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Status |
Public on Apr 11, 2014 |
Title |
TG_FT_8W_rep2 |
Sample type |
RNA |
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Source name |
TG_Fallopian_Tube_8Week
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Organism |
Mus musculus |
Characteristics |
genotype: mogp-TAg transgenic genetic background: C57BL6 gender: female tissue: fallopian tube age: 8 weeks old
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Treatment protocol |
Animals were euthanized and the fallopian tubes dissected for total RNA isolation at either 7, 8 or 9 weeks of age.
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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.
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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.
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Label |
Streptavidin-Cy3 bound to biotin labeled cRNA.
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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.
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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.
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Scan protocol |
Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
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Description |
TG_Fallopian_Tube_8Week
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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.
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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 |
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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 |
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