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Sample GSM4568442 Query DataSets for GSM4568442
Status Public on Jun 22, 2020
Title Hyperplastic Mammary gland Rep 1
Sample type RNA
 
Source name Hyperplastic Mammary gland Rep 1
Organism Mus musculus
Characteristics gender: Female
strain: C57Bl/6
Treatment protocol Normal mammary gland was recovered from female mices that were not exposed to either MPA nor DMBA. Hyperplastic mammary glands were recovered from female mice that underwent MPA/DMBA protocol but did not develop any tumor. Mammary gland tumors were recovered from female mice once the tumor reach the size of 0.7-1 cm^2
Growth protocol Fifty mg slow-release (90 days) medroxyprogesterone acetate (MPA) pellets (Innovative Research of America) were implanted subcutaneously by surgery into 6-9 week-old female (day 0). Mice were administered 200 µL of a 5 mg mL-1 7,12-dimethylbenz[a]anthracene (DMBA; from Sigma-Aldrich) solution in corn oil (Sigma-Aldrich), by oral gavage once a week on weeks 1, 2, 3, 5, 6 and 7 after implantation of the MPA pellet.
Extracted molecule total RNA
Extraction protocol Mammary gland tissue was removed from the mice and RNA freshly extracted using Qiagen RNeasy kits.
Label biotin
Label protocol 200 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) . Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.
 
Hybridization protocol After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MTA1.0 (Affymetrix) at 45°C for 17 hours
Scan protocol After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G
Data processing The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. RMA normalization is performed using Partek software with Affymetrix CDF file.
 
Submission date May 26, 2020
Last update date Jun 26, 2020
Contact name Aitziber Buque Martinez
Organization name Weill Cornell Medical College
Department Radiation Oncology
Street address 1300 York Avenue
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL20258
Series (1)
GSE151197 M/D-tumors vs non´-tumor mammary gland tissues

Data table header descriptions
ID_REF
VALUE Log2-RMA signal

Data table
ID_REF VALUE
TC0100000001.mm.1 5.275229
TC0100000002.mm.1 3.336306
TC0100000003.mm.1 2.828982
TC0100000004.mm.1 3.709571
TC0100000005.mm.1 3.240723
TC0100000006.mm.1 3.696385
TC0100000007.mm.1 3.465513
TC0100000008.mm.1 10.30756
TC0100000009.mm.1 3.309496
TC0100003860.mm.1 7.907321
TC0100003861.mm.1 8.712478
TC0100000011.mm.1 4.815864
TC0100000012.mm.1 3.441196
TC0100000013.mm.1 3.62114
TC0100000014.mm.1 8.263331
TC0100000015.mm.1 5.876186
TC0100000016.mm.1 4.548245
TC0100000017.mm.1 3.165733
TC0100000018.mm.1 4.315603
TC0100000019.mm.1 3.457284

Total number of rows: 58776

Table truncated, full table size 1544 Kbytes.




Supplementary file Size Download File type/resource
GSM4568442_7_H1_M8A1GM_MTA-1_0_.CEL.gz 25.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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