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

PRJNA495061: Gene expression in three tissues from two crab-eating macaques (Macaca fascicularis, cynomolgus monkey).

Source: NCBI / GSE120935
Submission Date: Oct 08 2018
Release Date: May 01 2019
Update Date: Jun 03 2019

Summary: We provide RNA-Seq data for cerebral cortex, liver and kidney cortex from two untreated female crab-eating macaques.

Overall Design: Three tissues from two animals, without treatment

GEN Datasets:
GEND000165
Strategy:
Species:
Tissue:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Total RNAs were individually extracted using the Ambion Magmax™-96 total RNA isolation kit (Life Sciences) according to the manufacturer’s instructions. Briefly, 5 mg of tissue was placed in the lysis solution and homogenised in Qiagen Tissuelyzer™ for a period of 30 sec. Nucleic acids were captured onto magnetic beads, washed and treated with DNase. Total RNA was then eluted in 50 μl elution buffer. RNA quality and concentration was measured using an RNA Pico chip on an Agilent Bioanalyzer.
Library Construction Protocol: The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) producing a 275bp fragment including adapters in average size. In the final step before sequencing, eight individual libraries were normalised and pooled together using the adapter indices supplied by the manufacturer. Pooled libraries have then been clustered on the cBot Instrument from Illumina using the TruSeq SR Cluster Kit v3 - cBot - HS(GD-401-3001, Illumina Inc, San Diego, CA) sequencing was then performed as 2x85bp, paired reads and 7 bases index read on an Illumina HiSeq3000 instrument using the TruSeq SBS Kit HS- v3 (50-cycle) (FC-401-3002, Illumina Inc, San Diego, CA).
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 3000
Strand-Specific: Specific
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
Exploiting orthology and de novo transcriptome assembly to refine target sequence information.
BMC medical genomics . 2019-05-23 [PMID: 31122257]