来自假种皮从头转录组组装的数据集。

Dataset from de novo transcriptome assembly of aril.

作者信息

Matra Deden Derajat, Ritonga Arya Widura, Natawijaya Azis, Poerwanto Roedhy, Widodo Winarso Drajad, Inoue Eiichi

机构信息

Department of Agronomy and Horticulture, Bogor Agricultural University, Indonesia.

Research and Development Division, Mekarsari Fruit Garden, Indonesia.

出版信息

Data Brief. 2018 Dec 14;22:566-569. doi: 10.1016/j.dib.2018.12.034. eCollection 2019 Feb.

DOI:10.1016/j.dib.2018.12.034

PMID:30627609

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6321968/

Abstract

(Rambutan), is one of tropical fruit in which - cultivated widely in Indonesia and has good taste and aroma. However, the transcriptomic study of rambutan has limited. In this study, we performed transcriptome assembly using paired-end Illumina technology. The assembled transcriptome was constructed using Trinity and after filtering and removal sequences redundancy produced 36,303 contigs. The contig ranged 201-11,770 bp and N50 has 1327 bp. The contig was annotated with several databases such as SwissProt, TrEMBL, and nr/nt of NCBI databases. The raw reads are deposited in the DDBJ with DRA accession number, DRA007359: https://www.ncbi.nlm.nih.gov/sra/?term=DRA007359. The assembled contigs of transcriptome are deposited in the DDBJ TSA repository with accession number IADQ01000001-IADQ01036303: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/tsa/IADQ.gz and also can be accessed at http://rujakbase.id.

摘要

红毛丹是一种热带水果，在印度尼西亚广泛种植，味道和香气俱佳。然而，红毛丹的转录组学研究有限。在本研究中，我们使用双末端Illumina技术进行转录组组装。组装的转录组使用Trinity构建，经过过滤和去除序列冗余后产生了36,303个重叠群。重叠群长度在201至11,770 bp之间，N50为1327 bp。这些重叠群用多个数据库进行注释，如SwissProt、TrEMBL以及NCBI数据库的nr/nt。原始读数存于DDBJ，DRA登录号为DRA007359：https://www.ncbi.nlm.nih.gov/sra/?term=DRA007359。转录组组装的重叠群存于DDBJ TSA库，登录号为IADQ01000001 - IADQ01036303：ftp://ftp.ddbj.nig.ac.jp/ddbj_database/tsa/IADQ.gz，也可在http://rujakbase.id访问。

相似文献

Dataset from de novo transcriptome assembly of aril.来自假种皮从头转录组组装的数据集。

Data Brief. 2018 Dec 14;22:566-569. doi: 10.1016/j.dib.2018.12.034. eCollection 2019 Feb.

Dataset of the first de novo transcriptome assembly of the arillode of ..假种皮首次从头转录组组装的数据集。需注意，原文中“of the arillode of.”后面似乎缺少具体内容，这可能会影响对整个句子更准确完整的理解。

Data Brief. 2018 Dec 13;22:332-335. doi: 10.1016/j.dib.2018.12.031. eCollection 2019 Feb.

Dataset of de novo assembly and functional annotation of the transcriptomes of three native oleaginous microalgae from the Peruvian Amazon.来自秘鲁亚马逊地区的三种本地产油微藻转录组的从头组装和功能注释数据集。

Data Brief. 2020 Jun 21;31:105917. doi: 10.1016/j.dib.2020.105917. eCollection 2020 Aug.

Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of "camu-camu".“卡姆果”种子萌发和幼苗初期生长过程中转录组的从头组装和功能注释数据集

Data Brief. 2020 Jun 11;31:105834. doi: 10.1016/j.dib.2020.105834. eCollection 2020 Aug.

Dataset of assembly and functional annotation of the transcriptome of blueberry ( spp.).蓝莓（spp.）转录组的组装与功能注释数据集。

Data Brief. 2019 Aug 12;25:104390. doi: 10.1016/j.dib.2019.104390. eCollection 2019 Aug.

De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.山竹（莽吉柿，Garcinia mangostana L.）果实的从头转录组组装

Genom Data. 2016 Sep 9;10:35-7. doi: 10.1016/j.gdata.2016.09.003. eCollection 2016 Dec.

Dataset for sequencing and assembly of the European endangered white-clawed crayfish () abdominal muscle transcriptome.用于欧洲濒危白爪小龙虾（）腹肌转录组测序和组装的数据集。

Data Brief. 2020 Jan 27;29:105166. doi: 10.1016/j.dib.2020.105166. eCollection 2020 Apr.

Dataset from transcriptome assembly of leaves using MinION nanopore sequencer.使用MinION纳米孔测序仪对叶片转录组进行组装得到的数据集。

Data Brief. 2022 Dec 17;46:108838. doi: 10.1016/j.dib.2022.108838. eCollection 2023 Feb.

transcriptome assembly of heavy metal tolerant .重金属耐受性的转录组组装

Genom Data. 2017 Jan 26;11:118-119. doi: 10.1016/j.gdata.2017.01.004. eCollection 2017 Mar.

The dataset of de novo assembly and inferred functional annotation of the transcriptome of , a bloom-forming, cosmopolitan raphidophyte.一种形成水华的世界性针胞藻转录组的从头组装和推断功能注释数据集。

Data Brief. 2023 Mar 22;48:109071. doi: 10.1016/j.dib.2023.109071. eCollection 2023 Jun.

引用本文的文献

De novo transcriptome datasets of leaves and basal stem in waterlogged and dry soil.淹水和干旱土壤中叶片和基部茎的从头转录组数据集。

Data Brief. 2019 Dec 14;28:104998. doi: 10.1016/j.dib.2019.104998. eCollection 2020 Feb.

The dataset of de novo transcriptome assembly of cambium from gall-rust () infected and non-infected tree.来自感染和未感染锈瘿（）树木形成层的从头转录组组装数据集。

Data Brief. 2019 Sep 7;26:104489. doi: 10.1016/j.dib.2019.104489. eCollection 2019 Oct.

Metabolomics dataset of underutilized Indonesian fruits; rambai (), nangkadak (), rambutan () and Sidempuan salak () using GCMS and LCMS.利用气相色谱-质谱联用仪（GCMS）和液相色谱-质谱联用仪（LCMS）对印度尼西亚未充分利用的水果（兰拜、南卡达克、红毛丹和西empuan蛇皮果）进行代谢组学数据集分析。

Data Brief. 2019 Mar 6;23:103706. doi: 10.1016/j.dib.2019.103706. eCollection 2019 Apr.

本文引用的文献

De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.山竹（莽吉柿，Garcinia mangostana L.）果实的从头转录组组装

Genom Data. 2016 Sep 9;10:35-7. doi: 10.1016/j.gdata.2016.09.003. eCollection 2016 Dec.

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes.Corset：为从头组装的转录组实现差异基因表达分析。

Genome Biol. 2014 Jul 26;15(7):410. doi: 10.1186/s13059-014-0410-6.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.无参考基因组的 RNA-Seq 数据的全长转录组组装。

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.Cd-hit：一个用于对大量蛋白质或核苷酸序列进行聚类和比较的快速程序。

Bioinformatics. 2006 Jul 1;22(13):1658-9. doi: 10.1093/bioinformatics/btl158. Epub 2006 May 26.

CAP3: A DNA sequence assembly program.CAP3：一个DNA序列组装程序。

Genome Res. 1999 Sep;9(9):868-77. doi: 10.1101/gr.9.9.868.

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验