title: year: 2003 - developmental stage: UD:0000035 34E-L - rep3

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 07/16/2003 (7 weeks post flowering) in the study site "Ai Molini" of the IASMA Institute. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicates. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2003_developmental stage: UD:0000035 34E-L


title: year: 2003 - developmental stage: UD:0000037 36E-L - rep3

status: Public on Aug 27 2011

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 08/06/2003 (10 weeks post flowering) in the study site "Ai Molini" of the IASMA Institute. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicates. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

hyb_protocol: Affy-Eukaryotic Target Hybridization

scan_protocol: Affy-Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

label: biotin

molecule: total RNA

organism: Vitis vinifera

source_name: fruit_year 2003_developmental stage: UD:0000037 36E-L

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: hot borate RNA extraction protocol

tag: germplasm name

value: clone entav 115

tag: organism part

tag: development stage

tag: growth media

value: field soil


title: year: 2003 - developmental stage: UD:0000037 36E-L - rep1


title: casein + tofu diet, biological rep1

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

country: Japan

institute: Akita Prefectural University

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.84563210469905
upper limit: 2.62548510224213
saturation: 3.06893179387779
gamma: 49.0522525995972
sigma: 0.764845808093679
mu: 1.99559279452815

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C, according to the manual supplied by Affymetrix (P/N 702232 Rev. 2). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with a GCS 3000 scanner (GCOS V1.2, Affymetrix).

data_processing: The data were analyzed by using SuperNORM (V 1.7, Skylight Biotech Inc.) accoring to a parametric method (Konishi, T., 2008, Stat Appl Genet Mol Biol 7: Article 25.). A row of the data table presents z-scores of the PM data of a gene, in accordance with the order of the Cell appears in the CDF file. The PM data are further summarized to find z-scores and pseudo data value of a gene. The signal intensity represents the pseudo data, of which center of intensity for each array was arbitrarily set to 256.  For details of the methodology, visit http://www.super-norm.com/eng/index.html.

organism: Rattus norvegicus

source_name: rat liver, casein + tofu diet fed for 14 days

label_protocol: Ten micrograms of total RNA was processed to prepare biotinylated cRNA using One-Cycle Target Labeling and Control Reagents (Afflymetrix).

growth_protocol: Male Sprague-Dawley rats were obtained from Charles River Japan (Kanagawa, Japan) at 4 week of age. Animals were housed individually in a room with a controlled temperature (20-22ºC), humidity (55-65%), and 12-h-light/-dark cycle. During their adaptation to the conditions, rats were fed a commercial non-purified diet (Type NMF; Oriental Yeast Co., Tokyo, Japan) for 5 days. Rats were allowed free access to diet and water.

extract_protocol: At the end of the experimental period, the animals were sacrificed by bleeding from the abdominal aorta under diethyl ether anesthesia, and the liver was quickly excised. Hepatic total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Each group was fed a diet containing 200 g/kg of protein in the form of casein, soy protein, or freeze-dried tofu. The experimental diets were as follows: 1) casein diet (C); 2) C containing isoflavone (CI); 3) soy protein diet (S); 4) S containing isoflavone (SI); 5) a diet containing 100 g/kg each of protein derived from casein and freeze-dried tofu (T10); and 6) a diet containing 200 g/kg of protein derived from freeze-dried tofu (T20) (Table 1). CI and SI were supplemented with a mixture of isoflavones to match the isoflavone level of T20.

tag: strain

value: Sprague-Dawley

tag: sex

value: male

tag: tissue

value: liver


title: soy protein+isoflavone diet, biological rep4

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.677428187182076
upper limit: 2.54902877609805
saturation: 2.99247546773371
gamma: 50.7010461092227
sigma: 0.784372127799414
mu: 1.9030062614181

source_name: rat liver, soy protein+isoflavone diet fed for 14 days


title: year: 2005 - developmental stage: UD:0000034 33E-L - rep2

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 07/06/2005 (5 weeks post flowering) in the study site "Ai Molini" of the IASMA Institute. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicates. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2005_developmental stage: UD:0000034 33E-L


title: casein + tofu diet, biological rep3

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.662136921953261
upper limit: 2.87014534590318
saturation: 3.13009685479305
gamma: 51.1232426243228
sigma: 0.805664772363052
mu: 1.80404583962506


title: year: 2003 - developmental stage: UD:0000035 34E-L - rep2


title: year: 2003 - developmental stage: UD:0000035 34E-L - rep1


title: year: 2003 - developmental stage: UD:0000034 33E-L - rep3

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 07/02/2003 (5 weeks post flowering) in the study site "Ai Molini" of the IASMA Institute. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicates. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2003_developmental stage: UD:0000034 33E-L


title: soy protein+isoflavone diet, biological rep3

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.600971861037998
upper limit: 2.44198991949634
saturation: 3.00776673296253
gamma: 57.824533449116
sigma: 0.818125028085515
mu: 1.85802377429247


title: soy protein+isoflavone diet, biological rep2

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.708010717639708
upper limit: 2.47257244995397
saturation: 3.11480558956424
gamma: 47.6800438827195
sigma: 0.780752527276917
mu: 1.84084290603167


title: soy protein+isoflavone diet, biological rep1

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.677428187182076
upper limit: 2.31965979766582
saturation: 3.09951432433542
gamma: 50.1405875503293
sigma: 0.78714426705743
mu: 1.8861780332224


title: Mer2, 3h meiosis

status: Public on Aug 28 2011

type: genomic

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

country: Austria

institute: University of Vienna, MFPL

hyb_protocol: Hybridization to Affymetrix S. cerevisiae Tiling  1.0R Arrays was carried out at 42C for 16 hours. The following washing and staining steps were done with an Affymetrix 450 station. All reagents used are described in the Affymetrix ChIP Assay Protocol.

scan_protocol: Each array was scanned by Genechip Scanner 3000 (Affymetrix, CA) at default settings

data_processing:
Primary data analysis was performed with GeneChip Operating Software (GCOS, Affymetrix). Resulting Cel files were analyzed by the Tiling Analysis Software (TAS, v 1.1.02, Affymetrix, two sample comparison analysis (IP versus WCE), without normalization and results in linear scale were exported as  RPT text file) in the format specified by Affymetrix.
Text files are in tab separated format provided by Affymetrix Tiling Analysis Software. The first column represents the chromosomal position, the second column "fold enrichment" over the control experiment (WCE, 4 hours, if not specified otherwise). The columns are separated by 25 headers specifying the identity of the chromosome; sequence #8-#23 contain chromosome1 to chromosome16, sequence #24 mitochondrial DNA, sequence #25 the yeast 2mikron plasmid.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Mer2-myc ChIP with anti-myc antibody

label_protocol: Two rounds of amplification, DNA fragmentation, and end-labeling, were performed according to the Affymetrix ChIP protocol.

growth_protocol: Meiotic cultures of diploid S. cerevisiae SK1 strain were set up as follows: A saturated YPD culture was used to inoculate 300 ml liquid SPS medium (.5% yeast extract, 1% Bacto peptone, 1% potassium acetate, .17% Yeast nitrgen base w/o aa, 0.05 M potassium biphtalate, pH 5.5) 1:400 and grown in a 3-liter baffled flask at 200 rpm at 30°C for 14 hrs. Cells were harvested, washed once, resuspended at an OD660 of  1.1 in sporulation medium (1% potassium acetate pH 7.0, supplemented with amino acids and  .001% PPG) and shaken at 200 rpm at 30°C for 4 hrs.

extract_protocol: Cells were fixed in 1% formaldehyde for 30min. 1X10^9 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka). Chromosomal DNA was shared into the average size of 500-1000bp by sonication. Chromatin IP was performed as described in Katou et al. (Methods Enzym., 409,389-410, 2006).

tag: genetic background

tag: genotype

value: FK3222:Mat a/alpha,  MER2-myc9::TRP

tag: bait protein

tag: antibody

value: mouse, anti-myc 9E11

tag: meiotic timepoint

value: 3 hours

value: wild type

source_name: WCE 4h meiosis

extract_protocol: Cells were fixed in 1% formaldehyde for 30min. 1X10^9 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka). Chromosomal DNA was shared into the average size of 500-1000bp by sonication. Isolation of genomic DNA was performed as described in Katou et al. (Methods Enzym., 409,389-410, 2006).

value: rad50S mutation


title: soy protein diet, biological rep4

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.509224269665103
upper limit: 2.50315498041161
saturation: 2.93131040681845
gamma: 47.7429734968628
sigma: 0.821522877054724
mu: 1.77052833797377

source_name: rat liver, soy protein diet fed for 14 days


title: soy protein diet, biological rep5

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.585680595809182
upper limit: 2.51844624564042
saturation: 3.03834926342016
gamma: 50.4191843356731
sigma: 0.806304439101245
mu: 1.87545072956943


title: soy protein diet, biological rep2

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.524515534893919
upper limit: 2.04441702354713
saturation: 2.96189293727608
gamma: 53.9501431841619
sigma: 0.813927872240782
mu: 1.868511803154


title: year: 2003 - developmental stage: UD:0000034 33E-L - rep2


title: soy protein diet, biological rep3

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.600971861037998
upper limit: 1.93737816694542
saturation: 2.99247546773371
gamma: 51.1245734954943
sigma: 0.790740131802435
mu: 1.90702133428734


title: liver, anti-miR-33 treated, 4 weeks, rep 5

city: San Diego

first: Christine

last: Esau

state: CA

address: 3545 John Hopkins Court

institute: Regulus Therapeutics

hyb_protocol: Hybridize fragmented, biotin-labeled cRNA to the Affymetrix GeneChip® Array overnight at 45oC for 16 to 18 hours (GeneChip Hybridization Oven 640) according to the manufacturer’s recommendations.

scan_protocol: Stain, wash (GeneChip Fluidics Station 450, EukGE-WS2v5_450 script) and scan (GCS 3000 7G with the GeneChip® AutoLoader) performed according to the manufacturer’s recommendations.

data_processing: The data were analyzed with Array Studio version 4.1 using Affymetrix default analysis settings and RMA as normalization method. The normalized signals were log-2 transformed.

organism: Chlorocebus aethiops

source_name: liver, anti-miR-33 treated, 4 weeks

label_protocol: Starting with 1 ug total RNA, produce amplified biotin-labeled cRNA targets using the Enzo Target Labeling method.

growth_protocol: African Green monkeys were fed normal chow for first 4 weeks of treatment period, then switched to high carbohydrate, moderate cholesterol diet for remaining 8 weeks of treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Monkeys were treated with 5mg/kg anti-miR-33 or control anti-miR twice weekly for two weeks, then weekly for an additional ten weeks. anti-miR was administered subcutaneously

tag: gender

tag: animal id

tag: timepoint (wks)

tag: common name

value: African green monkey

tag: diet

value: Normal chow


title: untreated (control)_28 days_after_veraison - rep1

description: untreated (control) grape berry skins sampled at 28 days after veraison. Repetition 1

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: total RNA isolation followed by RNeasy purification

value: PO 0009085 epicarp

value: PO:0001002 fruit development stages


title: liver, anti-miR-33 treated, 12 weeks, rep 4

source_name: liver, anti-miR-33 treated, 12 weeks

value: High carb/Med. Cholesterol


title: year: 2003 - developmental stage: UD:0000034 33E-L - rep1

tag: germplasm name


title: liver, control anti-miR, 4 weeks, rep 2

source_name: liver, control anti-miR, 4 weeks


title: liver, anti-miR-33 treated, 4 weeks, rep 6


title: liver, control anti-miR, 4 weeks, rep 1


title: liver, control anti-miR, 4 weeks, rep 5


title: liver, control anti-miR, 4 weeks, rep 4


title: liver, anti-miR-33 treated, 4 weeks, rep 4


title: liver, anti-miR-33 treated, 12 weeks, rep 5


title: liver, control anti-miR, 4 weeks, rep 6


title: untreated (control)_28 days_after_veraison - rep3

description: untreated (control) grape berry skins sampled at 28 days after veraison. Repetition 3

tag: organism part


title: liver, control anti-miR, 12 weeks, rep 6

source_name: liver, control anti-miR, 12 weeks


title: liver, anti-miR-33 treated, 4 weeks, rep 3


title: liver, anti-miR-33 treated, 12 weeks, rep 6


title: soy protein diet, biological rep1

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.524515534893919
upper limit: 2.47257244995397
saturation: 3.05364052864897
gamma: 53.2910812576872
sigma: 0.787983153664658
mu: 1.96181196415384


title: liver, anti-miR-33 treated, 4 weeks, rep 1


title: liver, anti-miR-33 treated, 4 weeks, rep 2


title: casein+isoflavone diet, biological rep5

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.362716655680217
upper limit: 2.42117340643909
saturation: 2.92865336567959
gamma: 51.529121802478
sigma: 0.814115956879256
mu: 1.84512227913562

source_name: rat liver, casein+isoflavone diet fed for 14 days


title: liver, control anti-miR, 4 weeks, rep 3


title: liver, control anti-miR, 12 weeks, rep 5


title: untreated (control)_28 days_after_veraison - rep2

description: untreated (control) grape berry skins sampled at 28 days after veraison. Repetition 2

tag: development stage


title: casein+isoflavone diet, biological rep3

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.371602882605761
upper limit: 2.09029081923358
saturation: 2.87014534590318
gamma: 57.232393129574
sigma: 0.819007322806815
mu: 1.80207447496484


title: untreated (control)_14 days_after_veraison - rep1

description: untreated (control) grape berry skins sampled at 14 days after veraison. Repetition 1

tag: growth media


title: year: 2005 - developmental stage: UD:0000037 36E-L - rep1

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 08/10/2005 (10 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2005_developmental stage: UD:0000037 36E-L


title: liver, control anti-miR, 12 weeks, rep 3


title: liver, control anti-miR, 12 weeks, rep 1


title: liver, anti-miR-33 treated, 12 weeks, rep 3


title: liver, anti-miR-33 treated, 12 weeks, rep 2


title: ABA treated_28 days_after_veraison - rep2

description: ABA-treated grape berry skins sampled at 28 days after veraison. Repetition 2


title: casein+isoflavone diet, biological rep2

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.600971861037998
upper limit: 2.05970828877595
saturation: 2.91601914158963
gamma: 49.8718611994404
sigma: 0.820267952255947
mu: 1.86088844530719

tag: strain


title: casein+isoflavone diet, biological rep4

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.295146556461682
upper limit: 2.12087334969121
saturation: 2.80898028498792
gamma: 58.4030111525954
sigma: 0.82370825129592
mu: 1.88380682615617

tag: sex


title: liver, control anti-miR, 12 weeks, rep 2

tag: tissue


title: casein + tofu diet, biological rep4

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.493933004436287
upper limit: 2.85485408067437
saturation: 3.43592215936937
gamma: 49.1723479621268
sigma: 0.782537444825238
mu: 1.86271311333722


title: untreated (control)_14 days_after_veraison - rep2

description: untreated (control) grape berry skins sampled at 14 days after veraison. Repetition 2


title: ABA treated_28 days_after_veraison - rep3

description: ABA-treated grape berry skins sampled at 28 days after veraison. Repetition 3


title: liver, anti-miR-33 treated, 12 weeks, rep 1


title: liver, untreated, (baseline) -5 weeks, rep 9

source_name: liver, untreated, (baseline) -5 weeks


title: casein diet, biological rep5

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.44805920874984
upper limit: 2.6866501631574
saturation: 2.96189293727608
gamma: 51.402117092976
sigma: 0.814710272760019
mu: 1.84522968287427

source_name: rat liver, casein diet fed for 14 days


title: casein+isoflavone diet, biological rep1

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.478641739207472
upper limit: 2.19732967583529
saturation: 2.91601914158963
gamma: 59.7605159567935
sigma: 0.804773592008036
mu: 1.8902015126249


title: liver, untreated, (baseline) -5 weeks, rep 11


title: liver, untreated, (baseline) -5 weeks, rep 10


title: ABA treated_28 days_after_veraison - rep1

description: ABA-treated grape berry skins sampled at 28 days after veraison. Repetition 1


title: ABA treated_14 days_after_veraison - rep3

description: ABA-treated grape berry skins sampled at 14 days after veraison. Repetition 3


title: liver, control anti-miR, 12 weeks, rep 4


title: liver, untreated, (baseline) -5 weeks, rep 12


title: liver, untreated, (baseline) -5 weeks, rep 8


title: liver, untreated, (baseline) -5 weeks, rep 7


title: liver, untreated, (baseline) -5 weeks, rep 6


title: casein diet, biological rep3

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.44805920874984
upper limit: 2.304368532437
saturation: 2.91601914158963
gamma: 57.232393129574
sigma: 0.819007322806815
mu: 1.80207447496484


title: casein diet, biological rep4

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.55509806535155
upper limit: 2.3961161238099
saturation: 2.885436611132
gamma: 55.3289259732241
sigma: 0.815271055423456
mu: 1.89732997602285


title: liver, untreated, (baseline) -5 weeks, rep 4


title: ABA treated_14 days_after_veraison - rep2

description: ABA-treated grape berry skins sampled at 14 days after veraison. Repetition 2


status: Public on Aug 26 2011

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_media= hlgABC-deletion strainderived from wild type USA300-rep 3

hyb_protocol: Samples were hybridized to the custom Affymetrix GeneChip (RMLchip7, GEO platform GPL8069) containing the USA300 genome at 100% coverage (2560/2560).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Sa genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

label_protocol: Fragmented and biotin-dUTP-labeled aRNA was generated from purified staphylococcal RNA followed by manufacturer protocol MessageAmp™ II-Bacteria Kit (Ambion).

growth_protocol: S. aureus USA300 strain was cultured in tryptic soy broth (TSB; Becton Dickinson) to mid-exponential growth phase (OD600~0.75), washed once with Dulbecco’s PBS (DPBS; Sigma-Aldrich) and added to fresh TSB media, human normal serum and human heparinized blood to a final concentration 107CFU/ml. Blood and serum were obtained from six healthy individuals. Each human subject included in the study gave informed consent. Bacteria were incubated with gentle rotation for up to 120 min at 37°C with 5% CO2. At chosen time points (0, 30, 60, 90 and 120 min) 10 ml samples were collected

extract_protocol: RNA was isolated from collected samples by RNeasy Mini Kit (Qiagen) with addition use of Bacterial-RNA Protect (Qiagen), and contaminating chromosomal DNA was removed by TurboDNase (Ambion/Applied Biosystem). To remove eukaryotic RNA, samples were subjected to MICROBEnrich™ (Ambion) treatment.

treatment_protocol: At chosen time points (0, 30, 60, 90 and 120 min) 10 ml samples were collected. Bacteria were washed with DPBS and plated on TSA for CFU count. Culture samples at all time points were stained with Wright-Giemsa stain and were examined under the microscope

value: USA300 hlgABC-deletion

tag: genotype/variation

value: hlgABC-deletion


title: liver, untreated, (baseline) -5 weeks, rep 2


title: casein diet, biological rep2

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.15752516940234
upper limit: 2.33495106289463
saturation: 2.885436611132
gamma: 56.5643189843982
sigma: 0.83911135170537
mu: 1.83092588714588


title: casein diet, biological rep1

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.539806800122735
upper limit: 2.51844624564042
saturation: 2.96189293727608
gamma: 59.2569798465073
sigma: 0.803859041516305
mu: 1.89208689083088


title: liver, untreated, (baseline) -5 weeks, rep 5


description: Gene expression data from_media= hlgABC-deletion strainderived from wild type USA300-rep 2


title: wild type USA300 strain-rep 3

description: Gene expression data from_media= wild type USA300 strain-rep 3

source_name: wild type USA300 strain-rep 3


title: wild type USA300 strain- rep 1

description: Gene expression data from_media= wild type USA300 strain- rep 1

source_name: wild type USA300 strain- rep 1


title: liver, untreated, (baseline) -5 weeks, rep 3


title: liver, untreated, (baseline) -5 weeks, rep 1


title: ABA treated_14 days_after_veraison - rep1

description: ABA-treated grape berry skins sampled at 14 days after veraison. Repetition 1


title: media= Blood , time point 120 , replicate 6

description:
Gene expression data from_media= Blood time point 120 replicate 6
3418_NM-1_Sa_78_Blood-120-6-90_01_9827

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: media= Blood time point 120 replicate 6

tag: growth protocol

value: Blood

tag: time

value: 120 min


title: wild type USA300 strain-rep 2

description: Gene expression data from_media= wild type USA300 strain-rep 2

source_name: wild type USA300 strain-rep 2


title: media= Serum , time point 90 , replicate 6

description:
Gene expression data from_media= Serum time point 90 replicate 6
3388_NM-1_Sa_48_Serum-90-6-84_01_9835

source_name: media= Serum time point 90 replicate 6

value: Serum

value: 90 min


description: Gene expression data from_media= hlgABC-deletion strainderived from wild type USA300-rep 1


title: media= Blood , time point 60 , replicate 6

description:
Gene expression data from_media= Blood time point 60 replicate 6
3406_NM-1_Sa_66_Blood-60-6-88_01_7537

source_name: media= Blood time point 60 replicate 6

value: 60 min


title: media= Blood , time point 90 , replicate 6

description:
Gene expression data from_media= Blood time point 90 replicate 6
3412_NM-1_Sa_72_Blood-90-6-89_01_9840

source_name: media= Blood time point 90 replicate 6


title: media= Serum , time point 120 , replicate 6

description:
Gene expression data from_media= Serum time point 120 replicate 6
3394_NM-1_Sa_54_Serum-120-6-85_01_9811

source_name: media= Serum time point 120 replicate 6


title: media= TSB , time point 120 , replicate 6

description:
Gene expression data from_media= TSB time point 120 replicate 6
3370_NM-1_Sa_30_TSB-120-6-80_01_3232

source_name: media= TSB time point 120 replicate 6

value: TSB


title: media= TSB , time point 30 , replicate 6

description:
Gene expression data from_media= TSB time point 30 replicate 6
3352_NM-1_Sa_12_TSB-30-6-77_01_9822

source_name: media= TSB time point 30 replicate 6

value: 30 min


title: media= Serum , time point 60 , replicate 6

description:
Gene expression data from_media= Serum time point 60 replicate 6
3382_NM-1_Sa_42_Serum-60-6-83_01_9808

source_name: media= Serum time point 60 replicate 6


title: media= Blood , time point 30 , replicate 6

description:
Gene expression data from_media= Blood time point 30 replicate 6
3400_NM-1_Sa_60_Blood-30-6-87_01_3221

source_name: media= Blood time point 30 replicate 6


title: media= TSB , time point 60 , replicate 6

description:
Gene expression data from_media= TSB time point 60 replicate 6
3358_NM-1_Sa_18_TSB-60-6-78_01_9830

source_name: media= TSB time point 60 replicate 6


title: media= Blood , time point 120 , replicate 5

description:
Gene expression data from_media= Blood time point 120 replicate 5
3417_NM-1_Sa_77_Blood-120-5-75_01_9831

source_name: media= Blood time point 120 replicate 5


title: media= TSB , time point 90 , replicate 6

description:
Gene expression data from_media= TSB time point 90 replicate 6
3364_NM-1_Sa_24_TSB-90-6-79_01_3225

source_name: media= TSB time point 90 replicate 6


title: media= TSB , time point 0 , replicate 6

description:
Gene expression data from_media= TSB time point 0 replicate 6
3346_NM-1_Sa_06_TSB-0-6-76_01_7520

source_name: media= TSB time point 0 replicate 6

value: 0 min


title: media= Blood , time point 30 , replicate 5

description:
Gene expression data from_media= Blood time point 30 replicate 5
3399_NM-1_Sa_59_Blood-30-5-72_01_9813

source_name: media= Blood time point 30 replicate 5


title: media= Serum , time point 30 , replicate 6

description:
Gene expression data from_media= Serum time point 30 replicate 6
3376_NM-1_Sa_36_Serum-30-6-82_01_7514

source_name: media= Serum time point 30 replicate 6


title: media= Blood , time point 90 , replicate 5

description:
Gene expression data from_media= Blood time point 90 replicate 5
3411_NM-1_Sa_71_Blood-90-5-74_01_9829

source_name: media= Blood time point 90 replicate 5


title: media= Serum , time point 90 , replicate 5

description:
Gene expression data from_media= Serum time point 90 replicate 5
3387_NM-1_Sa_47_Serum-90-5-69_01_9833

source_name: media= Serum time point 90 replicate 5


title: media= Serum , time point 30 , replicate 5

description:
Gene expression data from_media= Serum time point 30 replicate 5
3375_NM-1_Sa_35_Serum-30-5-67_01_7511

source_name: media= Serum time point 30 replicate 5


title: media= TSB , time point 120 , replicate 5

description:
Gene expression data from_media= TSB time point 120 replicate 5
3369_NM-1_Sa_29_TSB-120-5-65_01_7513

source_name: media= TSB time point 120 replicate 5


title: media= TSB , time point 90 , replicate 5

description:
Gene expression data from_media= TSB time point 90 replicate 5
3363_NM-1_Sa_23_TSB-90-5-64_01_7540

source_name: media= TSB time point 90 replicate 5


title: media= Serum , time point 120 , replicate 5

description:
Gene expression data from_media= Serum time point 120 replicate 5
3393_NM-1_Sa_53_Serum-120-5-70_01_9826

source_name: media= Serum time point 120 replicate 5


title: media= Serum , time point 60 , replicate 5

description:
Gene expression data from_media= Serum time point 60 replicate 5
3381_NM-1_Sa_41_Serum-60-5-68_01_7532

source_name: media= Serum time point 60 replicate 5


title: media= TSB , time point 60 , replicate 5

description:
Gene expression data from_media= TSB time point 60 replicate 5
3357_NM-1_Sa_17_TSB-60-5-63_01_9823

source_name: media= TSB time point 60 replicate 5


title: media= TSB , time point 30 , replicate 5

description:
Gene expression data from_media= TSB time point 30 replicate 5
3351_NM-1_Sa_11_TSB-30-5-62_01_3218

source_name: media= TSB time point 30 replicate 5


title: media= TSB , time point 0 , replicate 5

description:
Gene expression data from_media= TSB time point 0 replicate 5
3345_NM-1_Sa_05_TSB-0-5-61_01_7522

source_name: media= TSB time point 0 replicate 5


title: media= Blood , time point 60 , replicate 5

description:
Gene expression data from_media= Blood time point 60 replicate 5
3405_NM-1_Sa_65_Blood-60-5-73_01_9839

source_name: media= Blood time point 60 replicate 5


title: media= Blood , time point 30 , replicate 4

description:
Gene expression data from_media= Blood time point 30 replicate 4
3398_NM-1_Sa_58_Blood-30-4-57_01_9838

source_name: media= Blood time point 30 replicate 4


title: media= Blood , time point 120 , replicate 4

description:
Gene expression data from_media= Blood time point 120 replicate 4
3416_NM-1_Sa_76_Blood-120-4-60_01_9825

source_name: media= Blood time point 120 replicate 4


title: media= Serum , time point 90 , replicate 4

description:
Gene expression data from_media= Serum time point 90 replicate 4
3386_NM-1_Sa_46_Serum-90-4-54_01_7526

source_name: media= Serum time point 90 replicate 4


title: media= Serum , time point 120 , replicate 4

description:
Gene expression data from_media= Serum time point 120 replicate 4
3392_NM-1_Sa_52_Serum-120-4-55_01_7530

source_name: media= Serum time point 120 replicate 4


title: untreated (control)_14 days_after_veraison - rep3

description: untreated (control) grape berry skins sampled at 14 days after veraison. Repetition 3

value: field soil


title: media= Blood , time point 90 , replicate 4

description:
Gene expression data from_media= Blood time point 90 replicate 4
3410_NM-1_Sa_70_Blood-90-4-59_01_9834

source_name: media= Blood time point 90 replicate 4


title: media= Blood , time point 60 , replicate 4

description:
Gene expression data from_media= Blood time point 60 replicate 4
3404_NM-1_Sa_64_Blood-60-4-58_01_9810

source_name: media= Blood time point 60 replicate 4


title: media= Serum , time point 30 , replicate 4

description:
Gene expression data from_media= Serum time point 30 replicate 4
3374_NM-1_Sa_34_Serum-30-4-52_01_9800

source_name: media= Serum time point 30 replicate 4


title: media= Serum , time point 60 , replicate 4

description:
Gene expression data from_media= Serum time point 60 replicate 4
3380_NM-1_Sa_40_Serum-60-4-53_01_9806

source_name: media= Serum time point 60 replicate 4


title: media= TSB , time point 60 , replicate 4

description:
Gene expression data from_media= TSB time point 60 replicate 4
3356_NM-1_Sa_16_TSB-60-4-48_01_9815

source_name: media= TSB time point 60 replicate 4


title: media= TSB , time point 120 , replicate 4

description:
Gene expression data from_media= TSB time point 120 replicate 4
3368_NM-1_Sa_28_TSB-120-4-50_01_7533

source_name: media= TSB time point 120 replicate 4


title: media= TSB , time point 30 , replicate 4

description:
Gene expression data from_media= TSB time point 30 replicate 4
3350_NM-1_Sa_10_TSB-30-4-47_01_9799

source_name: media= TSB time point 30 replicate 4


title: media= TSB , time point 90 , replicate 4

description:
Gene expression data from_media= TSB time point 90 replicate 4
3362_NM-1_Sa_22_TSB-90-4-49_01_7545

source_name: media= TSB time point 90 replicate 4


title: media= TSB , time point 0 , replicate 4

description:
Gene expression data from_media= TSB time point 0 replicate 4
3344_NM-1_Sa_04_TSB-0-4-46_01_7544

source_name: media= TSB time point 0 replicate 4


title: media= Blood , time point 90 , replicate 3

description:
Gene expression data from_media= Blood time point 90 replicate 3
3409_NM-1_Sa_69_Blood-90-3-44_01_9816

source_name: media= Blood time point 90 replicate 3


title: media= Blood , time point 120 , replicate 3

description:
Gene expression data from_media= Blood time point 120 replicate 3
3415_NM-1_Sa_75_Blood-120-3-45_01_9809

source_name: media= Blood time point 120 replicate 3


title: media= Blood , time point 60 , replicate 3

description:
Gene expression data from_media= Blood time point 60 replicate 3
3403_NM-1_Sa_63_Blood-60-3-43_01_7527

source_name: media= Blood time point 60 replicate 3


title: media= Blood , time point 30 , replicate 3

description:
Gene expression data from_media= Blood time point 30 replicate 3
3397_NM-1_Sa_57_Blood-30-3-42_01_9798

source_name: media= Blood time point 30 replicate 3


title: media= Serum , time point 120 , replicate 3

description:
Gene expression data from_media= Serum time point 120 replicate 3
3391_NM-1_Sa_51_Serum-120-3-40_01_7531

source_name: media= Serum time point 120 replicate 3


title: media= TSB , time point 120 , replicate 3

description:
Gene expression data from_media= TSB time point 120 replicate 3
3367_NM-1_Sa_27_TSB-120-3-35_01_3189

source_name: media= TSB time point 120 replicate 3


title: media= TSB , time point 60 , replicate 3

description:
Gene expression data from_media= TSB time point 60 replicate 3
3355_NM-1_Sa_15_TSB-60-3-33_01_9817

source_name: media= TSB time point 60 replicate 3


title: media= TSB , time point 90 , replicate 3

description:
Gene expression data from_media= TSB time point 90 replicate 3
3361_NM-1_Sa_21_TSB-90-3-34_01_9828

source_name: media= TSB time point 90 replicate 3


title: media= Serum , time point 60 , replicate 3

description:
Gene expression data from_media= Serum time point 60 replicate 3
3379_NM-1_Sa_39_Serum-60-3-38_01_9821

source_name: media= Serum time point 60 replicate 3


title: media= Blood , time point 120 , replicate 2

description:
Gene expression data from_media= Blood time point 120 replicate 2
3414_NM-1_Sa_74_Blood-120-2-30_01_9802

source_name: media= Blood time point 120 replicate 2


title: media= Blood , time point 60 , replicate 2

description:
Gene expression data from_media= Blood time point 60 replicate 2
3402_NM-1_Sa_62_Blood-60-2-28_01_7517

source_name: media= Blood time point 60 replicate 2


title: media= Serum , time point 30 , replicate 3

description:
Gene expression data from_media= Serum time point 30 replicate 3
3373_NM-1_Sa_33_Serum-30-3-37_01_9818

source_name: media= Serum time point 30 replicate 3


title: media= Serum , time point 90 , replicate 3

description:
Gene expression data from_media= Serum time point 90 replicate 3
3385_NM-1_Sa_45_Serum-90-3-39_01_9803

source_name: media= Serum time point 90 replicate 3


title: media= Serum , time point 120 , replicate 2

description:
Gene expression data from_media= Serum time point 120 replicate 2
3390_NM-1_Sa_50_Serum-120-2-25_01_7529

source_name: media= Serum time point 120 replicate 2


title: media= Blood , time point 120 , replicate 1

description:
Gene expression data from_media= Blood time point 120 replicate 1
3413_NM-1_Sa_73_Blood-120-1-15_01_9812

source_name: media= Blood time point 120 replicate 1


title: media= TSB , time point 0 , replicate 3

description:
Gene expression data from_media= TSB time point 0 replicate 3
3343_NM-1_Sa_03_TSB-0-3-31_01_9804

source_name: media= TSB time point 0 replicate 3


title: media= Serum , time point 90 , replicate 2

description:
Gene expression data from_media= Serum time point 90 replicate 2
3384_NM-1_Sa_44_Serum-90-2-24_01_7542

source_name: media= Serum time point 90 replicate 2


title: media= TSB , time point 0 , replicate 2

description:
Gene expression data from_media= TSB time point 0 replicate 2
3342_NM-1_Sa_02_TSB-0-2-16_01_9841

source_name: media= TSB time point 0 replicate 2


title: media= TSB , time point 90 , replicate 2

description:
Gene expression data from_media= TSB time point 90 replicate 2
3360_NM-1_Sa_20_TSB-90-2-19_01_7523

source_name: media= TSB time point 90 replicate 2


title: media= Blood , time point 30 , replicate 2

description:
Gene expression data from_media= Blood time point 30 replicate 2
3396_NM-1_Sa_56_Blood-30-2-27_01_9842

source_name: media= Blood time point 30 replicate 2


title: media= Serum , time point 90 , replicate 1

description:
Gene expression data from_media= Serum time point 90 replicate 1
3383_NM-1_Sa_43_Serum-90-1-9_01_7510

source_name: media= Serum time point 90 replicate 1


title: media= Blood , time point 90 , replicate 2

description:
Gene expression data from_media= Blood time point 90 replicate 2
3408_NM-1_Sa_68_Blood-90-2-29_01_9832

source_name: media= Blood time point 90 replicate 2


title: media= TSB , time point 120 , replicate 2

description:
Gene expression data from_media= TSB time point 120 replicate 2
3366_NM-1_Sa_26_TSB-120-2-20_01_7519

source_name: media= TSB time point 120 replicate 2


title: media= Serum , time point 60 , replicate 1

description:
Gene expression data from_media= Serum time point 60 replicate 1
3377_NM-1_Sa_37_Serum-60-1-8_01_9843

source_name: media= Serum time point 60 replicate 1


title: media= Serum , time point 120 , replicate 1

description:
Gene expression data from_media= Serum time point 120 replicate 1
3389_NM-1_Sa_49_Serum-120-1-10_01_7518

source_name: media= Serum time point 120 replicate 1


title: media= Blood , time point 30 , replicate 1

description:
Gene expression data from_media= Blood time point 30 replicate 1
3395_NM-1_Sa_55_Blood-30-1-12_01_9805

source_name: media= Blood time point 30 replicate 1


title: media= Serum , time point 30 , replicate 1

description:
Gene expression data from_media= Serum time point 30 replicate 1
3371_NM-1_Sa_31_Serum-30-1-7_01_7512

source_name: media= Serum time point 30 replicate 1


title: media= TSB , time point 120 , replicate 1

description:
Gene expression data from_media= TSB time point 120 replicate 1
3365_NM-1_Sa_25_TSB-120-1-5_01_3190

source_name: media= TSB time point 120 replicate 1


title: media= Blood , time point 60 , replicate 1

description:
Gene expression data from_media= Blood time point 60 replicate 1
3401_NM-1_Sa_61_Blood-60-1-13_01_7534

source_name: media= Blood time point 60 replicate 1


title: media= TSB , time point 90 , replicate 1

description:
Gene expression data from_media= TSB time point 90 replicate 1
3359_NM-1_Sa_19_TSB-90-1-4_01_3222

source_name: media= TSB time point 90 replicate 1


title: media= Blood , time point 90 , replicate 1

description:
Gene expression data from_media= Blood time point 90 replicate 1
3407_NM-1_Sa_67_Blood-90-1-14_01_7528

source_name: media= Blood time point 90 replicate 1


title: media= TSB , time point 60 , replicate 1

description:
Gene expression data from_media= TSB time point 60 replicate 1
3353_NM-1_Sa_13_TSB-60-1-3_01_7524

source_name: media= TSB time point 60 replicate 1


title: media= TSB , time point 30 , replicate 1

description:
Gene expression data from_media= TSB time point 30 replicate 1
3347_NM-1_Sa_07_TSB-30-1-2_01_7521

source_name: media= TSB time point 30 replicate 1


title: media= TSB , time point 0 , replicate 1

description:
Gene expression data from_media= TSB time point 0 replicate 1
3341_NM-1_Sa_01_TSB-0-1-1_01_9836

source_name: media= TSB time point 0 replicate 1


title: L1234

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

description: Gene expression data were exported from BeadStudio software (Illumina).

hyb_protocol: Hybridized 16-20 hours at 58C temp. with rocker speed at 5.

scan_protocol: Illumina BeadStation 500GX, as per manufacturer's instructions.

data_processing:
For the expression array, unprocessed data were collected from BeadStudio (version 3.1.3.0) and processed using VST and quantile normalization with the R beadarray package (version 1.16.0). The processed data was analyzed using Limma (linear models for microarray data) analysis which uses moderated t-test to detect differentially expressed genes between two groups by taking into account natural variance within these groups and correcting for multiple testing using false discovery rate indicating the number of differentially expressed genes between two groups.

Bead-level raw data are available in the supplementary files that are linked to the Sample records.
Bead summary raw data are available in the 'GSE22855.non-normalized.txt' file, which is linked to the Series GSE22855 record.

organism: Homo sapiens

source_name: Growth Plate

label_protocol: Illumina TotalPrep RNA Amplification Kit according to manufacturer's instructions. Dye was biotin-NTP mix and label was streptavidin-Cy3.

extract_protocol: Tumor samples containing more than 80% tumor cells, as estimated on haematoxylin and eosin-stained frozen sections, were selected. RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Qiagen GmbH, Hilden, Germany) according to manufacturer's instructions. RNA concentration was measured spectrophotometrically and the fragment sizes were determined using the RNA 6000 Nano Labchip kit.

value: growth plate

tag: sample type

value: control


title: L2603

source_name: Cartilage

value: cartilage


title: L1686

source_name: Ollier Enchondroma

tag: disease

value: Ollier

value: enchondroma

tag: location of tumor

value: phalanx


title: L1683

tag: age

tag: gender

value: female

value: metacarpal


title: L2392


title: L910

description:
L206 and L910 enchondromas are from the same patient. These tumors were obtained from the patient during different operations.

Gene expression data were exported from BeadStudio software (Illumina).


title: L1251

value: male


title: L2103a


title: L1142


title: leiomyoma, patient MY65, MED12wt

city: Helsinki

first: Miika

last: Mehine

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: University of Helsinki

description: Leiomyoma gene expression data from patient MY65, MED12wt

hyb_protocol: Fragmented cRNA was hybridized according to the manufacturer´s intructions

scan_protocol: According to the standard Affymetrix procedures

data_processing: Gene expression data was processed and analyzed with Partek Genomic Suite™ v. 6.5 (Partek Incorporated, St. Louis, MO, USA) using Brainarray Custom CDF files (HGU133Plus2_Hs_ENSG,v.14.1.0, http://brainarray.mbni.med.umich.edu/ Brainarray/default.asp).

source_name: leiomyoma, patient MY65, MED12wt

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10ug of total RNA

extract_protocol: RNA was extracted using TRIzol® Reagent and purified with RNeasy® MinElute™ clean up kit according to manufacturers’ instructions

value: leiomyoma

value: mut+

tag: patient


title: leiomyoma, patient MY30, MED12wt

description: Leiomyoma gene expression data from patient MY30, MED12wt

source_name: leiomyoma, patient MY30, MED12wt


title: L2687


title: L2600


title: E4A03_42

city: Rochester

first: Shaji

middle: K

last: Kumar

state: MN

address: 200 First Street SW

department: Hematology

institute: Mayo Clinic

description: CD138 sorted cells

hyb_protocol: Appropriate amounts of labeled cRNA and control oligonucleotide B2 are added along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin to the hybridization buffer. The hybridization mixture is heated at 99°C for 5 minutes followed by incubation at 45°C for 5 minutes before applying the sample onto the GeneChip. Hybridization is performed at 45°C for 16 hours with mixing, following which the solutions are removed, and arrays washed and stained with streptavidin-phycoerythrin (Molecular Probes, Portland, OR).

scan_protocol: The arrays will be scanned using a Genechip 300 scanner and GeneChip 5.0 software (Affymetrix) will used to quantitatively analyze the scanned image. Algorithms in the software use probe cell ﬂuo¬rescence intensities to calculate an average intensity for each set of probe pairs representing a gene, which directly correlates with the amount of mRNA.

data_processing: The plasma cell gene expression from normal samples will be first compared to each of the patient groups. Subsequently, the individual patient groups will be compared to each other. The selection criteria for all genes reported as differentially expressed will be as follows: (1) in absolute analysis, a detection call of present; (2) a change either increased or decreased; (3) signal of greater than 1,000; and (4) greater than 2-fold differences in expression in all pairwise comparisons. Only genes with transcript levels that satisfied all 4 criteria will be considered as signiﬁcantly differentially expressed.

label: Biotin

source_name: Primary myeloma cells

label_protocol: The puriﬁed cDNA is used as the template for in vitro transcription reaction for synthesizing biotinylated complementary RNA (cRNA) using an RNA transcript labeling reagent (Af¬fymetrix). The quality of the frag-mented biotin–labeled cRNA in each experiment is evaluated before hybridizing by both gel electrophoresis and hybridizing (fraction of the sample) onto test-3 microarray and analyzing as a measure of quality control.

extract_protocol: Total RNA (5 μg) will be isolated from purified plasma cells using TRIZOL reagent (Life Technologies, Gaithersburg, MD) and further puri¬ﬁed using an afﬁnity resin column (RNeasy; Qiagen, Chatsworth, CA). Total RNA will be then converted to cDNA using the Superscript cDNA synthesis kit (Gibco-BRL, Gaithersburg, MD) followed by purification using phase lock gel (Eppendorf, Westbury, NY) with phenol/chloroform extraction.

tag: diagnosis

value: myeloma

tag: cell type

value: primary CD138+ sorted cells


title: E4A03_39

description: CD138 sorted cells


title: E4A03_37

description: CD138 sorted cells


title: leiomyoma, patient MY31, MED12mut+

description: Leiomyoma gene expression data from patient MY31, MED12mut+

source_name: leiomyoma, patient MY31, MED12mut+


title: E4A03_38

description: CD138 sorted cells


title: E4A03_45

description: CD138 sorted cells


title: E4A03_44

description: CD138 sorted cells


title: leiomyoma, patient MY52, MED12mut+

description: Leiomyoma gene expression data from patient MY52, MED12mut+

source_name: leiomyoma, patient MY52, MED12mut+


title: L206


title: E4A03_41

description: CD138 sorted cells


title: E4A03_40

description: CD138 sorted cells


title: E4A03_46

description: CD138 sorted cells


title: E4A03_36

description: CD138 sorted cells


title: leiomyoma, patient MY33, MED12mut+

description: Leiomyoma gene expression data from patient MY33, MED12mut+

source_name: leiomyoma, patient MY33, MED12mut+


title: KR426(PC-Brca1 flex2/flex2) Replicate 1

city: Cold Spring Harbor

first: Jude

last: Kendall

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: These samples were hybridized to one array

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min. The solution was then applied to the microarray and hybridized under a coverslide in an oven at 65 degrees C for 36 to 48 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada).

data_processing: The microarray image file was processed with Agilent Feature Extraction software using feature extraction protocol CGH-v4_95_Feb07 and array format 014695_D_20070207.  Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. The data was segmented using DNAcopy version 2.5.0.

organism: Mus musculus

label_protocol: DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.

extract_protocol: Qiagen Genomic DNA Isolation Kit

value: Ductal Breast Carcinoma

source_name: TAIL

tag: reference

value: Tail genomic DNA from the same conditional mutant mice.


title: KR609(PC-Brca1-flex2/FH-I26A) Replicate 1

data_processing: The microarray image file was processed with Agilent Feature Extraction software using feature extraction protocol CGH-v4_95_Feb07 and array format 014695_D_20070207.  Probes indicated as failed by the Agilent software were removed from analysis.  Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. The data was segmented using DNAcopy version 2.5.0.


title: E4A03_34

description: CD138 sorted cells


title: KR109(PC-Brca1+/+) Replicate 1

data_processing: The microarray image file was processed with Agilent Feature Extraction software using feature extraction protocol CGH-v4_91 and array format 014695_D_20060703.  Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. The data was segmented using DNAcopy version 2.5.0.


title: E4A03_43

description: CD138 sorted cells


title: media= TSB , time point 30 , replicate 3

description:
Gene expression data from_media= TSB time point 30 replicate 3
3349_NM-1_Sa_09_TSB-30-3-32_01_3197

source_name: media= TSB time point 30 replicate 3

value: TSB

value: 30 min


title: L1630

value: Iliac bone


title: time: Day 16 - stress: Salinity - rep3

type: other

description: Development stage: [2-year-old cuttings].  Part of organism: [Shoot tips to 4th leaf including tendrils, stem, leaves and vegetative apex].

molecule: other

source_name: time: Day 16 - stress: Salinity

growth_protocol: Plants grown in greenhouse with 16 h day supplemental lighting (mininum of 300 micro moles m-2 s-1 with Na halide lamps).

extract_protocol: Tris-LiCl

tag: organism part

tag: development stage

value: vegetative growth, PO:0007134

value: Scotts MetroMix 200


title: leiomyoma, patient MY29, MED12mut+

description: Leiomyoma gene expression data from patient MY29, MED12mut+

source_name: leiomyoma, patient MY29, MED12mut+


title: leiomyoma, patient M32, MED12mut+

description: Leiomyoma gene expression data from patient M32, MED12mut+

source_name: leiomyoma, patient M32, MED12mut+


title: leiomyoma, patient MY64, MED12mut+

description: Leiomyoma gene expression data from patient MY64, MED12mut+

source_name: leiomyoma, patient MY64, MED12mut+


title: E4A03_33

description: CD138 sorted cells


title: time: Day 16 - stress: Salinity - rep2

tag: growth media


title: E4A03_35

description: CD138 sorted cells


title: E4A03_30

description: CD138 sorted cells


title: time: Day 16 - stress: Salinity - rep1


title: time: Day 16 - stress: Water-Deficit - rep3

source_name: time: Day 16 - stress: Water-Deficit


title: E4A03_31

description: CD138 sorted cells


title: E4A03_25

description: CD138 sorted cells


title: leiomyoma, patient MY53, MED12mut+

description: Leiomyoma gene expression data from patient MY53, MED12mut+

source_name: leiomyoma, patient MY53, MED12mut+


title: E4A03_26

description: CD138 sorted cells


title: E4A03_28

description: CD138 sorted cells


title: time: Day 16 - stress: Water-Deficit - rep2


title: E4A03_24

description: CD138 sorted cells


title: myometrium, patient MY31, MED12wt

description: Myometrium gene expression data from patient MY31, MED12wt

source_name: myometrium, patient MY31, MED12wt

value: myometrium

value: wt


title: E4A03_23

description: CD138 sorted cells


title: time: Day 16 - stress: Control - rep3

source_name: time: Day 16 - stress: Control


title: time: Day 16 - stress: Control - rep2


title: time: Day 16 - stress: Water-Deficit - rep1


title: myometrium, patient MY29, MED12wt

description: Myometrium gene expression data from patient MY29, MED12wt

source_name: myometrium, patient MY29, MED12wt


title: myometrium, patient MY52, MED12wt

description: Myometrium gene expression data from patient MY52, MED12wt

source_name: myometrium, patient MY52, MED12wt


title: myometrium, patient M32, MED12wt

description: Myometrium gene expression data from patient M32, MED12wt

source_name: myometrium, patient M32, MED12wt


title: E4A03_22

description: CD138 sorted cells

source_name: Primary myeloma cells


title: E4A03_18

description: CD138 sorted cells


title: E4A03_17

description: CD138 sorted cells


title: E4A03_20

description: CD138 sorted cells


title: E4A03_19

description: CD138 sorted cells


title: myometrium, patient MY30, MED12wt

description: Myometrium gene expression data from patient MY30, MED12wt

source_name: myometrium, patient MY30, MED12wt


title: E4A03_16

description: CD138 sorted cells


title: E4A03_21

description: CD138 sorted cells


title: E4A03_15

description: CD138 sorted cells


title: time: Day 16 - stress: Control - rep1


title: time: Day 12 - stress: Salinity - rep3

source_name: time: Day 12 - stress: Salinity


title: E4A03_13

description: CD138 sorted cells


title: E4A03_29

description: CD138 sorted cells


title: myometrium, patient MY33, MED12wt

description: Myometrium gene expression data from patient MY33, MED12wt

source_name: myometrium, patient MY33, MED12wt


title: time: Day 12 - stress: Salinity - rep2


title: E4A03_11

description: CD138 sorted cells


title: E4A03_12

description: CD138 sorted cells


title: E4A03_14

description: CD138 sorted cells


title: myometrium, patient MY65, MED12wt

description: Myometrium gene expression data from patient MY65, MED12wt

source_name: myometrium, patient MY65, MED12wt


title: time: Day 12 - stress: Salinity - rep1


title: myometrium, patient MY64, MED12wt

description: Myometrium gene expression data from patient MY64, MED12wt

source_name: myometrium, patient MY64, MED12wt


title: time: Day 12 - stress: Water-Deficit - rep1

source_name: time: Day 12 - stress: Water-Deficit


title: time: Day 12 - stress: Water-Deficit - rep2


title: E4A03_10

description: CD138 sorted cells


title: E4A03_8

description: CD138 sorted cells


title: E4A03_9

description: CD138 sorted cells


title: E4A03_5

description: CD138 sorted cells


title: time: Day 12 - stress: Water-Deficit - rep3


title: myometrium, patient M70, MED12wt

description: Myometrium gene expression data from patient M70, MED12wt

source_name: myometrium, patient M70, MED12wt


title: time: Day 12 - stress: Control - rep2

source_name: time: Day 12 - stress: Control


title: myometrium, patient MY53, MED12wt

description: Myometrium gene expression data from patient MY53, MED12wt

source_name: myometrium, patient MY53, MED12wt


title: E4A03_3

description: CD138 sorted cells


title: time: Day 12 - stress: Control - rep3


title: E4A03_6

description: CD138 sorted cells


title: E4A03_2

description: CD138 sorted cells


title: E4A03_7

description: CD138 sorted cells


title: E4A03_4

description: CD138 sorted cells


title: E4A03_1

description: CD138 sorted cells


title: time: Day 12 - stress: Control - rep1


title: time: Day 8 - stress: Salinity - rep2

source_name: time: Day 8 - stress: Salinity


title: Expression data of LM-187

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

institute: University of Tokyo

description: TRAINING, LM-N

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Colorecal Cancer, Patient_187

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturerüfs instructions.

tag: Tissue

value: Colorecal Cancer


title: Expression data of LM-188

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_188


title: Expression data of LM-190

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_190


title: time: Day 8 - stress: Salinity - rep3


title: time: Day 8 - stress: Salinity - rep1


title: Expression data of LM-189

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_189


title: Expression data of LM-181

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_181


title: Expression data of LM-185

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_185


title: Expression data of LM-186

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_186


title: Expression data of LM-182

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_182


title: Expression data of LM-183

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_183


title: Expression data of LM-178

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_178


title: Expression data of LM-180

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_180


title: Expression data of LM-179

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_179


title: E4A03_32

description: CD138 sorted cells

source_name: Primary myeloma cells


title: time: Day 8 - stress: Water-Deficit - rep1

source_name: time: Day 8 - stress: Water-Deficit


title: time: Day 8 - stress: Water-Deficit - rep2


title: 6 weeks vs harvest fruit Royal Glory

city: Legnaro

first: claudio

last: Bonghi

state: Padova

address: Viale dell'UNiversità, 16

country: Italy

institute: University of Padova

description: Analysis used harvest fruit+1 day at room temperature RNA as control samples for comparison to the experimental samples taken after 6weeks at O°C + 1 day at room temperature.

hyb_protocol: Pre-hybridisations were carried out by soaking whole glass slides in a solution containing 5X SSC, 0.1% SDS, 5X Denhardt’s solution and 100ng/μL DNA carrier at 48°C for at least 2 h. Then the slides were washed once with a 0.2X SSC solution and dried by centrifuging for 4 min at 1000 rpm.  Hybridisations were carried out in 250 µL of hybridisation solution (5X SSC, 0.1% SDS, 25% formamide) containing 90-100 pmol of Cy3- and Cy5-labelled target cDNAs. The hybridisation solution was kept in place by means of a microarray gene frame (ABgene, UK), while the glass slides were placed in a hybridisation chamber (HybChamber, by Genomic Solutions, USA) kept on a rotary oven for at least 36 h. Then the slides were briefly rinsed with 1X SSC 0.1% SDS and washed once the same solution for 5 min. Three additional washes (one with 0.2XSSC 0.1% SDS and two with 0.2X SSC, for 5 min each) at room temperature were performed before drying the glass slides with a brief centrifugation. The probe design and these hybridisation/washing conditions allow the detection of specific genes even within gene families.

scan_protocol: The microarray was scanned with a two channel confocal microarray scanner (ScanArray® Lite, Perkin Elmer, USA) using its dedicated software (ScanArray Express 3.0.0., Perkin Elmer). The laser power and the photomultiplier tube (PMT) were set between 75 and 85 % of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing: Software from the TM4 (www.tm4.org) package developed at TIGR (www.tigr.org, Saeed et al., 2003) was used to analyze microarray data. Images were processed using the Spotfinder 2.2.3. software by means of the Otsu algorithm. Spots were also visually examined to delete the non-uniform ones. The expression data extracted by Spotfinder were normalized by MIDAS 2.18 using the LOWESS (Locally Weighted Regression Scatter Plot Smoothing, Cleveland, 1979) algorithm with the “block mode”. Normalized split data were loaded in MeV 4.3 and subjected to SAM (Significance Analysis of Microarrays, Tusher et al., 2001) analyses. Since each comparison was repeated at least twice, and a “percentage cutoff filter”, set to 75%, was used to eliminate those gene with less than 3 data points, there were at least 3 values for each gene to be used in the SAM analysis. Lists of clones with significant changes in expression were identified at delta values that gave a false discovery rate (FDR) of about 5%.

organism: Prunus persica

source_name: fruit stored for 6 weeks at 0° plus 1 day at room temperature

label_protocol: Total RNA (20 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dyes: the red-fluorescent cyanine5 (Cy5) and the green-fluorescent cyanine3 (Cy3) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Fruit material from the cultivars ‘Royal Glory’ and ‘Morettini No 2’ was used in the current study. ‘Royal Glory’ fruit are characterized by high tissue firmness retention that can fully ripen on the tree while still retaining satisfactory firmness and acceptable quality attributes after harvest or after removal from cold storage, without incidence of CI symptoms, while ‘Morettini No 2’ fruit are characterized by low tissue firmness and high susceptibility to physiological disorders (internal breakdown and flesh wooliness) after extended cold storage (Manganaris et al., 2008a). Fruit of both cultivars were collected during the last developmental stages, corresponding to 70, 77 and 84 days after full bloom (DAFB), respectively. These stages correspond to 4, 3 and 2 weeks before harvest, respectively. Fruit harvested at commercially mature stage, according to fruit size and skin background colour, were separated into three 30-fruit lots.

extract_protocol: Frozen fruit (3 g) was ground in liquid nitrogen to a fine powder and total RNA was extracted as described by Ruperti and co-workers (Physiologia. Plantarum 111, 336-344). Fifty μg of total RNA were treated with 10 units of RQ1 RNase-Free DNAse (Promega) and 1 unit of RNAguard (RNase INHIBITOR) (Amersham) for 30 min, and then purified by phenol-chlorophorm according to the manufacturer’s instructions. The concentration of RNA was quantified by measuring the absorbance at 260 nm and its integrity was checked electrophoretically on agarose gels.

treatment_protocol: One lot of fruit was allowed to ripen at room temperature (25°C) and fruit mesocarp (wedged-shape slices) was removed after 1, 3 and 5 days, respectively. The other lots were subjected to cold storage (0°C, R.H. 95%) for 4 and 6 weeks and mesocarp was sampled after removal from cold storage plus 1 day at room temperature. For each of the examined cultivars a common reference design was followed by using 0 weeks of cold storage plus 1 day of shelf life as a reference. Comparisons were carried out between (a) after harvest + 1 day of shelf life vs 4 weeks of cold storage + 1 day of shelf life and (b) after harvest + 1 day of shelf life vs 6 weeks + 1 day of shelf life. At least three biological replicates were created, repeating three times the same combination of targets of which one was a dye swap (in order to increase accuracy and to correct for dye-related differences).

tag: cultivar

value: Royal Glory

source_name: fruit stored for 0 weeks at 0° plus 1 day at room temperature

tag: tag


title: 6 weeks vs harvest fruit Morettini N°2

value: Morettini N°2


title: 4 weeks vs harvest fruit Royal Glory

description: Analysis used harvest fruit+1 day at room temperature RNA as control samples for comparison to the experimental samples taken after 4weeks at O°C + 1 day at room temperature.

source_name: fruit stored for 4 weeks at 0° plus 1 day at room temperature


title: Expression data of LM-184

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_184


title: Expression data of LM-177

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_177


title: Expression data of LM-174

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_174


title: E4A03_27

description: CD138 sorted cells


title: Expression data of LM-175

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_175


title: time: Day 8 - stress: Water-Deficit - rep3

description: Development stage: [2-year-old cuttings].  Part of organism: [Shoot tips to 4th leaf including tendrils, stem, leaves and vegetative apex].


title: Expression data of LM-176

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_176


title: 4 weeks vs harvest fruit Morettini N°2


title: time: Day 8 - stress: Control - rep2

source_name: time: Day 8 - stress: Control


title: AVIC sample#1 treated with DMSO

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description: Gene expression data from DMSO treated mouse replicate 1

hyb_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

scan_protocol: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

data_processing: Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA).  Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.

source_name: aortic valve cells treated with DMSO

label_protocol: Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

growth_protocol: Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin.  Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA.  AVICs between passage 3 and 8 were used for experiments.  Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.

treatment_protocol: Not applicable.

tag: strain

value: Sprague-Dawley

value: aortic valve interstitial cells


title: time: Day 8 - stress: Control - rep3


title: time: Day 8 - stress: Control - rep1


title: Expression data of LM-171

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_171


title: Expression data of LM-172

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_172


title: Expression data of LM-173

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_173


title: Expression data of LM-170

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_170


title: leiomyoma, patient M70, MED12mut+

description: Leiomyoma gene expression data from patient M70, MED12mut+

source_name: leiomyoma, patient M70, MED12mut+

tag: tissue

value: leiomyoma

value: mut+


title: AVIC sample#3 treated with DMSO

description: Gene expression data from DMSO treated mouse replicate 3


title: Expression data of LM-168

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_168


title: Expression data of LM-169

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_169


title: Expression data of LM-167

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_167


title: time: Day 4 - stress: Salinity - rep3

source_name: time: Day 4 - stress: Salinity


title: AVIC sample#2 treated with DAPT

description: Gene expression data from DAPT treated mouse replicate 2

source_name: aortic valve cells treated with DAPT


title: AVIC sample#2 treated with DMSO

description: Gene expression data from DMSO treated mouse replicate 2


title: Expression data of LM-165

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_165


title: AVIC sample#3 treated with DAPT

description: Gene expression data from DAPT treated mouse replicate 3


title: Expression data of LM-166

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_166


title: time: Day 4 - stress: Salinity - rep2


title: Expression data of LM-164

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_164


title: AVIC sample#1 treated with DAPT

description: Gene expression data from DAPT treated mouse replicate 1


title: Expression data of LM-161

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_161


title: time: Day 4 - stress: Salinity - rep1


title: time: Day 4 - stress: Water-Deficit - rep3

source_name: time: Day 4 - stress: Water-Deficit


title: Expression data of LM-163

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_163


title: Expression data of LM-162

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_162


title: Expression data of LM-160

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_160


title: time: Day 4 - stress: Water-Deficit - rep2


title: Expression data of LM-159

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_159


title: time: Day 4 - stress: Water-Deficit - rep1


title: Expression data of LM-156

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_156


title: time: Day 4 - stress: Control - rep3

source_name: time: Day 4 - stress: Control


title: time: Day 4 - stress: Control - rep2


title: Expression data of LM-158

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_158


title: Expression data of LM-150

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_150


title: time: Day 4 - stress: Control - rep1


title: Klf3 wild-type, splenic CD19+ B cell, rep4

city: Sydney

first: Richard

middle: Carden

last: Pearson

state: NSW

address: Gate 11 Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

hyb_protocol: RNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

scan_protocol: Arrays were scanned following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

data_processing: Data was normalised using RMA, using the Affymetrix Power Tools (v1.8.6)

source_name: Klf3 wildtype, splenic CD19+ B cell

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

growth_protocol: Wildtype and Klf3 knockout mice were housed in standard University of Sydney facilities, under SPF conditions

extract_protocol: RNA extraction was performed using TRI-Reagent, according to manufacturer’s guidelines (Sigma-Aldrich). RNA samples were further purified using RNeasy columns (Qiagen) and by treating with DNase I (Ambion).

treatment_protocol: total CD19+ splenic B cells were positively sorted using Magnetic-Activated Cell Sorting (Miltenyi Biotec)

tag: genotype

value: wildtype

tag: source  tissue

value: spleen

value: CD19+ B cell

tag: replicate

tag: genetic background

value: FVB/NJ


title: Expression data of LM-157

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_157


title: Klf3 knockout, splenic CD19+ B cell, rep4

source_name: Klf3 knockout, splenic CD19+ B cell

value: Klf3 knockout


title: Klf3 knockout, splenic CD19+ B cell, rep1


title: Expression data of LM-151

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_151


title: Klf3 wild-type, splenic CD19+ B cell, rep2


title: Klf3 wild-type, splenic CD19+ B cell, rep3


title: Klf3 knockout, splenic CD19+ B cell, rep3


title: time: Day 0 - stress: Control - rep2

source_name: time: Day 0 - stress: Control


title: Expression data of LM-154

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_154


title: Expression data of LM-152

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_152


title: time: Day 0 - stress: Control - rep3


title: Expression data of LM-153

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_153


title: Expression data of LM-155

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_155


title: Klf3 knockout, splenic CD19+ B cell, rep2


title: time: Day 0 - stress: Control - rep1


title: Expression data of LM-149

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_149


title: Expression data of LM-146

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_146


title: Expression data of LM-144

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_144


title: Klf3 wild-type, splenic CD19+ B cell, rep1


title: Expression data of LM-147

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_147


title: Expression data of LM-148

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_148


title: Expression data of LM-145

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_145


title: Expression data of LM-143

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_143


title: developmental stage: 6 weeks - temperature: Control - rep2

source_name: developmental stage: 6 weeks_temperature: Control

extract_protocol: Rapid Extraction of High Quality RNA from Recalcitrant Tissues

tag: development stages

tag: age

value: 11 years

value: soil


title: developmental stage: 6 weeks - temperature: Control - rep1


title: developmental stage: 6 weeks - temperature: High temperature - rep1

source_name: developmental stage: 6 weeks_temperature: High


title: Expression data of LM-134

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_134


title: Expression data of LM-140

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_140


title: developmental stage: 4 weeks - temperature: Control - rep2

source_name: developmental stage: 4 weeks_temperature: Control


title: Expression data of LM-137

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_137


title: Expression data of LM-136

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_136


title: Expression data of LM-138

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_138

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

tag: treatment response


title: Expression data of LM-135

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_135


title: developmental stage: 4 weeks - temperature: High temperature - rep2

source_name: developmental stage: 4 weeks_temperature: High


title: developmental stage: 6 weeks - temperature: High temperature - rep2


title: Expression data of LM-141

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_141


title: Expression data of LM-131

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_131


title: developmental stage: 4 weeks - temperature: High temperature - rep1


title: Expression data of LM-133

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_133


title: Expression data of LM-139

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_139


title: Expression data of LM-130

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_130


title: developmental stage: 4 weeks - temperature: Control - rep1


title: Expression data of LM-127

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_127


title: Expression data of LM-132

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_132


title: Expression data of LM-126

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_126


title: Expression data of LM-129

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_129


title: developmental stage: 2 weeks - temperature: Control - rep1

source_name: developmental stage: 2 weeks_temperature: Control


title: Expression data of LM-128

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_128


title: Expression data of LM-124

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_124


title: developmental stage: 2 weeks - temperature: Control - rep2


title: developmental stage: 2 weeks - temperature: High temperature - rep2

source_name: developmental stage: 2 weeks_temperature: High


title: Expression data of LM-125

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_125


title: Expression data of LM-121

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_121


title: Expression data of LM-120

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_120


title: Expression data of LM-118

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_118


title: Expression data of LM-115

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_115


title: Expression data of LM-122

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_122


title: Non-treated (control) - time: 3 days - rep2

description: non-treated (control) berry skins cultured in vitro which was sampled at 3 days after the treatment. Repetition 2.

source_name: epicarp_Non-treated_control_3 days

value: PO 0009085 epicarp

value: PO:0001002 fruit development stages

value: 0.3M sucrose solution


title: Expression data of LM-119

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_119

value: Colorecal Cancer


title: Non-treated (control) - time: 3 days - rep1

description: non-treated (Control) berry skins cultured in vitro which was sampled at 3 days after the treatment. Repetition 1.


title: ABA treated - time: 10 days - rep2

description: ABA treated berry skins cultured in vitro which was sampled at 10 days after the treatment. Repetition 2.

source_name: epicarp_ABA treated_10 days

value: 0.3M sucrose solution supplemented with abscisic acid


title: Expression data of LM-117

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_117


title: developmental stage: 2 weeks - temperature: High temperature - rep1


title: Expression data of LM-107

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_107


title: Non-treated (control) - time: 10 days - rep2

description: non-treated (Control) berry skins cultured in vitro which was sampled at 10 days after the treatment. Repetition 2.

source_name: epicarp_Non-treated_control_10 days


title: Non-treated (control) - time: 10 days - rep1

description: non-treated (Control) berry skins cultured in vitro which was sampled at 10 days after the treatment. Repetition 1.


title: Expression data of LM-104

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_104


title: Expression data of LM-110

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_110


title: Expression data of LM-111

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_111


title: Expression data of LM-105

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_105


title: Expression data of LM-113

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_113


title: Expression data of LM-108

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_108


title: Expression data of LM-109

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_109


title: Expression data of LM-103

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_103


title: Expression data of LM-123

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_123


title: ABA treated - time: 3 days - rep2

description: ABA treated berry skins cultured in vitro which was sampled at 3 days after the treatment. Repetition 2.

source_name: epicarp_ABA treated_3 days


title: Expression data of LM-102

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_102


title: Expression data of LM-116

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_116


title: Expression data of LM-112

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_112


title: pathogen infection: Virus-free - developmental stage name: Ripening - rep3

description: Uninfected and GLRaV-3-infected V. vinifera cv. Cabernet Sauvignon grapevines were obtained from the nursery of the Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile. Four uninfected and three virus infected vines were maintained separately in the field under similar growing conditions in the same experimental block. Uninfected plants in this study were defined as plants without any detectable levels of the following thirteen viruses as determined by RT-PCR: Grapevine virus A (GVA), Grapevine virus B (GVB), Grapevine fanleaf virus (GFLV), Grapevine fleck virus (GFkV), Tomato ringspot virus (ToRSV), Grapevine rootstock stem lesion associated virus (GRSLaV) and Grapevine leaf-roll-associated viruses (GLRaV) 1, 2, 3, 4, 5, 6 and 7. In addition, all uninfected plants were free of bacterial, fungal or viroids disease symptoms.

hyb_protocol: Affymetrix GeneChip Hyb

scan_protocol: GeneChip Expression Wash

tag: germplasm name

value: cabernet sauvignon

value: PO 0009001 fruit

value: fruit

value: field soil


title: pathogen infection: Virus-free - developmental stage name: Ripening - rep4


title: ABA treated - time: 10 days - rep1

description: ABA treated berry skins cultured in vitro which was sampled at 10 days after the treatment. Repetition 1.

source_name: epicarp_ABA treated_10 days


title: pathogen infection: Virus-free - developmental stage name: Ripening - rep2


title: Expression data of LM-100

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_100


title: Expression data of LM-097

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_097


title: ABA treated - time: 3 days - rep1

description: ABA treated berry skins cultured in vitro which was sampled at 3 days after the treatment. Repetition 1.


title: Expression data of LM-142

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_142


title: Expression data of LM-098

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_098


title: Expression data of LM-086

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_086


title: Expression data of LM-101

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_101


title: Expression data of LM-096

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_096


title: Expression data of LM-087

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_087


title: Expression data of LM-099

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_099


title: Expression data of LM-093

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_093


title: Expression data of LM-095

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_095


title: Expression data of LM-090

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_090


title: pathogen infection: Virus-free - developmental stage name: Ripening - rep1


title: pathogen infection: GLRaV-3 virus-infected - developmental stage name: Veraison - rep3


title: Expression data of LM-092

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_092


title: Expression data of LM-094

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_094


title: Expression data of LM-089

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_089


title: Expression data of LM-091

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_091


title: pathogen infection: Virus-free - developmental stage name: Veraison - rep1


title: pathogen infection: Virus-free - developmental stage name: Veraison - rep3


title: pathogen infection: GLRaV-3 virus-infected - developmental stage name: Ripening - rep1


title: cup2 null mutant strain replicate 4

city: Taipei

first: Jun-Yi

last: Leu

address: 128 Academia Road, Section 2, Nankang

department: Insititute of Molecular Biolody

country: Taiwan

institute: Academia Sinica

hyb_protocol: The hybridization protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

scan_protocol: Scanned on an Molecular Device AXON 4000B (version GenePix 6.0) and got .gpr files

data_processing: Subtracted background and lowess normalization. Dividing by ch2 (control) was used to log2 transform data (Agilent GeneSpring 7.3.1 software)

source_name: S. cerevisiae cup2 cup2 deletion

label_protocol: The label protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

growth_protocol: Yeast cells were grown in YPD medium with 1mM copper sulfate 1h, at 30 degree.

extract_protocol: The total RNA of the treated samples and the corresponding untreated control samples ( in YPD) was isolated by Qiagen RNeasy Midi Kit (Qiagen, Valencia, CA)

tag: genotype/variation

value: cup2 null mutant strain

value: EC

tag: treatment

value: YPD with 1mM copper sulfate

growth_protocol: Yeast cells were grown in YPD medium 1h, at 30 degree.

value: YPD


title: Expression data of LM-106

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_106


title: pathogen infection: Virus-free - developmental stage name: Veraison - rep4

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

tag: organism part

tag: development stage


title: pathogen infection: GLRaV-3 virus-infected - developmental stage name: Veraison - rep1

tag: growth media


title: pathogen infection: GLRaV-3 virus-infected - developmental stage name: Veraison - rep2


title: pathogen infection: GLRaV-3 virus-infected - developmental stage name: Ripening - rep3


title: pathogen infection: Virus-free - developmental stage name: Veraison - rep2


title: cup2 null mutant strain replicate 3


title: Expression data of LM-083

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_083


title: Expression data of LM-081

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_081

tag: Tissue


title: cup2 null mutant strain replicate 2


title: Expression data of LM-084

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_084


title: Expression data of LM-076

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_076


title: Expression data of LM-088

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_088


title: Expression data of LM-082

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_082


title: cup2 null mutant strain replicate 1


title: Expression data of LM-079

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_079


title: Expression data of LM-085

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_085


title: Expression data of LM-073

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_073


title: Expression data of LM-080

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_080


title: cup2 deletion strain replicate 3

source_name: S. cerevisiae cup2 deletion

value: cup2 deletion strain


title: Expression data of LM-077

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_077


title: Expression data of LM-078

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_078


title: cup2 deletion strain replicate 2


title: Expression data of LM-071

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_071


title: Expression data of LM-075

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_075


title: Expression data of LM-070

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_070


title: Expression data of LM-068

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_068


title: Expression data of LM-067

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_067


title: pathogen infection: GLRaV-3 virus-infected - developmental stage name: Ripening - rep2


title: Expression data of LM-064

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_064


title: Expression data of LM-072

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_072


title: Expression data of LM-065

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_065


title: Expression data of LM-069

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_069


title: Expression data of LM-062

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_062


title: Expression data of LM-063

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_063


title: Expression data of LM-074

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_074


title: Expression data of LM-066

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_066


title: cup2 deletion strain replicate 1


title: wild type strain replicate 4

source_name: S. cerevisiae

value: wild type strain


title: wild type strain replicate 1


title: Expression data of LM-061

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_061


title: Expression data of LM-060

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_060


title: wild type strain replicate 2


title: Expression data of LM-059

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_059


title: Expression data of LM-054

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_054


title: Expression data of LM-057

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_057


title: Expression data of LM-058

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_058


title: wild type strain replicate 3


title: Expression data of LM-055

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_055


title: Expression data of LM-051

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_051


title: Expression data of LM-056

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_056


title: Expression data of LM-052

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_052


title: Expression data of LM-053

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_053


title: Expression data of LM-050

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_050


title: Expression data of LM-049

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_049


title: Expression data of LM-048

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_048


title: Expression data of LM-038

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_038


title: Expression data of LM-042

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_042


title: Expression data of LM-047

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_047


title: Expression data of LM-039

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_039


title: Expression data of LM-044

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_044


title: Expression data of LM-036

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_036


title: Expression data of LM-035

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_035


title: Expression data of LM-046

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_046


title: Expression data of LM-040

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_040


title: Expression data of LM-041

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_041


title: Expression data of LM-043

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_043


title: Expression data of LM-037

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_037


title: Expression data of LM-045

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_045


title: Expression data of LM-032

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_032


title: Expression data of LM-031

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_031


title: Expression data of LM-029

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_029


title: Expression data of LM-033

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_033


title: Expression data of LM-028

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_028


title: Expression data of LM-030

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_030


title: Expression data of LM-034

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_034


title: Expression data of LM-025

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_025


title: L1974

scan_protocol: GeneChip GSC3000 7G Whole-Genome Association System. According to Affymetrix SNP 6.0 standard protocol.

data_processing: Genotyping was performed using the CRLMM algorithm in the Oligo package (Lin, 2008), copy number analysis using the aroma affymetrix package (Bengtsson, 2009), and we constructed LAIR plots to visualize regions of LOH and allelic imbalance (Corver, 2008) in R software (version 2.8). We have used CNCHP log ratio file as an input in Nexus (BioDiscovery, USA) software (version 4.1) and performed HMM based SNP-FASST segmentation for copy number analysis. Copy number inferred after correction with the 5 closest normals.

source_name: Ollier chondrosarcoma grade II

extract_protocol: DNA from fresh frozen tissue was isolated using the Wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.

tag: disease

value: Ollier

value: chondrosarcoma II

tag: tumor location

value: scapula

tag: gender

value: male


title: Expression data of LM-027

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_027


title: Expression data of LM-026

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_026