Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19884838_1.fastq.gz | Fastqsanger.gz | |||
| SRR19884838_2.fastq.gz | Fastqsanger.gz | |||
| SRR19884839_1.fastq.gz | Fastqsanger.gz | |||
| SRR19884839_2.fastq.gz | Fastqsanger.gz | |||
| SRR19884840_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Most of the morbidity associated with short bowel syndrome (SBS) are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition (TPN). We hypothesized that acute SBS alone has significant systemic effects, and tested this in a zebrafish SBS model. Methods: With IACUC approval, adult male wild-type zebrafish underwent SBS (laparotomy, proximal stoma, distal ligation,n=3) or sham (laparotomy alone,n=3) surgery. After 2 weeks, the proximal intestine was harvested, RNA isolated and external RNA controls consortium (ERCC) controls spiked into each sample, sequenced and aligned to reference genome with gene ontology (GO) enrichment analysis performed. CyclinD1, CyclinB1, SAA1, IFN-gamma, and CYP7A1 gene expression were confirmed by qPCR. Results: RNA-seq analysis identified 1346 up-regulated genes and 678 down-regulated genes in SBS zebrafish compared to sham. The up-regulated genes were involved in acute phase response signaling, complement system, coagulation, cell proliferation, cellular barrier, production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down-regulated genes were involved in folate synthesis, gluconeogenesis, glycogenolysis, fatty-acid oxidation & activation, and drug & steroid metabolism. CyclinD1 gene expression was 2-fold higher, CyclinB1 2.8-fold higher, SAA1 4.5-fold higher, IFN-gamma 2.1-fold higher, and CYP7A1 25-fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways, some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy.
2017-03-08 | GSE83195 | GEO
Project description:Lacticaseibacillus rhamnosus strain:SBS-CC-2110 | isolate:SBS-CC-2110 Genome sequencing
| PRJNA1047776 | ENA
Project description:Lactiplantibacillus plantarum strain:SBS-CC-2127 | isolate:SBS-CC-2127 Genome sequencing
| PRJNA1047774 | ENA
Project description:Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technologies like ‘massively parallel signature sequencing (MPSS)’ and ‘Sequencing by Synthesis’ (SBS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). Illumina’s SBS technology can generate large amounts of sequence data in a short time at low cost compared to traditional Sanger sequencing based methods. Using the MPSS technology, we previously analyzed the transcriptomes of 72 rice tissues. To validate the sequencing results from MPSS technology, we employed SBS technology and constructed SBS libraries from 32 rice tissues (47 libraries including replications). For SBS library construction, we used the same mRNA samples and same restriction enzyme (DpnII) that were used for the construction of the MPSS libraries. These libraries include six abiotic-stress libraries, eight pathogen-infected libraries, five insect-damaged libraries, three developing seed libraries, and 10 untreated rice tissue libraries. This study was carried out with the following objectives; a) Identification and quantification of expressed genes in rice at all developmental stages of plant growth, response to biotic and abiotic stresses, and developing seeds; b) Compare SBS signatures with rice genomic sequence to identify novel transcripts; c) To validate the transcriptional data obtained through MPSS technology; and To create query and analysis tools to facilitate public use of and access to rice MPSS and SBS data and to display abundance and chromosomal locations of rice MPSS and SBS signatures. The SBS data will be available at http://mpss.udel.edu/rice_sbs/.
2011-06-22 | GSE25596 | GEO
Project description:Citrobacter freundii SBS 197 Genome sequencing
| PRJNA228973 | ENA
Project description:Intestinal adaptation is crucial to improving outcomes in short bowel syndrome (SBS). We performed scRNA sequencing of human intestinal organoid explanted from mice with experimental SBS to examine the genes and pathways involved in this adaptation.
2024-08-16 | GSE271065 | GEO
Project description:Short bowel syndrome (SBS) is a rare condition resulting from the loss of portions of the small intestine, and can cause a spectrum of metabolic and physiologic disturbances.The objective of this study was to determine the longterm survival and parenteral nutrition dependence of adult patients with SBS.
| 114861 | ecrin-mdr-crc
Project description:Numerous cytokines have been shown to affect epithelial cell differentiation and proliferation through epithelial-mesenchymal interaction. Growing evidence suggests that platelet-derived growth factor (PDGF) signaling is an important mediator of these interactions. The purpose of this study was to evaluate the effect of PDGF-α on enterocyte turnover in a rat model of short bowel syndrome (SBS). Male rats were divided into four groups: Sham rats underwent bowel transection, Sham-PDGF-α rats underwent bowel transection and were treated with PDGF-α, SBS rats underwent a 75% bowel resection, and SBS-PDGF-α rats underwent bowel resection and were treated with PDGF-α. Parameters of intestinal adaptation, enterocyte proliferation and apoptosis were determined at sacrifice. Illumina's Digital Gene Expression (DGE) analysis was used to determine PDGF-related gene expression profiling. PDGF-α and PDGF-α receptor (PDGFR-α) expression was determined using Real Time PCR. Western blotting was used to determine p-ERK, Akt1/2/3, bax and bcl-2 protein levels. SBS rats demonstrated a significant increase in PDGF-α and PDGFR-α expression in jejunum and ileum compared to sham animals. SBS-PDGF-α rats demonstrated a significant increase in bowel and mucosal weight, villus height and crypt depth in jejunum and ileum compared to SBS animals. PDGF-α expression in crypts increased in SBS rats (vs sham) and was accompanied by increased cell proliferation following PDGF-α administration. A significant decrease in cell apoptosis in this group was correlated with lower bax protein levels. In conclusion, in a rat model of SBS, PDGF-α stimulates enterocyte turnover, which is correlated with up-regulated PDGF-α receptor expression in the remaining small intestine.
2012-02-29 | GSE36122 | GEO
Project description:Investigating how the Wnt-driven Mll1 epigenome regulates salivary gland and head and neck cancer. We performed mRNA-seq and ChIP-seq of H3K4me1, me2 and me3 on mouse salivary gland cancer cells that are kept in two different growth conditions, adherent culture and non-adherent sphere culture. Mouse salivary gland cancer cells were isolated from salivary gland of transgenic mouse that harbor K14-Cre-induced Wnt/β-catenin gain-of-function and Bmpr1a loss-of-function mutations. Anti-H3K4me1 (C15410194), -me2 (C15410035) and -me3 (C15410003-50) antibodies were purchased from Diagenode. ChIP-seq was performed according to the protocols provided by Diagenode using the iDeal ChIP-seq kit for histones and the iDeal library preparation kit. For mRNA-seq, mRNA was extracted according to the standard TRIzol protocol (Invitrogen) and subjected to library preparation using the TruSeq stranded mRNA library preparation kit. Sequencing was performed with the TruSeq SBS Kit v3-HS (2 X 200 cycles) on an Illumina HiSeq 2000 sequencer.
2018-12-24 | E-MTAB-7514 | biostudies-arrayexpress
Project description:Loss of the transcription factor Satb2 converts mouse colonic epithelium into an ileal type. Here, we report that Satb2 gene deletion alleviates SBS by replacing diminished absorptive function and by inducing lymphovascular channels in the proximal colon. Enhanced nutrient absorption following Satb2 loss increased body weight and survival of mice with SBS. Deletion of SATB2 by adeno-associated viral delivery of CRISPR Split Cas9 to human colon organoids, followed by xenotransplantation into mice, resulted in ileal morphology and expression of ileal marker genes. This approach offers a feasible strategy for future treatment of SBS.
2025-03-19 | GSE279770 | GEO