title: Heart 2 month old Taz KD rep1 (mouse 5973)

city: Saint Louis

first: Michael

middle: Andrew

last: Kiebish

state: MO

address: 660 South Euclid Avenue, Campus Box 8020

department: Internal Medicine

institute: Washington University School of Medicine

description: Taz shRNA KD replicate 2 625 mg/Kg Doxycycline diet

hyb_protocol: Standard Illumina hydridization protocols

scan_protocol: Standard Illumina scanning protocols

data_processing: The data were normalized using quantile normalization

source_name: Heart

label_protocol: Biotinylated cRMA were prepared with the Ambion MessageAMP kit for Illumina arrays

extract_protocol: Total RNA was extracted with Trizol folowed by Dnase treatment using Qiagen Rneasy minikit using manufacturers protocls.  Quality control was performed with Agilent 2100 Expert Bioanalyzer

tag: strain

value: transgenic shRNA Taz KD

tag: genetic background

value: heart

tag: age

value: 2 mo


title: G7

status: Public on Nov 05 2011

type: RNA

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

country: USA

institute: Vanderbilt

description: Gene expression data from Human RCC sample

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent model C scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: Data was retrieved from the UNC Microarray Database as LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). Missing data was imputed with KNN (k=10) in SAM.  Each array was standard normalized (subtract the mean of the array and divide by the standard deviation). See GSE3538 et al. sample data were re-downloaded from the Stanford Microarray Database (http://smd.stanford.edu/) with Entrez ID annotation as log2 normalized ratios (median).  Raw data from remaining studies utilized Affymetrix arrays and were retrieved from GEO (http://www.ncbi.nlm.nih.gov/geo/). For the See GSE22541 et al. dataset, metastatic tumors were excluded.  Raw data files were imported into Partek Genomics Suite software, version 6.5 (Partek Inc., St. Louis, MO) using RMA normalization.  Each Affymetrix array type was imported separately and data was subsequently merged into one file containing only the overlapping probes.  Entrez IDs common to all datasets were identified using MergeMaid in R, and the Affymetrix data was merged with the Agilent datasets.  This combined dataset was imported into Partek, and batch effect from each source removed.    All reanalyzed data is linked to GSEnnnnn as GSEnnnnn_reanalysis.txt.

molecule: total RNA

organism: Homo sapiens

source_name: mRNA from Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled using the Agilent Two-Color Microarray-Based Gene Expression Analysis v 5.2 protocol by UNC Lineberger Comprehensive Cancer Center Genomics Core.

growth_protocol: Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility

extract_protocol: RNA was extracted with a Qiagen RNeasy kit. RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology

tag: organism part

value: Kidney

tag: histology

value: Clear Cell

tag: biosource type

value: Frozen Sample

tag: biosource provider

value: University of North Carolina

source_name: Perou lab reference RNA

value: Cancer cell lines


title: LM003_TOP_high

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
ext114
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label: biotin

source_name: Colon cancer stem cell culture

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

tag: tissue

value: Colon CSC culture transduced with Wnt reporter construct

tag: cell type

tag: cell fraction

value: high


title: LM003_TOP_low

description:
ext112
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).

value: low


title: L1685

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

institute: LUMC

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing:
For the expression array, unprocessed data were collected from BeadStudio and processed using variance-stabilizing transformation (vst) and robust spline normalization (rsn) with the Bioconductor package lumi. The processed data was analyzed using LIMMA (linear models for microarray data) analysis, which uses moderated t-test to detect differentially expressed genes between two groups by taking into account natural variance within these groups and correcting for multiple testing using false discovery rate indicating the number of differentially expressed genes between two groups.

Raw data file description: On the Illumina BeadChips, each sample is hybridized on 2 chips, which together compromise all probes per sample. There are four columns in each file. The first column represents the bead (there are approximately 30 replicate beads per probe on random positions on the Illumina BeadChip arrays, so the data that is generated is higly robust), the second the signal, and the other 2 the X and Y locations on the chip. These 2 raw files can be imported into BeadStudio, the program developed by Illumina for analyzing these data, or into R package beadarray.

source_name: Ollier chondrosarcoma grade II

label_protocol: As per manufacturer's instructions.

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

tag: disease

value: Ollier chondrosarcoma

tag: tumor

value: chondrosarcoma grade II

tag: idh1/2 mutations

value: yes


title: co108_TOP_low

description:
ext247
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).


title: Heart 2 month old Taz KD rep3 (mouse 5974)

description: Taz shRNA KD replicate 3 625 mg/Kg Doxycycline diet

organism: Mus musculus


title: T-ALL sample #15

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: sample collected in human clinical trial E2993 (Marks et al., 2009)

hyb_protocol: 500 ng of RNA was amplified and biotinylated using the TotalPrep RNA Amplification Kit (Ambion) and hybridized to the HumanHT-12 v4 Expression BeadChip (Illumina)

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression profiling data from 57 adult T-ALL patients were transfomed to log2 scale and normalized using quantile normalization without background subtraction

source_name: TALL lymphoblast sample 15

label_protocol: 10ng of RNA from each T-cell subset was amplified using the Ovation® PicoSL WTA System (Nugen), labeled by the EncoreTM BiotinIL Module (Nugen)

extract_protocol: RNA isolation from lymphoblast obtained from adult T-ALL patient samples was achieved using the RNeasy plus mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: Leukemic DNA and cryopreserved lymphoblast samples were provided by the Eastern Cooperative Oncology Group (ECOG). All samples were collected in clinical trial E2993(Marks et al., 2009) and informed consent to use leftover material for research purposes was obtained from all the patients at trial entry according to the declaration of Helsinki. T-cell phenotype was confirmed by flow cytometry

value: cryopreserved lymphoblast


title: Heart 2 month old Taz KD rep1 (mouse 5975)

description: Taz shRNA KD replicate 4 625 mg/Kg Doxycycline diet


title: lm23_TOP_high

description:
ext248
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).


title: T-ALL sample #12

source_name: TALL lymphoblast sample 12


title: Heart 2 month old Taz KD rep1 (mouse 5972)

description: Taz shRNA KD replicate 1 625 mg/Kg Doxycycline diet


title: Colo100_TOP_low

description:
ext095
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).


title: Heart 2 month old WT rep4 (mouse 5971)

description: Wildtype replicate 4  625 mg/Kg Doxycycline diet

value: wild type


title: Colo100_TOP_high

description:
ext094
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).


title: co108_TOP_ high

description:
ext246
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).


title: Heart 4 month old CLS rep4 (mouse 5969)

description: Tg-CLS replicate 4

source_name: Heart 4 month old CLS rep4 (mouse 5969)

value: transgenic hCLS1

value: 4 mo


title: DON2.5 group, biological rep2

city: Zurich

first: Bruno

last: Dietrich

address: Tannenstrasse 1

department: Department of Agricultural and Food Sciences

country: Switzerland

institute: ETH Zurich

description: Gene expression data from the liver of chicken fed the DON2.5 diet (DON-contaminated, 2.5mg DON / kg feed) for 23 days ad libitum.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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 image data on each individual chip was scaled to target intensity 500.

organism: Gallus gallus

source_name: Chicken liver from group DON2.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Affymetrix One-Cycle Target Labeling - Expression Arrays, Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Chickens were held for 23 days and were fed ad libitium. The animal experiment was performed according to the regulations of the cantonal veterinary office in Zurich (Switzerland).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Then the total RNA was cleaned up with the Rneasy Mini Kit according  to the manufacturer's protocol.

treatment_protocol: The standard diet was formulated according to the National Research Council (1994) and basic diet was prepared for all groups. The control group received the basic diet plus the remaining uncontaminated wheat and in the DON groups uncontaminated wheat was exchanged with DON contaminated wheat up to the intended concentration. The livers were removed immediatly after slaughter and frozen in liquid nitrogen.

value: liver

value: 23 days

tag: breed

value: ROSS308, commercial broilers for meat production

tag: treatment

value: 2.5 mg DON / kg feed for 23 days ad libitum


title: Heart 2 month old WT rep3 (mouse 5970)

description: Wildtype replicate 3  625 mg/Kg Doxycycline diet

value: heart

value: 2 mo


title: Heart 2 month old WT rep2 (mouse 5981)

description: Wildtype replicate 2  625 mg/Kg Doxycycline diet


title: DON5 group, biological rep2

description: Gene expression data from the liver of chicken fed the DON5 diet (DON-contaminated, 5mg DON / kg feed) for 23 days ad libitum.

source_name: Chicken liver from group DON5

value: 5 mg DON / kg feed for 23 days ad libitum


title: Heart 4 month old WT rep4 (mouse 5967)

description: Wildtype replicate 4

source_name: Heart 4 month old WT rep4 (mouse 5967)


title: Heart 4 month old CLS rep2 (mouse 5968)

description: Tg-CLS replicate 2

source_name: Heart 4 month old CLS rep2 (mouse 5968)


title: DON5 group, biological rep3


title: DON5 group, biological rep1


title: DON2.5 group, biological rep3


title: Heart 2 month old WT rep1 (mouse 5980)

description: Wildtype replicate 1  625 mg/Kg Doxycycline diet


title: DON1 group, biological rep3

description: Gene expression data from the liver of chicken fed the DON1 diet (DON-contaminated, 1mg DON / kg feed) for 23 days ad libitum.

source_name: Chicken liver from group DON1

value: 1 mg DON / kg feed for 23 days ad libitum


title: Heart 4 month old CLS rep1 (mouse 5978)

description: Tg-CLS replicate 1

source_name: Heart 4 month old CLS rep1 (mouse 5978)


title: T-ALL sample #11

source_name: TALL lymphoblast sample 11


title: DON1 group, biological rep2


title: DON2.5 group, biological rep1


title: Colo200_TOP_high

description:
ext096
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).

value: Colon CSC culture transduced with Wnt reporter construct

value: high


title: malignant cells [GE1_1_POPT]

city: Timisoara

first: Diana

last: Narita

address: 2 Eftimie Murgu

department: Biochemistry

country: Romania

institute: University of Medicine and Pharmacy Victor Babes Timisoara

description: Gene expression malignant cells patient POP

hyb_protocol: The slides were blocked and prepared for hybridization (Gene Expression Hibridization Buffer, Agilent); after 17 h of hybridization, the slides were washed (Gene Expression Wash Buffer, Agilent) and stabilized (stabilization and drying Solution, Agilent).

scan_protocol: Slides were scanned on green dye channel, with 5 µm resolution (Agilent microarray scanner p/n G2565BA)

data_processing: Feature Extraction software 9.5 was used for data extraction.

source_name: Breast cancer tissue

label_protocol: Agilent One-Color Spike Mix dilutions were prepared; then, Agilent's Low Input Quick Amp Labeling Kit was used with a sample input RNA of 10 ng total RNA for one-color processing to synthesize cDNA with the help of AffinityScript-reverse transcriptase and oligo dT-promoter primers; this method uses T7 RNA polymerase to generate fluorescent cRNA (complimentary RNA) and simultaneously amplifies the target material and incorporates cyanine 3-labeled CTP; amplification is typically at least 100-fold from total RNA to cRNA; the antisense cRNA was then purified (Agilent Absolute RNA Nanoprep kit) and spectrophotometrically quantified (NanoDrop ND-1000 UV-VIS Spectrophotometer) in order to determine the yield and specific activity of each reaction - μg cRNA yield and specific activity (pmol Cy3 per μg cRNA)

extract_protocol: Laser-capture microdissection was used to select and procure only the desired cell types (malignant groups of cells or normal mammary acini), under direct microscopic visualization, using an UV cutting system (mmi SmartCut Plus, MMI Molecular Machines and Industries, Glattburg, Switzerland) with an Olympus microscope. RNA was extracted with RNAqueous-Micro kit (Ambion, Applied Biosystems, Germany) following exactly the manufacturer protocol for microdissected cells. RNA concentration and purity were quantified spectrophotometrically (NanoDrop ND1000) and the quality of RNA was evaluated on RNA electrophoregrams generated by the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France). RNA was stored at -80°C until further gene expression analyses.

treatment_protocol: Fresh samples were obtained during surgical resection and after macroscopic pathological assessment. Prelevated tissues (0.5 – 1/0.5 cm) were preserved in tubes with RNAlater solution, (Ambion, Applied Biosystems, Germany) for 24 hours at +4°C and then frozen at -80°C. Corresponding non-lesional tissues removed from the same patients served as normal controls and were treated in similar manner.

value: Breast cancer surgical resection

value: malignant cells

tag: gender

value: female


title: Heart 4 month old CLS rep3 (mouse 5979)

description: Tg-CLS replicate 3

source_name: Heart 4 month old CLS rep3 (mouse 5979)


title: malignant cells [GE1_1_105]

description: Gene expression malignant cells patient 105


title: malignant cells [GE1_1_104]

description: Gene expression malignant cells patient 104


title: DON1 group, biological rep1


title: malignant cells [GE1_1_95]

description: Gene expression malignant cells patient 95


title: malignant cells [GE1_1_124T]

description: Gene expression malignant cells patient 124


title: confluent monolayer in EGM-2 media rep2

status: Public on Nov 04 2011

city: San Francisco

first: Kevin

last: Wilhelmsen

state: CA

address: 513 Parnassus Ave.

department: Anesthesia

institute: University of California, San Francisco

description:
control
HUVEC_#2

data_processing:
For the normalization it uses the average of two housekeeping genes: HPRT1 , 18s
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold-change values were caluculated using 2^-deltadeltaCt, where deltadeltaCt=(average deltaCt_test - average deltaCt control) and reports test/control (i.e. THP1/THP1 and HUVEC/THP1) ratios [available as a Series Supplementary file].

label: FAM Taqman

label_protocol: PCR assays were performed using the TaqMan® Human Toll-Like Receptors Pathway Arrays (4418838) (Applied Biosystems) following the Manufacturer’s instructions. Reverse transcription was performed from 2000 ng total RNA using the  High Capacity RNA-to-cDNA Kit from Applied Biosystems). 2.5 ng cDNA used per well. Quantitative real-time PCR were performed (ABI Prism 7000 Sequence Detection System; Applied Biosystems) at 95°C for 20 sec was followed by 40 cycles of 1 sec at 95C and 20 sec at 60C.

growth_protocol: HUVEC: EGM-2 media (2% FBS) (Clonetics Corp; Walkersville, MD); THP1: RPMI 1640 supplemented with 10% FBS, L-glutamine, and antibiotics

extract_protocol: Total RNA was extracted with High Capacity RNA-to-cDNA Kit from AB (4387406)

tag: cell line

value: HUVEC

value: primary endothelial cell


title: Heart 4 month old WT rep3 (mouse 5966)

description: Wildtype replicate 3

source_name: Heart 4 month old WT rep3 (mouse 5966)

tag: strain

value: wild type


title: normal mammary acini [GE1_1_POPN]

description: Gene expression normal cells patient POP

source_name: Breast normal tissue

value: normal mammary acini


title: Heart 4 month old WT rep2 (mouse 5977)

description: Wildtype replicate 2

source_name: Heart 4 month old WT rep2 (mouse 5977)

tag: genetic background

value: 4 mo


title: Heart 4 month old WT rep1 (mouse 5976)

description: Wildtype replicate 1

source_name: Heart 4 month old WT rep1 (mouse 5976)

tag: age


title: DON control group, biological rep2

description: Gene expression data from the liver of chicken fed the control diet (uncontaminated) for 23 days ad libitum.

source_name: Chicken liver from control group

value: liver

value: 23 days


title: normal mammary acini [GE1_1_126N]

description: Gene expression normal cells patient 126


title: DON control group, biological rep3

value: ROSS308, commercial broilers for meat production

value: control diet (uncontaminated) for 23 days ad libitum


title: suspension cells grown in RPMI 1640 supplemented with 10% FBS, L-glutamine, and antibiotics rep1

description:
test
THP1_#1

value: monocytic cell


title: confluent monolayer in EGM-2 media rep1

description:
control
HUVEC_#1


title: C_parapsilosis_Low_Iron_rep6

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

hyb_protocol: Purified cDNA was denatured at 95 degrees Celsius  for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacturer's manual.

scan_protocol: Scanned with an Axon 4000B scanner at 10 µm resolution. Data was acquired using GenePix 5.0 software. The quality and concentration of the isolated RNA was analyzed using an Agilent 2100 Bioanalyzer.

data_processing: LOWESS normalized, no background correction using the LIMMA package from Bioconductor.

organism: Candida parapsilosis

source_name: Total RNA from Candida parapsilosis wild type CLIB214 cells, grown in SD medium supplemented with 200 μM BPS and labeled with Cy3

label_protocol: 24 µg of total RNA was used for cDNA labeling. Briefly RNA samples were incubated with 200 pmol of anchor oligonucleotide deoxyriboslthymine (Invitrogen) at 70°C for 10 min, after which following reaction reagents were added: 1 X First strand buffer, 20 µmol dATP, dTTP, and dGTP, 2 µmol dCTP, 400 pmol dithiothreitol, 400 U Superscript II reverse transcriptase (Invitrogen). 2 nmol Cy5-dCTP or Cy3-dCTP was then added into the mixture in the dark. The mixture was left at 42°C for two hours followed by adding additional 400 U Superscript II reverse transcriptase, and reaction was continued for one more hour. 50 µg/ml-1 RNase A and 0.05 U RNase H were added and the reaction was incubated for 30 min at 37°C.

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 50 ml of SD medium supplemented with 200 μM BPS, and culture was incubated at 200 rpm at 37 degree for 5 hours

extract_protocol: RNA was isolated using a RiboPure Yeast kit (Ambion)

tag: growth condition

value: 37 degrees celsius, SD medium supplemented with 200 μM BPS (Bathophenanthroline disulfonic acid disodium salt trihydrate)

tag: genotype/variation

source_name: Total RNA from Candida parapsilosis CLIB214 cells in SD medium and labeled with Cy3

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 50 ml of SD medium, and culture was incubated at 200 rpm at 37 degree for 5 hours

value: 37 degree Celsius, SD medium


title: MCF-7 cells DDT

city: new orleans

first: Melyssa

last: Bratton

address: 1430 Tulane Ave

institute: Tulane University School of Medicine

description:
DDT
S81588-DDT-raw-data.txt

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: MCF-7 cells, ATCC #HTB-22

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: MCF-7 cells were grown in DMEM supplemented with 10% FBS.  48 hrs prior to dosing, cells were incubated in phenol red free DMEM supplemented with 5% charcoal stripped FBS.

extract_protocol: small RNA was isolated using miRNeasy® mini column (Qiagen), following the manufacturer’s instructions.

treatment_protocol: Cells were treated for 18 hours with indicated drugs

value: MCF-7 breast cancer cell line

tag: atcc#

tag: agent

value: DDT


title: C_parapsilosis_Low_Iron_rep3

source_name: Total RNA from Candida parapsilosis wild type CLIB214 cells, grown in SD medium supplemented with 200 μM BPS and labeled with Cy5

source_name: Total RNA from Candida parapsilosis CLIB214 cells in SD medium and labeled with Cy5


title: C_parapsilosis_WT_v_bcr1_rep5

source_name: Total RNA from Candida parapsilosis CDb71 (bcr1 deletion), grown in SD medium supplemented with 50 mM glucose and 10% fetal calf serum and labeled with Cyanine-5.

growth_protocol: Overnight cultures of C. parapsilosis CDb71 were diluted to a A600 of 0.2 in 50 ml of SD medium supplemented with 50 mM glucose and 10% fetal calf serum, and culture was incubated at 200 rpm at 37 degree for 5 hours

value: 37 degree Celsius, SD medium supplemented with 50 mM glucose and 10% fetal calf serum

value: bcr1 deletion

source_name: Total RNA from Candida parapsilosis CLIB214 cells in SD medium supplemented with 50 mM glucose and 10% fetal calf serum and labeled with Cy3

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 50 ml of SD medium supplemented with 50 mM glucose and 10% fetal calf serum, and culture was incubated at 200 rpm at 37 degree for 5 hours


title: MCF-7 cells veh

description:
Control
S81588-control-raw-data.txt

value: Control


title: C_parapsilosis_WT_v_bcr1_rep1


title: C_parapsilosis_WT_v_bcr1_rep2


title: C_parapsilosis_Low_Iron_rep5


title: C_parapsilosis_Low_Iron_rep7


title: malignant cells [GE1_1_126T]

description: Gene expression malignant cells patient 126

tag: tissue

value: Breast cancer surgical resection

value: malignant cells

value: female


title: MCF-7 cells E2

description:
E2
S81588-E2-raw-data.txt


title: C_parapsilosis_WT_v_bcr1_rep6

source_name: Total RNA from Candida parapsilosis CDUHB6 (bcr1 deletion), grown in SD medium supplemented with 50 mM glucose and 10% fetal calf serum and labeled with Cyanine-3.

growth_protocol: Overnight cultures of C. parapsilosis CDUHB6 were diluted to a A600 of 0.2 in 50 ml of SD medium supplemented with 50 mM glucose and 10% fetal calf serum, and culture was incubated at 200 rpm at 37 degree for 5 hours

source_name: Total RNA from Candida parapsilosis CLIB214 cells in SD medium supplemented with 50 mM glucose and 10% fetal calf serum and labeled with Cy5

value: wild type


title: C_parapsilosis_Low_Iron_rep2


title: C_parapsilosis_WT_v_bcr1_rep4


title: C_parapsilosis_Low_Iron_rep1


title: DON control group, biological rep1


title: C_parapsilosis_Low_Iron_rep4


title: MCF-7 cells BPA

description:
BPA
S81588-BPA-raw-data.txt

value: BPA


title: C_parapsilosis_WT_v_bcr1_rep3


title: C_parapsilosis_WT_v_bcr1_rep7


title: S14b

city: Philadelphia

first: Joshua

last: Friedman

state: PA

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

description:
S14b
10214

hyb_protocol: 1 Warm Hybridization buffer to 56 degrees to completely resuspend any precipitates, cool to room temp     2 Combine Hy 3 and Hy 5 reactions (~22ul total) and adjust volume to 205ul with water (~183)     3 Add 205ul of 2x Hybridization buffer to labeled samples, mix by vortexing, spin to collect (410ul final volume)     4 Denature Samples at 95 degrees for 3 minutes     5 Snap cool sample on Ice for 2 minutes (but no more than 15)     6 Centifgue max speed for 1 minutes, put back on ice     7 Apply sample to Agilent Coverslip, apply slide, assemble hybridization aparatus     8 Hybridize 16hr at 56oC with rotation speed of 4

scan_protocol: Scanner=GenePix 4000B [81994]  FocusPosition=0  Temperature=33.346  LinesAveraged=1  Comment=  PMTGain=850 750  ScanPower=100 100  LaserPower=2.58339 2.79733  Filters=<Empty> <Empty>  ScanRegion=384,1104,3984,11592

data_processing: Using Partek Genomics Suite 6.2 (Partek Inc., St. Louis, MO, USA) for background subtraction, threshholding, Loess normalization

source_name: pcctrl

label_protocol: miRCURY Power Labeling Kit (Exiqon) for use with Exiqon miRNA arrays. Disolve spike-in controls in 30ul of nucleaqse free water, leave on ice 30 minutes, vortex (use 1ul/rxn)                      Dyes come dry.  If necessary, to avoid multiple freeze/thaw cycles, resuspend in 30ul of water and make 2ul aliquots (single use)                      miRNA enrichment is not necessary for labeling intact total RNA with this kit.  If RNA is degraded (FFPE), enrichment is recommended to reduce the number of RNA fragments to be labeled.                                   Thaw all kit components on ice for 15 to 20 minutes prior to use, mix thoroughly by gently vortexing and briefly centrifuge.                      Do not vortex or thaw enzymes, flick and spin only

growth_protocol: Newborn Balb/c mice

extract_protocol: Total RNA; miRvana kit (Ambion)

treatment_protocol: Injected on DOL0 with either saline or Rhesus rotavirus

value: Balb/c

tag: reference

value: Pooled common control

value: Saline

tag: time point

value: day 14


title: S14d

description:
S14d
10216


title: S8e

description:
S8e
10211

value: day 8


title: S14f

description:
S14f
10218


title: S8c

description:
S8c
10209


title: S8d

description:
S8d
10210


title: S14a

description:
S14a
10213


title: S3c

description:
S3c
10203

value: day 3


title: S14c

description:
S14c
10215


title: RRV14e

description:
RRV14e
10199

value: RRV


title: S8a

description:
S8a
10207


title: RRV14f

description:
RRV14f
10200


title: S3f

description:
S3f
10206


title: S3d

description:
S3d
10204


title: S3e

description:
S3e
10205


title: RRV14d

description:
RRV14d
10198


title: S8b

description:
S8b
10208


title: S3a

description:
S3a
10201


title: S8f

description:
S8f
10212


title: RRV14c

description:
RRV14c
10197


title: RRV8f

description:
RRV8f
10194


title: RRV14b

description:
RRV14b
10196


title: RRV14a

description:
RRV14a
10195


title: RRV8d

description:
RRV8d
10192


title: RRV8e

description:
RRV8e
10193


title: RRV8b

description:
RRV8b
10190


title: S3b

description:
S3b
10202


title: Colo200_TOP_low

description:
ext097
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).

source_name: Colon cancer stem cell culture

value: Colon CSC culture transduced with Wnt reporter construct

tag: cell type

tag: cell fraction

value: low


title: RRV8a

description:
RRV8a
10189


title: RRV3f

description:
RRV3f
10188


title: RRV3e

description:
RRV3e
10187


title: RRV8c

description:
RRV8c
10191


title: RRV3a

description:
RRV3a
10183


title: RRV3d

description:
RRV3d
10186


title: RRV3c

description:
RRV3c
10185


title: RRV3b

description:
RRV3b
10184


title: y1y8_AsV_60min_rep2

city: Oeiras

first: Liliana

middle: Batista

last: Nascimento

address: Avenida da Republica

department: Biological Chemistry

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica

data_processing:
All data were analyzed using both Partek® Genomics SuiteTM and dChip softwares. Principal Component Analysis (PCA) and
 Hierarchical Clustering (HC) were used on the expression data of the single
 arrays. Next it was done pair-wise comparisons. The comparison
 files state clearly what has been compared. As a cut-off for the fold
 change we have chosen a lower confidence bound (LCB) fold change of 1.2. This lower confidence bound takes into
 account the standard errors of the expression values, while the "fold
 change" value does not. In addition we have used permutation analysis to assess the false discovery rate for
 each comparison. This value can be found in the end of each file name (e.g.
> FDR 0.1 equals false discovery rate of 0.1%). Anything below 10% is
 considered acceptable. In addition we did a functional analysis of based on Gene Ontology
 terms for the genes identified in the comparisons. Here the cut-off for significance was a p-value of 0.005. Finally we have used Venn diagram analysis to see the overlaps in all
 comparisons.

organism: Saccharomyces cerevisiae

extract_protocol: Total yeast RNA was isolated by the hot phenol method

value: AsV


title: E0911N-B3

city: Gaithersburg

first: Wusheng

last: Yan

address: 8717 Grovemont Circle

institute: NCI

hyb_protocol: Per sample,15μg of biotin-labeled cRNA sample was fragmented and processed for hybridization to Human Genome U133A 2.0 Genechips (Affymetrix Inc., Santa Clara, CA), according to the Expression Kit User Manual (http://www.affymetrix.com/support/technical/manuals.affx)).

scan_protocol: Arrays were washed and stained using the Midi_euk2v3_450 protocol (V4).  Fluorescent intensity emitted by the labeled target was measured using a GeneChip Scanner 7G (Affymetrix Inc.).

data_processing: GCOS

source_name: LCM normal fragment

label_protocol: Two rounds of linear amplification were performed by combining reagents supplied in MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion, Catalog# AM1791, Austin, TX) and MessageAmp™ II aRNA Amplification Kit (Ambion, Catalog# AM1751), resulting in biotin-labeled antisense cRNA [21].

growth_protocol: Frozen tissue

extract_protocol: RNA was isolated using the PicoPure RNA Isolation kit (Arcturus Engineering, Inc. Mountain View, CA) digested with Dnase.

treatment_protocol: ESCC tumor and match normal

value: normal fragment

tag: sample type

value: frozen tissue


title: E0911N-C2


title: E0911N-C1-2


title: yap8_AsV_60min_rep2


title: yap8_AsV_60min_rep3


title: y1y8_AsV_60min_rep1


title: E0911N-C3


title: E0911N-B2


title: E0911N-A2


title: E0911C3

source_name: LCM tumor cluster

value: tumor cluster


title: E0911N-A1-2


title: E0911N-A1-1


title: E0911C2


title: E0911N-B1-1


title: E0911C1-2


title: E0911N-A3


title: E0911N-B1-2


title: E0911N-C1-1


title: yap8_AsV_60min_rep1


title: E0911C1-1


title: y1y8_AsV_60min_rep3


title: yap1_AsV_60min_rep2


title: yap1_AsV_60min_rep1


title: yap1_AsV_60min_rep3


title: E0911A1-2


title: WT_AsV_60min_rep2

value: WT


title: WT_AsV_60min_rep3


title: Emb2

city: new york

first: hui

last: zhao

address: 430 east 67th street

institute: MSKCC

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol (58 degrees for 16-20 hours)

data_processing: The data were normalized using the Shift to Median function in Partek

label: Biotin

source_name: Mus Musculus EHF embryo

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

growth_protocol: Standard

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Thermo Scientific nanodrop 1000.

tag: develpmental stage

value: early headfold (EHF) stage

value: embryo


title: Emb3

description: Replicate 3


title: E0911A2


title: E0911A3


title: Emb1

description: Replicate 1


title: E0911A1-1


title: E0782C1-2


title: E0782C3


title: 1264A3


title: MNNG-Lung 1233

city: Houston

first: Alexander

last: Yu

state: TX

institute: Baylor College of Medicine

description:
ZsGreen transduced tumor cells
MNNG_Lung_1233_JS_05122010

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 7G.

data_processing: Cel files were processed in BRB-ArrayTools using the Just-RMA algorithm

source_name: human osteosarcoma_orthotopic transplant_lung metastasis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from100ng total RNA (GeneChip 3' IVT Express kit, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and RNA was further purified with QIAGEN  DNAse I on column treatment.

tag: source cell line

value: MNNG/HOS

tag: tissue source

value: orthotopic transplant_lung metastasis

tag: tumor cell subpopulation

value: osteosarcoma lung metastasis


title: MNNG-Lung Mix

description:
ZsGreen transduced tumor cells
MNNG_Lung_Mix_JS_05122010


title: E0782A1-2


title: E0782C1-1-re-2


title: E0782A2


title: WT_notreatment_0min_rep3


title: MNNG-1235 High

description:
ZsGreen transduced tumor cells
MNNG_Bone_1235_high_JS_05122010

value: orthotopic bone tumors

value: PKH26Hi cells (TICs)

value: osteosarcoma tumor-initiating cells


title: E0782A1-1


title: MNNG-1235 Low

description:
ZsGreen transduced tumor cells
MNNG_Bone_1235_low_JS_05062010

value: PKH26Lo cells (non-TICs)

value: osteosarcoma bulk tumor cells


title: WT_AsV_60min_rep1


title: E0782C2-re-2


title: 1264A2


title: 1264C1-2


title: E0782A3


title: WT_notreatment_0min_rep2


title: WT_notreatment_0min_rep1


title: MNNG-1233 Low

description:
ZsGreen transduced tumor cells
MNNG_Bone_1233_low_JS_05062010


title: MNNG-1233 High

description:
ZsGreen transduced tumor cells
MNNG_Bone_1233_high_JS_05122010


title: 1264A1-1


title: MNNG-1232 Low

description:
ZsGreen transduced tumor cells
MNNG_Bone_1232_low_JS_05062010


title: C2C12 cells ZBED6 siRNA 96h rep3

city: Uppsala

first: Carl-Johan

last: Rubin

address: Husargatan 3

department: Dedp. Med. Biochem. & Microbiol.

country: Sweden

institute: Uppsala University

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using the lumi package implemented in the software FlexArray v. 1.4.1 using Robust spline normalization

source_name: C2C12 cells ZBED6 siRNA 96h rep3

label_protocol: Biotinylated probes were prepared from 250 ng of total RNA, using the Ambion Illumina TotalPrep RNA Amplification kit

growth_protocol: The C2C12 cells used for these studies were between passages 10 and 18. Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with L-glutamine (ATCC), supplemented with 10 % heat-inactivated fetal bovine serum and penicillin (0.2 U/mL)/streptomycin (0.2 μg/ml)/L-glutamine (0.2 μg/ml) (Gibco) at 37°C in a 5 % CO2 humidified atmosphere. At 70-80 % confluency, cells were trypsinized and seeded at 100,000 cells per well in 12-well plates (Falcon) for the transfection experiments.

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.

treatment_protocol: Cells were seeded in complete DMEM lacking antibiotics and reverse transfected with siRNA by lipofectamine 2000 (Invitrogen). ZBED6 silencing and validation of silencing was done by qPCR and western blotting as described (Markljung et al. 2009). Briefly, C2C12 cells were treated with ZBED6 or scrambled siRNAs for two days and four days in biological triplicates. Total RNA from each sample was extracted for qRT-PCR validation and microarray analysis.

tag: cell line

value: myoblast


title: C2C12 cells ZBED6 siRNA 96h rep2

source_name: C2C12 cells ZBED6 siRNA 96h rep2


title: MNNG-1231 Low

description:
ZsGreen transduced tumor cells
MNNG_Bone_1231_low_JS_05122010


title: C2C12 cells negative control siRNA 96h rep2


title: 143B-54&55 High

description:
ZsGreen transduced tumor cells
143B_Bone_54&55_High_JS_05262010


title: MNNG-1232 High

description:
ZsGreen transduced tumor cells
MNNG_Bone_1232_high_JS_05122010


title: E1310C1-2


title: 1264A1-2


title: JEG-3_IL11_24h

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description: Gene expression data from JEG-3 cells cultured for 24 h in the medium without fetal bovine serum and stimulated with IL-11 (200 ng/ml)

hyb_protocol: Fragmented and labeled cDNAs were hybridized to Affymetrix Exon 1 ST GeneChips (Affymetrix, Santa Clara, CA) at 45ºC for 17 h in hybridization oven at 60 rpm according to the Affymetrix protocols (Affymetrix).

scan_protocol: The chips were read using a GeneChip Scanner 3000

data_processing:
Raw images after scannning were converted to signal intensities, detection calls, comparison files, signal log ratios, and change calls.For normalizing and summarizing probe-level intensity measurements from GeneChips, GCRMA was used which converts .CEL files into expression set using the Robust Multi-array Average (RMA) with the help of probe sequence and with GC-content background correction.
Affymetrix Power Tools (APT)

source_name: JEG-3 cells stimulated with IL-11 (200ng/ml) for 24 h

label_protocol: Sense strand cDNA was prepared using the Ambion WT expression kit (Ambion Inc., Austin, Texas, USA), which was fragmented and biotin-labeled using the Affymetrix GeneChip WT terminal labeling kit (Affymetrix, High Wycombe, UK) according to the manufacturers’ recommendations.

growth_protocol: JEG-3 and HTR-8/SVneo cells were maintained in the medium supplemented with 10% foetal bovine serum containg antibiotic and antimycotic cocktail. For growth, cell were kept at 37⁰C in a humidified atmosphere containing 5%CO2 in air.

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

treatment_protocol: Cells (~0.1 million) were seeded onto the six well culture plates and cultured for 24 h in medium containing 10% foetal bovine serum. Cells were serum starved for 4 h before addition of IL-11 (200 ng/ml) for 24 h, keeping appropriate vehicle control.


title: E1310C1-1


title: E1310C3


title: C2C12 cells negative control siRNA 96h rep3


title: 143B-51&52 High

description:
ZsGreen transduced tumor cells
143B_Bone_51&52_High_JS_05262010


title: C2C12 cells ZBED6 siRNA 96h rep1

source_name: C2C12 cells ZBED6 siRNA 96h rep1


title: E1310A1-2


title: C2C12 cells ZBED6 siRNA 48h rep3

source_name: C2C12 cells ZBED6 siRNA 48h rep3


title: HTR-8/SVneo_IL11_24h

description: Gene expression data from HTR-8/SVneo cells cultured for 24 h in the medium without fetal bovine serum and stimulated with IL-11 (200 ng/ml)

source_name: HTR-8/SVneo cells stimulated with IL-11 (200ng/ml) for 24 h


title: C2C12 cells ZBED6 siRNA 48h rep2

source_name: C2C12 cells ZBED6 siRNA 48h rep2


title: 143B-1255 Low

description:
ZsGreen transduced tumor cells
143B_Bone_1255_Low_JS_05262010


title: Se-yeast group, biological rep5

description: Gene expression data from the liver of chicken fed the Se-yeast diet (Se supplemented) for 35 days ad libitum.

source_name: Chicken liver from Se-yeast supplemented group

growth_protocol: Chickens were held for 35 days and were fed ad libitium. The animal experiment was performed according to the regulations of the cantonal veterinary office in Zurich (Switzerland).

treatment_protocol: The standard diet was formulated according to the National Research Council (1994) and prepared for both groups. The control group received the standard diet and in the Se-yeast group selenized yeast (Sel-Plex®, Alltech, Lexington, Kentucky, USA) was added to achieve a Se supplementation of 0.5mg Se/kg diet. The livers were removed immediatly after slaughter and frozen in liquid nitrogen.

value: liver

value: 35 days

tag: breed

value: ROSS308, commercial broilers for meat production


title: E1310C2

value: frozen tissue


title: E1310A1-1

value: tumor cluster


title: MNNG-1231 High

description:
ZsGreen transduced tumor cells
MNNG_Bone_1231_High_JS_05122010


title: Se-yeast group, biological rep4

tag: age


title: 143B-1253 Low

description:
ZsGreen transduced tumor cells
143B_Bone_1253_Low_JS_05262010


title: E1310A3


title: Se-yeast group, biological rep3


title: HTR-8/SVneo_Control_24h

description: Gene expression data from HTR-8/SVneo cells cultured for 24 h in the medium without fetal bovine serum

source_name: HTR-8/SVneo cells cultured for 24 h without any kind of exogenous treatment

value: control (without IL-11)


title: C2C12 cells ZBED6 siRNA 48h rep1

source_name: C2C12 cells ZBED6 siRNA 48h rep1


title: 143B-1254 Low

description:
ZsGreen transduced tumor cells
143B_Bone_1254_Low_JS_05262010


title: JEG-3_Control_24h

description: Gene expression data from JEG-3 cells cultured for 24 h in the medium without fetal bovine serum

source_name: JEG-3 cells cultured for 24 h without any kind of exogenous treatment


title: 143B-1252 Low

description:
ZsGreen transduced tumor cells
143B_Bone_1252_Low_JS_05262010


title: Se-yeast group, biological rep2


title: C2C12 cells negative control siRNA 48h rep2


title: E1310A2


title: C2C12 cells negative control siRNA 48h rep1


title: Control group, biological rep4

description: Gene expression data from the liver of chicken fed the control diet (Se un-supplemented) for 35 days ad libitum.

source_name: Chicken liver from control group


title: T0404C3


title: Se-yeast group, biological rep1


title: T0404C1-2


title: 143B-1253 High

description:
ZsGreen transduced tumor cells
143B_Bone_1253_High_JS_05262010


title: T0404C1-1


title: Control group, biological rep1


title: C2C12 cells negative control siRNA 48h rep3


title: Control group, biological rep3


title: leaves, healthy, 13-17 wai, biological rep 2

city: Fort Pierce

first: Ute

last: Albrecht

state: FL

address: 2001 South Rock Road

institute: USDA, ARS, US Horticultural Research Laboratory

description: gene expression data from healthy leaves

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Citrus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: Data pre-processing and normalization were performed using the Affy package (B.M. Bolstad, R.A. Irizarry, M. Astrand, T.P. Speed, Bioinformatics 19 (2003), 1945-1951).

organism: Citrus sinensis

source_name: Valencia' leaves, mock-inoculated, 13 and 17 wai

label_protocol: Biotinylated cRNA were prepared according to Affymetrix GeneChip® 3’ IVT Express protocol from 250 ug total RNA (Affymetrix P/N 702646 Rev. 1).

growth_protocol: Plants were grown in the greenhouse and kept under natural light conditions at a temperature of 17 to 25 °C. Plants were irrigated as needed and fertilized using a 17N-6P-10K controlled release fertilizer (Scotts Sierra, Marysville, OH, USA).

extract_protocol: Total RNA was extracted according to Strommer et al. (J. Strommer, R. Gregerson, M. Vayda, in: B.M. Greenberg, B.R. Glick, (Eds.), Methods in Plant Molecular Biology and Biotechnology, CRC Press Inc., Boca Raton, FL, USA, 1993, pp. 49-65.) with slight modifications.  Phenol/chloroform/isoamylalcohol (25:24:1) extraction was followed by two extractions with chloroform/isoamylalcohol and precipitation of RNA with isopropanol at -20 °C overnight.  RNA was pelleted by centrifugation at 10,000 g and 4 °C for 1 h, resuspended in 5 mL water and precipitated overnight at 0 °C with an equal volume of 8 M LiCl.  After centrifugation at 10,000 g and 4 °C for 1h, RNA was washed twice with 70 % ethanol, air-dried and dissolved in 500 µL of water.  RNA was further purified using the RNeasy® MinElute Cleanup kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Plants were graft-inoculated with non-infected bark- or bud pieces from  greenhouse- grown 'Lisbon' lemon (C. limon) plants or Ca. L. asiaticus-infected bark- or bud pieces from field-grown 'Lisbon' lemon trees.

tag: type of plants

value: greenhouse-grown sweet orange scions on Cleopatra mandarin

tag: age of plants

value: 3 years

value: mature leaves


title: T0404C2


title: 143B-1251 Low

description:
ZsGreen transduced tumor cells
143B_Bone_1251_Low_JS_05262010


title: Control group, biological rep2


title: T0404B2


title: leaves, healthy, 13-17 wai, biological rep 1


title: T0404B1-2


title: T0404B3


title: leaves, healthy, 5-9 wai, biological rep 2

source_name: Valencia' leaves, mock-inoculated, 5 and 9 wai


title: leaves, infected, 13-17 wai, biological rep 3

description: gene expression data from symptomatic  leaves

source_name: Valencia' leaves, Las-inoculated, 13 and 17 wai


title: C_albicans_WT_v_bcr1_rep3

organism: Candida albicans

source_name: Total RNA from Candida albicans BCR1 knockout cells, grown in SD medium supplemented with 50 mM glucose and 10% feotal calf serum and labeled with Cyanine-3

label_protocol: 10 µg of total RNA was used for cDNA labeling. Briefly RNA samples were incubated with 0.2 pmol of Candida albicans specific RT primers mix (Eurogentec) and 200 pmol of anchor oligonucleotide deoxyriboslthymine (Invitrogen) at 70°C for 10 min, after which following reaction reagents were added: 1 X First strand buffer, 20 µmol dATP, dTTP, and dGTP, 2 µmol dCTP, 400 pmol dithiothreitol, 400 U Superscript II reverse transcriptase (Invitrogen). 2 nmol Cy5-dCTP or Cy3-dCTP was then added into the mixture in the dark. The mixture was left at 42°C for two hours followed by adding additional 400 U Superscript II reverse transcriptase, and reaction was continued for one more hour. 50 µg/ml-1 RNase A and 0.05 U RNase H were added and the reaction was incubated for 30 min at 37°C.

growth_protocol: Overnight cultures of C. albicans CJN702 were diluted to a A600 of 0.2 in 50 ml of SD medium supplemented with 50 mM glucose and 10% feotal calf serum, and culture was incubated at 200 rpm at 37 degree for 5 hours

tag: growth condition

value: 37 degree Celsius, SD medium supplemented with 50 mM glucose and 10% feotal calf serum

tag: strain

tag: genotype/variation

value: BCR1 knockout

source_name: Total RNA from Candida albicans DAY286 cells in SD medium supplemented with 50 mM glucose and 10% feotal calf serum and labeled with Cy5

growth_protocol: Overnight cultures of C. albicans DAY286 were diluted to a A600 of 0.2 in 50 ml of SD medium supplemented with 50 mM glucose and 10% feotal calf serum, and culture was incubated at 200 rpm at 37 degree for 5 hours

value: wild type


title: leaves, healthy, 5-9 wai, biological rep 1

tag: tissue


title: leaves, infected, 13-17 wai, biological rep 1


title: leaves, infected, 5-9 wai, biological rep 3

description: gene expression data from pre-symptomatic/symptomatic  leaves

source_name: Valencia' leaves, Las-inoculated, 5 and 9 wai


title: T0404B1-1

source_name: LCM tumor cluster


title: leaves, infected, 5-9 wai, biological rep 2


title: T0404A1-2


title: T0404A3


title: T0404A2


title: C_albicans_WT_v_bcr1_rep1

source_name: Total RNA from Candida albicans BCR1 knockout cells, grown in SD medium supplemented with 50 mM glucose and 10% feotal calf serum and labeled with Cyanine-5

source_name: Total RNA from Candida albicans DAY286 cells in SD medium supplemented with 50 mM glucose and 10% feotal calf serum and labeled with Cy3


title: C_albicans_WT_v_bcr1_rep2


title: leaves, infected, 5-9 wai, biological rep 1


title: leaves, infected, 13-17 wai, biological rep 2


title: T0404A1-1


title: C2C12 cells negative control siRNA 96h rep1


title: HC_CD4_251485038534_3

status: Public on Nov 03 2011

city: London

first: Alessandra

middle: De Paula Alves

last: Sousa

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

description: All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 90% (% of CD4 or CD8+ cells, determined by flow cytometry).

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65oC and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the “Gene Expression Hybridization Kit” (Agilent, 5188-5242). After posthybridization washes (“Wash Buffers 1 and 2 Kit”, Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: After processing, microarray slides were scanned at 535 nm and 5um/pixel resolution using a GenePix 4000B scanner and the software “GenePix Pro 6.0” (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Images were analyzed with the software “Agilent Feature Extraction 8.5” and extracted expression values (gProcessedSignal) were further normalized to the 75 percentile expression value, considering all non-control features (ControlType=0). Following normalization, replicate probes were averaged, resulting in the final set of 41,000 unique probes.

source_name: CD4+ T-lymphocytes, peripheral blood healthy control

label_protocol: Cy3-labelled cRNA was generated using the “Quick Amp Labeling Kit, one-color” (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA (“One Color RNA Spike-In Kit”, Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

extract_protocol:
Anti-biotin magnetic beads pre-loaded with biotinylated antibodies against human CD4 and CD8 (Miltenyi Biotec) were used to isolated specific T cells from PBMCs. The all samples included in this study showed purity more than 90% by cytometry analysis.
Peripheral blood mononuclear cells (PBMCs) were isolated from MS patients and healthy controls by centrifugation using Ficoll-Paque PLUS, and CD4+ and CD8+ T-cells were immunomagnetically purified using the positive cell Isolation Kit (Miltenyi Biotec).
Total RNA was extracted using TRIZOL-LS (Invitrogen), treated with DNase and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA). RNA quality was assessed by agarose gel electrophoresis and quantified using a NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA).

tag: disease

value: CD4+ T-lymphocytes

tag: group

value: healthy control

tag: gender

value: male


title: HC_CD8_251485038535_2

source_name: CD8+ T-lymphocytes, peripheral blood healthy control

tag: cell type

value: CD8+ T-lymphocytes

value: female


title: HC_CD4_251485038534_2


title: HC_CD4_251485038534_4


title: HC_CD8_251485038535_3


title: C_albicans_WT_v_bcr1_rep4


title: HC_CD4_251485038534_1


title: MS_CD8_2YR_251485036537_2

source_name: CD8+ T-lymphocytes, peripheral blood 2 years post-transplant

value: Multiple sclerosis

value: 2 years post-transplant


title: MS_CD8_2YR_251485036537_4


title: HC_CD8_251485038535_1


title: MS_CD8_2YR_251485036537_3


title: MS_CD8_2YR_251485036537_1


title: MS_CD8_1YR_251485033971_3

source_name: CD8+ T-lymphocytes, peripheral blood 1 year post-transplant

value: 1 year post-transplant


title: MS_CD8_6MO_251485033969_4

source_name: CD8+ T-lymphocytes, peripheral blood 6 month post-transplant

value: 6 month post-transplant


title: MSNI_CD8_PRE_251485033729_2

source_name: CD8+ T-lymphocytes, peripheral blood pre-transplant

value: pre-transplant


title: HC_CD8_251485038535_4


title: MSNI_CD8_PRE_251485033729_3


title: MS_CD8_6MO_251485033969_3


title: MSI_CD8_PRE_251485033973_2


title: MS_CD8_1YR_251485033971_4


title: MSI_CD8_PRE_251485033973_4


title: MS_CD8_6MO_251485033969_1


title: MS_CD8_1YR_251485033971_1


title: MSI_CD8_PRE_251485033973_1


title: MS_CD8_6MO_251485033969_2


title: MSI_CD8_PRE_251485033973_3


title: MS_CD4_2YR_251485036536_4

source_name: CD4+ T-lymphocytes, peripheral blood 2 years post-transplant


title: MS_CD8_1YR_251485033971_2


title: MS_CD4_2YR_251485036536_1


title: MSNI_CD8_PRE_251485033729_4


title: MSNI_CD8_PRE_251485033729_1


title: MS_CD4_2YR_251485036536_2


title: MS_CD4_1YR_251485033970_4

source_name: CD4+ T-lymphocytes, peripheral blood 1 year post-transplant


title: EBC-1_STY

type: genomic

city: Charlestown

first: Stephen

middle: Michael

last: Rothenberg

state: MA

address: 13th Street, Bldg. 149, 7th Floor

department: Cancer Center

institute: Massachusetts General Hospital

description:
Hybridized to 250K_Sty
EBC-1

hyb_protocol: Hybridization was performed as described in the 500k assay manual (P/N 701930 Rev. 2).

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000 with autoloader and 7G upgrade and images were acquired using GenChip operating software version 1.4.

data_processing:
CEL files and TXT files (generated by Affymetrix GTYPE using the Dynamic Model Mapping algorithm) were processed by dCHIP version 2008 using Model-based expression. The following parameters were used: Background subtraction--Mismatch probe (PM/MM difference); Normalization--Invariant set probe selection method and Running median smoothing method (baseline array NA06990); Raw copy number determination--Signal / (mean signal of normal samples at this SNP) * 2; log2 ratio--log2(Signal / mean signal of normal samples at this SNP); Inferred copy number method-- Median smoothing with window size of 3.

The SNP calls are available in the supplementary .txt file that is linked to this record. The data table containing the Signal values (analgous to the expression value in expression array analysis) for each SNP probe produced by dCHIP is available in the supplementary .txt file that is linked to the Series GSE20306 record.

molecule: genomic DNA

source_name: Lung:NSCLC cell line EBC-1

label_protocol: Labeling was performed as described in the 500k assay manual (P/N 701930 Rev. 2).

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted with the Qiagen Blood Amp kit (P/N 51161).

treatment_protocol: None.


title: MS_CD4_2YR_251485036536_3


title: BEN_STY

description:
Hybridized to 250K_Sty
BEN

source_name: Lung:NSCLC cell line BEN

value: BEN


title: SVts-8_STY

description:
Hybridized to 250K_Sty
SVts-8

source_name: Lung cell line SVts-8


title: VMRC-LCD_STY

description:
Hybridized to 250K_Sty
VMRC-LCD

source_name: Lung:NSCLC cell line VMRC-LCD

value: VMRC-LCD


title: MCF7_STY

description:
Hybridized to 250K_Sty
MCF7

source_name: Breast cell line MCF7


title: RERF-LC-MS_STY

description:
Hybridized to 250K_Sty
RERF-LC-MS

source_name: Lung:NSCLC cell line RERF-LC-MS

value: RERF-LC-MS


title: MS_CD4_6MO_251485033730_2

source_name: CD4+ T-lymphocytes, peripheral blood 6 months post-transplant

value: 6 months post-transplant


title: SK-ES-1_STY

description:
Hybridized to 250K_Sty
SK-ES-1

source_name: Bone cell line SK-ES-1


title: Saos-2_STY

description:
Hybridized to 250K_Sty
Saos-2

source_name: Bone cell line Saos-2


title: MS_CD4_1YR_251485033970_1


title: MS_CD4_6MO_251485033730_1


title: NCI-H647_STY

description:
Hybridized to 250K_Sty
NCI-H647

source_name: Lung:NSCLC cell line NCI-H647


title: MSI_CD4_PRE_251485033972_2

source_name: CD4+ T-lymphocytes, peripheral blood pre-transplant


title: MS_CD4_6MO_251485033730_4


title: MS_CD4_1YR_251485033970_3


title: MS_CD4_1YR_251485033970_2


title: MS_CD4_6MO_251485033730_3


title: MSI_CD4_PRE_251485033972_4


title: MSNI_CD4_PRE_251485033728_4


title: MSI_CD4_PRE_251485033972_1


title: MSI_CD4_PRE_251485033972_3


title: MSTO-211H_STY

description:
Hybridized to 250K_Sty
MSTO-211H

source_name: Lung cell line MSTO-211H


title: MSNI_CD4_PRE_251485033728_3


title: MRC-9_STY

description:
Hybridized to 250K_Sty
MRC-9

source_name: Lung cell line MRC-9


title: MSNI_CD4_PRE_251485033728_1


title: MKN7_STY

description:
Hybridized to 250K_Sty
MKN7

source_name: Stomach cell line MKN7


title: MSNI_CD4_PRE_251485033728_2


title: U-2 OS_STY

description:
Hybridized to 250K_Sty
U-2 OS

source_name: Bone cell line U-2 OS

value: U-2 OS


title: RERF-LC-MA_STY

description:
Hybridized to 250K_Sty
RERF-LC-MA

source_name: Lung cell line RERF-LC-MA

value: RERF-LC-MA


title: SK-BR-3_STY

description:
Hybridized to 250K_Sty
SK-BR-3

source_name: Breast cell line SK-BR-3


title: PC-3 [JPC-3]_STY

description:
Hybridized to 250K_Sty
PC-3 [JPC-3]

source_name: Lung:NSCLC cell line PC-3 [JPC-3]


title: LU99A_STY

description:
Hybridized to 250K_Sty
LU99A

source_name: Lung:NSCLC cell line LU99A


title: LOU-NH91_STY

description:
Hybridized to 250K_Sty
LOU-NH91

source_name: Lung:NSCLC cell line LOU-NH91


title: OCUM-1_STY

description:
Hybridized to 250K_Sty
OCUM-1

source_name: Stomach cell line OCUM-1


title: ABC-1_STY

description:
Hybridized to 250K_Sty
ABC-1

source_name: Lung:NSCLC cell line ABC-1


title: BT-20_STY

description:
Hybridized to 250K_Sty
BT-20

source_name: Breast cell line BT-20


title: BPH-1_STY

description:
Hybridized to 250K_Sty
BPH-1

source_name: Prostate cell line BPH-1


title: WPE1-NB14_STY

description:
Hybridized to 250K_Sty
WPE1-NB14

source_name: Prostate cell line WPE1-NB14


title: LNCaP clone FGC_STY

description:
Hybridized to 250K_Sty
LNCaP clone FGC

source_name: Prostate cell line LNCaP clone FGC

value: LNCaP clone FGC


title: SBC-5_STY

description:
Hybridized to 250K_Sty
SBC-5

source_name: Lung cell line SBC-5


title: SBC-2_STY

description:
Hybridized to 250K_Sty
SBC-2

source_name: Lung cell line SBC-2


title: SBC-3_STY

description:
Hybridized to 250K_Sty
SBC-3

source_name: Lung cell line SBC-3


title: RERF-LC-Ad2_STY

description:
Hybridized to 250K_Sty
RERF-LC-Ad2

source_name: Lung:NSCLC cell line RERF-LC-Ad2


title: OUS-11_STY

description:
Hybridized to 250K_Sty
OUS-11

source_name: Lung cell line OUS-11


title: NCI-H2196_STY

description:
Hybridized to 250K_Sty
NCI-H2196

source_name: Lung cell line NCI-H2196


title: NCI-H1693_STY

description:
Hybridized to 250K_Sty
NCI-H1693

source_name: Lung:NSCLC cell line NCI-H1693


title: COR-L 105_STY

description:
Hybridized to 250K_Sty
COR-L 105

source_name: Lung:NSCLC cell line COR-L 105

value: COR-L 105


title: DMS 153_STY

description:
Hybridized to 250K_Sty
DMS 153

source_name: Lung cell line DMS 153

value: DMS 153


title: NCI-H1666_STY

description:
Hybridized to 250K_Sty
NCI-H1666

source_name: Lung:NSCLC cell line NCI-H1666


title: Hs 936.T_STY

description:
Hybridized to 250K_Sty
Hs 936.T

source_name: Skin cell line Hs 936.T


title: NCI-H1755_STY

description:
Hybridized to 250K_Sty
NCI-H1755

source_name: Lung:NSCLC cell line NCI-H1755


title: Hs 891.T_STY

description:
Hybridized to 250K_Sty
Hs 891.T

source_name: Kidney cell line Hs 891.T


title: SNU-16_STY

description:
Hybridized to 250K_Sty
SNU-16

source_name: Stomach cell line SNU-16


title: Hs 834.T_STY

description:
Hybridized to 250K_Sty
Hs 834.T

source_name: Skin cell line Hs 834.T


title: Hs 908.T_STY

description:
Hybridized to 250K_Sty
Hs 908.T

source_name: Skin cell line Hs 908.T


title: NUGC-4_STY

description:
Hybridized to 250K_Sty
NUGC-4

source_name: Stomach cell line NUGC-4


title: 23132/87_STY

description:
Hybridized to 250K_Sty
23132/87

source_name: Stomach cell line 23132/87


title: Hs 852.T_STY

description:
Hybridized to 250K_Sty
Hs 852.T

source_name: Skin cell line Hs 852.T


title: Hs 895.T_STY

description:
Hybridized to 250K_Sty
Hs 895.T

source_name: Skin cell line Hs 895.T


title: COLO-680N_STY

description:
Hybridized to 250K_Sty
COLO-680N

source_name: Esophagus cell line COLO-680N


title: Calu-3_STY

description:
Hybridized to 250K_Sty
Calu-3

source_name: Lung:NSCLC cell line Calu-3


title: KYSE-140_STY

description:
Hybridized to 250K_Sty
KYSE-140

source_name: Esophagus cell line KYSE-140


title: KYSE-150_STY

description:
Hybridized to 250K_Sty
KYSE-150

source_name: Esophagus cell line KYSE-150


title: KYSE-180_STY

description:
Hybridized to 250K_Sty
KYSE-180

source_name: Esophagus cell line KYSE-180


title: KATO III_STY

description:
Hybridized to 250K_Sty
KATO III

source_name: Stomach cell line KATO III

value: KATO III


title: KYSE-270_STY

description:
Hybridized to 250K_Sty
KYSE-270

source_name: Esophagus cell line KYSE-270


title: Hs 573.T_STY

description:
Hybridized to 250K_Sty
Hs 573.T

source_name: Lung cell line Hs 573.T


title: KYSE-30_STY

description:
Hybridized to 250K_Sty
KYSE-30

source_name: Esophagus cell line KYSE-30


title: KYSE-410_STY

description:
Hybridized to 250K_Sty
KYSE-410

source_name: Esophagus cell line KYSE-410


title: KYSE-450_STY

description:
Hybridized to 250K_Sty
KYSE-450

source_name: Esophagus cell line KYSE-450


title: NCI-H1563_STY

description:
Hybridized to 250K_Sty
NCI-H1563

source_name: Lung:NSCLC cell line NCI-H1563


title: KYSE-70_STY

description:
Hybridized to 250K_Sty
KYSE-70

source_name: Esophagus cell line KYSE-70


title: NCI-H1623_STY

description:
Hybridized to 250K_Sty
NCI-H1623

source_name: Lung:NSCLC cell line NCI-H1623


title: NCI-H1522_STY

description:
Hybridized to 250K_Sty
NCI-H1522

source_name: Lung cell line NCI-H1522


title: MKN74_STY

description:
Hybridized to 250K_Sty
MKN74

source_name: Stomach cell line MKN74


title: MKN45_STY

description:
Hybridized to 250K_Sty
MKN45

source_name: Stomach cell line MKN45


title: NCI-H1651_STY

description:
Hybridized to 250K_Sty
NCI-H1651

source_name: Lung:NSCLC cell line NCI-H1651


title: MKN1_STY

description:
Hybridized to 250K_Sty
MKN1

source_name: Stomach cell line MKN1


title: NCI-H1573_STY

description:
Hybridized to 250K_Sty
NCI-H1573

source_name: Lung:NSCLC cell line NCI-H1573


title: NCI-H2081_STY

description:
Hybridized to 250K_Sty
NCI-H2081

source_name: Lung cell line NCI-H2081


title: NCI-H2122_STY

description:
Hybridized to 250K_Sty
NCI-H2122

source_name: Lung:NSCLC cell line NCI-H2122


title: NCI-H2171_STY

description:
Hybridized to 250K_Sty
NCI-H2171

source_name: Lung cell line NCI-H2171


title: T.T_STY

description:
Hybridized to 250K_Sty
T.T

source_name: Esophagus cell line T.T


title: NCI-H2172_STY

description:
Hybridized to 250K_Sty
NCI-H2172

source_name: Lung:NSCLC cell line NCI-H2172


title: SW 900_STY

description:
Hybridized to 250K_Sty
SW 900

source_name: Lung:NSCLC cell line SW 900


title: T.Tn_STY

description:
Hybridized to 250K_Sty
T.Tn

source_name: Esophagus cell line T.Tn


title: SK-MEL-3_STY

description:
Hybridized to 250K_Sty
SK-MEL-3

source_name: Skin cell line SK-MEL-3


title: NCI-H661_STY

description:
Hybridized to 250K_Sty
NCI-H661

source_name: Lung:NSCLC cell line NCI-H661


title: NCI-H441_STY

description:
Hybridized to 250K_Sty
NCI-H441

source_name: Lung:NSCLC cell line NCI-H441


title: KYSE-510_STY

description:
Hybridized to 250K_Sty
KYSE-510

source_name: Esophagus cell line KYSE-510


title: NCI-H2452_STY

description:
Hybridized to 250K_Sty
NCI-H2452

source_name: Lung cell line NCI-H2452


title: KYSE-520_STY

description:
Hybridized to 250K_Sty
KYSE-520

source_name: Esophagus cell line KYSE-520


title: NCI-H2286_STY

description:
Hybridized to 250K_Sty
NCI-H2286

source_name: Lung cell line NCI-H2286


title: NCI-H711_STY

description:
Hybridized to 250K_Sty
NCI-H711

source_name: Lung cell line NCI-H711


title: NCI-H2170_STY

description:
Hybridized to 250K_Sty
NCI-H2170

source_name: Lung:NSCLC cell line NCI-H2170


title: NCI-H2228_STY

description:
Hybridized to 250K_Sty
NCI-H2228

source_name: Lung:NSCLC cell line NCI-H2228


title: NCI-H2135_STY

description:
Hybridized to 250K_Sty
NCI-H2135

source_name: Lung:NSCLC cell line NCI-H2135


title: NCI-H2347_STY

description:
Hybridized to 250K_Sty
NCI-H2347

source_name: Lung:NSCLC cell line NCI-H2347


title: NCI-H2085_STY

description:
Hybridized to 250K_Sty
NCI-H2085

source_name: Lung:NSCLC cell line NCI-H2085


title: SK-MEL-1_STY

description:
Hybridized to 250K_Sty
SK-MEL-1

source_name: Skin cell line SK-MEL-1


title: NCI-H2009_STY

description:
Hybridized to 250K_Sty
NCI-H2009

source_name: Lung:NSCLC cell line NCI-H2009


title: NCI-H1734_STY

description:
Hybridized to 250K_Sty
NCI-H1734

source_name: Lung:NSCLC cell line NCI-H1734


title: NCI-H1568_STY

description:
Hybridized to 250K_Sty
NCI-H1568

source_name: Lung:NSCLC cell line NCI-H1568


title: KYSE-220_STY

description:
Hybridized to 250K_Sty
KYSE-220

source_name: Esophagus cell line KYSE-220


title: Hs 417.Lu_STY

description:
Hybridized to 250K_Sty
Hs 417.Lu

source_name: Lung cell line Hs 417.Lu

value: Hs 417.Lu


title: GCT_STY

description:
Hybridized to 250K_Sty
GCT

source_name: Miscellaneous cell line GCT

value: GCT


title: H69AR_STY

description:
Hybridized to 250K_Sty
H69AR

source_name: Lung cell line H69AR


title: Hs 781.T_STY

description:
Hybridized to 250K_Sty
Hs 781.T

source_name: Bone cell line Hs 781.T


title: Hs 894(E).Lu_STY

description:
Hybridized to 250K_Sty
Hs 894(E).Lu

source_name: Lung cell line Hs 894(E).Lu


title: NCI-H810_STY

description:
Hybridized to 250K_Sty
NCI-H810

source_name: Lung:NSCLC cell line NCI-H810


title: NCI-H1793_STY

description:
Hybridized to 250K_Sty
NCI-H1793

source_name: Lung:NSCLC cell line NCI-H1793


title: G-361_STY

description:
Hybridized to 250K_Sty
G-361

source_name: Skin cell line G-361


title: A375.S2_STY

description:
Hybridized to 250K_Sty
A375.S2

source_name: Skin cell line A375.S2


title: KYSE-50_STY

description:
Hybridized to 250K_Sty
KYSE-50

source_name: Esophagus cell line KYSE-50


title: 201T_STY

description:
Hybridized to 250K_Sty
201T

source_name: Lung:NSCLC cell line 201T


title: NCI-H727_STY

description:
Hybridized to 250K_Sty
NCI-H727

source_name: Lung cell line NCI-H727


title: 273T_STY

description:
Hybridized to 250K_Sty
273T

source_name: Lung:NSCLC cell line 273T


title: NCI-H82_STY

description:
Hybridized to 250K_Sty
NCI-H82

source_name: Lung cell line NCI-H82


title: Hs 751.T_STY

description:
Hybridized to 250K_Sty
Hs 751.T

source_name: Blood/Lymph cell line Hs 751.T


title: NCI-H1048_STY

description:
Hybridized to 250K_Sty
NCI-H1048

source_name: Lung cell line NCI-H1048


title: NCI-H1703_STY

description:
Hybridized to 250K_Sty
NCI-H1703

source_name: Lung:NSCLC cell line NCI-H1703


title: NCI-H2023_STY

description:
Hybridized to 250K_Sty
NCI-H2023

source_name: Lung:NSCLC cell line NCI-H2023


title: NCI-H1944_STY

description:
Hybridized to 250K_Sty
NCI-H1944

source_name: Lung:NSCLC cell line NCI-H1944


title: NCI-H841_STY

description:
Hybridized to 250K_Sty
NCI-H841

source_name: Lung cell line NCI-H841


title: NCI-H1581_STY

description:
Hybridized to 250K_Sty
NCI-H1581

source_name: Lung:NSCLC cell line NCI-H1581


title: NCI-H838_STY

description:
Hybridized to 250K_Sty
NCI-H838

source_name: Lung:NSCLC cell line NCI-H838


title: NCI-H1437_STY

description:
Hybridized to 250K_Sty
NCI-H1437

source_name: Lung:NSCLC cell line NCI-H1437


title: NCI-H1417_STY

description:
Hybridized to 250K_Sty
NCI-H1417

source_name: Lung cell line NCI-H1417


title: NCI-H650_STY

description:
Hybridized to 250K_Sty
NCI-H650

source_name: Lung:NSCLC cell line NCI-H650


title: NCI-H1155_STY

description:
Hybridized to 250K_Sty
NCI-H1155

source_name: Lung:NSCLC cell line NCI-H1155


title: NCI-H23_STY

description:
Hybridized to 250K_Sty
NCI-H23

source_name: Lung:NSCLC cell line NCI-H23


title: NL20-TA_STY

description:
Hybridized to 250K_Sty
NL20-TA

source_name: Lung cell line NL20-TA


title: NCI-H1650_STY

description:
Hybridized to 250K_Sty
NCI-H1650

source_name: Lung:NSCLC cell line NCI-H1650


title: HMCB_STY

description:
Hybridized to 250K_Sty
HMCB

source_name: Skin cell line HMCB

value: HMCB


title: NCI-H1792_STY

description:
Hybridized to 250K_Sty
NCI-H1792

source_name: Lung:NSCLC cell line NCI-H1792


title: WM-115_STY

description:
Hybridized to 250K_Sty
WM-115

source_name: Skin cell line WM-115


title: AN3CA_STY

description:
Hybridized to 250K_Sty
AN3CA

source_name: Uterus cell line AN3CA


title: C32_STY

description:
Hybridized to 250K_Sty
C32

source_name: Skin cell line C32


title: MEWO_STY

description:
Hybridized to 250K_Sty
MEWO

source_name: Skin cell line MEWO

value: MEWO


title: NCI-H1299_STY

description:
Hybridized to 250K_Sty
NCI-H1299

source_name: Lung:NSCLC cell line NCI-H1299


title: RPMI-7951_STY

description:
Hybridized to 250K_Sty
RPMI-7951

source_name: Skin cell line RPMI-7951


title: NCI-H460_STY

description:
Hybridized to 250K_Sty
NCI-H460

source_name: Lung:NSCLC cell line NCI-H460


title: WI-26 VA4_STY

description:
Hybridized to 250K_Sty
WI-26 VA4

source_name: Lung cell line WI-26 VA4

value: WI-26 VA4


title: NCI-H358_STY

description:
Hybridized to 250K_Sty
NCI-H358

source_name: Lung:NSCLC cell line NCI-H358


title: ChaGo-K-1_STY

description:
Hybridized to 250K_Sty
ChaGo-K-1

source_name: Lung:NSCLC cell line ChaGo-K-1


title: A549_STY

description:
Hybridized to 250K_Sty
A549

source_name: Lung:NSCLC cell line A549


title: HT 728.T_STY

description:
Hybridized to 250K_Sty
HT 728.T

source_name: Bone cell line HT 728.T


title: BT-483_STY

description:
Hybridized to 250K_Sty
BT-483

source_name: Breast cell line BT-483


title: WIL2 NS_STY

description:
Hybridized to 250K_Sty
WIL2 NS

source_name: Blood/Lymph cell line WIL2 NS

value: WIL2 NS


title: COR-L 23/CPR_STY

description:
Hybridized to 250K_Sty
COR-L 23/CPR

source_name: Lung:NSCLC cell line COR-L 23/CPR

value: COR-L 23/CPR


title: COLO 792_STY

description:
Hybridized to 250K_Sty
COLO 792

source_name: Skin cell line COLO 792

value: COLO 792


title: BICR 78_STY

description:
Hybridized to 250K_Sty
BICR 78

source_name: Head & Neck cell line BICR 78

value: BICR 78


title: A2780cis_STY

description:
Hybridized to 250K_Sty
A2780cis

source_name: Ovary cell line A2780cis


title: COLO 741_STY

description:
Hybridized to 250K_Sty
COLO 741

source_name: Intestine cell line COLO 741

value: COLO 741


title: HCC202_STY

description:
Hybridized to 250K_Sty
HCC202

source_name: Breast cell line HCC202


title: Eos-HL-60_STY

description:
Hybridized to 250K_Sty
Eos-HL-60

source_name: Blood/Lymph cell line Eos-HL-60


title: DOK_STY

description:
Hybridized to 250K_Sty
DOK

source_name: Head & Neck cell line DOK

value: DOK


title: NCI-H522_STY

description:
Hybridized to 250K_Sty
NCI-H522

source_name: Lung:NSCLC cell line NCI-H522


title: COR-L88_STY

description:
Hybridized to 250K_Sty
COR-L88

source_name: Lung cell line COR-L88


title: H-EMC-SS_STY

description:
Hybridized to 250K_Sty
H-EMC-SS

source_name: Bone cell line H-EMC-SS

value: H-EMC-SS


title: LS 123_STY

description:
Hybridized to 250K_Sty
LS 123

source_name: Intestine cell line LS 123


title: LUDLU-1_STY

description:
Hybridized to 250K_Sty
LUDLU-1

source_name: Lung:NSCLC cell line LUDLU-1


title: Hs 737.T_STY

description:
Hybridized to 250K_Sty
Hs 737.T

source_name: Blood/Lymph cell line Hs 737.T


title: EJ138_STY

description:
Hybridized to 250K_Sty
EJ138

source_name: Bladder cell line EJ138


title: HCT 116_STY

description:
Hybridized to 250K_Sty
HCT 116

source_name: Intestine cell line HCT 116

value: HCT 116


title: NCI-H2330_STY

description:
Hybridized to 250K_Sty
NCI-H2330

source_name: Lung cell line NCI-H2330


title: Sci-1_STY

description:
Hybridized to 250K_Sty
Sci-1

source_name: Blood/Lymph cell line Sci-1


title: U266B1_STY

description:
Hybridized to 250K_Sty
U266B1

source_name: Blood/Lymph cell line U266B1


title: DMS 92_STY

description:
Hybridized to 250K_Sty
DMS 92

source_name: Lung cell line DMS 92

value: DMS 92


title: RT112/84_STY

description:
Hybridized to 250K_Sty
RT112/84

source_name: Bladder cell line RT112/84


title: SW 1116_STY

description:
Hybridized to 250K_Sty
SW 1116

source_name: Intestine cell line SW 1116


title: PE/CA-PJ15_STY

description:
Hybridized to 250K_Sty
PE/CA-PJ15

source_name: Head & Neck cell line PE/CA-PJ15


title: RT4_STY

description:
Hybridized to 250K_Sty
RT4

source_name: Bladder cell line RT4


title: OAW28_STY

description:
Hybridized to 250K_Sty
OAW28

source_name: Ovary cell line OAW28


title: RO82-W-1_STY

description:
Hybridized to 250K_Sty
RO82-W-1

source_name: Thyroid cell line RO82-W-1


title: MOG-G-UVW_STY

description:
Hybridized to 250K_Sty
MOG-G-UVW

source_name: Brain cell line MOG-G-UVW

value: MOG-G-UVW


title: HT 1376_STY

description:
Hybridized to 250K_Sty
HT 1376

source_name: Bladder cell line HT 1376


title: HRT-18_STY

description:
Hybridized to 250K_Sty
HRT-18

source_name: Intestine cell line HRT-18


title: FLYA13_STY

description:
Hybridized to 250K_Sty
FLYA13

source_name: Miscellaneous cell line FLYA13


title: fR2_STY

description:
Hybridized to 250K_Sty
fR2

source_name: Breast cell line fR2


title: COLO 857_STY

description:
Hybridized to 250K_Sty
COLO 857

source_name: Skin cell line COLO 857

value: COLO 857


title: H69V_STY

description:
Hybridized to 250K_Sty
H69V

source_name: Lung cell line H69V


title: COLO 205_STY

description:
Hybridized to 250K_Sty
COLO 205

source_name: Intestine cell line COLO 205

value: COLO 205


title: COLO 685_STY

description:
Hybridized to 250K_Sty
COLO 685

source_name: Uterus cell line COLO 685

value: COLO 685


title: COLO 684_STY

description:
Hybridized to 250K_Sty
COLO 684

source_name: Uterus cell line COLO 684

value: COLO 684


title: 1321N1_STY

description:
Hybridized to 250K_Sty
1321N

source_name: Brain cell line 1321N1


title: DMS 273_STY

description:
Hybridized to 250K_Sty
DMS 273

source_name: Lung cell line DMS 273

value: DMS 273


title: WM 266-4_STY

description:
Hybridized to 250K_Sty
WM 266-4

source_name: Skin cell line WM 266-4


title: SR_STY

description:
Hybridized to 250K_Sty
SR

source_name: Blood/Lymph cell line SR

value: SR


title: NCI-H889_STY

description:
Hybridized to 250K_Sty
NCI-H889

source_name: Lung cell line NCI-H889


title: SNU-398_STY

description:
Hybridized to 250K_Sty
SNU-398

source_name: Liver cell line SNU-398


title: SW 1463_STY

description:
Hybridized to 250K_Sty
SW 1463

source_name: Intestine cell line SW 1463


title: SK-N-FI_STY

description:
Hybridized to 250K_Sty
SK-N-FI

source_name: Brain cell line SK-N-FI

value: SK-N-FI


title: NCI-H322_STY

description:
Hybridized to 250K_Sty
NCI-H322

source_name: Lung:NSCLC cell line NCI-H322


title: SK-CO-1_STY

description:
Hybridized to 250K_Sty
SK-CO-1

source_name: Intestine cell line SK-CO-1


title: Nthy-ori 3-1_STY

description:
Hybridized to 250K_Sty
Nthy-ori 3-1

source_name: Thyroid cell line Nthy-ori 3-1

value: Nthy-ori 3-1


title: PC-9_STY

description:
Hybridized to 250K_Sty
PC-9

source_name: Lung:NSCLC cell line PC-9


title: SK-LU-1_STY

description:
Hybridized to 250K_Sty
SK-LU-1

source_name: Lung:NSCLC cell line SK-LU-1


title: PC-14_STY

description:
Hybridized to 250K_Sty
PC-14

source_name: Lung:NSCLC cell line PC-14


title: COR-L23_STY

description:
Hybridized to 250K_Sty
COR-L23

source_name: Lung:NSCLC cell line COR-L23


title: PNT1A_STY

description:
Hybridized to 250K_Sty
PNT1A

source_name: Prostate cell line PNT1A


title: NUGC-3_STY

description:
Hybridized to 250K_Sty
NUGC-3

source_name: Stomach cell line NUGC-3


title: COR-L279_STY

description:
Hybridized to 250K_Sty
COR-L279

source_name: Lung cell line COR-L279


title: IM-95_STY

description:
Hybridized to 250K_Sty
IM-95

source_name: Stomach cell line IM-95


title: NCI-N87_STY

description:
Hybridized to 250K_Sty
NCI-N87

source_name: Stomach cell line NCI-N87


title: COLO 858_STY

description:
Hybridized to 250K_Sty
COLO 858

source_name: Skin cell line COLO 858

value: COLO 858


title: Hs 746T_STY

description:
Hybridized to 250K_Sty
Hs 746T

source_name: Stomach cell line Hs 746T

value: Hs 746T


title: AZ-521_STY

description:
Hybridized to 250K_Sty
AZ-521

source_name: Stomach cell line AZ-521


title: AGS_STY

description:
Hybridized to 250K_Sty
AGS

source_name: Stomach cell line AGS

value: AGS


title: RERF-GC-1B_STY

description:
Hybridized to 250K_Sty
RERF-GC-1B

source_name: Stomach cell line RERF-GC-1B


title: SNU-5_STY

description:
Hybridized to 250K_Sty
SNU-5

source_name: Stomach cell line SNU-5


title: 22RV1_STY

description:
Hybridized to 250K_Sty
22RV1

source_name: Prostate cell line 22RV1


title: Hs 600.T_STY

description:
Hybridized to 250K_Sty
Hs 600.T

source_name: Skin cell line Hs 600.T


title: WPE1-NB26_STY

description:
Hybridized to 250K_Sty
WPE1-NB26

source_name: Prostate cell line WPE1-NB26


title: WPE1-NB11_STY

description:
Hybridized to 250K_Sty
WPE1-NB11

source_name: Prostate cell line WPE1-NB11


title: NCI-H1915_STY

description:
Hybridized to 250K_Sty
NCI-H1915

source_name: Lung:NSCLC cell line NCI-H1915


title: WPE1-NA22_STY

description:
Hybridized to 250K_Sty
WPE1-NA22

source_name: Prostate cell line WPE1-NA22


title: RWPE2-W99_STY

description:
Hybridized to 250K_Sty
RWPE2-W99

source_name: Prostate cell line RWPE2-W99


title: NB69_STY

description:
Hybridized to 250K_Sty
NB69

source_name: Brain cell line NB69


title: SNU-1_STY

description:
Hybridized to 250K_Sty
SNU-1

source_name: Stomach cell line SNU-1


title: NCI-H2342_STY

description:
Hybridized to 250K_Sty
NCI-H2342

source_name: Lung:NSCLC cell line NCI-H2342


title: MES-SA_STY

description:
Hybridized to 250K_Sty
MES-SA

source_name: Uterus cell line MES-SA

value: MES-SA


title: RWPE-2_STY

description:
Hybridized to 250K_Sty
RWPE-2

source_name: Prostate cell line RWPE-2


title: RWPE-1_STY

description:
Hybridized to 250K_Sty
RWPE-1

source_name: Prostate cell line RWPE-1


title: LU65A_STY

description:
Hybridized to 250K_Sty
LU65A

source_name: Lung:NSCLC cell line LU65A


title: LU65_STY

description:
Hybridized to 250K_Sty
LU65

source_name: Lung:NSCLC cell line LU65


title: KHOS/NP_STY

description:
Hybridized to 250K_Sty
KHOS/NP

source_name: Bone cell line KHOS/NP

value: KHOS/NP


title: KHOS-240S_STY

description:
Hybridized to 250K_Sty
KHOS-240S

source_name: Bone cell line KHOS-240S


title: LU65B_STY

description:
Hybridized to 250K_Sty
LU65B

source_name: Lung:NSCLC cell line LU65B


title: JSC-1_STY

description:
Hybridized to 250K_Sty
JSC-1

source_name: Blood/Lymph cell line JSC-1


title: KHOS-312H_STY

description:
Hybridized to 250K_Sty
KHOS-312H

source_name: Bone cell line KHOS-312H


title: STC 1_STY

description:
Hybridized to 250K_Sty
STC 1

source_name: Lung cell line STC 1

value: STC 1


title: LK-2_STY

description:
Hybridized to 250K_Sty
LK-2

source_name: Lung:NSCLC cell line LK-2


title: RERF-LC-KJ_STY

description:
Hybridized to 250K_Sty
RERF-LC-KJ

source_name: Lung:NSCLC cell line RERF-LC-KJ

value: RERF-LC-KJ


title: RERF-LC-Sq1_STY

description:
Hybridized to 250K_Sty
RERF-LC-Sq1

source_name: Lung:NSCLC cell line RERF-LC-Sq1


title: HARA_STY

description:
Hybridized to 250K_Sty
HARA

source_name: Lung:NSCLC cell line HARA

value: HARA


title: LCLC-103H_STY

description:
Hybridized to 250K_Sty
LCLC-103H

source_name: Lung:NSCLC cell line LCLC-103H


title: HCC-78_STY

description:
Hybridized to 250K_Sty
HCC-78

source_name: Lung:NSCLC cell line HCC-78


title: Hs 633T_STY

description:
Hybridized to 250K_Sty
Hs 633T

source_name: Miscellaneous cell line Hs 633T

value: Hs 633T


title: HT55_STY

description:
Hybridized to 250K_Sty
HT55

source_name: Intestine cell line HT55


title: Ishikawa (Heraklio) 02 ER-_STY

description:
Hybridized to 250K_Sty
Ishikawa (Heraklio) 02 ER-

source_name: Uterus cell line Ishikawa (Heraklio) 02 ER-

value: Ishikawa (Heraklio) 02 ER-


title: Ishikawa_STY

description:
Hybridized to 250K_Sty
Ishikawa

source_name: Uterus cell line Ishikawa

value: Ishikawa


title: HCC-44_STY

description:
Hybridized to 250K_Sty
HCC-44

source_name: Lung:NSCLC cell line HCC-44


title: HGC-27_STY

description:
Hybridized to 250K_Sty
HGC-27

source_name: Stomach cell line HGC-27


title: NCI-H196_STY

description:
Hybridized to 250K_Sty
NCI-H196

source_name: Lung cell line NCI-H196


title: H33HJ-JA1_STY

description:
Hybridized to 250K_Sty
H33HJ-JA1

source_name: Blood/Lymph cell line H33HJ-JA1


title: NCI-H1435_STY

description:
Hybridized to 250K_Sty
NCI-H1435

source_name: Lung:NSCLC cell line NCI-H1435


title: UMC-11_STY

description:
Hybridized to 250K_Sty
UMC-11

source_name: Lung cell line UMC-11


title: NCI-H1781_STY

description:
Hybridized to 250K_Sty
NCI-H1781

source_name: Lung:NSCLC cell line NCI-H1781


title: BT-549_STY

description:
Hybridized to 250K_Sty
BT-549

source_name: Breast cell line BT-549


title: SW 1417_STY

description:
Hybridized to 250K_Sty
SW 1417

source_name: Intestine cell line SW 1417


title: SW 13_STY

description:
Hybridized to 250K_Sty
SW 13

source_name: Kidney cell line SW 13

value: SW 13


title: Hs 228.T_STY

description:
Hybridized to 250K_Sty
Hs 228.T

source_name: Bladder cell line Hs 228.T


title: OAW42_STY

description:
Hybridized to 250K_Sty
OAW42

source_name: Ovary cell line OAW42


title: SW 48_STY

description:
Hybridized to 250K_Sty
SW 48

source_name: Intestine cell line SW 48

value: SW 48


title: PNT2_STY

description:
Hybridized to 250K_Sty
PNT2

source_name: Prostate cell line PNT2


title: MES-SA/Dx-5_STY

description:
Hybridized to 250K_Sty
MES-SA/Dx-5

source_name: Uterus cell line MES-SA/Dx-5


title: MDST8_STY

description:
Hybridized to 250K_Sty
MDST8

source_name: Intestine cell line MDST8


title: SK-N-BE(2)_STY

description:
Hybridized to 250K_Sty
SK-N-BE(2)

source_name: Brain cell line SK-N-BE(2)


title: LS180_STY

description:
Hybridized to 250K_Sty
LS180

source_name: Intestine cell line LS180


title: MOG-G-CCM_STY

description:
Hybridized to 250K_Sty
MOG-G-CCM

source_name: Brain cell line MOG-G-CCM

value: MOG-G-CCM


title: HCT-8_STY

description:
Hybridized to 250K_Sty
HCT-8

source_name: Intestine cell line HCT-8


title: LS174T_STY

description:
Hybridized to 250K_Sty
LS174T

source_name: Intestine cell line LS174T


title: HMVII_STY

description:
Hybridized to 250K_Sty
HMVII

source_name: Skin cell line HMVII

value: HMVII


title: GA-10_STY

description:
Hybridized to 250K_Sty
GA-10

source_name: Blood/Lymph cell line GA-10


title: HCC-366_STY

description:
Hybridized to 250K_Sty
HCC-366

source_name: Lung:NSCLC cell line HCC-366


title: HCC-15_STY

description:
Hybridized to 250K_Sty
HCC-15

source_name: Lung:NSCLC cell line HCC-15


title: G-292 Clone A141B1_STY

description:
Hybridized to 250K_Sty
G-292 Clone A141B1

source_name: Bone cell line G-292 Clone A141B1

value: G-292 Clone A141B1


title: EB1_STY

description:
Hybridized to 250K_Sty
EB1

source_name: Blood/Lymph cell line EB1


title: Detroit 562_STY

description:
Hybridized to 250K_Sty
Detroit 562

source_name: Head & Neck cell line Detroit 562

value: Detroit 562


title: COR-L95_STY

description:
Hybridized to 250K_Sty
COR-L95

source_name: Lung cell line COR-L95


title: C8166_STY

description:
Hybridized to 250K_Sty
C8166

source_name: Blood/Lymph cell line C8166


title: ReferenceSample_NA17737

description:
Hybridized to 250K_Sty
NA17737

source_name: Reference Sample NA17737

tag: sample type

value: reference


title: ReferenceSample_NA07349

description:
Hybridized to 250K_Sty
NA07349

source_name: Reference Sample NA07349


title: ReferenceSample_NA06990

description:
Hybridized to 250K_Sty
NA06990

source_name: Reference Sample NA06990


title: H3255_STY

description:
Hybridized to 250K_Sty
H3255

source_name: Lung:NSCLC cell line H3255


title: ReferenceSample_NA17110

description:
Hybridized to 250K_Sty
NA17110

source_name: Reference Sample NA17110


title: ReferenceSample_NA17102

description:
Hybridized to 250K_Sty
NA17102

source_name: Reference Sample NA17102


title: HT115_STY

description:
Hybridized to 250K_Sty
HT115

source_name: Intestine cell line HT115


title: ReferenceSample_NA17733

description:
Hybridized to 250K_Sty
NA17733

source_name: Reference Sample NA17733


title: A373-C6_STY

description:
Hybridized to 250K_Sty
A373-C6

source_name: Skin cell line A373-C6


title: T47D_STY

description:
Hybridized to 250K_Sty
T47D

source_name: Breast cell line T47D


title: WiDr_STY

description:
Hybridized to 250K_Sty
WiDr

source_name: Intestine cell line WiDr

value: WiDr


title: COLO 201_STY

description:
Hybridized to 250K_Sty
COLO 201

source_name: Intestine cell line COLO 201

value: COLO 201


title: WILCL_STY

description:
Hybridized to 250K_Sty
WILCL

source_name: Blood/Lymph cell line WILCL

value: WILCL


title: BICR 10_STY

description:
Hybridized to 250K_Sty
BICR 10

source_name: Head & Neck cell line BICR 10

value: BICR 10


title: WI 38_STY

description:
Hybridized to 250K_Sty
WI 38

source_name: Lung cell line WI 38

value: WI 38


title: SK-OV-3_STY

description:
Hybridized to 250K_Sty
SK-OV-3

source_name: Ovary cell line SK-OV-3


title: A2780ADR_STY

description:
Hybridized to 250K_Sty
A2780ADR

source_name: Ovary cell line A2780ADR


title: SK-MES_STY

description:
Hybridized to 250K_Sty
SK-MES

source_name: Lung:NSCLC cell line SK-MES

value: SK-MES


title: MG-63_STY

description:
Hybridized to 250K_Sty
MG-63

source_name: Bone cell line MG-63


title: FTC-238_STY

description:
Hybridized to 250K_Sty
FTC-238

source_name: Thyroid cell line FTC-238


title: A2780_STY

description:
Hybridized to 250K_Sty
A2780

source_name: Ovary cell line A2780


title: BICR 31_STY

description:
Hybridized to 250K_Sty
BICR 31

source_name: Head & Neck cell line BICR 31

value: BICR 31


title: D341 Med_STY

description:
Hybridized to 250K_Sty
D341 Med

source_name: Brain cell line D341 Med

value: D341 Med


title: U373 MG_STY

description:
Hybridized to 250K_Sty
U373 MG

source_name: Brain:Glioblastoma cell line U373 MG

value: U373 MG


title: GP5d_STY

description:
Hybridized to 250K_Sty
GP5d

source_name: Intestine cell line GP5d


title: Bu25 TK-_STY

description:
Hybridized to 250K_Sty
Bu25 TK-

source_name: Cervix cell line Bu25 TK-

value: Bu25 TK-


title: COLO 853_STY

description:
Hybridized to 250K_Sty
COLO 853

source_name: Skin cell line COLO 853

value: COLO 853


title: FTC-133_STY

description:
Hybridized to 250K_Sty
FTC-133

source_name: Thyroid cell line FTC-133


title: Ca Ski_STY

description:
Hybridized to 250K_Sty
Ca Ski

source_name: Cervix cell line Ca Ski

value: Ca Ski


title: OE33_STY

description:
Hybridized to 250K_Sty
OE33

source_name: Esophagus cell line OE33


title: A673_STY

description:
Hybridized to 250K_Sty
A673

source_name: Muscle cell line A673


title: T84_STY

description:
Hybridized to 250K_Sty
T84

source_name: Intestine cell line T84


title: HT 1080_STY

description:
Hybridized to 250K_Sty
HT 1080

source_name: Miscellaneous cell line HT 1080


title: A431_STY

description:
Hybridized to 250K_Sty
A431

source_name: Skin cell line A431


title: C170_STY

description:
Hybridized to 250K_Sty
C170

source_name: Intestine cell line C170


title: OE19_STY

description:
Hybridized to 250K_Sty
OE19

source_name: Esophagus cell line OE19


title: HOS_STY

description:
Hybridized to 250K_Sty
HOS

source_name: Bone cell line HOS

value: HOS


title: H69_STY

description:
Hybridized to 250K_Sty
H69

source_name: Lung cell line H69


title: KG-1-C_STY

description:
Hybridized to 250K_Sty
KG-1-C

source_name: Brain cell line KG-1-C


title: QGP-1_STY

description:
Hybridized to 250K_Sty
QGP-1

source_name: Pancreas cell line QGP-1


title: JHH-1_STY

description:
Hybridized to 250K_Sty
JHH-1

source_name: Liver cell line JHH-1


title: CAMA-1_STY

description:
Hybridized to 250K_Sty
CAMA-1

source_name: Breast cell line CAMA-1


title: OE21_STY

description:
Hybridized to 250K_Sty
OE21

source_name: Esophagus cell line OE21


title: KP-3_STY

description:
Hybridized to 250K_Sty
KP-3

source_name: Pancreas cell line KP-3


title: SW 780_STY

description:
Hybridized to 250K_Sty
SW 780

source_name: Bladder cell line SW 780