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Sample GSM1099311 Query DataSets for GSM1099311
Status Public on Mar 16, 2013
Title HT-29, stimulated with NaB, replicate #1
Sample type RNA
Source name HT-29 cells stimulated with 2 mM NaB
Organism Homo sapiens
Characteristics cell line: HT-29
cell type: colonic epithelial cell line
treatment: NaB
Treatment protocol Culture media was discarded, cells were rinsed with PBS and stimulated with 2 mM NaB (Sigma) alone or in combination with 125/150 ug/ml ciprofloxacin (Sigma) in culture medium in the absence of fetal calf serum and penicillin-streptomycin for 24 hours at 37C in 5% CO2. Cells incubated with only culture medium served as an unstimulated control.
Growth protocol HT-29 (ATCC, HTB-38) was grown up to 80-90% confluence in culture medium (RPMI-1640 supplemented with 10% fetal calf serum, 25 mM HEPES, 2 mM L-glutamine amd penicillin-streptomycin [Invitrogen]) in 6-well tissue culture plates (Corning) at 37C in 5% CO2.
Extracted molecule total RNA
Extraction protocol Extraction of RNA from cells was performed utilizing the RNeasy RNA purification kit according to the manufacturer's instructions (Qiagen).
Label biotin
Label protocol Total RNA was converted to sense strand cRNA using the Ambion WT expression kit. For fragmentation and labeling, the GeneChip WT Target Labeling kit was used.
Hybridization protocol Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.
Scan protocol Array plates were scanned using a GeneTitan scanner.
Description PS02_NaB
Gene expression data from HT-29 cells stimulated with 2 mM NaB.
Data processing Preprocessing in Affymetrix Expression Console (v 1.1) using the following methods. Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.
Submission date Mar 15, 2013
Last update date Mar 16, 2013
Contact name Protim Sarker
Phone +8801772683211
Organization name icddr,b
Street address Mohakhali
City Dhaka
ZIP/Postal code 1212
Country Bangladesh
Platform ID GPL11532
Series (1)
GSE45220 Expression data from HT-29, a human colonic epithelial cell line

Data table header descriptions
VALUE Quantitative signal

Data table
7930148 163.11
8152115 31.17
7892743 3.86
8148867 67.88
8165663 80.15
8148902 83.45
7896750 70.21
8039340 276.01
8033987 60.98
8067652 1021.06
8109226 230.15
7980720 139.63
8158242 160.38
8030557 30.9
7912374 359.65
8027473 366.55
8164698 58.8
8021777 16.77
7920278 52.33
8076978 73.55

Total number of rows: 33297

Table truncated, full table size 460 Kbytes.

Supplementary file Size Download File type/resource
GSM1099311_PS02_NaB_A07.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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