after_p50_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + median normalization)
Gene_CLASS_after_p50_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + median normalization)
Gene_abundances_after_p95_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + 95th percentile normalization)
Gene_CLASS_after_p95_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + 95th percentile normalization)
Gene_abundances_after_TMM_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + TMM normalization)
Gene_CLASS_after_TMM_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + TMM normalization)
Gene_abundances_after_Q_normalization.txt: Summary table of abundance measurements in all samples, in all species (FPKM + quantile normalization)
Gene_CLASS_after_Q_normalization.txt: Prediction of transcript origin for all species (maternal/zygotic/maternal-zygotic), included their associated probability, based on an SVM classifier (FPKM + quantile normalization)
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| Submission date |
Apr 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mathilde Paris |
| Organization name |
CNRS
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| Department |
IGFL
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| Street address |
Faculte des sciences de Luminy, case 907
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| City |
LYON |
| ZIP/Postal code |
69007 |
| Country |
France |
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| Platform ID |
GPL13307 |
| Series (1) |
| GSE68062 |
Sex bias and maternal contribution to gene expression divergence in Drosophila blastoderm embryos |
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| Relations |
| BioSample |
SAMN03492553 |
| SRA |
SRX1000512 |
| 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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