It provides the QC metrics and expression tables, including overall read mapping statistics, QC report for a subset of GTEx samples, interactive gene expression visualization and analytical tools to gain insights about the data. Please click for interactive plots.

Shanrong Zhao, Li Xi, Jie Quan, Hualin Xi, Ying Zhang, David von Schack, Michael Vincent and Baohong Zhang

RNA-seq was performed using the Illumina TruSeq library construction protocol (non-stranded, polyA+ selection).

Total RNA was quantified using the Quant-iTTM RiboGreen®RNA Assay Kit and normalized to 5 ng per µL. An aliquot of 200 ng for each sample was transferred into library preparation, which was an automated variant of the Illumina Tru SeqTM RNA sample preparation protocol (Revision A, 2010). This method used oligo dT beads to select mRNA from the total RNA sample followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant cDNA then went through library preparation (end repair, base 'A' addition, adapter ligation, and enrichment) using Broad Institute-designed indexed adapters substituted in for multiplexing. After enrichment, the libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly. The entire process was performed in 96-well plates and all pipetting was performed by either Agilent Bravo or Hamilton Starlet liquid handlers with electronic tracking throughout the process in real-time, including reagent lot numbers, specific automation used, time stamps for each process step, and automatic registration.

Pooled libraries were normalized to 2 nM and denatured using 0.1 N NaOH prior to sequencing. Flow cell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the HiSeq 2000 or HiSeq 2500. Sequencing generated 76bp paired-end reads and an eight-base index barcode read, and was run with a coverage goal of 50M reads (the median achieved was ~82M total reads).

Click on the image above to access the interactive plot. Raw Data

Raw Read Counts on Genes

RPKM Values on Genes

sample.annotation.txt	sample annotation file
star-mapping-summary.txt	read mapping summary for STAR run
fc-counting-summary.txt	read counting summary for featureCounts run
RSeQC-read-distribution.txt	The distribution of mapped reads along gene elements
Gene-count-table.txt	counting table
Gene-count-table.flt.txt	filtered counting table. A gene is filtered if having 0 read in more than 50% samples
Gene-fpkm-table.txt	RPKM table, calculated from Gene-count-table.txt
Gene-fpkm-table.flt.txt	filtered RPKM table, calculated from Gene-count-table.flt.txt
RNASeq-expr-QC.txt	correlation based QC of expression profile
RNASeq-expr-corr.txt	All-against-all gene expression correlation matrix
RNASeq-snp-corr.txt	All-against-all SNP correlation matrix
RNASeq-merged-metrics.txt	Merged RNA-seq metrics from mapping, counting, distribution and QC
read_map_sum.10x7.png	plot of star-mapping-summary.txt. Intended for powerpoint presentation.
read_map_sum.png	plot of star-mapping-summary.txt. Intended for interactive HTML presentation.
read_count_sum.10x7.png	plot of fc-counting-summary.txt. Intended for powerpoint presentation.
read_count_sum.png	plot of fc-counting-summary.txt. Intended for interactive HTML presentation.
read_dist_sum.10x7.png	plot of RSeQC-read-distribution.txt. Intended for powerpoint presentation.
read_dist_sum.png	plot of RSeQC-read-distribution.txt. Intended for interactive HTML presentation.
expr_count_RPKM.10x7.png	plot the number of genes with a give RPKM cutoff. Intended for powerpoint presentation.
expr_count_RPKM.png	plot the number of genes with a give RPKM cutoff. Intended for interactive HTML presentation.
RNASeq-expr-corr.txt.corr.9x7.png	correlation plot for RNASeq-expr-corr.txt.Intended for powerpoint presentation.
RNASeq-expr-corr.txt.corr.png	correlation plot for RNASeq-expr-corr.txt.Intended for interactive HTML presentation.
RNASeq-snp-corr.txt.corr.9x7.png	correlation plot for RNASeq-snp-corr.txt.Intended for powerpoint presentation.
RNASeq-snp-corr.txt.corr.png	correlation plot for RNASeq-snp-corr.txt

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6. D3.js - Data-Driven Documents