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Sample GSM3440003 Query DataSets for GSM3440003
Status Public on Apr 07, 2021
Title C4: Healthy colon, biological rep.4
Sample type RNA
 
Source name Colon, normal
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Colon
treatment regime: Untreated
Treatment protocol Azoxymethane (AOM) was given a single (10mg/kg B.wt) intraperitonielly at day 0 and three bouts of 5% DSS at days 5-10, 25-30, 45-50. At day 140, the mice were sacrificed. Cardamonin was administered orally, at a dose of 10mg/kg, 5 times every week for simultaneous group. And treatment started at a dose of 10mg/kg, 5times every week from 16th week to 30th week for the ''after tumor formation''group.
Growth protocol Colon collected from mice treated with AOM+DSS, followed by Cardamonin simultaneously treated or after tumor development. Colon from normal, healthy mice were used as control.
Extracted molecule total RNA
Extraction protocol Colon dissected and rinsed in 1X PBS, followed by snap freezing in liquid nitrogen. This was ground in liquid nitrogen, and mirVana miRNA isolation kit was used for the subsequent steps.
Label Biotin
Label protocol Total RNA was used for the reaction, Poly(A) tailing was performed followed by biotin labelling of the RNA. This was done by Flash Tag Biotin HSR labelling kit by Affymetrix
 
Hybridization protocol Samples were hybridised using Affymetrix hybridisation kit. Briefly, biotin labelled sample and hybridisation master mix were incubated at 99oC for 5 mins, then at 45oC for 5 mins. 130ul was injected into the array and both septa covered with tough spots. Loaded into hybridisation oven and incubated at 48oC, 60rpm for 16-18hrs
Scan protocol The chips were then scanned with an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, California, United States).
Description miRNA expression from AOM treated colon
Data processing The Data generated from the scan was then analyzed using the Bioconductor packages (Oligo, limma)
 
Submission date Oct 22, 2018
Last update date Apr 07, 2021
Contact name Dr. Harikumar K B
E-mail(s) harikumar@rgcb.res.in
Phone +91-471-2529-596
Organization name Rajiv Gandhi centre for Biotechnology
Department Cancer Research Program
Lab CRP-7
Street address Poojappura
City Thycaud
State/province Kerala
ZIP/Postal code 695 014
Country India
 
Platform ID GPL19117
Series (1)
GSE121608 Cardamonin repel colitis and its associated colorectal cancer

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
14q0_st 1.067622549
14qI-1_st 1.072154104
14qI-1_x_st 1.077233619
14qI-2_st 0.966367752
14qI-3_x_st 1.057860426
14qI-4_st 0.88096167
14qI-4_x_st 0.939585989
14qI-5_st 1.018471383
14qI-6_st 0.694069377
14qI-7_st 2.204217037
14qI-8_st 0.79994822
14qI-8_x_st 0.805689423
14qI-9_x_st 1.190593869
14qII-1_st 1.187716372
14qII-1_x_st 1.388627815
14qII-10_st 1.238522334
14qII-11_st 1.165938421
14qII-12_st 0.957467906
14qII-12_x_st 0.902999216
14qII-13_st 0.587244521

Total number of rows: 36353

Table truncated, full table size 983 Kbytes.




Supplementary file Size Download File type/resource
GSM3440003_C4_miRNA-4_0.CEL.gz 818.6 Kb (ftp)(http) CEL
Processed data included within Sample table

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