title: head and neck squamous cell carcinoma 125

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue

value: peripheral blood


title: 1323-T

status: Public on Jul 01 2013

type: RNA

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

country: USA

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lung cancer specimen

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

extract_protocol: After homogenization, total RNA was extracted using TRI Reagent (Life Technologies, Grand Island, NY) according to manufacturer’s protocol. The nanodrop spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA (RIN number) was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA)

tag: histology

value: Adenocarcinoma

tag: gender

value: F

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: siPin1, TGF-b positive

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

country: Japan

institute: Yamanashi University

hyb_protocol: Following fragmentation, 7 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console and global scaling as normalization method.

organism: Mus musculus

source_name: NMuMG,TGF-b, 1h

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA. Single-stranded DNA were labeled using the GeneChip® WT Terminal Labeling Kit

growth_protocol: NMuMG cells were cultured in DMEM containing 10% fetal bovine serum.

extract_protocol: Total RNA was performed according to the manufacturer's instructions.

treatment_protocol: NMuMG cells were transfected with siRNAs (siControl, siOlig1 or siPin1) and treated with or without TGF-b for 1h.

tag: cell type

value: NMuMG

tag: transfection


title: head and neck squamous cell carcinoma 126

type: genomic

city: Tokyo

first: Mitsuyoshi

last: Urashima

address: Nishishimbashi 3-25-8, Minato-ku

institute: Jikei University School of Medicine

hyb_protocol: Scanned on an Agilent G4449A scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

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

molecule: genomic DNA

source_name: tumor sample

label_protocol: following manufacturer's instructions

growth_protocol: Clinical samples

extract_protocol: 0.5 µg of total DNA were extracted using DNeasy and primed following manufacturer's instructions

tag: age at operation (yrs)

value: female

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

source_name: healthy non-smoking volunteer

value: male

value: non-drinker control


title: head and neck squamous cell carcinoma 128

tag: gender

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 124

value: Sinonasal Cavity


title: A375_Passage 1 xenograft_R1

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description:
A375 P01 T1
Gene expression data from A375 Passage 1 xenograft.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner.

data_processing: Affymetrix Expression Console v1.3.

label: Biotin

source_name: A375, passage 1 xenograft

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.

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

tag: originating cell line

tag: tumor type

value: metastatic malignant melanoma

tag: in vivo passage


title: siPin1, TGF-b negative

source_name: NMuMG

tag: cell type

tag: transfection


title: FvB mouse, biological rep 1

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: Gene expression data from non transgenic mouse

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Signal intensities from each array were analyzed using Partek Genomic Suite version 6.4 (Partek©, Saint Louis, MI). Raw intensity probe values were normalized using robust multiarray analysis background correction (RMA). A two way ANOVA was performed to identify differentially expressed genes. Only genes with statistically significant differences in expression levels (p-value < 0.05) and a fold change criteria of ≥ 2 and ≤ -2 were included in the final set of differentially expressed genes. The microarray data were deposited to the NCBIGEO database [GEOID:]. To identify those biological processes altered by E7 and/or 17β-estradiol, we used Ingenuity Pathway software (Ingenuity Systems®, Redwood, CA), a bioinformatic tool for visualizing expression data in the context of KEGG-defined biological pathways.

source_name: Nontransgenic female mouse

label_protocol: Biotin

extract_protocol: K14E7 hemizygote and nontransgenic FvB control virgin female untreated and treated mice were sacrificed by cervical dislocation. Cervical biopsies were immediately stored in RNA later Solution (Ambion®, Carlsbad, CA) at 4ºC overnight. Tissue was recovered from RNA later solution with sterile forceps, quickly blotted to remove excess RNA later and immediately snap frozen in liquid nitrogen. Total RNA was extracted from snap frozen tissue using standard procedures (TRIzol reagent, Ambion®, Carlsbad, CA ). Total RNA collected from six female mice of each group was pooled. RNA quantity and quality were assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies©, Waldbronn, Germany). Only RNA samples with a RNA Integrity Number greater than 8.0 were further processed for microarray analysis. cDNA synthesis, amplification, and gene expression profiling were performed according to the manufacturer’s instructions (Affymetrix WT Sense Target labeling assay Manual). Each microarray experiment was performed as triplicates for each group.

treatment_protocol: The K14E7 and FvB mice have been described previously (Riley et al., 2003). All the mice were housed and treated according to the American Association of Laboratory Animal Care (AALAC), and all experiments and procedures were approved by the Research Unit for Laboratory Animal Care Committee (UPEAL-CINVESTAV-IPN, Mexico; NOM-062-ZOO-1999). One-month virgin female transgenic and nontransgenic mice were implanted in the dorsal skin with continuous release pellets delivering 0.05 mg of17-β estradiol over 60 days (Innovative Research of America, Sarasota, FL). We also used K14E7 and FvB (control) untreated mice of seven months old.

tag: genotype/variation

value: nontransgenic FvB

tag: treatment


title: K14E7 treated mouse, biological rep 3

description: Gene expression data from K14E7treated transgenic mouse

source_name: K14E7 hemizygote female treated mouse

value: K14E7 transgenic mouse

value: continuous release pellets delivering 0.05 mg of 17-beta estradiol over 60 days


title: head and neck squamous cell carcinoma 123

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

value: peripheral blood


title: 1289-T

tag: histology

value: Adenocarcinoma

value: F

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: siOlig1, TGF-b positive

tag: cell type


title: 1305-T

tag: gender

value: M

value: Caucasian

value: Y

value: IIIB


title: A375_originating cell line_R2

description:
A375 P0 T2
Gene expression data from A375 originating cell line.

source_name: A375, originating cell line

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: siControl, TGF-b positive

value: NMuMG

tag: transfection

value: siControl


title: siOlig1, TGF-b negative


title: A375_originating cell line_R1

description:
A375 P0 T1
Gene expression data from A375 originating cell line.


title: siControl, TGF-b negative


title: head and neck squamous cell carcinoma 122

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue


title: 786-0_Passage 10 xenograft_R4

description:
786-0 P10 T4
Gene expression data from 786-0 Passage 10 xenograft.

source_name: 786-0, passage 10 xenograft

tag: originating cell line

value: adenocarcinoma renal


title: 786-0_Passage 10 xenograft_R5

description:
786-0 P10 T5
Gene expression data from 786-0 Passage 10 xenograft.

tag: tumor type


title: 1303-T

tag: histology

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 786-0_Passage 10 xenograft_R2

description:
786-0 P10 T2
Gene expression data from 786-0 Passage 10 xenograft.

tag: in vivo passage


title: head and neck squamous cell carcinoma 120

tag: age at operation (yrs)

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking


title: head and neck squamous cell carcinoma 119

tag: gender

value: female

value: Oral Cavity

tag: sample type

tag: tissue

value: peripheral blood


title: 786-0_Passage 10 xenograft_R3

description:
786-0 P10 T3
Gene expression data from 786-0 Passage 10 xenograft.

tag: originating cell line

tag: tumor type


title: head and neck squamous cell carcinoma 118


title: 1284-T

tag: histology

value: Adenocarcinoma

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 786-0_Passage 10 xenograft_R1

description:
786-0 P10 T1
Gene expression data from 786-0 Passage 10 xenograft.

tag: in vivo passage


title: 1273-T

value: Squamous

value: M

value: Caucasian

value: N


title: 1282-T

value: F

value: Y

value: IA


title: head and neck squamous cell carcinoma 117

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

value: non-drinker control


title: 786-0_Passage 4 xenograft_R5

description:
786-0 P04 T5
Gene expression data from 786-0 Passage 4 xenograft.

source_name: 786-0, passage 4 xenograft

tag: originating cell line

tag: tumor type

value: adenocarcinoma renal


title: 1266-T

tag: histology

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival


title: 1240-T

value: A

tag: recurrence

tag: last follow-up recurrence


title: 1247-T

value: IIB


title: 1265-T


title: MLL-AF9/Nras LMN Suz12sh day5 sample3

city: Cold Spring Harbor

first: Junwei

last: Shi

state: NY

address: 1 Bungtown Rd

institute: cold spring harbor lab

description: Gene expression pattern of shRNA knockdown subunits of PRC2 complex

hyb_protocol: Hybridization, washing, and scan protocol were according to the manufacturer's instructions on Mouse Gene ST 1.0 GeneChips

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed by RMA

source_name: MLL-AF9/NrasG12D LMN murine cell line

label_protocol: The cDNA was then fragmented and terminally labeled with biotin, using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: Murine cell lines were cultured in RPMI1640 supplement with 10% FBS and penicillin/streptomycin

extract_protocol: total RNA was isolated by using RNeasy Mini Kit (QIAGEN, #74104)

treatment_protocol: The sample were transduced with indicted MSCV virus

tag: genotype

tag: knockdown

tag: genetic background


title: 1238-T

value: Asian

value: IIIA


title: MLL-AF9/Nras LMN Suz12sh day5 sample2


title: 786-0_Passage 4 xenograft_R3

description:
786-0 P04 T3
Gene expression data from 786-0 Passage 4 xenograft.

tag: in vivo passage


title: head and neck squamous cell carcinoma 116

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue

value: peripheral blood


title: 1237-T

tag: histology

value: Adenocarcinoma

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 786-0_Passage 4 xenograft_R1

description:
786-0 P04 T1
Gene expression data from 786-0 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 113

tag: age at operation (yrs)

value: female

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking


title: 786-0_Passage 4 xenograft_R2

description:
786-0 P04 T2
Gene expression data from 786-0 Passage 4 xenograft.


title: MLL-AF9/Nras LMN Suz12sh day5 sample1

tag: genotype

tag: knockdown

tag: genetic background


title: 1234-T

tag: histology

value: Squamous

tag: gender

value: M

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 110

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: sample type

tag: tissue


title: 786-0_Passage 4 xenograft_R4

description:
786-0 P04 T4
Gene expression data from 786-0 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 114

tag: gender

value: Hypopharyngeal

tag: smoking status

tag: alcohol drinking

value: non-drinker control


title: 786-0_Passage 1 xenograft_R4

description:
786-0 P01 T4
Gene expression data from 786-0 Passage 1 xenograft.

source_name: 786-0, passage 1 xenograft

value: adenocarcinoma renal


title: head and neck squamous cell carcinoma 111

tag: age at operation (yrs)

value: Oropharyngeal


title: MLL-AF9/Nras LMN Eedsh day5 sample2

tag: genotype

tag: knockdown

value: Eed

tag: genetic background


title: 786-0_Passage 1 xenograft_R5

description:
786-0 P01 T5
Gene expression data from 786-0 Passage 1 xenograft.


title: head and neck squamous cell carcinoma 115

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage


title: MLL-AF9/Nras LMN Eedsh day5 sample3


title: 786-0_Passage 1 xenograft_R3

description:
786-0 P01 T3
Gene expression data from 786-0 Passage 1 xenograft.


title: head and neck squamous cell carcinoma 108

value: Laryngeal

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status


title: head and neck squamous cell carcinoma 107

value: Sinonasal Cavity

tag: sample type

tag: tissue


title: 1213-T

tag: histology

tag: gender

tag: race

tag: tobacco history

value: Y

tag: final patient stage

value: IIIA

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 106

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: smoking status

tag: alcohol drinking

value: peripheral blood


title: 1218-T

tag: histology

value: Adenocarcinoma

tag: gender

tag: race

value: A


title: 786-0_Passage 1 xenograft_R2

description:
786-0 P01 T2
Gene expression data from 786-0 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 786-0_Passage 1 xenograft_R1

description:
786-0 P01 T1
Gene expression data from 786-0 Passage 1 xenograft.


title: head and neck squamous cell carcinoma 105

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 121

tag: age at operation (yrs)

value: female

tag: primary tumor site

tag: hpv infection


title: MLL-AF9/Nras LMN Rluc day5 sample2

tag: genotype

tag: knockdown

value: control

tag: genetic background


title: 1161-T

tag: histology

value: M

value: Caucasian

tag: tobacco history

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 103

tag: gender

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

value: male

tag: sample type

value: non-drinker control


title: 1168-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

value: IIA


title: 1157-T

value: Squamous

value: F

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival


title: 786-0_originating cell line_R1

description:
786-0 P0 T1
Gene expression data from 786-0 originating cell line.

source_name: 786-0, originating cell line

tag: originating cell line

tag: tumor type

value: adenocarcinoma renal

tag: in vivo passage


title: MLL-AF9/Nras LMN Eedsh day5 sample1

tag: genotype

tag: knockdown

value: Eed

tag: genetic background


title: 1183-T

tag: gender

value: N

value: IA

tag: recurrence

tag: last follow-up recurrence


title: 1129-T

tag: histology

value: Y


title: 786-0_originating cell line_R2

description:
786-0 P0 T2
Gene expression data from 786-0 originating cell line.


title: 786-0_originating cell line_R3

description:
786-0 P0 T3
Gene expression data from 786-0 originating cell line.


title: head and neck squamous cell carcinoma 104

tag: age at operation (yrs)

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue

value: peripheral blood


title: 1135-T

tag: race

value: African American

tag: tobacco history

tag: final patient stage

value: IIIA

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival


title: MLL-AF9/Nras LMN Rluc day5 sample3

tag: genotype

tag: knockdown

value: control

tag: genetic background


title: head and neck squamous cell carcinoma 101

tag: age at operation (yrs)

tag: gender

value: male

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy


title: head and neck squamous cell carcinoma 102

value: Oropharyngeal

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue


title: head and neck squamous cell carcinoma 100

value: Laryngeal


title: MLL-AF9/Nras LMN Rluc day5 sample1

tag: genotype


title: 1095-T

tag: histology

value: Squamous

value: M

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 1100-T

tag: gender

value: F

value: IIB


title: head and neck squamous cell carcinoma 98

tag: age at operation (yrs)

value: female

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: chemoradiotherapy

tag: relapse

tag: survival status


title: 1079-T

tag: histology

value: Adenocarcinoma

tag: race

value: Hispanic

tag: tobacco history

value: Y

value: IIA

value: N


title: 1087-T

tag: final patient stage

value: IA

tag: date of birth

tag: date of surgery


title: KIR+CD56+ T cell replicate 5

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 12.5 micrograms of biotinylated cRNA were hybridized for 16 hr at 45C on an Affymetrix GeneChip Mouse 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression values were summarized using the MAS5 algorithm as implemented in the GCOS v1.4 software (Affymetrix). Signals were variance adjusted by log-transformation prior to statistical analysis.  Analysis of variance (ANOVA) was performed using Partek Genomics Suite v6.4. The false discovery rate was controlled at a level of 0.05 unless otherwise stated.

source_name: Human peripheral blood monor nuclear cells

label_protocol: Biotinylated cRNA were prepared according to the two-cycle eukaryote target Affymetrix protocol starting from 10-100 nanograms of total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini/Micro kit accroding to the manufacturer's instructions.

treatment_protocol: Lymphocyte subsets were sorted with FACSAriaII (BD Biosciences, San Jose, CA).

tag: immunophenotype

value: KIR+CD3+CD56+ T-cell


title: iNKT cell replicate 5

value: CD3+TCRValpha+ iNKT-cell


title: KIR-CD56+ T cell replicate 5

value: KIR-CD3+CD56+ T-cell


title: 1064-T

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 99

tag: age at operation (yrs)

tag: gender

value: male

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: tumor grade

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: CD56+ T cell replicate 5

value: CD3+CD56+ T-cell


title: iNKT cell replicate 4


title: NK cell replicate 5

value: CD3-CD56+ NK cell


title: CD56- T cell replicate 5

value: CD3+CD56- T-cell


title: 1052-T

tag: histology

value: M

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

value: IB

value: A


title: 1041-T

value: Adenocarcinoma

value: F

value: African American

value: Y

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D


title: head and neck squamous cell carcinoma 96

value: Oropharyngeal

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: chemoradiotherapy

tag: relapse

tag: survival status


title: 1042-T

value: Squamous

tag: gender

value: IIIA

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: KIR-CD56+ T cell replicate 4

tag: immunophenotype

value: KIR-CD3+CD56+ T-cell


title: head and neck squamous cell carcinoma 97

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: tumor grade

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: head and neck squamous cell carcinoma 92

value: Sinonasal Cavity

tag: p16 protein immunohistochemistry

tag: tnm stage


title: head and neck squamous cell carcinoma 93

value: Hypopharyngeal

tag: chemoradiotherapy

tag: relapse


title: KIR+CD56+ T cell replicate 4

value: KIR+CD3+CD56+ T-cell


title: NK cell replicate 4

value: CD3-CD56+ NK cell


title: 1038-T2

tag: histology

value: Adenocarcinoma

tag: gender

value: M

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics


title: 1025-T

value: Y

value: D

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 94

tag: age at operation (yrs)

tag: primary tumor site

value: Laryngeal

tag: hpv infection

tag: tumor grade

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type


title: head and neck squamous cell carcinoma 90

tag: gender

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: chemoradiotherapy

tag: relapse

tag: tissue


title: head and neck squamous cell carcinoma 87


title: 999-T

tag: histology

value: F

tag: race

tag: tobacco history

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival


title: CD56+ T cell replicate 4

tag: immunophenotype

value: CD3+CD56+ T-cell


title: 963-T1

value: Squamous

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 83

tag: age at operation (yrs)

tag: gender

value: male

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: tumor grade

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

value: peripheral blood


title: UACC-62_Passage 10 xenograft_R4

description:
UACC-62 P10 T4
Gene expression data from UACC-62 Passage 10 xenograft.

source_name: UACC-62, passage 10 xenograft

tag: originating cell line

tag: tumor type

value: malignant melanoma

tag: in vivo passage


title: UACC-62_Passage 10 xenograft_R3

description:
UACC-62 P10 T3
Gene expression data from UACC-62 Passage 10 xenograft.


title: 993-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A


title: head and neck squamous cell carcinoma 82

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: chemoradiotherapy

tag: relapse

tag: tissue


title: head and neck squamous cell carcinoma 81

value: Oropharyngeal

tag: hpv infection

tag: tumor grade

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type


title: 952-T

tag: histology

value: Adenocarcinoma

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

value: IIA

tag: date of birth

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 931-T1

tag: gender

value: Y

value: IIIB

tag: date of surgery

tag: vital statistics

value: D


title: 922-T2

value: F

value: Asian

value: N

value: IA


title: 940-T

value: M

value: IIB


title: UACC-62_Passage 10 xenograft_R1

description:
UACC-62 P10 T1
Gene expression data from UACC-62 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: UACC-62_Passage 10 xenograft_R5

description:
UACC-62 P10 T5
Gene expression data from UACC-62 Passage 10 xenograft.


title: UACC-62_Passage 10 xenograft_R2

description:
UACC-62 P10 T2
Gene expression data from UACC-62 Passage 10 xenograft.


title: head and neck squamous cell carcinoma 85

tag: age at operation (yrs)

value: male

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

value: non-drinker control

tag: tissue


title: UACC-62_Passage 4 xenograft_R4

description:
UACC-62 P04 T4
Gene expression data from UACC-62 Passage 4 xenograft.

source_name: UACC-62, passage 4 xenograft

value: malignant melanoma


title: head and neck squamous cell carcinoma 79

tag: gender

value: Hypopharyngeal

tag: alcohol drinking

tag: sample type

value: peripheral blood


title: head and neck squamous cell carcinoma 80

value: Laryngeal


title: UACC-62_Passage 4 xenograft_R5

description:
UACC-62 P04 T5
Gene expression data from UACC-62 Passage 4 xenograft.

tag: originating cell line


title: head and neck squamous cell carcinoma 78


title: UACC-62_Passage 4 xenograft_R3

description:
UACC-62 P04 T3
Gene expression data from UACC-62 Passage 4 xenograft.

tag: tumor type


title: 896-T1

source_name: Lung cancer specimen

tag: histology

value: Adenocarcinoma

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: CD56- T cell replicate 4

tag: immunophenotype

value: CD3+CD56- T-cell


title: head and neck squamous cell carcinoma 77

tag: age at operation (yrs)

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: tissue


title: 917-T

tag: histology

value: Squamous

tag: gender

value: F

tag: race

tag: tobacco history

value: Y

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery


title: head and neck squamous cell carcinoma 73

tag: age at operation (yrs)

tag: primary tumor site

value: Oropharyngeal

tag: alcohol drinking

tag: sample type


title: head and neck squamous cell carcinoma 75

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade


title: R749H-amr RD40a

city: Rehovot

first: Rivka

last: Dikstein

address: 2 Hertzl st.

country: Israel

institute: The Weizmann Institute of Science

hyb_protocol: cDNA in 80 ul were hybridized to a Human Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: 4 slow

label_protocol: 200ng TotalRNA were used. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: HEK293T were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal calf serum.

extract_protocol: Total RNA was extracted with Tri-reagent (MRC inc.) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with plasmids directing the expression of α-amanitin-resistant variants of Pol II (Rpb1-amr and R749H-amr). α-amanitin was added and RNA was prepared 24 and 48 h later, respectively.

tag: cell line

tag: treatment


title: head and neck squamous cell carcinoma 74

source_name: tumor sample

value: female

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: tissue


title: 850-T

tag: histology

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

value: IIIA

tag: date of birth

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 819-T

value: IIIB

tag: date of surgery

value: D


title: 847-T1

value: N


title: R749H-amr RD36a

source_name: 1 slow

tag: cell line

tag: treatment


title: 814-T


title: 841-T

value: M

value: African American


title: R749H-amr RD38a

source_name: 3 slow


title: Rpb1-amr  RD39a

source_name: 4 wt


title: Rpb1-amr  RD37a

source_name: 3 wt


title: UACC-62_Passage 4 xenograft_R2

description:
UACC-62 P04 T2
Gene expression data from UACC-62 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

value: malignant melanoma

tag: in vivo passage


title: head and neck squamous cell carcinoma 71

tag: age at operation (yrs)

value: male

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

source_name: healthy non-smoking volunteer

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: head and neck squamous cell carcinoma 72

tag: gender

value: Oral Cavity


title: UACC-62_Passage 1 xenograft_R2

description:
UACC-62 P01 T2
Gene expression data from UACC-62 Passage 1 xenograft.

source_name: UACC-62, passage 1 xenograft

tag: originating cell line


title: UACC-62_Passage 1 xenograft_R4

description:
UACC-62 P01 T4
Gene expression data from UACC-62 Passage 1 xenograft.

tag: tumor type


title: UACC-62_Passage 4 xenograft_R1

description:
UACC-62 P04 T1
Gene expression data from UACC-62 Passage 4 xenograft.

tag: in vivo passage


title: MCF10A-SNAI1-3

city: Cologne

first: Soyoung

last: Lim

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: Cologne medical school

description: gene expression data MCF10A upon SNAI1 expression

hyb_protocol: Following fragmentation, biotinylated cRNA was hybridized to HG-U133Plus_2.0 microarrays (Affymetrix, Inc., Santa Clara, CA, USA).

scan_protocol: The arrays were scanned in a GeneChip scanner 3000 (Affymetrix).

data_processing: Raw data representing the signal values of gene expression were pre-processed with the GeneChip Operating Software (GCOS) 1.4 Expression console 1.1 was used to obtain quality control data after MAS 5.0 statistical algorithm.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA extraction using RNeasyMini Kit (Qiagen)

tag: cell type

value: mammary epithelial cells

tag: cell line


title: 799-T

tag: histology

value: Squamous

value: F

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 70

tag: age at operation (yrs)

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: UACC-62_Passage 1 xenograft_R3

description:
UACC-62 P01 T3
Gene expression data from UACC-62 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: UACC-62_Passage 1 xenograft_R5

description:
UACC-62 P01 T5
Gene expression data from UACC-62 Passage 1 xenograft.


title: Rpb1-amr  RD35a

source_name: 1 wt

tag: cell line

tag: treatment


title: 792-T

tag: histology

value: Adenocarcinoma

tag: gender

tag: race

tag: tobacco history

value: Y

tag: final patient stage

value: IA Vs IIIB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 69

tag: age at operation (yrs)

tag: primary tumor site

value: Laryngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 68

tag: gender

value: Hypopharyngeal


title: MCF10A-SNAI1-2

tag: cell type

tag: cell line


title: head and neck squamous cell carcinoma 66


title: UACC-62_originating cell line_R3

description:
UACC-62 P0 T3
Gene expression data from UACC-62 originating cell line.

source_name: UACC-62, originating cell line

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 67

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection


title: MCF10A 2

description: gene expression data MCF10A


title: 758-T1

tag: histology

value: M

tag: race

tag: final patient stage

value: IIIA

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: UACC-62_Passage 1 xenograft_R1

description:
UACC-62 P01 T1
Gene expression data from UACC-62 Passage 1 xenograft.

value: malignant melanoma


title: MCF10A-SNAI1-1

tag: cell type


title: head and neck squamous cell carcinoma 65

tag: gender

value: male

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue


title: head and neck squamous cell carcinoma 61

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

value: peripheral blood


title: MCF10A 1

description: gene expression data MCF10A

value: mammary epithelial cells

tag: cell line


title: 771-T

tag: histology

value: Squamous

tag: race

tag: tobacco history

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: 759-T3

value: Adenocarcinoma

tag: gender

value: Caucasian


title: U251_Passage 10 xenograft_R5

description:
U251 P10 T5
Gene expression data from U251 Passage 10 xenograft.

source_name: U251, passage 10 xenograft

tag: originating cell line

tag: tumor type

value: glioblastoma

tag: in vivo passage


title: 764-T

value: F

value: Y

value: IB


title: UACC-62_originating cell line_R2

description:
UACC-62 P0 T2
Gene expression data from UACC-62 originating cell line.


title: MCF10A 3

description: gene expression data MCF10A

tag: cell type


title: 724-T


title: head and neck squamous cell carcinoma 64

tag: age at operation (yrs)

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 59

tag: gender

value: Oral Cavity


title: head and neck squamous cell carcinoma 57

value: Hypopharyngeal


title: U251_Passage 10 xenograft_R3

description:
U251 P10 T3
Gene expression data from U251 Passage 10 xenograft.

tag: originating cell line

tag: tumor type


title: U251_Passage 10 xenograft_R4

description:
U251 P10 T4
Gene expression data from U251 Passage 10 xenograft.

tag: in vivo passage


title: UACC-62_originating cell line_R1

description:
UACC-62 P0 T1
Gene expression data from UACC-62 originating cell line.

value: malignant melanoma


title: U251_Passage 10 xenograft_R2

description:
U251 P10 T2
Gene expression data from U251 Passage 10 xenograft.


title: 756-T1

tag: histology

value: M

tag: race

tag: final patient stage

value: IIIA

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 56

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Laryngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

value: non-drinker control

value: peripheral blood


title: 722-T

tag: histology

value: Squamous

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

value: IIIB

value: D


title: U251_Passage 4 xenograft_R4

description:
U251 P04 T4
Gene expression data from U251 Passage 4 xenograft.

source_name: U251, passage 4 xenograft

tag: originating cell line

tag: tumor type

value: glioblastoma

tag: in vivo passage


title: 717-T

value: Adenocarcinoma

value: Caucasian

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 55

tag: age at operation (yrs)

tag: primary tumor site

value: Sinonasal Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: alcohol drinking

tag: sample type

tag: tissue


title: U251_Passage 10 xenograft_R1

description:
U251 P10 T1
Gene expression data from U251 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: U251_Passage 4 xenograft_R5

description:
U251 P04 T5
Gene expression data from U251 Passage 4 xenograft.


title: 720-T

tag: histology

tag: gender

value: F

tag: race

tag: tobacco history

value: Y

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

value: N


title: head and neck squamous cell carcinoma 53

tag: age at operation (yrs)

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: survival status

tag: smoking status


title: head and neck squamous cell carcinoma 54

tag: gender

value: Hypopharyngeal

tag: relapse

tag: alcohol drinking

tag: sample type

tag: tissue


title: 686-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: recurrence

tag: last follow-up recurrence


title: U251_Passage 4 xenograft_R3

description:
U251 P04 T3
Gene expression data from U251 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 697-T

value: IIB

tag: vital statistics

tag: last follow-up survival


title: 670-T

tag: gender

value: Hispanic

value: IA

value: A


title: head and neck squamous cell carcinoma 52

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Laryngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

value: non-drinker control

value: peripheral blood


title: 654-T2

tag: histology

value: Squamous

value: M

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

value: D

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 51

tag: age at operation (yrs)

tag: gender

value: female

tag: primary tumor site

tag: hpv infection

tag: sample type

tag: tissue


title: U251_Passage 1 xenograft_R5

description:
U251 P01 T5
Gene expression data from U251 Passage 1 xenograft.

source_name: U251, passage 1 xenograft

tag: originating cell line

tag: tumor type

value: glioblastoma

tag: in vivo passage


title: U251_Passage 4 xenograft_R2

description:
U251 P04 T2
Gene expression data from U251 Passage 4 xenograft.


title: 633-T2

tag: histology

value: Adenocarcinoma

value: Caucasian

value: Y

tag: vital statistics

tag: last follow-up survival

value: N


title: 630-T

value: F

tag: race

tag: tobacco history

tag: final patient stage

value: IIB


title: U251_Passage 1 xenograft_R4

description:
U251 P01 T4
Gene expression data from U251 Passage 1 xenograft.


title: head and neck squamous cell carcinoma 50

value: Hypopharyngeal

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking


title: 619-T2

tag: gender

tag: date of birth

tag: date of surgery

tag: recurrence

tag: last follow-up recurrence


title: 650-T2

tag: histology

value: IB

tag: vital statistics

value: A

tag: last follow-up survival


title: U251_Passage 1 xenograft_R3

description:
U251 P01 T3
Gene expression data from U251 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: U251_Passage 1 xenograft_R2

description:
U251 P01 T2
Gene expression data from U251 Passage 1 xenograft.


title: head and neck squamous cell carcinoma 49

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: sample type

tag: tissue


title: U251_Passage 4 xenograft_R1

description:
U251 P04 T1
Gene expression data from U251 Passage 4 xenograft.


title: head and neck squamous cell carcinoma 46

tag: gender

value: Laryngeal

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

value: non-drinker control

value: peripheral blood


title: head and neck squamous cell carcinoma 48


title: U251_originating cell line_R2

description:
U251 P0 T2
Gene expression data from U251 originating cell line.

source_name: U251, originating cell line

tag: originating cell line


title: 602-T

tag: histology

value: Squamous

value: M

tag: race

tag: tobacco history

tag: final patient stage

value: IA

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: U251_Passage 1 xenograft_R1

description:
U251 P01 T1
Gene expression data from U251 Passage 1 xenograft.

tag: tumor type

value: glioblastoma

tag: in vivo passage


title: head and neck squamous cell carcinoma 44

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 40

value: female

tag: survival status

tag: smoking status

tag: alcohol drinking


title: 589-T2

tag: histology

value: Adenocarcinoma

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: SW-620_Passage 10 xenograft_R5

description:
SW-620 P10 T5
Gene expression data from SW-620 Passage 10 xenograft.

source_name: SW-620, passage 10 xenograft

tag: originating cell line

tag: tumor type

value: adenocarcinoma colon

tag: in vivo passage


title: U251_originating cell line_R1

description:
U251 P0 T1
Gene expression data from U251 originating cell line.


title: head and neck squamous cell carcinoma 37

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 39

value: Hypopharyngeal

tag: survival status

tag: smoking status

tag: alcohol drinking


title: 590-T

tag: histology

value: F

tag: race

tag: tobacco history

tag: final patient stage

value: IIA

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 36

tag: age at operation (yrs)

tag: gender

value: male

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

value: non-drinker control


title: head and neck squamous cell carcinoma 43

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue

value: peripheral blood


title: 566-T

tag: histology

value: M

tag: race

tag: tobacco history

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival


title: 593-T

tag: gender

value: IIB

tag: recurrence

tag: last follow-up recurrence


title: 582-T

value: Squamous


title: SW-620_Passage 10 xenograft_R2

description:
SW-620 P10 T2
Gene expression data from SW-620 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 545-T

value: Adenocarcinoma

value: D


title: head and neck squamous cell carcinoma 33

tag: age at operation (yrs)

tag: primary tumor site

value: Laryngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking


title: SW-620_Passage 10 xenograft_R4

description:
SW-620 P10 T4
Gene expression data from SW-620 Passage 10 xenograft.


title: SW-620_Passage 10 xenograft_R3

description:
SW-620 P10 T3
Gene expression data from SW-620 Passage 10 xenograft.


title: 555-T

tag: histology

tag: gender

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival


title: SW-620_Passage 4 xenograft_R2

description:
SW-620 P04 T2
Gene expression data from SW-620 Passage 4 xenograft.

source_name: SW-620, passage 4 xenograft

tag: originating cell line

tag: tumor type

value: adenocarcinoma colon

tag: in vivo passage


title: 535-T

source_name: Lung cancer specimen

tag: recurrence

value: N

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 31

tag: age at operation (yrs)

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: sample type

tag: tissue


title: 556-T

tag: histology

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

value: IIIA

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival


title: 539-T

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 29

tag: age at operation (yrs)

value: male

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: smoking status

tag: alcohol drinking


title: SW-620_Passage 4 xenograft_R3

description:
SW-620 P04 T3
Gene expression data from SW-620 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: SW-620_Passage 4 xenograft_R1

description:
SW-620 P04 T1
Gene expression data from SW-620 Passage 4 xenograft.


title: head and neck squamous cell carcinoma 28

tag: gender

value: Hypopharyngeal

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: sample type

tag: tissue


title: SW-620_Passage 4 xenograft_R4

description:
SW-620 P04 T4
Gene expression data from SW-620 Passage 4 xenograft.


title: 568-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: SW-620_Passage 10 xenograft_R1

description:
SW-620 P10 T1
Gene expression data from SW-620 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 27

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

value: Sinonasal Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: smoking status

tag: alcohol drinking

value: non-drinker control


title: head and neck squamous cell carcinoma 35

tag: survival status

tag: sample type

tag: tissue

value: peripheral blood


title: head and neck squamous cell carcinoma 34


title: 497-T

tag: histology

value: M

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: SW-620_Passage 1 xenograft_R5

description:
SW-620 P01 T5
Gene expression data from SW-620 Passage 1 xenograft.

source_name: SW-620, passage 1 xenograft

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 534-T

tag: gender

value: F

value: IB


title: 501-T

value: Squamous


title: head and neck squamous cell carcinoma 26

source_name: tumor sample

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking


title: head and neck squamous cell carcinoma 30

tag: sample type

tag: tissue


title: 485-T

tag: histology

tag: race

value: Hispanic

tag: tobacco history

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: SW-620_Passage 1 xenograft_R4

description:
SW-620 P01 T4
Gene expression data from SW-620 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 5 of 10

city: New Delhi

first: Pankaj

last: Kumar

state: Delhi

address: Mall Road,

department: G N R Knowledge Center for Genome Informatics

country: India

institute: Institiue of Genomics and Integrative Biology

hyb_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).

scan_protocol: Arrays were scanned on a the Axon Genepix 4000B scanner at 5 microns for both 532nm and 635nm channels

data_processing: Scanned images were processed using NimbleScan

source_name: H4K16ac ChIP DNA from HEK293 cells

extract_protocol: DMEM high glucose with 10% FBS, culture at 37C in 5% CO2

tag: cell line

tag: antibody

source_name: Input DNA from HEK293 cells

value: input


title: head and neck squamous cell carcinoma 25

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type


title: SW-620_Passage 4 xenograft_R5

description:
SW-620 P04 T5
Gene expression data from SW-620 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

value: adenocarcinoma colon


title: GS-2 H2K9me2

city: Tsukuba

first: Rieko

last: Ikeda

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

institute: RIKEN

description: Chip-chip GS cells H3K9me2

hyb_protocol: Arrays were hybridized in Maui hybridization stations for 17 h at 42C, and then washed according to manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on NimbleGen MS200.

data_processing: Array data were processed using Nimblescan ChIP data extraction.

source_name: H3K9me2 ChIP DNA from GS cells

label_protocol: The labeled ChIP DNA was concentrated by precipitation, and hybridized to Oligomicroarray, Mouse ChIP-chip 2.1M Whole-Genome Tiling - Array 10 of 10 (#05542600001).

growth_protocol: GS cells were cultured on MEF fedder cells in supplements containing StemPro-34 SFM medium

extract_protocol: GS cells were subjected to plate purification procedure to remove feeder cells. Chromatin Immunoprecipitation with anti-histone H3K9me2 was performed using purified GS cells, and 1 µg of immpunoprecipitated DNA was labeled by random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

tag: cell type

value: GS cells

tag: strain

tag: chip antibody

value: H3K9me2 (6D11, gift from Hiroshi Kimura) (Kimura et al, 2008)

source_name: none, input DNA

value: none, input DNA


title: SW-620_Passage 1 xenograft_R3

description:
SW-620 P01 T3
Gene expression data from SW-620 Passage 1 xenograft.

tag: in vivo passage


title: GS-1 H2K9me2

description: Chip-chip GS cells H3K9me2


title: 495-T

tag: histology

value: Adenocarcinoma

tag: gender

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IIIA

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: SW-620_Passage 1 xenograft_R1

description:
SW-620 P01 T1
Gene expression data from SW-620 Passage 1 xenograft.

tag: originating cell line


title: 475-T

value: F

value: N


title: 482-T

value: M

value: IB


title: head and neck squamous cell carcinoma 21

tag: age at operation (yrs)

value: male

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

source_name: healthy non-smoking volunteer

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 7 of 10

label_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).

tag: cell line

tag: antibody

value: input


title: head and neck squamous cell carcinoma 23

tag: gender

value: female

value: Oropharyngeal


title: head and neck squamous cell carcinoma 22

value: Oral Cavity


title: head and neck squamous cell carcinoma 24


title: 471-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 20

tag: age at operation (yrs)

tag: primary tumor site

value: Sinonasal Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status


title: SW-620_originating cell line_R2

description:
SW-620 P0 T2
Gene expression data from SW-620 originating cell line.

source_name: SW-620, originating cell line

tag: originating cell line

tag: tumor type

value: adenocarcinoma colon

tag: in vivo passage


title: SR_Passage 10 xenograft_R5

description:
SR P10 T5
Gene expression data from SR Passage 10 xenograft.

source_name: SR, passage 10 xenograft

value: SR

value: poorly differentiated B cell origin leukemia


title: cumulus-1 H2K9me2

description: Chip-chip cumulus cells H3K9me2

source_name: H3K9me2 ChIP DNA from cumulus cells

tag: cell type

value: cumulus

tag: strain

tag: chip antibody

value: H3K9me2 (6D11, gift from Hiroshi Kimura) (Kimura et al, 2008)

value: none, input DNA


title: SW-620_originating cell line_R1

description:
SW-620 P0 T1
Gene expression data from SW-620 originating cell line.


title: SR_Passage 10 xenograft_R4

description:
SR P10 T4
Gene expression data from SR Passage 10 xenograft.


title: 440-T

tag: histology

value: Squamous

tag: gender

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 439-T

value: Adenocarcinoma

value: M

value: IA

value: N


title: SW-620_originating cell line_R3

description:
SW-620 P0 T3
Gene expression data from SW-620 originating cell line.

tag: originating cell line


title: head and neck squamous cell carcinoma 19

tag: age at operation (yrs)

value: male

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: SR_Passage 10 xenograft_R3

description:
SR P10 T3
Gene expression data from SR Passage 10 xenograft.

tag: tumor type

tag: in vivo passage


title: 432-T

tag: histology

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 17

tag: age at operation (yrs)

tag: primary tumor site

value: Laryngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status


title: 416-T

tag: histology

tag: gender

value: F

tag: race

tag: tobacco history

tag: final patient stage

value: IIIA


title: SR_Passage 10 xenograft_R2

description:
SR P10 T2
Gene expression data from SR Passage 10 xenograft.

tag: originating cell line

value: SR

tag: tumor type

value: poorly differentiated B cell origin leukemia

tag: in vivo passage


title: 426-T

value: Caucasian

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 16

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 15

tag: gender

value: Hypopharyngeal

tag: survival status

tag: smoking status


title: head and neck squamous cell carcinoma 14

value: Oral Cavity


title: SR_Passage 10 xenograft_R1

description:
SR P10 T1
Gene expression data from SR Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 412-T

tag: histology

value: Adenocarcinoma

tag: race

value: Hispanic

tag: tobacco history

value: Y

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: SR_Passage 4 xenograft_R5

description:
SR P04 T5
Gene expression data from SR Passage 4 xenograft.

source_name: SR, passage 4 xenograft


title: SW-620_Passage 1 xenograft_R2

description:
SW-620 P01 T2
Gene expression data from SW-620 Passage 1 xenograft.

value: adenocarcinoma colon


title: SR_Passage 4 xenograft_R3

description:
SR P04 T3
Gene expression data from SR Passage 4 xenograft.


title: head and neck squamous cell carcinoma 13

tag: age at operation (yrs)

value: male

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: 404-T

tag: histology

tag: gender

value: M

tag: race

tag: tobacco history

tag: final patient stage

value: IA

tag: date of birth

value: A

value: N


title: 468-T

value: Squamous

value: F

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: SR_Passage 4 xenograft_R2

description:
SR P04 T2
Gene expression data from SR Passage 4 xenograft.

tag: originating cell line

value: SR

tag: tumor type

value: poorly differentiated B cell origin leukemia

tag: in vivo passage


title: 386-T

value: Caucasian


title: 393-T

value: IB


title: head and neck squamous cell carcinoma 12

tag: age at operation (yrs)

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking


title: head and neck squamous cell carcinoma 10

tag: gender

value: female

value: Laryngeal

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 11

value: Sinonasal Cavity


title: 399-T

tag: histology

value: Adenocarcinoma

tag: race

tag: tobacco history

value: Y

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 9

tag: age at operation (yrs)

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

value: male

value: non-drinker control

value: peripheral blood


title: SR_Passage 4 xenograft_R4

description:
SR P04 T4
Gene expression data from SR Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: SR_Passage 4 xenograft_R1

description:
SR P04 T1
Gene expression data from SR Passage 4 xenograft.


title: cumulus-2 H2K9me2

description: Chip-chip cumulus cells H3K9me2

tag: cell type

value: cumulus

tag: strain

tag: chip antibody

value: H3K9me2 (6D11, gift from Hiroshi Kimura) (Kimura et al, 2008)

value: none, input DNA


title: head and neck squamous cell carcinoma 6

tag: gender

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 8

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry


title: SR_Passage 1 xenograft_R5

description:
SR P01 T5
Gene expression data from SR Passage 1 xenograft.

source_name: SR, passage 1 xenograft

value: SR


title: 289-T

tag: histology

value: Squamous

value: M

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 346-T

tag: gender

value: F

value: Caucasian

value: IB

value: A

value: N


title: SR_Passage 1 xenograft_R1

description:
SR P01 T1
Gene expression data from SR Passage 1 xenograft.

tag: originating cell line

tag: tumor type

value: poorly differentiated B cell origin leukemia

tag: in vivo passage


title: SR_Passage 1 xenograft_R3

description:
SR P01 T3
Gene expression data from SR Passage 1 xenograft.


title: 363-T

value: Adenocarcinoma

value: Y


title: head and neck squamous cell carcinoma 5

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Oropharyngeal

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue


title: 296-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence


title: 374-T

tag: gender

value: IA

tag: last follow-up recurrence


title: 309-T


title: SR_Passage 1 xenograft_R4

description:
SR P01 T4
Gene expression data from SR Passage 1 xenograft.

tag: originating cell line

value: SR

tag: tumor type

tag: in vivo passage


title: SR_Passage 1 xenograft_R2

description:
SR P01 T2
Gene expression data from SR Passage 1 xenograft.


title: head and neck squamous cell carcinoma 3

tag: age at operation (yrs)

value: female

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

value: peripheral blood


title: 8W_mouse_liver_rep1

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

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

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for 4x44k v2 array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.
(A total of 16,523 orthologs across the human 4x44K v.2 Agilent oligonucleotide array, and the mouse 4x44K v.2 Agilent oligonucleotide array.)

source_name: Liver cells from P8W mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: CD45- Ter119- liver cells

value: pooled

tag: age


title: head and neck squamous cell carcinoma 2

tag: gender

tag: sample type


title: SR_originating cell line_R3

description:
SR P0 T3
Gene expression data from SR originating cell line.

source_name: SR, originating cell line

tag: originating cell line

tag: tumor type


title: 250-T

tag: histology

value: M

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 96-T

value: Adenocarcinoma


title: SN12C_Passage 10 xenograft_R3

description:
SN12C P10 T3
Gene expression data from SN12C Passage 10 xenograft.

source_name: SN12C, passage 10 xenograft

value: carcinoma renal

tag: in vivo passage


title: 18-T

value: Squamous

value: Y

value: IIIA

value: N


title: SR_originating cell line_R1

description:
SR P0 T1
Gene expression data from SR originating cell line.

value: poorly differentiated B cell origin leukemia


title: SN12C_Passage 10 xenograft_R5

description:
SN12C P10 T5
Gene expression data from SN12C Passage 10 xenograft.


title: 157-T

value: IIB


title: SN12C_Passage 10 xenograft_R2

description:
SN12C P10 T2
Gene expression data from SN12C Passage 10 xenograft.


title: SR_originating cell line_R2

description:
SR P0 T2
Gene expression data from SR originating cell line.

value: SR


title: SN12C_Passage 10 xenograft_R4

description:
SN12C P10 T4
Gene expression data from SN12C Passage 10 xenograft.


title: Melanocytes 24 hrs replicate 2

city: Callaghan

first: Nikola

last: Bowden

state: NSW

address: University Dr

department: School of Medicine and Public Health

country: Australia

institute: University of Newcastle

description: Replicate 2

hyb_protocol: The biotinylated cRNA was hybridised to Whole Genome Gene Expression Human Ref8 V3 BeadChips

scan_protocol: The BeadChips were scanned using standard Bead Array Reader protocol.

data_processing: The transcript expression results were cubic spline normalised using BeadStudio 2.0 software (Illumina, USA), and the remaining analyses was performed using GeneSpring GX 11.0. To account for bias or skewing of expression results all the gene expression profiles and each individual gene were normalized to the median resulting in two way normalisation. For visualisation of the results the data was log transformed

source_name: Melanocyte cell line

label_protocol: Duplicate total RNA from all cell lines at all time points, was amplified and biotinylated using the Illumina TotalPrep kit (Ambion, USA)

growth_protocol: All cell lines were routinely tested for mycoplasma every 3 months and were found to be free of contamination. All of the melanoma cell lines were cultured in DMEM (5% FCS) and the melanocytes were cultured in Medium 254. All cell lines were maintained in exponential growth at 37°C and 5% CO2

extract_protocol: Total RNA was extracted from all cell lines at all time points in duplicate using the SV Total RNA Isolation System (Promega)

treatment_protocol: Cells were treated with 10μg/mL cisplatin (Pharmacia Upjohn) as previously described (Avery-Kiejda, 2008) and harvested before treatment and 6 and 24 hours after treatment for gene expression analysis.

tag: cell line

value: Melanocytes

tag: time post-treatment


title: Melanocytes 24 hrs replicate 1

description: Replicate 1


title: Melanocytes 6 hrs replicate 2

description: Replicate 2


title: 15-T

source_name: Lung cancer specimen

tag: gender

value: A


title: SN12C_Passage 4 xenograft_R5

description:
SN12C P04 T5
Gene expression data from SN12C Passage 4 xenograft.

source_name: SN12C, passage 4 xenograft


title: SN12C_Passage 10 xenograft_R1

description:
SN12C P10 T1
Gene expression data from SN12C Passage 10 xenograft.


title: P3_ mouse_liver_rep1

source_name: Liver cells from P3 mice

tag: tissue

value: CD45- Ter119- liver cells

tag: age


title: E17.5_mouse_liver_rep1

source_name: Liver cells from E17.5 mice

value: pooled


title: E19.5_mouse_liver_rep1

source_name: Liver cells from E19.5 mice


title: P0_mouse_liver

source_name: Liver cells from P0 mice


title: E15.5_mouse_liver_rep1

source_name: Liver cells from E15.5 mice


title: E13.5_mouse_liver_rep1

source_name: Liver cells from E13.5 mice


title: Melanocytes 6 hrs replicate 1

description: Replicate 1


title: elp2_wound_rep3

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

description:
Gene expression 3 hr after wounding with a needle
Replicate 3

hyb_protocol: For each array, 1.65 μg of Cy3 or Cy5 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr. Samples were hybridized to Agilent-021169 Arabidopsis 4 × 44k arrays (Agilent Technologies). The arrays were washed according to the manufacturer's protocol.

scan_protocol: The arrays were scanned on a G2505B scanner (Agilent Technologies).

data_processing:
Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies).
Data (individual signal intensity values) obtained from the microarray probes were background corrected using a normexp+offset method, in which a small positive offset (k = 50) was added to move the corrected intensities away from zero. The resulting data were log transformed (using 2 as the base) and normalized between individual samples by scaling the individual log-transformed signal intensities so that all datasets had comparable lower quartile, median and upper quartile values. The normalized data is generated by R(2.15.2). After normalization, the Student’s t-test was performed considering a probe-by-probe comparison between different genotypes at the same time point using wild type (Col-0) as the reference sample and between different time points of the same genotype using the 0-hr sample as the reference. In each comparison, a p-value and fold change (FC) were computed for each gene locus. The gene expression fold changes were computed based on the normalized log-transformed signal intensity data.

organism: Arabidopsis thaliana

source_name: elp2, wounded 3hr

label_protocol: cDNA was synthesized from 200 ng of total RNA and used as a template for in vitro transcription in the presence of T7 RNA Polymerase and cyanine labeled CTPs using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol. The amplified, labeled complementary RNA (cRNA) was purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

growth_protocol: Arabidopsis seeds were sown on autoclaved soil (Sunshine MVP, Sun Gro Horticulture, Agawam, MA) and vernalized at 4°C for 3 days. Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.

extract_protocol: About 100 mg leaf tissues were ground into a fine powder in liquid nitrgen and resuspended in 500 μL 80°C water-saturated phenol and 500 μL 80°C extraction buffer (100 mM LiCl, 100 mM Tris pH 8.0, 10 mM EDTA, 1% SDS). After brief vortexing and centrifugation at 14,000 rpm for 5 min, the aqueous phase was transferred to another cold tube containing 500 μL of 24:1 chloroform:isoamyl alcohol. After vortexing and centrifugation, the aqueous phase was transferred to a DEPC-treated tube with 1/10 volume of 3 M NaOAc and 2 volume of 100% ethanol. The tube was inverted to mix and placed at -80°C for 30 min and then spun at 14,000 rpm for 15 min. After removing the supernatant, the pellet was washed with 80% ethanol, dried briefly, and resuspended in DEPC-treated water.

treatment_protocol: Botrytis cinerea was grown on BD Difco Potato Dextrose Agar (Becton, Dickinson and Company, Sparks, MD) for about 10 days at 25°C. Spores were harvested, resuspended in BD Difco Potato Dextrose Broth (Becton, Dickinson and Company) at a density of 1-5×10^5 spores per mL, and incubated for 2 hr prior to inoculation. Five-μL spore suspensions were dropped on the adaxial surface of rosette leaves where the leaves were gently wounded with a needle. Leaf tissues were collected at the indicated time points. Leaves that were only gently wounded with a needle were also collected at 3 hr as controls.

tag: strain/background

tag: genotype/variation

value: elp2 mutant

value: leaves

tag: treatment

value: wounded, non-infected with Botrytis cinerea

tag: time point

value: 3 hr


title: E11.5_mouse_liver_rep1

source_name: Liver cells from E11.5 mice


title: SN12C_Passage 4 xenograft_R2

description:
SN12C P04 T2
Gene expression data from SN12C Passage 4 xenograft.

tag: originating cell line

tag: tumor type


title: Col-0_wound_rep3

source_name: Col-0, wounded 3hr

value: wild type


title: SN12C_Passage 4 xenograft_R3

description:
SN12C P04 T3
Gene expression data from SN12C Passage 4 xenograft.

value: carcinoma renal


title: E9.5_mouse_liver

source_name: Liver cells from E9.5 mice


title: Melanocytes 0 hrs replicate 2

description: Replicate 2


title: SN12C_Passage 4 xenograft_R4

description:
SN12C P04 T4
Gene expression data from SN12C Passage 4 xenograft.


title: Melanocytes 0 hrs replicate 1

description: Replicate 1


title: SN12C_Passage 1 xenograft_R5

description:
SN12C P01 T5
Gene expression data from SN12C Passage 1 xenograft.

source_name: SN12C, passage 1 xenograft


title: elp2_wound_rep2

description:
Gene expression 3 hr after wounding with a needle
Replicate 2


title: E10.5_mouse_liver

source_name: Liver cells from E10.5 mice


title: SN12C_Passage 4 xenograft_R1

description:
SN12C P04 T1
Gene expression data from SN12C Passage 4 xenograft.


title: Col-0_wound_rep2


title: head and neck squamous cell carcinoma 1

source_name: tumor sample

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

source_name: healthy non-smoking volunteer

tag: sample type

value: non-drinker control

value: peripheral blood


title: elp2_wound_rep1

description:
Gene expression 3 hr after wounding with a needle
Replicate 1

tag: strain/background

tag: genotype/variation

tag: tissue


title: Sk-mel-28 24 hrs replicate 1

description: Replicate 1

source_name: Melanoma cell line

tag: cell line

tag: time post-treatment


title: Sk-mel-28 6 hrs replicate 2

description: Replicate 2


title: Sk-mel-28 6 hrs replicate 1

description: Replicate 1


title: SN12C_Passage 1 xenograft_R2

description:
SN12C P01 T2
Gene expression data from SN12C Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: SN12C_Passage 1 xenograft_R3

description:
SN12C P01 T3
Gene expression data from SN12C Passage 1 xenograft.


title: Col-0_wound_rep1

tag: treatment

tag: time point


title: Col-0_B.cinerea_48hr_rep3

description:
Gene expression 48 hr after Botrytis cinerea infection.
Replicate 3

source_name: Col-0, infected, 48hr

value: Botrytis cinerea infection

value: 48 hr


title: SN12C_Passage 1 xenograft_R4

description:
SN12C P01 T4
Gene expression data from SN12C Passage 1 xenograft.


title: Sk-mel-28 24 hrs replicate 2

description: Replicate 2


title: elp2_B.cinerea_48hr_rep3

source_name: elp2, infected, 48hr


title: SN12C_Passage 1 xenograft_R1

description:
SN12C P01 T1
Gene expression data from SN12C Passage 1 xenograft.


title: Sk-mel-28 0 hrs replicate 1

description: Replicate 1


title: SN12C_originating cell line_R2

description:
SN12C P0 T2
Gene expression data from SN12C originating cell line.

source_name: SN12C, originating cell line


title: Col-0_B.cinerea_48hr_rep2

description:
Gene expression 48 hr after Botrytis cinerea infection.
Replicate 2


title: 259-T

source_name: Lung cancer specimen

tag: histology

value: Adenocarcinoma

tag: gender

value: F

tag: race

value: African American

tag: tobacco history

value: Y

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: SN12C_originating cell line_R1

description:
SN12C P0 T1
Gene expression data from SN12C originating cell line.


title: Col-0_B.cinerea_48hr_rep1

description:
Gene expression 48 hr after Botrytis cinerea infection.
Replicate 1

tag: strain/background

tag: genotype/variation

tag: tissue

value: leaves


title: elp2_B.cinerea_48hr_rep1

value: elp2 mutant


title: Col-0_B.cinerea_24hr_rep2

description:
Gene expression 24 hr after Botrytis cinerea infection.
Replicate 2

source_name: Col-0, infected, 24hr

value: 24 hr


title: Me4405 24 hrs replicate 2

description: Replicate 2

tag: cell line

tag: time post-treatment


title: SF-539_Passage 1 xenograft_R5

description:
SF-539 P01 T5
Gene expression data from SF-539 Passage 1 xenograft.

source_name: SF-539, passage 1 xenograft

tag: originating cell line

tag: tumor type

value: glioblastoma

tag: in vivo passage


title: Me4405 6 hrs replicate 2

description: Replicate 2


title: Me4405 0 hrs replicate 2

description: Replicate 2


title: SF-539_Passage 1 xenograft_R3

description:
SF-539 P01 T3
Gene expression data from SF-539 Passage 1 xenograft.


title: Me4405 24 hrs replicate 1

description: Replicate 1


title: Sk-mel-28 0 hrs replicate 2

description: Replicate 2


title: elp2_B.cinerea_48hr_rep2

tag: treatment

tag: time point


title: SF-539_Passage 1 xenograft_R4

description:
SF-539 P01 T4
Gene expression data from SF-539 Passage 1 xenograft.


title: Me4405 6 hrs replicate 1

description: Replicate 1


title: Col-0_B.cinerea_24hr_rep3

description:
Gene expression 24 hr after Botrytis cinerea infection.
Replicate 3

value: wild type


title: elp2_B.cinerea_24hr_rep3

source_name: elp2, infected, 24hr


title: Mel-RM 24 hrs replicate 1

description: Replicate 1

value: Mel-RM


title: elp2_B.cinerea_24hr_rep2


title: elp2_B.cinerea_24hr_rep1

description:
Gene expression 24 hr after Botrytis cinerea infection.
Replicate 1


title: Me4405 0 hrs replicate 1

description: Replicate 1


title: Mel-RM 24 hrs replicate 2

description: Replicate 2


title: Col-0_B.cinerea_24hr_rep1


title: SF-539_Passage 1 xenograft_R2

description:
SF-539 P01 T2
Gene expression data from SF-539 Passage 1 xenograft.


title: SF-539_Passage 1 xenograft_R1

description:
SF-539 P01 T1
Gene expression data from SF-539 Passage 1 xenograft.


title: SF-539_originating cell line_R2

description:
SF-539 P0 T2
Gene expression data from SF-539 originating cell line.

source_name: SF-539, originating cell line


title: SF-268_Passage 1 xenograft_R5

description:
SF-268 P01 T5
Gene expression data from SF-268 Passage 1 xenograft.

source_name: SF-268, passage 1 xenograft

value: anaplastic astrocytoma


title: SF-539_originating cell line_R1

description:
SF-539 P0 T1
Gene expression data from SF-539 originating cell line.


title: Mel-RM 6 hrs replicate 2

description: Replicate 2


title: elp2_B.cinerea_12hr_rep3

description:
Gene expression 12 hr after Botrytis cinerea infection.
Replicate 3

source_name: elp2, infected, 12hr

value: 12 hr


title: SF-268_Passage 1 xenograft_R4

description:
SF-268 P01 T4
Gene expression data from SF-268 Passage 1 xenograft.


title: Mel-RM 6 hrs replicate 1

description: Replicate 1


title: Mel-RM 0 hrs replicate 2

description: Replicate 2


title: SF-268_Passage 1 xenograft_R3

description:
SF-268 P01 T3
Gene expression data from SF-268 Passage 1 xenograft.


title: IgR3 24 hrs replicate 2

description: Replicate 2


title: elp2_B.cinerea_12hr_rep2

description:
Gene expression 12 hr after Botrytis cinerea infection.
Replicate 2


title: SF-268_Passage 1 xenograft_R1

description:
SF-268 P01 T1
Gene expression data from SF-268 Passage 1 xenograft.


title: Col-0_B.cinerea_12hr_rep2

source_name: Col-0, infected, 12hr


title: elp2_B.cinerea_12hr_rep1

description:
Gene expression 12 hr after Botrytis cinerea infection.
Replicate 1


title: Col-0_B.cinerea_12hr_rep3


title: IgR3 24 hrs replicate 1

description: Replicate 1


title: IgR3 6 hrs replicate 2

description: Replicate 2


title: Col-0_B.cinerea_6hr_rep3

description:
Gene expression 6 hr after Botrytis cinerea infection.
Replicate 3

source_name: Col-0, infected, 6hr

value: 6 hr


title: SF-268_Passage 1 xenograft_R2

description:
SF-268 P01 T2
Gene expression data from SF-268 Passage 1 xenograft.


title: SF-268_originating cell line_R1

description:
SF-268 P0 T1
Gene expression data from SF-268 originating cell line.

source_name: SF-268, originating cell line


title: SF-268_originating cell line_R2

description:
SF-268 P0 T2
Gene expression data from SF-268 originating cell line.


title: Mel-RM 0 hrs replicate 1

description: Replicate 1


title: Clinical case 1 (Identification of adenovirus responsible for an outbreak of flu-like infections)

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

hyb_protocol: Labeled DNA were mixed in 60 ul of hybridization and added to the 8×60K EOPM for hybridization overnight at 65℃ in hybridization oven (Agilent). Then EOPM microarrays were washed with 2×SSC, 0.005%Triton X-100 at room temperature for 1min,and second wash with 0.2×SSC at 37℃ for 1 min

scan_protocol: scanned using a dual-laser scanner (Agilent)

data_processing: The images were extracted and analyzed using Feature Extraction software (Agilent).

source_name: serum

label_protocol: the first cDNA strand was reverse transcribed with a random decamer heeled with a PCR primer (5’- GTTTCCCAGTCACGATCNNNNNNNNN -3'). Then the cDNA was synthesized to double-stranded DNA by using the same primer with Klenow enzyme (Takara, Daian, China). After that, the amplification of the double stranded cDNA of both patients and normal control was performed by PCR utilizing the heel primer. Products of the PCR were then purified and labeled with Cy3-dCTP for normal control and Cy5-dCTP for patient sample, respectively, by using Klenow enzyme (Takara)

extract_protocol: Microbial nucleic acid were extracted using TIANamp Virus DNA/RNA Kit (TIANGEN Biotech., Beijing, China). The carrier RNA from the kit was applied to extract virus nucleic acid with small molecular weight

tag: sample type

value: disease

label_protocol: The first cDNA strand was reverse transcribed with a random decamer heeled with a PCR primer (5’- GTTTCCCAGTCACGATCNNNNNNNNN -3'). Then the cDNA was synthesized to double-stranded DNA by using the same primer with Klenow enzyme (Takara, Daian, China). After that, the amplification of the double stranded cDNA of both patients and normal control was performed by PCR utilizing the heel primer. Products of the PCR were then purified and labeled with Cy3-dCTP for normal control and Cy5-dCTP for patient sample, respectively, by using Klenow enzyme (Takara)

value: healthy control


title: IgR3 6 hrs replicate 1

description: Replicate 1


title: Col-0_B.cinerea_12hr_rep1

value: Botrytis cinerea infection


title: IgR3 0 hrs replicate 2

description: Replicate 2


title: Clinical case 2 (Cardiovirus discovery in a hand-foot-and-mouth child)


title: RXF 393_Passage 10 xenograft_R3

description:
RXF 393 P10 T3
Gene expression data from RXF 393 Passage 10 xenograft.

source_name: RXF 393, passage 10 xenograft

value: RXF 393

value: poorly differentiated hypernephroma


title: elp2_B.cinerea_6hr_rep3

source_name: elp2, infected, 6hr


title: Col-0_B.cinerea_6hr_rep2

description:
Gene expression 6 hr after Botrytis cinerea infection.
Replicate 2


title: RXF 393_Passage 10 xenograft_R2

description:
RXF 393 P10 T2
Gene expression data from RXF 393 Passage 10 xenograft.


title: RXF 393_Passage 10 xenograft_R5

description:
RXF 393 P10 T5
Gene expression data from RXF 393 Passage 10 xenograft.


title: RXF 393_Passage 10 xenograft_R4

description:
RXF 393 P10 T4
Gene expression data from RXF 393 Passage 10 xenograft.


title: MM200 24 hrs replicate 2

description: Replicate 2

source_name: Melanoma cell line


title: Col-0_B.cinerea_6hr_rep1

description:
Gene expression 6 hr after Botrytis cinerea infection.
Replicate 1


title: elp2_B.cinerea_6hr_rep2


title: RXF 393_Passage 10 xenograft_R1

description:
RXF 393 P10 T1
Gene expression data from RXF 393 Passage 10 xenograft.


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 3 of 10

source_name: H4K16ac ChIP DNA from HEK293 cells

tag: antibody

source_name: Input DNA from HEK293 cells

value: input


title: elp2_B.cinerea_6hr_rep1


title: IgR3 0 hrs replicate 1

description: Replicate 1


title: MM200 24 hrs replicate 1

description: Replicate 1


title: MM200 6 hrs replicate 2

description: Replicate 2


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 2 of 10


title: MM200 6 hrs replicate 1

description: Replicate 1


title: elp2_B.cinerea_3hr_rep3

description:
Gene expression 3 hr after Botrytis cinerea infection.
Replicate 3

source_name: elp2, infected, 3hr

value: 3 hr


title: RXF 393_Passage 4 xenograft_R4

description:
RXF 393 P04 T4
Gene expression data from RXF 393 Passage 4 xenograft.

source_name: RXF 393, passage 4 xenograft


title: RXF 393_Passage 4 xenograft_R2

description:
RXF 393 P04 T2
Gene expression data from RXF 393 Passage 4 xenograft.


title: RXF 393_Passage 4 xenograft_R3

description:
RXF 393 P04 T3
Gene expression data from RXF 393 Passage 4 xenograft.


title: Col-0_B.cinerea_3hr_rep3

source_name: Col-0, infected, 3hr


title: MM200 0 hrs replicate 2

description: Replicate 2


title: RXF 393_Passage 4 xenograft_R1

description:
RXF 393 P04 T1
Gene expression data from RXF 393 Passage 4 xenograft.


title: MM200 0 hrs replicate 1

description: Replicate 1


title: elp2_B.cinerea_3hr_rep2

description:
Gene expression 3 hr after Botrytis cinerea infection.
Replicate 2


title: RXF 393_Passage 1 xenograft_R5

description:
RXF 393 P01 T5
Gene expression data from RXF 393 Passage 1 xenograft.

source_name: RXF 393, passage 1 xenograft


title: elp2_B.cinerea_3hr_rep1

description:
Gene expression 3 hr after Botrytis cinerea infection.
Replicate 1


title: Col-0_B.cinerea_3hr_rep2


title: Col-0_B.cinerea_3hr_rep1


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 1 of 10


title: RXF 393_Passage 1 xenograft_R4

description:
RXF 393 P01 T4
Gene expression data from RXF 393 Passage 1 xenograft.


title: elp2_B.cinerea_0hr_rep1

description:
Gene expression 0 hr after Botrytis cinerea infection.
Replicate 2

source_name: elp2, infected, 0hr

value: 0 hr


title: RXF 393_Passage 1 xenograft_R2

description:
RXF 393 P01 T2
Gene expression data from RXF 393 Passage 1 xenograft.


title: elp2_B.cinerea_0hr_rep2

description:
Gene expression 0 hr after Botrytis cinerea infection.
Replicate 1

value: leaves


title: Col-0_B.cinerea_0hr_rep1

source_name: Col-0, infected, 0hr


title: Col-0_B.cinerea_0hr_rep2


title: RXF 393_Passage 1 xenograft_R3

description:
RXF 393 P01 T3
Gene expression data from RXF 393 Passage 1 xenograft.


title: RXF 393_originating cell line_R3

description:
RXF 393 P0 T3
Gene expression data from RXF 393 originating cell line.

source_name: RXF 393, originating cell line


title: RXF 393_Passage 1 xenograft_R1

description:
RXF 393 P01 T1
Gene expression data from RXF 393 Passage 1 xenograft.