title: IHCC_IDH1_mutant_R132C_NoCollagen_Rep1

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to Affymetrix 430Av2 microarray chips overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.

scan_protocol: Scans were performed on Affymetrix confocal laser scanners.

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA).

source_name: HBs_R132C mutant IDH1_uncoated plates

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: HB cells were prepared from WT mice at embryonic day 14 and immortalized by plating at clonal density. HBs were maintained in HB media [DMEM/F-12 (Gibco Life Technologies, Grand Island NY) containing 10% fetal bovine serum, 1% penicillin-streptomycin, 50ng/mL epidermal growth factor, 30 ng/mL insulin-like growth factor II (PeproTech, Rocky Hill, NJ), 10 μg/mL insulin (Roche, Mannheim, Germany)] on plates coated with rat tail collagen (BD Biosciences, Bedford, MA) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA (1ug) was isolated using RNeasy Mini Kit (QIAGEN, Valencia, CA) and quality control performed using Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: For IDH1 experiments, culture media was supplemented with 25 ng/mL of doxycycline (d9891, Sigma-Aldrich). For hepatocyte differentiation assays, 5e6 HB cells were cultured on uncoated 10 cm tissue culture dishes in HB cell medium for up to 5 days and isolated for gene expression analysis.

tag: cell type

value: hepatoblasts (HBs) from E14 WT mouse

value: expressing R132C mutant IDH1

tag: culture plate

value: uncoated plate


title: 251_159

status: Public on Apr 30 2014

type: RNA

city: Columbus

first: Susan

middle: Elizabeth

last: Olivo-Marston

state: OH

address: 1841 Neil Avenue

department: Epidemiology

country: USA

institute: The Ohio State University

description: Calorie restriction or diet-induced obesity

hyb_protocol: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing: The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 4.0). Intensities of each spot were the median intensities of foreground. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. Each microRNA oligo is represented by quadruplicate spots on these arrays as two distant pairs of two adjacent spots. If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package and all replicate spots were averaged.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Colon tissue from mouse_calorie_restricted

label_protocol: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol: Tissues were flash frozen immediately after euthanasia. RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.

tag: disease

value: Colon cancer

tag: diet

value: Calorie restricted


title: IHCC_Vector_NoCollagen_Rep2

label: biotin

source_name: HBs_empty vector controls_uncoated plates

tag: genotype/variation

value: expressing empty vector controls


title: CN-10

type: genomic

city: Adelaide

first: Naiara

middle: G

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Quality control and data pre-processing was performed using lumi package (Bioconductor). Samples were background adjusted, processed for the colour channel adjustment and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor).

molecule: genomic DNA

organism: Homo sapiens

source_name: Oral rinse, control

label_protocol: Standard as recommended by Illumina.

extract_protocol: Genomic DNA was extracted and purified from oral rinse samples using the Gentra Puregene Buccal Cell Kit according to standard instructions.

tag: disease state

value: control

tag: Sex

value: male

value: buccal cells

tag: age

tag: tobacco

tag: alcohol


title: 246_145

treatment_protocol: Calorie restriction or diet-induced obesity


title: NCI10507

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

institute: University of North Carolina at Chapel Hill

description:
NCI10507
A_4x44_251485068447-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-194

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-189

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

tag: distance to tumor

value: Peritumoral

value: LumA


title: NCI10497

description:
NCI10497
A_4x44k_251485068452-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-193

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-188

value: LumB


title: 250_157


title: IHCC_IDH2_mutant_R172K_Collagen_Rep2

source_name: HBs_R172K mutant IDH2_collagen-coated plates

value: expressing R172K mutant IDH2

value: collagen-coated plate


title: IHCC_IDH2_WT_Collagen_Rep2

source_name: HBs_wild type IDH2_collagen-coated plates

value: expressing wild type IDH2


title: IHCC_Vector_NoCollagen_Rep1


title: IHCC_IDH1_mutant_R132C_NoCollagen_Rep2


title: 244_131


title: IHCC_IDH2_WT_Collagen_Rep1


title: 245_137


title: Col-0 5d uininfected, biological rep 2

city: Berkeley

first: Mary

middle: C

last: Wildermuth

state: CA

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

description: Gene expression data from 5d uninfected leaves of wild type Col-0 plants

hyb_protocol: Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 702646 Rev. 8.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip® Scanner 3000 7G at the Univeristy of California, Berkeley, functional genomics lab.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) using Partek Genomics Suite software (Partek, Inc).

organism: Arabidopsis thaliana

source_name: Col-0 5d uninfected leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds of wild type and mutant were equally distributed in each box using a template, with 6 plants each per box.  The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 3 weeks. Plants were grown in Percival AR66L growth chambers at 22°C, 70% RH, 12 h photoperiod with photosynthetically active radiation=150 µE m-2 s-1. Seeds for del1-1 were obtained from Vlieghe et al. 2005, Current Biology, 15:59–63.

extract_protocol: Total RNA was extracted using the RNeasy plant mini kit from Qiagen according to the manufacturer's instructions.  RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

treatment_protocol: At four weeks, a subset of boxes was infected with a moderate innoculum of G.orontii using a settling tower. Moderate innoculum is 2 half G.orontii.-infected leaves with conidia 10-14 dpi.  Infected plants were placed in a separate Percival growth chamber under the same conditions as the pathogen-free Percival. Infections were performed at 1 pm to standardize experiments and minimize circadian effects. Samples were harvested at 5 dpi. Uninfected 5 d samples were also collected.  For each sample, three fully expanded mature leaves were harvested per plant and immediately frozen in liquid nitrogen. Two independent experiments were performed with triplicate samples collected within each experiment.  Two biological replicates were processed.

value: wild type

value: 4 weeks old at time 0 (inoculation)

tag: tissue

value: mature, fully expanded leaves

tag: infected

value: no


title: NCI10483

description:
NCI10483
A_4x44k_251485068484-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-192

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-187


title: IHCC_IDH1_mutant_R132C_Collagen_Rep2

source_name: HBs_R132C mutant IDH1_collagen-coated plates

value: hepatoblasts (HBs) from E14 WT mouse

value: expressing R132C mutant IDH1


title: NCI10428

description:
NCI10428
A_4x44k_251485068474-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-191

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-186


title: IHCC_IDH2_mutant_R172K_Collagen_Rep1


title: 242_83

source_name: Colon tissue from mouse_control

value: Colon cancer

value: Control


title: 243_85


title: NCI10703

description:
NCI10703
A_4x44_251485068435-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-196

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-191


title: NCI10367

description:
NCI10367
A_4x44k_251485068451-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-189

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-184


title: NCI10382

description:
NCI10382
A_4x44k_251485068478-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-190

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-185

value: Claudin


title: 240_77


title: 239_73


title: 241_79


title: NCI10687

description:
NCI10687
A_4x44_251485068448-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-195

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-190


title: NCI10366

description:
NCI10366
A_4x44k_251485068478-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-188

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-183


title: IHCC_IDH1_mutant_R132C_Collagen_Rep1


title: IHCC_IDH1_WT_Collagen_Rep2

source_name: HBs_wild type IDH1_collagen-coated plates

value: expressing wild type IDH1


title: NCI10335

description:
NCI10335
A_4x44k_251485068450-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-187

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-182

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: NCI10301

description:
NCI10301
A_4x44k_251485068482-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-186

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-181

value: Peritumoral


title: 238_71


title: 237_63


title: 236_61


title: NCI10252

description:
NCI10252
A_4x44k_251485068455-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-185

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-180


title: 234_51


title: IHCC_IDH1_WT_Collagen_Rep1


title: IHCC_Vector_Collagen_Rep2

source_name: HBs_empty vector controls_collagen-coated plates

value: expressing empty vector controls


title: 235_55


title: NCI10239

description:
NCI10239
A_4x44k_251485068481-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-184

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-179


title: NCI10215

description:
NCI10215
A_4x44k_251485064369-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-183

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-178

value: LumB


title: NCI10211

description:
NCI10211
A_4x44k_251485068480-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-182

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-177

value: LumA


title: NCI10199

description:
NCI10199
A_4x44k_251485068480-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-181

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-176


title: IHCC_Vector_Collagen_Rep1

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to Affymetrix 430Av2 microarray chips overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

value: collagen-coated plate


title: NCI10197

description:
NCI10197
A_4x44k_251485068480-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-180

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-175

value: Basal


title: TP63 siRNA Adriamycin [S0781F0004]

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

hyb_protocol: In accordance with Affymetrix Genechio Whole Transcript (WT) Sense Target Labelling Assay Manual

scan_protocol: Affymetrix protocol

data_processing: Cel files were imported into Altanalyze  (Altanalyse version 2.0.6 beta) using RMA normalisation through Affymetrix Power Tools and Gene expression was summarized at an individual gene level for “Constitutive” exons (probe sets aligning to those exons regions most common among all transcripts) filtering for probes with DABG P<0.05 or expression below 1. Fold change and Log2 fold change for all samples was then calculated by comparing each sample relative to the mean of the no siRNA and scrambled untreated controls.

source_name: Human neonatal foreskin keratinocytes

label_protocol: RNA samples were amplified with WT ovation pico amplification kit and strand ceonversion conducted using NuGEN Exon module,Samples were then fragmented, labelled and hybridised using the FL-Ovation cDNA Biotin Module V2 accoriding to manufactureres instructions

growth_protocol: Human neonatal foreskin keratinocytes were grown in Epi-Life supplemented with HKGS (Lifetechnologies).

extract_protocol: RNA extracted using RNAeasy mini kit (Qiagen) according to manufacturers instructions and treated with DNAse-1 prior to QC on bioanlysers

treatment_protocol: Cells were transfected with siRNAs targetting p53, p63 or a scrambled control using Lipofectamine RNAimax (Invitrogen) according to manufacturers instruction and treated with 350nM Adriamycin or 25uM Cisplatin.

tag: transfection

value: TP53 siRNA

tag: treatment

value: Adriamycin


title: NCI10092

description:
NCI10092
A_4x44k_251485068453-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-177

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-172


title: 247_147

hyb_protocol: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

label_protocol: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

value: Calorie restricted


title: TP63 siRNA Cisplatin [S0781F0008]

value: Cisplatin


title: NCI10120

description:
NCI10120
A_4x44k_251485068454-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-178

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-173


title: TP63 siRNA Untreated [S0781F0006]


title: TP53 siRNA Adriamycin [S0781F0002]


title: NCI10073

description:
NCI10073
A_4x44k_251485064521-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-175

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-170


title: NCI10132

description:
NCI10132
A_4x44k_251485064532-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-179

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-174


title: NCI10065

description:
NCI10065
A_4x44k_251485064521-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-174

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-169


title: TP53 siRNA Cisplatin [S0781F0010]


title: TP53 siRNA Untreated [S0781F0007]


title: NCI10074

description:
NCI10074
A_4x44k_251485064535-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-176

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-171


title: Scrambled siRNA Cisplatin [S0781F0003]

value: Scrambled siRNA


title: NCI10014

description:
NCI10014
A_4x44k_251485064535-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-171

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-166


title: NCI10053

description:
NCI10053
A_4x44k_251485064370-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-173

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-168


title: NCI10020

description:
NCI10020
A_4x44k_251485068453-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-172

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-167


title: Scrambled siRNA Adriamycin [S0781F0012]


title: NBS10081_99274342_09

description:
NBS10081_99274342_09
A_4x44k_251485064321-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-170

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-165

value: Remote

tag: er status


title: Scrambled siRNA Untreated [S0781F0001]


title: No siRNA Adriamycin [S0781F0009]

value: No siRNA


title: No siRNA Cisplatin [S0781F0005]


title: NBS10081_99274342_06

description:
NBS10081_99274342_06
A_4x44k_251485064321-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-169

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-164


title: No siRNA Untreated [S0781F0011]


title: NBS10030_97636476_03

description:
NBS10030_97636476_03
A_4x44k_251485064411-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-166

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-161


title: NBS10084_98879026_06

description:
NBS10084_98879026_06
A_4x44k_251485064408-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-167

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-162


title: NBS10084_98879026_08

description:
NBS10084_98879026_08
A_4x44k_251485064408-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-168

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-163


title: NBS10118_96454897_08

description:
NBS10118_96454897_08
A_4x44_251485064825-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-165

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-160


title: NBS10077_95029484_08

description:
NBS10077_95029484_08
A_4x44k_251485064320-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-163

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-158


title: NBS10077_95029484_06

description:
NBS10077_95029484_06
A_4x44k_251485064320-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-162

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-157


title: NBS09012_94322229_03_rep4

description:
NBS09012_94322229_03_rep4
A_4x44k_251485064008-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-160

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-155


title: NBS10118_96454897_06

description:
NBS10118_96454897_06
A_4x44_251485064825-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-164

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-159


title: Normal_2203_new [screening set]

city: Rome

first: Monica

last: Messina

address: Via Benevento 26

department: Department of Cellular Biotechnologies and Hematology

country: Italy

institute: Sapienza University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files, CHP files and TXT files (generated by Affymetrix Genotyping Console using the Birdseed v2 algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm (see Matrix sheet and attached .cnmz files)

source_name: genomic DNA extracted from saliva

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from peripheral blood cells (>80% CD19/CD5 positive cells) obtained before the treatment resulting in chemorefractoriness or from peripheral blood granulocytes or saliva using the Qiagen DNA Blood Mini Kit or the Promega Wizard® Genomic DNA Purification Kit . DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Not applicable

tag: experimental set

value: screening

tag: tissue type

value: normal

tag: tissue source

value: Saliva


title: NBS10152_92998483_08

description:
NBS10152_92998483_08
A_4x44_251485068415-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-157

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-152

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: Normal_2209_new [screening set]


title: NBS10100_93627867_08

description:
NBS10100_93627867_08
A_4x44_251485064824-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-159

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-154


title: CR_CLL_6496 [screening set]

source_name: genomic DNA extracted from peripheral blood of patients affected by chronic lymphocytic leukemia at refractoriness

value: FR-CLL tumor

value: peripheral blood sampled at refractoriness


title: NBS10100_93627867_06

description:
NBS10100_93627867_06
A_4x44_251485064824-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-158

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-153


title: NBS10152_92998483_06

description:
NBS10152_92998483_06
A_4x44_251485068415-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-156

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-151


title: NBS10129_92367044_08

description:
NBS10129_92367044_08
A_4x44_251485064826-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-154

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-149


title: CR_CLL_3878 [screening set]


title: CR_CLL_4845 [screening set]


title: CR_CLL_9930 [screening set]


title: Normal_Affy_new [screening set]

source_name: Reference genomic DNA provided by Affymetrix


title: CR_CLL_4262 [screening set]


title: CR_CLL_3981 [screening set]


title: CR_CLL_7228 [screening set]


title: NBS10107_90998329_08

description:
NBS10107_90998329_08
A_4x44_251485064822-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-152

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-147


title: NBS10129_92367044_06

description:
NBS10129_92367044_06
A_4x44_251485064826-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-153

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148


title: NBS10134_90679705_06

description:
NBS10134_90679705_06
A_4x44_251485064372-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-149

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144


title: CR_CLL_9244 [screening set]


title: NBS10107_90998329_06

description:
NBS10107_90998329_06
A_4x44_251485064822-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-151

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146


title: CR_CLL_8081 [screening set]


title: CR_CLL_7916 [screening set]


title: CR_CLL_5675 [screening set]


title: CR_CLL_4047 [screening set]


title: NBS10084_98879026_04

description:
NBS10084_98879026_04
A_4x44k_251485064408-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

value: Peritumoral


title: NBS10081_99274342_02

description:
NBS10081_99274342_02
A_4x44k_251485064320-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141


title: NBS10081_99274342_04

description:
NBS10081_99274342_04
A_4x44k_251485064321-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-147

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142


title: CR_CLL_8253 [screening set]


title: CR_CLL_10320 [screening set]


title: CR_CLL_5977 [screening set]


title: NBS10118_96454897_02

description:
NBS10118_96454897_02
A_4x44_251485064825-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136


title: NBS10118_96454897_04

description:
NBS10118_96454897_04
A_4x44_251485064825-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137


title: CR_CLL_9303_new [screening set]


title: NBS10030_97636476_02

description:
NBS10030_97636476_02
A_4x44k_251485064411-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139


title: CR_CLL_9311_new [screening set]


title: NBS10047_95644548_02_rep2

description:
NBS10047_95644548_02_rep2
A_4x44k_251485064317-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135


title: NBS10038_95518494_02_rep2

description:
NBS10038_95518494_02_rep2
A_4x44k_251485064317-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134


title: CR_CLL_6944 [screening set]

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

label_protocol: As per manufacturer (Affymetrix)


title: NBS10077_95029484_04

description:
NBS10077_95029484_04
A_4x44k_251485064320-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133


title: CR_CLL_6342 [screening set]


title: CR_CLL_10649 [screening set]


title: CR_CLL_4232 [screening set]


title: NBS10077_95029484_02

description:
NBS10077_95029484_02
A_4x44k_251485064319-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132


title: NBS10100_93627867_02

description:
NBS10100_93627867_02
A_4x44k_251485064823-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: NBS10134_90679705_08

description:
NBS10134_90679705_08
A_4x44_251485064372-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-150

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145


title: CR_CLL_6012 [screening set]


title: siTR4A1_3

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell line

value: Panc1 pancreatic cancer cell line


title: NBS10100_93627867_04

description:
NBS10100_93627867_04
A_4x44_251485064824-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: NBS10152_92998483_02

description:
NBS10152_92998483_02
A_4x44_251485068415-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126


title: siTR4A1_2


title: NBS10129_92367044_02

description:
NBS10129_92367044_02
A_4x44_251485064826-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: NBS10129_92367044_04

description:
NBS10129_92367044_04
A_4x44_251485064826-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: NBS10152_92998483_04

description:
NBS10152_92998483_04
A_4x44_251485068415-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127


title: CR_CLL_12477 [screening set]


title: CR_CLL_11203_new [screening set]


title: CR_CLL_6550_new [screening set]


title: CR_CLL_5610_new [screening set]


title: NBS10134_90679705_04

description:
NBS10134_90679705_04
A_4x44_251485064372-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: CR_CLL-9B [discovery set]

source_name: genomic DNA extracted from saliva of patient 9

value: discovery

value: paired normal


title: CR_CLL-7B [discovery set]

source_name: genomic DNA extracted from saliva of patient 7


title: CR_CLL-10B [discovery set]

source_name: genomic DNA extracted from saliva of patient 10


title: siTR4A1_1


title: CR_CLL-8B [discovery set]

source_name: genomic DNA extracted from saliva of patient 8


title: siControl_2

value: siControl


title: CR_CLL-6B [discovery set]

source_name: genomic DNA extracted from peripheral blood granulocytes of patient 6

value: peripheral blood granulocytes


title: CR_CLL-3B [discovery set]

source_name: genomic DNA extracted from saliva of patient 3


title: NBS10134_90679705_02

description:
NBS10134_90679705_02
A_4x44_251485064372-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

source_name: Human Reference B

source_name: Normal Tissue Adjacent to Breast Tumor


title: CR_CLL-4B [discovery set]

source_name: genomic DNA extracted from saliva of patient 4


title: NBS10107_90998329_02

description:
NBS10107_90998329_02
A_4x44_251485064822-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126


title: CR_CLL_4885_new [screening set]


title: CR_CLL_13931_new [screening set]


title: NBS10107_90998329_04

description:
NBS10107_90998329_04
A_4x44k_251485064822-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127


title: siControl_3


title: yy1 control biological rep2

status: Public on Apr 29 2014

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

hyb_protocol: Standard Affymetrox protocol.

scan_protocol: Standard Affymetrox protocol.

data_processing: data were processed with dChip software

source_name: control crypt epithelium

label_protocol: total RNA was processed and hybridized according to Affymetrix instructions

growth_protocol: mouse jejunum crypt epithelium were isolated using EDTA treatment and filtering through a 70um filter.

extract_protocol: RNA was isolated using Trizol

treatment_protocol: Crypts were isolated from either control or YY1f/f; Vil-Cre-ERT2 mice treated with tamoxifen for 4 days

tag: strain

value: C57BL/6J enriched

tag: cell type

value: crypt epithelium

tag: genotype/variation

value: control


title: Cbx4 siRNA cumulus cell, biological rep. 4

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

description:
Gene expression data for cumulus cells treated for 72 h in vitro with Cbx4 siRNA
B6D1 F1 female

hyb_protocol: 12.5 ug of labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to MOE430V2 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: The data were preprocessed and analyzed with scripts written in R with Bioconductor libraries.  Probeset summarization was done with Robust Multiarray Averaging (RMA), using a custom Chip Definition File (CDF) . Custom CDF was developed from the original Affymetrix CDF by removing probes that do not align to intended targets or cross-hybridize with non-homologous transcripts were removed from the respective probesets. Custom annotation were compiled by aligning remaining probe sequences to RefSeq mRNA sequences (downloaded 7/01/2013) for genes in GRC38 genome assembly. Significance Analysis of Microarrays (SAM) was used for identification of differentially expressed probesets.

source_name: Cbx4 siRNA cumulus cell

label_protocol: Up to 50 ng of total RNA from each sample were subjected to two rounds of cDNA synthesis using the Arcturus RiboAmp HS Plus kit (Invitrogen).  Labeled cRNA was produced using the Affymetrix GeneChip Expression 3’ Amplification for IVT Labeling Kit (Affymetrix, Santa Clara, CA).  The biotin-labeled cRNA samples were fragmented and 10 µg were hybridized onto arrays.

growth_protocol: Cumulus cells were harvested from BDF1 mice that had been superovulated by injection of 5 IU equine chorionic gonadotropin followed by 5 IU human chorionic gonadotropin (hCG) 46-48 hours later.  Cumulus cells were isolated from ovulated MII stage cumulus-oocyte complexes, washed with M2 medium, re-suspended in MEM-a medium containing 10% FCS, penicillin and streptomycin, and then plated in six-well plates at a density of 2x104 cells/well.  They were cultured overnight before transfection.

extract_protocol: RNA was extracted three days after transfection using the Pico Pure RNA Isolation Kit (Arcturus/Life Technologies)

treatment_protocol: Double-stranded siRNAs (21-mer) targeting mouse CBX4 were purchased from Qiagen (Valencia, CA). The corresponding target mRNA sequences for the siRNAs were: Cbx4-6 (S102731834): CAGGAAGAGCGG-CAAGT ATTA, Cbx4-7 (S104446673): AAGGTCCGAAGTTGAGGGAAA. Scrambled siRNA was used as a negative control. Cumulus cells were transfected with siRNA (25 nM Cbx4-6 and 25nM Cbx4-7) using lipofectamine RNAiMAX reagent (Invitrogen/Life Technologies, Grand Island, NY) according to the manufacturer protocol. After overnight culture, the medium was replaced and the cells were transfected using the forward transfection method.  Thirty pmol of siRNA were diluted in 50 μl Opti-MEM medium (Invitrogen) and mixed with 1 μl of Lipofectamine RNAiMAX reagent (Invitrogen) diluted in 49 ml of Opti-MEM medium. After incubation for 20 minutes at room temperature, the mixture was added to wells containing the cumulus cells. Cumulus cells were harvested after 72 hours of incubation at 37 °C in a humidified 5% CO2 atmosphere.

tag: gender

value: female

value: cultured cumulus cell

value: Cbx4 knockdown


title: Cbx4 siRNA cumulus cell, biological rep. 1


title: PMN6 [expression]

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: GPL10558 (Illumina HumanHT-12 V4.0 expression beadchip)

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol (iScan)

data_processing: 39426 overlapping probes from the two versions of the Ht12 array were quantile normalized in GenomeStudio

source_name: bone marrow PMN cells donor 6

label_protocol: Biotinylated cRNA were prepared with the illumina totalprep rna amplification kitfor Illumina arrays.

extract_protocol: Total RNA was extracted using Trizol reagent.

value: male

tag: donor

value: bone marrow

value: PMN cells


title: yy1 knockout biological rep2

source_name: YY1 knockout crypt epithelium

value: YY1 knockout


title: CR_CLL-9A [discovery set]

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

value: FR-CLL tumor

value: peripheral blood sampled at refractoriness


title: siControl_1

value: Panc1 pancreatic cancer cell line


title: yy1 control biological rep1


title: PMN5 [expression]

source_name: bone marrow PMN cells donor 5


title: Cbx4 siRNA cumulus cell, biological rep. 3


title: WT zinc X zur zinc - rep2

city: São Paulo

first: Ricardo

middle: Ruiz

last: Mazzon

state: SP

address: Avenida Professor Lineu Prestes, 1374

department: Microbiology

country: Brazil

institute: Institute of Biomedical Sciences from University of São Paulo

description: RNA after 2 hours of addition of 200 micromolars of zinc

hyb_protocol: Standard Agilent protocol Agilent protocol

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excel and the log10 values extracted with no additional processing or filterin

organism: Caulobacter vibrioides NA1000

source_name: zur mutant zinc

label_protocol: Standard Cy3-dCTP and Cy5-dCTP incorporations

growth_protocol: Cultures were grown until midlog growing phase in M2 medium

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

treatment_protocol: The culture was supplemented with 200 µM ZnCl2 for 1 h.

value: zur mutant

tag: cultured with

value: 200 µM ZnCl2 for 1 h

source_name: WT zinc

value: wild type


title: PMN4 [expression]

source_name: bone marrow PMN cells donor 4


title: yy1 knockout biological rep1

description: YY1 KO_1


title: Cbx4 siRNA cumulus cell, biological rep. 2


title: CR_CLL_4380_new [screening set]

source_name: genomic DNA extracted from peripheral blood of patients affected by chronic lymphocytic leukemia at refractoriness

value: screening


title: WT zinc X zur zinc - rep4

scan_protocol: Standard Agilent protocol Agilent protocol


title: WT zinc X zur zinc - rep3


title: CR [U9]

city: Baltimore

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description:
Total RNA was reverse-transcribed with 'A' and 'B' stem-loop primer pools, pre-amplified with miRNA-specific primers in 'A' and 'B' primer pools, and loaded onto OpenArray medium-throughput slides using a Life Technologies liquid handling robot.
RT and pre-amp protocol: Reverse-transcription was done per manufacturer's protocol using miRNA Megaplex primers, pools A and B (Applied Biosystems) and 100 ng RNA per sample. cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, pools A and B (Applied Biosystems), then diluted per manufacturer's protocol.
qRT-PCR protocol: Diluted pre-amplified samples were provided to the Johns Hopkins DNA Analysis Facility of the Genetic Resources Core Facility, where samples were mixed with manufacturer's qPCR master mix and loaded onto OpenArray slides by liquid handling robot. qRT-PCR was performed with the QuantStudio system per manufacturer's recommendations.

data_processing:
Data collected by QuantStudio were downloaded from the Johns Hopkins Genetic Resources Core Facility GeneSifter server. Data for amplified wells with amplification score greater than 1.24 and Crt lower than 33 were exported from ExpressionSuite software (Life Technologies) as a .txt file.
Several features with abnormally low Crt values were discarded after amplification curve inspection; these included mmu-miRs-1894-3p, -1896, and -1942, and hsa-miRs-188-3p and -5p. Data were exported to Microsoft Excel. Replicate values were averaged. Data were quantile normalized using R/Bioconductor preprocesscore.

label: FAM

source_name: Mouse 9, control diet, radiation

label_protocol: TaqMan probe label: FAM

extract_protocol: RNA was isolated and purified from 20-30 mg mouse lung tissue using a modifed Trizol protocol with column clean-up. 20-30 mg frozen tissue was placed into 1 mL Trizol (Invitrogen) in 2 mL screw-cap tubes, and Lysing matrix D was added. Tissue was disrupted using a desktop bead beater at 2x30 seconds, with five minutes on ice interspersed. Tubes were spun to collect beads and homogenate, and 200 ul chloroform was added. Tubes were firmly capped and shaken vigorously for 1 minute, then centrifuged at 12,000 x g in an Eppendorf C2415 centrifuge for 15 minutes at 4C. The aqueous phase was transferred to a new tube, with care taken not to disturb the interphase. 100% ethanol was added in a volume at least 1.25x that of the recovered aqueous phase for each tube. Sample was then applied to columns from a mirVana total RNA isolation kit (Ambion). Washing and elution was done per manufacturer’s protocol. RNA concentration and purity was analyzed by NanoDrop. All RNA was stored at -80C.

treatment_protocol: C57BL/6 Black mice were fed a 10% Flaxseed diet for 21 days and/or given 13.5Gy radiation and sacrificed 48hrs post radiation

value: lung


title: Scrambled siRNA control cumulus cells, biological rep. 3

description:
Gene expression data from cumulus cells treated for 72 h in vitro with scrambled siRNA
B6D1 F1 female

source_name: Scrambled siRNA control cumulus cells


title: CR_CLL-2B [discovery set]

source_name: genomic DNA extracted from saliva of patient 2

value: discovery

value: paired normal

value: peripheral blood granulocytes


title: CR_CLL-8A [discovery set]


title: CR [U8]

source_name: Mouse 8, control diet, radiation


title: PMC5 [expression]

source_name: bone marrow PMC cells donor 5

value: PMC cells


title: Scrambled siRNA control cumulus cells, biological rep. 2

value: female

value: cultured cumulus cell

value: control


title: CC [U2]

source_name: Mouse 2, control diet, no radiation


title: CC [U5]

source_name: Mouse 5, control diet, no radiation


title: Scrambled siRNA control cumulus cells, biological rep. 1


title: PMC6 [expression]

source_name: bone marrow PMC cells donor 6

value: male

value: bone marrow


title: PMC4 [expression]

source_name: bone marrow PMC cells donor 4


title: GMP5 [expression]

source_name: bone marrow GMP cells donor 5

value: GMP cells


title: PMN3 [expression]

description: GPL6947 (Illumina HumanHT-12 V3.0 expression beadchip)

source_name: bone marrow PMN cells donor 3

value: PMN cells


title: PMC3 [expression]

source_name: bone marrow PMC cells donor 3


title: PMN2 [expression]

source_name: bone marrow PMN cells donor 2


title: PMC2 [expression]

source_name: bone marrow PMC cells donor 2


title: GMP6 [expression]

source_name: bone marrow GMP cells donor 6


title: CC [U4]

source_name: Mouse 4, control diet, no radiation


title: FR [U18]

source_name: Mouse 18, flaxseed diet, radiation


title: FR [U17]

source_name: Mouse 17, flaxseed diet, radiation


title: FR [U15]

source_name: Mouse 15, flaxseed diet, radiation


title: CR_CLL-7A [discovery set]

source_name: genomic DNA extracted from peripheral blood of patients affected by chronic lymphocytic leukemia at refractoriness

value: FR-CLL tumor

value: peripheral blood sampled at refractoriness


title: CF [U12]

source_name: Mouse 12, flaxseed diet, no radiation


title: CF [U13]

source_name: Mouse 13, flaxseed diet, no radiation


title: CR_CLL-6A [discovery set]


title: CR_CLL-10A [discovery set]


title: CF [U11]

source_name: Mouse 11, flaxseed diet, no radiation


title: GMP2 [expression]

source_name: bone marrow GMP cells donor 2


title: CMP6 [expression]

source_name: bone marrow CMP cells donor 6

value: CMP cells


title: CMP4 [expression]

source_name: bone marrow CMP cells donor 4


title: CR_CLL-5A [discovery set]


title: GMP4 [expression]

source_name: bone marrow GMP cells donor 4


title: ACC42

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

country: France

institute: Ligue Nationale contre le Cancer

hyb_protocol: Samples were hybridized with GeneChip Human Exon 2.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the RMA normalisation (Bioconductor R affy package) + ComBat (R sva package ) to generate log2 normalized intensity signal.  Data analysis and statistical evaluations were performed with customized R codes.

source_name: Frozen tissue of Adrenocortical carcinomas

label_protocol: The labeling of the extracted RNA was performed according to the manufacturer's instruction (Affymetrix)

growth_protocol: Samples stored at -80 C

extract_protocol: Tumor samples (10 to 50 mg) were powdered under liquid nitrogen. RNA were extracted using RNAble (Eurobio, Courtaboeuf, France), followed by a clean-up step on RNAeasy columns (Qiagen, Courtaboeuf, France).

tag: age (years)

value: M

value: Adrenocortical carcinoma


title: CMP2 [expression]

source_name: bone marrow CMP cells donor 2


title: CMP5 [expression]

source_name: bone marrow CMP cells donor 5


title: CMP3 [expression]

source_name: bone marrow CMP cells donor 3


title: CR_CLL-3A [discovery set]

label_protocol: As per manufacturer (Affymetrix)


title: ACC50

value: F


title: CR_CLL-4A [discovery set]

value: discovery


title: ACC45


title: GMP3 [expression]

source_name: bone marrow GMP cells donor 3


title: CR [U7]

source_name: Mouse 7, control diet, radiation

value: lung


title: ACC49


title: ACC38


title: CR_CLL-2A [discovery set]


title: ACC44


title: ACC35


title: ACC37


title: ACC39


title: ACC48


title: CR_CLL-1A [discovery set]


title: ACC40


title: CR_CLL-5B [discovery set]

source_name: genomic DNA extracted from peripheral blood granulocytes of patient 5

value: paired normal

value: peripheral blood granulocytes


title: CR_CLL-1B [discovery set]

source_name: genomic DNA extracted from peripheral blood granulocytes of patient 1


title: ACC36


title: ACC32


title: ACC18


title: ACC29


title: ACC19


title: ACC26


title: ACC22


title: ACC47


title: ACC23


title: ACC28


title: ACC16


title: ACC20


title: ACC24


title: ACC17


title: ACC27


title: ACC21


title: ACC33


title: ACC46


title: ACC8


title: ACC9


title: ACC13


title: ACC15


title: ACC11


title: SNU-739 vs Huh-7 cells replicate 2

city: Chuncheon

first: Hyung-Joo

last: Kwon

state: Gangwon-do

address: 1 Hallymdaehak-gil

department: Department of Microbiology

country: South Korea

institute: Hallym University College of Medicine

description: Biological replicate 2 of 2, SNU-739 vs Huh-7 cells, untreated, harvested after 3 days cell culture.

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

source_name: 3 days cultured SNU-739 cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: The Huh-7 and SNU-739 cells were maintained in RPMI 1640 medium containing 10% FBS at 37oC in an atmosphere of 95% air and 5% CO2

extract_protocol: Total RNAs from Huh-7 and SNU-739 cells were isolated using Trizol following manufacturer's instructions

treatment_protocol: Untreated

tag: age

value: day 3

value: hepatocarcinoma

source_name: 3 days cultured Huh-7 cells


title: ACC6


title: SNU-739 vs Huh-7 cells replicate 1

description: Biological replicate 1 of 2, SNU-739 vs Huh-7 cells, untreated, harvested after 3 days cell culture.

tag: tissue


title: ACC5


title: ACC4


title: ACC14


title: ACC10


title: ACA27

description: Adrenocortical adenoma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: Cy5 and Cy3

label_protocol: standard Illumina protocol

extract_protocol: Tumor samples were powdered under liquid nitrogen. DNA was extracted and purified by cesium chloride gradient ultracentrifugation or by proteinase K digestion and ethanol extraction, followed by a clean-up step on columns (QIAGEN, Courtaboeuf, France).

value: Adrenocortical adenoma


title: ACA29

description: Adrenocortical adenoma


title: ACA25

description: Adrenocortical adenoma


title: ACC1


title: ACA24

description: Adrenocortical adenoma


title: ACC43


title: ACA26

description: Adrenocortical adenoma


title: ACA22

description: Adrenocortical adenoma


title: ACA23

description: Adrenocortical adenoma


title: ACA30

description: Adrenocortical adenoma


title: ACC2


title: ACA19

description: Adrenocortical adenoma


title: ACA20

description: Adrenocortical adenoma


title: ACA17

description: Adrenocortical adenoma


title: ACA21

description: Adrenocortical adenoma


title: ACA28

description: Adrenocortical adenoma


title: ACA18

description: Adrenocortical adenoma


title: ACA14

description: Adrenocortical adenoma


title: ACA13

description: Adrenocortical adenoma


title: ACA15

description: Adrenocortical adenoma


title: ACA11

description: Adrenocortical adenoma


title: ACA16

description: Adrenocortical adenoma


title: ACA12

description: Adrenocortical adenoma


title: ACA10

description: Adrenocortical adenoma


title: ACA5

description: Adrenocortical adenoma


title: ACA6

description: Adrenocortical adenoma


title: ACA2

description: Adrenocortical adenoma


title: ACA7

description: Adrenocortical adenoma


title: ACA9

description: Adrenocortical adenoma


title: ACC52

description: Adrenocortical carcinoma


title: ACC50

description: Adrenocortical carcinoma


title: ACC55

description: Adrenocortical carcinoma


title: ACA4

description: Adrenocortical adenoma


title: ACA8

description: Adrenocortical adenoma


title: ACC47

description: Adrenocortical carcinoma


title: ACC49

description: Adrenocortical carcinoma


title: ACC48

description: Adrenocortical carcinoma


title: ACC41

description: Adrenocortical carcinoma


title: ACA3

description: Adrenocortical adenoma


title: ACC51

description: Adrenocortical carcinoma


title: ACC43

description: Adrenocortical carcinoma


title: ACC42

description: Adrenocortical carcinoma


title: ACA1

description: Adrenocortical adenoma


title: ACC46

description: Adrenocortical carcinoma


title: ACC39

description: Adrenocortical carcinoma


title: ACC44

description: Adrenocortical carcinoma


title: ACC40

description: Adrenocortical carcinoma


title: ACC37

description: Adrenocortical carcinoma


title: ACC25


title: ACC38

description: Adrenocortical carcinoma


title: ACC45

description: Adrenocortical carcinoma


title: ACC35

description: Adrenocortical carcinoma


title: ACC32

description: Adrenocortical carcinoma


title: ACC33

description: Adrenocortical carcinoma


title: ACC34

description: Adrenocortical carcinoma


title: ACC36

description: Adrenocortical carcinoma


title: ACC29

description: Adrenocortical carcinoma


title: ACC31

description: Adrenocortical carcinoma


title: ACC12


title: ACC30

description: Adrenocortical carcinoma


title: ACC20

description: Adrenocortical carcinoma


title: ACC26

description: Adrenocortical carcinoma


title: ACC22

description: Adrenocortical carcinoma


title: ACC13

description: Adrenocortical carcinoma


title: ACC24

description: Adrenocortical carcinoma


title: ACC23

description: Adrenocortical carcinoma


title: ACC17

description: Adrenocortical carcinoma


title: ACC15

description: Adrenocortical carcinoma


title: ACC16

description: Adrenocortical carcinoma


title: ACC25

description: Adrenocortical carcinoma


title: ACC19

description: Adrenocortical carcinoma


title: ACC10

description: Adrenocortical carcinoma


title: ACC18

description: Adrenocortical carcinoma


title: ACC12

description: Adrenocortical carcinoma


title: ACC11

description: Adrenocortical carcinoma


title: ACC14

description: Adrenocortical carcinoma


title: ACC6

description: Adrenocortical carcinoma


title: ACC7

description: Adrenocortical carcinoma


title: ACC4

description: Adrenocortical carcinoma


title: ACC3

description: Adrenocortical carcinoma


title: ACC5

description: Adrenocortical carcinoma


title: ACC9

description: Adrenocortical carcinoma


title: ACC2

description: Adrenocortical carcinoma


title: HaCaT obacunone 100 uM 2 set

city: Seoul

first: Jong Min

address: 209, Neungdong-ro, Gwangjin-gu

department: Bioscience and Biotechnology

institute: Sejong University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Avadis 3.3 software

source_name: HaCaT cell

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrep RNA Amplification kit

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS and antibiotics at 37°C in a humidified 5% CO2 incubator.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were seeded at a density of 1 x 106 cells in a 100 mm dish and incubated overnight. Next day, the cells were fed with fresh media containing 10% FBS and incubated with obacunone or 0.1% DMSO (vehicle control) for 4 h.

value: keratinocyte

tag: agent

value: obacunone 100 uM


title: ACC1

description: Adrenocortical carcinoma


title: HaCaT obacunone 100 uM 3 set

description: replicate 3


title: ACC28

description: Adrenocortical carcinoma


title: HaCaT obacunone 100 uM 1 set

description: replicate 1


title: HaCaT obacunone 50 uM 3 set

description: replicate 3

value: obacunone 50 uM


title: ACC21

description: Adrenocortical carcinoma


title: HaCaT obacunone 50 uM 2 set

description: replicate 2


title: HaCaT obacunone 50 uM 1 set

description: replicate 1


title: ACC28

description: Adrenocortical carcinoma

label: C-Bio and A-DNP


title: ACC25

description: Adrenocortical carcinoma


title: ACC16

description: Adrenocortical carcinoma


title: ACC29

description: Adrenocortical carcinoma


title: HaCaT obacunone 10 uM 3 set

description: replicate 3

value: obacunone 10 uM


title: ACC11

description: Adrenocortical carcinoma


title: ACC26

description: Adrenocortical carcinoma


title: ACC45

description: Adrenocortical carcinoma


title: ACC44

description: Adrenocortical carcinoma


title: HaCaT obacunone 10 uM 2 set

description: replicate 2


title: ACC41

description: Adrenocortical carcinoma


title: ACC39

description: Adrenocortical carcinoma


title: ACC24

description: Adrenocortical carcinoma


title: ACC27

description: Adrenocortical carcinoma


title: ACC40

description: Adrenocortical carcinoma


title: ACC34

description: Adrenocortical carcinoma


title: ACC38

description: Adrenocortical carcinoma


title: HaCaT obacunone 10 uM 1 set

description: replicate 1


title: ACC30

description: Adrenocortical carcinoma


title: ACC3

description: Adrenocortical carcinoma


title: ACC21

description: Adrenocortical carcinoma


title: ACC8

description: Adrenocortical carcinoma


title: HaCaT Vehicle control 2 set

description: replicate 2

value: 0.1% DMSO (vehicle control)


title: ACC7

description: Adrenocortical carcinoma


title: ACC32

description: Adrenocortical carcinoma


title: ACC43

description: Adrenocortical carcinoma


title: ACC23

description: Adrenocortical carcinoma


title: HaCaT Vehicle control 3 set

description: replicate 3


title: ACC35

description: Adrenocortical carcinoma


title: ACC22

description: Adrenocortical carcinoma


title: ACC6

description: Adrenocortical carcinoma


title: S2 Luc dsRNA 1

city: Helsinki

first: Emilia

last: Kuuluvainen

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

hyb_protocol: 10 µg of fragmented cRNA were hybridized on GeneChip Drosophila Genome 2.0 arrays according to Affymetrix standars protocols (Expression Analysis Technical Manual P/N 702232 Rev.2). Affymetrix Fluidics station 450 was used for washing and staining.

scan_protocol: GeneChips were scanned with Affymetrix 3000 scanner

data_processing: GeneSpring GX 12.1 GC-RMA

organism: Drosophila melanogaster

source_name: S2 cells

label_protocol: Biotinylated cRNA was prepared from 4µg total RNA according to standard Affymetrix protocol (Expression Analysis Technical Manual P/N 702232 Rev.2)

growth_protocol: Drosophila S2 cells were cultured in  Drosophila SFM media (Gibco) supplemented with 10% FBS, L-glutamine and antibiotics

extract_protocol: Total RNA, Qiagen RNeasy Plus Mini Kit according to manufcturers protocol

treatment_protocol: 1.2 million exponentially growing S2 cells were treated with 20µg dsRNA in 1 ml of serum free media on 6-well plates. Serum containing media was added 1h later for a final FBS concentration of 10%. Cells were cultured for 72h before sample collection.

value: S2 cells

tag: treated with

value: Luc dsRNA


title: S2 Luc dsRNA 2


title: HepG2 Obacunone-treated 6 h

description:
replicate1
SAMPLE 10

data_processing: The data were normalised using quantile normalisation with Avadis 3.3 software

source_name: HepG2 cell

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

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

treatment_protocol: Cells were seeded at a density of 1 x 106 cells in a 100 mm dish and incubated overnight. Next day, the cells were fed with fresh media containing 10% FBS and incubated with 100 uM obacunone or 0.1% DMSO (vehicle control)  for 0.5, 1, 3, 6, or 12 h.

value: hepatocellular carcinoma cell

value: 100 uM obacunone

tag: time point

value: 6 h


title: S2 Luc dsRNA 4


title: HaCaT Vehicle control 1 set

description: replicate 1


title: S2 Luc dsRNA 3


title: HepG2 Obacunone-treated 1 h

description:
replicate1
SAMPLE 8

value: 1 h


title: HepG2 Obacunone-treated 3 h

description:
replicate1
SAMPLE 9

value: 3 h


title: HepG2 Obacunone-treated 0.5 h

description:
replicate1
SAMPLE 7


title: ACC20

description: Adrenocortical carcinoma

value: Adrenocortical carcinoma


title: S2 GFP dsRNA 3

value: GFP dsRNA


title: S2 GFP dsRNA 1


title: HepG2 Vehicle control 12 h

description:
replicate1
SAMPLE 6

value: 0.1% DMSO vehicle control


title: HepG2 Obacunone-treated 12 h

description:
replicate1
SAMPLE 11


title: HepG2 Vehicle control 3 h

description:
replicate1
SAMPLE 4


title: S2 GFP dsRNA 2


title: HepG2 Vehicle control 6 h

description:
replicate1
SAMPLE 5


title: S2 Med13 dsRNA 4

value: Med13 dsRNA


title: HepG2 Vehicle control 1 h

description:
replicate1
SAMPLE 3


title: ACC14

description: Adrenocortical carcinoma


title: BMSCs from young mice 3

city: Changsha

first: Peng

last: Cheng

state: Hunan

address: 139# Middle Renmin Road

department: The Second Xiangya Hospital

country: China

institute: Central South University

description: microRNAs expression in young mice

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-046065 Mouse miRNA Microarray V19.0 8x60K(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained.

source_name: young mice 3

label_protocol: 0.1ug total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP（Cy3）using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer  version 3.2.1.

growth_protocol: We collected bone marrow cells from 3 or 18 months old female C57BL/6 mice and then incubated the cells aliquots for 20 min at 4°C with phycoerythrin (PE)-, FITC-, peridinin chlorophyll protein (Per CP)- and allophycocyanin (APC)-conjugated antibodies to mouse Sca-1, CD29, CD45 and CD11b. Acquisition was performed on a fluorescence-activated cell sorting (FACS) Aria model, and the analysis was performed using FACS DIVE software.The sorted CD29+Sca-1+CD45−CD11b− cells were BMSCs.

extract_protocol: total RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: 1ml Trizol was added to BMSCs per 3.5cm dish and then transferred into freezing tubes.The tubes were preserved in liquid nitrogen and then sent to company in dry ice.

tag: background strain

value: bone marrow

value: female

value: 3 months


title: HepG2 Vehicle control 0.5 h

description:
replicate1
SAMPLE 2


title: S2 Med13 dsRNA 3


title: ACC18

description: Adrenocortical carcinoma


title: S2 Med12 dsRNA 4

value: Med12 dsRNA


title: S2 Med13 dsRNA 2


title: ACC12

description: Adrenocortical carcinoma


title: S2 GFP dsRNA 4


title: S2 Med13 dsRNA 1


title: HaCaT Obacunone-treated 12 h

description:
replicate1
SAMPLE 11

value: keratinocyte


title: BMSCs from young mice 1

description: microRNAs expression in young mice

source_name: young mice 1


title: HepG2 Vehicle control 0 h

description:
replicate1
SAMPLE 1

value: 0 h


title: ACC4

description: Adrenocortical carcinoma


title: BMSCs from age mice 3

description: microRNAs expression in aged mice

source_name: aged mice 3

value: 18 months


title: BMSCs from age mice 2

description: microRNAs expression in aged mice

source_name: aged mice 2


title: BMSCs from age mice 1

description: microRNAs expression in aged mice

source_name: aged mice 1


title: S2 Med12 dsRNA 3

value: S2 cells


title: S2 Med12 dsRNA 1


title: BMSCs from young mice 2

description: microRNAs expression in young mice

source_name: young mice 2


title: HaCaT Obacunone-treated 0.5 h

description:
replicate1
SAMPLE 7


title: HaCaT Vehicle control 12 h

description:
replicate1
SAMPLE 6


title: S2 Med12 dsRNA 2


title: ACC9

description: Adrenocortical carcinoma


title: HaCaT Obacunone-treated 1 h

description:
replicate1
SAMPLE 8


title: HaCaT Obacunone-treated 6 h

description:
replicate1
SAMPLE 10


title: ACC2

description: Adrenocortical carcinoma


title: HaCaT Obacunone-treated 3 h

description:
replicate1
SAMPLE 9


title: S2 CycC dsRNA 2

value: CycC dsRNA


title: HH_TOX shRNA knockdown replicate 3

city: Vancouver

first: Youwen

last: Zhou

state: BC

address: Room 490, 828 West 10th Ave.

department: Dermatology and Skin Science

country: Canada

institute: UBC

description: Biological replicate 3 of 3. Control vector vs. TOX shRNA vector transduced HH cells.

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: HH sh3 5

label_protocol: A total of 100 ng RNA for each sample was reverse-transcribed into cDNA and linearly amplified by in vitro transcription with Cy3 or Cy5 dye using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Mississauga, Canada).

growth_protocol: Human CTCL cell line Hut78 and HH (ATCC no. TIB-161, CRL-2105, respectively) were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 10−4 M β-mercaptoethanol (STEMCELL Technologies, Vancouver, BC, Canada). Transduced-CTCL cells were cultured in the above medium plus 1ug/mL puromycin (Invitrogen, Burlington, Ontario, Canada).

treatment_protocol: PLKO.1 vector containing shRNA inserts that specifically target human TOX (sh2 and sh3), and a non-targeting shRNA control (002) were used to be packed into lentiviral particles. The virus-ontaining medium (35 mL per construct) was ﬁltered and concentrated in 100 uL RPMI 1640 medium. CTCL cells (2×105 cells in 1mL media) were incubated with 5 ul concentrated lentiviral particles for 24 hours. After another 24 hours, puromycin (1ug/mL) was added to select transduced populations. Bulk populations transduced by either control or TOX-shRNA viruses were used in this study.

value: HH

tag: transduction

value: TOX shRNA

value: Control


title: S2 CycC dsRNA 1


title: HH_TOX shRNA knockdown replicate 2

description: Biological replicate 2 of 3. Control vector vs. TOX shRNA vector transduced HH cells.

source_name: HH sh3 4


title: Hut78_TOX shRNA knockdown replicate 3

description: Biological replicate 3 of 3. TOX shRNA vector vs. control vector transduced Hut78 cells.

source_name: Hut78 sh3 9


title: HH_TOX shRNA knockdown replicate 1

description: Biological replicate 1 of 3. Control vector vs. TOX shRNA vector transduced HH cells.

source_name: HH sh2 4


title: HaCaT Vehicle control 0.5 h

description:
replicate1
SAMPLE 2


title: HaCaT Vehicle control 1 h

description:
replicate1
SAMPLE 3

value: 1 h


title: S2 Cdk8 dsRNA 1

value: Cdk8 dsRNA


title: ACC1

description: Adrenocortical carcinoma

value: Adrenocortical carcinoma


title: Hut78_TOX shRNA knockdown replicate 1

description: Biological replicate 1 of 3. TOX shRNA vector vs. control vector transduced Hut78 cells.

source_name: Hut78 sh2 10


title: ACC36

description: Adrenocortical carcinoma


title: S2 Cdk8 dsRNA 2


title: Hut78_TOX shRNA knockdown replicate 2

description: Biological replicate 2 of 3. TOX shRNA vector vs. control vector transduced Hut78 cells.

source_name: Hut78 sh3 8


title: ACC31

description: Adrenocortical carcinoma


title: ACC37

description: Adrenocortical carcinoma


title: ACC17

description: Adrenocortical carcinoma


title: ZR-75-1

status: Public on Apr 28 2014

city: Macclesfield

first: Mark

last: Wappett

address: Alderley Park

department: Oncology

institute: AstraZeneca

description: Untreated

hyb_protocol: Affymetrix protocol

data_processing: The data were analysed with the robust multichip analysis algorithm.  The data is returned in log2 normalised format. The RMA version used was from the bioconductor package affy, stable release version number 1.40.

source_name: AZ GENE EXPRESSION

label_protocol: Affymetrix protocol

extract_protocol: RNA was extracted from cell lines using the Qiagen RNeasy kit as per the manufacturer's instructions. RNA quantity was determined using a Nanodrop spectrophotometer and both 260/280 and 260/230 ratios were evaluated. RNA quality was assessed using an Agilent RNA 6000 Nano Chip and the RNA Integrity Number (RIN) value of each sample was determined.

value: Breast

tag: disease

value: ductal carcinoma Derived from metastatic site:ascites


title: ACC42

description: Adrenocortical carcinoma


title: ACC19

description: Adrenocortical carcinoma


title: ACC13

description: Adrenocortical carcinoma


title: Bx051b_030 HG2

description: Untreated

source_name: Kudos 95 Cell Panel

value: Ductal Carcinoma


title: S2 CycC dsRNA 3


title: HaCaT Vehicle control 6 h

description:
replicate1
SAMPLE 5

source_name: HaCaT cell

value: 0.1% DMSO vehicle control

value: 6 h


title: S2 CycC dsRNA 4

source_name: S2 cells


title: ACC33

description: Adrenocortical carcinoma


title: ACC10

description: Adrenocortical carcinoma


title: WSU-DCL2 ghp280606

description: Untreated

value: Hematopoietic System

value: B-NHL (B-cell non-Hodgkins Lymphoma) / DLCL (Diffuse Large Cell Lymphoma)


title: HaCaT Vehicle control 0 h

description:
replicate1
SAMPLE 1

value: 0 h

value: keratinocyte


title: WiDr ap121105

description: Untreated

value: WIDR

value: Colon

value: colorectal adenocarcinoma


title: WiDr

description: Untreated


title: EA09076_118378_HG-U133_PLUS_2_CO015_08

description: Untreated

value: Rectum carcinoma


title: ACC5

description: Adrenocortical carcinoma


title: EA10068_111341

description: Untreated

value: AML


title: EA09076_118379_HG-U133_PLUS_2_CO015_09

description: Untreated


title: EA10068_203551_HG-U133_PLUS_2_ULA

description: Untreated

value: ULA

value: DLBCL


title: SR5072_HUMAN_U133_PLUS2_250310

description: Untreated

value: Bladder


title: SB11010-2_D4S1C0040R_(HG-U133_Plus_2)

description: Untreated

value: VMRCLCP

value: Lung

value: SqLC


title: EA09076_118380_HG-U133_PLUS_2_CO015_10

description: Untreated

value: Cecum carcinoma


title: EA10068_203553_HG-U133_PLUS_2_WILL-2

description: Untreated


title: WSU-NHL ghp231105

description: Untreated

value: WSUNHL

value: B-NHL (B-cell non-Hodgkins Lymphoma) / DLBL (Diffuse Large B-cell Lymphoma )


title: SR5074_HUMAN_U133_PLUS2_250310

description: Untreated


title: EA10068_203552_HG-U133_PLUS_2_WILL-1

description: Untreated

value: Hematopoietic System


title: EA10068_203562_HG-U133_PLUS_2_U-698-M

description: Untreated


title: A1631-09

description: Untreated

value: VCAP

value: Prostate


title: U937 ghp280606

description: Untreated

value: Histocytic Lymphoma


title: EA08079_80509_ZR-75-1

description: Untreated

value: Breast


title: EA09076_118377_HG-U133_PLUS_2_CO015_07

description: Untreated

value: Colon

value: carcinoma


title: HaCaT Vehicle control 3 h

description:
replicate1
SAMPLE 4

value: 0.1% DMSO vehicle control

value: 3 h

value: keratinocyte


title: EA10068_111344

description: Untreated

value: AML


title: Bx058-19 HG2

description: Untreated

value: Brain

value: glioblastoma; astrocytoma


title: U266B1 ghp150606

description: Untreated

value: Myeloma


title: ACC15

description: Adrenocortical carcinoma

value: Adrenocortical carcinoma


title: SBCG2008008-D3S1CO001R

description: Untreated

value: TT

value: Thyroid Gland

value: Esophageal cancer


title: Bx058-16 HG2

description: Untreated

value: glioblastoma


title: Bx051b_069 HG2

description: Untreated

value: Ovary

value: primary malignant adenocarcinoma; clear cell carcinoma


title: SBCG2008008-D3S1C0015R

description: Untreated

value: Esophagus


title: SBCG2008008-D3S1CO002R

description: Untreated

value: TTN


title: T47D

description: Untreated

value: Breast

value: ductal carcinoma Derived from metastatic site:pleural effusion


title: EA10068_203549_HG-U133_PLUS_2_U2932

description: Untreated

value: Hematopoietic System

value: DLBCL


title: EA10068_203550_HG-U133_PLUS_2_U-2940

description: Untreated


title: EA10068_203548_HG-U133_PLUS_2_TMD8

description: Untreated


title: SBCG2008008-D3S1C0016R

description: Untreated


title: Bx058-15 HG2

description: Untreated


title: 81 TCC Sup

description: Untreated

value: TCCSUP

value: Bladder


title: THP-1 ghp231105

description: Untreated

value: AML (Acute Myeloid Leukemia)


title: TF-1 ghp231105

description: Untreated


title: Bx051b_019 HG2

description: Untreated

value: Ductal Carcinoma


title: SBCG2008008-D3S1C0014R

description: Untreated


title: Bx042-050

description: Untreated

value: Colon

value: colorectal carcinoma


title: SR5165_HUMAN_U133_PLUS2_250310

description: Untreated


title: 90 T24 sauvage

description: Untreated


title: 87 T24 WT k6

description: Untreated


title: EA08079_80508_T-47D

description: Untreated


title: Bx051b_076 HG2

description: Untreated

value: primary malignant adenocarcinoma; endometrioid carcinoma


title: SBCG2008008-D3S1CO017R

description: Untreated

value: Esophageal cancer


title: Bx040_0012_R

description: Untreated

value: Pancreas

value: Adenocarcinoma


title: 88 T24 Neo 3 correct

description: Untreated


title: Bx051b_090 HG2

description: Untreated


title: A1385-17

description: Untreated


title: Bx058-05 HG2

description: Untreated

value: Brain

value: Glioblastoma multiforme


title: 85 T24 R2WT K10

description: Untreated


title: 89 T24 Neo 1 correct

description: Untreated


title: 86 T24 WT y

description: Untreated


title: SW620_1

description: Untreated

value: colorectal adenocarcinoma


title: Bx042-054

description: Untreated


title: Bx042-045r

description: Untreated

value: adenocarcinoma


title: SR5083_HUMAN_U133_PLUS2_250310

description: Untreated


title: Bx042-013

description: Untreated


title: Bx051b_100 HG2

description: Untreated

value: Thyroid Gland

value: squamous cell carcinoma


title: Bx042-011

description: Untreated


title: Bx051b_049 HG2

description: Untreated


title: Bx051b_009 HG2

description: Untreated


title: SW48

description: Untreated


title: Bx051b_056 HG2

description: Untreated


title: SR5068_HUMAN_U133_PLUS2_250310

description: Untreated


title: Bx042-010

description: Untreated


title: Bx058-14 HG2

description: Untreated

value: astrocytoma


title: SR5080_HUMAN_U133_PLUS2_250310

description: Untreated


title: SW620

description: Untreated


title: SW48_1

description: Untreated


title: Bx051b_079 HG2

description: Untreated

value: Breast

value: Invasive Ductal Carcinoma


title: SW480_1

description: Untreated


title: Bx042-048

description: Untreated


title: Bx051b_017 HG2

description: Untreated


title: SW1116

description: Untreated


title: SW1116 ap121105

description: Untreated


title: EA08079_80513_SUM52PE

description: Untreated


title: SW480

description: Untreated


title: Bx051b_004 HG2

description: Untreated


title: SW579 ap270406

description: Untreated


title: Bx030_031 HG2

description: Untreated

value: Hematopoietic System


title: Bx058-04 HG2

description: Untreated

value: Astrocytoma


title: Bx042-060

description: Untreated

value: Colon


title: Bx051b_063 HG2

description: Untreated

value: invasive ductal carcinoma;


title: Bx030_030 HG2

description: Untreated


title: EA10068_203555_HG-U133_PLUS_2_SUDHL8

description: Untreated

value: DLBCL


title: SU-DHL-4 ghp231105

description: Untreated

value: B-NHL (B-cell non-Hodgkins Lymphoma) / DLBL (Diffuse Large B-cell Lymphoma )


title: EA10068_203559_HG-U133_PLUS_2_SUDHL10

description: Untreated


title: Bx042-001

description: Untreated

value: colorectal carcinoma


title: A1385-13

description: Untreated

value: Pancreas


title: EA10068_203547_HG-U133_PLUS_2_SUDHL2

description: Untreated


title: SBCG2008008-D2S1CO17R

description: Untreated

value: Liver

value: Liver Cancer


title: SBCG2008008-D2S1CO16R

description: Untreated


title: SBCG2008008-D2S1CO18R

description: Untreated


title: SK-MES-1 ghp030206

description: Untreated

value: Lung

value: Carcinoma


title: SBCG2008008-D1S1CO19R

description: Untreated

value: Stomach

value: Gastric Cancer


title: SBCG2008008-D2S1CO15R

description: Untreated


title: SBCG2008008-D1S1CO18R

description: Untreated


title: SBCG2008008-D1S1CO15R

description: Untreated


title: Bx030_013 HG2

description: Untreated


title: SBCG2008008-D1S1CO31R

description: Untreated


title: SBCG2008008-D1S1CO11R

description: Untreated


title: Bx051b_008 HG2

description: Untreated

value: Ovary

value: adenocarcinoma


title: SBCG2008008-D2S1C0013R

description: Untreated


title: SBCG2008008-D2S1CO05R

description: Untreated


title: SBCG2008008-D1S1CO10R

description: Untreated


title: SBCG2008008-D1S1CO16R

description: Untreated


title: SBCG2008008-D2S1CO14R

description: Untreated


title: SBCG2008008-D1S1CO17R

description: Untreated


title: SKMM2 ghp150606

description: Untreated

value: Myeloma


title: SBCG2008008-D1S1COO9R

description: Untreated


title: SBCG2008008-D2S1CO21R

description: Untreated


title: SBCG2008008-S5

description: Untreated


title: SKM-1 ghp231105

description: Untreated

value: Hematopoietic System

value: AML (Acute Myeloid Leukemia)


title: SBCG2008008-D3S1C0013R

description: Untreated

value: Esophagus

value: Esophageal cancer


title: Bx042-019

description: Untreated

value: Colon

value: colorectal adenocarcinoma


title: Bx051b_059 HG2

description: Untreated


title: SKCO-1 ap121105

description: Untreated

value: colorectal adenocarcinoma Derived from metastatic site:ascites


title: SkBr3

description: Untreated

value: Breast

value: adenocarcinoma Derived from metastatic site:pleural effusion


title: EA08079_80492_SK-BR-3

description: Untreated


title: Bx051b_036 HG2

description: Untreated

value: Adenocarcinoma


title: SBCG2008008-D2S1CO26R

description: Untreated

value: Liver

value: Liver Cancer


title: Bx056_03 HG2

description: Untreated

value: Lung

value: small cell lung cancer; carcinoma


title: EA10068_203546_HG-U133_PLUS_2_RI-1

description: Untreated

value: DLBCL


title: EA10068_111345

description: Untreated

value: AML


title: SCC-9 ap150606

description: Untreated

value: Tongue

value: Squamous Cell Carcinoma


title: SR5075_HUMAN_U133_PLUS2_250310

description: Untreated

value: SCABER

value: Bladder


title: A1631-11

description: Untreated

value: Prostate


title: EA10068_111349

description: Untreated

value: Hematopoietic System

value: ALL


title: Bx051b_107 HG2

description: Untreated

value: Nasal Septum


title: RPMI8226 ghp280606

description: Untreated

value: Myeloma


title: RPMI2650 ap270406

description: Untreated

value: squamous cell carcinoma from pleural effusion


title: SCC25 ap270406

description: Untreated

value: squamous cell carcinoma


title: SB11010-1-2_D4S1C0041R_(HG-U133_Plus_2)

description: Untreated

value: SqLC


title: SBCG2008008-D1S1CO04R

description: Untreated

value: Stomach

value: Gastric Cancer


title: Bx030_004 HG2

description: Untreated

value: REH


title: 84 RT 112

description: Untreated


title: Bx030_008 HG2

description: Untreated


title: 79 SD 148

description: Untreated


title: 80 Scaber

description: Untreated


title: EA10068_203554_HG-U133_PLUS_2_RC-K8

description: Untreated

value: DLBCL


title: SR5079_HUMAN_U133_PLUS2_250310

description: Untreated


title: SR5082_HUMAN_U133_PLUS2_250310

description: Untreated


title: Bx042-005

description: Untreated

value: RKO

value: Colon

value: carcinoma


title: Bx042-065

description: Untreated

value: rectum


title: Bx051b_032 HG2

description: Untreated

value: Carcinoma


title: SC1 ghp280606

description: Untreated

value: B-NHL (B-cell non-Hodgkins Lymphoma) / FL (Follicular Lymphoma)


title: Bx030_012 HG2

description: Untreated

value: RAMOS

value: Hematopoietic System


title: Raji ghp280606

description: Untreated

value: RAJI

value: Burkitts lymphoma


title: Ramos ghp231105

description: Untreated


title: SCC-4 ap270406

description: Untreated

value: Tongue


title: Raji ghp231105

description: Untreated


title: A1631-10

description: Untreated

value: Prostate


title: PE CA PJ49 ap200406

description: Untreated

value: oral squamous cell carcinoma


title: A1385-16

description: Untreated

value: Pancreas


title: SBCG2008008-D2S1CO02R

description: Untreated

value: Liver

value: Liver Cancer


title: PE CA PJ15 ap200406

description: Untreated

value: squamous cell carcinoma


title: SBCG2008008-D2S1CO10R

description: Untreated


title: Bx030_029 HG2

description: Untreated


title: Bx051b_068 HG2

description: Untreated

value: Oral cavity

value: basaloid squamous cell carcinoma


title: Bx051b_106 HG2

description: Untreated


title: PC9 parental ap290806

description: Untreated

value: Lung

value: NSCLC


title: Bx051b_083 HG2

description: Untreated


title: Bx051b_071 HG2

description: Untreated

value: Adenocarcinoma


title: EA10068_111340

description: Untreated

value: APL


title: A1385-11

description: Untreated


title: PE CA PJ34 ap200406

description: Untreated


title: Bx040_0010_R

description: Untreated


title: Bx042-032r

description: Untreated

value: PCJW

value: Colon

value: Colorectal adenocarcinoma


title: A1385-10

description: Untreated


title: SR5058_HUMAN_U133_PLUS2_250310

description: Untreated


title: PC9 r2

description: Untreated


title: SR5064_HUMAN_U133_PLUS2_250310

description: Untreated


title: PC3

description: Untreated

value: adenocarcinoma


title: Bx051b_082 HG2

description: Untreated

value: Tongue


title: PE CA PJ41 ap200406

description: Untreated


title: PC9 ZD ap290806

description: Untreated


title: PC-9_1

description: Untreated


title: A1385-09

description: Untreated


title: SR5059_HUMAN_U133_PLUS2_250310

description: Untreated

value: Prostate


title: Bx051b_066 HG2

description: Untreated


title: A1385-08

description: Untreated


title: RKO

description: Untreated

value: RKO

value: carcinoma


title: A1385-07

description: Untreated

value: Pancreas


title: SBCG2008008-D1S1COO8R

description: Untreated

value: Stomach

value: Gastric Cancer


title: Bx051b_064 HG2

description: Untreated

value: Ovary

value: teratocarcinoma


title: PANC1

description: Untreated

value: epithelioid carcinoma


title: Bx051b_080 HG2

description: Untreated


title: Bx051b_105 HG2

description: Untreated

value: malignant papillary serous adenocarcinoma


title: Bx040_0009_R

description: Untreated

value: Carcinoma


title: Bx051b_042 HG2

description: Untreated

value: Adenocarcinoma


title: Bx051b_047 HG2

description: Untreated


title: Bx051b_097 HG2

description: Untreated

value: Esophagus

value: oesophageal squamous cell carcinoma


title: OPM-2 ghp280606

description: Untreated

value: Hematopoietic System

value: Myeloma


title: SB11010-2_D4S1C0039R_(HG-U133_Plus_2)

description: Untreated

value: Lung

value: SqLC


title: EA08079_89053_OCI-MY1

description: Untreated


title: EA08079_89054_OCI-MY5

description: Untreated


title: Bx051b_044 HG2

description: Untreated


title: EA10068_111343

description: Untreated

value: AML


title: OE21 ap270406

description: Untreated

value: squamous cell carcinoma


title: EA08079_89052_OCI-LY8

description: Untreated


title: OCI-LY19 ghp280606

description: Untreated

value: B-NHL (B-cell non-Hodgkins Lymphoma) / DLCL (Diffuse Large Cell Lymphoma)


title: EA08079_89051_OCI-LY7

description: Untreated


title: EA08079_89049_OCI-LY3

description: Untreated


title: EA08079_89047_OCI-LY10

description: Untreated


title: EA08079_89050_OCI-LY4

description: Untreated


title: EA08079_89046_OCI-LY1

description: Untreated


title: EA08079_89048_OCI-LY18

description: Untreated


title: Bx030_028 HG2

description: Untreated


title: Bx030_002 HG2

description: Untreated


title: Bx051b_099 HG2

description: Untreated

value: ovarian cystadenocarcinoma


title: Bx030_027 HG2

description: Untreated


title: Bx051b_085 HG2

description: Untreated


title: SBCG2008008-D1S1CO24R

description: Untreated

value: Stomach

value: Gastric Cancer


title: A1385-15

description: Untreated

value: Pancreas


title: OCI-AML5 ghp280606

description: Untreated

value: AML (Acute Myeloid Leukemia)


title: Bx051b_006 HG2

description: Untreated

value: Ovary

value: adenocarcinoma


title: OVCAR3 ghp101105

description: Untreated


title: NCI-87 ap071105

description: Untreated

value: gastric carcinoma


title: EA10068_203561_HG-U133_PLUS_2_NU-DHL-1

description: Untreated

value: DLBCL


title: Bx030_007 HG2

description: Untreated


title: SBCG2008008-D1S1CO037R

description: Untreated


title: H838 ap150606

description: Untreated

value: Adenocarcinoma


title: Bx042-039

description: Untreated

value: Colon

value: colorectal adenocarcinoma


title: NCLH929 ghp280606

description: Untreated

value: Hematopoietic System

value: Myeloma


title: OVCAR3 ap121105

description: Untreated


title: H-810 re-hyb

description: Untreated

value: Lung

value: carcinoma; non-small cell lung cancer


title: Bx056_10 HG2

description: Untreated


title: EA08073_86096_BX062-08

description: Untreated


title: SBCG2008008-S2

description: Untreated


title: NCI-H838 ghp030206

description: Untreated


title: Bx051b_094 HG2

description: Untreated


title: NCI-H596 ghp030206

description: Untreated

value: adenosquamous carcinoma


title: NCI-H82 ghp030206

description: Untreated

value: carcinoma; small cell lung cancer Derived from metastatic site:pleural effusion


title: NCI-H522

description: Untreated

value: adenocarcinoma; non-small cell lung cancer


title: H647 r2

description: Untreated

value: adenosquamous carcinoma; non-small cell lung cancer


title: Bx056_01 HG2

description: Untreated

value: variant small cell lung cancer; carcinoma


title: Bx056_06 HG2

description: Untreated


title: NCI-H460 dn p53

description: Untreated

value: carcinoma; large cell lung cancer Derived from metastatic site:pleural effusion


title: H727 NSCLC rpt

description: Untreated

value: carcinoid


title: Bx042-038

description: Untreated


title: H522 r2

description: Untreated


title: NCI-H520 ghp030206

description: Untreated

value: Carcinoma


title: NCI-H460 r2

description: Untreated


title: Bx051b_012 HG2

description: Untreated

value: carcinoma; large cell lung cancer


title: SB11016-2_D4S1C0049R_(HG-U133_Plus_2)

description: Untreated

value: SqLC


title: H358 r2

description: Untreated

value: bronchioalveolar carcinoma; non-small cell lung cancer


title: H3255 ap150606

description: Untreated

value: Adenocarcinoma


title: NCI-H460

description: Untreated


title: NCI-H322 r2

description: Untreated

value: Lung Carcinoma


title: SBCG2008008-D1S1CO25R

description: Untreated

value: Stomach

value: Gastric Cancer


title: Bx051b_001 HG2

description: Untreated

value: Lung

value: bronchioloalveolar adenocarcinoma


title: EA10068_203564_HG-U133_PLUS_2_H3122-CR

description: Untreated

value: NSCLC


title: H2347 nsclc rpt

description: Untreated


title: H2342 (AP) NSCLC rpt

description: Untreated


title: EA10068_203563_HG-U133_PLUS_2_H3122-P

description: Untreated


title: H2444

description: Untreated

value: non-small cell lung cancer


title: SB11016-2_D4S1C0053R_(HG-U133_Plus_2)

description: Untreated


title: Bx051b_025 HG2

description: Untreated

value: adenocarcinoma; non-small cell lung cancer


title: H23 nsclc rpt

description: Untreated


title: H2228 x nsclc rpt

description: Untreated


title: NCI-H226 ghp030206

description: Untreated

value: squamous cell carcinoma; mesothelioma [23570] Derived from metastatic site:pleural effusion


title: NCI-H2122

description: Untreated


title: H2135 x nsclc rpt

description: Untreated


title: H2291 x r2

description: Untreated

value: adenocarcinoma; non-small cell lung cancer Derived from metastatic site:lymph node


title: H23

description: Untreated


title: Bx051b_028 HG2

description: Untreated

value: squamous cell carcinoma; mesothelioma


title: Bx056_02 HG2

description: Untreated

value: small cell lung cancer; carcinoma


title: H2073 x NSCLC rpt

description: Untreated


title: H2172

description: Untreated


title: H2030 GB P1 A NSCLC rpt

description: Untreated


title: Bx056_04 HG2

description: Untreated


title: H1838 A nsclc rpt

description: Untreated


title: H1869 (AP) nsclc rpt

description: Untreated


title: H2085 r2

description: Untreated


title: NCI-H1793

description: Untreated


title: Bx051b_031 HG2

description: Untreated


title: H2122 r2

description: Untreated


title: SB11016-2_D4S1C0052R_(HG-U133_Plus_2)

description: Untreated


title: H1975 x nsclc rpt

description: Untreated


title: H1563 x nsclc rpt

description: Untreated


title: Bx030_005 HG2

description: Untreated

value: Hematopoietic System


title: MV-4-11 ghp231105

description: Untreated

value: AML (Acute Myeloid Leukemia)


title: H1703 A nsclc rpt

description: Untreated


title: Bx030_025 HG2

description: Untreated


title: H1650 x nsclc rpt

description: Untreated


title: H1666 ap150606

description: Untreated


title: Bx051b_084 HG2

description: Untreated


title: NCI-H1437

description: Untreated


title: NCI-H1299 nsclc rpt

description: Untreated

value: carcinoma; non-small cell lung cancer Derived from metastatic site:lymph node


title: NB4

description: Untreated


title: Namalwa ghp231105

description: Untreated

value: NAMALWA

value: Burkitts lymphoma


title: Bx030_009 HG2

description: Untreated


title: MOLM13

description: Untreated

value: acute myeloid leukemia


title: MOLP8 ghp280606

description: Untreated

value: Myeloma


title: Bx051b_061 HG2

description: Untreated


title: NCI-1781 ap071105

description: Untreated


title: H1651 B nsclc rpt

description: Untreated


title: H1734 nsclc rpt

description: Untreated


title: H1623 x nsclc rpt

description: Untreated


title: Bx058-18 HG2

description: Untreated

value: MOGGUVW

value: Brain

value: astrocytoma


title: H1437 r2

description: Untreated

value: Lung


title: ML-2 ghp231105

description: Untreated


title: Bx051b_043 HG2

description: Untreated

value: carcinoma; non-small cell lung cancer


title: Bx056_05 HG2

description: Untreated

value: squamous cell; adenocarcinoma; non-small cell lung cancer


title: Bx030_015 HG2

description: Untreated


title: EA08079_89045_MM1.S

description: Untreated


title: Bx030_026 HG2

description: Untreated


title: SBCG2008008-D1S1CO22R

description: Untreated

value: Stomach

value: Gastric Cancer


title: Bx056_14 HG2

description: Untreated

value: gastric adenocarcinoma


title: EA08079_89044_MM1.R

description: Untreated


title: Bx058-17 HG2

description: Untreated

value: MOGGCCM


title: SBCG2008008-D1S1CO23R

description: Untreated


title: Mia-Pa-a-2

description: Untreated

value: Pancreas

value: carcinoma


title: Bx040_0008_R

description: Untreated

value: Carcinoma


title: Bx051b_073 HG2

description: Untreated


title: SBCG2008008-D2S1CO09R

description: Untreated

value: Liver

value: Liver Cancer


title: A1631-08

description: Untreated

value: Bladder


title: SBCG2008008-D2S1CO32R

description: Untreated


title: H2126 r2

description: Untreated

value: adenocarcinoma; non-small cell lung cancer


title: SBCG2008008-D1S1COO7R

description: Untreated


title: MelJuSo ap071105

description: Untreated

value: MELJUSO

value: Skin

value: melanoma


title: 91 MGH-U3

description: Untreated


title: Bx030_024 HG2

description: Untreated

value: Hematopoietic System


title: EA10068_111348

description: Untreated

value: CML


title: MEC1 ghp280606

description: Untreated

value: B-CLL (Chronic Lymphocytic B-Leukemia )


title: EA08079_89055_ME1

description: Untreated


title: MDA-MB-453

description: Untreated

value: Breast

value: metastatic carcinoma Derived from metastatic site:pericardial effusion


title: Bx051b_050 HG2

description: Untreated

value: Metastatic Ductal Carcinoma


title: SBCG2008008-D2S1CO07R

description: Untreated


title: EA08079_80504_MDAMB436

description: Untreated


title: MDAMB 468 ghp101105

description: Untreated

value: adenocarcinoma


title: Bx051b_104 HG2

description: Untreated

value: Adenocarcinoma


title: Bx051b_038 HG2

description: Untreated

value: metastatic carcinoma


title: EA08079_80493_MDAMB453

description: Untreated


title: Bx051b_048 HG2

description: Untreated


title: EA08079_80505_MDAMB468

description: Untreated


title: EA08079_80495_MDAMB361

description: Untreated


title: Bx051b_023 HG2

description: Untreated


title: EA08079_80501_MDAMB157

description: Untreated


title: MDAMB 361 ghp071105

description: Untreated

value: adenocarcinoma Derived from metastatic site:brain


title: Bx051b_020 HG2

description: Untreated


title: Bx058-06 HG2

description: Untreated

value: Brain

value: malignant glioblastoma; glioma; glial cell


title: MDA-MB-231

description: Untreated

value: adenocarcinoma Derived from metastatic site:pleural effusion


title: A1631-03

description: Untreated


title: EA08079_80507_MCF7

description: Untreated


title: Bx051b_101 HG2

description: Untreated


title: SB11010-2_D4S1C0038R_(HG-U133_Plus_2)

description: Untreated

value: Lung

value: SqLC


title: Bx042-017

description: Untreated

value: Colon


title: LS180

description: Untreated

value: colorectal adenocarcinoma


title: MCF7-mdf+

description: Untreated

value: Breast Adenocarcinoma


title: Bx030_017 HG2

description: Untreated

value: Hematopoietic System


title: Bx042-051

description: Untreated


title: MDA-MB-157

description: Untreated

value: medulallary carcinoma