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Sample GSM3506984 Query DataSets for GSM3506984
Status Public on Jun 12, 2019
Title 237_DIFF_1h_0,5mM
Sample type RNA
 
Source name d-EpOCs from Ctrl (237), 1h incubation, 0.5 mM butyrate stimulation
Organism Homo sapiens
Characteristics patient id: 237
differentiated_organoid: d-EpOCs
stimulus_time: 1h
stimulus_conc: 0.5mM
Treatment protocol At day 5 of in vitro expansion, EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated. d-EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated.
Growth protocol Crypts from descending/sigmoid colon samples were isolated by EDTA treatment. Crypt units were embedded in Matrigel, expanded for 3-4 days in stem medium and dissociated. Single epithelial cells were replated in fresh stem medium according to a 1:3 dilution to generate EpOCs. Part of the EpOCs was induced to differentiate (d-EpOCs) by the addition of fresh differentiation medium.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol+RNA Cleanup protocol by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol
 
Hybridization protocol Standard Affymetrix protocol
Scan protocol Standard Affymetrix protocol using a Gene chip scanner 3000
Description 1h 0.5mM
237_14
Data processing The data were analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using GC-RMA as normalization method.
 
Submission date Dec 10, 2018
Last update date Jun 12, 2019
Contact name Azucena Salas
E-mail(s) asalas1@recerca.clinic.cat
Organization name IDIBAPS
Department Gastroenterology
Street address Rosselló, 149-153
City Barcelona
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL20650
Series (1)
GSE123553 Expression data of butyrate stimulated epithelial organoid cultures generated from intestinal mucosa

Data table header descriptions
ID_REF
VALUE log2 GC-RMA signal

Data table
ID_REF VALUE
10000_at 4.365484267
10001_at 9.562436302
10002_at 4.463550057
100037417_at 5.269869094
100038246_at 5.012183379
10003_at 4.1635749
100048912_at 4.981118319
100049587_at 4.541919768
10004_at 4.363523737
10005_at 8.3967602
10006_at 10.16663865
10007_at 7.76469764
10008_at 9.084851072
100093630_at 11.3456554
10009_at 6.883077144
1000_at 4.701500771
100101467_at 4.994571014
10010_at 9.248692152
100113393_at 4.733710193
100113407_at 6.809801607

Total number of rows: 18512

Table truncated, full table size 375 Kbytes.




Supplementary file Size Download File type/resource
GSM3506984_237_14_260716_F02.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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