GEO DataSets

(Submitter supplied) Purpose: This study aims to the downstream transcriptional networks controlled by JUN and DDIT which are critical for RGC death Methods: RNA was isolated from the retinas of wild-type mice and mice deficient in Jun, Ddit3, and both Jun and Ddit3 three days after mechanical optic nerve crush injury (CONC), and was subjected to RNA-sequecing. Results: This study identified downstream transcriptional changes after injury included both neuronal survival and pro-inflammatory signaling that were attenuated to differing degrees by loss of Ddit3, Jun, and Ddit3/Jun. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

38 Samples

Download data: TXT

(Submitter supplied) PROgECT (ClinicalTrials.gov Identifier: NCT01988961) was a multicenter, open-label study evaluating the accuracy of a probe-set panel in predicting response to golimumab treatment in participants with moderately to severely active ulcerative colitis (UC). Biopsy samples (collected 15 to 20 cm from the anal verge) were taken at screening from 84 patients and used for RNA extraction and profiling by microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

84 Samples

Download data: CEL

(Submitter supplied) UNITI-2 was a phase 3 clinical trial (ClinicalTrials.gov Identifier: NCT01369342) comparing the effects (both positive and negative) of an initial treatment with ustekinumab to a placebo over 8 weeks in patients with moderately to severely active Crohn's disease.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

148 Samples

Download data: CEL

(Submitter supplied) UNIFI was a randomized placebo-controlled phase 3 clinical trial evaluating the efficacy and safety of ustekinumab (ClinicalTrials.gov Identifier: NCT02407236). Gene expression profiling by microarrays was carried out at baseline on biopsies from the sigmoid colon (15-20cm from anal verge) of patients (n=550) with moderate-to-severe ulcerative colitis and of healthy subjects (n=18). Ulcerative colitis patients received placebo (n=186) or ustekinumab (n=364). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

568 Samples

Download data: CEL, TSV

(Submitter supplied) Mapping of transcriptional changes elicited by cytokines mediating Th2 and Th9 responses in human colonic organoids

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) Mapping of transcriptional changes elicited by cytokines mediating canonical immune responses in human colonic organoids

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

24 Samples

Download data: TXT

(Submitter supplied) Purpose: The purpose of this study was　to use RNA-seq to investigate the molecular mechanisms of damage in the early stages of the response to axonal injury, before the onset of RGC death. Methods: 12-week-old wild-type (WT) mice were used in this study. The experiment group underwent an optic nerve crush (ONC) procedure to induce axonal injury in the right eye, and the control group underwent a sham procedure. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: CSV

(Submitter supplied) In this study, we performed RNA-seq of injured and FACS-purified RGCs receiving CRISPR-mediated knockout of ATF3, ATF4, CEBPγ or CHOP

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

21 Samples

Download data: TSV

(Submitter supplied) In this study, we profiled epigenetic and transcriptional landscapes in injured RGCs to identify transcription factors driving critical chromatin state and gene expression changes in reponse to injury.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

30 Samples

Download data: TSV, TXT

(Submitter supplied) RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

61 Samples

Download data: CSV

(Submitter supplied) Intestinal organoids have the potential to replicate cellular diversity and functional biology of the human gut, suggesting their application in Inflammatory Bowel Disease (IBD) research. Insufficient characterization at the molecular, cellular, and functional level has remained a barrier to their use in drug discovery. We profile intestinal organoids and Transwell-monolayers derived from ileum and colon tissue of control and IBD subjects. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

211 Samples

Download data: TXT

(Submitter supplied) In order to investigate the response of epithelium to butyrate, we generated in vitro epithelial organoid cultures from colon samples of non-IBD controls and they were stimulated with different doses of butyrate. The transcriptional signature revealed that butyrate negatively regulated proliferation and cell cycle, induced a protective response to oxidative stress and regulated genes related to the immune response.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20650

95 Samples

Download data: CEL

(Submitter supplied) Treatment of inflammatory bowel disease (IBD) is challenging, with a series of available drugs each helping only a fraction of patients. Patients may face time-consuming drug trials while the disease is active, thus there is an unmet need for biomarkers and assays to predict drug effect. It is well known that the intestinal epithelium is an important factor in disease pathogenesis, exhibiting physical, biochemical and immunologic driven barrier dysfunctions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

36 Samples

Download data: SF

(Submitter supplied) Athough anti-TNF therapies can be used to treat colitis associated with inflammatory bowel disease, in mice the loss of the TNF receptor TNFR1 (Tnfrsf1a) in the Il10-/- spontaneous colitis background results in acceleration of disease onset. Whereas Il10-/- mice on the Bl/6 background are relatively protected from colitis throughout life, Il10-/- Tnfr1-/- mice develop colitis beginning at 4 wks of age. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: CSV

(Submitter supplied) The loss of TNFR1 (Tnfrsf1a) in the Il10-/- spontaneous mouse colitis background results in acceleration of disease onset. Whereas Il10-/- mice on the Bl/6 background are relatively protected from colitis throughout life, Il10-/- Tnfr1-/- mice develop colitis beginning at 4 wks of age. Their disease results in nearly 50% mortality by 12 wks of age. We hypothesized that this early-onset colitis was due to dysregulation of immune signals in early life, defining a key period known as the "weaning reaction" in which proinflammatory signals help induce mucosal tolerance of the microbiome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV

(Submitter supplied) We have compared mRNA expression in full-thickness mouse colon between wildtype mice and mice with a genetic deletion in tumor necrosis factor receptor 1 (TNFR1, encoded by the Tnfrsf1a gene). This experiment was motivated by our observation that Il10-/- Tnfr1-/- double-knockout mice develop very-early-onset colitis at the time of weaning, significantly earlier than disease onset in Il10-/- single-knockout mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) To further understand different gene expression of miR-31 knockout mouse colon and normal colon, we have employed colonic epithelium microarray expression profiling as a discovery platform to identify different genes with miR-31 knockout mouse colon and normal colon.comparision with normal colonic epithelium,upgene is 285 and downgene is 178 in knockout group.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

6 Samples

Download data: TXT

(Submitter supplied) Activation of inflammatory pathways in human IBD IL-6:STAT3 pathways are activated in the affected colon in IBD. However, the functional implications of this are not known. We hypothesized that pro-inflammatory IL-6:STAT3 dependent networks would be up regulated in the colon of pediatric patients with Crohn Disease (CD) and Ulcerative Colitis (UC), and that these would regulate leukocyte survival, proliferation, and recruitment to the gut. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5760

33 Samples

Download data: CEL

(Submitter supplied) A human colon carcinoma-derived cell line LS174T was modified to overexpress NICD, intracellular domain of Notch1, upon doxycycline addition (designated as LS174T-tetON-NICD cells), using the T-rex system (Invitrogen). We have previously shown that these cells can overexpress NICD under the control of CMV promoter (Okamoto R et al, Am J Physiol, 296(1):G23-35, 2009), and the amont of the overexpressed NICD protein reaches to the maximal level in early as 3 hours from doxycycline addition (100ng/ml), which persists for up to 24 hours. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13915

3 Samples

Download data: TXT

(Submitter supplied) The intestinal epithelium is an immunologically active barrier adapted for a low oxygen environment. Its role is implicated in the pathophysiology of various diseases, including inflammatory bowel disease (IBD) and colorectal cancer. Patient-derived intestinal epithelial organoids (IEOs) mimic the architecture and cell type composition of the intestine and can be used for disease modeling and personalized drug screening. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: SF