title: 2239-T

tag: histology

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


title: A673_CloneAsp14_Dox_72h_1

status: Public on Jul 01 2013

type: RNA

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 72 hours, replica 1

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol: DMEM + GlutaMAXTM-I (+ 4,5g/L D-Glucose + Pyruvate) (Gibco/invitrogen 31966)  + Penicillin/Streptomycin (1x) (100x Stock PAA)  +  50 µg/ml Zeocin (for the shRNA expression vector) (powder Cayla)  and 2 µg/ml Blasticidin (for the TR expression vector)(powder Invitrogen)

extract_protocol: RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.

treatment_protocol: 72 hours after addition of 1 µg/ml Doxycyline

tag: treatment

value: 1 ug/ml doxycyline

tag: time

tag: cell line

tag: transgene

value: doxycyclin  inducible EWS-FLI1 knockdown

tag: sample type


title: 2237-T

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

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)

value: Adenocarcinoma

tag: gender

value: F

value: Y

value: A

tag: recurrence

value: N

tag: last follow-up recurrence


title: CAKI-1_Passage 10 xenograft_R4

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description:
CAKI-1 P10 T4
Gene expression data from CAKI-1 Passage 10 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: CAKI-1, passage 10 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: carcinoma renal cell

tag: in vivo passage


title: 2259-T

tag: histology

tag: race

value: African American

tag: tobacco history

value: IA


title: head and neck squamous cell carcinoma 252

type: genomic

city: Tokyo

first: Mitsuyoshi

last: Urashima

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

country: Japan

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

tag: alcohol drinking

source_name: healthy non-smoking volunteer

value: male

value: non-drinker control

tag: tissue

value: peripheral blood


title: A673_CloneAsp14_Dox_36h_2

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 36 hours, replica 2

treatment_protocol: 36 hours after addition of 1 µg/ml Doxycyline

tag: treatment

tag: time

tag: cell line

tag: transgene

tag: sample type

value: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct


title: CAKI-1_Passage 10 xenograft_R3

description:
CAKI-1 P10 T3
Gene expression data from CAKI-1 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: CAKI-1_Passage 10 xenograft_R1

description:
CAKI-1 P10 T1
Gene expression data from CAKI-1 Passage 10 xenograft.


title: 2212-T

tag: histology

tag: gender

tag: race

value: Asian

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

tag: recurrence

tag: last follow-up recurrence


title: A673_CloneAsp14_Dox_53h_1

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 53 hours, replica 1

treatment_protocol: 53 hours after addition of 1 µg/ml Doxycyline

tag: treatment

value: 1 ug/ml doxycyline

tag: time

tag: cell line

value: doxycyclin  inducible EWS-FLI1 knockdown


title: CAKI-1_Passage 10 xenograft_R2

description:
CAKI-1 P10 T2
Gene expression data from CAKI-1 Passage 10 xenograft.

tag: originating cell line


title: A673_CloneAsp14_Dox_53h_2

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 53 hours, replica 2

tag: transgene

tag: sample type


title: 2230-T

tag: histology

value: Adenocarcinoma

value: F

value: Caucasian


title: 2207-T

tag: gender

value: N

value: A


title: A673_CloneAsp14_Dox_36h_3

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 36 hours, replica 3


title: 2211-T

value: Squamous

value: M

tag: race

value: Y

value: IIB


title: CAKI-1_Passage 4 xenograft_R5

description:
CAKI-1 P04 T5
Gene expression data from CAKI-1 Passage 4 xenograft.

source_name: CAKI-1, passage 4 xenograft

tag: tumor type

value: carcinoma renal cell

tag: in vivo passage


title: A673_CloneAsp14_Dox_36h_1

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 36 hours, replica 1


title: head and neck squamous cell carcinoma 248

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

value: non-drinker control

tag: tissue


title: head and neck squamous cell carcinoma 251

tag: sample type

value: peripheral blood


title: A673_CloneAsp14_Dox_18h_3

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 18 hours, replica 3

treatment_protocol: 18 hours after addition of 1 µg/ml Doxycyline

tag: treatment

tag: time

tag: cell line

tag: transgene

value: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct


title: 2269-T

tag: histology

tag: gender

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

tag: last follow-up recurrence


title: CAKI-1_Passage 4 xenograft_R4

description:
CAKI-1 P04 T4
Gene expression data from CAKI-1 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 2204-T

value: IB


title: head and neck squamous cell carcinoma 250

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: alcohol drinking

tag: sample type

tag: tissue


title: CAKI-1_Passage 4 xenograft_R3

description:
CAKI-1 P04 T3
Gene expression data from CAKI-1 Passage 4 xenograft.


title: head and neck squamous cell carcinoma 245

tag: gender


title: head and neck squamous cell carcinoma 244

value: Hypopharyngeal


title: MLL5 chromatin profiling (replicates 1-3)

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

description:
DamID-based MLL5 chromatin profiling
Three biological replicates:
rep1 = A
rep2 = B
rep3 = C

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
For DamID chromatin profiling, raw signals of corresponding experimental replicates were loess normalized within arrays and quantile normalized between arrays (C2C12A,B,C). The mean was calculated (C2C12_mean_normalized.wig).  Enrichment statistics (test versus control signals) were computed using the ‘sam’ algorithm within Bioconductor . Fdr values of the sam statistic were determined using ‘locfdr’ . Region summarization was performed using the HMM algorithm of TileMap (Straub et al., 2008) . Probes were considered to be bound significantly if the posterior probability of the HMM was greater than 0.9 and the enriched region was larger than 0.5 Kb (MLL5 bound regions.txt). To evaluate overlaps between MLL5 bound promoters and histone modifications in C2C12, we lift-over the MLL5 bound regions from the built mm8 to mm9. Overlaps were analyzed using Galaxy (Goecks, J., 2010, Blankenberg D., 2010, Giardine B., 2005)
value definition (in the nomalized/processed data files): Log 2 ratio (Dam_MLL5 vs Dam)

organism: Mus musculus

source_name: Dam_MLL5 expressed in myoblast C2C12 cells

label_protocol: 1 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers ( DNA isolated from DamMLL5 expressing cells) or with Cy3 nonamers (DNA isolated from Dam expressing cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Dam_MLL5 transfected cells cells were incubated for 48h at 37 C

extract_protocol: For DamID experiments, genomic DNA from DamMLL5- or Dam- expressing cells was recovered, DpnI digested, fractionated and amplified according to Vogel, M.J., et al ( Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2, 1467-78 (2007))

treatment_protocol: C2C12 cells were transduced with DamMLL5 expressing viruses

tag: cell line

value: Undifferentiated C2C12 Cells

tag: transfection

value: Dam_MLL5 expressing virus

source_name: Dam expressed in myoblast C2C12 cells

growth_protocol: Dam transfected cells cells were incubated for 48h at 37 C

treatment_protocol: C2C12 cells were transduced with Dam expressing viruses

value: Dam expressing virus


title: head and neck squamous cell carcinoma 243


title: CAKI-1_Passage 1 xenograft_R4

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

source_name: CAKI-1, passage 1 xenograft

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 2190-T

tag: histology

value: Adenocarcinoma

value: F

tag: race

value: Hispanic

tag: tobacco history

value: N

tag: final patient stage

value: IA

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: CAKI-1_Passage 4 xenograft_R2

description:
CAKI-1 P04 T2
Gene expression data from CAKI-1 Passage 4 xenograft.

value: carcinoma renal cell


title: 2185-T

value: Caucasian

value: Y

value: IIIA


title: CAKI-1_Passage 4 xenograft_R1

description:
CAKI-1 P04 T1
Gene expression data from CAKI-1 Passage 4 xenograft.


title: A673_CloneAsp14_Dox_0h_4

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 4

treatment_protocol: control at timepoint of doxycyclin  addition

tag: treatment

value: control

tag: time

value: 0 h

tag: transgene

value: doxycyclin  inducible EWS-FLI1 knockdown

tag: sample type

value: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct


title: A673_CloneAsp14_Dox_0h_3

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 3

tag: cell line


title: A673_CloneAsp14_Dox_0h_1

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 1


title: A673_CloneAsp14_Dox_18h_1

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 18 hours, replica 1

value: 1 ug/ml doxycyline


title: CAKI-1_Passage 1 xenograft_R5

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

tag: originating cell line

tag: tumor type


title: A673_CloneAsp14_Dox_18h_2

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 18 hours, replica 2


title: 2192-T

tag: histology

tag: gender

value: M

value: IB


title: 2177-T

value: Squamous

tag: race

tag: tobacco history

value: IIA


title: CAKI-1_Passage 1 xenograft_R2

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

tag: in vivo passage


title: head and neck squamous cell carcinoma 242

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

value: non-drinker control

tag: tissue

value: peripheral blood


title: head and neck squamous cell carcinoma 240

value: Sinonasal Cavity

tag: sample type


title: 2178-T

tag: histology

tag: gender

value: F

value: Caucasian

tag: final patient stage

value: IIIB

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: A673_CloneAsp14_Dox_0h_2

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 2

tag: treatment

value: control

tag: time

value: 0 h

tag: cell line

tag: transgene


title: 2172-T

value: Adenocarcinoma

tag: race

value: Asian

tag: tobacco history

value: N

value: IA

value: Y


title: CAKI-1_Passage 1 xenograft_R3

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

tag: originating cell line

tag: tumor type

value: carcinoma renal cell

tag: in vivo passage


title: head and neck squamous cell carcinoma 239

tag: age at operation (yrs)

tag: gender

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

tag: tissue


title: CAKI-1_Passage 1 xenograft_R1

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

tag: originating cell line


title: head and neck squamous cell carcinoma 241

value: Oropharyngeal


title: 2167-T

tag: histology

value: Squamous

tag: race

tag: tobacco history

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: head and neck squamous cell carcinoma 238

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

value: non-drinker control

value: peripheral blood


title: head and neck squamous cell carcinoma 237

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 236


title: 2078-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: A

tag: last follow-up survival


title: 2086-T

tag: gender

value: F

tag: recurrence

tag: last follow-up recurrence


title: 2155-T

value: Adenocarcinoma


title: head and neck squamous cell carcinoma 235

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


title: CA46_Passage 10 xenograft_R3

description:
CA46 P10 T3
Gene expression data from CA46 Passage 10 xenograft.

source_name: CA46, passage 10 xenograft

tag: originating cell line

tag: tumor type

value: lymphoblastic Burkitt's lymphoma

tag: in vivo passage


title: CA46_Passage 10 xenograft_R4

description:
CA46 P10 T4
Gene expression data from CA46 Passage 10 xenograft.


title: CA46_Passage 10 xenograft_R5

description:
CA46 P10 T5
Gene expression data from CA46 Passage 10 xenograft.


title: 2135-T

tag: histology

tag: race

value: Asian

tag: tobacco history

value: N

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery


title: CAKI-1_originating cell line_R1

description:
CAKI-1 P0 T1
Gene expression data from CAKI-1 originating cell line.

source_name: CAKI-1, originating cell line

value: carcinoma renal cell


title: CA46_Passage 10 xenograft_R2

description:
CA46 P10 T2
Gene expression data from CA46 Passage 10 xenograft.


title: CA46_Passage 4 xenograft_R5

description:
CA46 P04 T5
Gene expression data from CA46 Passage 4 xenograft.

source_name: CA46, passage 4 xenograft


title: 2035-T

value: Squamous

tag: gender

value: Y

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: CA46_Passage 4 xenograft_R4

description:
CA46 P04 T4
Gene expression data from CA46 Passage 4 xenograft.


title: head and neck squamous cell carcinoma 231

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: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: 2029-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

value: IIIA

tag: date of birth

tag: date of surgery

value: D


title: head and neck squamous cell carcinoma 234

tag: age at operation (yrs)

tag: gender

tag: chemoradiotherapy

tag: relapse

value: non-drinker control

value: peripheral blood


title: CAKI-1_originating cell line_R2

description:
CAKI-1 P0 T2
Gene expression data from CAKI-1 originating cell line.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 2076-T

value: M

value: Caucasian

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 2024-T

tag: histology

value: F

value: IB

value: A


title: 2031-T

tag: race

value: IIB


title: CA46_Passage 10 xenograft_R1

description:
CA46 P10 T1
Gene expression data from CA46 Passage 10 xenograft.

value: lymphoblastic Burkitt's lymphoma


title: head and neck squamous cell carcinoma 226

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: 2006-T

tag: gender

tag: tobacco history

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery


title: head and neck squamous cell carcinoma 232

tag: age at operation (yrs)

tag: chemoradiotherapy

tag: relapse


title: head and neck squamous cell carcinoma 230

tag: primary tumor site

tag: hpv infection


title: CA46_Passage 4 xenograft_R3

description:
CA46 P04 T3
Gene expression data from CA46 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 233

value: female

value: Oral Cavity

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: survival status

tag: smoking status


title: head and neck squamous cell carcinoma 228

tag: gender

value: male

tag: alcohol drinking

tag: sample type

tag: tissue


title: 1992-T

tag: histology

value: Squamous

tag: race

tag: tobacco history

value: Y

tag: final patient stage

value: IA

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: 1987-T

value: Adenocarcinoma

value: D


title: 1985-T

value: Caucasian


title: head and neck squamous cell carcinoma 229

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

value: non-drinker control

value: peripheral blood


title: CA46_Passage 4 xenograft_R2

description:
CA46 P04 T2
Gene expression data from CA46 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: CA46_Passage 1 xenograft_R5

description:
CA46 P01 T5
Gene expression data from CA46 Passage 1 xenograft.

source_name: CA46, passage 1 xenograft


title: CA46_Passage 4 xenograft_R1

description:
CA46 P04 T1
Gene expression data from CA46 Passage 4 xenograft.


title: head and neck squamous cell carcinoma 223

tag: gender

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: Epididymal's luminal fluid from cauda, replicate 3

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Labeled miRNA was hybridized on the GeneChip miRNA Array (Affymetrix, Santa Clara, CA, USA) according to the protocol described in the FlashTag Biotin HSR system (Genisphere).

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix).

data_processing: Data were analyzed using the miRNA QC Tool software for quality control (www.affymetrix.com), and CEL files were imported and analyzed with the Partek Genomics Suite 6.5 software (Partek Incorporated, St Louis, MO). Signals were RMA normalized.

organism: Bos taurus

source_name: cauda luminal fluid

label_protocol: 100 ng of each miRNA sample was labeled with the FlashTag Biotin HSR (Genisphere, Hatfield, PA, USA) following the manufacturer's recommendations.

extract_protocol: miRNAs were extracted from perfused epithelia as previously described (Belleannee et al., 2010). Briefly, tissues were frozen in liquid nitrogen, then powdered in a pestle and mortar, and homogenized in mirVana lysis/binding buffer (Life technologies, Burlington, ON, Canada). Small RNAs were purified with the mirVana kit as described above.

treatment_protocol: Epididymides from sexually mature bulls were obtained from a commercial slaughterhouse. Six epididymides provided from 3 different bulls were dissected and kept on ice prior to perfusion. The technique of intraluminal perfusion was adapted from Belleannee et al., 2010 (PMID 20692385) in order to portrait miRNAs contained in epididymosomes and their surrounding epithelium in caput and cauda epididymal regions. Briefly, after removal of the connective tissues from the middle caput region of the epididymidis, a small incision was made to insert a catheter into the isolated tubule. The lumen was perfused with PBS (137 mM NaCl, 3 mM KCl, 8 mM Na2HPO4 and 1.5 mM KH2PO4) at a rate of 10 μl/min controlled by a syringe pump, and the perfusate flowing out of the tubule was collected until obtaining a clear sperm-free perfusate. Epididymal fluid from the cauda region was obtained by retrograde perfusion with a syringe inserted in the proximal portion of the vas deferens. In order to maximize the yield of epididymosome purification from each animal, perfusates collected from the same regions of two paired epididymides were pooled. Spermatozoa were isolated from caput and cauda epididymal fluids by two centrifugations at 3000 x g for 20 min and supernatants were kept at -80oC prior to epididymosome preparation. Once perfused, sperm-free tissues were directly frozen in liquid nitrogen and kept at -80oC prior to miRNA extraction and purification. Epididymosomes were prepared as previously described (Frenette et al., 2006). Briefly, the 3000 × g supernatants were ultracentrifuged at 120 000 × g at 4°C for 2 hrs in a swinging bucket rotor (MLS-50; Beckman). Pellets were resuspended in cold PBS and subjected to another ultracentrifugation at 120 000 × g at 4°C for 2 hrs. Pellets were either fixed for scanning electron microscopy or resuspended in 50 µl of PBS prior to Bradford protein assay. Between 240 and 410 µg of protein-containing epididymosomes were recovered from the different samples and were directly subjected to miRNA extraction and purification.

value: epididymosomes

tag: epididymal region

value: cauda


title: Epididymal's luminal fluid from cauda, replicate 2


title: head and neck squamous cell carcinoma 227

tag: age at operation (yrs)

tag: primary tumor site

value: Laryngeal


title: Epididymal's luminal fluid from caput, replicate 3

source_name: caput luminal fluid

value: caput


title: Epididymal's luminal fluid from cauda, replicate 1


title: head and neck squamous cell carcinoma 224

tag: hpv infection

tag: p16 protein immunohistochemistry


title: 1974-T

tag: histology

value: M

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

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 222

tag: gender

value: female

value: Sinonasal Cavity

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

value: male

tag: sample type


title: Epididymal's luminal fluid from caput, replicate 2

tag: tissue

tag: epididymal region


title: 1972-T

tag: histology

value: F

tag: race

value: Asian

tag: tobacco history

value: Y

tag: final patient stage

value: IA

tag: date of birth

value: A


title: 1978-T

value: Squamous

value: Caucasian

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: CA46_Passage 1 xenograft_R4

description:
CA46 P01 T4
Gene expression data from CA46 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

value: lymphoblastic Burkitt's lymphoma

tag: in vivo passage


title: head and neck squamous cell carcinoma 221

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: survival status

tag: smoking status

tag: alcohol drinking

value: non-drinker control

value: peripheral blood


title: Epididymal's luminal fluid from caput, replicate 1

tag: tissue

value: epididymosomes

tag: epididymal region

value: caput


title: 1966-T

tag: histology

value: Adenocarcinoma

value: M

tag: race

value: African American

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: head and neck squamous cell carcinoma 220

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

tag: sample type


title: head and neck squamous cell carcinoma 218

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: tissue


title: CA46_Passage 1 xenograft_R2

description:
CA46 P01 T2
Gene expression data from CA46 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: CA46_Passage 1 xenograft_R1

description:
CA46 P01 T1
Gene expression data from CA46 Passage 1 xenograft.


title: 1964-T

tag: histology

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

tag: recurrence

tag: last follow-up recurrence


title: 1956-T

tag: gender

value: F


title: CA46_originating cell line_R2

description:
CA46 P0 T2
Gene expression data from CA46 originating cell line.

source_name: CA46, originating cell line


title: Epididymal's epithelial cells from cauda, replicate 3

source_name: cauda epithelial cells

value: epididymis

tag: epididymal region

value: cauda


title: head and neck squamous cell carcinoma 217

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

tag: sample type


title: head and neck squamous cell carcinoma 216

tag: tissue


title: Epididymal's epithelial cells from cauda, replicate 2


title: Epididymal's epithelial cells from cauda, replicate 1


title: 1947-T

tag: histology

value: Squamous

tag: race

value: Caucasian

tag: tobacco history

value: Y

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


title: 1944-T

value: Adenocarcinoma

tag: gender

value: Hispanic

value: IIIB

tag: last follow-up recurrence


title: 1942-T

value: D


title: Epididymal's epithelial cells from caput, replicate 2

source_name: caput epithelial cells

tag: epididymal region

value: caput


title: AsPC-1_Passage 10 xenograft_R5

description:
AsPC-1 P10 T5
Gene expression data from AsPC-1 Passage 10 xenograft.

source_name: AsPC-1, passage 10 xenograft

tag: originating cell line

tag: tumor type

value: adenocarcinoma pancreatic

tag: in vivo passage


title: Epididymal's epithelial cells from caput, replicate 3


title: AsPC-1_Passage 10 xenograft_R3

description:
AsPC-1 P10 T3
Gene expression data from AsPC-1 Passage 10 xenograft.


title: 1936-T

source_name: Lung cancer specimen

value: M

value: N

value: IV


title: AsPC-1_Passage 10 xenograft_R4

description:
AsPC-1 P10 T4
Gene expression data from AsPC-1 Passage 10 xenograft.


title: AsPC-1_Passage 10 xenograft_R2

description:
AsPC-1 P10 T2
Gene expression data from AsPC-1 Passage 10 xenograft.


title: 1933-T

value: F

value: African American

value: IIIA


title: head and neck squamous cell carcinoma 214

source_name: tumor sample

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

value: peripheral blood


title: AsPC-1_Passage 10 xenograft_R1

description:
AsPC-1 P10 T1
Gene expression data from AsPC-1 Passage 10 xenograft.


title: CA46_originating cell line_R1

description:
CA46 P0 T1
Gene expression data from CA46 originating cell line.

value: lymphoblastic Burkitt's lymphoma


title: head and neck squamous cell carcinoma 213

tag: gender

source_name: healthy non-smoking volunteer

tag: tissue


title: head and neck squamous cell carcinoma 215


title: head and neck squamous cell carcinoma 211

value: Oropharyngeal


title: head and neck squamous cell carcinoma 212


title: heart_basal_male3

city: Bethesda

first: Delong

last: Liu

address: 10 Central Drive

department: NHLBI

institute: NIH

hyb_protocol: labeled miRNA was analyzed for quality using 79 the Genisphere ELOSA QC assay and hybridized to a Affymetrix GeneChip miRNA 1.0 array for 16 hours

scan_protocol: Affymetrix GeneChip scanner

data_processing: MiRNA QC tool software (now, merged into Affymetrix Expression Console) was used to extract log2 signal intensities on the mouse miRNA probesets.

source_name: heart homogenate male mouse 3

label_protocol: Genisphere FlashTag Biotin HSR RNA labeling kit (Hatfield, PA, USA)

extract_protocol: miRNA was extracted using Qiagen miRNAeasy extraction kit

value: heart homogenate


title: heart_basal_male2

source_name: heart homogenate male mouse 2


title: heart_basal_male4

source_name: heart homogenate male mouse 4


title: heart_basal_female4

source_name: heart homogenate female mouse 4

value: female


title: AsPC-1_Passage 4 xenograft_R4

description:
AsPC-1 P04 T4
Gene expression data from AsPC-1 Passage 4 xenograft.

source_name: AsPC-1, passage 4 xenograft

tag: originating cell line


title: 1921-T

tag: histology

value: Adenocarcinoma

tag: race

value: Caucasian

tag: tobacco history

value: Y

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 210

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


title: CA46_Passage 1 xenograft_R3

description:
CA46 P01 T3
Gene expression data from CA46 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 1908-T

tag: histology

tag: gender

tag: race

tag: tobacco history

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

value: N


title: AsPC-1_Passage 4 xenograft_R1

description:
AsPC-1 P04 T1
Gene expression data from AsPC-1 Passage 4 xenograft.

value: adenocarcinoma pancreatic


title: heart_basal_female3

source_name: heart homogenate female mouse 3

tag: tissue


title: 1913-T

value: F

value: IA

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 207

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: smoking status

tag: alcohol drinking

tag: sample type


title: 1930-T

tag: histology

tag: gender

value: M

tag: race

value: African American

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery


title: AsPC-1_Passage 4 xenograft_R5

description:
AsPC-1 P04 T5
Gene expression data from AsPC-1 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: AsPC-1_Passage 4 xenograft_R2

description:
AsPC-1 P04 T2
Gene expression data from AsPC-1 Passage 4 xenograft.


title: heart_basal_female2

source_name: heart homogenate female mouse 2

tag: tissue


title: AsPC-1_Passage 4 xenograft_R3

description:
AsPC-1 P04 T3
Gene expression data from AsPC-1 Passage 4 xenograft.


title: head and neck squamous cell carcinoma 209

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: survival status

value: non-drinker control

value: peripheral blood


title: AsPC-1_Passage 1 xenograft_R5

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

source_name: AsPC-1, passage 1 xenograft


title: AsPC-1_Passage 1 xenograft_R4

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


title: head and neck squamous cell carcinoma 205

tag: gender

tag: chemoradiotherapy

tag: relapse

tag: smoking status

tag: alcohol drinking

tag: sample type


title: head and neck squamous cell carcinoma 219

value: Oropharyngeal


title: head and neck squamous cell carcinoma 202

value: Laryngeal


title: head and neck squamous cell carcinoma 204


title: RadioresistantBxPC3 subline #2

city: Shanghai

first: Peng

last: Wang

address: 270 Dong An Road

department: Department of Integrative Oncology

country: China

institute: Fudan University Shanghai Cancer Center

hyb_protocol: The total amount of RNA was hybridized to the arrays for 16 hours at 48C with rotation at 60rpm.

scan_protocol: Samples were scanned using the GCS 3000 7G Scanner and processed using miRNA_1-0_2xgain library files.

data_processing: The data was preprocessed using the Affymetrix miRNA QC tool where Individual feature intensities were flagged by detection calls, background subtracted, transformed through addition of a small constant and median summarized.

source_name: RadioresistantBxPC3 subline #2

label_protocol: A total of 500-1000ng of total RNA was labelled using the Genisphere HSR labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html).

growth_protocol: Cell lines were grown in DMEM + 10% FCS

extract_protocol: miRNAs were isolated with MirVana® miRNA isolation Kit, Ambion, AM1560

tag: cell type

value: Human pancreatic duct cells

tag: cell line


title: head and neck squamous cell carcinoma 203


title: 1888-T

tag: histology

value: Adenocarcinoma

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IIB

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: heart_basal_female1

source_name: heart homogenate female mouse 1

tag: gender

value: female

tag: tissue

value: heart homogenate


title: 1898-T

value: F

value: IIIB

value: A

value: N


title: Radioresistant BxPC3 subline #1

source_name: Radioresistant BxPC3 subline #1


title: head and neck squamous cell carcinoma 201

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

value: male


title: AsPC-1_Passage 1 xenograft_R3

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

tag: originating cell line

tag: tumor type

value: adenocarcinoma pancreatic

tag: in vivo passage


title: BxPC3 cell line

source_name: BxPC3 cell line

tag: cell type

tag: cell line


title: AsPC-1_originating cell line_R3

description:
AsPC-1 P0 T3
Gene expression data from AsPC-1 originating cell line.

source_name: AsPC-1, originating cell line


title: 1894-T

tag: histology

tag: gender

value: M

tag: race

tag: tobacco history

tag: final patient stage

value: IA

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 1872-T

value: IV


title: head and neck squamous cell carcinoma 199

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

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: 1884-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


title: AsPC-1_Passage 1 xenograft_R1

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

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 1870-T

value: IB

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 198

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: alcohol drinking


title: head and neck squamous cell carcinoma 197

tag: gender

value: Laryngeal

tag: sample type

tag: tissue


title: AsPC-1_Passage 1 xenograft_R2

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

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: AsPC-1_originating cell line_R2

description:
AsPC-1 P0 T2
Gene expression data from AsPC-1 originating cell line.


title: head and neck squamous cell carcinoma 195

tag: age at operation (yrs)

value: female


title: TR.VITRO.72hr#2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Affymetrix WT Sense Target Labeling Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 14 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 72hr

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Male


title: 1867-T

source_name: Lung cancer specimen

tag: histology

value: Adenocarcinoma

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: A

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: Epididymal's epithelial cells from caput, replicate 1

source_name: caput epithelial cells

tag: tissue

value: epididymis

tag: epididymal region

value: caput


title: 1858-T2

tag: gender

value: F

value: African American


title: 1844-T

value: Squamous

value: Caucasian

value: Y

value: IIIA

value: D


title: TR.VITRO.2hr#2

tag: age

value: 14 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

value: In vitro 1.25ug/ml of KT3 stimulation for 2hr


title: TR.VITRO.8hr#2

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 8hr

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Male


title: AsPC-1_originating cell line_R1

description:
AsPC-1 P0 T1
Gene expression data from AsPC-1 originating cell line.

tag: originating cell line

tag: tumor type

value: adenocarcinoma pancreatic

tag: in vivo passage


title: AS283_Passage 10 xenograft_R4

description:
AS283 P10 T4
Gene expression data from AS283 Passage 10 xenograft.

source_name: AS283, passage 10 xenograft

value: AIDs related Burkitts lymphoma


title: TR.VITRO.24hr#2

value: In vitro 1.25ug/ml of KT3 stimulation for 24hr


title: head and neck squamous cell carcinoma 196

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: head and neck squamous cell carcinoma 194

tag: gender

value: Hypopharyngeal

tag: tissue


title: 1853-T

tag: histology

value: Adenocarcinoma

value: M

tag: race

value: Caucasian

tag: tobacco history

value: Y

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: AS283_Passage 10 xenograft_R3

description:
AS283 P10 T3
Gene expression data from AS283 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 1837-T

value: IIIA

value: D


title: AS283_Passage 10 xenograft_R2

description:
AS283 P10 T2
Gene expression data from AS283 Passage 10 xenograft.


title: head and neck squamous cell carcinoma 193

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


title: TR.VITRO.0hr#2

tag: age

value: 14 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 0hr

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Male


title: heart_basal_male1

source_name: heart homogenate male mouse 1

tag: gender

value: male

tag: tissue

value: heart homogenate


title: TC.VITRO.72hr#2

value: In vitro 1.25ug/ml of KT3 stimulation for 72hr


title: head and neck squamous cell carcinoma 192

tag: age at operation (yrs)

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: sample type

value: non-drinker control

value: peripheral blood


title: TC.VITRO.24hr#2

value: In vitro 1.25ug/ml of KT3 stimulation for 24hr


title: 1833-T

tag: histology

value: Adenocarcinoma

value: M

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

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 1839-T

tag: gender

value: A


title: 1911-T

value: IA

value: N


title: 1834-T

value: D


title: 1824-T

value: Squamous

value: IIIA


title: TC.VITRO.0hr#2

tag: age

value: 14 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 0hr

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Male


title: TC.VITRO.8hr#2

value: In vitro 1.25ug/ml of KT3 stimulation for 8hr


title: 1809-T

tag: histology

value: Adenocarcinoma

value: M

tag: race

tag: tobacco history


title: AS283_Passage 4 xenograft_R5

description:
AS283 P04 T5
Gene expression data from AS283 Passage 4 xenograft.

source_name: AS283, passage 4 xenograft

tag: originating cell line

tag: tumor type

value: AIDs related Burkitts lymphoma

tag: in vivo passage


title: AS283_Passage 4 xenograft_R4

description:
AS283 P04 T4
Gene expression data from AS283 Passage 4 xenograft.


title: AS283_Passage 10 xenograft_R1

description:
AS283 P10 T1
Gene expression data from AS283 Passage 10 xenograft.


title: TR.VITRO.72hr#1

value: 9 Weeks Old

value: In vitro 1.25ug/ml of KT3 stimulation for 72hr

value: Female


title: TC.VITRO.2hr#2

value: In vitro 1.25ug/ml of KT3 stimulation for 2hr


title: head and neck squamous cell carcinoma 191

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

value: peripheral blood


title: head and neck squamous cell carcinoma 190

tag: gender

value: Oropharyngeal


title: AS283_Passage 4 xenograft_R3

description:
AS283 P04 T3
Gene expression data from AS283 Passage 4 xenograft.

tag: originating cell line


title: head and neck squamous cell carcinoma 188

value: Oral Cavity


title: head and neck squamous cell carcinoma 187


title: head and neck squamous cell carcinoma 186

value: female


title: AS283_Passage 4 xenograft_R2

description:
AS283 P04 T2
Gene expression data from AS283 Passage 4 xenograft.

tag: tumor type


title: head and neck squamous cell carcinoma 184

value: Laryngeal


title: 1805-T

tag: histology

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

value: N

tag: last follow-up recurrence


title: TR.VITRO.24hr#1

tag: age

value: 9 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 24hr

tag: separation method

value: MoFlo Sorter

tag: Sex


title: TR.VITRO.2hr#1

value: In vitro 1.25ug/ml of KT3 stimulation for 2hr

value: Female


title: 1804-T

tag: histology

value: Adenocarcinoma

tag: gender

value: M

tag: race

value: Hispanic

value: D


title: AS283_Passage 4 xenograft_R1

description:
AS283 P04 T1
Gene expression data from AS283 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

value: AIDs related Burkitts lymphoma

tag: in vivo passage


title: 1793-T

value: F

value: Caucasian

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: head and neck squamous cell carcinoma 185

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Hypopharyngeal

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

value: non-drinker control

tag: tissue

value: peripheral blood


title: TR.VITRO.8hr#1

tag: age

value: 9 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 8hr

tag: separation method

tag: Sex


title: 1785-T

tag: histology

value: Squamous

tag: gender

tag: race

tag: tobacco history

value: Y

tag: final patient stage

value: IIIB

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: 1736-T

value: Adenocarcinoma

value: IB

value: A


title: AS283_Passage 1 xenograft_R5

description:
AS283 P01 T5
Gene expression data from AS283 Passage 1 xenograft.

source_name: AS283, passage 1 xenograft

tag: originating cell line

tag: tumor type

value: AIDs related Burkitts lymphoma

tag: in vivo passage


title: 1729-T

value: F

value: Caucasian


title: AS283_Passage 1 xenograft_R3

description:
AS283 P01 T3
Gene expression data from AS283 Passage 1 xenograft.


title: head and neck squamous cell carcinoma 181

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

tag: sample type

tag: tissue


title: TC.VITRO.24hr#1

tag: age

tag: inclusion markers

tag: strain

tag: genotype/variation

tag: source prep

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 24hr

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Female


title: 1761-T

tag: histology

tag: gender

value: M

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

tag: recurrence

tag: last follow-up recurrence


title: AS283_Passage 1 xenograft_R2

description:
AS283 P01 T2
Gene expression data from AS283 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: TC.VITRO.72hr#1

tag: age

value: 9 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 72hr


title: head and neck squamous cell carcinoma 183

tag: age at operation (yrs)

tag: gender

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

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: AS283_Passage 1 xenograft_R4

description:
AS283 P01 T4
Gene expression data from AS283 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

value: AIDs related Burkitts lymphoma

tag: in vivo passage


title: TR.VITRO.0hr#1

tag: age

tag: inclusion markers

tag: strain

tag: genotype/variation

tag: source prep

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 0hr

tag: separation method

tag: Sex


title: TC.VITRO.8hr#1

value: In vitro 1.25ug/ml of KT3 stimulation for 8hr


title: AS283_originating cell line_R2

description:
AS283 P0 T2
Gene expression data from AS283 originating cell line.

source_name: AS283, originating cell line


title: AS283_Passage 1 xenograft_R1

description:
AS283 P01 T1
Gene expression data from AS283 Passage 1 xenograft.


title: AS283_Passage 10 xenograft_R5

description:
AS283 P10 T5
Gene expression data from AS283 Passage 10 xenograft.


title: head and neck squamous cell carcinoma 179

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: chemoradiotherapy

tag: relapse


title: head and neck squamous cell carcinoma 180

value: Oral Cavity

tag: tumor grade

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 178


title: TR.VIVO.ctrl24hr#2

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

tag: genotype/variation

tag: source prep

value: Treg cells from a RatIgG-treated Foxp3-IRES-GFP mouse were purified at 24h post-Rat IgG iv injection.

tag: cell treatment

value: Purified by cell sorting (CD4+ GFP+)

value: MoFlo Sorter


title: A549/Asc-1_Passage 10 xenograft_R5

description:
A549/Asc-1 P10 T5
Gene expression data from A549/Asc-1 Passage 10 xenograft.

source_name: A549/Asc-1, passage 10 xenograft

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: TC.VITRO.0hr#1

value: 9 Weeks Old

value: NOD

tag: separation method

tag: Sex

value: Female


title: 1718-T

tag: histology

value: Adenocarcinoma

tag: gender

value: M

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

value: N

tag: last follow-up recurrence


title: A549/Asc-1_Passage 10 xenograft_R3

description:
A549/Asc-1 P10 T3
Gene expression data from A549/Asc-1 Passage 10 xenograft.


title: TC.VITRO.2hr#1

tag: age

tag: inclusion markers

tag: strain

tag: genotype/variation

tag: source prep

value: Splenocytes from a Foxp3-IRES-GFP mouse in culture

tag: cell treatment

value: In vitro 1.25ug/ml of KT3 stimulation for 2hr


title: 1723-T

tag: histology

value: F

value: IA


title: TR.VIVO.72hr#2

value: 8 Weeks Old

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 72h post-KT3 iv injection.

value: Purified by cell sorting (CD4+ GFP+)

tag: separation method

tag: Sex


title: AS283_originating cell line_R1

description:
AS283 P0 T1
Gene expression data from AS283 originating cell line.

tag: originating cell line

tag: tumor type

value: AIDs related Burkitts lymphoma

tag: in vivo passage


title: A549/Asc-1_Passage 10 xenograft_R4

description:
A549/Asc-1 P10 T4
Gene expression data from A549/Asc-1 Passage 10 xenograft.

value: adenocarcinoma lung


title: TR.VIVO.24hr#2

value: NOD

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 24h post-KT3 iv injection.

value: MoFlo Sorter

value: Female


title: A549/Asc-1_Passage 10 xenograft_R2

description:
A549/Asc-1 P10 T2
Gene expression data from A549/Asc-1 Passage 10 xenograft.


title: 1714-T

value: Adenocarcinoma

tag: gender

value: M

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

value: D


title: head and neck squamous cell carcinoma 175

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

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: 1692-T

tag: histology

value: Squamous

tag: gender

value: F

tag: race

tag: tobacco history

value: IA

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: TR.VIVO.8hr#2

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 8h post-KT3 iv injection.

tag: cell treatment

value: Purified by cell sorting (CD4+ GFP+)

tag: separation method

value: MoFlo Sorter

tag: Sex


title: 1671-T

value: Adenocarcinoma

value: M

value: Caucasian

value: Y

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery


title: 1662-T

tag: histology

tag: gender

tag: race

value: Hispanic

value: IB


title: head and neck squamous cell carcinoma 176

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

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: head and neck squamous cell carcinoma 177


title: head and neck squamous cell carcinoma 182


title: A549/Asc-1_Passage 10 xenograft_R1

description:
A549/Asc-1 P10 T1
Gene expression data from A549/Asc-1 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: head and neck squamous cell carcinoma 171

tag: gender


title: head and neck squamous cell carcinoma 172

tag: age at operation (yrs)

value: Hypopharyngeal


title: TR.VIVO.2hr#2

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at  2h post-KT3 iv injection.

tag: cell treatment

tag: separation method

tag: Sex

value: Female


title: TC.VIVO.2hr#2

value: Tconv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 2h post-KT3 iv injection.

value: Purified by cell sorting (CD4+ GFP-)

value: MoFlo Sorter


title: A549/Asc-1_Passage 1 xenograft_R3

description:
A549/Asc-1 P01 T3
Gene expression data from A549/Asc-1 Passage 1 xenograft.

source_name: A549/Asc-1, passage 1 xenograft


title: A549/Asc-1_Passage 4 xenograft_R2

description:
A549/Asc-1 P04 T2
Gene expression data from A549/Asc-1 Passage 4 xenograft.

source_name: A549/Asc-1, passage 4 xenograft


title: A549/Asc-1_Passage 1 xenograft_R2

description:
A549/Asc-1 P01 T2
Gene expression data from A549/Asc-1 Passage 1 xenograft.


title: 1601-T

tag: histology

value: Adenocarcinoma

value: M

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: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 1727-T

tag: gender

value: African American

value: IA

value: N


title: 1576-T

value: F

value: IIB


title: A549/Asc-1_Passage 1 xenograft_R5

description:
A549/Asc-1 P01 T5
Gene expression data from A549/Asc-1 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: TR.VIVO.0hr#2

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Treg cells from a non-treated mouse.

tag: cell treatment

value: Purified by cell sorting (CD4+ GFP+)


title: head and neck squamous cell carcinoma 174

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

value: peripheral blood


title: TC.VIVO.24hr#2

tag: age

tag: inclusion markers

tag: strain

value: Tconv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 24h post-KT3 iv injection.

value: Purified by cell sorting (CD4+ GFP-)

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Female


title: TC.VIVO.72hr#2

tag: genotype/variation

tag: source prep

value: Tconv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 72h post-KT3 iv injection.

tag: cell treatment


title: head and neck squamous cell carcinoma 168

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

value: Oropharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage


title: TC.VIVO.0hr#2

value: T conv cells from a non-treated mouse.


title: 1623-T

tag: histology

value: Squamous

value: M

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IIIB

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: TC.VIVO.ctrl24hr#2

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Tconv cells from a RatIgG-treated Foxp3-IRES-GFP mouse were purified at 24h post-Rat IgG iv injection.

tag: cell treatment

tag: separation method

tag: Sex


title: head and neck squamous cell carcinoma 163

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

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: TR.VIVO.24hr#1

tag: age

tag: inclusion markers

tag: strain

tag: genotype/variation

tag: source prep

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 24h post-KT3 iv injection.

tag: cell treatment

value: Purified by cell sorting (CD4+ GFP+)

value: MoFlo Sorter

value: Female


title: head and neck squamous cell carcinoma 160

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

tag: hpv infection


title: head and neck squamous cell carcinoma 162

value: female

value: Oral Cavity

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy


title: TR.VIVO.8hr#1

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 8h post-KT3 iv injection.

tag: separation method

tag: Sex


title: 1598-T2

tag: histology

value: Adenocarcinoma

value: F

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: A

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: 1551-T

tag: gender

value: IA


title: A549/Asc-1_originating cell line_R2

description:
A549/Asc-1 P0 T2
Gene expression data from A549/Asc-1 originating cell line.

source_name: A549/Asc-1, originating cell line

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: 1510-Tx

value: M

value: IB


title: 1502-T2

value: IIA

value: D


title: TR.VIVO.2hr#1

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 2h post-KT3 iv injection.

tag: cell treatment

value: Purified by cell sorting (CD4+ GFP+)

value: MoFlo Sorter


title: TR.VIVO.72hr#1

value: Treg cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 72h post-KT3 iv injection.

tag: separation method

tag: Sex

value: Female


title: head and neck squamous cell carcinoma 167

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

tag: alcohol drinking

value: male

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: 1549-T

tag: histology

value: Adenocarcinoma

tag: gender

value: F

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: A

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: A549/Asc-1_Passage 1 xenograft_R1

description:
A549/Asc-1 P01 T1
Gene expression data from A549/Asc-1 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: head and neck squamous cell carcinoma 159

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: alcohol drinking


title: A549/Asc-1_Passage 1 xenograft_R4

description:
A549/Asc-1 P01 T4
Gene expression data from A549/Asc-1 Passage 1 xenograft.


title: A549/Asc-1_originating cell line_R1

description:
A549/Asc-1 P0 T1
Gene expression data from A549/Asc-1 originating cell line.


title: 1607-T

tag: histology

tag: gender

value: M

tag: race

tag: tobacco history

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival


title: TC.VIVO.8hr#2

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Tconv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 8h post-KT3 iv injection.

tag: cell treatment

value: Purified by cell sorting (CD4+ GFP-)

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Female


title: 1498-T

tag: histology

value: Adenocarcinoma

value: IB

tag: recurrence

tag: last follow-up recurrence


title: 1496-T

tag: gender

value: F

tag: race

value: Caucasian

tag: tobacco history


title: A549/Asc-1_Passage 4 xenograft_R1

description:
A549/Asc-1 P04 T1
Gene expression data from A549/Asc-1 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 1591-T

value: Squamous

value: Y

tag: final patient stage

value: IIA

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival


title: A549_Passage 10 xenograft_R3

description:
A549 P10 T3
Gene expression data from A549 Passage 10 xenograft.

source_name: A549, passage 10 xenograft

value: adenocarcinoma lung


title: A549/Asc-1_Passage 4 xenograft_R3

description:
A549/Asc-1 P04 T3
Gene expression data from A549/Asc-1 Passage 4 xenograft.


title: A549_Passage 10 xenograft_R5

description:
A549 P10 T5
Gene expression data from A549 Passage 10 xenograft.


title: head and neck squamous cell carcinoma 156

tag: age at operation (yrs)

value: female

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: male

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: head and neck squamous cell carcinoma 164

tag: gender

value: Oropharyngeal


title: head and neck squamous cell carcinoma 157


title: 1476-T

tag: histology

tag: race

tag: tobacco history

tag: final patient stage

tag: date of birth

tag: date of surgery

tag: recurrence

value: N

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 155

tag: age at operation (yrs)

tag: primary tumor site

value: Laryngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade


title: A549_Passage 10 xenograft_R1

description:
A549 P10 T1
Gene expression data from A549 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 154

tag: gender

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: A549_Passage 10 xenograft_R4

description:
A549 P10 T4
Gene expression data from A549 Passage 10 xenograft.


title: A549_Passage 10 xenograft_R2

description:
A549 P10 T2
Gene expression data from A549 Passage 10 xenograft.


title: TR.VIVO.0hr#1

tag: age

value: 8 Weeks Old

tag: inclusion markers

tag: strain

value: NOD

tag: genotype/variation

tag: source prep

value: Treg cells from a non-treated mouse.

tag: cell treatment

value: Purified by cell sorting (CD4+ GFP+)

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Female


title: 1477-T

tag: histology

value: Squamous

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

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: TC.VIVO.72hr#1

tag: age

tag: inclusion markers

value: T conv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 72h post-KT3 iv injection.

value: Purified by cell sorting (CD4+ GFP-)


title: head and neck squamous cell carcinoma 158

tag: age at operation (yrs)

tag: gender

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: TC.VIVO.24hr#1

tag: strain

tag: genotype/variation

tag: source prep

value: T conv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 24h post-KT3 iv injection.

tag: cell treatment

tag: separation method

tag: Sex


title: head and neck squamous cell carcinoma 153

tag: age at operation (yrs)

tag: gender

tag: primary tumor site

value: Laryngeal

tag: hpv infection


title: head and neck squamous cell carcinoma 161

value: Oropharyngeal

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy


title: TC.VIVO.8hr#1

tag: age

value: 8 Weeks Old

tag: inclusion markers

value: NOD

value: T conv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 8h post-KT3 iv injection.


title: head and neck squamous cell carcinoma 152

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue


title: TC.VIVO.0hr#1

tag: strain

tag: genotype/variation

tag: source prep

value: T conv cells from a non-treated mouse.

tag: cell treatment

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Female


title: TC.VIVO.2hr#1

value: T conv cells from a KT3-treated Foxp3-IRES-GFP mouse were purified at 2h post-KT3 iv injection.


title: 1462-T

tag: histology

value: Adenocarcinoma

tag: gender

value: M

tag: race

value: Caucasian

tag: tobacco history

value: Y

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: A549_Passage 4 xenograft_R4

description:
A549 P04 T4
Gene expression data from A549 Passage 4 xenograft.

source_name: A549, passage 4 xenograft

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: 1454-T

value: IIIA


title: A549_Passage 4 xenograft_R2

description:
A549 P04 T2
Gene expression data from A549 Passage 4 xenograft.


title: A549_Passage 4 xenograft_R5

description:
A549 P04 T5
Gene expression data from A549 Passage 4 xenograft.


title: 1424-T

value: Squamous

value: D


title: A549_Passage 4 xenograft_R3

description:
A549 P04 T3
Gene expression data from A549 Passage 4 xenograft.


title: A549_Passage 4 xenograft_R1

description:
A549 P04 T1
Gene expression data from A549 Passage 4 xenograft.


title: head and neck squamous cell carcinoma 151

tag: age at operation (yrs)

value: male

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

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: 1465-T

tag: histology

tag: gender

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

tag: recurrence

tag: last follow-up recurrence


title: 1434-T

value: Adenocarcinoma


title: KO (Rnh1-/-) -1

city: EPALINGES

first: ramanjaneyulu

last: allam

state: Vaud

address: Chemin des Boveresses 155

department: Biochemistry

country: Switzerland

institute: University of lausanne

description:
KO1; Rnh1 Knock out-1
Gene expression data from Rnh1 knock out yolk sac at E 9.5 day

hyb_protocol: Following fragmentation, we used standard Affymetrix procedures for hybridization

scan_protocol: standard Affymetrix procedures were done using GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with RMA normalization method (Expression Console 1.2.1.20).

source_name: Rnh1 Knock out  embryo yolk sac

label_protocol: For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affymetrix, Cat.no. 900223); 5.5μg of the resulting sense cDNA was fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal labelling kit  (Affymetrix Cat.no. 900671)

growth_protocol: Yolk sacs were isolated from E9.5 embryo without contaminating maternal tissue and placed in to RLT buffer.

extract_protocol: RNA was prepared using RNAeasy Mini Kit  according manufacturer-suggested protocol

treatment_protocol: No treatment were done.

tag: strain background

value: mixed (SV 129/C57BL/6)

tag: genotype/variation

value: Rnh1 Knock out (Rnh1-/-)

tag: age

value: embryonic day E9.5

value: yolk sac


title: HET(Rnh1+/-) -3

description:
HET3; Rnh1 Heterozygous-3
Gene expression data from Rnh1 heterzygous yolk sac at E 9.5 day

source_name: Rnh1 heterozygous embryo yolk sac

value: Rnh1 Heterozygous (Rnh1+/-)


title: 1443-T

source_name: Lung cancer specimen

value: Caucasian

value: N

value: A

value: Y


title: 1405-T

value: IIIA

value: D


title: head and neck squamous cell carcinoma 150

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: smoking status

tag: alcohol drinking


title: KO (Rnh1-/-) -3

description:
KO3; Rnh1 Knock out-3
Gene expression data from Rnh1 knock out yolk sac at E 9.5 day

tag: tissue


title: A549_Passage 1 xenograft_R4

description:
A549 P01 T4
Gene expression data from A549 Passage 1 xenograft.

source_name: A549, passage 1 xenograft

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: head and neck squamous cell carcinoma 149

tag: gender

value: Oropharyngeal

tag: sample type

value: non-drinker control

value: peripheral blood


title: 1416-T

tag: histology

value: Adenocarcinoma

value: F

tag: race

tag: tobacco history

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: KO (Rnh1-/-) -2

description:
KO2; Rnh1 Knock out-2
Gene expression data from Rnh1 knock out yolk sac at E 9.5 day

tag: strain background

value: mixed (SV 129/C57BL/6)

tag: genotype/variation

value: Rnh1 Knock out (Rnh1-/-)

tag: age

value: embryonic day E9.5

value: yolk sac


title: head and neck squamous cell carcinoma 147

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

tag: tissue


title: HET(Rnh1+/-) -2

description:
HET2; Rnh1 Heterozygous-2
Gene expression data from Rnh1 heterzygous yolk sac at E 9.5 day

value: Rnh1 Heterozygous (Rnh1+/-)


title: A549_Passage 1 xenograft_R5

description:
A549 P01 T5
Gene expression data from A549 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 148

tag: gender

value: Hypopharyngeal

tag: sample type


title: head and neck squamous cell carcinoma 146

tag: age at operation (yrs)


title: HET(Rnh1+/-) -1

description:
HET1; Rnh1 Heterozygous-1
Gene expression data from Rnh1 heterzygous yolk sac at E 9.5 day

tag: strain background

tag: genotype/variation

tag: age


title: head and neck squamous cell carcinoma 145

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage


title: A549_Passage 1 xenograft_R3

description:
A549 P01 T3
Gene expression data from A549 Passage 1 xenograft.


title: head and neck squamous cell carcinoma 144

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status


title: A549_Passage 1 xenograft_R1

description:
A549 P01 T1
Gene expression data from A549 Passage 1 xenograft.

tag: originating cell line


title: 1402-T

tag: histology

value: Squamous

tag: race

value: Caucasian

tag: tobacco history

value: Y

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: A549_Passage 1 xenograft_R2

description:
A549 P01 T2
Gene expression data from A549 Passage 1 xenograft.

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: WT(Rnh1+/+) -2

description:
WT2; Wild type-2
Gene expression data from wild type yolk sac at E 9.5 day

source_name: Wild type embryo yolk sac

tag: strain background

tag: genotype/variation

value: wild type (Rnh1 +/+)

tag: age

tag: tissue


title: 1380-T

value: Adenocarcinoma

tag: gender

value: N

value: IB

value: A


title: 1396-T

tag: histology

value: F


title: WT(Rnh1+/+) -3

description:
WT3; Wild type-3
Gene expression data from wild type yolk sac at E 9.5 day

value: mixed (SV 129/C57BL/6)

value: embryonic day E9.5


title: 1401-T

tag: race

value: IIIA


title: 1360-T

value: M

tag: tobacco history


title: 1375-T

tag: final patient stage


title: head and neck squamous cell carcinoma 142

source_name: tumor sample

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: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

value: peripheral blood


title: 1361-T

value: Squamous

tag: gender

value: Caucasian

value: Y

value: IA

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 139

tag: age at operation (yrs)

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

source_name: healthy non-smoking volunteer

tag: tissue


title: head and neck squamous cell carcinoma 143

value: female

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy


title: A549_originating cell line_R1

description:
A549 P0 T1
Gene expression data from A549 originating cell line.

source_name: A549, originating cell line

tag: originating cell line

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: A549_originating cell line_R3

description:
A549 P0 T3
Gene expression data from A549 originating cell line.


title: FvB treated 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 treated 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 treated 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

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


title: A375_Passage 10 xenograft_R4

description:
A375 P10 T4
Gene expression data from A375 Passage 10 xenograft.

source_name: A375, passage 10 xenograft

value: metastatic malignant melanoma


title: A549_originating cell line_R2

description:
A549 P0 T2
Gene expression data from A549 originating cell line.


title: FvB treated mouse, biological rep 2


title: A375_Passage 10 xenograft_R2

description:
A375 P10 T2
Gene expression data from A375 Passage 10 xenograft.


title: FvB treated mouse, biological rep 3


title: FvB control mouse, biological rep 3

description: Gene expression data from non transgenic mouse

source_name: Nontransgenic female mouse


title: FvB control mouse, biological rep 1


title: A375_Passage 10 xenograft_R3

description:
A375 P10 T3
Gene expression data from A375 Passage 10 xenograft.


title: A375_Passage 10 xenograft_R5

description:
A375 P10 T5
Gene expression data from A375 Passage 10 xenograft.


title: head and neck squamous cell carcinoma 138

tag: gender

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type


title: head and neck squamous cell carcinoma 136

tag: age at operation (yrs)

tag: primary tumor site

value: Laryngeal

tag: hpv infection


title: 1357-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

value: A

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: A375_Passage 10 xenograft_R1

description:
A375 P10 T1
Gene expression data from A375 Passage 10 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 135

tag: gender

value: male

value: Oropharyngeal

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: 1355-T

tag: histology

tag: race

value: Caucasian

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: FvB mouse, biological rep 3

tag: genotype/variation

tag: treatment


title: 1376-T

tag: gender

value: M

value: Y

value: IIB

tag: recurrence

tag: last follow-up recurrence


title: WT(Rnh1+/+) -1

description:
WT1; Wild type-1
Gene expression data from wild type yolk sac at E 9.5 day

tag: strain background

value: mixed (SV 129/C57BL/6)

value: wild type (Rnh1 +/+)

tag: age

value: embryonic day E9.5

value: yolk sac


title: head and neck squamous cell carcinoma 141

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

value: peripheral blood


title: FvB control mouse, biological rep 2

tag: genotype/variation

value: nontransgenic FvB

tag: treatment


title: 1378-T

tag: histology

value: Adenocarcinoma

tag: gender

value: F

tag: race

tag: tobacco history

tag: final patient stage

value: IA

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: 1354-T

value: N

value: D


title: head and neck squamous cell carcinoma 137

tag: age at operation (yrs)

value: female

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

value: male

value: non-drinker control

tag: tissue


title: head and neck squamous cell carcinoma 133

tag: gender

value: Oral Cavity

tag: smoking status

tag: alcohol drinking

tag: sample type


title: 1353-T

tag: histology

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

tag: last follow-up survival


title: head and neck squamous cell carcinoma 132

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade


title: A375_Passage 4 xenograft_R5

description:
A375 P04 T5
Gene expression data from A375 Passage 4 xenograft.

source_name: A375, passage 4 xenograft

tag: originating cell line

tag: tumor type

value: metastatic malignant melanoma

tag: in vivo passage


title: A375_Passage 4 xenograft_R3

description:
A375 P04 T3
Gene expression data from A375 Passage 4 xenograft.


title: 1350-T

tag: histology

value: Squamous

tag: gender

value: M

value: IIIA

tag: recurrence

tag: last follow-up recurrence


title: head and neck squamous cell carcinoma 131

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

tag: tissue

value: peripheral blood


title: head and neck squamous cell carcinoma 134

tag: age at operation (yrs)

tag: primary tumor site

tag: hpv infection

tag: p16 protein immunohistochemistry


title: 1346-T

value: Adenocarcinoma

tag: race

tag: tobacco history

tag: final patient stage

value: IV

tag: date of birth

tag: date of surgery

tag: vital statistics

tag: last follow-up survival


title: A375_Passage 4 xenograft_R4

description:
A375 P04 T4
Gene expression data from A375 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: head and neck squamous cell carcinoma 130

tag: gender

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking


title: FvB mouse, biological rep 2

tag: genotype/variation

value: nontransgenic FvB

tag: treatment


title: K14E7 treated mouse, biological rep 1

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 129

tag: age at operation (yrs)

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: sample type

tag: tissue


title: A375_Passage 4 xenograft_R2

description:
A375 P04 T2
Gene expression data from A375 Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: A375_Passage 4 xenograft_R1

description:
A375 P04 T1
Gene expression data from A375 Passage 4 xenograft.


title: 1330-T

tag: histology

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: K14E7 treated mouse, biological rep 2

tag: genotype/variation

tag: treatment


title: K14E7 mouse, biological rep 3

description: Gene expression data from K14E7 transgenic mouse

source_name: K14E7 hemizygote female untreated mouse


title: A375_Passage 1 xenograft_R4

description:
A375 P01 T4
Gene expression data from A375 Passage 1 xenograft.

source_name: A375, passage 1 xenograft


title: head and neck squamous cell carcinoma 127

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


title: K14E7 mouse, biological rep 2


title: A375_Passage 1 xenograft_R2

description:
A375 P01 T2
Gene expression data from A375 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 1325-T

tag: histology

tag: gender

tag: race

value: Caucasian

tag: tobacco history

tag: final patient stage

value: IIIB

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: A375_Passage 1 xenograft_R5

description:
A375 P01 T5
Gene expression data from A375 Passage 1 xenograft.

value: metastatic malignant melanoma


title: 1332-T

value: African American

value: Y

value: IIB


title: 1309-T

value: F

value: N


title: K14E7 mouse, biological rep 1

tag: genotype/variation

tag: treatment


title: A375_Passage 1 xenograft_R3

description:
A375 P01 T3
Gene expression data from A375 Passage 1 xenograft.


title: 1311-T

value: Adenocarcinoma