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Sample GSM1257528 Query DataSets for GSM1257528
Status Public on Apr 11, 2014
Title TG_FT_8W_rep2
Sample type RNA
 
Source name TG_Fallopian_Tube_8Week
Organism Mus musculus
Characteristics genotype: mogp-TAg transgenic
genetic background: C57BL6
gender: female
tissue: fallopian tube
age: 8 weeks old
Treatment protocol Animals were euthanized and the fallopian tubes dissected for total RNA isolation at either 7, 8 or 9 weeks of age.
Growth protocol Female C57BL6 mice and mogp-TAg transgenic mice (Dr. I. Myoshi/Nagoya University, Japan) were housed under standard conditions with food and water ad libitum.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using Invitrogen Trizol (Life Technologies, Inc. Carlsbad, CA) following the manufacturer's specifications. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.
Label Streptavidin-Cy3 bound to biotin labeled cRNA.
Label protocol Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description TG_Fallopian_Tube_8Week
Data processing Data was extracted using the Illumina GenomeStudio software, ver 1.6.0. Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std.
ID_REF = Unique identifiers from GPL6885-5840
Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.6.0.
 
Submission date Nov 01, 2013
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6885
Series (1)
GSE52011 A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high-grade serous carcinoma development

Data table header descriptions
ID_REF
VALUE Z transformation of the natural log of the raw intensity values
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -0.642109371 0.26316
ILMN_1212612 -0.661680879 0.34461
ILMN_1212619 -0.64599596 0.27569
ILMN_1212628
ILMN_1212632 -0.403505433 0.01003
ILMN_1212636 1.622777922 0
ILMN_1212637 0.440552465 0
ILMN_1212645 -0.903608697 0.97744
ILMN_1212648 0.517217345 0
ILMN_1212653 0.460699987 0
ILMN_1212672 6.75893E-05 0
ILMN_1212682
ILMN_1212683 -0.717021012 0.59524
ILMN_1212685
ILMN_1212692 1.547585864 0
ILMN_1212693 0.413599118 0
ILMN_1212695
ILMN_1212698
ILMN_1212702 3.271490354 0
ILMN_1212703 -0.28606123 0.00376

Total number of rows: 25697

Table truncated, full table size 619 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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