Mouse Lymphedema RNA Sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15150 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1589230.fastq.gz | Fastqsanger.gz | |||
| ERR1589240.fastq.gz | Fastqsanger.gz | |||
| ERR1589231.fastq.gz | Fastqsanger.gz | |||
| ERR1589232.fastq.gz | Fastqsanger.gz | |||
| ERR1589233.fastq.gz | Fastqsanger.gz |
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Project description:OBJECTIVE: To analyze genome-wide changes in chondrocyte gene expression in a surgically induced model of early osteoarthritis (OA) in rats, to assess the similarity of this model to human OA, and to identify genes and mechanisms leading to OA pathogenesis. METHODS: OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression. Expression patterns of selected dysregulated genes, including Col2a1, Mmp13, Adamts5, Ctsc, Ptges, and Cxcr4, were validated by real-time polymerase chain reaction, immunofluorescence, or immunohistochemistry 2, 4, and 8 weeks after surgery. RESULTS: After normalization, comparison of OA and sham-operated samples showed 1,619 differentially expressed probe sets with changes in their levels of expression >/=1.5-fold, 722 with changes >/=2-fold, 135 with changes >/=4-fold, and 20 with changes of 8-fold. Dysregulated genes known to be involved in human OA included Mmp13, Adamts5, and Ptgs2, among others. Several dysregulated genes (e.g., Reln, Phex, and Ltbp2) had been identified in our earlier microarray study of hypertrophic chondrocyte differentiation. Other genes involved in cytokine and chemokine signaling, including Cxcr4 and Ccl2, were identified. Changes in gene expression were also observed in the contralateral knee, validating the sham operation as the appropriate control. CONCLUSION: Our results demonstrate that the animal model mimics gene expression changes seen in human OA, supporting the relevance of newly identified genes and pathways to early human OA. We propose new avenues for OA pathogenesis research and potential targets for novel OA treatments, including cathepsins and cytokine, chemokine, and growth factor signaling pathways, in addition to factors controlling the progression of chondrocyte differentiation. Experiment Overall Design: OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees, 28 days post-surgery. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression.
2009-04-23 | E-GEOD-8077 | biostudies-arrayexpress
Project description:Transcriptional profiling of infrarenal aortic tissue from Male 10-week-old C57BL/6J mice after AAA-induction with porcine pancreatic elastase, compared with sham-operated mice. Includes samples obtained 7 days after aneurysm induction. Goal was to examine gene expression in developing AAA in this model, and compare with miRNA profiling performed using the same tissue. Two condition experiment, one infrarenal aorta per array. Sham vs. PPE at Day 7 post-operatively. Total 10 arrays: 5 sham D7, 5 PPE D7.
2014-08-31 | E-GEOD-51227 | biostudies-arrayexpress
Project description:Transcripts were measured in infraspinatus muscle before (PRE) and after 2 weeks of tendon release (POST) in the operated muscle.
2020-04-03 | GSE144394 | GEO
Project description:We investigated the inflammatory gene profile of surgically-repaired lacerated muscles during the recovery phase and examined if it was influenced by the integrity/injury of the IM, intramuscular nerve using 3 lacerated rat muscle models: DN, where the IM-nerve was concomitantly cut; RN, where the IM-nerve was crushed but leaving an intact nerve sheath; and PN, a control where the IM-nerve was preserved intact. After 2, 4 and 8 weeks, the animals were sacrificed and their gastrocnemius muscles were removed and total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini Kit according to manufacturers instructions. Biotin-labelled cRNA probes were synthesized from total RNA by using a TrueLabeling-AMP Linear RNA amplification kit (SABiosciences Corp, Frederick, MD). The labeled cRNA probes were hybridized to oligonucleotide fragments spotted on the gene array membranes. Membranes were washed to remove any unincorporated probe and incubated with alkaline phosphatase-conjugated streptavidin (AP-streptavidin). Relative expression levels of specific genes were detected from signals generated by chemiluminescence from the alkaline phosphatase substrate, CDP-Star. The luminizing blots were used to expose X-ray films and quantified by spot densitometry with the aid of GEArray expression analysis suite (SABiosciences Corp, Frederick, MD). The abundance of each transcript was normalized to the normal un-operated muscle of the opposite limb, and to the housekeeping gene markers on each array (Aldoa, GAPdH and BAS2C). The results were presented as log2-fold expression with PN used as a control, to compare the two different types of nerve injuries (RN and DN).
2012-01-11 | E-MTAB-755 | biostudies-arrayexpress
Project description:36 Yucatan minipigs underwent anterior cruciate ligament (ACL) transection and were randomly assigned in equal numbers to no further treatment, reconstruction or ligament repair. Cartilage was harvested at 1 and 4 weeks post-operatively and histology and RNA-sequencing performed. The generated data served to identify the molecular pathophysiology present in early post-traumatic osteoarthritis (PTOA), as well as differences between surgical treatments.
2017-10-22 | E-MTAB-5879 | biostudies-arrayexpress
Project description:C57BL/6N animals received at the age of 6 weeks either adeno associated virus from serotype 9 (AAV9) leading to cardiac overexpression of luciferase (Luc, as control) or amino acids 1-201 of histone deacetyase 4 (HDAC4-NT) under the control of the cardiac myocyte-specific CMV-enhanced short (260bp) myosin light chain promoter (CMVenh/MLC260). Transaortic constriction (TAC) and sham operation was conducted 6 weeks later in 12 week old mice to induce pathological pressure overload. Organs were harvested 4 weeks after TAC at the age of 16 weeks and total RNA was used for microarray analysis. Three groups were compared: 1) sham-operated mice that were pretreated with AAV9 (CMVenh/MLC260)-Luc, 2) TAC-operated mice that were pretreated with AAV9 (CMVenh/MLC260)-Luc, 3) TAC-operated mice that were pre-treated with AAV9 (CMVenh/MLC260)-HDAC4-NT.
2016-07-27 | GSE72904 | GEO
Project description:36 Yucatan minipigs underwent anterior cruciate ligament (ACL) transection and were randomly assigned in equal numbers to no further treatment, reconstruction or ligament repair. Peri-meniscal synovium was harvested at 1 and 4 weeks post-operatively and histology and RNA-sequencing performed. The generated data served to identify the molecular pathophysiology present in inflamed synovium during the early development of post-traumatic osteoarthritis (PTOA), as well as differences between surgical treatments.
2018-04-21 | E-MTAB-6664 | biostudies-arrayexpress
Project description:Tissue from cleared mammary fat pad and sham-operated controlateral control was removed before and at 10, 15,17, and 19 days of pregnancy. Cleared vs. controlateral tissue was hybridized in dye-swap design to in-house cDNA microarry platform. This design aims to identify factors signaling from the epithelial part of the mammary gland to the surrounding fat pad to initiate adipo-epithelial transdifferentiation. We surgically removed the epithelial part of the 4th mammary gland (including the nipple and the rudimentary ductal tree) in three weeks old CD1 mice where the ductal anlage is confined to the proximal part of the mammary fat pad close to the nipple. The controlateral gland was sham-operated as control. This leaves a cleared mammary fat pad in its endogenous environment. The dissected tissues were subjected to whole mount analysis to judge if the removal of epithelial tissue was complete. At the age of 10 to 15 weeks the tissues were harvested before and 10, 15, 17, and 19 days after the start of pregnancy. RNA from cleared fat pads were compared to sham-operated contralateral controls by competitive hybridization on two-channel microarrays. If enough material was available three different pools of RNA (= three biological replicates) were used for hybridization (from d19 material only two replicates were obtained) in a dye-swap configuraiton (one biological replicate of d17 and d19 samples did not provide sufficient amount for a dyw-swap pair).
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Project description:OBJECTIVE: To analyze genome-wide changes in chondrocyte gene expression in a surgically induced model of early osteoarthritis (OA) in rats, to assess the similarity of this model to human OA, and to identify genes and mechanisms leading to OA pathogenesis. METHODS: OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression. Expression patterns of selected dysregulated genes, including Col2a1, Mmp13, Adamts5, Ctsc, Ptges, and Cxcr4, were validated by real-time polymerase chain reaction, immunofluorescence, or immunohistochemistry 2, 4, and 8 weeks after surgery. RESULTS: After normalization, comparison of OA and sham-operated samples showed 1,619 differentially expressed probe sets with changes in their levels of expression >/=1.5-fold, 722 with changes >/=2-fold, 135 with changes >/=4-fold, and 20 with changes of 8-fold. Dysregulated genes known to be involved in human OA included Mmp13, Adamts5, and Ptgs2, among others. Several dysregulated genes (e.g., Reln, Phex, and Ltbp2) had been identified in our earlier microarray study of hypertrophic chondrocyte differentiation. Other genes involved in cytokine and chemokine signaling, including Cxcr4 and Ccl2, were identified. Changes in gene expression were also observed in the contralateral knee, validating the sham operation as the appropriate control. CONCLUSION: Our results demonstrate that the animal model mimics gene expression changes seen in human OA, supporting the relevance of newly identified genes and pathways to early human OA. We propose new avenues for OA pathogenesis research and potential targets for novel OA treatments, including cathepsins and cytokine, chemokine, and growth factor signaling pathways, in addition to factors controlling the progression of chondrocyte differentiation. Keywords: disease state analysis
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