Comparison of Liver Tumor Models to Regenerating Liver Tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus Rattus norvegicus
PROVIDER: GSE75677 | GEO | 2017/11/19
SECONDARY ACCESSION(S): PRJNA305035
REPOSITORIES: GEO
Similar Datasets
Project description:Comparison of Liver Tumor Models to Regenerating Liver Tissues
| PRJNA305035 | ENA
Project description:Regenerating intestine tissues were compared with normal (non-regenerating tissues) to determine the gene expression profile at early stages of regeneration (3, 7 and 14 days post- evisceration (dpe)). Immuno activated tissues with LPS were compared with Normal (non-regenerating tissues) and regenerating tissues (3 and 7 dpe) to determine the gene expression of immune related genes in the sea cucumber and it's expression during early stages of regeneration. 16 Total arrays. 8 comparisons with 8 dye swap replicates. Normal Vs. (3, 7 and 14 days of regeneration), and Vs. (LPS) 2 microarray slides used. Each slide with 8 Arrays (8 x 15k). 15,744 probes printed per array. (all 16 arrays are identically printed). 7,209 ESTs from Normal, 3 dpe and 7 dpe tissues were used to design the probes. Two probes per EST from diferent regions of the sequence (as a technical replicate). 536 technical controls and more than 600 internal biological controls (from different species).
2010-05-18 | E-GEOD-16182 | biostudies-arrayexpress
Project description:The therapeutic regimens of adjuvant and neoadjuvant chemotherapy for colorectal cancer (CRC) remain largely relied on clinical experience, and thus preclinical models are needed to guide individualized medicine. The investigators are going to establish 3D bioprinted CRC models and organoids from surgically resected tumor tissues of CRC patients with or without liver metastases. In vitro 3D models and organoids will be treated with the same chemotherapy drugs with the corresponding patients from whom the models are derived. The sensitivity of chemotherapy drugs will be tested in these two types of in vitro models, and the actual response to chemotherapy in patients will be evaluated. The predictive ability of 3D models for chemotherapy sensitivity in CRC patients will be compared with that of the organoids. This observational study will validate the potential value of 3D bioprinted tumor models in predicting the response to chemotherapy in CRC.
| 2367475 | ecrin-mdr-crc
Project description:Regenerating intestine tissues were compared with normal (non-regenerating tissues) to determine the gene expression profile at early stages of regeneration (3, 7 and 14 days post- evisceration (dpe)). Immuno activated tissues with LPS were compared with Normal (non-regenerating tissues) and regenerating tissues (3 and 7 dpe) to determine the gene expression of immune related genes in the sea cucumber and it's expression during early stages of regeneration.
2009-05-21 | GSE16182 | GEO
Project description:We used microarrays to identify genes in regenerating mouse liver after OGFRL1-expressing cell administration
2017-09-15 | GSE103857 | GEO
Project description:Plant roots can regenerate after complete excision of their tip, including the stem cell niche, but it is not clear what developmental program mediates such repair. Here, we use a combination of lineage tracing, single-cell RNA-seq, and marker analysis to test different models of tissue reassembly. We show that rapid cell-identity transitions lead to the formation of a new stem cell niche from multiple remnant tissues. The transcriptome of regenerating cells prior to stem cell activation resembled that of the embryonic root progenitor, and regeneration defects were more severe in embryonic versus adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirrored their embryonic dynamics, and manipulation of both hormones altered the position of new tissues and stem cell niche markers. Our findings suggest that plant organ regeneration resembles the developmental stages of embryonic patterning and is guided by spatial information laid down by complementary hormone domains. 215 single cells isolated from marked stele tissue (either using WOL or AHP6 promoters), before, at 3h, 16h and 46h post root tip decapitation
2016-04-01 | E-GEOD-74488 | biostudies-arrayexpress
Project description:Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control. Keywords: Stress response, injury response. Two time points, 18-24 hours post amputation (hpa) and 48 hpa, of regenerating fin fold were analyzed. We performed one replicate per each time point. For microarray expression profiling, total RNA was extracted from regenerating and uncut caudal fin folds of AB strain larvae. Tail tissues of 16-24 hpa, 48 hpa, and uncut siblings of the respective stages including 3-5 posterior somite segments were collected on ice. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, California, United States) according to the manufacturerâs instruction. The quantity and quality of total RNA were assessed by absorbance at 260 nm and 280 nm and by gel electrophoresis. Approx. 9 μg of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 μg, from ~130 tail tissues at 48 hpa or uncut control tissues. Probes for microarray analysis were labeled with cy3 (amputated fin fold at 16-24 hpa and uncut control at 48 hpa) or cy5 (uncut control at 16-24 hpa and amputated fin fold at 48 hpa), and used for hybridization.
2010-05-19 | E-GEOD-11391 | biostudies-arrayexpress
Project description:Defining conserved molecular pathways in animal models of successful cardiac regeneration could yield insight into why adult mammals have inadequate cardiac regeneration after injury. Here we describe a cross-species transcriptomic screen to identify evolutionarily conserved pathways in the early events of cardiac regeneration in three species that can regenerate myocardium after a major injury. In this study, we performed RNA-seq on regenerating hearts from three model organisms - axolotl, zebrafish and mouse. Apical resection was performed to amputate ~10 - 20% of the left ventricle in all three model organisms. Following resection, hearts were harvested at 12, 24 and 48 hours post-resection and subjected to RNA-seq. RNA-seq on sham controls (no ventricular amputation) was used as interanal control. This approach revealed upregulation of inflammatory genes in all three organisms during regeneration. Furthermore, upregulation of Complement 5a receptor1 (C5aR1) expression in the regenerating hearts of zebrafish, axolotls and mice was observed.
2018-02-01 | GSE108493 | GEO
Project description:To identify the molecular targets of orosomucoid (Orm1) during liver regeneration, GeneChip analysis was performed at 48 h after partial hepatectomy (PH) in regenerating mouse liver treated with siControl or siOrm. A total of 180 differentially expressed genes in Orm1 konckdown mouse liver by comparing with siControl were identified with a fold change more than 2. Then, pathway analysis performed on the altered gene expression profiles using Ingenuity Pathways Analysis (IPA) program revealed that cell cycle, Toll-like receptor and TGF-beta receptor signaling pathways were under control of Orm1 in regenerating mouse livers. Three days post In vivo knockdown of Orm1 with its siRNA administered to mice using Invivofectamine 3.0 by a single injection, 40% PH was perfomred and gene expression prolifes of regenerating mouse livers at 48 h after PH was measued using Affymetrix GeneChip Mouse Genome 430A 2.0 Array.
2016-07-01 | E-GEOD-83733 | biostudies-arrayexpress
Project description:RNA seq analysis of regenerating hearts from three models of successful cardiac regeneration
| PRJNA427437 | ENA