Comment[GEAAccession]	E-GEAD-315
MAGE-TAB Version	1.1
Investigation Title	Reference transcriptomic data in silkworm, Bombyx mori
Experiment Description	Total RNAs was extracted from 10 tissues (Anterior silk gland, Anterior part of the middle silk gland, Middle part of the middle silk gland, osterior part of the middle silk gland, Posterior silk gland, Fat body, Midgut, Malpighian tubules, Testis, Ovary) of Bombyx mori (P50T strain) fifth instar day 3 larvae.  These total RNAs were sequenced by Illumina NovaSeq 6000. Firstly, the sequenced fastq data after quality control processes were done was mapped to new reference genome by Hisat2 and based on mapping data, reference transcript sequence data constructed by Stringtie. Consequently, expression amounts of the transcripts in the multiple tissues plus midgut, silk gland, fat body, Malpighian tubules, testis, and ovary from other Bombyx mori (SRA accession numbers are DRA005094, DRA005878.) was quantified by kallisto.
Experimental Design	case control design	organism part comparison design	reference design	replicate design
Experimental Factor Name	tissue
Experimental Factor Type	tissue
Person Last Name	Yokoi
Person First Name	Kakeru
Person Affiliation	Division of Applied Genetics/Insect Genome Research and Engineering Unit, Institute of Agrobiological Sciences, The National Agriculture and Food Research Organization
Person Roles	submitter
Public Release Date	2019-10-17
Protocol Name	P-GEAD-205	P-GEAD-206	P-GEAD-207	P-GEAD-208	P-GEAD-209
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Silkworm daizo strain was reared on an artificial diet (Nihon Nosan Kogyo, Yokohama, Japan) at 25????????C under a 12-hours light/dark photoperiod. Tissues of silk gland, fat body, midgut, Malpighian tubules, testis and ovary were dissected on the 3rd day of fifth instar larva. The silk gland was further subdivided into anterior silk gland (ASG), anterior part of the middle silk gland (MSG-A), middle part of the middle silk gland (MSG-M), posterior part of the middle silk gland (MSG-P) and posterior silk gland (PSG). Each tissue was dissected from one individual and totally three biological replicates were obtained and analyzed separately.	The tissues were homogenized using ISOGEN (NIPPON GENE, Tokyo, Japan) and SV Total RNA Isolation System (Promega, Madison, WI) was used for RNA extraction.	The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, \"tagmentation\" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.	For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are ready for sequencing. Illumina SBS technology utilizes a proprietary reversible terminator-based method that detects single bases as they are incorporated into DNA template strands. As all 4 reversible, terminator-bound dNTPs are persent during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error rates compared to other technologies. The result is highly accurate base-by-base sequencing that virtually eliminates sequence-context-specific errors, even within repetitive sequence regions and homopolymers.	Quality control and trimming for short read data were performed by Trimmomatic-0.36.
SDRF File	E-GEAD-315.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB8614
Comment[Last Update Date]	2019-10-17