Dataset Information

Circular transcriptome sequencing of the middle silk gland and posterior silk gland in the Bombyx mori.

ABSTRACT: Circular transcriptome sequencing of the middle silk gland (MSG) and posterior silk gland (PSG) in the Bombyx mori are presented. The middle silk gland and posterior silk gland were collected from the third day of fifth-instar B.mori larvae. The circular RNAs enriched by using RNase R to degrade the linear RNA molecules, and circular RNA sequencing (circRNA-seq) was performed using an Illumina Hiseq. 2500 sequencing platform. Samples are described in the SRA portal (SRP100385) and FASTQ files have been deposited in Sequence Read Archive (accession numbers: SRX2577343 and SRX2577342). The interpretation of these data is presented in the following research article: "Identification of circular RNA in the Bombyx mori silk gland" [1] (Gan et al., 2017).

SUBMITTER: Gan H

PROVIDER: S-EPMC5671477 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Circular transcriptome sequencing of the middle silk gland and posterior silk gland in the Bombyx mori.

Gan Huaiyan H Feng Tieshan T Wu Yuqian Y Liu Chun C Xia Qingyou Q Cheng Tingcai T

Data in brief 20171018

Circular transcriptome sequencing of the middle silk gland (MSG) and posterior silk gland (PSG) in the <i>Bombyx mori</i> are presented. The middle silk gland and posterior silk gland were collected from the third day of fifth-instar <i>B.mori</i> larvae. The circular RNAs enriched by using RNase R to degrade the linear RNA molecules, and circular RNA sequencing (circRNA-seq) was performed using an Illumina Hiseq. 2500 sequencing platform. Samples are described in the SRA portal (SRP100385) and ...[more]

PMID: 29124095

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Project description:To identify functions that distinguish the posterior and median cells producing fibroin and sericin in the silk gland of Bombyx mori, serial analysis of gene expression (SAGE) profiles from both silk gland regions were analyzed and compared. The construction of a B. mori reference tag collection extracted from a set of 38000 Bombyx EST sequenced from the 3’ side, helped annotating the SAGE libraries. Most of the tags appeared at similar relative concentration in the two libraries except for those corresponding to silk proteins that were found region-specific and highly abundant. Strikingly, besides tags from silk protein mRNAs, 19 tags were found in the class of high abundance in the median cell library, which were absent in the posterior cell tag collection. Except tags from SP1 mRNA, no PSG specific tags were found in the same class of abundance. The analysis of MSG-specific different transcripts led to suggest that middle silk gland cell realizes more diversified functions as those already known, of synthesis and secretion of the silk sericins. EST libraries from 11 silkworm tissues were 3’-sequenced to ensure the identification of the most terminal tag. 37,920 sequences were analyzed on ABI 3700 or 3730XL sequencers. Electrophoregrams were processed with KB Basecaller (3730XL traces) or with PHRED (3700 traces) to obtain the .phd files from which were extracted text sequences and their corresponding quality files in Fasta format (Phd2Fasta, Green and Ewing, 1995; 2002). Vector sequences and bad quality regions were removed with an home made software after identification by Lucy (Chou and Holmes, 2001). Chimera were removed by an home made software and retrotransposon sequences were masked by RepeatMasker (http://repeatmasker.org). The cleaned sequences were clusterized with TGICL package (TIGR) and assembled into contigs with CAP3 (Huang and Madan, 1999). Contigs were identified with Blastn and Blastx on GenBank and SwissProt/TREMBL, respectively. Some clusters, splitted by CAP3 procedure, have been regrouped on the basis of Blastx identity. Identitag (Keime et al., 2004) was used to extract all possible tags (forward and reverse) to create a reference database. Moreover, a quality index is attached to each tag depending to the presense of poly-A, polyadenylation signal and its proximity to 3-prime extremity in the original mRNA sequence. This database was supplemented with the tags extracted from public B. mori sequences (GenBank, Silkbase) with the same software. Tags were extracted from MSG and PSG libraries (from 2304 and 3072 sequenced inserts respectively) with the Sagenhaft software (Beissbarth et al., 2004) then identified and compared with Identitag. The assessment of significant differences among the two libraries was performed by using the Z-test used for comparison of SAGE libraries of different size (Kal et al., 1999). For graphic purpose and to avoid division by zero we used a tag value of 1 for tags that were not detected in MSG or PSG libraries. Since the two SAGE libraries showed up different TAG number, we used the Z-test for comparing the two mRNA populations.

Dataset Information

Circular transcriptome sequencing of the middle silk gland and posterior silk gland in the Bombyx mori.

Publications

Circular transcriptome sequencing of the middle silk gland and posterior silk gland in the Bombyx mori.

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