Sample Set Annotation Tool: Expression data from IBS patients before and after treatment

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Increased numbers of mast cells and their products have been linked to symptom onset and severity in patients with chronic diarrhea and abdominal pain. Although mast-cell inhibition ameliorates clinical manifestations and reduces mucosal inflammation, underlying molecular mechanisms remain unknown.

Hypothesis

Experimental Design

Diarrhea-irritable bowel syndrome (d-IBS) patients were studied at baseline, or 6 months after natural evolution (control) or oral cromoglycate treatment. Jejunal biopsies were subjected to chip analysis (Affymetrix Human Genome U133 Plus 2.0 GeneChips).

Experimental Variables

Oral cromoglycate treatment

Controls

Natural evolution of the disease

Methods

Chip analysis were done on jejunal biopsies of 5 Diarrhea-irritable bowel syndrome (d-IBS) patients at baseline, 6 months after natural evolution (control) or oral cromoglycate treatment.

Additional Information

Expected Samples:

14 Samples Loaded: 14

Species

Human (Homo sapiens)

Sample Source

Jejunal biopsies

Disease

Diarrhea-irritable bowel syndrome

Treatment Protocol

Biopsies were placed in RNA later solution and stored at -80ºC until processed.

Growth Protocol

Jejunal biopsies were obtained using the Watson's capsule in all participants. The instrument was orally inserted under fluoroscopic control 5 to 10 cm distal to the Treitz’s angle. Then, a tissue sample was obtained by suction with a 50 ml syringe.

Extraction Protocol

Biopsies were placed in RNA later solution and stored at -80ºC until processed. Extraction of total RNA was performed using the Rneasy mini kit (Qiagen) according to the manufacturer's instructions.

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	tissue	treatment	disease	location	Sample Type
GSM371301	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy
GSM371302	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy
GSM371303	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy
GSM371304	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy
GSM371305	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy

Please log in in order to upload files.

File
GSE14842_annotation_ori.csv Sample Set Spreadsheet
GSE14842_annotation_ori.csv Sample Set Spreadsheet
GSE14842_annotation_v1.csv Sample Set Spreadsheet
GSE14842_annotation_v2.csv Sample Set Spreadsheet
GSE14842_annotation_v2.csv Sample Set Spreadsheet
GSE14842_v1.csv Sample Set Spreadsheet

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID	Tissue	Treatment	Disease	Location	Sample Type	Repetition
GSM371301	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep1
GSM371302	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep2
GSM371303	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep3
GSM371304	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep4
GSM371305	jejunal mucosa	baseline	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep5
GSM371310	jejunal mucosa	control	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep1
GSM371311	jejunal mucosa	control	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep2
GSM371312	jejunal mucosa	control	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep3
GSM371313	jejunal mucosa	control	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep4
GSM371314	jejunal mucosa	control	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep5
GSM371315	jejunal mucosa	treatment	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep1
GSM371316	jejunal mucosa	treatment	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep2
GSM371317	jejunal mucosa	treatment	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep3
GSM371318	jejunal mucosa	treatment	diarrhea-IBS	10 cm from Treitz	Jejunal biopsy	rep4

Group Sets View in Gene Expression Browser

Name
All Samples		View
Patient		View
Treatment	Default	View
In order to make new Group Sets or change settings, please log in.

Module Analysis

Group Set
All Samples
Patient
Treatment

SIDRA