John Calley
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Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis Open
Metastasis is the primary cause of cancer mortality. The primary tumors of colorectal cancer (CRC) often metastasize to the liver. In this study, we have collected 122 samples from 45 CRC patients. Among them, 32 patients have primary tumo…
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers Open
MicroRNAs (miRNAs) are small RNAs that regulate mRNA expression and have been targeted as biomarkers of organ damage and disease. To explore the utility of miRNAs to assess injury to specific tissues, a tissue atlas of miRNA abundance was …
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions Open
The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) Consortium …
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database Open
RATEmiRs provides a new platform for identification of TE, TS and OS miRNAs in a broad array of rat tissues. RATEmiRs is available at: https://www.niehs.nih.gov/ratemirs.
The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
A microRNA body atlas for rat and dog was useful in identifying new candidate miRNA biomarkers of organ toxicity in 2 toxicologically relevant species.
Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons Open
Our proposed HTR2A and HTR2A-AS1 gene structures dramatically differ from current annotations, now including overlapping exons on the sense and anti-sense strands. We also find orthologous transcript isoforms expressed in mice, providing o…
Additional file 8: Table S5. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
MiRNAs tested in qPCR validation. Tissue enriched miRNAs and their sequences are displayed. MiRNA abundance was measured through qPCR in order to correlate their tissue enrichment status to deep sequencing results. (XLSX 15Â kb)
Additional file 8: Table S4. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons Open
Mouse Htr2a exons and coordinates. (XLSX 12Â kb)
Additional file 11: Table S5. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons Open
Mouse Htr2a-AS1 exons and coordinates. (XLSX 12Â kb)
Additional file 7: Table S3. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons Open
Predicted HTR2A-AS1 transcripts and open reading frames. (XLSX 13Â kb)
Additional file 6: Table S2. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons Open
Splice junctions and counts for human HTR2A-AS1. (XLSX 12Â kb)
Additional file 15: Table S7. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
P-values of rat caerulein toxicity study. Statistical analysis of miRNA and clinical chemistry biomarkers measured in the rat caerulein toxicity study are presented in this table with their associated fold changes and p-values indicated at…
Additional file 3: Table S1. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
List of miRNAs in common in HESI analysis. Tissue enriched miRNAs mutually identified by independent data analysis techniques employed by Eli Lilly, NIEHS and Maastricht University are listed including tissue (s) in which the miRNA is most…
Additional file 16: Table S8. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
P-values of dog caerulein toxicity study. Statistical analysis of miRNA biomarkers measured in the dog caerulein toxicity study are displayed in this table with their associated p-values, Lsmean, lower confidence intervals, upper confidenc…
Additional file 6: Table S3. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
Tissue Enriched miRNAs identified by NIEHS. Tissue enriched miRNAs identified by NIEHS are listed under the organ in which they are most abundantly expressed. (XLSX 42Â kb)
Additional file 15: Table S1. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons Open
Mapping statistics for human DLPFC RNA-Seq samples (XLSX 22Â kb)
Additional file 9: Table S6. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
Correlations of miRNAs to sequencing data. Correlation of tissue enriched miRNA measurements using deep sequencing and qPCR are depicted with a correlation of â 1.0 being highly correlated and â 0.0 representing poor correlation. (XLSX 10Â…
Additional file 4: Table S2. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
Tissue specific and enriched miRNAs identified by Lilly. Tissue specific and tissue enriched miRNAs identified by Eli Lilly are listed under the organ in which they are most abundantly expressed. Tissue specific miRNAs are in bold text and…
Additional file 2: of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog Open
Sequences of miRNAs and Exiqon qPCR assay identification. (XLSX 14Â kb)
Additional file 14: Table S6. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons Open
Predicted splicing proteins bound to human HTR2A rs6313 alleles. (XLSX 11Â kb)