title: CSM vs EC1118 Experiment 1

city: Burjassot

first: Agustin

last: Aranda

state: Valencia

address: Moliner 50

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia

hyb_protocol: Yeast 6.4Kv7 microarray slides from the Microarray Center of University Health Network (Canada) were used. Microarrays were prehybridized for 45 min at 42º C in 3xSSC (0.15M NaCl and 0.015M sodium citrate), 0.1% (w/v) sodium dodecyl sulphate (SDS) and 0.1 mg/mL bovine serum albumin. Before hybridization, equal amounts of Cy5- and Cy3-labelled cDNA, 50% (v/v) formamide, 5xSSC and 0.1% (w/v) SDS were mixed and denatured for 1 min at 95ºC. The mixture was applied to the prehybridized microarrays, covered with a Hybri-slip (Sigma-Aldrich) and hybridization took place for 16 h in a humidified chamber in a water bath at 42º C. Hybridized microarrays were washed for 5 min at 42ºC in 2xSSC, 0.1% (w/v) SDS for 20 min at room temperature in 0.1xSSC, 0.1% (w/v) SDS, for 6 min at room temperature in 0.1_SSC and for 1 min at room temperature in 0.01xSSC.

scan_protocol: After washing, microarrays were immediately scanned with an Axon 4100A scanner at a resolution of 10 mm and the data were analysed using the GENEPIX PRO 6.1. software package (Axon Instruments).

data_processing: Data were ratio-based normalized and processed using ACUITY 4.0 (Axon Instruments). A false discovery rate of 10% was used to select the statistically significant data.

organism: Saccharomyces cerevisiae

source_name: CSM c

label_protocol: cDNA was synthesized by combining 20 microg of total RNA and 1 microg of oligo (dT) (Roche), dithiothreitol (0.1M),  dNTPs mixture at 10mM each (Invitrogen), aminoallyl- dUTP 50mM (Fermentas), RNase inhibitor and Superscript III reverse transcriptase (Invitrogen). Aminoallyl-cDNA was purified using the MinElute PCR Purification Kit (Qiagen) according to the manufacturer’s instructions. A labelling reaction was produced by incubating 1.5–2 mg of aminoallyl-cDNA with 3 mL of the Cy3 and Cy5 fluorophores (Amersham) at a basic pH (0.2M Na2CO3, pH 9) for 2 h at room temperature. Labelled cDNA was purified using the aforementioned kit.

growth_protocol: Growth in in synthetic grape juice for 6 days

extract_protocol: Acid phenol extraction in LETS buffer plus LiCl precipitation.

tag: strain

value: CSM


title: S 1 rep2

status: Public on Oct 26 2011

type: RNA

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cross-correlation normalisation in R or Matlab

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: tumor sphere

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: lung tumor sphere


title: S 1 rep1

description: replicate 1


title: Root cap_rep2

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description:
RXP4001_002
Gene expression of root cap.

hyb_protocol: At least 1,100 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4x44K microarray RAP-DB (Agilent; G2519F#15241) at 65℃ for 17 hours. Hybridization and washing of the hybridized slide were performed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75th percentile normalization and log2 transformation with GeneSpring GX11 (Agilent).

organism: Oryza sativa Japonica Group

source_name: Root cap

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction, and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by the RNeasy Mini Kit (Qiagen), and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: Rice seeds were sterilized with 70% (v/v) ethanol solution and 1% (v/v) sodium hypochlorite solution, imbibed in distilled water in the dark at 25°C for 2 days, and transferred onto a nylon net floated in distilled water in a growth chamber (60% humidity; 14 h light period at 30°C and 10 h dark period at 25°C). After 3 days of germination, the seedlings were transferred to a nutrient solution (based on Yoshida nutrient solution; pH 5.5) and allowed to grow for another 7 days. The pH of the nutrient solution was adjusted using 1N NaOH and maintained using MES (buffer), and the solution was renewed every 2 days.

extract_protocol: Total RNA was extracted from each sample with a Pico-Pure RNA isolation kit (Arcturus) according to the manufacturer’s protocol. The quantity and quality of the obtained RNAs were checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: The crown roots of 10-day-old seedlings with length more than 5 cm were used for the gene expression profiling. The samples were fixed in 99.5% cold ethanol or 100% cold acetone. Sample fixation and paraffin-embedding were performed using the Microwave Processor (Energy Beam Sciences, East Granby, CT). The paraffin-embedded samples were cut into 12-20 µm thick sections using a microtome (Leica RM2255) and used for laser microdissection with the Veritas Laser Microdissection System LCC1704 (Arcturus).

tag: cultivar

value: Nipponbare

tag: tissue

value: root

tag: developmental stage

value: root cap


title: Elongation zone_rep3

description:
RXP4001_009
Gene expression of 1-2 mm region from root tip corresponding to elongation zone.

source_name: Elongation zone_1-2 mm from root tip

value: elongation zone


title: CSM vs EC1118 Experiment 2


title: CSM vs EC1118 Experiment 3

source_name: CSM a


title: Root cap_rep1

description:
RXP4001_001
Gene expression of root cap.


title: MS121 OA

status: Public on Oct 25 2011

city: Madrid

first: Manuel

middle: J

last: Del Rey

address: Avda Córdoba s/n

department: Grupo de Enfermedades Inflamatorias y Autoinmunes

institute: Instituto de Investigación Hospital 12 de Octubre

description: OASF (osteoarthritis arthritis synovial fibroblasts) gene expression under basal conditions

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: OASF, basal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs from synovial fibroblasts was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality control was performed in 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). In all cases, RIN (RNA integrity number) was higher than or equal to 9.

treatment_protocol: Synovial tissues were obtained from 9 patients with RA and 11 sex and age matched patients with OA at the time of knee prostetic replacement surgery. Healthy synovial tissues were obtained from 4 adult donors without history of joint disease and macroscopically healthy joints at necropsy and from additional 7 patients with minor traumatic lesions. Fibroblast cultures were established by explant growth in Dulbecco’s modified Eagle’s medium supplemented with 10% heat inactivated fetal bovine serum (FBS) (Cambrex Bio Science, Verviers, Belgium). Cultures were used after passage 4 in order to avoid contamination by other cell types.

value: Synovial fibroblasts culture

tag: disease status

tag: gender

value: Female

tag: age


title: ytpQ mutant, methylglyoxal (MG) treated, rep2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description:
ytpQ_2_MG
ytpQ mutant vs. wild type_MG treated_second biological replicate

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Bacillus subtilis

source_name: wild type, 2.8 mM MG

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: B. subtilis 168 wild type, delta ytpQ mutant, and delta spx mutant cells were grown under vigorous agitation at 37 °C in a minimal medium described before (Stülke et al., 1993, J Gen Microbiol 139, 2041-2045).

extract_protocol: Total RNA was isolated by the acid phenol method as described (Majumdar et al., 1991, Biotechniques 11: 94-101).

treatment_protocol: At OD500 of 0.4, cells were treated for 10 minutes with 2.8 mM methylglyoxal.

tag: genotype

value: wild type

tag: treatment

value: methylglyoxal (MG)

source_name: ytpQ deletion mutant, 2.8 mM MG

value: ytpQ deletion mutant


title: ytpQ mutant, methylglyoxal (MG) treated, rep1

description:
ytpQ_1_MG
ytpQ mutant vs. wild type_MG treated_first biological replicate


title: ytpQ mutant, untreated, rep1

description:
ytpQ_1_control
ytpQ mutant vs. wild type_untreated_first biological replicate

source_name: wild type, untreated

source_name: ytpQ deletion mutant, untreated


title: ytpQ mutant, methylglyoxal (MG) treated, rep3

description:
ytpQ_3_MG
ytpQ mutant vs. wild type_MG treated_third biological replicate


title: spx mutant, untreated, rep3

description:
spx_3_control
spx mutant vs. wild type_untreated_third biological replicate

source_name: spx deletion mutant, untreated

value: spx deletion mutant


title: Root cap_rep3

description:
RXP4001_003
Gene expression of root cap.


title: MS140 OA

value: OASF (osteoarthritis arthritis synovial fibroblasts)

value: Male


title: ytpQ mutant, untreated, rep2

description:
ytpQ_2_control
ytpQ mutant vs. wild type_untreated_second biological replicate


title: MFH1NR

city: Kashihara

first: Kanya

last: Honoki

state: Nara

address: 840 Shijo-cho

department: Department of Orthopedic Surgery

institute: Nara Medical University

description: Gene expression of rat MFH cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: rat malignant fibrous histiocytoma MFH1NR

extract_protocol: RNA was prepared using the FastTrack® 2.0 mRNA Isolation Kit  (K1593-02, Invitrogen) following the manufacturer's recommendations.  Five hundreds nanogrm total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: malignant fibrous histiocytoma


title: ytpQ mutant, untreated, rep3

description:
ytpQ_3_control
ytpQ mutant vs. wild type_untreated_third biological replicate


title: spx mutant, untreated, rep1

description:
spx_1_control
spx mutant vs. wild type_untreated_first biological replicate


title: MS132 OA


title: MS136 OA


title: MS64 OA


title: rMSC

description: Gene expression of rat mesenchymal stem cells

source_name: rat mesenchymal stem cells

value: mesenchymal stem cells


title: spx mutant, untreated, rep2

description:
spx_2_control
spx mutant vs. wild type_untreated_second biological replicate


title: MS120 OA


title: COS1NR

description: Gene expression of rat osteosarcoma cells

source_name: rat osteosarcoma COS1NR

value: osteosarcoma


title: MS60 OA


title: MS63 OA


title: MS94 Sano

description: HSF (healthy synovial fibroblasts) gene expression under basal conditions

source_name: HSF, basal

value: HSF (healthy synovial fibroblasts)


title: 07/1180 Sano


title: MS150 Sano


title: 07/775 Sano


title: MS85 OA


title: 09/940 Sano


title: MS97 Sano


title: MS141 Sano


title: MS77 AR

description: RASF (rheumatoid arthritis synovial fibroblasts) gene expression under basal conditions

source_name: RASF, basal


title: MS96 Sano


title: MS81 OA


title: MS124 OA


title: MS90 Sano


title: MS86 Sano


title: MS82 AR

value: RASF (rheumatoid arthritis synovial fibroblasts)


title: MS98 AR


title: MS80 AR


title: MS52 AR


title: MS95 AR


title: MS83 AR


title: MS147 AR


title: 07/967 Sano


title: MS114 AR


title: (NBF164) Normal fibroblast technical replicate 4

city: Montreal

first: Mark

last: Basik

state: QC

address: 3755 Cote Ste Catherine

department: Oncology

country: Canada

institute: Lady Davis Institute

description: Technical Replicate of NBF164

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned with Agilent Technologies Scanner G2505B US22502597

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Normal Breast fibroblast

label_protocol: standard Agilent protocol

growth_protocol: All samples were cultured in DMEM media with 2% fetal bovine serum and harvested at subconfluency

extract_protocol: standard Agilent protocol

value: breast fibroblast

tag: disease state

value: normal

source_name: Pooled cancer cell lines

tag: sample type

value: reference


title: (T65CAF) Cancer associated fibroblast biological replicate 17

description: Biological replicate of other CAFs

source_name: Breast carcinoma associated fibroblast

value: breast carcinoma associated fibroblast

value: carcinoma


title: (T114CAF) Cancer associated fibroblast biological replicate 23

description: Biological replicate of other CAFs


title: (T68CAF) Cancer associated fibroblast biological replicate 19

description: Biological replicate of other CAFs


title: (T89CAF) Cancer associated fibroblast biological replicate 22

description: Biological replicate of other CAFs


title: (NBF164) Normal fibroblast biological replicate 4

description: Biological replicate of other normal breast fibroblasts


title: (BERK067) Normal fibroblast biological replicate 1


title: (T73CAF) Cancer associated fibroblast biological replicate 20

description: Biological replicate of other CAFs


title: (hMSC298) Mesenchymal stem cell biological replicate 2

description: Biological replicate of other mesenchymal stem cells

source_name: Mesenchymal Stem Cells

value: femur bone marrow aspirate


title: (hMSC300) Mesenchymal stem cell biological replicate 3


title: (T179CAF) Cancer associated fibroblast biological replicate 16

description: Biological replicate of other CAFs


title: (hMSC304) Mesenchymal stem cell biological replicate 5


title: (T92CAF) Cancer associated fibroblast Technical Replicate 12

description: Technical Replicate of T92CAF


title: (BERK897) Normal fibroblast biological replicate 3


title: (Norm2) Normal fibroblast biological replicate 5


title: (T105CAF) Cancer associated fibroblast biological replicate 15

description: Biological replicate of other CAFs


title: (BERK833) Normal fibroblast biological replicate 2


title: (T77CAF) Cancer associated fibroblast Technical Replicate 11

description: Technical Replicate of T77CAF


title: (hMSC296) Mesenchymal stem cell biological replicate 1


title: (T71CAF) Cancer associated fibroblast Technical Replicate 10

description: Technical Replicate of T71CAF


title: (BERK833) Normal fibroblast technical replicate 2

description: Technical Replicate of BERK833


title: (T48CAF) Cancer associated fibroblast Technical Replicate 8

description: Technical Replicate of T48CAF


title: (hMSC303) Mesenchymal stem cell biological replicate 4


title: (T63CAF) Cancer associated fibroblast Technical Replicate 9

description: Technical Replicate of T63CAF


title: (BERK897) Normal fibroblast technical replicate 3

description: Technical replicate of BERK897


title: (T66CAF) Cancer associated fibroblast biological replicate 18

description: Biological replicate of other CAFs


title: (T50CAF) Cancer associated fibroblast biological replicate 14

description: Biological replicate of other CAFs


title: (T79CAF) Cancer associated fibroblast biological replicate 21

description: Biological replicate of other CAFs


title: (T44CAF) Cancer associated fibroblast Technical Replicate 7

description: Technical Replicate of T44CAF


title: (T112CPF) Counterpart fibroblast biological replicate 13

description: Biological replicate of other CPF

source_name: Breast Counterpart fibroblast

value: breast counterpart fibroblast


title: (T35CAF) Cancer associated fibroblast biological replicate 13

description: Biological replicate of other CAFs


title: (T98CAF) Cancer associated fibroblast biological replicate 11

description: Biological replicate of other CAFs


title: (T98CPF) Counterpart fibroblast biological replicate 12

description: Biological replicate of other CPF


title: (T38CAF) Cancer associated fibroblast Technical Replicate 6

description: Technical Replicate of T38CAF


title: (T77CPF) Counterpart fibroblast biological replicate 11

description: Biological replicate of other CPF


title: (T77CAF) Cancer associated fibroblast biological replicate 9

description: Biological replicate of other CAFs


title: (T35CPF) Counterpart fibroblast biological replicate 9

description: Biological replicate of other CPF


title: (NBF164) Normal fibroblast technical replicate 2

description: Technical replicate of NBF164


title: (T44CPF) Counterpart fibroblast biological replicate 10

description: Biological replicate of other CPF


title: (T44CAF) Cancer associated fibroblast Technical Replicate 4

description: Technical Replicate of T44CAF


title: (T114CPF) Counterpart fibroblast biological replicate 7

description: Biological replicate of other CPF


title: (T48CAF) Cancer associated fibroblast biological replicate 8

description: Biological replicate of other CAFs


title: (T38CAF) Cancer associated fibroblast Technical Replicate 3

description: Technical Replicate of T38CAF


title: HH1-60, biological replicate 1

city: Beijing

first: Jie

last: Zhao

address: No. 2 Yuan Ming Yuan West Street

country: China

institute: Institute of Plant Protection, Chinese Academe of Agricultural Sciences

description: Gene expression data from HH1 at the age of 60-day old

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C using an Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained at Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa

source_name: HH1 seedlings

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

growth_protocol: Rice seeds were surface-disinfected and then soaked in distilled sterile water for germination at 28°C for 2 days. Rice seedlings were grown in pots fertilized with half-strength of basal macro- and micro-salt nutrition components of MS medium (Murashige and Skoog, 1962) in a controlled climate chamber at 16-h-light (30°C)/8-h-dark (26°C) cycle.

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

treatment_protocol: At the age of 30-day, 60-day, 75-day and 90-day old, seedling samples were collected; seedlings, at the age of 30-day old, were treated with high-temperature (45°C) and low-temperature (12°C) respectively at climate chambers, and samples were collected 6 hours after treatment; Seedlings were inoculated respectively with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI and  Pxo99 strains, rice leaf streak disease pathogen of Xanthomonas oryzae pv. oryzicola Rs105 strain and rice non-host pathogen of Xanthomonas compestris pv. vesicatoria Xv5 strain at the age of 75-day old.

value: leaves

value: Minghui 63

tag: genotype/variation


title: (T112CAF) Cancer associated fibroblast biological replicate 12

description: Biological replicate of other CAFs


title: (T48CAF) Cancer associated fibroblast Technical Replicate 5

description: Technical Replicate of T48CAF


title: (T106CPF) Counterpart fibroblast biological replicate 6

description: Biological replicate of other CPF


title: (BERK897) Normal fibroblast technical replicate 1

description: Technical replicate of BERK897


title: (T104CAF) Cancer associated fibroblast biological replicate 4

description: Biological replicate of other CAFs


title: (T92CPF) Counterpart fibroblast biological replicate 4

description: Biological replicate of other CPF


title: (T138CPF) Counterpart fibroblast biological replicate 8

description: Biological replicate of other CPF


title: (T71CPF) Counterpart fibroblast biological replicate 3

description: Biological replicate of other CPF


title: (T92CAF) Cancer associated fibroblast biological replicate 10

description: Biological replicate of other CAFs


title: (T104CPF) Counterpart fibroblast biological replicate 5

description: Biological replicate of other CPF


title: (T106CAF) Cancer associated fibroblast biological replicate 5

description: Biological replicate of other CAFs


title: (T138CAF) Cancer associated fibroblast biological replicate 6

description: Biological replicate of other CAFs


title: (T44CAF) Cancer associated fibroblast biological replicate 7

description: Biological replicate of other CAFs


title: (T68CAF) Cancer associated fibroblast Technical Replicate 2

description: Technical replicate of T68CAF


title: (T63CPF) Counterpart fibroblast biological replicate 2

description: Biological replicate of other CPF


title: (T38CPF) Counterpart fibroblast biological replicate 1

description: Biological replicate of other CPF


title: (T63CAF) Cancer associated fibroblast biological replicate 2

description: Biological replicate of other CAFs


title: (T71CAF) Cancer associated fibroblast biological replicate 3

description: Biological replicate of other CAFs


title: (T38CAF) Cancer associated fibroblast biological replicate 1

description: Biological replicate of other CAFs


title: Tenotomy-Control-Day14-Rep5

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

country: USA

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

source_name: Gastroc Muscle, Tenotomy Control, Day 14

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

tag: animal number

value: Muscle;Gastrocnemius

tag: tissue location

value: Right

tag: timepoint

value: Day 14


title: (T48CAF) Cancer associated fibroblast Technical Replicate 1

description: Technical replicate of T48CAF


title: Tenotomy-Control-Day14-Rep1

value: Male

tag: strain


title: Tenotomy-Control-Day7-Rep1

source_name: Gastroc Muscle, Tenotomy Control, Day 7

value: Day 7


title: Tenotomy-Control-Day2-Rep1

source_name: Gastroc Muscle, Tenotomy Control, Day 2

value: Day 2


title: Tenotomy-Treatment-Day2-Rep1

source_name: Gastroc Muscle, Tenotomy Treatment, Day 2

value: Left

value: Tenotomy


title: Tenotomy-Control-Day7-Rep3


title: Tenotomy-Treatment-Day7-Rep6

source_name: Gastroc Muscle, Tenotomy Treatment, Day 7


title: Tenotomy-Treatment-Day14-Rep4

source_name: Gastroc Muscle, Tenotomy Treatment, Day 14


title: Tenotomy-Control-Day14-Rep2


title: Tenotomy-Treatment-Day2-Rep3


title: Tenotomy-Treatment-Day14-Rep1


title: Tenotomy-Treatment-Day14-Rep5


title: Tenotomy-Control-Day2-Rep5


title: Tenotomy-Control-Day7-Rep2


title: Tenotomy-Treatment-Day14-Rep3


title: Tenotomy-Control-Day7-Rep5


title: Tenotomy-Control-Day7-Rep7


title: Tenotomy-Treatment-Day7-Rep2


title: Tenotomy-Control-Day7-Rep6


title: Tenotomy-Treatment-Day7-Rep3


title: Tenotomy-Treatment-Day7-Rep1


title: Tenotomy-Treatment-Day7-Rep7


title: Tenotomy-Treatment-Day7-Rep4


title: Control patient 2, intact skin sample

city: Helsinki

first: Kristo

middle: Juhana

last: Nuutila

address: Haartmaninkatu 8, Biomedicum 1

department: Institute of Biomedicine

country: Finland

institute: University of Helsinki

hyb_protocol: According to Affymetrix GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Chip scanning was performed with a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data analysis was performed with GeneSpring GX software, version 11.0.1 (Agilent Technologies), normalized to the median, and filtered by expression. Statistical analysis was performed, using GeneSpring GX software, version 11.0.1 (Agilent Technologies).  Differences between the groups were compared using 2-way analysis of variance (ANOVA) with Benjamini-Hochberg posttesting.

source_name: Punch biopsy from healthy intact skin

label_protocol: According to Affymetrix GeneChip 3' IVT Express Kit

extract_protocol: The skin samples were homogenized using the Precellys 24 tissue homogenizer with a Cryolys temperature controller unit (Bertin Technologies SA, Montigny-le-Bretonneux, France).Total RNA was extracted from the homogenized tissue samples with an RNeasy® mini kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: The skin biopsies were immediately immersed in RNAlater® (Qiagen) buffer, were incubated at +4°C for one day, and stored thereafter at -80°C until RNA isolation.

tag: patient

value: patient 2

value: control


title: Tenotomy-Control-Day14-Rep3


title: Tenotomy-Control-Day7-Rep4


title: Negative-pressure-treated patient 4, 7th post operative day sample

source_name: Punch biopsy from split-thickness skin graft donor site wound

value: patient 4

value: Negative-pressure-treated


title: Control patient 2, 7th post operative day sample


title: Negative-pressure-treated patient 3, 7th post operative day sample

value: patient 3


title: Tenotomy-Control-Day14-Rep4


title: Tenotomy-Treatment-Day2-Rep2


title: Negative-pressure-treated patient 1, intact skin sample

value: patient 1


title: Negative-pressure-treated patient 2, intact skin sample


title: Tenotomy-Control-Day2-Rep3


title: Tenotomy-Control-Day2-Rep4


title: Tenotomy-Control-Day2-Rep2


title: Control patient 1, intact skin sample


title: Tenotomy-Treatment-Day7-Rep5


title: Tenotomy-Treatment-Day14-Rep2


title: Negative-pressure-treated patient 3, intact skin sample


title: Negative-pressure-treated patient 2, 7th post operative day sample


title: Control patient 1, 7th post operative day sample


title: Tenotomy-Treatment-Day2-Rep5


title: Negative-pressure-treated patient 4, intact skin sample


title: Negative-pressure-treated patient 1, 7th post operative day sample


title: SW480 Snail (2)

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: SW480-Snail, Snail expressing stable line

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA through R based affy module

label: Biotin

source_name: SW480, colon cancer cell

label_protocol: standard Affymetrix procedures

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM-high glucose; Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco)

extract_protocol: Total RNA were extracted by RNeasy mini kit (Cat. 74106; Qiagen, Hilden, Germany), and 100 ng to 1 ug of total RNA were subjected into reverse transcription using the SuperScriptTM III Reverse transcriptase kit (Invitrogen) as directed by the manufacturer.


title: Immature exosome replica 4

city: Pittsburgh

first: Adrian

middle: Eduardo

last: Morelli

state: PA

address: E1546. Biomedical Science Tower. 200 Lothrop St.

department: T.E. Starzl Transplantation Institute. Dept. of Surgery

institute: University of Pittsburgh

description: Immature exosome replica 4

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: BeadStudio v3.3 was used to generate data. No normalization, J5 test for finding differentially expressed miRNAs.

source_name: Immature exosome

label_protocol: Cy3-labelled cDNAs were prepared with the Illumina microRNA Expression Profiling Assay.

growth_protocol: Bone marrow-derived DCs were grown in complete RPMI-1640 medium supplemented with 10% FCS, GM-CSF (1000U/ml) and IL-4 (500 U/ml).

extract_protocol: BMDCs and BMDC-derived exosomes (the latter purified by sucrose gradient and treated with 2microg/ml Rnase A, 37C, 10min) were disrupted with Trizol. RNA isolation was carried out with the miRNeasy Mini Kit (Quiagen). Samples were quantified by picogreen assay.

treatment_protocol: For generation of immature DCs, cultures were supplemented with 10nM vitamin D3 beginning on day 2. For generation of mature DCs, LPS (200ng/ml) was added 24 hr before exosomes harvesting. Exosomes were isolated from DC-culture supernatants of DCs maintained in medium with exosome-free FCS (overnight 100,000g centrifugation) during the last 48 hr of culture. DC-cultures were incubated with 100nM ionomycin (1 hr) before collecting the supernatants for exosome purification.

tag: cell type

value: Immature exosomes


title: Immature DC replica 2

description: Immature DC replica 2

source_name: Immature DC

value: Immature Dendritic cells


title: Mature exosome replica 4

description: Mature exosome replica 4

source_name: Mature exosome

value: Mature exosomes


title: Tenotomy-Treatment-Day2-Rep4

tag: tissue

value: Muscle;Gastrocnemius


title: SW480 Snail (1)

value: SW480-Snail, Snail expressing stable line


title: SW480 Vector (2)

description: SW480-Vector, vector control treated stable line

source_name: SW480, colon cancer cells


title: Casting-Treatment-Day14-Rep2

source_name: Gastroc Muscle, Casting, Day 14

value: Right

value: Casting

value: Day 14


title: SW480 Vector (1)

growth_protocol:
SW480 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM-high glucose; Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco)
atmosphere: air, 95%; carbon dioxide (CO2), 5%
temperature: 37.0°

value: SW480-Vector, vector control treated stable line


title: Mature DC replica 2

description: Mature DC replica 2

source_name: Mature DC

value: Mature Dendritic cells


title: Immature exosomes replica 3

description: Immature exosomes replica 3

source_name: Immature exosomes


title: Immature exosomes replica 2

description: Immature exosomes replica 2


title: Casting-Control-Day14-Rep6

source_name: Gastroc Muscle, Casting Control, Day 14

value: Male

value: Left


title: Casting-Treatment-Day14-Rep9


title: Casting-Treatment-Day14-Rep8


title: HT29 parental control(1)

description: HT29, colon cancer cells

source_name: colon cancer cells

growth_protocol:
the medium for this cell line is dmem. to make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.
atmosphere: air, 95%; carbon dioxide (CO2), 5%
temperature: 37.0°C

value: HT29, colon cancer cells


title: Casting-Treatment-Day14-Rep3


title: Casting-Control-Day14-Rep1


title: Casting-Control-Day14-Rep3


title: HT29 1st spheres (2)

description: HT29 cancer spheres

growth_protocol: Cells were cultured in tumor sphere medium consisting of DMEM-F12 (Gibco) with N2 Plus Supplement (R＆D,  Minneapolis, MN, USA ), 10 ng/ml recombinant bFGF (PeproTech Asia, Rehovot, Israel), 10 ng/ml EGF (PeproTech Asia, Rehovot, Israel) and 1% penicillin-streptomycine (Gibco).

value: HT29, cancer spheres


title: Immature DC replica 1

description: Immature DC replica 1


title: HT29 1st sphere(1)

description: HT29 cancer spheres

source_name: Colon cancer cells


title: Casting-Control-Day14-Rep7


title: Mature exosome replica 2

description: Mature exosome replica 2


title: Mature exosome replica 3

description: Mature exosome replica 3


title: Immature exosomes replica 1

description: Immature exosomes replica 1


title: HT29 parental control (2)

description: HT29, colon cancer cells

growth_protocol:
The medium for this cell line is DMEM. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.
atmosphere: air, 95%; carbon dioxide (CO2), 5%
temperature: 37.0°C


title: Casting-Treatment-Day14-Rep1


title: Mature exosome replica 1

description: Mature exosome replica 1


title: Casting-Treatment-Day14-Rep5


title: Casting-Control-Day14-Rep5


title: Casting-Treatment-Day14-Rep4


title: Casting-Control-Day14-Rep9


title: Casting-Control-Day14-Rep4


title: Mature DC replica 1

description: Mature DC replica 1


title: Casting-Treatment-Day14-Rep6


title: Casting-Control-Day14-Rep8


title: Casting-Control-Day14-Rep2


title: Casting-Control-Day7-Rep8

source_name: Gastroc Muscle, Casting Control, Day 7

value: Day 7


title: Casting-Treatment-Day14-Rep7


title: a pool of neonatal foreskin melanocytes from 4 individuals

type: genomic

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: a pool of cultured neonatal foreskin melanocytes from 4 individuals

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: The beta values for each site were calculated using the standard Illumina procedure using GenomeStudio software 2008.1 and provides a continuous, quantitative measurement of DNA methylation, ranging from 0 (completely unmethylated) to 1 (completely methylated).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: normal foreskin

label_protocol: Standard Illumina Protocol

growth_protocol: All cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum. Primary human melanocytes were obtained from neonatal foreskins and cultured in 10% heat-inactivated fetal calf serum (CSL, Melbourne, Australia) in RPMI-1640 medium supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 3 mM HEPES with the addition of 6 ng/ml cholera toxin and 16.2 nM phorbol 12-myristate 13-acetate (PMA).

extract_protocol: QIAGEN DNeasy Blood and Tissue Kits were used to isolate genomic DNA from cells in log phase growth as per the manufacturer’s instructions

treatment_protocol: Extracted genomic DNA was bisulfite treated using an EZ-96 DNA methylation kit (Zymo Research) as per the manufacturer’s instructions

value: normal

value: neonatal foreskin melanocytes (pooled from 4 individuals)


title: Casting-Treatment-Day7-Rep2

source_name: Gastroc Muscle, Casting, Day 7


title: Casting-Control-Day7-Rep5


title: Casting-Control-Day7-Rep7


title: Casting-Treatment-Day7-Rep4


title: Casting-Control-Day7-Rep4


title: Casting-Treatment-Day7-Rep7


title: Casting-Treatment-Day7-Rep1


title: melanoma cell line MM603

description: cultured melanoma cell line

source_name: melanoma tumor

value: MM

tag: matching cn sample id

tag: matching expn sample id


title: Casting-Treatment-Day7-Rep5

tag: gender


title: melanoma cell line MM386

description: cultured melanoma cell line


title: Casting-Control-Day7-Rep6


title: Casting-Treatment-Day7-Rep6


title: Casting-Control-Day7-Rep2


title: melanoma cell line D41

description: cultured melanoma cell line


title: Casting-Treatment-Day7-Rep3


title: Diseased plants rep4

city: Bonn

first: Muna

last: Sultan

address: nussalle 9

institute: university of Bonn

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suitesoftware.

data_processing: The microarray data normalization and background correction was performed using Guanine Cytosine Robust Multi-Array Analysis (GCRMA)

organism: Solanum lycopersicum

source_name: tomato leaves from inoculated plants with Phytophthora infestans

label_protocol: Biotinylated cRNA was labeled using a biotinylated nucleotide analog/ribonucleotide mix using GeneChip IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: Tomato plants cv. Money Maker of 5 weeks old were grown under greenhouse conditions. The plants were inoculated with 105 sporangia ml-1 of Phytophthora infestans (Mont.) de Bary. The whole plants were kept at 100% RH in the dark at 18°C and 12 hours post inoculation the leaves from both healthy non-inoculated and pathogen inoculated plants were used to extract the RNA.

extract_protocol: Total RNA isolation was performed using NucleoSpinTM 8 RNA Isolation Kit (Machery-Nagel GmbH & Co. KG, Düren, Germany) according to the manufacturer's instruction.

tag: cultivar

value: Money Maker

tag: tissue type

value: leaves

value: 12 hours post inoculation


title: Diseased plants rep2


title: melanoma cell line MM466

description: cultured melanoma cell line


title: melanoma cell line CJM

description: cultured melanoma cell line

value: CJM


title: melanoma cell line MM253

description: cultured melanoma cell line


title: melanoma cell line D24

description: cultured melanoma cell line


title: Diseased plants rep3


title: melanoma cell line MM96L

description: cultured melanoma cell line


title: melanoma cell line MM415

description: cultured melanoma cell line


title: melanoma cell line A06

description: cultured melanoma cell line


title: Casting-Control-Day7-Rep3

value: Muscle;Gastrocnemius

tag: treatment


title: melanoma cell line MM329

description: cultured melanoma cell line

tag: cell line


title: Healthy plants rep3

source_name: tomato leaves from non-inoculated plants


title: Diseased plants rep1


title: Casting-Control-Day7-Rep1


title: Healthy plants rep2


title: Healthy plants rep1


title: unmodified CK2α alone_Rep2

type: protein

city: Baltimore

first: Mary Katherine

last: Tarrant

state: MD

address: 725 N. Wolfe Street, 317 Hunterian Bldg.

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins University School of Medicine

description:
There were no cells, organisms, or extracts used in this study.  Semisynthetic and recombinant protein samples were used to catalyze phosphorylation of the proteins spotted on the microarray.
50 nM CK2α

hyb_protocol: Kinase assays were performed on the microarray by applying 50 mM Hepes pH 7.5, 80 mM NaCl, 10 mM MgCl2, 1 mM MnCl2,1 mM DTT, 0.1% NP-40, 100 μM ATP, 6 μCi [33P]γ-ATP, with 50 nM CK2α ± 100 nM Pin1 to the microarray and incubating at 30ᵒC for 30 min after the microarrays was blocked with SuperBlock blocking buffer (Thermo Scientific, 37535) for 3h at 4°C.  The microarrays were then washed in PBS/T, followed by washes with 0.1% SDS at RT and 0.1% SDS at 50°C, rinsed with ddH2O before being dried by spinning at 2000 RPM for 2 min.

scan_protocol: The microarray chips were exposed to x-ray film for 4 weeks, the film was scanned with a HP Scanjet 8300 scanner, and the results were inported into Gene Pix Pro Software.

data_processing: The scanned images of the exposed film for the microarray were imported into GenePix Pro Software.  The signal intensity of each spot on the microarray chips was quantified by dividing the median foreground intensity by its median background intensity.  To correct for the variance that are non-uniformly distributed on the chips, signal intensities of a set of spots within a block on a chip were normalized by setting the median intensity of that block equal to one, based on the assumption that proteins are randomly printed and only a limited number of proteins on a microarray are substrates of a kinase.

molecule: protein

organism: synthetic construct

source_name: semisynthetic unmodfied CK2α protein

label_protocol: 33P-γ-ATP was used in the reaction mixture.  CK2 is responsible for catalyzing the addition of the 33P labeled phosphoryl group to its protein substrates.

treatment_protocol: For the samples where both CK2α andPin1 were used, the two proteins were allowed to incubate together on ice for 30 min prior being added to the reaction mixture and applied to the microarray.

tag: tag

value: N-terminal HA-tag


title: pThr344 CK2α alone_Rep1

source_name: semisynthetic pThr344 CK2α protein


title: pThr344 CK2α alone_Rep2


title: pThr344 CK2α with Pin1_Rep1

description:
There were no cells, organisms, or extracts used in this study.  Semisynthetic and recombinant protein samples were used to catalyze phosphorylation of the proteins spotted on the microarray.
50 nM CK2α + 100 nM Pin1

source_name: semisynthetic pThr344 CK2α protein with recombinant Pin1


title: Casting-Control-Day2-Rep3

source_name: Gastroc Muscle, Casting Control, Day 2

value: Day 2


title: pThr344 CK2α with Pin1_Rep2


title: Casting-Treatment-Day2-Rep3

source_name: Gastroc Muscle, Casting, Day 2

value: Right

value: Casting


title: Casting-Treatment-Day2-Rep7

value: Male


title: Casting-Treatment-Day2-Rep8


title: Pfa modified CK2α alone_Rep2

description:
There were no cells, organisms, or extracts used in this study.  Semisynthetic and recombinant protein samples were used to catalyze phosphorylation of the proteins spotted on the microarray.
20 nM CK2α

hyb_protocol: Kinase assays were performed on the microarray by applying 50 mM Hepes pH 7.5, 80 mM NaCl, 10 mM MgCl2, 1 mM DTT, 0.1% NP-40, 100 μM ATP, 6 μCi [33P]γ-ATP, with 20 nM CK2α ± 24 nM CK2β to the microarray and incubating at 30ᵒC for 30 min after the microarrays was blocked with SuperBlock blocking buffer (Thermo Scientific, 37535) for 3h at 4°C.  The microarrays were then washed in PBS/T, followed by washes with 0.1% SDS at RT and 0.1% SDS at 50°C, rinsed with ddH2O before being dried by spinning at 2000 RPM for 2 min.

source_name: semisynthetic Pfa344 CK2α protein

treatment_protocol: For the samples where both CK2α andCK2β were used, the two proteins were allowed to incubate together on ice for 30 min prior being added to the reaction mixture and applied to the microarray.


title: control_no kinase

type: other

description:
There were no cells, organisms, or extracts used in this study.  Semisynthetic and recombinant protein samples were used to catalyze phosphorylation of the proteins spotted on the microarray.
reaction mixture only

molecule: other

source_name: no enzyme, reaction mixture only


title: unmodified CK2α with Pin1_Rep2

source_name: semisynthetic unmodfied CK2α protein with recombinant Pin1


title: Casting-Treatment-Day2-Rep4


title: unmodified CK2α alone_Rep2

source_name: semisynthetic unmodified CK2α protein


title: Casting-Control-Day2-Rep4

value: Left


title: unmodified CK2α with Pin1_Rep1


title: unmodified CK2α alone_Rep1


title: 4966_Glioblastoma_SID_6147

city: Los Angeles

first: Reshmi

last: Chowdhury

state: CA

address: 635 Charles E. Young Drive South

department: Neuro-Oncology

institute: UCLA

description: IDH1 status = MUT

hyb_protocol: Cy-3 and Cy-5 labeled amplicons were co-hybridized at 65oC for 40 hours to Agilent CpG Island microarrays according to manufacture's instructions.  After hybridization, slides were washed consecutively.

scan_protocol: Scanned by Agilent DNA Microarray Scanner G2505B

data_processing: Agilent Feature Extraction 10.5.3 (FE) Was used for extraction only.  Data analysis was done on unnormalized data from FE output (rProcessedSignal and gProcessSignal).  Probes were mapped to corresponding fragment from BfaI digestion (refer to ProbeFragmentMap.txt).  Loess curve was constructed based on insensitive fragments and Loess correction was applied to the the entire arrays. Data analysis follows method described in In silico enhanced restriction enzyme based methylation analysis of the human glioblastoma genome using Agilent 244K CpG Island microarrays By Tran et al (Frontiers In Neuroscience 2010).

source_name: HpaII Digested, Pre-treatment brain tumor cells

label_protocol: HpaII and MspI digests were labeled with Cyanine 5-dUTP and Cyanine 3-dUTP respectively (Perkin-Elmer, Waltham, MA) using Bioprime Array CGH Genomics Labeling Module (Invitrogen, Carlsbad, CA) according to manufacture's instructions.

extract_protocol: DNA was extracted using Qiagen Dneasy Blood and Tissue Kit (Qiagen, Valencia, CA)

treatment_protocol: Methylation-specific restriction enzyme: 750 ng of each genomic sample was digested with 25 units of BfaI (NEB, MA) for 6 hours at 37oC.  Digested DNA was then ligated to oligonucleotide linkers consisting of annealed H-12 (5'-TAATCCCTCGGA-3') and H-24 (5'-AGGCAACTGTGCTATCCGAGGGAT - 3') oligonucleotides.  Following ligation, the genomic DNA was divided into two equal portions for separate digestion with 20 units of HpaII (methylation-sensitive isoschizomer) or 40 units of MspI (methylation-insensitive isoschizomer) (NEB).    Each digest was subjected to PCR amplification using the same H-12/H-24 primers with the following conditions: 72°C for 5 minutes, followed by 16 cycles of 97°C for 1 minutes, 62°C for 30 seconds, 72°C for 3 minutes, followed by 72°C for 10 minutes.

tag: tumor type

value: Glioblastoma

tag: restriction enzyme

value: HpaII

tag: idh1 status

value: MUT

source_name: MspI Digested, Pre-treatment brain tumor cells

value: MspI


title: 5449_Anaplastic_Astrocytoma_SID_6403

description: IDH1 status = WT

value: Anaplastic

value: WT


title: Casting-Control-Day2-Rep1

tag: animal number

tag: tissue location


title: unmodified CK2α alone_Rep1


title: 5308_Lowgrade_Astrocytoma_SID_6134

description: IDH1 status = MUT

value: Lowgrade


title: 4969_Glioblastoma_SID_6167

description: IDH1 status = WT


title: Casting-Control-Day2-Rep5

tag: strain

tag: timepoint


title: 4591_Glioblastoma_SID_5845

description: IDH1 status = WT


title: 4877_Glioblastoma_SID_5889

description: IDH1 status = WT


title: 4970_Glioblastoma_SID_5656

description: IDH1 status = MUT


title: S-GlcNAc modified CK2α alone_Rep2

source_name: semisynthetic S-GlcNAc-Ser347 CK2α protein


title: Pfa modified CK2α alone_Rep1


title: Casting-Treatment-Day2-Rep2


title: Casting-Control-Day2-Rep2


title: 4968_Glioblastoma_SID_5638

description: IDH1 status = WT


title: Casting-Treatment-Day2-Rep5


title: Casting-Treatment-Day2-Rep1


title: Sham-Day14-Rep8

source_name: Gastroc Muscle, Sham, Day 14

value: Sham Surgery

value: Day 14


title: Casting-Control-Day2-Rep7


title: Casting-Control-Day2-Rep8


title: S-GlcNAc modified CK2α with CK2β_Rep2

description:
There were no cells, organisms, or extracts used in this study.  Semisynthetic and recombinant protein samples were used to catalyze phosphorylation of the proteins spotted on the microarray.
20 nM CK2α + 24 nM CK2β

source_name: semisynthetic S-GlcNAc-Ser347 CK2α protein with recombinant CK2β


title: 4576_Glioblastoma_SID_5574

description: IDH1 status = WT


title: Casting-Treatment-Day2-Rep9


title: Pfa modified CK2α with CK2β_Rep2

source_name: semisynthetic Pfa344 CK2α protein with recombinant CK2β


title: 4954_Glioblastoma_SID_5548

description: IDH1 status = WT


title: unmodified CK2α with CK2β_Rep1

source_name: semisynthetic unmodified CK2α protein with recombinant CK2β


title: Sham-Day14-Rep5


title: 4274_Glioblastoma_SID_5573

description: IDH1 status = WT


title: S-GlcNAc modified CK2α alone_Rep1


title: 4230_Glioblastoma_SID_5578

description: IDH1 status = WT


title: Pfa modified CK2α with CK2β_Rep1


title: Naïve-Day0-Rep1

source_name: Gastroc Muscle, Naive, Day 0

value: Day 0


title: unmodified CK2α with CK2β_Rep2


title: Sham-Day2-Rep2

source_name: Gastroc Muscle, Sham, Day 2

value: Muscle;Gastrocnemius


title: 4878_Glioblastoma_SID_5502

description: IDH1 status = WT


title: SC4

city: Toon

first: Alejandro

last: Mayorca-Guiliani

state: Ehime

address: Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

description: SAMPLE 1

hyb_protocol: RNA hybridization was conducted with GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays (Affymetrix, USA) using the GeneAtlas System.

scan_protocol: Arrays were scanned by the GeneAtlas Imaging Station incorporated on the GeneAtlas System.

data_processing: Data was generated by the GeneAtlas Instrument Control Software and the Partek express software for statistical analysis. The data was the filtered using the GeneSpring GX software. The processing algorithm used is RMA

source_name: SASL1m Cells

label_protocol: RNA was labeled with the 3'-IVT Labeling Kit (Affymetrix) according to manufacturer's instructions.

growth_protocol: Both cell lines were cultured in DMEM supplemented with Fetal Bovine Serum 10% and Penicillin-Streptomycin 1% until confluence.

extract_protocol: Culture medium was aspirated from plates. The plates were flushed with 1 ml of ISOGEN (Nippongene, Japan). The mix was collected and centrifuged. The fraction containing Total RNA was collected, the rest discarded. RNA was then decanted and concentrated to 1ɥg/ɥl. RNA was the checked for purity (Eukaryote Total RNA nano Series II, Agilent, USA).

tag: cell type

value: Oral Squamous Cell Carcinoma


title: Sham-Day7-Rep5

source_name: Gastroc Muscle, Sham, Day 7

tag: tissue

value: Day 7


title: 4273_Glioblastoma_SID_5506

description: IDH1 status = WT


title: Sham-Day2-Rep1

value: Right

value: Day 2


title: 4967_Glioblastoma_SID_5438

description: IDH1 status = WT


title: 4879_Glioblastoma_SID_5425

description: IDH1 status = WT


title: AC-1

description: SAMPLE 2

source_name: ACC2 Cells

value: Adenoid Cystic Carcinoma


title: S-GlcNAc modified CK2α with CK2β_Rep1

value: N-terminal HA-tag


title: Sham-Day14-Rep7

value: Male


title: 4595_Glioblastoma_SID_5356

description: IDH1 status = WT

value: Glioblastoma

value: HpaII


title: 4955_Glioblastoma_SID_5388

description: IDH1 status = WT

value: MspI


title: 4953_Glioblastoma_SID_5396

description: IDH1 status = WT


title: iPS4 from HFF1-b

city: Berlin

first: Ying

last: Wang

address: Ihnestrasse 63

department: Vertebrate Genomics

institute: Max Planck Institute for Molecular Genetics

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

source_name: iPS4 from HFF1

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand  reverse transcription step, followed by a single in vitro transcription  (IVT) amplification that incorporates biotin-labeled nucleotides.  Subsequent steps include array hybridization, washing, blocking, and  streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively  detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion  (RNase-free DNase Set, Quiagen) has been applied on the columns during  isolation.

value: iPSCs

tag: cell stage

value: Passage 10


title: iPS4 from HFF1-a

description: replicate 1


title: Naïve-Day0-Rep7


title: H9

description: replicate 2

value: Passage 55

value: hESCs


title: iPS2 from HFF1-a

description: replicate 1

source_name: iPS2 from HFF1


title: Sham-Day14-Rep6

value: Sham Surgery

value: Day 14


title: Sham-Day7-Rep2

value: Muscle;Gastrocnemius


title: iPS2 from HFF1-b

description: replicate 2


title: H1

description: replicate 1


title: 4593_Glioblastoma_SID_5359

description: IDH1 status = WT

value: WT


title: Sham-Day7-Rep6

value: Day 7


title: 4574_Glioblastoma_SID_5386

description: IDH1 status = WT


title: Sham-Day2-Rep3

value: Right


title: 4594_Glioblastoma_SID_5303

description: IDH1 status = MUT

value: MUT


title: 1327_Glioblastoma_SID_5256

description: IDH1 status = WT


title: HFF1-48 h post-transduction-b

description: replicate 2

value: OSKM-transduced HFF1 cells after 48h

value: 48h post-transduction

value: OSKM-transduced neonatal foreskin fibroblasts


title: Sham-Day14-Rep4

value: Male


title: Sham-Day14-Rep1


title: HFF1-72 h post-transduction-a

description: replicate 1

value: OSKM-transduced HFF1 cells after 72h

value: 72h post-transduction


title: 5639_Glioblastoma_IDH1_positive_SID_5234

description: IDH1 status = MUT

value: Glioblastoma

value: HpaII

value: MspI


title: HFF1-24 h post-transduction-b

description: replicate 2

value: OSKM-transduced HFF1 cells after 24h

value: 24h post-transduction


title: Sham-Day14-Rep2

value: Sham Surgery

value: Day 14


title: HFF1-72 h post-transduction-b

description: replicate 2


title: Sham-Day7-Rep3

value: Muscle;Gastrocnemius


title: 5642_Glioblastoma_IDH1_positive_SID_5239

description: IDH1 status = MUT


title: HFF1-48 h post-transduction-a

description: replicate 1


title: 4249_Glioblastoma_SID_4916

description: IDH1 status = WT

value: WT


title: 5448_Anaplastic_Astrocytoma_SID_5264

description: IDH1 status = WT

value: Anaplastic


title: HFF1-a

description: replicate 1

value: HFF1 (purchased from ATCC)

value: Passage 8

value: neonatal foreskin fibroblasts


title: 5447_Anaplastic_Astrocytoma_SID_4771

description: IDH1 status = WT


title: 4228_Glioblastoma_SID_4927

description: IDH1 status = WT


title: Naïve-Day0-Rep2

value: Right

value: Day 0


title: 4275_Glioblastoma_SID_4687

description: IDH1 status = MUT

value: MUT


title: 5459_Anaplastic_Astrocytoma_SID_4578

description: IDH1 status = MUT


title: HFF1-24 h post-transduction-a

description: replicate 1

value: OSKM-transduced neonatal foreskin fibroblasts


title: 5311_Lowgrade_Astrocytoma_SID_4791

description: IDH1 status = MUT

value: Lowgrade


title: HFF1-b

description: replicate 2


title: Naïve-Day0-Rep6

value: Male


title: Sham-Day14-Rep3


title: Sham-Day7-Rep4

value: Day 7


title: Naïve-Day0-Rep3


title: Sham-Day7-Rep7


title: 5458_Anaplastic_Astrocytoma_SID_2470

description: IDH1 status = WT

value: HpaII

value: MspI


title: 5436_Anaplastic_Astrocytoma_SID_2180

description: IDH1 status = MUT


title: Naïve-Day0-Rep4


title: Casting-Control-Day2-Rep6

source_name: Gastroc Muscle, Casting Control, Day 2

value: Left

value: Day 2


title: Naïve-Day0-Rep5

value: Muscle;Gastrocnemius


title: 5306_Lowgrade_Astrocytoma_SID_4432

description: IDH1 status = WT

value: WT


title: Olive_oil_fed_70perc-pool3

status: Public on Oct 24 2011

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description:
Olive_oil_70p_3
hepatic gene expression
70-OO-P12.CEL

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: CEL files were generated using GCOS and utilized for analysis using GeneSpring  v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values

source_name: rat liver

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol:
Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

treatment_protocol: Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.

value: Sprague-Dawley

tag: dietary oil

value: Olive oil

tag: oil concentration

value: male


title: Sham-Day7-Rep1

tag: gender

value: Sham Surgery


title: Casting-Treatment-Day2-Rep10

source_name: Gastroc Muscle, Casting, Day 2

value: Right

value: Casting


title: Corn_oil_fed_70perc-pool2

description:
Corn_oil_70p_2
hepatic gene expression
70-CO-P8.CEL

value: Corn oil


title: Casting-Control-Day2-Rep9


title: Corn_oil_fed_70perc-pool3

description:
Corn_oil_70p_3
hepatic gene expression
70-CO-P9.CEL


title: Casting-Treatment-Day2-Rep6


title: 5310_Lowgrade_Astrocytoma_SID_3454

description: IDH1 status = MUT

source_name: HpaII Digested, Pre-treatment brain tumor cells

value: MUT


title: 5643_Glioblastoma_IDH1_positive_SID_2376

description: IDH1 status = MUT

value: Glioblastoma

source_name: MspI Digested, Pre-treatment brain tumor cells


title: 5309_Lowgrade_Astrocytoma_SID_2206

description: IDH1 status = MUT

value: Lowgrade


title: Olive_oil_fed_70perc-pool1

description:
Olive_oil_70p_1
hepatic gene expression
70-OO-P10.CEL


title: 5646_Anaplastic_Astrocytoma_SID_747

description: IDH1 status = MUT

value: Anaplastic


title: Olive_oil_fed_70perc-pool2

description:
Olive_oil_70p_2
hepatic gene expression
70-OO-P11.CEL


title: 5640_Glioblastoma_IDH1_positive_SID_2009

description: IDH1 status = MUT

value: HpaII


title: Corn_oil_fed_70perc-pool1

description:
Corn_oil_70p_1
hepatic gene expression
70-CO-P7.CEL


title: Olive_oil_fed_5perc-pool1

description:
Olive_oil_5p_1
hepatic gene expression
5-OO-P4.CEL


title: Corn_oil_fed_5perc-pool3

description:
Corn_oil_5p_3
hepatic gene expression
5-CO-P3.CEL


title: Corn_oil_fed_5perc-pool2

description:
Corn_oil_5p_2
hepatic gene expression
5-CO-P2.CEL


title: Corn_oil_fed_5perc-pool1

description:
Corn_oil_5p_1
hepatic gene expression
5-CO-P1.CEL


title: Olive_oil_fed_5perc-pool2

description:
Olive_oil_5p_2
hepatic gene expression
5-OO-P5.CEL


title: Olive_oil_fed_5perc-pool3

description:
Olive_oil_5p_3
hepatic gene expression
5-OO-P6.CEL


title: NS2

first: Jose

last: Silva

state: Cambridgeshire

address: Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: Wellcome Trust Centre for Stem Cell Research

description: replicate 2

hyb_protocol: Hybrization were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).

scan_protocol: Staining and scanning were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).

data_processing: The data were filtered removing any probes with a detection p-value above 0.01 for all the samples in the set. This remove any probes not detected at all in the set. It has been done before transformation via variance stabilisation and normalisation in order to reduce the noise of the set before normalisation. The data were then transformed using VST (Variance Stabilizing Transform) and normalised by quantile normalisation.

source_name: nanog null neural stem cell 2

label_protocol: Amplification and labeling of RNA were performed according to the TotalPrep-96 RNA Amplification Kit for the Illumina platform (Ambion).

growth_protocol: iPS and ES cells were cultured in N2B27 medium (Stem Cell Sciences, SCS-SF-NB-02) supplemented with LIF and 2i inhibitors (Ying et al., 2008), CHIR99021 (3μM) and PD0325901 (1μM).

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen)

value: nanog null neural stem cells


title: mNanog iPS 5

description: replicate 5

source_name: mouse Nanog iPS cells

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen)

value: mouse Nanog iPS cells


title: cNanog iPS 1

description: replicate 1

source_name: chick Nanog iPS cells

value: chick Nanog iPS cells


title: zNanog iPS 2

description: replicate 2

source_name: zebrafish Nanog iPS cells

value: zebrafish Nanog iPS cells


title: cNanog iPS 2

description: replicate 2


title: NS3

description: replicate 3

source_name: nanog null neural stem cell 3


title: mNanog iPS 4

description: replicate 4


title: zNanog iPS 1

description: replicate 1


title: ES1

description: replicate 1

source_name: embryonic stem cell1

value: embryonic stem cells


title: ES2

description: replicate 2

source_name: embryonic stem cell 2


title: NS1

description: replicate 1

source_name: nanog null neural stem cell 1


title: ES3

description: replicate 3

source_name: embryonic stem cell 3


title: RE:A498 (69227)

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description: Renal cancer cell line RE:A498 compared to Male human reference

hyb_protocol: Hybridization was carried out at NimbleGen. In brief, the Cy3-labeled test sample and Cy5-labeled reference sample were combined and hybridized overnight at 42°C in NimbleGen Hybridization Buffer (NimbleGen Systems).  Arrays were washed with the NimbleGen Wash Buffer System (NimbleGen Systems) and immediately dried down by centrifugation.

scan_protocol: Arrays were scanned (at NimbleGen) at 5 um resolution using the GenePix4000B scanner (Axon Instruments). Data was extracted from scanned images using NimbleScan 2.0 software (NimbleGen Systems) and the extracted intensity for each spot was saved as raw data.

data_processing: Probes were mapped to human genome reference HG19 (NCBI 37) to provide chromosome and position annotations. After taking ratio of sample/reference, log to the base 2 was taken. Dye bias was calculated using the one sample (LC:A549) with dye flips and subtracted from all arrays. Probe bias was calculated as described in article and subtracted from all probes. R (64-bit ver. 2.13.0) was used to do log2 transformation of the ratio (sample/reference). The log ratio was corrected for dye and probe bias (as described in article).

label_protocol: Purified genomic DNA (1 ug) was fragmented and labeled by random priming with Cy3- or Cy5-labeled random 9mer oligos.

growth_protocol: As described previously (Pubmed ID: 17272646) using conditions based on those adopted by DTP for their drug screen and harvested at ~80% confluence.

extract_protocol: Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions.  Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).

treatment_protocol: Untreated

tag: tissue of origin

value: Renal

tag: age

tag: Sex

value: F

tag: epithelial

value: yes

tag: ploidy

value: 3n, Triploid (69)

tag: p53 mutation

value: WT

tag: doubling time

tag: sample description

value: Adenocarcinoma

source_name: Male human reference

value: M

value: Pool of six normal male samples


title: RE:RXF-393 (69230)

description: Renal cancer cell line RE:RXF-393 compared to Male human reference

tag: cell line

tag: prior treatment

value: MT

value: hypernephroma-poor differentiation


title: hNanog iPS 3

description: replicate 3

source_name: human Nanog iPS 3

value: nanog iPS cells

tag: strain


title: RE:UO-31 (69232)

description: Renal cancer cell line RE:UO-31 compared to Male human reference

value: Renal cell carcinoma-very poorly differentiated


title: hNanog iPS 1

description: replicate 1

source_name: human Nanog iPS 1

tag: cell type


title: hNanog iPS 2

description: replicate 2

source_name: human Nanog iPS 2


title: mNanog iPS 3

description: replicate 3


title: PR:PC-3 (69226)

description: Prostate cancer cell line PR:PC-3 compared to Male human reference

value: Prostate

value: 4n, Tetraploid (92)


title: OV:NCI/ADR-RES (69223)

description: Ovarian cancer cell line OV:NCI/ADR-RES compared to Male human reference

value: Ovarian


title: OV:OVCAR-4 (69220)

description: Ovarian cancer cell line OV:OVCAR-4 compared to Male human reference

value: CyPh/CsPt/Adr

value: Adenocarcinoma-moderate differentiation


title: RE:786-0 (69229)

description: Renal cancer cell line RE:786-0 compared to Male human reference

value: Renal


title: OV:OVCAR-5 (69221)

description: Ovarian cancer cell line OV:OVCAR-5 compared to Male human reference

value: F

value: 2n+, Hyperdiploid (47-57)

value: Adenocarcinoma-well differentiated


title: ME:UACC-62 (69219)

description: Melanoma cancer cell line ME:UACC-62 compared to Male human reference

value: Melanoma

value: no

value: WT

value: Melanotic melanoma


title: RE:SN12C (69231)

description: Renal cancer cell line RE:SN12C compared to Male human reference

value: M

value: yes

value: 3n, Triploid (69)

value: MT

value: Renal cell carcinoma-poor differentiation

value: Pool of six normal male samples


title: RE:ACHN (69228)

description: Renal cancer cell line RE:ACHN compared to Male human reference

value: Rad/VB/CCNU/Mto/Pred

value: Renal cell carcinoma-poor to moderate differentiation


title: OV:SKOV3 (69224)

description: Ovarian cancer cell line OV:SKOV3 compared to Male human reference

value: Ovarian

value: Thiotepa

tag: source

value: Ascites


title: Control_rep4

city: Oxford

first: Natasha

last: Sahgal

address: Old Road Campus

department: Ludwig Institute of Cancer Research

institute: University of Oxford

description: replicate 4

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background corrected, filtered and then normalised using the vsn package in R

source_name: Cysts

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

extract_protocol: Total RNA extracted using MirVana (Ambion) as per protocol

value: 15 weeks

tag: genotype/variation

value: Control


title: OV:OVCAR-8 (69222)

description: Ovarian cancer cell line OV:OVCAR-8 compared to Male human reference

value: F

value: Ctx/Adr/CsPt/CyPh

value: 2n+, Hyperdiploid (47-57)

value: Carcinoma-undifferentiated


title: Control_rep2

description: replicate 2


title: Control_rep3

description: replicate 3


title: PR:DU-145 (69225)

description: Prostate cancer cell line PR:DU-145 compared to Male human reference

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: prostate; metastatic site:brain; carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)


title: mNanog iPS 2

description: replicate 2

value: nanog iPS cells


title: ME:SK-MEL-5 (69216)

description: Melanoma cancer cell line ME:SK-MEL-5 compared to Male human reference

value: Melanoma

value: no

value: 4n+, Hypertetraploid (93-103)

value: WT

value: Malignant melanotic melanoma

value: Pool of six normal male samples


title: Control_rep1

description: replicate 1

value: 15 weeks

value: Control


title: Hif1a/Fh1 KO_rep3

description: replicate 3

value: Hif1a/Fh1 KO


title: OV:IGROV-1 (69218)

description: Ovarian cancer cell line OV:IGROV-1 compared to Male human reference

value: Ovarian

value: F

value: Rad

value: yes

value: MT


title: Hif1a/Fh1 KO_rep4

description: replicate 4


title: ME:SK-MEL-2 (69214)

description: Melanoma cancer cell line ME:SK-MEL-2 compared to Male human reference

value: M

value: Metastasis

value: 4n-, Hypotetraploid (81-91)


title: LE:MOLT-4 (66649)

description: Leukemia cancer cell line LE:MOLT-4 compared to Male human reference

value: Leukemia

value: PB

value: 4n, Tetraploid (92)

value: ALL (cells were taken when patient was in relapse)


title: ME:MALME-3M (69209)

description: Melanoma cancer cell line ME:MALME-3M compared to Male human reference

value: Melanoma

value: no

value: WT

value: Malignant melanotic melanoma


title: mNanog iPS 1

description: replicate 1

value: nanog iPS cells


title: LC:NCI-H226 (64901)

description: Non-Small Cell Lung cancer cell line LC:NCI-H226 compared to Male human reference

value: Non-Small Cell Lung

value: None (non smoker)

value: 3n, Triploid (69)

value: Squamous cell carcinoma-very poorly differentiated

value: Pool of six normal male samples


title: ME:MDA-N (69213)

description: Melanoma cancer cell line ME:MDA-N compared to Male human reference

value: F

value: Pleural effusion

value: MT

value: Ductal carcinoma-mammary gland; breast; duct; metastatic site:pleural effusion;

value: M


title: Hif1a/Fh1 KO_rep1

description: replicate 1

value: 15 weeks

value: Hif1a/Fh1 KO


title: Fh1 KO_ rep4

description: replicate 4

value: Fh1 KO


title: ME:SK-MEL-28 (69215)

description: Melanoma cancer cell line ME:SK-MEL-28 compared to Male human reference

value: Melanoma

value: no

value: 4n-, Hypotetraploid (81-91)


title: OV:OVCAR-8 (64899)

value: Ovarian

value: Ctx/Adr/CsPt/CyPh

value: yes

value: 2n+, Hyperdiploid (47-57)

value: Carcinoma-undifferentiated


title: Hif1a/Fh1 KO_rep2

description: replicate 2


title: Fh1 KO_ rep3

description: replicate 3


title: Fh1 KO_ rep2

description: replicate 2


title: OV:OVCAR-3 (64892)

description: Ovarian cancer cell line OV:OVCAR-3 compared to Male human reference

value: CyPh/CsPt/Adr

value: Ascites

value: Adenocarcinoma-moderate differentiation

value: Pool of six normal male samples


title: RE:CAKI-1 (64887)

description: Renal cancer cell line RE:CAKI-1 compared to Male human reference

value: Renal

value: Metastasis

value: 3n, Triploid (69)

value: WT

value: Clear cell carcinoma


title: LE:SR (61073)

description: Leukemia cancer cell line LE:SR compared to Male human reference

value: Leukemia

value: M

value: Lymphoma


title: Fh1 KO_ rep1

description: replicate 1

value: 15 weeks

value: Fh1 KO


title: ME:UACC-257 (64895)

description: Melanoma cancer cell line ME:UACC-257 compared to Male human reference

value: Melanoma

value: no

value: 3n+, Hypertriploid (70-80)

value: Melanotic melanoma


title: kidney-non infected control-BR2-3

city: Greifswald

first: Maren

last: Depke

address: Friedrich-Ludwig-Jahn-Straße 15a

hyb_protocol: The host RNA expression profile was analyzed on GeneChip Mouse Gene 1.0 ST arrays (Affymetrix) using the Whole Transcript (WT) Sense Target Labeling and Control reagents according to the manufacturer’s instructions. Arrays were washed and stained in a GeneChip FluidicsStation 450 and scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The array image files (CEL) were first quality controlled in the Expression Console software (Affymetrix) and then imported into the Rosetta Resolver software (Rosetta Biosoftware) for data analysis. Signals were generated and normalized using the RMA algorithm. Groups were compared in log-transformed space using error-weighted one-way ANOVA with Benjamini-Hochberg False Discovery Rate multiple testing correction and p* < 0.01 was regarded as significant.  The control sequences and sequences that were not considered expressed on all arrays belonging to the selected group comparison (with p > 0.01 on intensity profile level in Rosetta Resolver software) were not included in statistical testing. Afterwards, sequence sets were translated into EntrezGene records using the Rosetta Resolver annotation of December 2009. Two criteria were used for definition of differential expression: Significance in ANOVA statistical testing and a minimal absolute fold change of 2. Further criteria only applied to the comparison of infection with non-infected controls: Significance in ANOVA statistical testing and a minimal absolute fold change of 2 in at least one of two comparisons (“infection with HG001” vs. “control”; “infection with HG001 ΔsigB” vs. “control”). Genes significant in ANOVA but with a minimal absolute fold change of only 1.5 in at least one of two comparisons were considered to be regulated by trend.

source_name: murine kidney d5 control

extract_protocol: Kidneys were explanted and immediately frozen in liquid nitrogen. Afterwards, both kidneys of the mice were homogenized using a mortar filled with liquid nitrogen.  Kidney tissue was mixed with 0.5 ml TRIzol (Invitrogen) under liquid nitrogen and then mechanically disintegrated at 2600 rpm for 2 min in a bead mill (Mikrodismembrator S, B. Braun Biotech International GmbH). After addition of further 0.5 ml TRIzol and incubation for 10 min at room temperature, RNA isolation was performed according to the manufacturer’s protocol with the following modifications: i) overnight RNA precipitation at -20°C; ii) pelleting the RNA precipitate for 30 min at 20000 x g.  The resulting RNA was DNase treated (6.8 Kunitz units) for 10 min at room temperature (QIAGEN GmbH) and afterwards purified using a RNA Clean-Up and Concentration Kit (Norgen Biotek Corp.). RNA concentrations were determined photometrically (NanoDrop Technologies), and the quality was controlled with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Female BALB/c mice (Charles River) were i.v. infected in two biological replicates with 5E+07 to 7E+07 colony-forming units (CFUs) of S. aureus HG001 or 5E+07 to 8E+07 CFUs of S. aureus HG001 ΔsigB. As a control, another group of mice received an injection of 100 µl physiological saline solution. Mice were sacrificed after 4 (1. biological replicate) or 5 days (2. biological replicate).

value: BALB/c

value: female

tag: tissue

value: kidney


title: kidney-non infected control-BR2-4

scan_protocol: Arrays were washed and stained in a GeneChip FluidicsStation 450 and scanned with a GeneChip Scanner 3000 (Affymetrix).

label_protocol: The host RNA expression profile was analyzed on GeneChip Mouse Gene 1.0 ST arrays (Affymetrix) using the Whole Transcript (WT) Sense Target Labeling and Control reagents according to the manufacturer’s instructions.


title: kidney-non infected control-BR2-1


title: kidney-non infected control-BR2-5


title: kidney-infected with S aureus HG001 ΔsigB-BR2-3

description: BR2_inf sigB

source_name: murine kidney d5 post infection with HG001 ΔsigB


title: ME:MDA-MB-435 (60774)

description: Melanoma cancer cell line ME:MDA-MB-435 compared to Male human reference

value: F

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)

value: MT

value: Ductal carcinoma-mammary gland; breast; duct; metastatic site:pleural effusion;

value: Pool of six normal male samples


title: kidney-infected with S aureus HG001 ΔsigB-BR2-4

description: BR2_inf sigB


title: kidney-non infected control-BR2-2


title: kidney-infected with S aureus HG001 ΔsigB-BR2-5

description: BR2_inf sigB


title: LE:K-562 (60043)

description: Leukemia cancer cell line LE:K-562 compared to Male human reference

value: Leukemia

value: Bisulfan/PiBr

value: 3n-, Hypotriploid (58-68)

value: CML

value: M


title: LE:HL-60 (60085)

description: Leukemia cancer cell line LE:HL-60 compared to Male human reference

value: no

value: PBL

value: Pro myelocytic leukemia


title: kidney-infected with S aureus HG001 ΔsigB-BR2-2

description: BR2_inf sigB

value: BALB/c


title: LC:HOP-92 (59214)

description: Non-Small Cell Lung cancer cell line LC:HOP-92 compared to Male human reference

value: Non-Small Cell Lung

value: yes

value: Large cell-undifferentiated


title: kidney-infected with S aureus HG001-BR2-4

description: BR2_inf wt

source_name: murine kidney d5 post infection with HG001

value: female

value: kidney


title: LC:EKVX (59988)

description: Non-Small Cell Lung cancer cell line LC:EKVX compared to Male human reference

value: MT

value: Adenocarcinoma-moderate differentiation


title: kidney-infected with S aureus HG001-BR2-2

description: BR2_inf wt


title: kidney-infected with S aureus HG001-BR2-3

description: BR2_inf wt


title: kidney-infected with S aureus HG001-BR2-5

description: BR2_inf wt


title: LE:RPMI-8226 (60698)

description: Leukemia cancer cell line LE:RPMI-8226 compared to Male human reference

value: PB

value: WT

value: Myeloma

value: Pool of six normal male samples


title: RE:TK10 (59234)

description: Renal cancer cell line RE:TK10 compared to Male human reference

value: Renal

value: 4n, Tetraploid (92)

value: Renal Spindle cell carcinoma


title: kidney-infected with S aureus HG001 ΔsigB-BR1-5

description: BR1_inf sigB

source_name: murine kidney d4 post infection with HG001 ΔsigB


title: kidney-infected with S aureus HG001-BR2-1

description: BR2_inf wt


title: ME:LOXIMVI (59327)

description: Melanoma cancer cell line ME:LOXIMVI compared to Male human reference

value: Melanoma

value: M

value: no

value: Malignant amelanotic melanoma


title: LC:NCI-H23 (59209)

description: Non-Small Cell Lung cancer cell line LC:NCI-H23 compared to Male human reference

value: Non-Small Cell Lung

value: yes

value: 2n+, Hyperdiploid (47-57)

value: Adenocarcinoma-undifferentiated


title: LE:CCRF-CEM (59223)

description: Leukemia cancer cell line LE:CCRF-CEM compared to Male human reference

value: Leukemia

value: F

value: Rad/Mtx/Cyx

value: MT

value: ALL


title: LC:HOP-62 (59212)

description: Non-Small Cell Lung cancer cell line LC:HOP-62 compared to Male human reference

value: 4n+, Hypertetraploid (93-103)

value: adenocarcinoma-undifferentiated

value: Pool of six normal male samples


title: CO:SW620 (58607)

description: Colon cancer cell line CO:SW620 compared to Male human reference

value: Colon

value: Carcinoma-undifferentiated


title: LC:NCI-H322M (59134)

description: Non-Small Cell Lung cancer cell line LC:NCI-H322M compared to Male human reference

value: M

value: Small cell Bronchioalveolar Carcinoma


title: LC:NCI-H460 (59507)

description: Non-Small Cell Lung cancer cell line LC:NCI-H460 compared to Male human reference

value: Pleural effusion

value: WT

value: Large Cell Carcinoma-undifferentiated


title: LC:NCI-H522 (57901)

description: Non-Small Cell Lung cancer cell line LC:NCI-H522 compared to Male human reference

value: Non-Small Cell Lung

value: yes


title: kidney-infected with S aureus HG001 ΔsigB-BR1-1

description: BR1_inf sigB

value: BALB/c

value: female

value: kidney


title: ME:M14 (58192)

description: Melanoma cancer cell line ME:M14 compared to Male human reference

value: Melanoma

value: no

value: MT

value: Melanotic melanoma


title: kidney-infected with S aureus HG001-BR1-3

description: BR1_inf wt

source_name: murine kidney d4 post infection with HG001


title: kidney-infected with S aureus HG001 ΔsigB-BR1-4

description: BR1_inf sigB


title: kidney-infected with S aureus HG001 ΔsigB-BR2-1

description: BR2_inf sigB


title: CO:KM12 (57550)

description: Colon cancer cell line CO:KM12 compared to Male human reference

value: Adenocarcinome-poor differentiation

value: Pool of six normal male samples


title: CO:HCT116 (57428)

description: Colon cancer cell line CO:HCT116 compared to Male human reference

value: Colon

value: 2n-, Hypodiploid (35-45)

value: carcinoma-very poorly differentiated


title: BR:MCF7 (59116)

description: Breast cancer cell line BR:MCF7 compared to Male human reference

value: Breast

value: F

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: Adenocarcinoma-mammary gland; breast; metastatic site:pleural effusion;

value: M


title: kidney-infected with S aureus HG001 ΔsigB-BR1-3

description: BR1_inf sigB

value: BALB/c

value: female


title: CO:HCC-2998 (57480)

description: Colon cancer cell line CO:HCC-2998 compared to Male human reference

value: yes

value: carcinoma


title: kidney-infected with S aureus HG001 ΔsigB-BR1-2

description: BR1_inf sigB

value: kidney


title: CNS:U251 (57445)

description: CNS cancer cell line CNS:U251 compared to Male human reference

value: CNS

value: no

value: 2n+, Hyperdiploid (47-57)

value: MT

value: Glioblastoma-undifferentiated


title: CO:HCT-15 (57425)

description: Colon cancer cell line CO:HCT-15 compared to Male human reference

value: Colon

value: Adenocarcinoma-poor to moderate differentiation

value: Pool of six normal male samples


title: CO:COLO205 (57442)

description: Colon cancer cell line CO:COLO205 compared to Male human reference

value: Ascites

value: 3n, Triploid (69)

value: Adenocarcinoma


title: kidney-infected with S aureus HG001-BR1-4

description: BR1_inf wt


title: OmpR-dependent genes - Slide D

first: Dongsheng

last: Zhou

address: NO.20 Dongdajie, Fengtai

institute: Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China

description: Slide D

hyb_protocol: For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5 xSSC, 0.1% SDS and 0.1% BSA) at 42 °C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then dried with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5 ×SSC, 0.1% SDS, 5 ×Denhardt’s solution, and 0.5µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98 °C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42 °C for 18 to 20 hr in a hybridization incubator (Robbins Scientific).

scan_protocol: After hybridization, the slides were washed in 1 ×SSC with 0.06 % SDS for 2 min, then in 0.06 ×SSC for 2 min and finally in ethanol for 1 min. The resulting slides were dried and then scanned at a resolution of 10 µm by using a GenePix Personal 4100A Microarray Scanner (Axon Instruments).

data_processing:
For microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Accordingly, for each time point, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. The scanning images were processed and the data were further analyzed by using GenePix Pro 4.1 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two fold of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods. The normalized log2 ratio of ΔompR /WT signal for each spot was recorded. Genes with less than six data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the four replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software. After the SAM analysis, only genes with at least two-fold changes in expression were collected for further analysis.

Raw data are unavailable due to computer disk failure.

organism: Yersinia pestis

source_name: WT

label_protocol: Genome directed primers (GDPs) were designed by using FindGDPs software (University of Texas Southwestern Medical Center at Dallas). The desired length of GDPs was set as hexamers, and 50% of the 3' end of each ORF was defined as target region to scan for GDPs. Finally, 42 GDPs were picked out for annealing to all the 4005 genes of Y. pestis represented on the microarray. Three separated labeled probes for each RNA preparation were made as technical replicates. For the total of six replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70 °C for 10 min, and cooled quickly on ice. 1 µl of rRNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42 °C for 1 hr, followed by the addition of a 200 U of Superscript II reverse transcriptase. The mixture was incubated at 42 °C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65 °C for 20 min. The mixture was neutralized by the addition of HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50 °C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 or Cy3 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH 9.3) and incubated for 2h at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50 °C, and was stored at -20 °C until use.

extract_protocol: Total RNA was extracted from four independent cell cultures. Before bacterial harvest, double-volume of RNAprotect Bacteria Reagent (Qiagen) was added immediately to each cell culture. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter). RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

tag: biovar

value: microtus

source_name: ompR null mutant (ΔompR)


title: CNS:SF-268 (56799)

description: CNS cancer cell line CNS:SF-268 compared to Male human reference

value: F

value: Rad

value: M


title: kidney-infected with S aureus HG001-BR1-1

description: BR1_inf wt

value: BALB/c

tag: gender

value: female


title: OmpR-dependent genes - Slide B

description: Slide B


title: OmpR-dependent genes - Slide A

description: Slide A


title: OmpR-dependent genes - Slide C

description: Slide C


title: kidney-infected with S aureus HG001-BR1-2

description: BR1_inf wt

value: kidney


title: LC:A549 (57014)

description: Non-Small Cell Lung cancer cell line LC:A549 compared to Male human reference

tag: tissue of origin

value: Non-Small Cell Lung

value: yes

value: WT


title: LC:A549 (57365)

description: Non-Small Cell Lung cancer cell line LC:A549 compared to Male human reference (dye flipped)

tag: age


title: Migrated_EX0802_09

city: Amsterdam

first: Marijke

last: Maijenburg

address: Plesmanlaan 125

department: Experimental Immunohematology

country: Netherlands

institute: Sanquin Research

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: RMA + GC correction by Partek software version 6.4

source_name: Fetal bone marrow

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: Cultured in Low Glucose DMEM, 30% FBS, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM ultraglutamine

extract_protocol: Rneasy column purification

value: Fetal bone marrow

tag: cell phenotype

value: Migrated

tag: growth condition


title: Non-Migrated_EX0802_06

value: Non-Migrated

value: Cultured in Low Glucose DMEM, 30% FBS, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM ultraglutamine


title: Non-Migrated_EX0802_10


title: LC:A549 (56899)

tag: Sex

tag: epithelial

tag: ploidy

value: Adenocarcinoma-poor to moderate differentiation

value: Pool of six normal male samples


title: CNS:SF-539 (56197)

description: CNS cancer cell line CNS:SF-539 compared to Male human reference

value: CNS

value: no

tag: p53 mutation

tag: doubling time

tag: sample description

value: Glial cell neoplasm


title: CNS:SF-268 (57296)

tag: cell line

value: F

tag: prior treatment

value: Rad

value: 2n+, Hyperdiploid (47-57)

value: MT

value: Glioblastoma-undifferentiated


title: Non-Migrated_EX0802_03


title: Migrated_EX0802_02


title: Migrated_EX0802_05


title: CNS:SNB19 (56256)

description: CNS cancer cell line CNS:SNB19 compared to Male human reference

value: M


title: CNS:SNB-75 (56391)

description: CNS cancer cell line CNS:SNB-75 compared to Male human reference

value: Astrocytoma


title: BR:T47D (56166)

description: Breast cancer cell line BR:T47D compared to Male human reference

value: Breast

value: yes

value: infiltrating ductal carcinoma


title: LC:A549 (55668)

value: Non-Small Cell Lung

value: WT


title: LC:A549 (55650)

value: Adenocarcinoma-poor to moderate differentiation


title: BR:HS578T (41076)

description: Breast cancer cell line BR:HS578T compared to Male human reference

tag: source

value: Primary

value: Carcinosarcoma-mammary gland; breast

value: Pool of six normal male samples


title: BR:MDA-MB-231 (56003)

description: Breast cancer cell line BR:MDA-MB-231 compared to Male human reference

value: Pleural effusion

value: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site:pleural effusion;


title: CO:HCT116 (38029)

value: Colon

value: 2n-, Hypodiploid (35-45)

value: carcinoma-very poorly differentiated


title: BR:MCF7 (42606)

value: F

value: 3n-, Hypotriploid (58-68)

value: Adenocarcinoma-mammary gland; breast; metastatic site:pleural effusion;


title: PR:DU-145(ATCC) (38074)

description: Prostate cancer cell line PR:DU-145(ATCC) compared to Male human reference

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: Derived from metastatic site:brain (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)


title: BR:MCF7 (37968)

value: Breast

value: yes

value: WT


title: HCI-012 xenograft 1st passage [expression]

status: Public on Oct 23 2011

city: Salt Lake City

first: Alana

last: Welm

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute / University of Utah

description: IDC Stage 99

hyb_protocol: Agilent one-color heterologous gene expression hybridization and wash protocol.

scan_protocol: Microarray slides were scanned on an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing:
TIFF images from the scanned microarrays were processed using Agilent Feature Extraction software version 10.5.1.1.
gProcessedSignal values were filtered to remove control features,  non-uniform outliers and feature population outliers. Remaining values were average to yield a single value for each unique probe.
Probe intensities were log transformed (log base 2) and quantile normalized.

label_protocol: Agilent one-color quick-amp labeling protocol.

growth_protocol: Flash frozen tumor tissue from human subject or mouse xenograft

extract_protocol: Total RNA isolated using Trizol

tag: tumor type

value: metastatic

tag: er status

tag: pr status

tag: her2 status

tag: Stage

value: IDC Stage 99

tag: tumor id

tag: sample type

value: xenograft 1st passage

value: metastatic breast cancer tumor


title: BR:MCF7 (42605)

tag: tissue of origin

tag: age

value: Pleural effusion

value: Pool of six normal male samples


title: PR:RC01 (37986)

description: Prostate cancer cell line PR:RC01 compared to Male human reference

tag: Sex

tag: epithelial

value: Drug resistant variant of DU145(ATCC)


title: CNS:SF-295 (56192)

description: CNS cancer cell line CNS:SF-295 compared to Male human reference

value: CNS

value: F

value: Rad

value: no

tag: ploidy

tag: p53 mutation

value: MT

value: Glioblastoma-undifferentiated


title: HCI-012 original tumor [expression]

description: IDC Stage 99

source_name: HCI-012 original tumor [expression]

value: original tumor

tag: tissue


title: BR:BT-549 (41075)

description: Breast cancer cell line BR:BT-549 compared to Male human reference

tag: cell line

value: Breast

value: Metastasis

tag: doubling time

tag: sample description

value: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: M


title: HCI-011 original tumor [expression]

description: ILC Stage 3C

source_name: HCI-011 original tumor [expression]

tag: tumor type

value: metastatic

value: ILC Stage 3C


title: HCI-010 xenograft 1st passage [expression]

description: IDC Stage 2C

tag: er status

value: IDC Stage 2C

value: xenograft 1st passage

value: metastatic breast cancer tumor


title: HCI-011 xenograft 1st passage [expression]

description: ILC Stage 3C

tag: pr status


title: HCI-010 original tumor [expression]

description: IDC Stage 2C

source_name: HCI-010 original tumor [expression]

tag: her2 status


title: HCI-009 xenograft 4th passage [expression]

description: Poorly differentiated adenocarcinoma Stage 99

tag: Stage

value: xenograft 4th passage


title: HCI-009 original tumor [expression]

source_name: HCI-009 original tumor [expression]

value: Poorly differentiated adenocarcinoma Stage 99

tag: tumor id


title: HCI-009 xenograft 1st passage [expression]

tag: sample type


title: HCI-007 xenograft 1st passage [expression]

description: ILC Stage 2B

value: ILC Stage 2B


title: HCI-008 original tumor [expression]

description: Inflammatory breast cancer Stage 2B

source_name: HCI-008 original tumor [expression]

value: Inflammatory breast cancer Stage 2B


title: HCI-006 original tumor [expression]

description: ILC Stage 2B

source_name: HCI-006 original tumor [expression]


title: HCI-007 original tumor [expression]

description: ILC Stage 2B

source_name: HCI-007 original tumor [expression]


title: HCI-008 xenograft 1st passage [expression]

description: Inflammatory breast cancer Stage 2B