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Sample GSM1662148

Query DataSets for GSM1662148

Status

Public on Apr 21, 2015

Title

yak.M.3

Sample type

SRA

Source name

D. yakuba_Whole embryo_male

Organism

Drosophila yakuba

Characteristics

Sex: Male
developmental stage: Blastoderm
tissue: Whole embryo

Growth protocol

Egg laying and development at room temperature, until embryos have reached the blastoderm stage, according to morphological criteria.

Extracted molecule

total RNA

Extraction protocol

Trizol extraction (Invitrogen), according to the manufacturer's instructions.
Liraries were made using the standard Illumina Truseq protocol

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

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)

Submission date

Apr 20, 2015

Last update date

May 15, 2019

Contact name

Mathilde Paris

Organization name

CNRS

Department

IGFL

Street address

Faculte des sciences de Luminy, case 907