Comment[GEAAccession]	E-GEAD-390
MAGE-TAB Version	1.1
Investigation Title	Transcriptome analysis of chicken-quail F1 hybrid blastoderms
Experiment Description	We quantified gene expression in parental species and chicken- and quail-derived allele-specific expression in the hybrids at the early blastoderm and preprimitive streak stages by mRNA sequencing.
Experimental Design	development or differentiation design
Experimental Factor Name	organism
Experimental Factor Type	organism
Person Last Name	Ishishita
Person First Name	Satoshi
Person Affiliation	Matsuda Group, Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University
Person Roles	submitter
Public Release Date	2020-09-28
Protocol Name	P-GEAD-611	P-GEAD-612	P-GEAD-613	P-GEAD-614	P-GEAD-615
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	To extract total RNAs from blastoderms at the stage X, blastoderms were collected from the eggs that were laid on each day, which were preserved at 12 degree C immediately after being laid. To extract total RNAs of blastoderms at the stage XIII/XIV, we began the incubation of the eggs within 3 d after they were collected and preserved at 12 degree C, and blastoderms were collected after 7.5-10.0 h of incubation.	Cell suspensions were lysed in TORIZOL reagent, Life Technologies, Carlsbad, CA, USA, immediately after tissue sampling. The solutions including blastodermal tissues were transferred into QIAshredder Mini Spin Columns, Qiagen, Hilden, Germany, and spun down. The flow-through samples were stored at -80 degree C until use. The frozen samples were thawed on ice, and total RNAs were purified according to the manufacturers instructions. The aqueous phases were transferred into Buffer RLT of RNeasy Plus Micro Kit Qiagen and then total RNAs were purified.	RNA quality was assessed using Bioanalyzer Pico Chips, Agilent Technologies, Santa Clara, USA. RNAs whose RNA Integrity Numbers were over 7.5 were used for mRNA sequencing. We converted oligodT-selected RNA into cDNA libraries for mRNA sequencing using the SureSelect Strand Specific RNA Library preparation kit, Agilent Technologies, according to the manufacturers instructions.	The libraries were sequenced on an Illumina HiSeq 2500 platform using paired-end sequencing (100 bp). A total of 174 GB was obtained from 48 libraries (average of 3.6 GB per sample).	We trimmed the adapter sequences from the reads using Trimmomatic v0.33, and then mapped the reads to the reference genome (Accession codes: GCF_000002315.5 for chickens and GCF_001577835.1 for quail) using HISAT2 v2.1.0. Multi-mapped reads and reads with >2 mismatches were filtered out using SAMtools v1.9, and orphan reads were eliminated using a custom Perl script. Read counts per gene were calculated by HTSeq v0.11.2 using concordantly aligned read pairs. For the analysis of allelic expression in the hybrids, reads that were mapped to both reference genomes of parental species were removed before the calculation of read counts per gene using Bash scripts.
SDRF File	E-GEAD-390.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB3482
Comment[Last Update Date]	2020-09-28