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Sample GSM3440013 Query DataSets for GSM3440013
Status Public on Apr 07, 2021
Title G3-3: Colon, AOM+DSS treated, Cardamonin treatment after 16 week, biol.rep.1
Sample type RNA
Source name Colon, AOM, Cardamonin after 16 week
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Colon
treatment regime: Treated - Cardamonin after tumor formation
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 1.478351981
14qI-1_st 1.25113348
14qI-1_x_st 1.204296384
14qI-2_st 1.218706009
14qI-3_x_st 1.671504722
14qI-4_st 1.110338283
14qI-4_x_st 1.00546202
14qI-5_st 1.363837654
14qI-6_st 1.327516209
14qI-7_st 2.129859639
14qI-8_st 1.325156702
14qI-8_x_st 1.420974705
14qI-9_x_st 1.279108869
14qII-1_st 0.963725705
14qII-1_x_st 1.258732891
14qII-10_st 1.54632928
14qII-11_st 2.227567101
14qII-12_st 1.418208084
14qII-12_x_st 1.469814227
14qII-13_st 2.133367006

Total number of rows: 36353

Table truncated, full table size 983 Kbytes.

Supplementary file Size Download File type/resource
GSM3440013_G3_3_miRNA-4_0.CEL.gz 670.5 Kb (ftp)(http) CEL
Processed data included within Sample table

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