Transcriptomics

Dataset Information

0

Rhizophora mucronata Lam. de novo transcriptome - Gene expression estimation


ABSTRACT: Rhizophora mucronata Lam., a prevalent mangrove variety of Indo-Pacific region is reported to defy saline stress up to 40 ppt, but the genome or transcriptome behind this tolerance is yet to be investigated. As an initiative to create a reference sequence database, we have forged a set of 46,366,348 paired end RNA-Seq raw reads of Rhizophora mucronata Lam. leaf tissues from Illumina HiSeq 2500 platform (SRA study accession SRP093200 ; Bioproject accession PRJNA345155). All possible gene transcripts were then reconstructed from the RNA raw seq data and 93960 Trinity assembled, annotated transcripts that are being actively expressed at a given time is proposed (TSA accession GGEC00000000). To estimate gene transcript expression, we used Bowtie 2 programme and successfully aligned back up to 95.14% of the filtered reads to the assembled transcriptome. We allowed up to 1-mismatches in the seed region (length =31bp) and all multiple mapped position were reported. Of all filtered reads about 95.14% of reads from each sample were properly aligned back to the assembled transcriptome. Overall we found 52,153 unique transcripts which have expression >=1 FPKM.

ORGANISM(S): Rhizophora mucronata

PROVIDER: GSE112162 | GEO | 2018/03/22

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2019-04-02 | GSE112607 | GEO
2023-09-12 | GSE175506 | GEO
2024-04-21 | GSE253342 | GEO
2018-12-14 | GSE123821 | GEO
2019-03-21 | GSE112166 | GEO
2022-09-06 | GSE186354 | GEO
2011-09-23 | E-GEOD-25759 | biostudies-arrayexpress
2018-05-02 | GSE110620 | GEO
2017-02-11 | GSE62700 | GEO
2014-06-30 | E-MTAB-2557 | biostudies-arrayexpress