Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJCA002998: The RNA-seq data of fibre development in two upland cotton cultivars (Nongdamian13 and Nongda601)

Source: NGDC / CRA002927
Submission Date: Jul 02 2020
Release Date: Jul 03 2020
Update Date: -

Summary: To detect the changes of the genes expression during the fiber development stage

Overall Design: Growing bolls from the two upland cotton cultivars nongdamian13 (high quality) and Nongda601 (normal quality) were collected at the initiation stage (0 DPA, day post anthesis), cell-elongation stage (5, 10, 15 DPA), and secondary-wall synthesis stage (20, 25, and 30 DPA). The qualified RNA was extracted from these samples and applied for the RNA-seq.

GEN Datasets:
GEND000318
Strategy:
Species:
Tissue:
Development Stage:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: -
Library Construction Protocol: Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik . 2020-09-07 [PMID: 32894321]