title: VAP 1 KO 2

city: Turku

first: Kaisa

last: Auvinen

address: Tykistökatu 6

department: Medicity Research Laboratory

country: Finland

institute: University of Turku

hyb_protocol: 1500 ng  of  each sample was hybridized to chips at 58 °C overnight (18 h) according to Illumina Whole-Genome Gene Expression with IntelliHyb -protocol, revision B

scan_protocol: Chips were scanned with Illumina BeadArray Reader with default setting of the scanner.

data_processing: Data were analyzed using R2 bioconductor with quantile normalisation method.

source_name: mouse B16 melanoma tissue

label_protocol: 100 ng total RNA was amplified with Ambion's Illumina RNA TotalPrep Amplification kit. IVT reaction was carried out overnight (14h) and cRNA was biotinylated.

growth_protocol: B16-F10-luc-G5 melanoma cells (Xenogen) were subcutaneously injected into abdominal area of anesthetized mice. After 10 days, mice were euthanized and tumors were dissected.

extract_protocol: total RNA was isolated from dissected tumors using Qiagen RNA extraction kit

tag: female C57/BL/6 VAP-1 -/- mouse

tag: tumor nodule


title: pSUPER-scramble replicate 2

status: Public on Oct 27 2009

type: RNA

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

description: Gene expression data from HUVEC over-expressing a scramble control sequence

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  HG-U133_Plus_2.1sq. GeneChip.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Summarized signal intensities were generated in BRB ArrayTools using justRMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC infected by retroviral vectors bearing a control scramble sequence

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HUVEC were grown in EGM-2 (Lonza) containing 2% FBS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

treatment_protocol: To obtain stable miR-210 over-expressing cells, HUVEC were infected by retroviral vectors bearing pre-miR-210 sequence or a control scramble sequence. To inhibit miR-210, Locked Nucleic Acid (LNA) oligonucleotides against miR-210 or a control scramble sequence (Exiqon) were transfected by siRNA Transfection Reagent (Santa Cruz), following manufacturer instructions, in 40% confluent HUVEC (4X103/cm2) at the final concentration of 40 nM.

tag: cell line

value: HUVEC


title: pSUPER-scramble replicate 3


title: Wild type 3

label: Biotin

organism: Mus musculus

tag: female C57/BL/6 wild-type mouse


title: Liver, F2 Control Pool (n=156) vs. 5903a-liver

status: Public on Oct 26 2009

city: Seattle

first: Radu

last: Dobrin

state: WA

address: 401 Terry Ave N

country: USA

institute: Merck and Co. Inc.

description: The expression profile in mouse liver tissue from individuals in a M16xICR cross given as a normalized ratio as reported from Rosetta Resolver.

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver? system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Liver, F2 Control Pool (n=156)

label_protocol: 5 ug of total RNA was used for each amplification reaction.  The method used a custom, automated version of the RT/IVT method referenced in Hughes et al, 2001 (Hughes 2001, Shannon 2000 patent ref).  mRNA amplification utilized a Moloney Murine Leukemia Virus Reverse Transcriptase (MMLV-RT) mediated reverse transcription that utilized a poly-T primer that incorporated a T7 RNA polymerase start site, followed by in vitro transcription incorporating amino-allyl UTP.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: tissue

value: liver

tag: reference

value: F2 Control Pool (n=156)

tag: genotype

value: F2 M16xICR cross


title: Liver, F2 Control Pool (n=156) vs. 6008b-liver


title: Liver, F2 Control Pool (n=156) vs. 6004b-liver


title: Liver, F2 Control Pool (n=156) vs. 6002a-liver


title: Liver, F2 Control Pool (n=156) vs. 6006b-liver


title: Liver, F2 Control Pool (n=156) vs. 6002b-liver


title: Liver, F2 Control Pool (n=156) vs. 5905a-liver


title: Liver, F2 Control Pool (n=156) vs. 6005b-liver


title: Liver, F2 Control Pool (n=156) vs. 5806b-liver


title: Liver, F2 Control Pool (n=156) vs. 5907a-liver


title: pSUPER-mir-210 replicate 1

description: Gene expression data from HUVEC over-expressing miR-210

source_name: HUVEC infected by retroviral vectors bearing pre-miR-210 sequence


title: Liver, F2 Control Pool (n=156) vs. 5902a-liver


title: Liver, F2 Control Pool (n=156) vs. 5805b-liver


title: Wild type 2


title: VAP 1 KO 1


title: pSUPER-scramble replicate 1


title: Liver, F2 Control Pool (n=156) vs. 5904a-liver


title: Liver, F2 Control Pool (n=156) vs. 5803a-liver


title: Liver, F2 Control Pool (n=156) vs. 5607b-liver


title: Liver, F2 Control Pool (n=156) vs. 5703b-liver


title: Liver, F2 Control Pool (n=156) vs. 5802a-liver


title: Liver, F2 Control Pool (n=156) vs. 5802b-liver


title: Liver, F2 Control Pool (n=156) vs. 5608a-liver


title: Liver, F2 Control Pool (n=156) vs. 5407a-liver


title: Liver, F2 Control Pool (n=156) vs. 5603a-liver


title: Liver, F2 Control Pool (n=156) vs. 5606a-liver


title: Liver, F2 Control Pool (n=156) vs. 5604a-liver


title: Liver, F2 Control Pool (n=156) vs. 5405a-liver


title: Liver, F2 Control Pool (n=156) vs. 5605b-liver


title: Liver, F2 Control Pool (n=156) vs. 5608b-liver


title: Liver, F2 Control Pool (n=156) vs. 5201a-liver


title: Liver, F2 Control Pool (n=156) vs. 5402a-liver


title: Liver, F2 Control Pool (n=156) vs. 5507b-liver


title: Liver, F2 Control Pool (n=156) vs. 5501b-liver


title: Liver, F2 Control Pool (n=156) vs. 5505b-liver


title: Liver, F2 Control Pool (n=156) vs. 5401a-liver


title: Liver, F2 Control Pool (n=156) vs. 5204a-liver


title: Liver, F2 Control Pool (n=156) vs. 5607a-liver


title: Liver, F2 Control Pool (n=156) vs. 5206a-liver


title: Liver, F2 Control Pool (n=156) vs. 5404a-liver


title: Liver, F2 Control Pool (n=156) vs. 5202a-liver


title: Liver, F2 Control Pool (n=156) vs. 5606b-liver


title: Liver, F2 Control Pool (n=156) vs. 5403a-liver


title: Liver, F2 Control Pool (n=156) vs. 5108a-liver


title: Liver, F2 Control Pool (n=156) vs. 5106a-liver


title: Liver, F2 Control Pool (n=156) vs. 5103a-liver


title: Liver, F2 Control Pool (n=156) vs. 5102a-liver


title: Liver, F2 Control Pool (n=156) vs. 5005b-liver


title: Liver, F2 Control Pool (n=156) vs. 5003b-liver


title: Liver, F2 Control Pool (n=156) vs. 4205b-liver


title: Liver, F2 Control Pool (n=156) vs. 4203b-liver


title: Liver, F2 Control Pool (n=156) vs. 4204a-liver


title: Liver, F2 Control Pool (n=156) vs. 4207a-liver


title: Liver, F2 Control Pool (n=156) vs. 5001b-liver


title: Liver, F2 Control Pool (n=156) vs. 5008b-liver


title: Liver, F2 Control Pool (n=156) vs. 4502a-liver


title: Liver, F2 Control Pool (n=156) vs. 5006b-liver


title: Liver, F2 Control Pool (n=156) vs. 4302b-liver


title: Liver, F2 Control Pool (n=156) vs. 4205a-liver


title: Liver, F2 Control Pool (n=156) vs. 4202b-liver


title: Liver, F2 Control Pool (n=156) vs. 4308b-liver


title: Liver, F2 Control Pool (n=156) vs. 4307b-liver


title: Liver, F2 Control Pool (n=156) vs. 4504b-liver


title: Liver, F2 Control Pool (n=156) vs. 4204b-liver


title: Liver, F2 Control Pool (n=156) vs. 4108a-liver


title: Liver, F2 Control Pool (n=156) vs. 4107a-liver


title: Liver, F2 Control Pool (n=156) vs. 4007a-liver


title: Liver, F2 Control Pool (n=156) vs. 4201b-liver


title: Liver, F2 Control Pool (n=156) vs. 5105a-liver


title: Liver, F2 Control Pool (n=156) vs. 4006b-liver


title: Liver, F2 Control Pool (n=156) vs. 4002b-liver


title: Liver, F2 Control Pool (n=156) vs. 4001b-liver


title: Liver, F2 Control Pool (n=156) vs. 3908b-liver


title: Liver, F2 Control Pool (n=156) vs. 3803b-liver


title: Liver, F2 Control Pool (n=156) vs. 3701b-liver


title: Liver, F2 Control Pool (n=156) vs. 3707a-liver


title: Liver, F2 Control Pool (n=156) vs. 3802b-liver


title: Liver, F2 Control Pool (n=156) vs. 3306a-liver


title: Liver, F2 Control Pool (n=156) vs. 3806a-liver


title: Liver, F2 Control Pool (n=156) vs. 3707b-liver


title: Liver, F2 Control Pool (n=156) vs. 4006a-liver


title: Liver, F2 Control Pool (n=156) vs. 3801b-liver


title: Liver, F2 Control Pool (n=156) vs. 3302a-liver


title: Liver, F2 Control Pool (n=156) vs. 3205b-liver


title: Liver, F2 Control Pool (n=156) vs. 3506a-liver


title: Liver, F2 Control Pool (n=156) vs. 3208a-liver


title: Liver, F2 Control Pool (n=156) vs. 3207a-liver


title: Liver, F2 Control Pool (n=156) vs. 3804b-liver


title: Liver, F2 Control Pool (n=156) vs. 3808b-liver


title: Liver, F2 Control Pool (n=156) vs. 3407b-liver


title: Liver, F2 Control Pool (n=156) vs. 3206a-liver


title: Liver, F2 Control Pool (n=156) vs. 3504b-liver


title: Liver, F2 Control Pool (n=156) vs. 4004a-liver


title: Liver, F2 Control Pool (n=156) vs. 3405b-liver


title: Liver, F2 Control Pool (n=156) vs. 3205a-liver


title: Liver, F2 Control Pool (n=156) vs. 3203a-liver


title: Liver, F2 Control Pool (n=156) vs. 3303a-liver


title: Liver, F2 Control Pool (n=156) vs. 3202a-liver


title: Liver, F2 Control Pool (n=156) vs. 3006a-liver


title: Liver, F2 Control Pool (n=156) vs. 3108b-liver


title: Liver, F2 Control Pool (n=156) vs. 3005a-liver


title: Liver, F2 Control Pool (n=156) vs. 3104b-liver


title: Liver, F2 Control Pool (n=156) vs. 3002a-liver


title: Liver, F2 Control Pool (n=156) vs. 3101b-liver


title: Liver, F2 Control Pool (n=156) vs. 2702a-liver


title: Liver, F2 Control Pool (n=156) vs. 3106b-liver


title: Liver, F2 Control Pool (n=156) vs. 3001a-liver


title: Liver, F2 Control Pool (n=156) vs. 2606a-liver


title: Liver, F2 Control Pool (n=156) vs. 2705a-liver


title: Liver, F2 Control Pool (n=156) vs. 2503a-liver


title: Liver, F2 Control Pool (n=156) vs. 2401a-liver


title: Liver, F2 Control Pool (n=156) vs. 2708a-liver


title: Liver, F2 Control Pool (n=156) vs. 2505a-liver


title: Liver, F2 Control Pool (n=156) vs. 2603a-liver


title: Liver, F2 Control Pool (n=156) vs. 2604a-liver


title: Liver, F2 Control Pool (n=156) vs. 2402a-liver


title: Liver, F2 Control Pool (n=156) vs. 2506a-liver


title: Liver, F2 Control Pool (n=156) vs. 2308a-liver


title: Liver, F2 Control Pool (n=156) vs. 2601a-liver


title: Liver, F2 Control Pool (n=156) vs. 2504a-liver


title: Liver, F2 Control Pool (n=156) vs. 2408a-liver


title: Liver, F2 Control Pool (n=156) vs. 2501a-liver


title: Liver, F2 Control Pool (n=156) vs. 2508a-liver


title: Liver, F2 Control Pool (n=156) vs. 2307a-liver


title: Liver, F2 Control Pool (n=156) vs. 2305a-liver


title: Liver, F2 Control Pool (n=156) vs. 2003b-liver


title: Liver, F2 Control Pool (n=156) vs. 2002b-liver


title: Liver, F2 Control Pool (n=156) vs. 2303a-liver


title: Liver, F2 Control Pool (n=156) vs. 2107a-liver


title: Liver, F2 Control Pool (n=156) vs. 2006b-liver


title: Liver, F2 Control Pool (n=156) vs. 1901b-liver


title: Liver, F2 Control Pool (n=156) vs. 2304a-liver


title: Liver, F2 Control Pool (n=156) vs. 1806a-liver


title: Liver, F2 Control Pool (n=156) vs. 1807a-liver


title: Liver, F2 Control Pool (n=156) vs. 1808a-liver


title: Liver, F2 Control Pool (n=156) vs. 1404b-liver


title: Liver, F2 Control Pool (n=156) vs. 1305a-liver


title: Liver, F2 Control Pool (n=156) vs. 1303a-liver


title: Liver, F2 Control Pool (n=156) vs. 1907a-liver


title: Liver, F2 Control Pool (n=156) vs. 1805a-liver


title: Liver, F2 Control Pool (n=156) vs. 1306a-liver


title: Liver, F2 Control Pool (n=156) vs. 1407a-liver


title: Liver, F2 Control Pool (n=156) vs. 1806b-liver


title: Liver, F2 Control Pool (n=156) vs. 1403b-liver


title: Liver, F2 Control Pool (n=156) vs. 1807b-liver


title: Liver, F2 Control Pool (n=156) vs. 1904b-liver


title: Liver, F2 Control Pool (n=156) vs. 1205a-liver


title: Liver, F2 Control Pool (n=156) vs. 1407b-liver


title: Liver, F2 Control Pool (n=156) vs. 1002b-liver


title: Liver, F2 Control Pool (n=156) vs. 1007b-liver


title: Liver, F2 Control Pool (n=156) vs. 1201a-liver


title: Liver, F2 Control Pool (n=156) vs. 2001b-liver


title: Liver, F2 Control Pool (n=156) vs. 1001b-liver


title: Liver, F2 Control Pool (n=156) vs. 1003a-liver


title: Liver, F2 Control Pool (n=156) vs. 0808b-liver


title: Liver, F2 Control Pool (n=156) vs. 1006a-liver


title: Liver, F2 Control Pool (n=156) vs. 0805b-liver


title: Liver, F2 Control Pool (n=156) vs. 0608b-liver


title: Liver, F2 Control Pool (n=156) vs. 0806b-liver


title: Liver, F2 Control Pool (n=156) vs. 0801b-liver


title: Liver, F2 Control Pool (n=156) vs. 0804b-liver


title: Liver, F2 Control Pool (n=156) vs. 0607a-liver


title: Liver, F2 Control Pool (n=156) vs. 0605a-liver


title: Liver, F2 Control Pool (n=156) vs. 5908-liver


title: Liver, F2 Control Pool (n=156) vs. 0606b-liver


title: Liver, F2 Control Pool (n=156) vs. 0604b-liver


title: Liver, F2 Control Pool (n=156) vs. 5903-liver


title: Liver, F2 Control Pool (n=156) vs. 5807-liver


title: Liver, F2 Control Pool (n=156) vs. 5904-liver


title: Liver, F2 Control Pool (n=156) vs. 0602b-liver


title: Liver, F2 Control Pool (n=156) vs. 0606a-liver


title: Liver, F2 Control Pool (n=156) vs. 0608a-liver


title: Liver, F2 Control Pool (n=156) vs. 0601a-liver


title: Liver, F2 Control Pool (n=156) vs. 0605b-liver


title: Liver, F2 Control Pool (n=156) vs. 5806-liver


title: Liver, F2 Control Pool (n=156) vs. 5404-liver


title: Liver, F2 Control Pool (n=156) vs. 5902-liver


title: Liver, F2 Control Pool (n=156) vs. 5506-liver


title: Liver, F2 Control Pool (n=156) vs. 5805-liver


title: Liver, F2 Control Pool (n=156) vs. 5503-liver


title: Liver, F2 Control Pool (n=156) vs. 5401-liver


title: Liver, F2 Control Pool (n=156) vs. 5802-liver


title: Liver, F2 Control Pool (n=156) vs. 5405-liver


title: Liver, F2 Control Pool (n=156) vs. 5505-liver


title: Liver, F2 Control Pool (n=156) vs. 5207-liver


title: Liver, F2 Control Pool (n=156) vs. 5208-liver


title: Liver, F2 Control Pool (n=156) vs. 5402-liver


title: Liver, F2 Control Pool (n=156) vs. 5206-liver


title: Liver, F2 Control Pool (n=156) vs. 5205-liver


title: Liver, F2 Control Pool (n=156) vs. 5204-liver


title: Liver, F2 Control Pool (n=156) vs. 5403-liver


title: Liver, F2 Control Pool (n=156) vs. 0506b-liver


title: Liver, F2 Control Pool (n=156) vs. 5203-liver


title: Liver, F2 Control Pool (n=156) vs. 0504b-liver


title: Liver, F2 Control Pool (n=156) vs. 501b-liver


title: Liver, F2 Control Pool (n=156) vs. 4505-liver


title: Liver, F2 Control Pool (n=156) vs. 5202-liver


title: Liver, F2 Control Pool (n=156) vs. 4506-liver


title: Liver, F2 Control Pool (n=156) vs. 4507-liver


title: Liver, F2 Control Pool (n=156) vs. 4501-liver


title: Liver, F2 Control Pool (n=156) vs. 4503-liver


title: Liver, F2 Control Pool (n=156) vs. 4205-liver


title: Liver, F2 Control Pool (n=156) vs. 4007-liver


title: Liver, F2 Control Pool (n=156) vs. 4008-liver


title: Liver, F2 Control Pool (n=156) vs. 4204-liver


title: Liver, F2 Control Pool (n=156) vs. 4103-liver


title: Liver, F2 Control Pool (n=156) vs. 4104-liver


title: Liver, F2 Control Pool (n=156) vs. 4208-liver


title: Liver, F2 Control Pool (n=156) vs. 4004-liver


title: Liver, F2 Control Pool (n=156) vs. 4207-liver


title: Liver, F2 Control Pool (n=156) vs. 1006b-liver


title: Liver, F2 Control Pool (n=156) vs. 4102-liver


title: Liver, F2 Control Pool (n=156) vs. 4202-liver


title: Liver, F2 Control Pool (n=156) vs. 4101-liver


title: Liver, F2 Control Pool (n=156) vs. 4006-liver


title: Liver, F2 Control Pool (n=156) vs. 3908-liver


title: Liver, F2 Control Pool (n=156) vs. 4003-liver


title: Liver, F2 Control Pool (n=156) vs. 4002-liver


title: Liver, F2 Control Pool (n=156) vs. 3907-liver


title: Liver, F2 Control Pool (n=156) vs. 3906-liver


title: Liver, F2 Control Pool (n=156) vs. 4206-liver


title: Liver, F2 Control Pool (n=156) vs. 4005-liver


title: Liver, F2 Control Pool (n=156) vs. 4001-liver


title: Liver, F2 Control Pool (n=156) vs. 0403a-liver


title: Liver, F2 Control Pool (n=156) vs. 3904-liver


title: Liver, F2 Control Pool (n=156) vs. 3905-liver


title: Liver, F2 Control Pool (n=156) vs. 3708-liver


title: Liver, F2 Control Pool (n=156) vs. 3403-liver


title: Liver, F2 Control Pool (n=156) vs. 3804-liver


title: Liver, F2 Control Pool (n=156) vs. 3702-liver


title: Liver, F2 Control Pool (n=156) vs. 3404-liver


title: Liver, F2 Control Pool (n=156) vs. 3402-liver


title: Liver, F2 Control Pool (n=156) vs. 3202-liver


title: Liver, F2 Control Pool (n=156) vs. 3205-liver


title: Liver, F2 Control Pool (n=156) vs. 3204-liver


title: Liver, F2 Control Pool (n=156) vs. 3107-liver


title: Liver, F2 Control Pool (n=156) vs. 3207-liver


title: Liver, F2 Control Pool (n=156) vs. 3406-liver


title: Liver, F2 Control Pool (n=156) vs. 0306b-liver


title: Liver, F2 Control Pool (n=156) vs. 3103-liver


title: Liver, F2 Control Pool (n=156) vs. 0304a-liver


title: Liver, F2 Control Pool (n=156) vs. 0308a-liver


title: Liver, F2 Control Pool (n=156) vs. 3108-liver


title: Liver, F2 Control Pool (n=156) vs. 0307b-liver


title: Liver, F2 Control Pool (n=156) vs. 3102-liver


title: Liver, F2 Control Pool (n=156) vs. 0306a-liver


title: Liver, F2 Control Pool (n=156) vs. 0305b-liver


title: Liver, F2 Control Pool (n=156) vs. 0304b-liver


title: Liver, F2 Control Pool (n=156) vs. 0303b-liver


title: Liver, F2 Control Pool (n=156) vs. 3002-liver


title: Liver, F2 Control Pool (n=156) vs. 0302a-liver


title: Liver, F2 Control Pool (n=156) vs. 3008-liver


title: Liver, F2 Control Pool (n=156) vs. 2808-liver


title: Liver, F2 Control Pool (n=156) vs. 2805-liver


title: Liver, F2 Control Pool (n=156) vs. 3004-liver


title: Liver, F2 Control Pool (n=156) vs. 2804-liver


title: Liver, F2 Control Pool (n=156) vs. 2801-liver


title: Liver, F2 Control Pool (n=156) vs. 3005-liver


title: Liver, F2 Control Pool (n=156) vs. 2802-liver


title: Liver, F2 Control Pool (n=156) vs. 2806-liver


title: Liver, F2 Control Pool (n=156) vs. 0207b-liver


title: Liver, F2 Control Pool (n=156) vs. 0208b-liver


title: Liver, F2 Control Pool (n=156) vs. 2004-liver


title: Liver, F2 Control Pool (n=156) vs. 2007-liver


title: Liver, F2 Control Pool (n=156) vs. 0202b-liver


title: Liver, F2 Control Pool (n=156) vs. 2002-liver


title: Liver, F2 Control Pool (n=156) vs. 2001-liver


title: Liver, F2 Control Pool (n=156) vs. 2005-liver


title: Liver, F2 Control Pool (n=156) vs. 1707-liver


title: Liver, F2 Control Pool (n=156) vs. 1901-liver


title: Liver, F2 Control Pool (n=156) vs. 1903-liver


title: Liver, F2 Control Pool (n=156) vs. 1706-liver


title: Liver, F2 Control Pool (n=156) vs. 1701-liver


title: Liver, F2 Control Pool (n=156) vs. 1703-liver


title: Liver, F2 Control Pool (n=156) vs. 0204b-liver


title: Liver, F2 Control Pool (n=156) vs. 1702-liver


title: Liver, F2 Control Pool (n=156) vs. 1503-liver


title: Liver, F2 Control Pool (n=156) vs. 1908-liver


title: Liver, F2 Control Pool (n=156) vs. 1704-liver


title: Liver, F2 Control Pool (n=156) vs. 1501-liver


title: Liver, F2 Control Pool (n=156) vs. 1506-liver


title: Liver, F2 Control Pool (n=156) vs. 1306-liver


title: Liver, F2 Control Pool (n=156) vs. 1407-liver


title: Liver, F2 Control Pool (n=156) vs. 1402-liver


title: Liver, F2 Control Pool (n=156) vs. 1305-liver


title: Liver, F2 Control Pool (n=156) vs. 1308-liver


title: Liver, F2 Control Pool (n=156) vs. 1304-liver


title: Liver, F2 Control Pool (n=156) vs. 1206-liver


title: Liver, F2 Control Pool (n=156) vs. 1105-liver


title: Liver, F2 Control Pool (n=156) vs. 1207-liver


title: Liver, F2 Control Pool (n=156) vs. 1301-liver


title: Liver, F2 Control Pool (n=156) vs. 0104-liver


title: Liver, F2 Control Pool (n=156) vs. 1307-liver


title: Liver, F2 Control Pool (n=156) vs. 0204-liver


title: Liver, F2 Control Pool (n=156) vs. 1005-liver


title: Liver, F2 Control Pool (n=156) vs. 1302-liver


title: Liver, F2 Control Pool (n=156) vs. 1008-liver


title: Liver, F2 Control Pool (n=156) vs. 0206-liver


title: Liver, F2 Control Pool (n=156) vs. 0207-liver


title: Liver, F2 Control Pool (n=156) vs. 1106-liver


title: Liver, F2 Control Pool (n=156) vs. 0103-liver


title: Liver, F2 Control Pool (n=156) vs. 1004-liver


title: Liver, F2 Control Pool (n=156) vs. 0108-liver


title: Liver, F2 Control Pool (n=156) vs. 0106-liver


title: Liver, F2 Control Pool (n=156) vs. 0102-liver


title: F2 Adipose Control Pool (n=160) vs. 5204

description: The expression profile in mouse adipose tissue from individuals in a M16xICR cross given as a normalized ratio as reported from Rosetta Resolver.

source_name: F2 Adipose Control Pool (n=160)

value: adipose

value: Control Pool (n=160)


title: F2 Adipose Control Pool (n=160) vs. 1307


title: F2 Adipose Control Pool (n=160) vs. 3202


title: F2 Adipose Control Pool (n=160) vs. 2806


title: F2 Adipose Control Pool (n=160) vs. 3404


title: F2 Adipose Control Pool (n=160) vs. 5203


title: F2 Adipose Control Pool (n=160) vs. 4003


title: F2 Adipose Control Pool (n=160) vs. 2804


title: F2 Adipose Control Pool (n=160) vs. 1008


title: F2 Adipose Control Pool (n=160) vs. 5205


title: F2 Adipose Control Pool (n=160) vs. 5207


title: F2 Adipose Control Pool (n=160) vs. 1407


title: F2 Adipose Control Pool (n=160) vs. 4002b


title: F2 Adipose Control Pool (n=160) vs. 1205


title: F2 Adipose Control Pool (n=160) vs. 5902


title: F2 Adipose Control Pool (n=160) vs. 1004


title: F2 Adipose Control Pool (n=160) vs. 1002


title: F2 Adipose Control Pool (n=160) vs. 2005


title: F2 Adipose Control Pool (n=160) vs. 5407a


title: F2 Adipose Control Pool (n=160) vs. 2508a


title: F2 Adipose Control Pool (n=160) vs. 5404


title: F2 Adipose Control Pool (n=160) vs. 2801


title: F2 Adipose Control Pool (n=160) vs. 1206


title: F2 Adipose Control Pool (n=160) vs. 4208


title: F2 Adipose Control Pool (n=160) vs. 3204


title: F2 Adipose Control Pool (n=160) vs. 3402


title: F2 Adipose Control Pool (n=160) vs. 5401


title: F2 Adipose Control Pool (n=160) vs. 5202


title: F2 Adipose Control Pool (n=160) vs. 1402


title: F2 Adipose Control Pool (n=160) vs. 1207


title: F2 Adipose Control Pool (n=160) vs. 1406


title: F2 Adipose Control Pool (n=160) vs. 2308a


title: F2 Adipose Control Pool (n=160) vs. 2802


title: F2 Adipose Control Pool (n=160) vs. 5904


title: F2 Adipose Control Pool (n=160) vs. 2501a


title: F2 Adipose Control Pool (n=160) vs. 5908


title: F2 Adipose Control Pool (n=160) vs. 2304a


title: F2 Adipose Control Pool (n=160) vs. 4006a


title: F2 Adipose Control Pool (n=160) vs. 6004b


title: F2 Adipose Control Pool (n=160) vs. 607a


title: F2 Adipose Control Pool (n=160) vs. 606a


title: F2 Adipose Control Pool (n=160) vs. 1005


title: F2 Adipose Control Pool (n=160) vs. 4006


title: F2 Adipose Control Pool (n=160) vs. 4307b


title: F2 Adipose Control Pool (n=160) vs. 5404a


title: F2 Adipose Control Pool (n=160) vs. 4203a


title: F2 Adipose Control Pool (n=160) vs. 5903a


title: F2 Adipose Control Pool (n=160) vs. 4205b


title: F2 Adipose Control Pool (n=160) vs. 5402a


title: F2 Adipose Control Pool (n=160) vs. 306a


title: F2 Adipose Control Pool (n=160) vs. 4204a


title: F2 Adipose Control Pool (n=160) vs. 3002a


title: F2 Adipose Control Pool (n=160) vs. 3005a


title: F2 Adipose Control Pool (n=160) vs. 4507


title: F2 Adipose Control Pool (n=160) vs. 2402a


title: F2 Adipose Control Pool (n=160) vs. 2107a


title: F2 Adipose Control Pool (n=160) vs. 5907a


title: F2 Adipose Control Pool (n=160) vs. 2505a


title: F2 Adipose Control Pool (n=160) vs. 5905a


title: F2 Adipose Control Pool (n=160) vs. 3104


title: F2 Adipose Control Pool (n=160) vs. 2106a


title: F2 Adipose Control Pool (n=160) vs. 2305a


title: F2 Adipose Control Pool (n=160) vs. 1306a


title: F2 Adipose Control Pool (n=160) vs. 608a


title: F2 Adipose Control Pool (n=160) vs. 4205a


title: F2 Adipose Control Pool (n=160) vs. 3407b


title: F2 Adipose Control Pool (n=160) vs. 5902a


title: F2 Adipose Control Pool (n=160) vs. 4505


title: F2 Adipose Control Pool (n=160) vs. 5403a


title: F2 Adipose Control Pool (n=160) vs. 3103


title: F2 Adipose Control Pool (n=160) vs. 308a


title: F2 Adipose Control Pool (n=160) vs. 5401a


title: F2 Adipose Control Pool (n=160) vs. 801b


title: F2 Adipose Control Pool (n=160) vs. 1407b


title: F2 Adipose Control Pool (n=160) vs. 202b


title: F2 Adipose Control Pool (n=160) vs. 3707a


title: F2 Adipose Control Pool (n=160) vs. 4502a


title: F2 Adipose Control Pool (n=160) vs. 3107


title: F2 Adipose Control Pool (n=160) vs. 1808a


title: F2 Adipose Control Pool (n=160) vs. 5904a


title: F2 Adipose Control Pool (n=160) vs. 1805a


title: F2 Adipose Control Pool (n=160) vs. 1806a


title: F2 Adipose Control Pool (n=160) vs. 304a


title: F2 Adipose Control Pool (n=160) vs. 4204b


title: F2 Adipose Control Pool (n=160) vs. 1305a


title: F2 Adipose Control Pool (n=160) vs. 4506


title: F2 Adipose Control Pool (n=160) vs. 4308b


title: F2 Adipose Control Pool (n=160) vs. 4007a


title: F2 Adipose Control Pool (n=160) vs. 806b


title: F2 Adipose Control Pool (n=160) vs. 5405a


title: F2 Adipose Control Pool (n=160) vs. 3006a


title: F2 Adipose Control Pool (n=160) vs. 2401a


title: F2 Adipose Control Pool (n=160) vs. 1907a


title: F2 Adipose Control Pool (n=160) vs. 1303a


title: F2 Adipose Control Pool (n=160) vs. 1407a


title: F2 Adipose Control Pool (n=160) vs. 5903


title: F2 Adipose Control Pool (n=160) vs. 6002b


title: F2 Adipose Control Pool (n=160) vs. 4108a


title: F2 Adipose Control Pool (n=160) vs. 3001a


title: F2 Adipose Control Pool (n=160) vs. 1807a


title: F2 Adipose Control Pool (n=160) vs. 4107a


title: F2 Adipose Control Pool (n=160) vs. 302a


title: F2 Adipose Control Pool (n=160) vs. 608b


title: F2 Adipose Control Pool (n=160) vs. 5402


title: F2 Adipose Control Pool (n=160) vs. 4004


title: F2 Adipose Control Pool (n=160) vs. 2002


title: F2 Adipose Control Pool (n=160) vs. 2408a


title: F2 Adipose Control Pool (n=160) vs. 4202


title: F2 Adipose Control Pool (n=160) vs. 4102


title: F2 Adipose Control Pool (n=160) vs. 6006b


title: F2 Adipose Control Pool (n=160) vs. 2004


title: F2 Adipose Control Pool (n=160) vs. 208b


title: F2 Adipose Control Pool (n=160) vs. 808b


title: F2 Adipose Control Pool (n=160) vs. 4201b


title: F2 Adipose Control Pool (n=160) vs. 4001


title: F2 Adipose Control Pool (n=160) vs. 4001b


title: F2 Adipose Control Pool (n=160) vs. 4008


title: F2 Adipose Control Pool (n=160) vs. 1403b


title: F2 Adipose Control Pool (n=160) vs. 3804b


title: F2 Adipose Control Pool (n=160) vs. 4002


title: F2 Adipose Control Pool (n=160) vs. 3207


title: F2 Adipose Control Pool (n=160) vs. 1904b


title: F2 Adipose Control Pool (n=160) vs. 4202b


title: F2 Adipose Control Pool (n=160) vs. 4204


title: F2 Adipose Control Pool (n=160) vs. 5008b


title: F2 Adipose Control Pool (n=160) vs. 5206


title: F2 Adipose Control Pool (n=160) vs. 4005


title: F2 Adipose Control Pool (n=160) vs. 2808


title: F2 Adipose Control Pool (n=160) vs. 606b


title: F2 Adipose Control Pool (n=160) vs. 4205


title: F2 Adipose Control Pool (n=160) vs. 207b


title: F2 Adipose Control Pool (n=160) vs. 4103


title: F2 Adipose Control Pool (n=160) vs. 5208


title: F2 Adipose Control Pool (n=160) vs. 1806b


title: F2 Adipose Control Pool (n=160) vs. 4206


title: F2 Adipose Control Pool (n=160) vs. 1901b


title: F2 Adipose Control Pool (n=160) vs. 2006b


title: F2 Adipose Control Pool (n=160) vs. 604b


title: F2 Adipose Control Pool (n=160) vs. 4207


title: F2 Adipose Control Pool (n=160) vs. 3808b


title: F2 Adipose Control Pool (n=160) vs. 2506a


title: F2 Adipose Control Pool (n=160) vs. 304b


title: F2 Adipose Control Pool (n=160) vs. 3104b


title: F2 Adipose Control Pool (n=160) vs. 5806b


title: F2 Adipose Control Pool (n=160) vs. 3707b


title: F2 Adipose Control Pool (n=160) vs. 3403


title: F2 Adipose Control Pool (n=160) vs. 6005b


title: F2 Adipose Control Pool (n=160) vs. 3504b


title: F2 Adipose Control Pool (n=160) vs. 1404b


title: F2 Adipose Control Pool (n=160) vs. 5703b


title: F2 Adipose Control Pool (n=160) vs. 3806a


title: F2 Adipose Control Pool (n=160) vs. 1002b


title: F2 Adipose Control Pool (n=160) vs. 306b


title: F2 Adipose Control Pool (n=160) vs. 3205b


title: F2 Adipose Control Pool (n=160) vs. 1807b


title: F2 Adipose Control Pool (n=160) vs. 5608b


title: F2 Adipose Control Pool (n=160) vs. 303b


title: F2 Adipose Control Pool (n=160) vs. 4006b


title: F2 Adipose Control Pool (n=160) vs. 3801b


title: F2 Adipose Control Pool (n=160) vs. 4302b


title: F2 Adipose Control Pool (n=160) vs. 5802b


title: F2 Adipose Control Pool (n=160) vs. 804b


title: F2 Adipose Control Pool (n=160) vs. 305b


title: F2 Adipose Control Pool (n=160) vs. 504b


title: F2 Adipose Control Pool (n=160) vs. 5606b


title: F2 Adipose Control Pool (n=160) vs. 204b


title: F2 Adipose Control Pool (n=160) vs. 602b


title: F2 Adipose Control Pool (n=160) vs. 805b


title: F2 Adipose Control Pool (n=160) vs. 5501b


title: F2 Adipose Control Pool (n=160) vs. 5006b


title: F2 Adipose Control Pool (n=160) vs. 3205


title: F2 Adipose Control Pool (n=160) vs. 4504b


title: F2 Adipose Control Pool (n=160) vs. 5003b


title: F2 Adipose Control Pool (n=160) vs. 101


title: F2 Adipose Control Pool (n=160) vs. 3405b


title: F2 Adipose Control Pool (n=160) vs. 1706


title: F2 Adipose Control Pool (n=160) vs. 5005b


title: F2 Adipose Control Pool (n=160) vs. 1006b


title: F2 Adipose Control Pool (n=160) vs. 1908


title: F2 Adipose Control Pool (n=160) vs. 3803b


title: F2 Adipose Control Pool (n=160) vs. 5505b


title: F2 Adipose Control Pool (n=160) vs. 2504a


title: F2 Adipose Control Pool (n=160) vs. 3701b


title: F2 Adipose Control Pool (n=160) vs. 307b


title: F2 Adipose Control Pool (n=160) vs. 2307a


title: F2 Adipose Control Pool (n=160) vs. 4207a


title: F2 Adipose Control Pool (n=160) vs. 1301


title: F2 Adipose Control Pool (n=160) vs. 3708


title: F2 Adipose Control Pool (n=160) vs. 506b


title: F2 Adipose Control Pool (n=160) vs. 601a


title: F2 Adipose Control Pool (n=160) vs. 605b


title: F2 Adipose Control Pool (n=160) vs. 1007b


title: F2 Adipose Control Pool (n=160) vs. 106


title: F2 Adipose Control Pool (n=160) vs. 4007


title: F2 Adipose Control Pool (n=160) vs. 3106b


title: F2 Adipose Control Pool (n=160) vs. 1205a


title: F2 Adipose Control Pool (n=160) vs. 1304


title: F2 Adipose Control Pool (n=160) vs. 1306


title: F2 Adipose Control Pool (n=160) vs. 1302


title: F2 Adipose Control Pool (n=160) vs. 1703


title: F2 Adipose Control Pool (n=160) vs. 1006a


title: F2 Adipose Control Pool (n=160) vs. 1707


title: F2 Adipose Control Pool (n=160) vs. 202


title: F2 Adipose Control Pool (n=160) vs. 1003a


title: F2 Adipose Control Pool (n=160) vs. 2007


title: F2 Adipose Control Pool (n=160) vs. 5801


title: F2 Adipose Control Pool (n=160) vs. 6008b


title: F2 Adipose Control Pool (n=160) vs. 4104


title: F2 Adipose Control Pool (n=160) vs. 4101


title: F2 Adipose Control Pool (n=160) vs. 3506a


title: F2 Adipose Control Pool (n=160) vs. 5807


title: F2 Adipose Control Pool (n=160) vs. 1201a


title: F2 Adipose Control Pool (n=160) vs. 2303a


title: F2 Adipose Control Pool (n=160) vs. 1305


title: F2 Adipose Control Pool (n=160) vs. 108


title: F2 Adipose Control Pool (n=160) vs. 5805


title: F2 Adipose Control Pool (n=160) vs. 2503a


title: F2 Adipose Control Pool (n=160) vs. 102


title: F2 Adipose Control Pool (n=160) vs. 5405


title: F2 Adipose Control Pool (n=160) vs. 1704


title: F2 Adipose Control Pool (n=160) vs. 2805


title: F2 Adipose Control Pool (n=160) vs. 3702


title: F2 Adipose Control Pool (n=160) vs. 204


title: F2 Adipose Control Pool (n=160) vs. 1702


title: F2 Adipose Control Pool (n=160) vs. 2001


title: F2 Adipose Control Pool (n=160) vs. 104


title: F2 Adipose Control Pool (n=160) vs. 207


title: F2 Adipose Control Pool (n=160) vs. 1701


title: F2 Adipose Control Pool (n=160) vs. 605a


title: F2 Adipose Control Pool (n=160) vs. 103


title: F2 Adipose Control Pool (n=160) vs. 201


title: F2 Adipose Control Pool (n=160) vs. 5806


title: F2 Adipose Control Pool (n=160) vs. 3406


title: F2 Adipose Control Pool (n=160) vs. 1308


title: F2 Adipose Control Pool (n=160) vs. 206


title: F2 Adipose Control Pool (n=160) vs. 3005


title: F2 Adipose Control Pool (n=160) vs. 1501


title: F2 Adipose Control Pool (n=160) vs. 1106


title: F2 Adipose Control Pool (n=160) vs. 1901


title: F2 Adipose Control Pool (n=160) vs. 3908


title: F2 Adipose Control Pool (n=160) vs. 3002


title: F2 Adipose Control Pool (n=160) vs. 5506


title: F2 Adipose Control Pool (n=160) vs. 3904


title: F2 Adipose Control Pool (n=160) vs. 3804


title: F2 Adipose Control Pool (n=160) vs. 5505


title: F2 Adipose Control Pool (n=160) vs. 5802


title: F2 Adipose Control Pool (n=160) vs. 5403


title: F2 Adipose Control Pool (n=160) vs. 3008


title: F2 Adipose Control Pool (n=160) vs. 3102


title: F2 Adipose Control Pool (n=160) vs. 1503


title: F2 Adipose Control Pool (n=160) vs. 3905


title: F2 Adipose Control Pool (n=160) vs. 1506


title: F2 Adipose Control Pool (n=160) vs. 4503


title: F2 Adipose Control Pool (n=160) vs. 3004


title: F2 Adipose Control Pool (n=160) vs. 1903


title: F2 Adipose Control Pool (n=160) vs. 1105


title: F2 Adipose Control Pool (n=160) vs. 5503


title: F2 Adipose Control Pool (n=160) vs. 3907


title: F2 Adipose Control Pool (n=160) vs. 4504


title: F2 Adipose Control Pool (n=160) vs. 3108


title: F2 Adipose Control Pool (n=160) vs. 4501


title: F2 Adipose Control Pool (n=160) vs. 3906


title: F2 Adipose Control Pool (n=160) vs. 3205a


title: F2 Adipose Control Pool (n=160) vs. 5103a


title: F2 Adipose Control Pool (n=160) vs. 2002b


title: F2 Adipose Control Pool (n=160) vs. 5605b


title: F2 Adipose Control Pool (n=160) vs. 403a


title: F2 Adipose Control Pool (n=160) vs. 6002a


title: F2 Adipose Control Pool (n=160) vs. 501b


title: F2 Adipose Control Pool (n=160) vs. 5507b


title: F2 Adipose Control Pool (n=160) vs. 3302a


title: F2 Adipose Control Pool (n=160) vs. 5604a


title: F2 Adipose Control Pool (n=160) vs. 3208a


title: F2 Adipose Control Pool (n=160) vs. 2705a


title: F2 Adipose Control Pool (n=160) vs. 5805b


title: F2 Adipose Control Pool (n=160) vs. 3108b


title: F2 Adipose Control Pool (n=160) vs. 2603a


title: F2 Adipose Control Pool (n=160) vs. 3908b


title: F2 Adipose Control Pool (n=160) vs. 2001b


title: F2 Adipose Control Pool (n=160) vs. 1001b


title: F2 Adipose Control Pool (n=160) vs. 3207a


title: F2 Adipose Control Pool (n=160) vs. 2702a


title: F2 Adipose Control Pool (n=160) vs. 5607b


title: F2 Adipose Control Pool (n=160) vs. 3206a


title: F2 Adipose Control Pool (n=160) vs. 3101b


title: F2 Adipose Control Pool (n=160) vs. 3203a


title: F2 Adipose Control Pool (n=160) vs. 5606a


title: F2 Adipose Control Pool (n=160) vs. 3202a


title: F2 Adipose Control Pool (n=160) vs. 2601a


title: F2 Adipose Control Pool (n=160) vs. 5607a


title: F2 Adipose Control Pool (n=160) vs. 2708a


title: F2 Adipose Control Pool (n=160) vs. 2604a


title: F2 Adipose Control Pool (n=160) vs. 2003b


title: F2 Adipose Control Pool (n=160) vs. 5802a


title: F2 Adipose Control Pool (n=160) vs. 3303a


title: F2 Adipose Control Pool (n=160) vs. 5106a


title: F2 Adipose Control Pool (n=160) vs. 5608a


title: F2 Adipose Control Pool (n=160) vs. 3306a


title: F2 Adipose Control Pool (n=160) vs. 5201a


title: F2 Adipose Control Pool (n=160) vs. 5206a


title: F2 Adipose Control Pool (n=160) vs. 5108a


title: F2 Adipose Control Pool (n=160) vs. 5204a


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1307-hypo

description: The expression profile in mouse hypothalamus tissue from individuals in a M16xICR cross given as a normalized ratio as reported from Rosetta Resolver.

source_name: Hypothalamus, F2 Control Pool  (n=156)

label_protocol: 100 ng of total RNA from each hypothalamus sample was amplified using an automated 2 cycle version of the method used for the other 3 tissues as described previously (Brandish et al.).  This method utilizes MMLV-RT reverse transcription and double stranded cDNA production, followed by T7 RNA polymerase transcription.  The resultant RNA is further amplified with a second round of reverse transcription and in vitro transcription incorporating amino-allyl UTP.

value: hypothalamus

value: M16xICR F2 cross


title: F2 Adipose Control Pool (n=160) vs. 5603a


title: F2 Adipose Control Pool (n=160) vs. 5102a


title: F2 Adipose Control Pool (n=160) vs. 5202a


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5203-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2806-hypo


title: F2 Adipose Control Pool (n=160) vs. 2606a


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5204-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4003-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2804-hypo


title: F2 Adipose Control Pool (n=160) vs. 5105a


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5207-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3204-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2005-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4002b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2508a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1205-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3404-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5205-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2801-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5404-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3202-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5407a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5902-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1407-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1008-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1004-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1002-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1206-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4208-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5202-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5904-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5401-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4006-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3402-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1402-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1406-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1207-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4205b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5908-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3005a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4307b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4203a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2802-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5404a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0606a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 6004b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0607a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0306a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2308a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4204a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4006a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5903a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2304a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4507-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3002a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5402a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2107a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5907a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1005-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2505a-hypo


title: F2 Adipose Control Pool (n=160) vs. 5803a


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3104-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5905a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1306a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2402a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2305a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3103-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4505-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2106a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0308a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4502a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3407b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5403a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4205a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5902a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3107-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5401a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3707a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1806a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0608a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4308b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1805a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0202b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0801b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4204b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1808a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1407b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4506-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0806b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3006a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2401a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5405a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 6002b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4007a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0304a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1305a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2501a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5903-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4108a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1303a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1407a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1907a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5402-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2408a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1807a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4107a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 6006b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0208b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0608b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4001-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1904b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4202-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4004-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4008-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4202b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2004-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4001b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4102-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4002-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0302a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3804b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3207-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4201b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0808b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1403b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0606b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4207-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4204-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2506a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0604b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1901b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5206-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4205-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5008b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2808-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3808b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4103-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5904a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0207b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2006b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4005-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3104b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5208-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5806b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0304b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3001a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3403-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0306b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1806b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3707b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3205b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4206-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 6005b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5703b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1404b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0305b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1002b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1807b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0805b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0303b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4302b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3806a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3504b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0204b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2002-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5608b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5006b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0602b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4006b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0804b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5501b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5606b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0504b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3205-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1908-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3801b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0101-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1706-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5003b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 6008b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4504b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3405b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2504a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3803b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5005b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1007b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3701b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5505b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0506b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4007-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0307b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3106b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0106-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1301-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0601a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0605b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2805-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1006a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1703-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1304-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1003a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1306-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3708-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4207a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1302-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5801-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1707-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3702-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0202-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4104-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2007-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1201a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2303a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0102-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4101-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3506a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0108-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5805-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2503a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0204-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5807-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5405-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2001-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1704-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5806-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0207-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0201-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1702-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1701-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0103-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5403-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1501-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1308-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0605a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0104-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3406-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3005-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3002-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3906-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5503-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1901-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5505-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4501-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1106-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3905-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3904-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3108-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1506-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3908-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3004-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3907-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3102-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3804-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5802-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0206-hypo


title: Patient without BC #10: control

status: Public on Feb 28 2010

city: Cologne

first: Thomas

last: Zander

address: Kerpenerstr. 62

country: Germany

institute: University Hospital Cologne

description: All samples were taken from smokers. EPIC cases were taken from the EPIC trial (a large prospective epidemiological trial in Europe, and are incident cases), Cosmos and BC cases are prevalent cases from a Cologne, Germany based epidemiological trial.

hyb_protocol: For hybridization samples were applied to the arrays and assembled into HybCartridges (Illumina). BeadChips were hybridized for 16h at 55°C on the BeadChip Hyb Wheel. 1.5 μg biotin labeled cRNA was hybridized to Sentrix® whole genome bead chips 6 x 2 V1 and V2 (Illumina, USA) according to the manufacturers instruction. Arrays were washed according to Illumina Wash BeadChip 6 x 2 protocol. Signals were developed with streptavidin Cy3.

scan_protocol: Scanning was performed on the Illumina(r) BeadStation 500x.

data_processing: BeadStudio raw data were normalized using R

source_name: peripheral blood

label_protocol: Biotin labeled cRNA preparation was performed using the Ambion® Illumina RNA amplification kit (Ambion, UK). Quality was controlled using a PCR based system1.

extract_protocol: weWe used snap frozen PBMC enriched blood (~ 300 µl) from the EPIC study for RNA extraction. Blood samples were directly thawed in 5ml of TRI Reagent BD (Molecular Research Center, Inc, USA). RNA was extracted according to the manufactures instruction and stored in 70% ethanol until finalization of preparation and dilution in H2O. For further RNA purification we applied Qiagen MinElute columns (Qiagen, Germany). By this method we extracted 960ng RNA (mean; range 120 – 2500ng). One sample contained no RNA. The OD ratio 260/280 was 2.01 in mean (range 1.76-2.06). For the LC-group, we drew 2.5 ml blood directly into PAXgene vials providing stabilization of the gene expression profile. Samples were rested over night at room temperature and then stored at -80°C until further preparation. RNA was extracted according to the manufactures instruction (Qiagen, Hilden, Germany).

tag: control


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4503-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5506-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 4504-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2705a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1903-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3008-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5802b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1105-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1503-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 6002a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2002b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3202a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2001b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5103a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5606a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2702a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5607b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5605b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1001b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5604a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3302a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3205a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5507b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1006b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3908b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3207a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3108b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2603a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2307a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3206a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2601a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0501b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 0403a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3101b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2708a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2606a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5607a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5805b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3208a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3303a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5608a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3306a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5201a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5802a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5206a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5106a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2604a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 3203a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 2003b-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5803a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5204a-hypo


title: cow_7198_PEB_rightrear_noninfectedquarter_cy3

city: Tjele

first: Kasey

middle: M

last: Moyes

address: Blichers Allé 20, P.O. BOX 50

department: Animal Health, Welfare, and Disease

country: Denmark

institute: University of Aarhus

hyb_protocol: A 13,257 oligonucleotide microarray was used for gene expression profiling (Loor et al., 2007). Prior to hybridization, slides were denatured in boiling water, rinsed in ethanol, and blocked in prehybridization buffer. Probes, consisting of the experimental sample and reference (control), were denatured by boiling and hybridized to the array under cover slips for 2 d at 42 oC. Slides were then washed for 4 min each in 1 x SSC 0.03% SDS, 0.2 x SSC, 0.1 x SSC, and 0.05 x SSC prior to scanning. All samples were hybridized to duplicate slides and repeated with reverse labeling for a total of 2 slides, or 4 spots per gene per experiment.

scan_protocol: Slides were scanned for both dye channels (Cy3 and Cy5) with a Scanarray 4000 (GSI-Lumonics, Billerica,MA) dual-laser confocal scanner and images were edited and processed using GenePix 6.0 (Axon Instruments, Inc., CA).

data_processing:
Oligonucleotides that were flagged with -100 by GenePix were removed from the analysis, and the remaining data were normalized to control for dye effects using the median of control elements on the microarray.  In a subsequent normalization step, the log2 normalized ratio of mammary versus reference (i.e., RNA mixture of different tissues including mammary) signal intensities were adjusted for global dye and microarray effects and normalized by Lowess.  A mixed-effects model was then fitted to the adjusted ratios (mammary/reference) using Proc MIXED of SAS (2003).  The model consisted of treatment (TRT; NEB and PEB), infection (INF; YES and NO), and the TRT × INF interaction.  YES identifies mammary quarters inoculated with 5,000 cfu of S. uberis; and NO identifies contralateral rear control quarters (i.e., non-inoculated).  The fixed effect was dye with cow and microarray as random effects.  Statistical significance probability values for TRT, INF and TRT × INF effects were adjusted for the number of comparisons using Benjamini and Hochberg’s FDR.  Differentially expressed genes were based on FDR P-value ≤ 0.05, which corresponded to an unadjusted P ≤ 0.01.

The ID_REFs in the supplementary raw data .txt file correspond to the IDs in Platform GPL2853, which is the non-condensed version of Platform GPL8776. See the GSE15344_raw_data_readme.txt file, which is linked to the GSE15344 record, for a description of the raw data file contents.

organism: Bos taurus

source_name: Pooled RNA from bovine tissues

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) according to manufacturer's instructions. Samples were purified using the QIAGEN PCR purification kit before hybridization.

extract_protocol: Total RNA was extracted using TRIZol (Invitrogen) and cleaned using the RNeasy mini kit Column (QIAGEN).

value: mixed

tag: sample type

value: reference standard

source_name: mammary tissue, PEB, right rear, non-infected

tag: breed

value: Holstein

value: mammary

tag: diet

value: ad libitum

tag: s. uberis infection

value: non-infected


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5603a-hypo


title: cow_7384_NEB_leftrear_infectedquarter_cy5

description: 7384 LR- 5

source_name: mammary tissue, NEB, left rear, infected

value: restricted

value: infected


title: cow_7384_NEB_leftrear_infectedquarter_cy3

description: 7384 LR- 3


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5105a-hypo


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5202a-hypo


title: cow_7198_PEB_leftrear_infectedquarter_cy5

description: 7198 LR- 5

source_name: mammary tissue, PEB, left rear, infected


title: Liver, F2 Control Pool (n=156) vs. 0101-liver


title: cow_7384_NEB_rightrear_noninfectedquarter_cy3

source_name: mammary tissue, NEB, right rear, non-infected


title: cow_7585_NEB_leftrear_infectedquarter_cy3

description: 7585 LR-3


title: cow_7198_PEB_leftrear_infectedquarter_cy3

description: 7198 LR- 3


title: cow_7384_NEB_rightrear_noninfectedquarter_cy5


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5108a-hypo


title: cow_7390_NEB_rightrear_noninfectedquarter_cy3

description: 7390 RR-3


title: Hypothalamus, F2 Control Pool  (n=156) vs. 5102a-hypo


title: cow_7585_NEB_rightrear_noninfectedquarter_cy5

description: 7585 RR-5


title: cow_7390_NEB_leftrear_infectedquarter_cy5


title: cow_7390_NEB_rightrear_noninfectedquarter_cy5

description: 7390 RR-5


title: cow_7585_NEB_rightrear_noninfectedquarter_cy3

description: 7585 RR-3


title: cow_7390_NEB_leftrear_infectedquarter_cy3


title: cow_7585_NEB_leftrear_infectedquarter_cy5

description: 7585 LR-5


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1205a-hypo


title: cow_7697_NEB_leftrear_noninfectedquarter_cy3

source_name: mammary tissue, NEB, left rear, non-infected


title: cow_7697_NEB_rightrear_infectedquarter_cy3

source_name: mammary tissue, NEB, right rear, infected


title: cow_7697_NEB_leftrear_noninfectedquarter_cy5

description: 7697 LR- 5


title: cow_7698_PEB_leftrear_noninfectedquarter_cy3

description: 7698 LR-3

source_name: mammary tissue, PEB, left rear, non-infected


title: cow_7697_NEB_rightrear_infectedquarter_cy5


title: cow_7698_PEB_rightrear_infectedquarter_cy3

description: 7698 RR-3

source_name: mammary tissue, PEB, right rear, infected


title: cow_7703_PEB_leftrear_noninfectedquarter_cy5

description: 7703 LR-5


title: cow_7743_NEB_leftrear_noninfectedquarter_cy3

description: 7743 LR-3


title: cow_7743_NEB_leftrear_noninfectedquarter_cy5

description: 7743 LR-5


title: cow_7698_PEB_rightrear_infectedquarter_cy5

description: 7698 RR -5


title: Dissected axillary meristem

city: Parkville

first: Chui

middle: E

last: WONG

state: Victoria

address: University of Melbourne

department: Land and Food

country: Australia

institute: University of Melbourne

description: The experiment consisted of six replicates of shoot apical meristem and one each of root apical meristem, axillary meristem and non-meristematic tissues.

scan_protocol: The Cy5- hybridized chip was then scanned using Genepix 4000B microarray scanner (Axon Instruments, CA, USA) according to manufacturer's instructions.

data_processing: The red channel intensities were background subtracted, quantile normalised and log2 transformed.  Differential expression was assessed using linear modelling and empirical Bayes moderated t-statistics (Smyth, 2004).  This approach allows variance information to be borrowed across both samples and genes, resulting in reliable statistical inference even for the groups with only one sample.  A number of genes were identified as significantly differentially expressed in different comparisons from this model at a 1% false discovery rate using the method of Benjamini and Hochberg (1995) (Benjamini and Hochberg, 1995).

organism: Lathyrus oleraceus

source_name: Dissected 10-day-old axillaryl meristem

label_protocol: Target preparation and hybridization were performed in Australian Genome Research Facility Ltd (AGRF) according to the standard CombiMatrix protocol described in detail at www.combimatrix.com. One microgram of total RNA from plant material was labeled using the Kreatech ampULSe kit to generate Cy5 labeled targets. The Cy5- labeled cDNA was then hybridized to the chip.

growth_protocol: Grown under the greenhouse condition in the University of Melbourne for 10 days after sowing the seeds

extract_protocol: Using Qiagen RNAEasy minikit

tag: Axillary meristem micro-dissected from 10-day-old garden pea (cultivar Torsdag)


title: cow_7703_PEB_rightrear_infectedquarter_cy5

description: 7703 RR-5


title: cow_7703_PEB_leftrear_noninfectedquarter_cy3

description: 7703 LR-3


title: cow_7698_PEB_leftrear_noninfectedquarter_cy5

description: 7698 LR-5


title: cow_7743_NEB_rightrear_infectedquarter_cy3

description: 7743 RR-3


title: Dissected 10-day-old shoot apical meristem Replicate 6

hyb_protocol: Target preparation and hybridization were performed in Australian Genome Research Facility Ltd (AGRF) according to the standard CombiMatrix protocol described in detail at www.combimatrix.com.

tag: Shoot apical meristem micro-dissected from 10-day-old garden pea (cultivar Torsdag)


title: cow_7743_NEB_rightrear_infectedquarter_cy5

description: 7743 RR-5


title: Hypothalamus, F2 Control Pool  (n=156) vs. 1305-hypo


title: Dissected 10-day-old shoot apical meristem Replicate 5


title: Root apical meristem

source_name: Root apical meristem tissue

tag: Root apical meristem (0.5 mm of root tip) from 10-day-old garden pea (cultivar Torsdag)


title: cow_7703_PEB_rightrear_infectedquarter_cy3

description: 7703 RR-3


title: Dissected 10-day-old shoot apical meristem Replicate 4


title: Non-meristematic tissues

source_name: Non-meristematic tissues harvested from 10-day-old garden pea

tag: Non-meristematic tissues (tendril, leaf, stem, and mature root tissues) from 10-day-old garden pea (cultivar Torsdag). Equal mix of RNA harvested from each of these tissues was used in the microarray experiment.


title: cow_7750_PEB_leftrear_infectedquarter_cy5

description: 7750 LR-5


title: cow_7750_PEB_rightrear_noninfectedquarter_cy3

description: 7750 RR-3


title: Dissected 10-day-old shoot apical meristem Replicate 3


title: cow_7783_PEB_leftrear_infectedquarter_cy5

description: 7783 LR-5


title: 50

status: Public on Oct 23 2009

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

hyb_protocol: According to Manufacturer's Specifications

data_processing: Data was quantile normalized with plate scaling for samples run on multiple 96-well Universal Array Matrices

label: Cy3 , Cy5

source_name: Radical prostatectomy

extract_protocol: Specimen Type: FFPE tissues sections or cores; Required Reagents: Recoverall RNA Isolation Kit, Ambion, Inc., Austin, TX (Cat#: AM1975); Initial quality of RNA will be determined by spectrophotometry, using the NanoDrop. The absorbance is measured at 230, 260, and 280 nm, and the A260/A280 and A260/A230 ratios of 2 are ideal. In addition, expression of a ribosomal housekeeping gene, Rpl13a, will be measured to determine how many useful RNA molecules are present in the sample. Ideally, the Ct value should be less than 29. The samples that fail QC will not be further analyzed. Procedural Steps (general): 1. Assemble FFPE sections equivalent to up to 80 µm sections (5 – 20 µm sections). 2. Add 1 ml of 100% xylene; vortex briefly; heat at 50°C for 3 min. 3. Centrifuge for 2 min at max. speed; discard xylene. 4. Wash the pellet with 100% EtOH; vortex; centrifuge for 2 min at max. speed. 5. Repeat step 4. one more time. 6. Air dry for 10 – 15 min. 7. Add digestion buffer to each sample. 8. Add protease to each sample; swirl each tube to mix. 9. Incubate at 50°C for overnight [can store at -20°C at this point]. 10. DNA and RNA isolation procedures are identical from this point forward; add 480 µl   Isolation Additive; vortex to mix. 11. Add 1.1 ml of 100% EtOH; mix by pipetting. 12. Pipet 700 µl of the sample/EtOH mixture onto the column and close the lid. 13. Centrifuge at 10,000 RPM for 30-60 sec; discard the flow-through. 14. Repeat steps 11 and 12 until all the mix has passed through the filter (3x). 15. Add 700 µl of Wash 1 to the filter cartridge. 16. Centrifuge for 30 sec at 10,000 RPM; discard flow-through. 17. Add 500 µl of Wash 2/3 . 18. Centrifuge for 30 sec at 10,000 RPM; discard flow-through. 19. Preheat the Elution solution or nuclease-free water to 95°C . 20. For RNA isolation (per sample):   6 µl 10 DNase Buffer.   4 µl DNase. 50 µl Nuclease-free water. a. Add 60 µl of the DNase mix to the center of each filter. b. Incubate at RT for 30 min. 21. Add 700 µl Wash 1 to the filter cartridge; Incubate at RT for 30-60 sec. 22. Centrifuge at 10,000 RPM for 30 sec; discard flow-through. 23. Add 500 µl Wash 2/3. 24. Centrifuge at 10,000 RPM for 30 sec; discard flow-through. 25. Repeat steps 22a and 23 one more time. 26. Centrifuge at 10,000 RPM for 1 min to dry. 27. Transfer filter cartridge to a fresh collection tube. 28. Add 30 µl of elution solution or water heated to 95°C to the center of the filter. 29. Incubate at RT for 1 min. 30. Centrifuge at full speed for 1 min. 31. Repeat steps 27 to 29 with an additional aliquot of water. 32. Store at -20°C or colder (if only a small amount of nucleic acid is collected, store in non-stick tubes)

tag: age

tag: psa

tag: gleason score

tag: recurrence

value: No Rec

tag: follow-up (months)

value: ERG Fusion:No Fusion

tag: positive surgical margin

value: No Positive Margin

tag: grade

tag: pathologic stage category

value: organ confined


title: 57

scan_protocol: According to Manufacturer's Specifications

value: Rec

value: ERG Fusion:Fusion

value: Positive Margin

value: extraprostatic


title: 53

label_protocol: According to Manufacturer's Specifications


title: 51


title: 58


title: cow_7750_PEB_rightrear_noninfectedquarter_cy5

description: 7750 RR-5

tag: tissue


title: 59


title: 52


title: cow_7783_PEB_leftrear_infectedquarter_cy3

description: 7783 LR-3

tag: sample type


title: cow_7783_PEB_rightrear_noninfectedquarter_cy3

description: 7783 RR-3

tag: breed


title: 49


title: WT3 vs D3

status: Public on Oct 25 2009

city: Smithville

first: Xuetong

last: Shen

state: TX

address: 1808 Park Road 1-C

institute: MD Anderson Cancer Center

hyb_protocol: According to manufacturer's recommendations using the Agilent document, 'Two-Color Microarray-Based Gene Expression Analysis' v5.5, p.26.

scan_protocol: Scanned on an Agilent G2505B Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: MeanFG-medianBG signal intensities from FE software results were used (reference: WT, exp: ino80), loess normalized, replicate probes averaged, Bayesian moderated t-test performed using Bioconductor package limma.  For the final results available as a supplementary file on the Series record, values were calculated using all samples:  logFC: average log2 ratio; AveExpr: average log2 signal intensity;  t: moderated t-statistic;  P.Value: raw p-value;  adj.P.Value:  adjusted p-value;  Significant Expression Difference: signficant=1, significant if |logFC| >= 0.585 & adj.P.val <= 0.05.

organism: Saccharomyces cerevisiae

source_name: WT replica 3

label_protocol: According to manufacturer's recommendations following the Amplification and Modified Amino-Allyl Incorporation for Agilent Arrays (For total RNA) protocol (Agilent).

growth_protocol: Yeast cell were grown in YPD to early log phase, cells were arrested at G1 with alpha-factor.

extract_protocol: Total RNA was isolated using total RNA isolation kit from Ambion.

treatment_protocol: G1-arrested cells were released into S-phase in the presence of 0.02% MMS to induce DNA damage.

tag: genome/variation

value: wild type

source_name: ino80 replica 3

value: ino80 mutant


title: D1 vs W1

source_name: ino80 replica 1

source_name: WT replica 1


title: D3 vs W3


title: WT1 vs D1


title: cow_7783_PEB_rightrear_noninfectedquarter_cy5

description: 7783 RR-5

tag: diet

tag: s. uberis infection

source_name: Pooled RNA from bovine tissues

value: mixed

value: reference standard


title: D2 vs W2

source_name: ino80 replica 2

source_name: WT replica 2


title: WT2 vs D2


title: Dissected 10-day-old shoot apical meristem Replicate 2

tag: Shoot apical meristem micro-dissected from 10-day-old garden pea (cultivar Torsdag)


title: 48


title: 46


title: 47


title: 45


title: 44

value: seminal vesicle invasion


title: 43


title: 40


title: 42


title: PPP_233

source_name: Breast tumor primary biopsy

tag: er

value: ER+

tag: pr

value: PR+


title: PPP_218


title: 41

tag: age


title: 34

tag: psa


title: PPP_220


title: 37

tag: gleason score


title: 35

tag: recurrence


title: PPN_271


title: PPN_269


title: PPN_267


title: 33

tag: follow-up (months)


title: PPN_261


title: PPP_207


title: PPN_260


title: 39

tag: positive surgical margin


title: PPP_219


title: 31

tag: grade


title: 32

tag: pathologic stage category


title: PPN_252


title: PPN_258


title: 29


title: 28


title: PPN_253


title: PPN_254


title: PPN_251


title: 27


title: 24


title: 25


title: PPN_232


title: cow_7750_PEB_leftrear_infectedquarter_cy3

description: 7750 LR-3

tag: tissue

source_name: mammary tissue, PEB, left rear, infected

value: Holstein

value: mammary

value: ad libitum


title: PPN_248


title: cow_7198_PEB_rightrear_noninfectedquarter_cy5

source_name: mammary tissue, PEB, right rear, non-infected

value: non-infected

tag: sample type


title: 23

value: No Rec

value: No Positive Margin


title: PPN_270


title: PPN_226


title: 22


title: PPN_227


title: PPN_231


title: 30

value: ERG Fusion:No Fusion


title: 21


title: 19


title: PPN_225


title: 26

value: ERG Fusion:Fusion

value: organ confined


title: 17

value: Positive Margin


title: 16

value: extraprostatic


title: PPN_250


title: 15


title: 14


title: PPN_224


title: PPN_214


title: PPN_222


title: 13


title: 11


title: 8


title: PPN_211


title: PPN_201


title: PPN_208


title: PPN_209


title: PPN_206


title: 7


title: 9


title: 10


title: PPN_200


title: PPN_203


title: 6

value: Rec


title: PNN_216

value: PR-


title: PPN_198


title: 3


title: 5


title: 4


title: PNN_215


title: NNP_245

value: ER-


title: PNN_195


title: PNN_217


title: 2


title: PPP_864


title: PPP_9045


title: 1


title: NNP_221


title: NNN_223


title: PPP_6106


title: NNN_197


title: PPP_5571


title: PPP_394


title: PPP_5431


title: NNN_194


title: PPP_3076


title: PPP_316


title: PPP_173


title: NNN_192


title: NNN_191


title: PPP_12602


title: NNN_190


title: NNN_189


title: NNN_196


title: PPN_939


title: PPP_12390


title: PPN_8602


title: PPN_5070


title: NNN_183


title: NNN_182


title: PPN_4874


title: PPN_4761


title: NNN_181


title: PPN_435


title: PPN_4150


title: NNN_179


title: PPN_4389


title: NNN_187


title: NNN_184


title: NNN_175


title: NNN_174


title: NNN_176


title: PNN_202


title: PPN_3987


title: PPN_7444


title: NNN_173


title: NNN_171


title: PPN_2710


title: PPN_2709


title: NNN_170


title: PPN_2575


title: NNN_168


title: NNN_167


title: PPN_4756


title: NNN_178


title: NNN_162


title: NNN_163


title: NNN_157


title: PPN_1777


title: PPN_2168


title: NNN_161


title: PPN_1858


title: PPN_1890


title: PPN_2388


title: PPN_1655


title: NNN_155


title: PPN_2181


title: NNN_156


title: NNN_153


title: NNN_152


title: PPN_1448


title: PPN_1474


title: PPN_1610


title: NNN_151


title: PNP_913


title: PNP_836


title: NNN_150


title: NNN_145


title: NNN_144


title: Dissected 10-day-old shoot apical meristem Replicate 1


title: PNP_6130


title: NNN_141


title: PNP_5860


title: NNN_137


title: PNP_3552


title: PNP_1014


title: NNN_128


title: PPN_1166


title: NNN_131


title: PNP_12508


title: NNN_130


title: NNN_127


title: PNN_8889


title: NNN_125


title: NNN_126


title: NNN_140


title: NNN_123


title: NNN_124


title: PNN_8245


title: PNN_7599


title: PNN_8163


title: NNN_122


title: PNN_945


title: PNN_7407


title: NNN_120


title: PNN_6791


title: NNN_119


title: NNN_118


title: NNN_117


title: PNN_2848


title: NNN_116


title: PNN_5174


title: PNN_4803


title: PNN_5514


title: NNN_94


title: NNN_115


title: NNN_113


title: PNN_1639


title: PNN_1995


title: PNN_2557


title: NNN_93


title: PNN_1034


title: NNP_8509


title: NNN_77


title: NNN_80


title: NNN_90


title: PNN_1100


title: NNN_87


title: NNN_76


title: PNN_12422


title: NNP_2799


title: NNN_74


title: NNP_6353


title: NNP_6337


title: NNN_63


title: NNN_72


title: NNN_70


title: NNP_2374


title: NNN_61


title: NNN_54


title: NNP_16458


title: NNP_2063


title: NNN_927


title: NNN_52


title: NNP_160


title: NNN_865


title: NNP_6875


title: NNN_9043


title: NNN_8632


title: NNN_48


title: PNP_6962


title: NNN_8557


title: NNN_47


title: NNN_7792


title: NNN_46


title: NNN_50


title: NNN_7564


title: NNN_42


title: NNN_41


title: NNN_40


title: NNN_6577


title: NNN_5925


title: NNN_7381


title: NNN_39


title: NNN_36


title: NNN_35


title: NNN_33


title: NNN_5383


title: NNN_7549


title: NNN_32


title: NNN_4554


title: NNN_38


title: NNN_4057


title: NNN_30


title: NNN_2380


title: NNN_25


title: NNN_2565


title: NNN_28


title: NNN_5138


title: NNN_2239


title: NNN_24


title: PNP_3442


title: NNN_10533


title: NNN_22


title: NNN_21


title: 159


title: NNN_26


title: NNN_15


title: 158


title: NNN_13


title: NNN_14


title: NNN_11


title: 153


title: 157


title: NNN_17


title: 149


title: 155


title: NNN_2220


title: NNN_4


title: NNN_7


title: NNN_8


title: NNN_3


title: NNN_6


title: 152


title: 148


title: 156


title: 147


title: 144


title: 142


title: 143


title: NNN_1


title: NNN_2


title: 151


title: PNN_4150


title: 141


title: PPN_1777


title: 140


title: 137


title: NNN_5149


title: PPP_9045


title: 135


title: NNP_16458


title: 134


title: 139


title: PPN_7444


title: 130


title: PNN_8245


title: NNN_5383


title: NNN_5925


title: 138


title: PNN_4803


title: PNN_6791


title: 133


title: PNN_2848


title: NNN_4057


title: PPN_2575


title: PPN_2168


title: 136


title: 126


title: 129


title: PPN_1610


title: 124


title: 125


title: PPP_864


title: NNN_8557


title: NNN_7830


title: PPP_12390


title: NNN_8632


title: NNN_12


title: 128


title: 121


title: 123


title: 122


title: 119


title: NNN_7564


title: PNP_6962


title: 115


title: NNP_968


title: PNP_12508


title: NNN_7381


title: 116


title: 118


title: 113

value: seminal vesicle invasion


title: 114


title: NNP_6353


title: 111


title: PPP_5571

value: ER+


title: PNP_6130


title: PPP_5431

value: PR+


title: NNN_5149


title: 109


title: PPN_5070


title: 108


title: 105


title: 106


title: NNN_2380


title: PPN_4389


title: 107


title: PPN_2557


title: 104


title: PNP_3442


title: 102


title: 103


title: PPN_2710


title: NNN_2220


title: 112


title: 101


title: PPN_4756


title: 100


title: 98


title: PPN_1858


title: PPN_1655


title: PPN_1448


title: 97


title: PNP_913


title: PPN_939


title: 94


title: 95


title: PNN_12422


title: 96


title: 91


title: PPP_316


title: 89


title: 120


title: 90


title: PPP_12602


title: NNN_10533


title: PPN_8602


title: NNN_9043


title: 117


title: 87


title: NNN_7549


title: NNP_8509


title: 83


title: NNN_7792


title: 84


title: NNN_6984


title: PNN_7407


title: PNN_8163


title: 86


title: 80


title: NNP_6875


title: 77


title: NNN_6577


title: 79


title: 78


title: NNP_6337


title: PNP_5860


title: 75


title: PNN_5514


title: 82


title: NNN_5415


title: 74


title: 73


title: PNN_5174


title: 72


title: 76


title: NNN_5138


title: PPN_4761


title: 71


title: 69


title: NNN_4554


title: PNP_3552


title: PPN_3987


title: 68


title: 70


title: PPN_2709


title: PPP_3076


title: 64


title: PPN_4874


title: NNN_2565


title: 67


title: NNP_2799


title: 65


title: 63


title: PPN_2388


title: 61


title: NNN_2239


title: 60


title: PPN_2181


title: NNP_2063


title: PNN_1639


title: PPN_1474


title: 62


title: PNN_1100


title: NNN_865


title: PNN_945


title: NNN_927


title: PNP_836


title: PPP_173


title: PPP_6106


title: 127


title: PPP_394


title: P19 cells derived pluripotent stem cells, biological rep2

city: Beijing

first: Vetto

last: Chang

address: No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing

country: China

institute: NIBS

description: Gene expression data from cancer cells derived pluripotent stem cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G.

data_processing: The raw data was analyzed by R/BioConductor software and then output for further analysis.  RMA was used to normalize the data with scale median=500. Then one way ANOVA (Matlab 7.5 )was used to screen out the differentially expressed genes.

source_name: P19 cells derived pluripotent stem cells cultured in in vitro

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: P19 cells, P19 cells derived pluripotent stem cells and R1 ES cell were all cultured in DMED containing 15%FBS, nonessential amino acids, 2-mercaptoethanol, and 1000 units/ml leukemia inhibitory factor (LIF). All cells were cultured in incubator containing 5% CO2 at 37℃.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: We change culture medium for these kinds of cells everyday; and all the manipulations were the same.

tag: cell type

value: embryonal carcinoma cells derived pluripotent stem cells


title: R1 ES cells, biological rep1

description: Gene expression data from ES cells

source_name: R1 ES cells cultued in vitro

value: embryonic stem cells


title: Sox2+ sample 17

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

description: flow-sorted cells

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the HSC Microarray Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were background corrected and normalized using standard RMA procedure implemented in the Affymetrix Expression Console software. The preprocessed  data were analysed using the LIMMA Bioconductor package to identify genes that show significant evidence of differential expression between SKPs and Sox:EGFP-positive cells.

source_name: Sox2:EGFP-positive, CD34-negative blackskin cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Neonatal back skin (P4) from Sox2:EGFP mice was processed as described in the paper to yield a single cell suspension. Cells were stained with biotin conjugated anti-cd34 antibody and visualized with a PECy7 conjugated streptavidin secondary antibody. Sox2:EGFP-positive, cd34-negative cells were sorted directly into RNAlater (Ambion). For RNA isolation of  SKPs, primary SKPs were generated from neonatal (P4) mouse skin as described in the paper. Spherical SKP colonies were collected.

extract_protocol: RNA was extracted using Trizol (Invitrogen).

tag: passage

value: primary


title: R1 ES cells, biological rep2

description: Gene expression data from ES cells


title: R1 ES cells, biological rep3

description: Gene expression data from ES cells


title: P19 cells derived pluripotent stem cells, biological rep1


title: 08SE869HGU133Plus2.0

city: Campus de la Universidad Autónoma de Madrid

first: Ismael

last: Santa-Maria

state: Madrid

address: Nicolás Cabrera 1

department: Biologia Molecular

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45ºC on a GeneChip Human U133Plus2.0 Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450, and they were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with GeneSpring GX software using RMA and global median normalization method.

source_name: Human entorhinal cortex

label_protocol: IVT labeling kit affymetrix

extract_protocol: Rneasy Mini Kit and QIAshredder (Qiagen)

value: brain


title: Sox2+ sample 20

description: flow-sorted cells

value: Sox2:EGFP-positive, CD34-negative blackskin cells


title: 81

value: No Rec


title: P19 cells, biological rep2

description: Gene expression data from cancer cells

source_name: P19 cells cultured in vitro

value: embryonal carcinoma cells


title: P19 cells, biological rep3

description: Gene expression data from cancer cells


title: P19 cells derived pluripotent stem cells, biological rep3


title: 08SE868HGU133Plus2.0


title: Parathyroid tissue cultured with low and high-calcium medium 1

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

country: Japan

institute: Tokyo Women's Medical University

description: Parathyroid tissues were precultured for 7 days with MEM medium supplemented with 10% fetal calf serum, and then cultured with low (0.6mM) and high (1.6mM) calcium medium for 7 days.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Images were quantified using Agilent Microarray Scanner

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: parathyroid tissue - low calcium (0.6mM)

label_protocol: 0.5 µg of total RNA were primed with 1.2 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

growth_protocol: Parathyroid tissues explants were precultured for 7 days with MEM medium supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted from parathyroid tissue explants using the RNeasy Minikit (Quiagen, Tokyo, Japan)

treatment_protocol: Total RNA was prepared from parathyroid tissue exlants cultured in low (0.6mM) and high (1.6mM) calcium medium for 7 days.

value: parathyroid

tag: medium

value: low calcium (0.6mM)

source_name: parathyroid tissue - high calcium (1.6mM)

value: high calcium (1.6mM)


title: ES cells in 5 mM H2O2 30 min-rep5

city: New York

first: Christine

last: Richardson

state: NY

address: St Nicholas Av

department: Institute for Cancer Genetics

institute: Columbia University

description: ESC incubated in PBS/H2O2 for 30 min followed by 1 hr recovery in normal medium at 37 degrees and 5% CO3

hyb_protocol: Following fragmentation, 12 ul of cRNA were hybridized for 16 hr at 45C on Mouse MG_U74Av2 Oligonucleotide Array. Arrays were washed and stained in the Affymetrix Fluidics Station using protocol EukGE-WS2v5_450

scan_protocol: Arrays were scanned using scanner M10

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. Filtering and Statistical Analysis was done using GeneSpring version 6.

source_name: mouse ES cells, treated with 5 mM H2O2 30 min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: E14tg2a mouse embryonic stem cells having two targeted I-SceI sites (Clone C2, Ref:Richardson and Jasin, Nature 2000) were cultured at 37 C and 5% CO2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: C2 cells were treated in PBS with or without 100 uM or 5 mM hydrogen peroxide for 15 or 30 min, respectively. Following treatment cells were recovered in maintenance medium for 1 hour before RNA extraction and microarray hybridization.

tag: genotype

value: E14tg2a with two I-Sce sites

tag: agent

tag: dose

value: high dose


title: Sox2+ sample 2

description: flow-sorted cells


title: P19 cells, biological rep1

description: Gene expression data from cancer cells


title: 08SE867HGU133Plus2.0


title: Parathyroid tissue cultured with low and high-calcium medium 2


title: ES cells in 5 mM H2O2 30 min-rep3


title: Sox2+ sample 16

description: flow-sorted cells


title: ES cells in 5 mM H2O2 30 min-rep4


title: ES cells in 100 µM H2O2 15 min-rep4

description: ESC incubated in PBS/H2O2 for 15 min followed by 1 hr recovery in normal medium at 37 degrees and 5% CO2

source_name: mouse ES cells, treated with 100 µM H2O2 15 min

value: low dose


title: 88

source_name: Radical prostatectomy

value: Rec

value: ERG Fusion:Fusion

value: Positive Margin

value: extraprostatic


title: Granulosa cell with Wnt4, biological rep3

city: Saint-Hyacinthe

first: Derek

last: Boerboom

state: QC

address: 3200 Sicotte

department: Département de biomédecine Vétérinaire

institute: Université de Montréal, Faculty of veterinary medicine

description: Gene expression data from the effect of Wnt4

hyb_protocol: hybridization was done by the Microarray Core Facility of the Baylor College of Medicine (Houston, TX).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 High-Resolution Scanning Patch.

data_processing: Microarray data were analyzed using FlexArray 1.3 software (Génome Québec, Montréal, Québec, Canada). Ad-Wnt4, Ad-Cre and control Ad-GFP data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation.Robustness of the data was further enhanced by the EB (Wright and Simon) algorithm and P-value calculation. A P-value threshold of 0.05 and 3-fold (Ad-Wnt4) or 2-fold (Ad-Cre) change cut-off values were used for identification of differentially expressed genes. Overlap between genes regulated by Ad-Wnt4 and Ad-Cre was also determined using this software.

source_name: Granulosa cells were obtained from 20-26 day-old mice of various genotypes 48h after eCG treatment.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Granulosa cells were obtained from 20-26 day-old mice of various genotypes 48h after eCG treatment, using the needle puncture method. For experiments involving cell culture, cells were suspended in DMEM/F-12 medium (Invitrogen) with 1% fetal bovine serum and allowed to attach overnight at a final density of ~50%.

extract_protocol: RNeasy mini kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were infected with adenoviruses to express eGFP or Cre, or overexpress WNT4 for 24h in serum-free medium.

tag: treatment protocol

value: Cells were then infected with adenoviruses to express Wnt4.

value: granulosa cell


title: SKP sample 4

description: SKP colonies

source_name: skin-derived precursor cells

value: primary

value: skin-derived precursor cells


title: ES cells in 5 mM H2O2 30 min-rep1


title: Granulosa cell with Wnt4, biological rep2


title: 08SE866HGU133Plus2.0

value: brain


title: ES cells in 100 µM H2O2 15 min-rep2


title: 08SE865HGU133Plus2.0


title: ES cells in 5 mM H2O2 30 min-rep2


title: 08SE864HGU133Plus2.0


title: 08SE863HGU133Plus2.0


title: Granulosa cell with Wnt4, biological rep1


title: 08SE861HGU133Plus2.0


title: MCF-7 PARG Replicate 3

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: Standard hybridization to Affymetrix U133A 2.0 microarray.

scan_protocol: Standard scanning protocol using GeneChip Scanner.

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling. Signals were then used in further analysis, namely batch effect adjusted and log2 median-normalized using COMBAT R.

source_name: MCF-7 PARG Replicate 3

label_protocol: Seven μg of total RNA were subjected to One-Cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray.

extract_protocol: Total RNA was prepared using Trizol Reagent according to the manufacturer’s instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen).

tag: MCF-7 PARG Replicate 3


title: Granulosa cell with Cre, biological rep3

description: Gene expression data from the effect of Cre

value: Cells were then infected with adenoviruses to express Cre.


title: ES cells in 100 µM H2O2 15 min-rep3


title: Granulosa cell with Cre, biological rep2


title: SKP sample 3

description: SKP colonies


title: MCF-7 PARG Replicate 2

source_name: MCF-7 PARG Replicate 2

tag: MCF-7 PARG Replicate 2


title: SKP sample 5

description: SKP colonies


title: ES cells in 100 µM H2O2 15 min-rep1


title: Granulosa cell with Cre, biological rep1


title: 08SE862HGU133Plus2.0


title: Granulosa cell with GFP, biological rep2

description: Control group

value: Cells were then infected with adenoviruses to express eGFP.


title: MCF-7 PARG Replicate 1

source_name: MCF-7 PARG Replicate 1

tag: MCF-7 PARG Replicate 1


title: ES cells in PBS-rep2

description: ESC cultured in PBS alone at 37 degrees and 5% CO2

source_name: mouse ES cells control

value: control


title: 08SE860HGU133Plus2.0


title: ES cells in PBS-rep3


title: MCF-7 PARP-1 Replicate 3

source_name: MCF-7 PARP-1 Replicate 3

tag: MCF-7 PARP-1 Replicate 3


title: Granulosa cell with GFP, biological rep3

description: Control group


title: 08SE859HGU133Plus2.0


title: MCF-7 PARP-1 Replicate 1

source_name: MCF-7 Cells PARP-1 Knockdown

tag: MCF-7 Cells PARP-1 Knockdown


title: Sox2+ sample 18

description: flow-sorted cells

value: Sox2:EGFP-positive, CD34-negative blackskin cells