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 on for interactive plots.

Stefka Gyoneva1, Raghavendra Hosur, Anne C. Cotleur, David Gosselin, Zhengyu Ouyang, Michael Peterson, Ravi Challa, Patrick Cullen, Kelly Miao, Norm Allaire, Taylor L. Reynolds, Christopher K. Glass, Chris Roberts, Baohong Zhang, Linda Burkly and Richard M. Ransohoff

RNA (containing microRNAs) was isolated with the Qiagen Universal AllPrep kit (Qiagen 80004) according to the manufacturer's instruction. RNA samples were treated on the column with DNAse I (Qiagen 79254) to remove potential DNA contamination. RNA concentration was quantified with the Quant-iT RiboGreen reagent (Molecular Probes MP11490). RNA quality was determined on a Bioanalyzer with the RNA Pico 6000 kit (Agilent 5067-1513), according to the manufacturer's instructions.

Because of the low RNA content of microglia and our desire to use each animal as an individual sample, we employed low RNA input protocols for RNA-Seq library preparation. cDNA for RNA-Seq libraries was prepared using 10 ng of RNA using the SmartSeq v4 Ultra Low RNA Input Library prep protocol (Clontech 634889) according to the manufacturer's instruction. The cDNA (250 ng starting material) was then tagged and fragmented with the NexteraXT DNA Library Preparation kit (Illumina FC-131-1024) according to the manufacturer's instructions. Quality of amplified cDNA and fragmented libraries was assessed on a Bioanalyzer with the High Sensitivity DNA chips (Agilent 5067-4627). Tagged libraries were pooled (8 nM total DNA) and sequenced on an Illumina HiSeq2500 sequencer, with target depth of 20 million of 50 bp paired end reads.

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

TPM Values on Genes

RPKM (FPKM) Values on Genes

Raw Read Counts on Genes

sample.annotation.txt	sample annotation file
run.config.txt	configuration file
star-mapping-summary.txt	read mapping summary for STAR run
fc-counting-summary.txt	read counting summary for featureCounts run
fc-gene-counts.txt	gene counts table
fc-gene-rpkm.txt	RPKM (FPKM) table, calculated from fc-gene-counts.txt
rsem-gene-tpm.txt	TPM table, calculated by RSEM algorithm
expr-gene-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