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Sample GSM1099312 Query DataSets for GSM1099312
Status Public on Mar 16, 2013
Title HT-29, stimulated with NaB and ciprofloxacin, replicate #1
Sample type RNA
Source name HT-29 cells stimulated with 2 mM NaB and 125 ug/ml ciprofloxacin
Organism Homo sapiens
Characteristics cell line: HT-29
cell type: colonic epithelial cell line
treatment: NaB and ciprofloxacin
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 PS03_NaB_Cip125
Gene expression data from HT-29 cells stimulated with 2 mM NaB and 125 ug/ml ciprofloxacin.
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 147.58
8152115 26.76
7892743 1.28
8148867 51.75
8165663 40.1
8148902 40.23
7896750 34.85
8039340 309.49
8033987 77.74
8067652 900.12
8109226 211.85
7980720 135.82
8158242 184.59
8030557 31.61
7912374 430.83
8027473 562.88
8164698 168.07
8021777 13.72
7920278 18.15
8076978 55.82

Total number of rows: 33297

Table truncated, full table size 462 Kbytes.

Supplementary file Size Download File type/resource
GSM1099312_PS03_NaB_Cip125_A09.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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