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

PRJNA578754: Non-floral Cascade RNA-seq

Source: NCBI / GSE139215
Submission Date: Oct 21 2019
Release Date: Oct 22 2019
Update Date: Oct 22 2019

Summary: This is an RNA-seq study looking at different non-floral hop tissue (stems, meristems and leaves) in the cultivar 'Cascade'

Overall Design: Tissue-specific RNA-seq studies in hop cultivar Cascade. There are two sample replicates for each tissue, including leaf, meristem, and stem.

GEN Datasets:
GEND000650
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: Cascade plants were grown in a glasshouse with active control of insects and plant pathogens. Young tissue of leaves, stems actively growing and apical meristems were harvested and immediately immersed in liquid nitrogen, then transferred into -80 C freezer until RNA extraction.
Treatment Protocol: There were no treatments applied to different tissue other than chemical sprays controlling insects and fungal pathogens.
Extract Protocol: RNA from hop tissues was extracted using RNeasy Plant Mini Kit (Qiagen), using glass hooks to remove RNA from tubes. 
Library Construction Protocol: Three TruSeq RNA (Qiagen) libraries were developed from leaf, stem, and meristem tissues with each library sequenced on a single lane.
Sequencing
Molecule Type: polyA(+) RNA
Library Source:
Library Layout: PAIRED
Library Strand: Reverse
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 3000
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
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 Condition 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