Transcription profiling by array of pancreas from KrasG12D, Ela-Tgfa and KrasG12D Ela-Tgfa mice
Concomitant pancreatic activation of Kras(G12D) and Tgfa results in cystic papillary neoplasms reminiscent of human IPMN.
Age, Specimen part
View SamplesDBZ (dibenzazepine) treatment in C57BL/6 mice, pancreatic gene expression
Notch signaling is required for exocrine regeneration after acute pancreatitis.
Sex, Age, Specimen part, Disease, Compound, Time
View SamplesWe examined transcriptome-wide effects of 4SC-202 in L3.6, BXPC3 and PANC1 cells as well as its effect on TGFß signaling Overall design: We performed mRNA sequencing from L3.6, BXPC3 and PANC1 cells following following DMSO, 4SC-202 and/or TGFß treatment. The mRNA-Seq includes following conditions: 4SC-202 vs DMSO (for L3.6, BXPC3 and PANC1 cells), TGFß vs DMSO and 4SC-202+TGFß vs TGFß (for PANC1 cells). The libraries were performed in triplicates.
Histone deacetylase class-I inhibition promotes epithelial gene expression in pancreatic cancer cells in a BRD4- and MYC-dependent manner.
Cell line, Subject
View SamplesObjective
A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling.
No sample metadata fields
View SamplesIdentification of genes enriched in the presumptive primary mouth. Dissected tissues from the primary mouth anlage and two other anterior regions for comparison, the anterior dorsal and ventral plus cement gland.
The Wnt antagonists Frzb-1 and Crescent locally regulate basement membrane dissolution in the developing primary mouth.
No sample metadata fields
View SamplesThe goal of the project was to isolate single miRNA-expressing cells labelled by GFP reporter genes under the control of endogenous miRNA promoters and analyze expression levels of miRNA target genes in these cells. GFP-positive miRNA-expressing cells and GFP-negative cells from the rest of the embryos were purified at the same developmental stage to the cellular resolution using fluorescent activated cell sorting (FACS). Focus was on regulation by miR-206 and miR-133 in the developing somites and miR-124 in the developing central nervous system. Comparison of wild-type embryos and those lacking miRNAs revealed predicted
Coherent but overlapping expression of microRNAs and their targets during vertebrate development.
No sample metadata fields
View SamplesHere, we use ribosome-footprint profiing and mRNA-seq to determine the average ribosome density on each gene in S. cerevisiae. We then perform quantitative modeling to identify the molecular determinants of ribosome density. Overall design: Analysis of S. cerevisiae
Poly(A)-tail profiling reveals an embryonic switch in translational control.
Cell line, Subject
View SamplesPolyA Position Profiling (3P-seq) for S. cerevisiae Overall design: Analysis of S. cerevisiae
Poly(A)-tail profiling reveals an embryonic switch in translational control.
Cell line, Subject
View SamplesGene expression profiles of human cell (THP-1) lines exposed to a novel Daboiatoxin (DbTx) isolated from Daboia russelli russelli, and specific cytokines and inflammatory pathways involved in acute infection caused by Burkholderia pseudomallei.
Gene Microarray Analyses of Daboia russelli russelli Daboiatoxin Treatment of THP-1 Human Macrophages Infected with Burkholderia pseudomallei.
No sample metadata fields
View SamplesThe post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3'' untranslated regions (3''UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-Seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-Seq reads substantially increased and improved existing 3''UTR annotations, resulting in confidently identified 3''UTRs for more than 78.79% of the annotated protein-coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant 3''UTRs at different stages. 3''UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3''UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3''UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At two hours post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3''UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P-Seq was used to map the 3'' ends of protein-coding genes in the zebrafish genome
Extensive alternative polyadenylation during zebrafish development.
No sample metadata fields
View Samples