title: 48h C2 tubes_rep1

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized and summarized using RMA in the lumi package of Bioconductor

source_name: C2C12 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: C2C12 myoblasts were cultured in DMEM supplemented with 10% BCS. If needed, 100% confluent myoblasts were induced to differentiate into myotubes in DMEM supplemented with 2% heat-inactive horse serum, 10ug/ml insulin, and 10ug/ml transferrin

extract_protocol: total RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: cell type

value: myotube

tag: time


title: Female Hypox + 2GH mouse liver/Female Hypox mouse liver/Replicate #1

status: Public on Jan 27 2010

type: RNA

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

description: The RNA expression profile for a Hypox + 2 GH injections adult female liver pool (n = 3) and a Hypox adult female liver pool (n = 2) is given as a normalized ratio. The purpose of this comparison is to highlight differences in female Hypox + treatment with 2 GH injections vs female Hypox mouse liver gene expression.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)

label: Alexa 647

molecule: total RNA

organism: Mus musculus

source_name: Frozen adult mouse liver

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of RNA

tag: strain

value: ICR

tag: treatment

value: Hypophysectomy ('Hypox')

tag: sex

value: Female

tag: tissue

value: Liver

tag: age

value: 8 wks

label: Alexa 555

value: Hypophysectomy ('Hypox') + 2 GH injections


title: Female Hypox + GH (90 min) mouse liver/Female Hypox mouse liver/Replicate #2

description: The RNA expression profile for a Hypox + single GH injection (90 min) adult female liver pool (n = 3) and a Hypox adult female liver pool (n = 2) is given as a normalized ratio. The purpose of this comparison is to highlight differences in female Hypox + GH treatment (90 min) vs female Hypox mouse liver gene expression.

value: Hypophysectomy ('Hypox') + GH injection (90 min)


title: Female Hypox + 2GH mouse liver/Female Hypox mouse liver/Replicate #2


title: 24h C2 tubes_rep2

description: replicate 2

label: biotin


title: T cell_Eur_Male_43y.o._Control_6h_Sample ID 002

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

hyb_protocol: 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x)

scan_protocol: Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing:
LOWESS normalized, background subtracted, batch adjusted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction. Batch effect removal was performed on 8 experimental array batches, matched for race, age, gender and treatment using Distance Weighted Discrimination, in three steps, as follows. Step1 A >80% presence call-filter was applied on all genes. Step 2 Missing expression values were added by KNN imputation (PMID: 11395428). Step 3 Batch effect was removed by the DWD method (PMID: 14693816)  merging batch pairs (1-2), (3-4), (5-6) and (7-8). Step 4; merging batch quadruplets (1-2-3-4) and (5-6-7-8). Step 5; merging all 8 batches together (1-2-3-4-5-6-7-8).
Sample table represents unfiltered data. The filtered data (ie, passed the 75% presence call filter) have been linked as a supplementary file on the Series GSE17952  record.

organism: Homo sapiens

source_name: Magnetic bead-selected CD3+ T cells, untreated control, 6h

label_protocol: 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion).

extract_protocol: Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions

tag: sample type

value: test

tag: race

value: European American

tag: gender

value: M

value: Control

tag: treatment pairs

tag: master set

value: Yes

tag: training set

tag: test set

value: No

tag: repeat set

tag: repeat samples derived from dentical donors

value: B

tag: array batch

value: Batch No.2

source_name: PBMCs, untreated control

value: control


title: Male Hypox mouse liver/Female Hypox mouse liver/Replicate #2

description: The RNA expression profile for a Hypox adult male liver pool (n = 3) and a Hypox adult female liver pool (n = 2) is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in Hypox mouse liver gene expression.

value: Male


title: T cell_Eur_Fem_64y.o._Control_6h_Sample ID 003

value: F

value: Batch No.1


title: 24h C2 tubes_rep1

tag: cell line

tag: cell type

value: myotube


title: 48h C2 tubes_rep2

description: replicate 2

tag: time


title: Arabidopsis bSC2

city: Davis

first: John

middle: J

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

description:
Laser capture microdissected (LCM) general seed coat at the bending cotyledon stage, biological replicate 2
General seed coat collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

hyb_protocol: Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G System.

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis bending cotyledon stage general seed coat captured by LCM

label_protocol: 5 to 6 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50%-70% relative humidity.

extract_protocol: Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.

treatment_protocol: Siliques containing bending cotyledon stage seeds were collected from 38-46 day old plants. Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on sections using a Leica LMD6000 system.

tag: genome/variation

value: general seed coat

tag: developmental stage

value: bending cotyledon stage


title: Female Hypox + GH (90 min) mouse liver/Female Hypox mouse liver/Replicate #1

description: The RNA expression profile for a Hypox + single GH injection (90 min) adult female liver pool (n = 4) and a Hypox adult female liver pool (n = 2) is given as a normalized ratio. The purpose of this comparison is to highlight differences in female Hypox + GH treatment (90 min) vs female Hypox mouse liver gene expression.

tag: strain

value: ICR

tag: treatment

value: Hypophysectomy ('Hypox')

tag: sex

value: Female

tag: tissue

value: Liver

value: 8 wks


title: Female Hypox + GH (30 min) mouse liver/Female Hypox mouse liver/Replicate #2

description: The RNA expression profile for a Hypox + single GH injection (30 min) adult female liver pool (n = 3) and a Hypox adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in female Hypox + GH treatment (30 min) vs female Hypox mouse liver gene expression.

tag: age

value: Hypophysectomy ('Hypox') + GH injection (30 min)


title: Male Hypox mouse liver/Female Hypox mouse liver/Replicate #1

description: The RNA expression profile for a Hypox adult male liver pool (n = 3) and a Hypox adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in Hypox mouse liver gene expression.


title: 48h C2 tubes_rep3

description: replicate 3


title: 24h C2 tubes_rep3

description: replicate 3


title: T cell_Afr_Male_39y.o._Control_6h_Sample ID 020

tag: sample type

value: test

tag: race

value: African American

tag: gender

value: M

value: Control

tag: treatment pairs

value: Yes

value: J


title: Female Hypox + GH (30 min) mouse liver/Female Hypox mouse liver/Replicate #1

description: The RNA expression profile for a Hypox + single GH injection (30 min) adult female liver pool (n = 4) and a Hypox adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in female Hypox + GH treatment (30 min) vs female Hypox mouse liver gene expression.


title: T cell_Afr_Male_41y.o._Control_6h_Sample ID 001

tag: master set

value: No

tag: training set

tag: test set

tag: repeat set

value: A

value: Batch No.2

value: control


title: T cell_Afr_Male_41y.o._IFNa_6h_Sample ID 001

source_name: Magnetic bead-selected CD3+ T cells, IFNa-treated, 6h

value: IFNa

tag: repeat samples derived from dentical donors

tag: array batch


title: 50% C2 blasts_rep3

description: replicate 3

tag: cell line

tag: cell type

value: myoblast

tag: confluence


title: Male Hypox + 2GH mouse liver/Male Hypox mouse liver/Replicate #2

description: The RNA expression profile for a Hypox + 2 GH injections adult male liver pool (n = 4) and a Hypox adult male liver pool (n = 5) is given as a normalized ratio. The purpose of this comparison is to highlight differences in male Hypox + treatment with 2 GH injections vs male Hypox mouse liver gene expression.

tag: strain

value: ICR

tag: treatment

value: Hypophysectomy ('Hypox')

value: Male

value: Hypophysectomy ('Hypox') + 2 GH injections


title: 50% C2 blasts_rep2

description: replicate 2


title: CONT_CD14_14

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

hyb_protocol: Biotin-labeled cRNA was then fragmented at 94 C for 35 min with 5X fragmentation buffer  (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C

scan_protocol: Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).

data_processing: Affymetrix Microarray Suite version 5.0

source_name: peripheral blood of control donor

label_protocol: Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24  primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).

growth_protocol: Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed

extract_protocol: Fibroblasts and monocytes were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA).  Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA).  cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY).  Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.

value: peripheral blood monocytes

tag: disease

value: normal


title: 95% C2 blasts_rep2

description: replicate 2


title: Arabidopsis bSC1

description:
Laser capture microdissected (LCM) general seed coat at the bending cotyledon stage, biological replicate 1
General seed coat collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

tag: genome/variation

value: general seed coat

tag: developmental stage

value: bending cotyledon stage


title: Female Hypox mouse liver/Female intact mouse liver comparison/Replicate #1

description: The RNA expression profile for a Hypox adult female liver pool (n = 3) and an intact adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in female Hypox vs intact female mouse liver gene expression.

value: Untreated

tag: sex

value: Female

tag: tissue

value: Liver

tag: age

value: 8 wks


title: Arabidopsis bCZE1-2

description:
Laser capture microdissected (LCM) chalazal endosperm at the bending cotyledon stage, biological replicate 1
Chalazal endosperm collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis bending cotyledon stage chalazal endosperm captured by LCM

value: chalazal endosperm


title: Arabidopsis bCZE2-2

description:
Laser capture microdissected (LCM) chalazal endosperm at the bending cotyledon stage, biological replicate 2
Chalazal endosperm collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.


title: 50% C2 blasts_rep1


title: 95% C2 blasts_rep1


title: Male Hypox + 2GH mouse liver/Male Hypox mouse liver/Replicate #1


title: CONT_CD14_1


title: Male Hypox + GH (90 min) mouse liver/Male Hypox mouse liver/Replicate #2

description: The RNA expression profile for a Hypox + single GH injection (90 min) adult male liver pool (n = 3) and a Hypox adult male liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in male Hypox + GH treatment (90 min) vs male Hypox mouse liver gene expression.

value: Hypophysectomy ('Hypox') + GH injection (90 min)


title: Female Hypox mouse liver/Female intact mouse liver comparison/Replicate #2

description: The RNA expression profile for a Hypox adult female liver pool (n = 2) and an intact adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in female Hypox vs intact female mouse liver gene expression.


title: Male Hypox + GH (90 min) mouse liver/Male Hypox mouse liver/Replicate #1

description: The RNA expression profile for a Hypox + single GH injection (90 min) adult male liver pool (n = 4) and a Hypox adult male liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in male Hypox + GH treatment (90 min) vs male Hypox mouse liver gene expression.


title: CONT_CD14_2


title: Arabidopsis bCZSC2

description:
Laser capture microdissected (LCM) chalazal seed coat at the bending cotyledon stage, biological replicate 2
Chalazal seed coat collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis bending cotyledon stage chalazal seed coat captured by LCM

value: chalazal seed coat


title: CONT_CD14_3


title: RAW264.7-10ug/ml AF-SWCNT-24hrs-replicate3

city: Beijing

first: Bin

last: Wan

address: 18 shuangqing road, Haidian District

country: China

institute: Research centre for eco-environmental sciences, CAS

description: no

hyb_protocol: cDNA probes were dissolved in 3×SSC( 0.2%SDS, 5×Denhart’s, 25%Formamide), and hybrized for overnight at 42℃. after that, the arrays were washed for 5min with solution (0.2% SDS，2×SSC) at 42℃, followed by 5 min wash with 0.2×SSC at Room Temperature。The arrays were then centrifuged to dry for scanning.

scan_protocol: Arrays were scanned with a confocal LuxScan 10KA scanner (CapitalBio), and the data of obtained images were extracted with LuxScan 3.0 software (CapitalBio).

data_processing: A space and intensity-dependent normalization based on a LOWESS program was employed. Genes with the signal intensity (Cy3 or Cy5)>800 were regarded as the expressed ones. If there were only one valid observation for a gene within a condition, that datum was disregarded for analysis.

source_name: cy5 labelled treatment sample replicate3

label_protocol: Five micrograms DNase-treated total RNA was prepared and fluorescent dye (Cy5-dCTP)-labeled cDNA, produced through Eberwine’s linear RNA amplification method (Van Gelder et al., 1990) and subsequent enzymatic reaction, were then hybridized to an array.

extract_protocol: We extracted total cellular RNA from each sample using Trizol reagent according to the mannual provided by manufactor(Invitrogen) . The quality of purified total RNA was assessed by Nanodrop 1000 (Thermo Fisher Scientific Inc., MA, USA), and quantity was assessed by absorbance at 260 nm.

treatment_protocol: 10ug/ml AF-SWCNTs for 24 hrs.

source_name: cy3 labelled control sample replicate3

label_protocol: Five micrograms DNase-treated total RNA was prepared and fluorescent dye (Cy3-dCTP)-labeled cDNA, produced through Eberwine’s linear RNA amplification method (Van Gelder et al., 1990) and subsequent enzymatic reaction, were then hybridized to an array.

treatment_protocol: incubated 24 hours without any treatment.


title: RAW264.7-10ug/ml AF-SWCNT-24hrs-replicate2

description: no

source_name: cy5 labelled treatment sample replicate2

source_name: cy3 labelled control sample replicate2


title: CONT_FB_18

source_name: primary FB cultures from control donor

growth_protocol: Skin biopsy was obtained from CHM affected patients and an age-matched healthy control group and incubated for 10-14 days until fibroblasts started to attach to the plate.Cells at passage 2-7 were used for microarrays.

value: primary fibroblasts cultures


title: Male Hypox + GH (30 min) mouse liver/Male Hypox mouse liver/Replicate #2

description: The RNA expression profile for a Hypox + single GH injection (30 min) adult male liver pool (n = 3) and a Hypox adult male liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in male Hypox + GH treatment (30 min) vs male Hypox mouse liver gene expression.

value: Hypophysectomy ('Hypox') + GH injection (30 min)


title: CHM_CD14_9

source_name: peripheral blood of CHM patient

value: choroideremia


title: Male Hypox + GH (30 min) mouse liver/Male Hypox mouse liver/Replicate #1

description: The RNA expression profile for a Hypox + single GH injection (30 min) adult male liver pool (n = 4) and a Hypox adult male liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in male Hypox + GH treatment (30 min) vs male Hypox mouse liver gene expression.

value: ICR

value: Hypophysectomy ('Hypox')


title: CHM_CD14_29


title: RAW264.7-1ug/ml AF-SWCNT-24hrs-replicate3

description: no

treatment_protocol: 1ug/ml AF-SWCNTs for 24 hrs.


title: CHM_CD14_7


title: TUB-GFP IP, biological replicate 4

type: other

city: Madison

first: Judith

last: Kimble

state: WI

address: 433 Babcock Drive

department: HHMI / Biochemistry

institute: University of Wisconsin-Madison

description:
RNA from GFP immunoprecipitation
mRNA associated with TUBULIN-GFP

hyb_protocol: 100% or up to 10 µg of FBF-GFP IP amplified RNA (aRNA) and the same amount of TUB-GFP IP aRNA by volume was hybridized in the GeneChip 640 Hybridization Oven (Affymetrix), and arrays post-processed in GeneChip Fluidics Station 450 (Affymetrix) .

scan_protocol: Arrays were scanned using GC3000 G7 scanner (Affymetrix)

data_processing: The data were extracted using GeneChip Operating Software (GCOS) v.1.4, and unscaled signal intensities were exported to Excel (Microsoft) and converted into log2 ratios (FBF/TUB).  Data were normalized by median centering of the control AFFX features.

molecule: other

organism: Caenorhabditis elegans

source_name: C. elegans adult extracts used to immunoprecipitate TUB-GFP

label_protocol: Biotinylated cRNAs were prepared using the MessageAmp Biotin-II Enhanced kit (Ambion), according the manufacturer's instructions

growth_protocol: Synchronized adults were grown at 20C until 24 hours after L4 stage.

extract_protocol: Trizol followed by Rneasy Minelute columns, following the manufacturer's instructions.

treatment_protocol: Adults were washed extensively and used to prepare extracts

value: Ppie-1::TUBULIN-GFP (strain AZ244)


title: FBF-GFP IP, biological replicate 4

description:
RNA from GFP immunoprecipitation
mRNA associated with FBF-GFP

source_name: C. elegans adult extracts used to immunoprecipitate FBF-GFP

value: Ppie-1::FBF-1-GFP (strain JK4198)


title: RAW264.7-10ug/ml AF-SWCNT-24hrs-replicate1

description: no

source_name: cy5 labelled treatment sample replicate1

source_name: cy3 labelled control sample replicate1


title: KB1-VC+MeOH versus MeOH-rep6

city: Toronto

first: Elizabeth

middle: A

last: Edwards

address: 200 College st.

department: Department of Chemical Engineering and Applied Chemistry

country: Canada

institute: University of toronto

description: 19,000 spot Custom shotgun metagenome microarrays constructed from short insert gDNA libraries of dechlorinating microbial community KB1.

hyb_protocol: The cDNA was then combined with 80 μL of hybridization solution (80 μL DIG Easy Hyb (Roche, Indianapolis, IN), 4 uL calf thymus DNA (SIGMA, 10 mg/mL) and 4 uL yeast tRNA (Invitrogen, 10 mg/mL).  After mixing the hybridization mixture was heated up to 65 0 C for 3 minutes and then allowed to cool to room temperature before being applied to the slide.  The slide was then place in a hybridization chamber and placed in a 37 0 C incubator for 16-18 hours.

scan_protocol: After removing the coverslip in 1X SSC, two 15 minute washes were carried out at 55 0 C in 1XSSC/0.1%SDS each with intermittent agitation.  Then an additional wash was performed in 0.1XSSC/0.1%SDS.  The slides were then rinsed twice at room temperature in 0.1XSSC.  The slides were subsequently dried by centrifugation at 600 rpm for 5 minutes in a slide box lined with Whatman paper and then immediately scanned with an Axon scanner using GenePix Pro software

data_processing: Data analysis was performed in the R programming language using programs available from Bioconductor such as Linear Analysis of Microarrays (Limma), gplots and other graphing programs.  The mean values from each channel were log2 transformed and normalizedwithin each array using the LOWESS algorithm to remove intensity dependent effects. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios for each slide.  Cy3/Cy5 ratios were then normalized between arrays using the 'scale' method that log ratios were scaled to have the same median-absolute-deviation across the arrays .  Then linear modell to average, and bayesian to assess statistical significance. and biological repeats (seperate chemostat runs)with all replicates combined. Data was compiled from two biological repelicates, totalling six replicates all comparing VC+MeOH to MeOH-only.

organism: dechlorinating enrichment culture KB-1

source_name: VC + Methanol - March experiment

label_protocol: The RNA was labelled using an indirect method in which amino allyl-dUTPs were incorporated during reverse transcription (RT), and then monoreactive Cyanine dyes were coupled to the aminoallyl cDNA in a separate reaction.  First strand cDNA synthesis was carried out using 10-20 μg of total RNA, and 10 ng control RNA (Arabadopsis chlorophyll synthetase gene).  The Cy3 or Cy5 labelled cDNA was purified then quantified using the NanoDrop ND-1000 to ensure that an appropriate amount of dye was incorporated (>100 pmoles) at an appropriate frequency (25-50 nucleotides per dye molecules).  The labeled-cDNA was then hybridized to the slide at 37 0 C for 16-18 hours.  The slides were then washed, dried and scanned with an Axon scanner using GenePix Pro software.

growth_protocol: Experiments were set up to examine gene expression in KB1 during vinyl chloride degradation using a robust and stable KB1 enrichment that had been maintained on TCE and MeOH for 5 years (T3MP1).  This culture routinely degrades 200 µmoles of TCE to ethene every week.  For each experiment the T3MP1 culture was purged with N2/CO2 (80:20 vol%) to remove trace chlorinated compounds and left to starve for four days to remove mRNA.  Subsequently, 1.2 L of culture was split into two equal treatments of 600 mL in 1L bottles (Pyrex, VWR, Mississauga, ON) in an anaerobic glovebox (Coy Laboratory products, Grass Lake, MI).  Into one treatment 5 mL (200 µmoles) of vinyl chloride was added as the electron acceptor and 15 µL (370 µmoles) methanol as the electron donor (VC+MeOH treatment).  In the other treatment only the electron donor methanol was added (MeOH only).  For the first set of arrays, RNA was extracted from the MeOH only and VC+MeOH treatments after 3 hours when 35 µmoles of ethene had been produced in the VC+MeOH treatment.  A second set of experiments was performed a month later with the same set-up.  For these, RNA was extracted after 3.5 hours when 50 µmoles of ethene had been produced in the VC+MeOH treatment.  Within each biological set there were dye-switched duplicates, and technical replicates resulting in 6 arrays comparing the same treatments.

extract_protocol: For RNA extraction, 50 ml samples were withdrawn from the culture bottles inside an anaerobic chamber.  After lysis with SDS and bead beating RNA was extracted using an ice-cold acid-phenol:chloroform:isoamyl alcohol method(Waller et al., 2005).  The RNA solution was further purified using an RNeasy spin column (Qiagen,Valencia, California), and contaminating DNA was removed using the DNA-free kit (Ambion, Austin, TX).  The quantity of the RNA was assessed using a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and the quality was assessed by electrophoresis on a 1% agarose gel or using the 2100 Bioanalyzer (Agilent Technologies).

tag: strain description

value: Mixed microbial community containing Dehalococcoides, Geobacter,

source_name: Methanol only - March experiment


title: KB1-VC+MeOH versus MeOH-rep5


title: TUB-GFP IP, biological replicate 3


title: Male mouse liver/Female mouse liver comparison/Replicate #1

description: The RNA expression profile for an intact adult male liver pool (n = 4) and an intact adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in intact mouse liver gene expression.

source_name: Frozen adult mouse liver

value: Male


title: FBF-GFP IP, biological replicate 3


title: Male Hypox mouse liver/Male intact mouse liver comparison/Replicate #2

description: The RNA expression profile for a Hypox adult male liver pool (n = 3) and an intact adult male liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight differences in male Hypox vs intact male mouse liver gene expression.


title: Male mouse liver/Female mouse liver comparison/Replicate #2

description: The RNA expression profile for an intact adult male liver pool (n = 3) and an intact adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in intact mouse liver gene expression.


title: CHM_FB_26

source_name: primary FB cultures from CHM patients


title: RAW264.7-1ug/ml AF-SWCNT-24hrs-replicate2

description: no


title: CHM_CD14_15

value: peripheral blood monocytes


title: TUB-GFP IP, biological replicate 2


title: RAW264.7-1ug/ml AF-SWCNT-24hrs-replicate1

description: no


title: CHM_FB_19


title: Male Hypox mouse liver/Male intact mouse liver comparison/Replicate #1

description: The RNA expression profile for a Hypox adult male liver pool (n = 3) and an intact adult male liver pool (n = 4) is given as a normalized ratio. The purpose of this comparison is to highlight differences in male Hypox vs intact male mouse liver gene expression.

value: Untreated


title: CHM_FB_21


title: KB1-VC+MeOH versus MeOH-rep4

source_name: VC + Methanol - February batch

source_name: Methanol only - February experiment


title: FBF-GFP IP, biological replicate 2


title: 95% C2 blasts_rep3

description: replicate 3

source_name: C2C12 cell line

value: myoblast


title: FBF-GFP IP, biological replicate 1


title: TUB-GFP IP, biological replicate 1


title: KB1-VC+MeOH versus MeOH-rep3


title: KB1-VC+MeOH versus MeOH-rep1

source_name: Methanol only - February batch

source_name: VC + Methanol - February experiment


title: CHM_CD14_13


title: KB1-VC+MeOH versus MeOH-rep2


title: imiquimod4

status: Public on Jan 26 2010

city: Seattle

first: Lynn

middle: M

last: Amon

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

description: replicate 4

hyb_protocol: biotin-labeled cRNA were hybridized to Sentrix Mouse Ref-8 Expression Bead Chip v1.0a

data_processing: Trimmed mean intensities were log2 transformed and quantile normalized using affy package from Bioconductor.org.

source_name: spontaneous mammary tumor

label_protocol: labeled cRNA were generated using the Illumina TotalPrep RNA Amplification kit from Ambion (cat# IL1791)

growth_protocol: spontaneous tumors in neu transgenic mice

extract_protocol: RNA was extracted from tumors using RNAqueous4PCR kit (Ambion)

treatment_protocol: topical imiquimod

value: FVB/N-TgN (MMTVneu)-202Mul

value: imiquimod cream


title: control3

description: replicate 3

value: control cream


title: control2

description: replicate 2


title: control4

description: replicate 4


title: imiquimod2

description: replicate 2


title: imiquimod1

description: replicate 1


title: CHM_CD14_10

growth_protocol: Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed and separated using AutoMacs magnetic sorting to CD14+ and CD14- populations.


title: miR-145 target genes in TE13

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

description: miRNA treated 72hr

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: control miRNA transfected TE13

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

source_name: miR-145 transfected TE13


title: mssa_time4_rep_5

status: Public on Jan 25 2010

city: Bilthoven

first: Tessa

middle: E

last: Pronk

address: A.v Leeuwenhoeklaan 9

department: GBO

country: Netherlands

institute: RIVM

description: The common reference was created by pooling 400 ng Cy5-labeled RNA sample of each time point of each growth curve, 35 points in total.

hyb_protocol: Labeled cDNA was hybridized according to manufacturer’s protocol (Agilent Technologies). A total of 300 ng Cy3-labeled cDNA and 300 ng Cy5-labeled common reference was mixed, 10x Blocking agent was added to a total volume of 25 µl. The mixture was heated to 95°C for 3 min, followed by addition of 2x hybridization buffer to a volume of 50 µl. A total of 40 µl was loaded onto an 8x15k array and hybridized for 18 hours at 65°C and 20 rpm in a dedicated hybridization oven (Agilent Technologies). After the hybridization the arrays were washed in buffer 1 for 1 min at RT, then 5 min in wash buffer 1 at RT and finally 1 min in wash buffer 2 at 37°C (Agilent Technologies). Slides were spun for 3 min at 300 rpm to dry and scanned immediately.

scan_protocol: Data was extracted and processed using Feature Extractiontm software (version 9.5.1, Agilent Technologies). Median spot intensities were extracted by Feature Extraction software (version 9.5.1, Agilent Technologies).

data_processing: Processing of the data was performed using R (version 2.7.0) and the Bioconductor MAANOVA package (version 1.10.0). All slides were subjected to a set of quality control checks, i.e. visual inspection of the scans, examination of the consistency among the replicated samples by principal component analysis, testing against criteria for signal to noise ratios, testing for consistent performance of the labelling dyes and visual inspection of pre- and post-normalized data with box and ratio-intensity plots. After log2 transformation, the data were normalized by a LOWESS smoothing procedure to correct for dye bias effects.

organism: Staphylococcus aureus subsp. aureus MSSA476

source_name: common reference

label_protocol: Total RNA was labeled in a one-step labeling with fluorescent dyes by direct labeling. A total of 10 µg RNA was randomly primed with Superscript II reverse transcriptase (Invitrogen) and random hexamers, in a total volume of 30 µl, for 2 h at 42°C with the incorporation of Cy5- or Cy3-dUTP (Agilent Technologies) with a ratio dUTP/dTTP of 3/1, yielding approximately 4 µg labeled cDNA. RNA template was removed by hydrolysis with 3 µl 2.5 M NaOH (Sigma-Aldrich) for 15 min at 70°C. Hydrolysis was stopped by neutralization with 15 µl 2 M MOPS (Sigma-Aldrich) and put on ice. Labeled cDNA was purified using Qia-quick PCR purification kit (Qiagen, Valencia, CA, USA). Incorporation of Cy3 or Cy5 was determined using a NanoDrop ND-1000.

growth_protocol: MSSA476 was grown overnight in Iscove’s Modified Dulbecco’s Medium (IMDM) (Invitrogen, Carlsbad, CA, USA). These overnight cultures were diluted in fresh prewarmed IMDM and grown twice to mid-log phase culture (A660 ~0.5) prior to the growth experiment. The second midlog phase culture was diluted to an A660 of 0.3 with prewarmed IMDM and directly transferred to fresh prewarmed IMDM to obtain an A660 of 0.03. Samples were taken at 1, 2, 3, 4, 5, 6 and 9 h post inoculation (p.i.). A660 was measured and dilutions were plated on sheep blood-agar plates to determine colony forming units (CFUs). Cultures were incubated at 37°C and 180 rpm.

extract_protocol: RNA extraction was performed at room temperature (RT) unless stated otherwise. RNA was purified using the NucleoSpin RNA II total RNA isolation kit (Macherey-Nagel, Düren, Germany) according to manufacturer’s protocol with some adjustments. Bacteria were spun 30 sec at 13000 rpm, immediately resuspended in 350 µl RA1 buffer supplemented with 3.5 µl β-mercaptoethanol (Sigma-Aldrich, Zwijndrecht, The Netherlands) and vortexed vigorously. Resuspended bacteria were added to 0.5 ml 0.1 mm silica beads (Merlin, Breda, The Netherlands), disrupted using a mini-Beadbeater (BioSpec Products, Bartlesville, OK, USA) for 30 sec at 5000 rpm and samples were frozen at -20°C overnight. The samples were thawed slowly and purified. Total RNA was eluted in 60 µl RNase free MilliQ. RNA yield was measured using a NanoDrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and quality was measured using a 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA). Both the RNA integrity number (RIN) and the presence of degradation products were checked.

source_name: sample taken at four hours post inoculation


title: miR-145 target genes in TE2

description: miRNA treated 72hr

source_name: control miRNA transfected TE2

source_name: miR-145 transfected TE2


title: miR-133a target genes in HSC3

description: miRNA treated 72hr

source_name: control miRNA transfected HSC3

source_name: miR-133a transfected HSC3


title: miR-133a target genes in SAS

description: miRNA treated 72hr

source_name: control miRNA transfected SAS

value: SAS

source_name: miR-133a transfected SAS


title: CHM_FB_27

source_name: primary FB cultures from CHM patients


title: mssa_time5_rep_2

treatment_protocol: The common reference was created by pooling 400 ng Cy5-labeled RNA sample of each time point of each growth curve, 35 points in total.

source_name: sample taken at five hours post inoculation


title: mssa_time1_rep_2

source_name: sample taken at one hour post inoculation


title: mssa_time5_rep_3


title: mssa_time2_rep_4

source_name: sample taken at two hours post inoculation


title: mssa_time9_rep_4

source_name: sample taken nine hours post inoculation


title: mssa_time3_rep_4

source_name: sample taken at three hours post inoculation


title: 256 cell H3K27me3

type: genomic

city: Shanghai

first: Yong

last: Zhang

address: 1239 Siping Road

institute: Tongji University

description: 256 cell stage H3K27me3 ChIP-chip

scan_protocol: Probe intensities were extracted using the standard ChIP analysis settings provided in the Nimblescan® software (NimbleGen, Madison WI).

data_processing: Each array was normalized by MA2C. Each probe was assigned a MA2Cscore to reflect the normalized and window averaged log2 ratio of ChIP enrichment over control (see MA2Cscore.wig supplementary file).

molecule: genomic DNA

organism: Danio rerio

source_name: H3K27me3 ChIP DNA from 256 cell stage

label_protocol: ChIP material was amplified using the Sigma GenomePlex Kit performing one round of amplification. Sample labeling, hybridization, washing and scanning were performed as described in the NimbleChip Arrays User’s Guide. All coprecipitated DNA fragments from ChIP experiments were labeled and hybridized to the custom array design using the standard NimbleGen protocol (Madison, WI).

extract_protocol: For each condition, ~200 embryos were carefully staged, dechorionated and fixed in 1.85% formaldehyde for 15 minutes at room temperature. Formaldehyde was quenched by adding glycine to a final concentration of 0.125M. Embryos were rinsed 3 times in ice-cold PBS, immediately resuspended in cell lysis buffer (10mM Tris-HCl pH7.5/10mM NaCl/0.5%NP40) and lysed for 15 min on ice. Nuclei were collected by centrifugation, resuspended in nuclei lysis buffer (50mM Tris-HCl pH7.5/10mM EDTA/1%SDS) and lysed for 10 min on ice. Samples were diluted 3 times in IP dilution buffer (16.7mM Tris-HCl pH7.5/167mM NaCl/1.2mM EDTA/0.01%SDS) and sonicated to obtain fragments of ~500 bp. Triton was added to a final concentration of 0.75% and the lysate was incubated overnight while rotating at 4°C with 50 to 100ul of protein G magnetic Dynabeads (Invitrogen) that had been pre-bound to an excess amount of antibody. Bound complexes were extensively washed with RIPA (50mM HEPES pH7.6/1mM EDTA/0.7%DOC/1%Igepal/0.5MLiCl) and TBS and then eluted from the beads with elution buffer (50mM NaHCO3/1%SDS). Cross-links were reversed o/n at 65°C, RNA degraded by a 30 min RNAseA treatment and DNA purified by QIAquick PCR purification kit (QIAGEN).

value: 256 cell

tag: fraction

value: ChIP (test)

tag: antibody

source_name: H3 ChIP DNA from 256 cell stage

value: ChIP (control)


title: mssa_time2_rep_3


title: mssa_time1_rep_3


title: mssa_time6_rep_4

source_name: sample taken at six hours post inoculation


title: 4hpf H3K4me3 rep2

description: 4hpf stage H3K4me3 ChIP-chip rep2

hyb_protocol: All coprecipitated DNA fragments from ChIP experiments were labeled and hybridized to the custom array design using the standard NimbleGen protocol (Madison, WI).

source_name: H3K4me3 ChIP DNA from 4hpf stage (rep 2)

value: 4hpf (dome/30%)

source_name: H3 ChIP DNA from 4hpf stage


title: 4hpf H3K27me3 rep2

description: 4hpf stage H3K27me3 ChIP-chip rep2

source_name: H3K27me3 ChIP DNA from 4hpf stage (rep 2)


title: mssa_time6_rep_3

source_name: common reference

source_name: sample taken six hours post inoculation


title: 4hpf H3K27me3 rep1

description: 4hpf stage H3K27me3 ChIP-chip rep1

source_name: H3K27me3 ChIP DNA from 4hpf stage (rep 1)


title: 4hpf polII rep1

description: 4hpf stage polII ChIP-chip rep1

source_name: PolII ChIP DNA from 4hpf stage (rep 1)

value: anti-PolII

source_name: Input DNA from 4hpf stage

value: Input


title: mssa_time9_rep_1

source_name: sample taken at 9 hours post inoculation


title: 4hpf H3K36me3 rep1

description: 4hpf stage H3K36me3 ChIP-chip rep1

source_name: H3K36me3 ChIP DNA from 4hpf stage (rep 1)


title: 4hpf polII rep2

description: 4hpf stage polII ChIP-chip rep2

source_name: PolII ChIP DNA from 4hpf stage (rep 2)


title: 256 cell polII

description: 256 cell stage polII ChIP-chip

source_name: PolII ChIP DNA from 256 cell stage

source_name: Input DNA from 256 cell stage


title: 256 cell H3K36me3

description: 256 cell stage H3K36me3 ChIP-chip

source_name: H3K36me3 ChIP DNA from 256 cell stage


title: 256 cell H3K4me3

description: 256 cell stage H3K4me3 ChIP-chip

source_name: H3K4me3 ChIP DNA from 256 cell stage


title: mssa_time3_rep_5

source_name: sample taken at three hours post inoculation


title: 4hpf H3K4me3 rep1

description: 4hpf stage H3K4me3 ChIP-chip rep1

source_name: H3K4me3 ChIP DNA from 4hpf stage (rep 1)


title: mssa_time3_rep_1


title: 4hpf H3K36me3 rep2

description: 4hpf stage H3K36me3 ChIP-chip rep2

source_name: H3K36me3 ChIP DNA from 4hpf stage (rep 2)


title: mssa_time4_rep_3

source_name: sample taken at four hours post inoculation


title: mssa_time3_rep_2


title: mssa_time6_rep_1

source_name: sample taken at six hours post inoculation


title: mssa_time1_rep_4

source_name: common reference

source_name: sample taken at one hour post inoculation


title: mssa_time2_rep_1

source_name: sample taken at two hours after inoculation


title: mssa_time9_rep_2

source_name: sample taken at nine hours post inoculation


title: mssa_time4_rep_4


title: mssa_time5_rep_4

source_name: sample taken at five hours post inoculation


title: mssa_time2_rep_5

source_name: sample taken at two hours post inoculation


title: mssa_time5_rep_1

source_name: sample taken five hours after inoculation


title: control1

description: replicate 1

source_name: spontaneous mammary tumor


title: mssa_time7_rep_3

source_name: sample taken 9 hours post inoculation


title: mssa_time5_rep_5

source_name: sample taken five hours post inoculation


title: mssa_time3_rep_3

source_name: sample taken three hours post inoculation


title: mssa_time2_rep_2

source_name: sample taken two hours post inoculation


title: mssa_time6_rep_2

source_name: sample taken 6 hours after inoculation


title: mssa_time1_rep_1

source_name: sample taken one hour post inoculation


title: mssa_time6_rep_5

source_name: sample taken six hours post inoculation


title: mssa_time1_rep_5

source_name: sample was taken one hour post inoculation


title: wt_3

status: Public on Jan 24 2010

city: Santa Cruz

first: Manny

last: Ares

address: 1125 High St

department: Molecular and Cellular Biology

institute: UCSC

description: mouse quadricep muscle wt cells

hyb_protocol: Targets were hybridized to chips in 7% DMSO solution for 16 hrs overnight at 50. Microarrays were washed, processed with anti-biotin antibodies and streptavidin-phycoerythrin according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix procedures

data_processing: Intensity values from the DNA arrays were normalized using a quantile normalization (Bolstad et al., 2003), and probe set summaries were derived using the Robust Multi-chip Analysis (RMA) procedure (Irizarry et al., 2003a; Irizarry et al., 2003b) with two modifications. The first modification was to remove all probes with 17 or more continuous bases that match to any other mouse transcript in order to minimize cross-hybridization issues. The second modification was to use the mode of the probe intensity values of similar GC content probes for the background estimate of a particular probe.

source_name: quadricep muscle

label_protocol: Total RNA was primed with random hexamers and reverse transcribed. After the reaction was completed, RNA was removed from the reaction by alkaline hydrolysis and the cDNA was purified using Qiagen PCR Quick Purification Kit. A typical reaction started with 5-6ug of total RNA usually yielded ~3ug of cDNA. The cDNA was then fragmented using DNAseI in an empirically controlled reaction that yields DNA fragments of 50-200 bases. This fragmented cDNA was then end labeled using terminal deoxynucleotidyl transferase and "DNA-Labeling-Reagent-1a (DLR-1a)", which is a biotinylated dideoxynucleoside triphosphate.

extract_protocol: Total RNA was extracted using Invitrogen Trizol reagent. RNA samples were quantified using NanoDrop ND-1000 Spectrophotometer.

tag: genotype

value: wildtype


title: arp2 yeast vs arp2 hyphae (replica 2)

status: Public on Jan 23 2010

city: Montréal

first: Elias

last: Epp

address: 1205 Docteur Penfield

department: Biology

institute: McGill University

description: Arrays are organized in 48 sub-arrays containing 280 spots each.

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: arp2 under hyphae conditions (10% FBS, 37°C, 3 hours)

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: RNeasy Mini kit (Qiagen) as described in Epp et al., PLoS Pathogen, 2010 (in press)

treatment_protocol: Overnight cultures grown in YPD media were diluted 1:200 in YPD (yeast conditions) or YPD+10% FBS (hyphae conditions) and placed for three hours at either 30°C (yeast) or 37°C (hyphae).

source_name: arp2 under yeast conditions (30°C, 3 hours)


title: nrg1/arp2 hyphae vs arp2 hyphae (replica 2)

source_name: nrg1/arp2 under hyphae conditions (10% FBS, 37°C, 3 hours)


title: nrg1/arp2 hyphae vs arp2 hyphae (replica 1)


title: nrg1/arp2 hyphae vs arp2 hyphae (replica 3)


title: mssa_time4_rep_2

source_name: common reference

source_name: mssa taken 4hours post inoculation


title: wt_4

description: mouse quadricep muscle wt cells


title: arp2 yeast vs arp2 hyphae (replica 3)


title: wt_2

description: mouse quadricep muscle wt cells


title: HSA8

description: mouse quadricep muscle HSA cells

value: HSALR


title: mssa_time9_rep_5

source_name: sample taken nine hours post inoculation


title: mssa_time4_rep_1

source_name: mssa476 taken 4 hours after inoculation


title: MBNLko_12

description: mouse quadricep muscle Mbnl ko cells

value: MBNL1 knockout


title: arp2 yeast vs arp2 hyphae (replica 1)


title: MBNLko_10

description: mouse quadricep muscle Mbnl ko cells


title: HSA6

description: mouse quadricep muscle HSA cells


title: MBNLko_9

description: mouse quadricep muscle Mbnl ko cells


title: nrg1/arp2 hyphae vs WT hyphae (replica 3)

source_name: WT under hyphae conditions (10% FBS, 37°C, 3 hours)


title: wt_1

description: mouse quadricep muscle wt cells


title: nrg1/arp2 hyphae vs WT hyphae (replica 1)


title: arp2 hyphae vs WT hyphae (replica 3)


title: arp2 hyphae vs WT hyphae (replica 2)


title: HSA7

description: mouse quadricep muscle HSA cells


title: arp2 yeast vs WT yeast (replica 3)

source_name: WT under yeast conditions (30°C, 3 hours)


title: arp2 hyphae vs WT hyphae (replica 1)


title: nrg1/arp2 hyphae vs WT hyphae (replica 2)


title: arp2 yeast vs WT yeast (replica 2)


title: arp2 yeast vs WT yeast (replica 1)


title: WT yeast vs WT hyphae (replica 1)


title: WT yeast vs WT hyphae (replica 3)


title: WT yeast vs WT hyphae (replica 2)


title: HFD+Tel-2 (high fat-fed C57BL/6 mouse treated with telmisartan)

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: High fat-fed C57BL/6 mouse treated with telmisartan.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

source_name: epididymal fat tissue, high-fat diet, telmisartan

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the epididymal fat tissue using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

treatment_protocol: Six-week-old male C57BL/6J mice were purchased from CLEA Japan.  The mice were fed a chow that contained 10% of its calories from fat (control) or a high-fat diet (HFD) that contained 30% of its calories from fat for 24 weeks.　The high fat-fed mice were randomized to 3 groups.  Either telmisartan (~3 mg/kg/day) in drinking water (HFD+Tel), candesartan (~3 mg/kg/day) in drinking water (HFD+Can), or a HFD without any drugs (HFD) was administered for the next 5 weeks.  Epididymal adipose tissues were rapidly removed from each mouse.

tag: gender

value: male

value: epididymal fat tissue

tag: diet

value: high fat

value: telmisartan


title: HFD+Can-1 (high fat-fed C57BL/6 mouse treated with candesartan)

description: High fat-fed C57BL/6 mouse treated with candesartan.

source_name: epididymal fat tissue, high-fat diet, candesartan

value: candesartan


title: HFD+Can-2 (high fat-fed C57BL/6 mouse treated with candesartan)


title: HFD-2 (high fat-fed C57BL/6 mouse)

description: High fat-fed C57BL/6 mouse.

source_name: epididymal fat tissue, high-fat diet


title: HFD+Tel-1 (high fat-fed C57BL/6 mouse treated with telmisartan)


title: H3K4 methylation in RL cells

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description: ChIP-chip, RL cells, H3K4me3.

hyb_protocol: The Input and ChIP samples were co-hybridized onto the NimbleGen promoter microarray (Roche-NimbleGen, Madison, WI) according to manufacturer's protocols.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: The array data were extracted according to standard operating procedures by NimbleGen Systems, Inc. The peaks were identified with a cut-off of false discovery rate (FDR) of <0.05 using NimbleGen SignalMap software.

source_name: H3K4me3 ChIP DNA from RL cells

label_protocol: For hybridization to the microarrays, 10ng each of Input and ChIP DNA samples was amplified using the GenomePlex WGA kit (Sigma-Aldrich, St. Louis, MO). The Input and ChIP samples were labeled with Cy3 and Cy5 fluorescent dye, respectively.

growth_protocol: RL cells were cultured in RPMI media.

extract_protocol: ChIP experiments were carried out using a Magna ChIP kit (Millipore, Billerica, MA) following the manufacturer’s suggested protocols. For each ChIP experiment, 5×106 RL cells were crosslinked with 10% formaldehyde at 37°C for 10 minutes. The following antibodies were used: anti-trimethyl-H3K27 (Upstate, no. 07-449), anti-trimethyl-H3K4 (Upstate, no. 04-745), and anti-Suz12 (Abcam, ab-12073).

treatment_protocol: Untreated.

tag: cell line

value: RL

value: follicular lymphoma cells

value: t(14,18) gene rearrangement

tag: chip antibody

source_name: Input DNA from RL cells


title: 11 dpi OSKM-infected MEFs biological replicate 2

status: Public on Jan 22 2010

city: Singapore

first: Dominic

middle: Jian Chien

last: Heng

address: 60 Biopolis Street #02-01, Genome Building

department: Stem Cell and Developmental Biology

country: Singapore

institute: Genome Institute of Singapore

description: Gene expression data from 11 dpi OSKM-infected MEFs

hyb_protocol: 1.5 ug of cRNA were hybridized to Illumina Mouse-6 Expression BeadChip v1.1 for 20 hr at 58oC on Ilumina Hybridization Oven.

scan_protocol: Illumina Mouse-6 Expression BeadChip v1.1 were washed and stained with streptavidin-Cy3 before scanning using the Illumina Bead Reader.

data_processing: The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.

label: Biotin

source_name: 11 dpi OSKM-infected MEFs

label_protocol: Biotinylated cRNA were prepared from 500 ng of total RNA according to the standard protocol (TotalPrep RNA Amplification Kit, Instruction Manual, Catalog #IL1791, Illumina).

growth_protocol: Infected MEFs were cultured at 37°C with 5% CO2 in relevant media cited in methods.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purified with RNeasy minikit (Qiagen).

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)


title: 7 dpi N2OSKM-infected MEFs biological replicate 3

description: Gene expression data from 7 dpi N2OSKM-infected MEFs

source_name: 3 dpi N2OSKM-infected MEFs


title: 11 dpi N2OSKM-infected MEFs biological replicate 3

description: Gene expression data from 3 dpi N2OSKM-infected MEFs

source_name: 11 dpi N2OSKM-infected MEFs


title: HFD-1 (high fat-fed C57BL/6 mouse)

description: High fat-fed C57BL/6 mouse.

tag: strain


title: 11 dpi N2OSKM-infected MEFs biological replicate 1

description: Gene expression data from 11 dpi N2OSKM-infected MEFs


title: Suz12 binding in RL cells

description: ChIP-chip, RL cells, Suz12.

source_name: Suz12 ChIP DNA from RL cells

extract_protocol: ChIP experiments were carried out using a Magna ChIP kit (Millipore, Billerica, MA) following the manufacturer’s suggested protocols. For each ChIP experiment, 5×106 RL cells were crosslinked with 10% formaldehyde at 37°C for 10 minutes.


title: H3K27 methylation in RL cells

description: ChIP-chip, RL cells, H3K27me3.

source_name: H3K27me3 ChIP DNA from RL cells


title: 11 dpi OSKM-infected MEFs biological replicate 1


title: 11 dpi N2OSKM-infected MEFs biological replicate 2


title: MBNLko_11

description: mouse quadricep muscle Mbnl ko cells

source_name: quadricep muscle


title: Control-1 (chow-fed C57BL/6 mouse)

description: Chow-fed C57BL/6 mouse.

source_name: epididymal fat tissue, control chow

value: normal chow

tag: treatment


title: 7 dpi OSKM-infected MEFs biological replicate 3

description: Gene expression data from 7 dpi OSKM-infected MEFs

source_name: 7 dpi OSKM-infected MEFs


title: 7 dpi N2OSKM-infected MEFs biological replicate 1

source_name: 7 dpi N2OSKM-infected MEFs


title: 7 dpi N2OSKM-infected MEFs biological replicate 2


title: 11 dpi OSKM-infected MEFs biological replicate 3


title: 7 dpi OSKM-infected MEFs biological replicate 2


title: 3 dpi N2OSKM-infected MEFs biological replicate 2


title: 7 dpi OSKM-infected MEFs biological replicate 1


title: 3 dpi OSKM-infected MEFs biological replicate 2

description: Gene expression data from 3 dpi OSKM-infected MEFs

source_name: 3 dpi OSKM-infected MEFs


title: Actin-GFP MEF, biological replicate 1

description: Actin-GFP transgenic mice were from the Jackson Laboratory, Stock No 003516. Actin-GFP MEFs were prepared from E13.5  embryos obtained from the intercross between male Actin-GFP mice and female wild-type CD1 mice.

source_name: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven  by Actin promoter.

growth_protocol: MEFs were cultured at 37°C with 5% CO2. MEFs were maintained in 15% FBS-DMEM containing 20 ug ml-1 gentamicin.


title: iPSC N2SK #B11, biological replicate 2

description: N2SK-induced iPSCs

source_name: mouse induced pluripotent stem cells (iPSCs)

growth_protocol: Mouse iPS cells were cultured at 37°C with 5% CO2. Mouse iPS cells were maintained on mitomycin C-treated MEF feeders in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid and 1,000 units/ml of LIF (Chemicon).


title: iPSC N2SK #B3, biological replicate 2

description: N2SK-induced iPSCs

value: mouse induced pluripotent stem cells (iPSCs)


title: iPSC N2SK #B3, biological replicate 1

description: N2SK-induced iPSCs


title: Pou5f1-GFP MEF, biological replicate 1

description: Pou5f1-GFP transgenic mice were from the Jackson Laboratory, Stock No 004654. Pou5f1-GFP MEFs were prepared from E13.5  embryos obtained from the intercross between male Pou5f1-GFP mice and female wild-type C57BL/6J mice.

source_name: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven  by Pou5f1 promoter


title: 3 dpi OSKM-infected MEFs biological replicate 3


title: iPSC N2SKM, biological replicate 2

description: N2SKM-induced iPSCs


title: iPSC OSKM, biological replicate 2

description: OSKM-induced iPSCs


title: 3 dpi N2OSKM-infected MEFs biological replicate 3


title: iPSC N2SK #B11, biological replicate 1

description: N2SK-induced iPSCs


title: Actin-GFP MEF, biological replicate 2

value: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven by Actin promoter.


title: ESC, biological replicate 2

description: mouse v6.4 ESCs

source_name: v6.4 mouse embryonic stem cells (ESCs)

growth_protocol: Mouse ES cells were cultured at 37°C with 5% CO2. Mouse ES cells were maintained on mitomycin C-treated MEF feeders in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid and 1,000 units/ml of LIF (Chemicon).

value: v6.4 mouse embryonic stem cells (ESCs)


title: Patient 4450_rep2

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

hyb_protocol: Sample and control probes were mixed together in a final volume of 90 µl of hybridisation buffer : DIG Easy Hyb (Roche, Laval, QC) + 0.5 µg/µl salmon sperm (Invitrogen, Carlsbad, CA) + 0.5 µg/µl yeast tRNA (Invitrogen, Carlsbad, CA). Mix was heated at 95ºC for 5 min and put on the arrray. After adding a coverslip, arrays were incubated in a hybridisation chamber at 37ºC for 16h. Arrays were then washed three times in SSC0.1X, SDS 0.1%, four times in SSC 0.1X and centrifuge to dry them.

scan_protocol: Slides were scanned in a ScanArray Lite (GSI Luminomics, Billerica, MA).

data_processing: Spot intensity was quantified using QuantArray (GSI Luminomics, Billerica, MA). The Lowess scatter-smoothing normalization was performed in the GeneSpring 7.0 software package (Agilent, Santa Clara, CA).

source_name: LCM-captured brain tumor cells, pediatric

label_protocol: 5 µg of aRNA were reverse transcribed with Superscript II RT (Invitrogen, Carlsbad, CA). cDNA were direct-labelled with Cy3dCTP or Cy5dCTP (GE Healtcare, Baie d'Urfe, QC) and purified using the QIAquick PCR Purification kit (Qiagen, Mississauga, ON). Labelled probes were then dried to get a final volume of 3 to 6 µl.

extract_protocol: After LCM, RNA was extracted with PicoPure RNA Isolation (Molecular Devices, Sunnyvale, CA). Then, 30-40 ng were amplified with the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: All biological samples were flash-frozen in liquid nitrogen immediately after surgery. Interesting cells were isolated by Laser Capture Microdissection (LCM).

value: type IV glioblastoma

tag: pediatric patient

value: yes

tag: angiogenesis score

value: neg

tag: p53 score

tag: egfr score

tag: ras score

tag: survival

value: M

tag: primary tumor?

source_name: Pooled normal brain, pediatric

value: brain


title: iPSC N2SKM, biological replicate 1

description: N2SKM-induced iPSCs


title: Pou5f1-GFP MEF, biological replicate 2

value: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven by Pou5f1 promoter


title: 3 dpi N2OSKM-infected MEFs biological replicate 1


title: 3 dpi OSKM-infected MEFs biological replicate 1


title: ESC, biological replicate 1

description: mouse v6.4 ESCs


title: U87MG-cell culture [Illumina]

city: Los Angeles

first: Stanley

middle: F

last: Nelson

address: 695 Young Dr S

department: Human Genetics

institute: UCLA

description: genomic DNA library from 10ug of source DNA extracted from cultured U87MG cells

hyb_protocol: Standard Illumina Beadchip protocol

scan_protocol: Standard Illumina Beadchip protocol

data_processing: Sample was run alongside a large number of normal samples in a series, and these were used together to normalize the data with the Illumina Beadstudio program.

label: C-Bio and A-DNP

source_name: brain tumor cell line

label_protocol: Standard Illumina Beadchip protocol

growth_protocol: Cells were grown in DMEM with 10% FBS.

extract_protocol: DNA was extracted using the Qiagen Gentra DNA isolation protocol


title: Patient 3948_rep3

tag: tissue

value: no

tag: sex

value: F


title: Patient 4450_rep1


title: Patient 272_rep1


title: Patient 3948_rep2


title: HSA5

description: mouse quadricep muscle HSA cells

tag: genotype

value: HSALR


title: Patient 272_rep2


title: Patient 184_rep2

value: pos


title: Control-2 (chow-fed C57BL/6 mouse)

description: Chow-fed C57BL/6 mouse.

tag: gender

value: male

value: epididymal fat tissue


title: Patient P4211_rep2


title: Patient 184_rep1


title: Patient 151_rep1


title: Patient P4211_rep1


title: Patient P4011_rep1


title: Patient P4011_rep3


title: Patient P143_rep2


title: Patient 3948_rep1


title: Patient 63_rep1


title: Patient 151_rep2


title: Patient P4011_rep4


title: Patient 63_rep2


title: Patient P4011_rep2


title: Patient P143_rep1


title: iPSC OSKM, biological replicate 1

description: OSKM-induced iPSCs


title: PHA, biological rep18

city: Iowa City

first: Ferhaan

last: Ahmad

state: IA

address: 100 Newton Road, 1191D ML

department: Internal Medicine

institute: University of Iowa

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. Gene expression data from a  Lung with pulmonary arterial hypertension.

hyb_protocol: Following fragmentation, 1.5 ug of cRNA were hybridized for 17 hr at 65C on Agilent 4x44k Whole Human Genome Array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Agilent Scanner protocol

data_processing: We ran cyclic LOESS algorithm for all probes containing annotations for Entrez Gene ID. Then we took the average over "Probe Names" for those containing multiple replicates.

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep18

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol from 500ng total RNA.

extract_protocol: RNA was isolated from lung tissue using Trizol (Invitrogen) and purified using the RNeasy Mini kit (Qiagen).

value: Tissue from a patient with pathological diagnosis of pulmonary arterial hypertension.


title: PHA, biological rep17

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep17


title: Patient 612_rep2


title: Patient 3948_rep4


title: Patient 612_rep3


title: Patient 434_rep4


title: Patient 612_rep4


title: PHA, biological rep16

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep16


title: Patient 434_rep1


title: Patient 434_rep3


title: PHA, biological rep15

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep15


title: PHA, biological rep14

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep14


title: Patient 429_rep1


title: PHA, biological rep10

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep10


title: Patient 429_rep4


title: Patient 612_rep1


title: PHA, biological rep11

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep11


title: Patient 434_rep2


title: Patient 1013_rep2


title: Patient 1013_rep1


title: PHA, biological rep13

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep13


title: PHA, biological rep8

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep8


title: PHA, biological rep7

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep7


title: PHA, biological rep9

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep9


title: PHA, biological rep5

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep5


title: PHA, biological rep6

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep6


title: Patient 429_rep2


title: PHA, biological rep4

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep4


title: PHA, biological rep3

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep3


title: Patient 66_rep1

source_name: LCM-captured brain tumor cells, pediatric

source_name: Pooled normal brain, pediatric


title: PAH, biological rep1

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. Gene expression data from a lung with pulmonary arterial hypertension.

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep1


title: PHA, biological rep12

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep12


title: PAH, biological rep2

source_name: Lung tissue with pulmonary arterial hypertension (PAH), biological rep2


title: IPF with PH, biological rep8

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. Gene expression data from a lung with pulmonary hypertension secondary to idiopathic pulmonary fibrosis.

source_name: Lung tissue with pulmonary hypertension secondary to idiopathic pulmonary fibrosis (IPF), biological rep7

value: Tissue from a patient with pathological diagnosis of pulmonary hypertension secondary to idiopathic pulmonary fibrosis.


title: Patient OP25_rep3

source_name: LCM-captured brain tumor cells, adult


title: Patient OP25_rep2


title: Patient OP13_rep2


title: Patient OP25_rep4


title: Patient 870_rep2


title: Patient OP13_rep1


title: Patient 870_rep1


title: IPF with PH, biological rep4

source_name: Lung tissue with pulmonary hypertension secondary to idiopathic pulmonary fibrosis (IPF), biological rep4


title: IPF with PH, biological rep5

source_name: Lung tissue with pulmonary hypertension secondary to idiopathic pulmonary fibrosis (IPF), biological rep5


title: Patient OP25_rep1


title: Patient 889_rep1


title: IPF with PH, biological rep7


title: IPF with PH, biological rep1

source_name: Lung tissue with pulmonary hypertension secondary to idiopathic pulmonary fibrosis (IPF), biological rep1


title: IPF with PH, biological rep2

source_name: Lung tissue with pulmonary hypertension secondary to idiopathic pulmonary fibrosis (IPF), biological rep2


title: IPF with PH, biological rep6

source_name: Lung tissue with pulmonary hypertension secondary to idiopathic pulmonary fibrosis (IPF), biological rep6


title: Patient 889_rep2


title: control, biological rep13

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. Gene expression data from a control lung.

source_name: normal lung tissues, control, biological rep13

value: Normal lung tissues obtained from the disease free margins with normal histology of lung cancer resection.


title: IPF with PH, biological rep3

source_name: Lung tissue with pulmonary hypertension secondary to idiopathic pulmonary fibrosis (IPF), biological rep3


title: control, biological rep12

source_name: normal lung tissues, control, biological rep12


title: Patient 821_rep4


title: Patient 861_rep2


title: control, biological rep11

source_name: normal lung tissues, control, biological rep11


title: Patient 821_rep6


title: Patient 429_rep3


title: Patient 821_rep5


title: Patient 821_rep2


title: Patient 813_rep4


title: control, biological rep10

source_name: normal lung tissues, control, biological rep10


title: Patient 821_rep1


title: control, biological rep9

source_name: normal lung tissues, control, biological rep9


title: Patient 821_rep3

source_name: Pooled normal brain, pediatric


title: control, biological rep8

source_name: normal lung tissues, control, biological rep8


title: control, biological rep4

source_name: normal lung tissues, control, biological rep4


title: control, biological rep7

source_name: normal lung tissues, control, biological rep7


title: control, biological rep6

source_name: normal lung tissues, control, biological rep6


title: control, biological rep2

source_name: normal lung tissues, control, biological rep2


title: control, biological rep3

source_name: normal lung tissues, control, biological rep3


title: Patient 813_rep3

source_name: LCM-captured brain tumor cells, adult


title: control, biological rep5

source_name: normal lung tissues, control, biological rep5


title: Patient 813_rep2


title: Patient 813_rep1


title: MRK090_Stroma

city: North Wales

first: James

last: Hardwick

state: PA

address: 351 N. Sumneytown Pike

department: Molecular Profiling

institute: Merck & Co., Inc.

description: Individual LCM stroma from esophageal disease

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

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4415
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

source_name: Stratagene Universal Human Reference RNA

label_protocol: Custom automated version of the aminoallyl MessageAmp II kit from Ambion.  Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

extract_protocol: Messenger RNA was extracted from stromal cells microdissected from 5x 8 μm sections using PicoPureRNA reagents according to Molecular Devices' instructions

treatment_protocol: Human tissue specimens were surgically excised and snap frozen in liquid nitrogen

value: Reference RNA Pool

value: stromal cells (laser-capture microdissected)

tag: disease stage

value: Dysplasia


title: control, biological rep1

source_name: normal lung tissues, control, biological rep1


title: Sample M84 versus breast cancer cell line reference pool

city: Bethesda

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: Sample M84; ER status: -; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: -; TNM: T2 N1 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

hyb_protocol: Equal amounts of labeled cDNA for the test sample and the reference sample were hybridized to cDNA array for each tumor.

scan_protocol: Fluorescent intensities were measured using an Agilent scanner, and scanned images were analyzed using DeArray software.

data_processing: Significance analysis of microarray was used for data mining and analysis. Supervised clustering was done, where each sample was identified as brain metastasis or primary tumor.

source_name: M84, breast tumor

label_protocol: cDNA microarray analysis: Cy3-dUTP–labeled or Cy5- dUTP–labeled cDNA (GE Healthcare) was synthesized from 50 to 100 μg of amplified aRNA using random primed polymerization with SuperScript II reverse transcriptase (Invitrogen).

extract_protocol: All samples were subjected to LCM and RNA amplification. Briefly, 8-μm frozen tissue sections were thawed 15 s at room temperature and stained using the Histogene LCM Frozen Section Staining kit (Arcturus Engineering) following the manufacturer's instructions with the addition of a 5-min incubation in 100% ethanol before xylene. Approximately 2,000 laser-captured pulses were collected for each sample using the PixCell II Laser Capture Microdissection System (Arcturus Engineering) in a 15-min period. Captured cells were lysed off the LCM caps in PicoPure RNA Extraction buffer (Pico- Pure RNA Isolation kit, Arcturus Engineering) for 30 min at 55°C and frozen at −80°C until ready to proceed. Total RNA was extracted according to the manufacturer's instructions for the PicoPure RNA Isolation kit. Quality and quantity of RNA were assessed using the RNA 6000 Pico Assay for the 2100 Bioanalyzer (Agilent Technologies). A minimum of 10 ng of RNA was then subjected to two rounds of a T7 RNA polymerase catalyzed amplification protocol using the RiboAmp RNA Amplification kit (Arcturus Engineering). Quality and quantity of the amplified aRNA were assessed using the RNA 6000 Nano Assay for the 2100 Bioanalyzer. A reference RNA sample consisting of a pool of six breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D) was simultaneously amplified.

tag: er status

tag: erbb2 status (fish)

tag: histology

value: Ductal

tag: metastatic

tag: tnm stage

value: T2 N1

source_name: Breast cancer cell line reference pool

tag: cell lines

value: breast cancer

tag: sample type

value: reference


title: Sample M107 versus breast cancer cell line reference pool

description: Sample M107; ER status: +; ERBB2 status by FISH: +; Histology: Ductal; Metastatic: -; TNM: T1 N0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: M107, breast tumor

value: T1 N0

tag: cell type


title: Sample M141 versus breast cancer cell line reference pool

description: Sample M141; ER status: -; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: -; TNM: T2 N1 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: M141, breast tumor


title: MRK084_Stroma

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

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4411
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Intestinal metaplasia


title: MRK089_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4414
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Sample BM20 versus breast cancer cell line reference pool

description: Sample BM20; ER status: +; ERBB2 status by FISH: +; Histology: Ductal; Metastatic: +; TNM: T3 N2 M0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: BM20, brain metastasis

value: T3 N2 M0


title: Sample M129 versus breast cancer cell line reference pool

description: Sample M129; ER status: -; ERBB2 status by FISH: -; Histology: Lobular; Metastatic: -; TNM: T2 N1 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: M129, breast tumor

value: Lobular


title: Sample BM12 versus breast cancer cell line reference pool

description: Sample BM12; ER status: +; ERBB2 status by FISH: -; Histology: Lobular; Metastatic: +; TNM: T3 N2 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: BM12, brain metastasis

value: T3 N2


title: MRK085_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4412
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK079_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4408
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK073_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4405
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK076_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4406
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK078_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4407
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Sample M116 versus breast cancer cell line reference pool

description: Sample M116; ER status: -; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: -; TNM: T1 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: M116, breast tumor


title: Sample BM19 versus breast cancer cell line reference pool

description: Sample BM19; ER status: -; ERBB2 status by FISH: -; Histology: Inflammatory; Metastatic: +; TNM: T3 N1 M0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: BM19, brain metastasis

value: Inflammatory

value: T3 N1 M0


title: MRK080_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4409
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK081_Stroma

data_processing:
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4410
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Sample M125 versus breast cancer cell line reference pool

description: Sample M125; ER status: -; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: -; TNM: T2 N0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: M125, breast tumor

value: T2 N0


title: Sample HD612 versus breast cancer cell line reference pool

description: Sample HD612; ER status: -; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: -; TNM: T3 N2 Mx versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: HD612, breast tumor

value: T3 N2 Mx