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Sample GSM3440000 Query DataSets for GSM3440000
Status Public on Apr 07, 2021
Title C1: Healthy colon, biological rep.1
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 form normal 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
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
VALUE RMA signal intensity

Data table
14q0_st 0.768494612
14qI-1_st 1.43114339
14qI-1_x_st 1.336377131
14qI-2_st 0.765041593
14qI-3_x_st 1.048289326
14qI-4_st 0.390923525
14qI-4_x_st 0.77246403
14qI-5_st 0.774730681
14qI-6_st 0.621894454
14qI-7_st 1.742751088
14qI-8_st 0.738242529
14qI-8_x_st 0.689200833
14qI-9_x_st 0.763046612
14qII-1_st 1.133830085
14qII-1_x_st 1.598878167
14qII-10_st 1.208016361
14qII-11_st 1.000638067
14qII-12_st 1.605091986
14qII-12_x_st 1.485705714
14qII-13_st 0.635129305

Total number of rows: 36353

Table truncated, full table size 983 Kbytes.

Supplementary file Size Download File type/resource
GSM3440000_C1_miRNA-4_0.CEL.gz 838.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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