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Sample GSM3440009 Query DataSets for GSM3440009
Status Public on Apr 07, 2021
Title G1-9: Colon, AOM+DSS treated, Vehicle control, biological rep.4
Sample type RNA
Source name Colon, AOM treated
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Colon
treatment regime: Treated - vehicle control
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 and cardamonin treated samples
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 0.9120058
14qI-1_st 1.448368153
14qI-1_x_st 1.581263247
14qI-2_st 2.547493261
14qI-3_x_st 1.106702909
14qI-4_st 1.346511139
14qI-4_x_st 1.014485712
14qI-5_st 1.165781188
14qI-6_st 0.60869107
14qI-7_st 1.702791842
14qI-8_st 1.820070504
14qI-8_x_st 1.313729078
14qI-9_x_st 1.044550111
14qII-1_st 1.046364988
14qII-1_x_st 1.313729078
14qII-10_st 1.382033521
14qII-11_st 2.031316449
14qII-12_st 1.944606273
14qII-12_x_st 1.470170618
14qII-13_st 1.109684603

Total number of rows: 36353

Table truncated, full table size 982 Kbytes.

Supplementary file Size Download File type/resource
GSM3440009_G1-9_miRNA-4_0.CEL.gz 667.9 Kb (ftp)(http) CEL
Processed data included within Sample table

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