title: Adjacent normal tissue from patient 120

description: Adjacent normal tissue from patient 120

source_name: Adjacent normal tissue from patient 120

value: patient 120


title: HB1.F5

status: Public on Aug 01 2014

type: RNA

city: Suwon

first: Myung Ae

last: Lee

state: Gyeonggi-do

address: Woncheon-dong, Yeongtong-gu

country: South Korea

institute: ajou univ school of medicine 607

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: GeneChip 3.0 software (Affymetrix) was used for scanning and for first pass analysis and generation of raw data cell intensity (.cel) files. Data were subsequently submitted to a relational database for quality control assessment to include RNA quality, GeneChip sensitivity, and process quality determinations. Hierarchical clustering was performed and several distinct functional clusters were identified, including a cluster of genes possessed Nurr1-binding elements in promoter region. Hierarchical clustering using hamming distance correlation of the list of differentially expressed genes was conducted using EisenSoftware (Eisen lab, Lawrence Berkeley National Lab).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Neural Stem cell line(Maternal transcript)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 701021 Rev 5., Affymetrix).

growth_protocol: Immortalized hNSC lines were maintained and passaged on uncoated culture dishes in DMEM with 10% Fetal bovine serum. All cells transduced with pLPCX or pLPC-Nurr1 were maintained in the same culture condition.

extract_protocol: Total RNA was extracted according to the manufacturer’s protocol (Affymetrix).

treatment_protocol: The retroviral vector pLPCX encoding human Nurr1 gene was infected into the PA317 amphotropic packaging cell line. Human NSC lines were infected with a retrovirus encoding human Nurr1 or control. All studies were performed within one week after transduction of retrovirus to avoid shut-down of Nurr1 gene expression in human neural stem cell lines.

tag: cell type

value: Immortalized human neural stem cell

tag: cell line

tag: treatment

value: control


title: pTH5257_ME_8mer_308

type: protein

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

country: USA

institute: Cincinnati Children's Hospital

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: Cebpg_ME design

label_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector, in most cases.  See paper supplemental web site (http://hugheslab.ccbr.utoronto.ca/supplementary-data/CisBP/) for exceptions.

tag: dbd

tag: platform_id_id design

value: ME

tag: dbd source organism


title: HB1.F5-Nurr1

source_name: Human Neural Stem cell line with Nurr1 overexpression

value: Nurr1 overexpression


title: Adjacent normal tissue from patient 108

city: Beijing

first: Jiagen

last: Li

address: 17 Panjiayuannanli Chaoyang District

country: China

institute: Cancer Institute, CAMS

description: Adjacent normal tissue from patient 108

hyb_protocol: The labeled RNA was purified and hybridized to miRNA arrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The miRNA array data were analyzed for data summarization, normalization and quality control by using the Percentile Shift (90th percentile) with GeneSpring software V11.5 (Agilent).

source_name: Adjacent normal tissue from patient 108

label_protocol: The extracted RNA were labeled according to the Agilent manufacturer's instructions. Briefly, the miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (100 ng) was dephosphorylated and ligated with pCp-Cy3.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: tissue type

value: Adjacent normal tissue

tag: patient

value: patient 108


title: pTH5257_HK_8mer_1305

source_name: Cebpg_HK design

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

value: HK


title: HB1.F3-Nurr1


title: HB1.F3


city: boston

first: Thorley-Lawson

last: David

state: MA

address: 150 harrison ave

institute: Tufts University

description: Gene expression data from BJAB 24 hour posttransfection with EBV miRNA BART 18-5p

hyb_protocol: Hybridization was perfomred at Genetic Analysis Platform in Broad Institute of Massachusetts Institute of Technology

scan_protocol: Scanning was perfomred at Genetic Analysis Platform in Broad Institute of Massachusetts Institute of Technology

data_processing: The data were analyzed with dChip using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Lymphoma cell line BJAB transfected with  EBV miRNA BART 18-5p, biological rep2

label_protocol: Labelling was perfomred at Genetic Analysis Platform in Broad Institute of Massachusetts Institute of Technology

growth_protocol: Burkitt's lymphoma cell lines BL2 and BJAB were maintained in RPMI 1640 medium with 10% fetal bovine serum (FBS), 2 mM sodium pyruvate, 2 mM glutamine, and 100 IU of penicillin-streptomycin

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, except that the precipitation of RNA pellet was done by using 100% ethanol at -20 degree overnight instead of isopropanol.

treatment_protocol: Synthetic miRNA mimics were purchased from Thermo scientific. EBV 18-5p miRNA mimic mature sequence is 5’-UCAAGUUCGCACUUCCUAUACA-3’. Mimic negative control #1 (MC) is based on C. elegan’s cel-miR-67 and the mature sequence is 5’-UCACAACCUCCUAGAAAGAGUAGA-3’. 100 pmol miRNA mimics were transfected into 2.5x 106 cells using an Amaxa nucleofector (Lonza), the V kit solution, and program C-009. Cells were harvested at 24 hr posttransfection, rinsed with DPBS, spun and resuspened in the Trizol solution (Invitrogen) on ice.

value: BJAB

value: Burkitt's lymphoma-derived B cell

tag: tissue

value: blood

tag: developmental stage

value: neonatal


title: pTH5253_ME_8mer_2505

source_name: Cebpe_ME design


title: Cancer tissue from patient 122

description: Cancer tissue from patient 122

source_name: Cancer tissue from patient 122

value: Cancer tissue

value: patient 122

tag: dataset

value: training

tag: age

tag: gender

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: family history

value: negative

tag: tumor location

value: upper

tag: tumor grade

value: poorly

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: status

value: dead


title: pTH5250_ME_8mer_437

source_name: Cebpd_ME design

tag: dbd

tag: platform_id_id design

value: ME

tag: dbd source organism


title: DC_Control_0h_R2

city: London

first: Raphael

last: Zollinger

state: London

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute (QMUL)

description: Sorted Dendritic Cells from healthy human blood

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: Data normalised in R using default settinsg of GCRMA package

source_name: freshly purified sample (Control_0h)

label_protocol: Affymetrix double amplification

growth_protocol: After purification, cells where either lysed immediatlely or cultured for 6h in RPMI (Gibco) medium containing 10% FBS (Hyclone) at 37 degree Celsius and 5% CO2 containing environment.

extract_protocol: Qiagen Rneasy microkit with on-column DNAse digestion.

treatment_protocol: Treatment stimuli were given from the start of culture.

tag: tissue type

tag: cell type

value: dendritic cells


title: Cancer tissue from patient 148

description: Cancer tissue from patient 148

source_name: Cancer tissue from patient 148

tag: patient

value: patient 148

tag: dataset

value: test

value: no

value: positive

value: middle

value: well


title: pTH5253_HK_8mer_2537

source_name: Cebpe_HK design

value: HK


title: Cancer tissue from patient 120

description: Cancer tissue from patient 120

source_name: Cancer tissue from patient 120

value: Cancer tissue

value: patient 120

tag: age

tag: gender

value: moderately

value: III


source_name: Lymphoma cell line BJAB transfected with  EBV miRNA BART 18-5p, biological rep1

tag: cell line

value: BJAB

value: Burkitt's lymphoma-derived B cell

tag: tissue

value: blood

tag: developmental stage

value: neonatal


description: Gene expression data from BJAB 24 hour posttransfection with EBV miRNA BART 10

source_name: Lymphoma cell line BJAB transfected with  EBV miRNA BART 10, biological rep2


title: pTH5250_HK_8mer_1295

source_name: Cebpd_HK design


description: Gene expression data from BJAB 24 hour posttransfection with EBV miRNA BART 14*

source_name: Lymphoma cell line BJAB transfected with  EBV miRNA BART 14*, biological rep1


title: pTH5169_HK_8mer_536

source_name: Arid3a_HK design

value: ARID


title: pTH5169_ME_8mer_225

source_name: Arid3a_ME design

value: ME


source_name: Lymphoma cell line BJAB transfected with  EBV miRNA BART 14*, biological rep2


title: pTH5168_HK_8mer_535

source_name: DDB_G0275333_HK design


source_name: Lymphoma cell line BJAB transfected with  EBV miRNA BART 10, biological rep1


title: Cancer tissue from patient 108

description: Cancer tissue from patient 108

source_name: Cancer tissue from patient 108

value: patient 108

value: training

value: female

tag: tobacco use

tag: alcohol use

tag: family history

value: negative

tag: tumor location

value: upper

tag: tumor grade

value: poorly

value: dead


title: Cancer tissue from patient 119

description: Cancer tissue from patient 119

source_name: Cancer tissue from patient 119

value: Cancer tissue

value: patient 119

value: no

value: middle

value: well

tag: t stage

tag: n stage

tag: tnm stage

tag: status


title: Adjacent normal tissue from patient 80

description: Adjacent normal tissue from patient 80

source_name: Adjacent normal tissue from patient 80

tag: tissue type

value: Adjacent normal tissue

value: patient 80


title: Adjacent normal tissue from patient 81

description: Adjacent normal tissue from patient 81

source_name: Adjacent normal tissue from patient 81

tag: patient

value: patient 81


title: pTH5168_ME_8mer_223

source_name: DDB_G0275333_ME design

tag: dbd

value: ARID

tag: platform_id_id design

tag: dbd source organism


description: Gene expression data from BJAB 24 hour posttransfection with MC

source_name: Lymphoma cell line BJAB transfected with MC, biological rep1

tag: cell line

value: BJAB

tag: cell type

value: Burkitt's lymphoma-derived B cell

value: blood

value: neonatal


source_name: Lymphoma cell line BJAB transfected with MC, biological rep2

tag: tissue

tag: developmental stage


title: pTH5164_ME_8mer_2290

source_name: Olig3_ME design

value: HLH

value: ME


title: pTH5166_ME_8mer_371

source_name: Cebpa_ME design


title: pTH5166_HK_8mer_1586

source_name: Cebpa_HK design

value: HK


title: Adjacent normal tissue from patient 68

description: Adjacent normal tissue from patient 68

source_name: Adjacent normal tissue from patient 68

value: patient 68


title: Adjacent normal tissue from patient 30

description: Adjacent normal tissue from patient 30

source_name: Adjacent normal tissue from patient 30

value: patient 30


title: pTH5164_HK_8mer_2164

source_name: Olig3_HK design


title: Cancer tissue from patient 80

description: Cancer tissue from patient 80

source_name: Cancer tissue from patient 80

value: Cancer tissue

tag: dataset

value: training

tag: age

tag: gender

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: positive

value: upper

value: III

value: dead


title: Cancer tissue from patient 68

description: Cancer tissue from patient 68

source_name: Cancer tissue from patient 68

value: test

tag: family history

value: negative

tag: tumor location

tag: tumor grade

value: poorly

tag: t stage

tag: n stage


title: pTH5161_ME_8mer_239

source_name: Srebf1_ME design

tag: dbd


description: Gene expression data from BL2 24 hour posttransfection with EBV miRNA BART 10

source_name: Lymphoma cell line BL2 transfected with EBV miRNA BART 10, biological rep2

value: Burkitt's lymphoma-derived B cell

value: blood


description: Gene expression data from BL2 24 hour posttransfection with EBV miRNA BART 14*

source_name: Lymphoma cell line BL2 transfected with EBV miRNA BART 14*, biological rep2


title: Cancer tissue from patient 30

description: Cancer tissue from patient 30

source_name: Cancer tissue from patient 30

tag: tissue type

tag: patient

value: middle

tag: tnm stage

tag: status


title: BL2 transfected with mimic control (MC), biological rep2

description: Gene expression data from BL2 24 hour posttransfection with MC

source_name: Lymphoma cell line BL2 transfected with MC, biological rep2

tag: cell line

tag: cell type

tag: tissue


source_name: Lymphoma cell line BL2 transfected with EBV miRNA BART 14*, biological rep1


source_name: Lymphoma cell line BL2 transfected with EBV miRNA BART 10, biological rep1


title: Cancer tissue from patient 81

description: Cancer tissue from patient 81

source_name: Cancer tissue from patient 81

value: patient 81

tag: dataset

tag: age

value: lower

value: II


title: pTH5159_ME_8mer_504

source_name: Arnt2_ME design

value: HLH

tag: platform_id_id design

value: ME

tag: dbd source organism


title: pTH5161_HK_8mer_1588

source_name: Srebf1_HK design

value: HK


title: Adjacent normal tissue from patient 29

description: Adjacent normal tissue from patient 29

source_name: Adjacent normal tissue from patient 29

value: Adjacent normal tissue

value: patient 29


title: BL2 transfected with  mimic control (MC), biological rep1

source_name: Lymphoma cell line BL2 transfected with MC, biological rep1


title: pTH5128_ME_8mer_1023

source_name: 21.m00216_ME design

value: ARID


title: Adjacent normal tissue from patient 288

description: Adjacent normal tissue from patient 288

source_name: Adjacent normal tissue from patient 288

value: patient 288


title: Adjacent normal tissue from patient 287

description: Adjacent normal tissue from patient 287

source_name: Adjacent normal tissue from patient 287

value: patient 287


description: Gene expression data from BL2 24 hour posttransfection with EBV miRNA BART 18-5p

source_name: Lymphoma cell line BL2 transfected with EBV miRNA BART 18-5p, biological rep2


title: Adjacent normal tissue from patient 285

description: Adjacent normal tissue from patient 285

source_name: Adjacent normal tissue from patient 285

value: patient 285


title: pTH5159_HK_8mer_1304

source_name: Arnt2_HK design


source_name: Lymphoma cell line BL2 transfected with EBV miRNA BART 18-5p, biological rep1


title: EJ cells control rep3

city: Sheffield

first: James

middle: WF

last: Catto

address: Beech Hill Road

department: School of Medicine

institute: University of Sheffield

description: PUV 1.3

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus 2 GeneChip in a hybridization solution according to the Affymetrix protocol. hybridization took place overnight in a rotating hybridization platform at 45°C for 16 hours. Post hybridization stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

source_name: EJ Bladder cancer cells, transfected with empty pUC19 vector

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

growth_protocol: Cells were grown in DMEM+10% FCS

extract_protocol: Extracted with mIRvana kit (Ambion)

treatment_protocol: 90mm dish of EJ Bladder cancel cells at 70% conf transfected with 24ug DNA + Lipofectamine 2000

value: EJ Bladder cancer cells

tag: transfected with

value: pUC19 (Empty)


title: Cancer tissue from patient 29

description: Cancer tissue from patient 29

source_name: Cancer tissue from patient 29

value: Cancer tissue

value: test

tag: gender

value: male

tag: tobacco use

value: no

tag: alcohol use

value: yes

tag: family history

value: negative

tag: tumor location

value: well

value: III

value: survival


title: pTH5128_HK_8mer_534

source_name: 21.m00216_HK design

tag: dbd

value: HK


title: pTH5124_HK_8mer_532

source_name: GSPATP00004674001_HK design


title: pTH5124_ME_8mer_217

source_name: GSPATP00004674001_ME design

value: ME


title: EJ cells control rep1

description: PUV 1.1


title: pTH5122_ME_8mer_215

source_name: e_gw.4.260.1_ME design

value: ARID


title: Cancer tissue from patient 288

description: Cancer tissue from patient 288

source_name: Cancer tissue from patient 288

tag: tissue type

tag: patient

value: patient 288

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

value: dead


title: pTH5122_HK_8mer_6167

source_name: e_gw.4.260.1_HK design


title: EJ cells FOXA1 rep3

description: FOX 1.3

source_name: EJ Bladder cancer cells, transfected with FOXA1 construct

tag: cell line

value: EJ Bladder cancer cells


title: Cancer tissue from patient 287

description: Cancer tissue from patient 287

source_name: Cancer tissue from patient 287

value: Cancer tissue

value: patient 287

tag: dataset

value: training

value: positive

tag: tnm stage

value: II

tag: status


title: Cancer tissue from patient 285

description: Cancer tissue from patient 285

source_name: Cancer tissue from patient 285

value: patient 285

tag: age

value: female

value: no

value: negative


title: Adjacent normal tissue from patient 284

description: Adjacent normal tissue from patient 284

source_name: Adjacent normal tissue from patient 284

value: Adjacent normal tissue

value: patient 284


title: Adjacent normal tissue from patient 281

description: Adjacent normal tissue from patient 281

source_name: Adjacent normal tissue from patient 281

value: patient 281


title: Adjacent normal tissue from patient 280

description: Adjacent normal tissue from patient 280

source_name: Adjacent normal tissue from patient 280

value: patient 280


title: pTH5121_ME_8mer_210

source_name: Arid5a_ME design

value: ARID

tag: platform_id_id design

value: ME

tag: dbd source organism


title: EJ cells control rep2

description: PUV 1.2

tag: transfected with

value: pUC19 (Empty)


title: Cancer tissue from patient 284

description: Cancer tissue from patient 284

source_name: Cancer tissue from patient 284

tag: gender

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: middle

value: moderately

value: I

value: dead


title: Cancer tissue from patient 281

description: Cancer tissue from patient 281

source_name: Cancer tissue from patient 281

value: Cancer tissue

value: training

tag: family history

tag: tumor location

value: III


title: Adjacent normal tissue from patient 279

description: Adjacent normal tissue from patient 279

source_name: Adjacent normal tissue from patient 279

tag: tissue type

tag: patient

value: patient 279


title: EJ cells FOXA1 rep1

description: FOX 1.1

value: EJ Bladder cancer cells


title: Cancer tissue from patient 279

description: Cancer tissue from patient 279

source_name: Cancer tissue from patient 279

value: negative

tag: tumor grade

tag: t stage

value: II

value: survival


title: pTH5120_HK_8mer_333

source_name: zgc:158706_HK design

tag: dbd

value: ARID

value: HK


title: EJ cells FOXA1 rep2

description: FOX 1.2

tag: cell line


title: pTH5121_HK_8mer_531

source_name: Arid5a_HK design


title: Adjacent normal tissue from patient 277

description: Adjacent normal tissue from patient 277

source_name: Adjacent normal tissue from patient 277

value: Adjacent normal tissue

value: patient 277


title: pTH5118_ME_8mer_212

source_name: cfi-1_ME design

value: ME


title: pTH5119_ME_8mer_410

source_name: retn_ME design


title: pTH5118_HK_8mer_331

source_name: cfi-1_HK design


title: Adjacent normal tissue from patient 275

description: Adjacent normal tissue from patient 275

source_name: Adjacent normal tissue from patient 275

value: patient 275


title: Adjacent normal tissue from patient 274

description: Adjacent normal tissue from patient 274

source_name: Adjacent normal tissue from patient 274

value: patient 274


title: Adjacent normal tissue from patient 273

description: Adjacent normal tissue from patient 273

source_name: Adjacent normal tissue from patient 273

value: patient 273


title: pTH5117_HK_8mer_330

source_name: DGIL_AUG5s5606g1t1_HK design


title: pTH5120_ME_8mer_214

source_name: zgc:158706_ME design


title: pTH5119_HK_8mer_530

source_name: retn_HK design


title: pTH5117_ME_8mer_428

source_name: DGIL_AUG5s5606g1t1_ME design


title: pTH5112_HK_8mer_1364

source_name: Msc_HK design

value: HLH


title: Cancer tissue from patient 280

description: Cancer tissue from patient 280

source_name: Cancer tissue from patient 280

value: Cancer tissue

value: patient 280

tag: dataset

value: male

value: yes

value: no

value: middle

value: moderately

tag: n stage

tag: tnm stage


title: pTH5111_ME_8mer_503

source_name: Arnt_ME design

tag: platform_id_id design


title: Cancer tissue from patient 275

description: Cancer tissue from patient 275

source_name: Cancer tissue from patient 275

value: test

tag: age

value: negative

value: II

tag: status

value: dead


title: Cancer tissue from patient 274

description: Cancer tissue from patient 274

source_name: Cancer tissue from patient 274

tag: gender

value: lower

value: I

value: survival


title: Cancer tissue from patient 277

description: Cancer tissue from patient 277

source_name: Cancer tissue from patient 277

value: patient 277

value: female

tag: tobacco use

value: poorly

value: III


title: Adjacent normal tissue from patient 269

description: Adjacent normal tissue from patient 269

source_name: Adjacent normal tissue from patient 269

value: Adjacent normal tissue

value: patient 269


title: pTH5108_HK_8mer_1303

source_name: Fosl2_HK design

value: HK

tag: dbd source organism


title: Cancer tissue from patient 273

description: Cancer tissue from patient 273

source_name: Cancer tissue from patient 273

value: Cancer tissue

value: patient 273

value: male

value: yes

tag: alcohol use

tag: family history

value: positive


title: pTH5111_HK_8mer_1302

source_name: Arnt_HK design

value: HLH


title: Adjacent normal tissue from patient 266

description: Adjacent normal tissue from patient 266

source_name: Adjacent normal tissue from patient 266

tag: tissue type

value: patient 266


title: pTH5112_ME_8mer_231

source_name: Msc_ME design

value: ME


title: pTH5108_ME_8mer_2509

source_name: Fosl2_ME design


title: pTH5102_ME_8mer_263

source_name: Hey2_ME design


title: pTH5105_HK_8mer_1363

source_name: Figla_HK design


title: pTH5102_HK_8mer_1596

source_name: Hey2_HK design


title: Adjacent normal tissue from patient 264

description: Adjacent normal tissue from patient 264

source_name: Adjacent normal tissue from patient 264

tag: patient

value: patient 264


title: pTH5105_ME_8mer_228

source_name: Figla_ME design


title: pTH5101_ME_8mer_207

source_name: Tcf4_ME design


title: pTH5101_HK_8mer_1582

source_name: Tcf4_HK design


title: 3D_4

city: Basel

first: Sophie

last: Brachat

address: Novartis Campus

department: Muskuloskeletal

country: Switzerland

institute: Novartis Institutes For Biomedical Research

hyb_protocol: Affymetrix Hybridization control kit (including B2)

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization followed by 2% trimmed mean scaling. Probesets with scaled RMA values below 50 in all groups were filtered out

label: FL cDNA Biotin Module V2

source_name: Tibialis anterior muscle

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2

extract_protocol: Total cellular RNA (40ug) was extracted from 2D or 3D-perfusion expanded CD45- cells, obtained from 5 independent experiments/donors, using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer.

treatment_protocol: Nucleated cells were isolated from human bone marrow aspirates by means of red blood cells lyses buffer (pH 7.2) containing 0.15M NH4CL, 1mM KHCO3 (both from Sigma, Switzerland) and 0.1mM Na2EDTA (Fluka, Switzerland). Nucleated cells were then seeded into a 3D-perfusion bioreactor system using a pure hydroxyapatite ceramic scaffold and in conventional Petri dishes (2D). Cells from both systems were cultured for 19 days using an alpha-Modified Eagle’s Medium supplemented with 10% fetal bovine serum (FBS), 10mM HEPES buffer, 1mM sodium pyruvate, 10000U/ml penicillin and 10000ug/ml streptomycin (all from GIBCO, Switzerland), 5ng/ml fibroblast growth factor-2 (FGF-2, R&D systems, Europe), 10 nM dexamethasone and 0.1 mM L-ascorbic acid-2-phosphate (both from Sigma, Switzerland). After 19 days of culture, 3D-perfusion expanded cells were extracted by substituting the culture medium with a solution of 0.3% collagenase (collagenase) and perfusing the ceramic constructs for 40min followed by 0.05% trypsin/0.53 mM EDTA solution (trypsin) for additional 15 min both at 400 μm per second. 2D-expanded cells were retrieved by using the same enzymatic solutions, i.e. collagenase for 40min and trypsin for 5min.  Extracted cells from both 3D-perfusion and 2D systems were subsequently sorted using anti-CD45-coated magnetic beads (Miltenyi Biotec, Auburn, CA), according to the manufacturer’s instructions.

tag: culture


title: pTH5099_ME_8mer_501

source_name: Myf6_ME design


title: 3D_3


title: 3D_5


title: Cancer tissue from patient 266

description: Cancer tissue from patient 266

source_name: Cancer tissue from patient 266

value: test

value: negative

tag: tumor location

value: middle

tag: tumor grade

value: moderately

tag: t stage

value: II

value: dead


title: Cancer tissue from patient 265

description: Cancer tissue from patient 265

source_name: Cancer tissue from patient 265

value: patient 265

tag: dataset

value: training

value: survival


title: Cancer tissue from patient 269

description: Cancer tissue from patient 269

source_name: Cancer tissue from patient 269

value: Cancer tissue

value: patient 269

value: poorly

tag: n stage

value: III


title: Adjacent normal tissue from patient 265

description: Adjacent normal tissue from patient 265

source_name: Adjacent normal tissue from patient 265

value: Adjacent normal tissue


title: Adjacent normal tissue from patient 262

description: Adjacent normal tissue from patient 262

source_name: Adjacent normal tissue from patient 262

value: patient 262


title: Cancer tissue from patient 264

description: Cancer tissue from patient 264

source_name: Cancer tissue from patient 264

value: male

value: no

tag: tnm stage


title: 3D_1


title: 2D_4


title: 3D_2


title: Adjacent normal tissue from patient 260

description: Adjacent normal tissue from patient 260

source_name: Adjacent normal tissue from patient 260

value: patient 260


title: pTH5098_HK_8mer_1193

source_name: Mafg_HK design

tag: dbd

tag: platform_id_id design

value: HK


title: 2D_5


title: pTH5099_HK_8mer_1280

source_name: Myf6_HK design

value: HLH


title: Adjacent normal tissue from patient 259

description: Adjacent normal tissue from patient 259

source_name: Adjacent normal tissue from patient 259

value: patient 259


title: 2D_1


title: pTH5098_ME_8mer_205

source_name: Mafg_ME design

value: ME


title: pTH5083_HK_8mer_1192

source_name: Atf2_HK design


title: pTH5087_ME_8mer_2499

source_name: Tcf21_ME design


title: pTH5087_HK_8mer_1342

source_name: Tcf21_HK design


title: pTH5083_ME_8mer_427

source_name: Atf2_ME design


title: 2D_2

source_name: Tibialis anterior muscle


title: 2D_3


title: Cancer tissue from patient 261

description: Cancer tissue from patient 261

source_name: Cancer tissue from patient 261

value: patient 261

tag: age

value: yes

value: negative

value: middle

value: moderately

tag: status

value: dead


title: Adjacent normal tissue from patient 261

description: Adjacent normal tissue from patient 261

source_name: Adjacent normal tissue from patient 261


title: 38_HPX_1

city: Boston

first: Patricia

last: Maiso

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from hypoxic cells.

hyb_protocol: The cRNA is hybridized to a microarray chip. The bound cRNA is stained with fluorescent streptavidin.

scan_protocol: The microarray chip is then scanned using a laser, and the positions and intensities of the fluorescent emissions are captured. These measurements provide the basis of subsequent biostatistical analysis.

data_processing: The data were analyzed using d-Chip software.

source_name: MM1S Hypoxia

label_protocol: RNA of interest is converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen).

treatment_protocol: Hypoxic exposure for 24 hours.

tag: cell line

tag: condition

value: hypoxia


title: Cancer tissue from patient 259

description: Cancer tissue from patient 259

source_name: Cancer tissue from patient 259

value: Cancer tissue

value: test

tag: gender

value: female

tag: tobacco use

tag: alcohol use

value: III


title: pTH5082_HK_8mer_1293

source_name: Nfil3_HK design

tag: dbd source organism


title: Adjacent normal tissue from patient 258

description: Adjacent normal tissue from patient 258

source_name: Adjacent normal tissue from patient 258

tag: tissue type

value: Adjacent normal tissue

tag: patient

value: patient 258


title: Cancer tissue from patient 262

description: Cancer tissue from patient 262

source_name: Cancer tissue from patient 262

value: patient 262

value: no

tag: family history

value: positive

tag: tumor location

tag: tumor grade

value: II


title: Adjacent normal tissue from patient 256

description: Adjacent normal tissue from patient 256

source_name: Adjacent normal tissue from patient 256

value: patient 256


title: Adjacent normal tissue from patient 253

description: Adjacent normal tissue from patient 253

source_name: Adjacent normal tissue from patient 253

value: patient 253


title: Cancer tissue from patient 260

description: Cancer tissue from patient 260

source_name: Cancer tissue from patient 260

value: patient 260

tag: dataset

value: training

value: negative

value: well

tag: t stage

tag: n stage


title: pTH5081_ME_8mer_187

source_name: Atf7_ME design

tag: dbd

tag: platform_id_id design

value: ME


title: 35_HPX_0

value: hypoxia


title: pTH5082_ME_8mer_188

source_name: Nfil3_ME design


title: 39_HPX_2


title: pTH5081_HK_8mer_1187

source_name: Atf7_HK design

value: HK


title: pTH5078_HK_8mer_1189

source_name: Tef_HK design


title: pTH5080_ME_8mer_358

source_name: Creb1_ME design


title: 36_NMX_1

description: Gene expression data from normoxic cells.

source_name: MM1S Normoxia

value: normoxia


title: pTH5080_HK_8mer_1581

source_name: Creb1_HK design


title: 37_NMX_2


title: Adjacent normal tissue from patient 251

description: Adjacent normal tissue from patient 251

source_name: Adjacent normal tissue from patient 251

value: patient 251


title: esophageal squamous cell carcinoma_responder_biological rep11

city: Guangzhou

first: Jing

last: Wen

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description:
BH12036-3_122_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on the GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in in a Fluidics Station 450 (Affymetrix).

scan_protocol: The array was scanned on GeneChip Scanner 3000 (Affymetrix)

data_processing: Genespring 12.0 (Agilent technologies) was used to analyze the microarray data. The microarray data were processed using the MAS5.0 summarization algorithm without baseline transformation.

source_name: ESCC from patient responsing to preoperative chemoradiotherapy (CRT)

label_protocol: Biotin-labeled cRNA was in vitro transcribed from the cDNA, which was reverse-transcribed from RNA, using the 3' IVT Express Kit (Affymetrix).

growth_protocol: Patients were eligible in the study if they fulfill all of the following criteria: with Stage IIB-III squamous cell carcinoma of the thoracic esophagus according to the 6th AJCC Cancer Staging which were potentially resectable; no previous anticancer-treatment; an age range from 18 to 70 years; a Karnofsky performance status (KPS) of 90 or more; and medical fitness for surgery. ; and approval for tissue collection during the diagnostic endoscopic procedure.

extract_protocol: Total RNA were isolated using mirVana miRNA Isolation Kit (Ambion) according to the manufacture's instruction.

treatment_protocol: For the 28 patients who received preoperative chemoradiotherapy composed of vinorelbine and cisplatin and subsequent surgical resection, tumor tissues were collected during preoperative endoscopy. Normal esophageal epithelia of 10 stage IIB-III ESCC patients receiving surgery alone were collected at surgery. All the tissue specimens were snap frozen in liquid nitrogen and stored at -80℃ until use.

tag: age

value: male

tag: tissue

value: esophageal squamous cell carcinoma (ESCC)

tag: tumor stage

tag: pathological response to crp

value: pathological complete response


title: Cancer tissue from patient 258

description: Cancer tissue from patient 258

source_name: Cancer tissue from patient 258

value: Cancer tissue

value: patient 258

tag: gender

value: female

tag: tobacco use

value: no

value: middle

value: poorly

tag: tnm stage

tag: status

value: dead


title: esophageal squamous cell carcinoma_responder_biological rep10

description:
BH12036-3_120_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy


title: Cancer tissue from patient 256

description: Cancer tissue from patient 256

source_name: Cancer tissue from patient 256

tag: tissue type

tag: patient

value: patient 256

value: training

value: yes

tag: alcohol use

value: negative

value: lower

value: moderately

value: III


title: pTH5078_ME_8mer_513

source_name: Tef_ME design

value: ME

tag: dbd source organism


title: pTH5077_ME_8mer_425

source_name: Fosl1_ME design


title: esophageal squamous cell carcinoma_responder_biological rep9

description:
BH12036-3_119_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

value: male

value: esophageal squamous cell carcinoma (ESCC)


title: pTH5077_ME_8mer_183


title: esophageal squamous cell carcinoma_responder_biological rep7

description:
BH12036-3_117_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

value: pathological complete response


title: pTH5072_ME_8mer_306

source_name: Tcfeb_ME design

value: HLH


title: pTH5074_HK_8mer_1349

source_name: Atoh1_HK design

value: HK


title: Adjacent normal tissue from patient 226

description: Adjacent normal tissue from patient 226

source_name: Adjacent normal tissue from patient 226

value: Adjacent normal tissue

value: patient 226


title: 34_NMX_0

tag: cell line

tag: condition

value: normoxia


title: Adjacent normal tissue from patient 225

description: Adjacent normal tissue from patient 225

source_name: Adjacent normal tissue from patient 225

value: patient 225


title: esophageal squamous cell carcinoma_responder_biological rep5

description:
BH12036-3_111_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

value: female


title: esophageal squamous cell carcinoma_responder_biological rep4

description:
BH12036-3_108_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy


title: pTH5074_ME_8mer_180

source_name: Atoh1_ME design


title: Cancer tissue from patient 253

description: Cancer tissue from patient 253

source_name: Cancer tissue from patient 253

value: Cancer tissue

value: patient 253

tag: dataset

value: training

value: no

tag: family history

tag: tumor location

value: middle

tag: tumor grade

value: poorly

tag: t stage

tag: n stage

value: II

value: survival


title: Adjacent normal tissue from patient 224

description: Adjacent normal tissue from patient 224

source_name: Adjacent normal tissue from patient 224

value: patient 224


title: Cancer tissue from patient 251

description: Cancer tissue from patient 251

source_name: Cancer tissue from patient 251

value: patient 251

value: test

tag: age

value: male

value: yes

value: negative

value: lower

value: moderately

value: III

value: dead


title: esophageal squamous cell carcinoma_responder_biological rep3

description:
BH12036-3_105_2_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

tag: gender

value: female

tag: tissue

value: esophageal squamous cell carcinoma (ESCC)

tag: tumor stage

tag: pathological response to crp

value: pathological complete response


title: esophageal squamous cell carcinoma_responder_biological rep6

description:
BH12036-3_113_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy


title: Adjacent normal tissue from patient 227

description: Adjacent normal tissue from patient 227

source_name: Adjacent normal tissue from patient 227

tag: tissue type

value: Adjacent normal tissue

value: patient 227


title: pTH5071_ME_8mer_176

source_name: Tcf12_ME design

tag: dbd

value: HLH

tag: platform_id_id design

value: ME


title: pTH5072_HK_8mer_1369

source_name: Tcfeb_HK design

value: HK

tag: dbd source organism


title: esophageal squamous cell carcinoma_responder_biological rep2

description:
BH12036-3_104_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy


title: Cancer tissue from patient 227

description: Cancer tissue from patient 227

source_name: Cancer tissue from patient 227

value: Cancer tissue

tag: patient

value: training

tag: tobacco use

tag: alcohol use

value: no

value: middle

tag: tnm stage

value: II

tag: status

value: survival


title: esophageal squamous cell carcinoma_responder_biological rep1

description:
BH12036-3_31_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

source_name: ESCC from patient responsing to preoperative chemoradiotherapy (CRT)

value: male


title: pTH5068_ME_8mer_173

source_name: Id2_ME design


title: esophageal squamous cell carcinoma_non_responder_biological rep16

description:
BH12036-3_123_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy

source_name: ESCC from patient not responsing to preoperative chemoradiotherapy (CRT)

value: not pathological complete response


title: pTH5070_ME_8mer_175

source_name: Mlx_ME design


title: esophageal squamous cell carcinoma_non_responder_biological rep17

description:
BH12036-3_126_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: pTH5071_HK_8mer_1362

source_name: Tcf12_HK design


title: esophageal squamous cell carcinoma_non_responder_biological rep15

description:
BH12036-3_121_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: Cancer tissue from patient 226

description: Cancer tissue from patient 226

source_name: Cancer tissue from patient 226

value: patient 226

tag: dataset

tag: family history

value: negative

tag: tumor location

tag: tumor grade

value: moderately

value: dead


title: Cancer tissue from patient 225

description: Cancer tissue from patient 225

source_name: Cancer tissue from patient 225

value: patient 225

value: test

tag: age

tag: gender

value: yes

value: lower

tag: t stage

tag: n stage


title: pTH5070_HK_8mer_1361

source_name: Mlx_HK design

value: HLH

value: HK


title: Cancer tissue from patient 224

description: Cancer tissue from patient 224

source_name: Cancer tissue from patient 224

tag: tissue type

value: Cancer tissue

value: patient 224

value: III


title: D10 ΔIDH/ΔKDH 36 hours post invasion

city: University Park

first: Heather

middle: J

last: Painter

state: Pennsylvania

address: Millennium Science Center

department: Biochemistry and Molecular Biology

institute: Penn State University

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2505B Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and dye bias correction.  Princeton University Microarray Database (https://puma.princeton.edu/) was utilized for log2 ratio calculation and data normalization.

organism: Plasmodium falciparum

source_name: D10 ΔIDH/ΔKDH 36h RNA

growth_protocol: P. faciparum wild-type D10 and ΔIDH/ΔKDH highly synchronized parasites were grown under standard culturing conditions

extract_protocol: Starting at 0 hours post invasion, samples were harvested in Trizol for total RNA extraction every 6 hours for 48 hours.

tag: strain

value: D10 ΔIDH/ΔKDH

tag: hours post invasion

source_name: 3D7 Mixed Stage Reference Pool


title: pTH5067_ME_8mer_172

source_name: Tcfap4_ME design

tag: dbd

tag: platform_id_id design

value: ME

tag: dbd source organism


title: D10 ΔIDH/ΔKDH 42 hours post invasion

source_name: D10 ΔIDH/ΔKDH 42h RNA

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: pTH5065_HK_8mer_1356

source_name: Tcfec_HK design


title: D10 ΔIDH/ΔKDH 24 hours post invasion

source_name: D10 ΔIDH/ΔKDH 24h RNA


title: esophageal squamous cell carcinoma_non_responder_biological rep13

description:
BH12036-3_114_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy

value: male

tag: tissue

value: esophageal squamous cell carcinoma (ESCC)

tag: tumor stage

tag: pathological response to crp


title: pTH5067_HK_8mer_1300

source_name: Tcfap4_HK design


title: esophageal squamous cell carcinoma_non_responder_biological rep10

description:
BH12036-3_107_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy

value: not pathological complete response


title: esophageal squamous cell carcinoma_non_responder_biological rep12

description:
BH12036-3_110_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: pTH5064_HK_8mer_1360

source_name: Arntl_HK design


title: esophageal squamous cell carcinoma_non_responder_biological rep14

description:
BH12036-3_115_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: D10 ΔIDH/ΔKDH 30 hours post invasion

source_name: D10 ΔIDH/ΔKDH 30h RNA


title: D10 ΔIDH/ΔKDH 18 hours post invasion

source_name: D10 ΔIDH/ΔKDH 18h RNA


title: D10 ΔIDH/ΔKDH 6 hours post invasion

source_name: D10 ΔIDH/ΔKDH 6h RNA


title: D10 ΔIDH/ΔKDH 12 hours post invasion

source_name: D10 ΔIDH/ΔKDH 12h RNA


title: pTH5064_ME_8mer_169

source_name: Arntl_ME design


title: pTH5059_ME_8mer_164

source_name: Hes1_ME design


title: pTH5060_HK_8mer_1308

source_name: Bhlhe41_HK design


title: pTH5065_ME_8mer_170

source_name: Tcfec_ME design


title: esophageal squamous cell carcinoma_non_responder_biological rep11

description:
BH12036-3_109_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy

source_name: ESCC from patient not responsing to preoperative chemoradiotherapy (CRT)


title: esophageal squamous cell carcinoma_non_responder_biological rep6

description:
BH12036-3_79_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: pTH5060_ME_8mer_166

source_name: Bhlhe41_ME design


title: D10 ΔIDH/ΔKDH 0 hours post invasion

source_name: D10 ΔIDH/ΔKDH 0h RNA

source_name: 3D7 Mixed Stage Reference Pool


title: esophageal squamous cell carcinoma_non_responder_biological rep8

description:
BH12036-3_103_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: esophageal squamous cell carcinoma_non_responder_biological rep7

description:
BH12036-3_102_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: esophageal squamous cell carcinoma_non_responder_biological rep9

description:
BH12036-3_106_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy

value: female


title: Wildtype 24 hours post invasion

source_name: D10 24h RNA

value: D10 wild-type


title: esophageal squamous cell carcinoma_non_responder_biological rep5

description:
BH12036-3_28_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: pTH5058_ME_8mer_163

source_name: Sohlh2_ME design


title: Wildtype 30 hours post invasion

source_name: D10 30h RNA


title: pTH5059_HK_8mer_1368

source_name: Hes1_HK design


title: Wildtype 36 hours post invasion

source_name: D10 36h RNA


title: pTH5058_HK_8mer_1343

source_name: Sohlh2_HK design


title: pTH5057_ME_8mer_162

source_name: Tcfe3_ME design


title: Wildtype 42 hours post invasion

source_name: D10 42h RNA


title: esophageal squamous cell carcinoma_non_responder_biological rep4

description:
BH12036-3_26_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: esophageal squamous cell carcinoma_non_responder_biological rep2

description:
BH12036-3_18_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: pTH5057_HK_8mer_1600

source_name: Tcfe3_HK design


title: esophageal squamous cell carcinoma_non_responder_biological rep1

description:
BH12036-3_11_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: esophageal squamous cell carcinoma_non_responder_biological rep3

description:
BH12036-3_21_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy


title: pTH5056_ME_8mer_128

source_name: Clock_ME design


title: Wildtype 12 hours post invasion

source_name: D10 12h RNA


title: esophageal squamous cell carcinoma_responder_biological rep8

description:
BH12036-3_118_(HG-U133_Plus_2)
Gene expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

source_name: ESCC from patient responsing to preoperative chemoradiotherapy (CRT)

value: pathological complete response


title: pTH5056_HK_8mer_1359

source_name: Clock_HK design


title: normal esophageal epithelia_biological rep10

description:
BH12036-3_580_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients

source_name: normal esophageal epithelium from patient with esophageal squmaous cell carcinoma

value: normal esophageal epithelium


title: Wildtype 18 hours post invasion

source_name: D10 18h RNA


title: Wildtype 6 hours post invasion

source_name: D10 6h RNA


title: Wildtype 0 hours post invasion

source_name: D10 0h RNA

source_name: 3D7 Mixed Stage Reference Pool


title: pTH5033_ME_8mer_127

source_name: Twist2_ME design


title: normal esophageal epithelia_biological rep9

description:
BH12036-3_15_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: normal esophageal epithelia_biological rep6

description:
BH12036-3_11_2_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: pTH5033_HK_8mer_2214

source_name: Twist2_HK design


title: normal esophageal epithelia_biological rep5

description:
BH12036-3_6_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: normal esophageal epithelia_biological rep7

description:
BH12036-3_12_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: pTH5024_ME_8mer_126

source_name: Creb3l2_ME design


title: pTH5018_HK_8mer_1351

source_name: Atf3_HK design


title: normal esophageal epithelia_biological rep8

description:
BH12036-3_13_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: pTH5018_ME_8mer_2295

source_name: Atf3_ME design


title: 315K

city: Columbus

first: David

middle: Jingxin

last: Wang

state: Ohio

department: Comprehensive Cancer Center

institute: The Ohio State University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: dCHIP. Log2 ratios are available on the series level.

organism: Mus musculus

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

growth_protocol: DMEM + 10%FBS

extract_protocol: Trizol total RNA isolation

treatment_protocol: p65+/+ and p65-/- MEFs were infected with pBabe-HRASG12V-Hygro to make p65+/+Ras and p65-/-Ras cells. Then p65+/+Ras or p65-/-Ras cells were injected into SCID mice. After tumor appearance, tumors were removed and put back into culture after collagenase treatment and selected with Hygromycin for 2 weeks. Then total RNA were isolated from cells before or after tumor formation

tag: cell type

value: MEF

tag: genotype


title: 315R


title: normal esophageal epithelia_biological rep2

description:
BH12036-3_2_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: normal esophageal epithelia_biological rep4

description:
BH12036-3_4_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: normal esophageal epithelia_biological rep1

description:
BH12036-3_1_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: pTH5005_HK_8mer_2534

source_name: Atf1_HK design


title: normal esophageal epithelia_biological rep3

description:
BH12036-3_3_(HG-U133_Plus_2)
Gene expression data from normal esophageal epithelia of esophageal squamous cell carcinoma patients


title: pTH5019_HK_8mer_1190

source_name: Xbp1_HK design


title: pTH5068_HK_8mer_1365

source_name: Id2_HK design


title: 36K


title: pTH5019_ME_8mer_122

source_name: Xbp1_ME design


title: pTH5005_ME_8mer_2502

source_name: Atf1_ME design


title: pTH5024_HK_8mer_1186

source_name: Creb3l2_HK design


title: 36R


title: Index, patient2

city: Riyadh

first: Dilek

last: Colak

address: MBC03, PO Box 3354

department: Biostatistics, Epidemiology and Scientific Computing

country: Saudi Arabia

institute: KFSHRC

description: Gene expression data from index patient.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed in the Affymetrix automated fluidic station.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 G7 scanner.

data_processing: The open source R/Bioconductor packages (Fred Hutchinson Cancer Research Center, Seattle, WA, USA) were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. High-level analyses were performed using MEV and PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.

source_name: Affected

label_protocol: cDNA and biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

growth_protocol: Whole blood from affecteds and controls according to protocols approved by the institutional review board.

extract_protocol: The Paxgene Blood RNA kit was used for total RNA isolation according to the manufacturer's instructions.

value: whole blood

tag: disease state

value: global developmental delay and autistic features


title: Index, patient1


title: pTH5002_ME_8mer_417

source_name: Crem_ME design


title: Oct4 positive Klf4 positive EpCAM negative MEFs

city: Stanford

first: Yury

last: Goltsev

address: 3220 CCRS, Baxter lab,

department: Department of Microbiology and Immunology

institute: Stanford Medical School

description: RNA from fixed permeablized stained and sorted MEFs

hyb_protocol: Following fragmentation, 5 ug of amplified DNA were hybridized for 16 hr at 45C on HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

data_processing: The data were analyzed by RMA-express software using original cdf file (Mouse430_2.cdf)

label_protocol: Biotinylated amplified cDNA was prepared according to Ovation Pico WTA kit (NuGEN)

extract_protocol: RNA was isolated from fixed permeabilized stained and sorted cells by protocol descrived in accompanying manuscript, RecoverALL (Ambion)


title: pTH4588_ME_8mer_159

source_name: Mnt_ME design

value: HLH


title: Oct4 positive Klf4 negative MEFs

source_name: Oct4 positive Klf4 negative MEFs

value: Oct4 positive Klf4 negative MEFs


title: pTH4582_HK_8mer_1297

source_name: Bhlha15_HK design

value: HK


title: Control, biological rep12

description: Gene expression data from normal control.

source_name: Control

value: healthy


title: Control, biological rep9


title: pTH5002_HK_8mer_1307

source_name: Crem_HK design


title: pTH4582_ME_8mer_157

source_name: Bhlha15_ME design


title: pTH4588_HK_8mer_1350

source_name: Mnt_HK design


title: Control, biological rep10


title: pTH4998_HK_8mer_12

source_name: Sp4_HK design


title: pTH4998_ME_8mer_31

source_name: Sp4_ME design


title: Time point 4 h after Non-thermal plasma treated 3 min, biological rep3

city: Hefei

first: Wei

last: Han

state: Anhui

address: #155 Shushanghu Road

institute: Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences

description:
Gene expression of A549 treated by 3min plasma, collected sample at 4 hr post treatment
Treat3m_4h_3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on PrimeView Human Chip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, US). Affymetrix GCOS software was used for image analysis to generate raw intensity data.

data_processing: The data were analyzed with Bioconductor.Normalization was performed with the RMA algorithm which included the global background adjustment and quantile normalization.

source_name: A549, Helium Plasma 3min treatment, 4h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: The human lung adenocarcinoma epithelial cell line A549 were stored by our laboratory and cultured in DMEM (Hyclone, Logan, US) supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, US), 1% penicillin/streptomycin and 2 mM L-glutamine. All cultures were grown in a humidified 5% CO2 atmosphere at 37℃.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Qualified total RNA was further purified using the RNeasy micro kit (QIAGEN, GmBH, Germany) and genomic contamination was removed by RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: The A549 cells were seeded into plates and treated by 1 min or 3 min plasma gas, then after, the cells were collected at 1, 2, 4 hr post treatment.

tag: cell line

tag: tumor

value: non-small cell lung cancer

tag: treatment

value: non-thermal plasma gas

tag: treatment time

value: 3 min

tag: collection time (post-treatment)

value: 4 hr


title: Oct4 positive Klf4 positive EpCAM positive MEFs


title: Control, biological rep6


title: In vivo B cell activation PF-303:597937

city: Cambridge

first: Andrew

last: Hill

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

description:
0624P1G9_164325_geatp_3
C4 0d2h0m_B Lymphocytes;Spleen;CD23+

hyb_protocol: GeneChip hybridization, wash and stain kit (Affymetrix) was used for sample hybridization to the mouse arrays on a Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) with autoloader following the standard protocol.

data_processing: Gene expression profiling data was extracted using the Affymetrix Microarray Suite 5.0 (MAS 5.0) software and used for subsequent statistical analyses.

source_name: Anti-IgD + PF-303

label_protocol: Following manufacturer’s recommendations, 150 ng of total RNA from each sample were used to prepare biotinylated cRNA for analysis on the Mouse Genome 430 2.0 expression arrays (Affymetrix). Sample generation, processing, labeling and fragmenting were performed using the GeneChip 3' IVT Express kit (Affymetrix).

extract_protocol: Qiagen RNAeasy columns with DNAse digestion

tag: injected with

tag: activated with

value: anti-IgD (in vivo B-cell activation)

value: spleen

value: B Lymphocytes; CD23+


title: In vivo B cell activation PF-303:597429

description:
0624P1G7_164323_geatp_3
A3 0d2h0m_B Lymphocytes;Spleen;CD23+

source_name: PBS + vehicle

tag: strain

value: Vehicle

value: PBS (control)


title: Oct4 negative MEFs

source_name: Oct4 negative MEFs

value: Oct4 negative MEFs


title: pTH4576_ME_8mer_155

source_name: Tcfl5_ME design

tag: dbd

value: ME


title: pTH4580_HK_8mer_1366

source_name: Tcf3_HK design

tag: platform_id_id design


title: Time point 4 h after Non-thermal plasma treated 3 min, biological rep2

description:
Gene expression of A549 treated by 3min plasma, collected sample at 4 hr post treatment
Treat3m_4h_2

value: lung adenocarcinoma epithelial cell line A549


title: In vivo B cell activation PF-303:598096

description:
0624P1G3_164319_geatp_3
D3 0d2h0m_B Lymphocytes;Spleen;CD23+

source_name: PBS + PF-303


title: Time point 2 h after Non-thermal plasma treated 3 min, biological rep2

description:
Gene expression of A549 treated by 3min plasma, collected sample at 2 hr post treatment
Treat3m_2h_2

source_name: A549, Helium Plasma 3min treatment, 2h

value: 2 hr


title: Control, biological rep11

value: whole blood


title: Control, biological rep2


title: Control, biological rep8


title: Control, biological rep13


title: In vivo B cell activation PF-303:597938

description:
0624P1F6_164314_geatp_3
C2 0d2h0m_B Lymphocytes;Spleen;CD23+


title: In vivo B cell activation PF-303:597427

description:
0624P1F5_164313_geatp_3
A1 0d2h0m_B Lymphocytes;Spleen;CD23+


title: Control, biological rep7


title: Control, biological rep5


title: Control, biological rep3


title: In vivo B cell activation PF-303:598098

description:
0624P1F4_164312_geatp_3
D1 0d2h0m_B Lymphocytes;Spleen;CD23+


title: Control, biological rep4


title: Time point 2 h after Non-thermal plasma treated 3 min, biological rep3

description:
Gene expression of A549 treated by 3min plasma, collected sample at 2 hr post treatment
Treat3m_2h_3


title: pTH4580_ME_8mer_156

source_name: Tcf3_ME design

value: HLH

tag: dbd source organism


title: In vivo B cell activation PF-303:597939

description:
0624P1F10_164318_geatp_3
C3 0d2h0m_B Lymphocytes;Spleen;CD23+

tag: tissue


title: Time point 4 h after Non-thermal plasma treated 3 min, biological rep1

description:
Gene expression of A549 treated by 3min plasma, collected sample at 4 hr post treatment
Treat3m_4h_1


title: In vivo B cell activation PF-303:597775

description:
0624P1E9_164309_geatp_3
B1 0d2h0m_B Lymphocytes;Spleen;CD23+

source_name: Anti-IgD + vehicle


title: pTH4576_HK_8mer_1373

source_name: Tcfl5_HK design

value: HK


title: Control, biological rep1

source_name: Control

value: healthy


title: In vivo B cell activation PF-303:597776

description:
0624P1E3_164303_geatp_3
B2 0d2h0m_B Lymphocytes;Spleen;CD23+


title: Time point 1 h after Non-thermal plasma treated 3 min, biological rep3

description:
Gene expression of A549 treated by 3min plasma, collected sample at 1 hr post treatment
Treat3m_1h_3

source_name: A549, Helium Plasma 3min treatment, 1h

value: non-small cell lung cancer

value: 1 hr


title: Time point 2 h after Non-thermal plasma treated 3 min, biological rep1

description:
Gene expression of A549 treated by 3min plasma, collected sample at 2 hr post treatment
Treat3m_2h_1

value: non-thermal plasma gas

value: 3 min


title: Time point 1 h after Non-thermal plasma treated 3 min, biological rep2

description:
Gene expression of A549 treated by 3min plasma, collected sample at 1 hr post treatment
Treat3m_1h_2


title: pTH4426_ME_8mer_1170

source_name: Arid5b_ME design

value: ARID


title: In vivo B cell activation PF-303:598100

description:
0624P1E10_164310_geatp_3
D5 0d2h0m_B Lymphocytes;Spleen;CD23+

value: spleen


title: In vivo B cell activation PF-303:597777

description:
0624P1D7_164300_geatp_3
B4 0d2h0m_B Lymphocytes;Spleen;CD23+

value: anti-IgD (in vivo B-cell activation)

value: B Lymphocytes; CD23+


title: In vivo B cell activation PF-303:597428

description:
0624P1C9_164296_geatp_3
A2 0d2h0m_B Lymphocytes;Spleen;CD23+

value: Vehicle

value: PBS (control)


title: pTH4425_ME_8mer_1138

source_name: Arid3b_ME design

value: ME


title: In vivo B cell activation PF-303:597935

description:
0624P1C5_164293_geatp_3
C5 0d2h0m_B Lymphocytes;Spleen;CD23+


title: Non-thermal plasma sham, biological rep3

description:
Gene expression of A549 sham control
Control_3

source_name: A549, Helium Plasma sham

value: lung adenocarcinoma epithelial cell line A549

value: control


title: pTH4426_HK_8mer_1183

source_name: Arid5b_HK design


title: Time point 4 h after Non-thermal plasma treated 1 min, biological rep3

description:
Gene expression of A549 treated by 1min plasma, collected sample at 4 hr post treatment
Treat1m_4h_3

source_name: A549, Helium Plasma 1min treatment, 4h

value: 1 min

value: 4 hr


title: pTH4425_HK_8mer_1152

source_name: Arid3b_HK design

value: HK


title: Time point 4 h after Non-thermal plasma treated 1 min, biological rep1

description:
Gene expression of A549 treated by 1min plasma, collected sample at 4 hr post treatment
Treat1m_4h_1


title: Time point 4 h after Non-thermal plasma treated 1 min, biological rep2

description:
Gene expression of A549 treated by 1min plasma, collected sample at 4 hr post treatment
Treat1m_4h_2


title: pTH4377_ME_8mer_414

source_name: Dbp_ME design


title: In vivo B cell activation PF-303:597936

description:
0624P1C3_164328_geatp_3
C1 0d2h0m_B Lymphocytes;Spleen;CD23+

source_name: Anti-IgD + PF-303


title: tumor tissue at age < 35 years (SA-BC12)

description:
SA-BC12.CEL
Gene expression data from tumor tissue at age < 35 years

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed in the Affymetrix automated fluidic station and scanned with Affymetrix G7 3000 scanner.

scan_protocol: GeneChips were scanned using  Affymetrix G7 3000 scanner.

data_processing: The open source  R/Bioconductor  packages, (Fred Hutchinson Cancer Research Center, Seattle, WA, USA)were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. The CEL files or CEL/CHP files were utilized for further analysis using dChip, MEV,  and PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.

source_name: tumor tissue at age < 35 years

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

growth_protocol: Tumors and adjacent disease free tissues obtained at time of surgical resection, according to institutional review board approved protocols.

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

tag: sample id

tag: tumor/normal

value: T

tag: grade

tag: er

tag: pr

tag: type

value: IDC

tag: age (years)


title: pTH4377_HK_8mer_1309

source_name: Dbp_HK design


title: pTH4381_ME_8mer_855

source_name: Max_ME design

value: HLH


title: In vivo B cell activation PF-303:597774

description:
0624P1C4_164292_geatp_3
B5 0d2h0m_B Lymphocytes;Spleen;CD23+

tag: cell type


title: tumor tissue at age < 35 years (532 T)

description:
532 T.CEL
Gene expression data from tumor tissue at age < 35 years


title: In vivo B cell activation PF-303:598097

description:
0624P1B9_164290_geatp_3
D4 0d2h0m_B Lymphocytes;Spleen;CD23+

source_name: PBS + PF-303


title: pTH4376_ME_8mer_376

source_name: Usf1_ME design


title: pTH4381_HK_8mer_1346

source_name: Max_HK design


title: tumor tissue at age < 35 years (436 T)

description:
436 T.CEL
Gene expression data from tumor tissue at age < 35 years


title: tumor tissue at age < 35 years (147 T)

description:
147 T.CEL
Gene expression data from tumor tissue at age < 35 years

value: DCIS


title: In vivo B cell activation PF-303:598099

description:
0624P1B5_164286_geatp_3
D2 0d2h0m_B Lymphocytes;Spleen;CD23+


title: normal tissue at age < 35 years (187N)

description:
187N.CEL
Gene expression data from normal tissue at age < 35 years

source_name: normal tissue at age < 35 years

value: N

value: NORMAL


title: Non-thermal plasma sham, biological rep1

description:
Gene expression of A549 sham control
Control_1

tag: cell line

tag: tumor

value: non-small cell lung cancer

tag: treatment

tag: treatment time


title: In vivo B cell activation PF-303:597430

description:
0624P1B3_164327_geatp_3
A4 0d2h0m_B Lymphocytes;Spleen;CD23+

source_name: PBS + vehicle

tag: strain

tag: injected with

tag: activated with

value: spleen


title: pTH4337_ME_8mer_1049

source_name: Jun_ME design

tag: dbd

tag: platform_id_id design

tag: dbd source organism


title: tumor tissue at age < 35 years (187T)

description:
187T.CEL
Gene expression data from tumor tissue at age < 35 years

tag: sample id

tag: tumor/normal


title: tumor tissue at age < 35 years (SA_BC375T)

description:
SA_BC375T.CEL
Gene expression data from tumor tissue at age < 35 years

tag: grade

tag: er


title: Non-thermal plasma sham, biological rep2

description:
Gene expression of A549 sham control
Control_2

tag: collection time (post-treatment)


title: NJ001 Treated SPC-A1 Cells Replicate 3

city: Nanjing

first: Shiyang

last: Pan

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Laboratory Medicine

institute: the First Affiliated Hospital of Nanjing Medical University

description: Gene expression data from mAb NJ001 treated SPC-A1 cells

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

scan_protocol: GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: SPC-A1 treated with NJ001

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: SPC-A1 cells were grown in RPMI1640 medium supplemented with L-glutamine, 100 units/ml penicillin, 100 mg/ml streptomycin and 10% (v/v) fetal bovine serum (FBS) (Gibco Invitrogen, Carlsbad, California, USA) at 37 °C in a humidified 5% CO2 incubator. Cells were harvested for passaging or analysis using trypsin/EDTA.

treatment_protocol: SPC-A1 cells were seeded in 6-well plates at 2 ×106 cells per well and, after overnight incubation, cultured with or without NJ001 (300 ng/μl) for 36 h. Total RNA was extracted from SPC-A1 cells using Trizol (Invitrogen, Carlsbad, California, USA).

value: lung adenocarcinoma


title: Control SPC-A1 Cells Replicate 3

description: Gene expression data from control SPC-A1 cells


title: pTH4376_HK_8mer_1592

source_name: Usf1_HK design


title: normal tissue at age < 35 years (341N)

description:
341N.CEL
Gene expression data from normal tissue at age < 35 years

tag: pr

tag: type

tag: age (years)


title: normal tissue at age < 35 years (SA_BC375N)

description:
SA_BC375N.CEL
Gene expression data from normal tissue at age < 35 years


title: normal tissue at age < 35 years (SA_BC147N)

description:
SA_BC147N.CEL
Gene expression data from normal tissue at age < 35 years


title: Control SPC-A1 Cells Replicate 2

tag: cell line

tag: cell type


title: normal tissue at age < 35 years (SA-BC24)

description:
SA-BC24.CEL
Gene expression data from normal tissue at age < 35 years


title: NJ001 Treated SPC-A1 Cells Replicate 2


city: Dublin

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T24 rep6

hyb_protocol: Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays. Following the hybridisation for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

scan_protocol: All Affymetrix Bovine Genome Array microarrays were scanned using an Affymetrix GeneChip® Scanner 3000.

data_processing: Affymetrix® GeneChip® Bovine Genome Array data were analysed using Bioconductor [http://www.bioconductor.org] contained within the R statistical package (http://www.r-project.org). Normalisation of raw data was performed using the Factor Analysis for Robust Microarray Summarization (FARMS) algorithm.

organism: Bos taurus

source_name: Bovine monocyte-derived macrophages cultured for 25 hr

label_protocol: Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The single stranded cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2. The enzymatically and chemically fragmented product (50-100 nt) was labelled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

growth_protocol: For monocyte isolation, 300 ml of whole blood was collected in acid citrate dextrose buffer (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) in sterile bottles. Blood was layered onto Accuspin™ tubes containing Histopaque® 1077 (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and following density gradient centrifugation, peripheral blood mononuclear cells (PBMC) were collected. Contaminating red blood cells (RBC) were removed following resuspension and subsequent incubation of the PBMC in RBC lysis buffer (10mM KHCO3, 150mM NH4Cl, 0.1mM EDTA pH 8.0) for 5 minutes at room temperature. After incubation, PBMC were washed twice with phosphate-buffered saline (PBS) before resuspending cells in phosphate-buffered saline (PBS) containing 1% bovine serum albumin (BSA, Sigma-Aldrich Ireland Ltd., Dublin, Ireland). Monocytes were then isolated using the MACS protocol and a human anti-CD14 antibody (Miltenyi Biotec Ltd., Surrey, UK), which has been shown to be cross-reactive with bovine monocytes. All procedures were carried out according to the manufacturers’ instructions. The identity and purity of monocytes was confirmed by flow cytometry using an anti-CD14 FITC labelled antibody (data not shown). This method has been previously shown by us to yield a purity of CD14+ cells >= 99%. Purified monocytes were seeded at 1+E6/ml in 24-well tissue culture plates in RPMI 1640 medium (Invitrogen Ltd., Paisley, UK) containing 15% heat inactivated foetal calf serum (FCS; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), 1% non-essential amino acids (NEAA; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), gentamicin (5 µg/ml; Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and incubated at 37°C, 5% CO2. Following 24 hours incubation (day one) the media was replaced with 1ml fresh antibiotic-containing media to remove any non-adhered cells. On day three, media was replaced with 1 ml antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only). To ensure that the same number of MDM were subjected to different treatments between experiments, cells were dissociated on day five using a non-enzymatic cell dissociation solution (Sigma-Aldrich Ireland Ltd., Dublin, Ireland), counted and then re-seeded at 2+E5 cells/well in 24-well tissue culture plates (Sarstedt, County Wexford, Ireland) using antibiotic-free culture media. By day eight, 80-100% confluent monolayers of MDM were generated that displayed the characteristic macrophage morphology as confirmed by Giemsa staining. Day eight MDM were used for the in vitro challenge experiments.

extract_protocol: All RNA extractions were performed in the CL3 laboratory using an RNeasy kit incorporating an on-column DNase treatment step (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions. RNA quantity and quality was assessed using both the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the on an Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Cork, Ireland). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) greater than 8.5. cDNA labelling, hybridisation and scanning for the microarray experiments were performed using a one-cycle amplification/labelling protocol on the Affymetrix GeneChip Bovine Genome Array (http://www.affymetrix.com). This array represents over 23,000 transcripts and includes approximately 19,000 UniGene clusters.

treatment_protocol: Culturing of BCG (Pasteur strain) was performed in a Biosafety Containment Level 3 (CL3) laboratory and conformed to the national guidelines on the use of Hazard Group 3 infectious organisms. BCG stocks for the in vitro MDM infection experiments were cultured in Middlebrook 7H9 medium (Difco, Becton, Dickinson Ltd., Oxford, UK) containing 10% (vol/vol) BBL Middlebrook OADC Enrichment (Difco, Becton, Dickinson Ltd., Oxford, UK), 0.05% Tween 80 (Sigma-Aldrich, Dublin, Ireland) and 0.50% (weight/vol) glycerol (Sigma-Aldrich Ltd., Dublin, Ireland) at 37°C. Bacterial cultures were grown to mid-logarithmic phase as determined by spectrophotometric analysis prior to the challenge experiments using the purified bovine MDM. Colony-forming unit (cfu) counting was performed using Middlebrook 7H11 medium (Difco, Becton- Dickinson Ltd., Dublin, Ireland) containing 10% (vol/vol) Middlebrook (ADC) enrichment (Difco, Becton-Dickinson Ltd., Dublin, Ireland) and 0.50% (vol/vol) glycerol (Sigma-Aldrich, Dublin, Ireland). MDM (seeded at 2 × 105 cells per well) were challenged with BCG (4 × 105 cells per well) prepared in antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only). BCG cell counts were performed using a Petroff Hausser chamber (Fisher Scientific Ltd., Dublin, Ireland) following sterile filtering to prevent clumping using a 5 micron filter (Millipore Ireland Ltd., County Cork, Ireland). BCG cell numbers were then adjusted and 4 × 105 bacilli were added to the appropriate wells giving a multiplicity of infection (MOI) of 2:1. Subsequent cfu for BCG counting also yielded a mean MOI of 2:1. Once challenged, MDM were incubated at 37°C, 5% CO2 for 2 h, 6 h and 24 h.

tag: time

value: 25 hr

tag: treatment

value: challenged with M. bovis BCG

value: monocyte-derived macrophage

tag: cattle breed

value: Holstein-Friesian

tag: Sex

value: Female

tag: age

value: 3 years


title: pTH4330_HK_8mer_1355

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

source_name: Bhlhe40_HK design

label_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector, in most cases.  See paper supplemental web site (http://hugheslab.ccbr.utoronto.ca/supplementary-data/CisBP/) for exceptions.

tag: dbd

tag: platform_id_id design


title: NJ001 Treated SPC-A1 Cells Replicate 1


title: tumor tissue at age36-45 years (563 T)

description:
563 T.CEL
Gene expression data from tumor tissue at age36-45 years

source_name: tumor tissue at age36-45 years

tag: sample id


title: pTH4330_ME_8mer_2878

source_name: Bhlhe40_ME design

value: ME

tag: dbd source organism


title: pTH4337_HK_8mer_2174

source_name: Jun_HK design

value: HK


title: pTH4327_ME_8mer_2498

source_name: Srebf2_ME design


title: tumor tissue at age36-45 years (455 T)

description:
455 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: tumor/normal

value: T

tag: grade


title: tumor tissue at age36-45 years (408 T)

description:
408 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: er

value: IDC


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T24 rep5


title: pTH4062_HK_8mer_1471

source_name: Zfp711_HK design


title: tumor tissue at age36-45 years (447 T)

description:
447 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: pr


title: tumor tissue at age36-45 years (431 T)

description:
431 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: type


title: pTH4327_HK_8mer_2530

source_name: Srebf2_HK design

value: HLH


title: tumor tissue at age36-45 years (542 T)

description:
542 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: age (years)


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T24 rep2


title: dorsal trunk SKPs sample 3

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

description: Gene expression data from adult rat dorsal trunk SKPs - reanalysis of GSM590218

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 1.0 ST Arrays (Affymetrix) and scanned at the HSC Microarray Facility.

scan_protocol: The hybridized microarray image was scanned with the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw probe intensity values were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) algorithm at the gene level in the Affymetrix Expression Console program.

organism: Rattus norvegicus

source_name: adult rat dorsal trunk SKPs

label_protocol: Single-stranded cDNA was generated from the cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Dorsal trunk skin samples were cut into small pieces and enzymatically digested and filtered until single cells were isolated.  These cells were cultured in proliferation-promoting conditions as previously described.  The resulting SKP spheres were harvested for RNA or plated in Schwann cell growth media.  Sciatic nerves were dissected and enzymatically digested to liberate single cells.  These were plated and grown in Schwann cell growth media.

extract_protocol: Trizol extraction of total RNA was performed with the RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: SKPs proliferated as spheres.  After one or two passages, spheres were placed in Trizol reagent.  Schwann cells or SKP-Schwann cells were passaged once, grown until confluent, then washed and placed in Trizol reagent.

tag: strain

value: Sprague Dawley rat

tag: tissue

value: dermis

value: dorsal trunk SKPs


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T24 rep3

tag: time

tag: cell type


title: Control SPC-A1 Cells Replicate 1

tag: cell line


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T24 rep4

tag: treatment

tag: cattle breed

tag: Sex


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T24 rep7

tag: age


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T6 rep7

source_name: Bovine monocyte-derived macrophages cultured for 6 hr

value: 6 hr


title: dorsal trunk SKPs sample 2

description: Gene expression data from adult rat dorsal trunk SKPs - reanalysis of GSM590217


title: dorsal trunk SKP-derived Schwann cell sample 3

description: Gene expression data from adult rat dorsal trunk SKP-derived Schwann cells

value: dorsal trunk SKP-derived Schwann cell


title: dorsal trunk SKPs sample 1

description: Gene expression data from adult rat dorsal trunk SKPs - reanalysis of GSM590216


title: pTH3802_ME_8mer_1993

city: Cincinnati

last: Weirauch

institute: Cincinnati Children's Hospital

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

source_name: Gm5294_ME design

tag: dbd

tag: platform_id_id design


title: tumor tissue at age36-45 years (385 T)

description:
385 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: sample id

tag: tumor/normal

value: DCIS


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T24 rep1

value: 25 hr


title: dorsal trunk SKP-derived Schwann cell sample 2

source_name: adult rat dorsal trunk SKP-derived Schwann cells


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T6 rep6

value: challenged with M. bovis BCG


title: Time point 1 h after Non-thermal plasma treated 3 min, biological rep1

description:
Gene expression of A549 treated by 3min plasma, collected sample at 1 hr post treatment
Treat3m_1h_1

source_name: A549, Helium Plasma 3min treatment, 1h

value: lung adenocarcinoma epithelial cell line A549

tag: tumor

value: non-small cell lung cancer

value: non-thermal plasma gas

tag: treatment time

value: 3 min

tag: collection time (post-treatment)

value: 1 hr


title: tumor tissue at age36-45 years (384 T)

description:
384 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: grade

tag: er

tag: pr

tag: type

tag: age (years)


title: pTH4062_ME_8mer_1335

source_name: Zfp711_ME design

value: ME

tag: dbd source organism


title: tumor tissue at age36-45 years (SA_BC384T)

description:
SA_BC384T.CEL
Gene expression data from tumor tissue at age36-45 years

value: T


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T6 rep5

tag: time

tag: treatment

tag: cell type

value: monocyte-derived macrophage

value: Holstein-Friesian

value: Female

value: 3 years


title: dorsal trunk SKP-derived Schwann cell sample 1

tag: strain

value: Sprague Dawley rat

tag: tissue

value: dermis


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T6 rep2

value: 6 hr

tag: cattle breed

tag: Sex

tag: age


title: pTH3802_HK_8mer_1472

source_name: Gm5294_HK design

tag: dbd

tag: platform_id_id design

value: HK


title: sciatic nerve Schwann cells sample 2

description: Gene expression data from adult rat sciatic nerve Schwann cells

source_name: adult rat sciatic nerve Schwann cells

value: sciatic nerve Schwann cells


title: sciatic nerve Schwann cells sample 3


title: pTH3475_ME_8mer_243

source_name: Irf7_ME design

value: IRF


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T6 rep3

value: challenged with M. bovis BCG


title: tumor tissue at age36-45 years (SA_BC371T)

description:
SA_BC371T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: sample id

tag: tumor/normal

value: IDC


title: sciatic nerve Schwann cells sample 1


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T6 rep4


title: pTH3475_HK_8mer_6166

source_name: Irf7_HK design


title: tumor tissue at age36-45 years (349 T)

description:
349 T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: grade

tag: er


title: pTH3466_ME_8mer_770

source_name: Nr2c1_ME design


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T6 rep1


title: pTH3466_HK_8mer_1413

source_name: Nr2c1_HK design


title: tumor tissue at age36-45 years (366 T)

description:
366 T.CEL
Gene expression data from tumor tissue at age36-45 years

source_name: tumor tissue at age36-45 years

tag: pr

tag: type

value: DCIS


title: pTH2880_ME_8mer_656

source_name: Rxrg_ME design

tag: dbd source organism


title: tumor tissue at age36-45 years (289T)

description:
289T.CEL
Gene expression data from tumor tissue at age36-45 years

tag: age (years)


title: tumor tissue at age36-45 years (290T)

description:
290T.CEL
Gene expression data from tumor tissue at age36-45 years


title: pTH2861_HK_8mer_1395

source_name: Rxrb_HK design


title: tumor tissue at age36-45 years (180T)

description:
180T.CEL
Gene expression data from tumor tissue at age36-45 years


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T2 rep5

source_name: Bovine monocyte-derived macrophages cultured for 2 hr

tag: time

value: 2 hr

tag: treatment


title: tumor tissue at age36-45 years (277T)

description:
277T.CEL
Gene expression data from tumor tissue at age36-45 years


title: pTH2880_HK_8mer_1396

source_name: Rxrg_HK design


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T2 rep6

tag: cell type


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T2 rep4


title: tumor tissue at age36-45 years (SA-BC18)

description:
SA-BC18.CEL
Gene expression data from tumor tissue at age36-45 years


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T2 rep2


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T2 rep3


title: pTH2808_ME_8mer_7666

source_name: Foxb1_ME design


description: gene expression data from bovine monocyte-derived macrophage challenged with M. bovis BCG at T2 rep7


title: tumor tissue at age36-45 years (278T)

description:
278T.CEL
Gene expression data from tumor tissue at age36-45 years


title: pTH2861_ME_8mer_655

source_name: Rxrb_ME design


title: tumor tissue at age36-45 years (SA-BC20)

description:
SA-BC20.CEL
Gene expression data from tumor tissue at age36-45 years


title: LP1 JQ1 Treated - 24 hours - mAdbID:117876

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 117876

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: LP1 JQ1 Treated - 24 hours

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was prepared by the TRIzol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).

treatment_protocol:
Treatment type: small molecule
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 24 hours

tag: cell line

value: multiple myeloma cells

tag: disease state

value: multiple myeloma

source_name: LP1 DMSO Treated

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol: Agent: DMSO (Dimethyl sulfoxide)


title: tumor tissue at age36-45 years (SA-BC19)

description:
SA-BC19.CEL
Gene expression data from tumor tissue at age36-45 years

value: T


title: pTH2673_ME_8mer_1949

first: Matthew

address: 3333 Burnet Avenue

source_name: Foxc1_ME design

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

value: ME


title: pTH2804_ME_8mer_630

source_name: Rarb_ME design


title: pTH2808_HK_8mer_600

source_name: Foxb1_HK design


title: tumor tissue at age36-45 years (SA-BC14)

description:
SA-BC14.CEL
Gene expression data from tumor tissue at age36-45 years