Computational protocol: Zeb1-Hdac2-eNOS circuitry identifies early cardiovascular precursors in naive mouse embryonic stem cells

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Protocol publication

[…] Next-generation sequencing was performed on Ion Torrent Proton sequencing platform (Thermo Fisher) using the Ion Total RNA-Seq Kit v2 (Thermo Fisher) with minor modifications. Total RNA for transcriptome analysis was isolated with miRNeasy Micro Kit (Qiagen) from a 60 mm2 dish per sample. The integrity of RNA was checked on Bioanalyzer 2100 (Agilent), and 5 μg of RNA with RIN >9 were used for ribosomal depletion using the Ribo-Minus Eukaryote Kit v2 (Invitrogen). Following modifications to the standard RNA-seq Library protocol were performed: fragmented RNA was concentrated to 3 μL with SpeedVac (Eppendorf) for 10–15 min, and all 3 μL were used for further steps. The number of amplification cycles was reduced to 8–12 cycles resulting in lower PCR duplication levels without any influence to quality/contribution of obtained reads. To maximize data, recovery libraries were size selected using the LabChipXT system (Perkin Elmer) with an isolation window between 180 and 270 bp (corresponding to 60–150 bp insert size). Obtained RNA libraries were quantified on Qubit 2.0 and diluted to 100 pM and used in a final concentration of 10 pM for template preparation on Ion OneTouch2 instrument (Thermo Fisher). For each run on the PI Ion Torrent V2 Chip, 2 RNA libraries were pooled in equimolar ratios to obtain between 37 and 63 M raw reads per sample. The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at [http://www.bioinformatics.babraham.ac.uk/projects/fastqc]). Reaper version 13–100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene (see Supplementary Table ). Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62. Only genes with a minimum fold change of ±2, a maximum Benjamini–Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)). The correlation of replicate gene counts was assessed with the Spearman ranked correlation algorithm included in R 3.11 (R: A language and environment for statistical computing). MA plots were computed using the script run_DE_analysis.pl included in Trinity version 20140717 which employs R functions for plotting. After pairwise comparison of GS/DM, NO/GS, and NO/DM the overlapping extent of differentially expressed genes among experimental conditions was analyzed in up- and downregulated RNAs (±2 log2 fold change, basemean >5, fdr <0.05) by Venn diagrams (Venny 2.1.0 [http://bioinfogp.cnb.csic.es/tools/venny/]). Gene ontology on genes exclusively regulated by NO (±2 log2 fold change, basemean >5, FDR <0.05) was performed using Cytoscape 3.2.1 plugin BINGO, which allows to determine statistically overrepresented GO categories in the derived biological networks. […]

Pipeline specifications

Software tools FastQC, Kraken, STAR, Subread, DESeq2, Trinity, VENNY, BiNGO
Databases UniProt
Application RNA-seq analysis
Organisms Mus musculus
Diseases Leukemia
Chemicals Nitric Oxide