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Sample GSM1349611 Query DataSets for GSM1349611
Status Public on Jun 01, 2014
Title D2.2
Sample type RNA
 
Source name Day 2 Repeat 2
Organism Mus musculus
Characteristics strain: CD-1
tissue: Multi-layered secondary follicles (150-180 µm in diameter) mechanically isolated from ovaries of 16-day-old mice
age: 16-day-old mice
Treatment protocol At each time point, follicles were pooled (for the microarray, 20-40 follicles per group, n = 3 independent experiments) and transferred into 1 ml of Liebovitz L-15 medium containing 10 U/ml alginate lyase (Sigma) for 20 min at 37°C to remove them from alginate. Follicles were aspirated, transferred into microcentrifuge tubes, flash frozen in liquid nitrogen, and stored at -80°C until RNA isolation was performed.
Growth protocol Multi-layered secondary follicles (150-180 µm in diameter) were mechanically isolated from ovaries of 16-day-old mice and individually encapsulated in alginate (FMC BioPolymers, Philadelphia, PA) as previously described (Kreeger et al. , 2006, West-Farrell et al., 2009, Xu et al. , 2006a). Alginate-encapsulated follicles were placed in individual wells of a 96-well plate containing 100 µl of growth medium (alpha minimum essential medium (alphaMEM) supplemented with 10 mIU/ml recombinant FSH (Organon, Roseland, NJ), 3 mg/ml bovine serum albumin (MP Biomedicals, Irvine, CA), 1 mg/ml bovine fetuin (Sigma, St. Louis, MO), 5 µg/ml insulin, 5 µg/ml transferrin, and 5 ng/ml selenium and cultured for 2, 4, 5, 6, or 8 days for microarray analysis. Half of the culture medium was exchanged every 2 days.
Extracted molecule total RNA
Extraction protocol RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA).
Label biotin
Label protocol mRNA samples were in vitro labeled using the TargetAmp 1-Round Aminoallyl-aRNA Kit (Epicentre, Madison, WI) a
 
Hybridization protocol randomly hybridized to BeadChips
Scan protocol Raw signal intensities of each probe were obtained using BeadStudio (Illumina).
Description TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-5
Data processing Statistical analyses were done in R (2008). Inadequate Illumina microarray probes due to misannotations or intronic coverage were removed from analysis using the Mouse WG V2.0 R0 file within ReMOAT (http://remoat.sysbiol.cam.ac.uk) (Barbosa-Morais et al. , 2010). Adequately annotated probes were considered to be above background if at least 2 of the 3 replicates measured were above background at P ≤ 0.01. The data were transformed using the variance stabilization transformation method (Lin et al. , 2008) and normalized by robust spline normalization (Du et al. , 2008).
 
Submission date Mar 17, 2014
Last update date Jun 01, 2014
Contact name and PhD
E-mail(s) bpenalver@surgery.bsd.chicago.edu
Organization name University of Chicago
Department Department of Surgery
Lab AB540
Street address 5841 South Maryland Avenue, MC 5032 Room AB540
City Chicago
State/province Illinois
ZIP/Postal code 60208
Country USA
 
Platform ID GPL6885
Series (1)
GSE55969 Dynamic study of In vitro murine follicle maturation in 3% alginate gels

Data table header descriptions
ID_REF
VALUE robust spline normalized signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 7.811529218 0.2130326
ILMN_1212612 7.806787476 0.2280702
ILMN_1212619 8.070139685 0.002506266
ILMN_1212628 7.751615104 0.6278195
ILMN_1212632 7.852204282 0.1065163
ILMN_1212636 11.11122443 0
ILMN_1212637 10.07537922 0
ILMN_1212645 7.748814583 0.6766917
ILMN_1212648 8.89743054 0
ILMN_1212653 8.291710502 0
ILMN_1212672 8.780940109 0
ILMN_1212682 7.94946597 0.01629073
ILMN_1212683 7.773188108 0.3972431
ILMN_1212685 7.743610739 0.735589
ILMN_1212692 7.957815101 0.01378446
ILMN_1212693 8.562680431 0
ILMN_1212695 7.761201165 0.5
ILMN_1212698 7.737421025 0.8120301
ILMN_1212717 8.727100463 0
ILMN_1212720 8.774438539 0

Total number of rows: 23286

Table truncated, full table size 730 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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