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

Glomerular enriched tissue was isolated by mechanical sieving of kidney cortex using an established protocol. Briefly, fresh cortex tissue (approximately one and a half kidneys per animal) was passed through a serial stack of mesh filters of 180, 106, and 75μ pore size. An optimal yield and enrichment of glomeruli was obtained by gently forcing cortex tissue through the 180μ mesh with the flat end of a 30 mL syringe plunger, followed by gravity flow collection on the lower mesh sizes with large volume PBS rinses. Materials trapped on the 106μ and 75μ mesh filters were collected in PBS by gentle flushing towards and aspiration from the edge of the mesh filter, combined, and placed back on a clean 75μ mesh for additional large volume PBS rinses and final collection. The material was then pelleted, resuspended in Qiazol (Qiagen Cat# 79306), and stored at -80°C prior to RNA isolation. Total RNA was isolated for all samples after study termination on the same day using miRNeasy RNA isolation kits (Qiagen Cat# 217004) on a Qiacube instrument (Qiagen). For all samples, RNA quality and integrity was confirmed on an Agilent 2100 bioanalyzer. RNA sequencing was performed on oligo(dT) purified poly(A)+ mRNA. A standard TruSeq mRNA library was constructed using TruSeq RNA Sample Prep Kit v2 (Illumina, Cat.# RS-122-2001). The library was sequenced by Illumina HiSeq 2000 using a paired-end run (2×100 bases). After sequencing, 40M 217 100 bp pair-end reads were generated for downstream analysis.

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