title: NS cardiac myocytes at T0 biological rep 3

source_name: NS neonatal rat cardiac myocytes, DOX 0hr

value: NS cardiac myocytes 0hr Dox


title: NS cardiac myocytes at T0 biological rep 2

status: Public on Oct 01 2015

type: RNA

city: Miami

first: Sumit

last: Jain

state: Florida

address: 1600 NW 10th Avenue RMSB 6041

department: Molecular and Cellular Pharmacology

country: USA

institute: University of Miami

description: Cardiac myocytes transfected with Non-silencing siRNA

hyb_protocol: Biotinylated and fragmented cDNA (5.5 ug/samples) was diluted in hybridization buffer along with hybridization controls and control oligo. The mixture was denatured for 5 minutes at 99C and then loaded on to the surface of Affmetrix Rat Gene ST 1.0 GeneChips and hybridized for 16-18 hours at 45C under constant rotation in a Affymetrix Model 640 hybridization oven.

scan_protocol: The Affymetrix 3000 7G Plus Scanner controlled by Affymetrix AGCC software was used for data acquisition.

data_processing: Expression Console Version 1.1 software was used to generate probe set intensities using .CEL files. Specifically the RMA algorithm was used for background adjustment, quantile normalization, and probe set summarization; then untransformed probe set intensities were outputted for presentation and archiving. Log2-transformed probe intensities were outputted for purposes of statistical analysis.

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Total RNA samples were converted to antisense cRNA and then to sense-strand cDNA using the Ambion (Carlsbad, CA) WT Expression kit. Sense strand cDNA generated was fragmented and biotin labeled using the Affymetrix (Santa Clara, CA) GeneChip® WT Terminal Labeling kit.

growth_protocol: The final myocyte cultures contained >90% cardiac myocytes at 60-70%% confluence; 0.1mmol/L bromodeoxyuridine was included in the medium for the first 4 days after plating to inhibit fibroblast growth. Cells were serum-starved for two days with TIB (MEM supplemented with transferrin, vitamin B12, insulin) before experiments.

extract_protocol: Total RNA was extracted using miRVana RNA isolation kit from AMBION using manufacturer's protocol.

treatment_protocol: Neonatal rat cardiac myocytes were cultured for 2 days in complete MEM media containing 1% BrdU, then transfected with either non-silencing (NS) or p300 (p300kd) siRNA. Following transfection and two additional days in complete medium, cells were cultured for an additional 48 hrs in serum-free TIB media before initiation of experiments.  Cells were then treated with 1 micromolar Doxorubicin (Dox) for either 0 or 8 hrs.

tag: strain

value: Sprague Dawley

tag: cell type

value: neonatal rat cardiac myocytes

tag: treatment group


title: Treg.CD45RO+.CD71+.rep3

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16-18 hours in GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450.

scan_protocol: Microarrays were immediately scanned using Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental *.mps file)

label: biotin

organism: Homo sapiens

source_name: Human Treg subsets from peripheral blood

label_protocol: 100 ng of total RNA was amplified and labeled with Ambion® WT Expression Kit Protocol (Life Technologies) and GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

growth_protocol: All the samples are sorted ex vivo cells from human peripheral blood.

extract_protocol: Total RNA was extracted with Qiagen RNeasy mini columns according to the manufacturer's instructions.

treatment_protocol: Buffy coat from human peripheral blood was processed through RosetteSe Human CD4+ T Cell Enrichment Cocktail, followed by antibody staining and washing.

value: Treg CD45RO+ CD71+

tag: sample type

value: Sorted ex vivo Treg subset


title: Treg.CD45RO+.CLA-.rep2

value: Treg CD45RO+ CLA-


title: p300kd cardiac myocytes at T0 biological rep 1

description: Cardiac myocytes transfected with anti-p300 siRNA

source_name: p300kd neonatal rat cardiac myocytes, DOX 0 hr

value: p300kd cardiac myocytes 0hr Dox


title: p300kd cardiac myocytes at T8 biological rep 1

source_name: p300kd neonatal rat cardiac myocytes, DOX 8 hr

value: p300kd cardiac myocytes 8hr Dox


title: Treg.CD45RO+.CLA-.rep1


title: NS cardiac myocytes at T0 biological rep 1

source_name: NS neonatal rat cardiac myocytes, DOX 0 hr


title: UPN727 cells, TN14 PL09 at 9 month

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensities.  Each sample was independently analyzed (3 arrays per patient, at baseline, 9, and 12 months into treatment, 189 arrays in total).  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANalysis Of VAriation (ANOVA) using Partek Genomics Suite 6.5.

source_name: UPN727 cells stimulated with TN14_PL09_M9 serum

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

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

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

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% serum from recent-onset (RO) T1D patients that were given Placebo or Canakinumab at their respective time points.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN727 cells

tag: patient

tag: timepoint

value: 9 month into treatment


title: p300kd cardiac myocytes at T0 biological rep 2


title: UPN727 cells, TN14 PL10 at 9 month

source_name: UPN727 cells stimulated with TN14_PL10_M9 serum


title: UPN727 cells, TN14 PL10 at baseline

source_name: UPN727 cells stimulated with TN14_PL10_BL serum

value: at baseline


title: UPN727 cells, TN14 PL09 at 12 month

source_name: UPN727 cells stimulated with TN14_PL09_M12 serum

value: 12 month into treatment


title: 064KK-UM-IU_787

type: genomic

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
uninvolved margin of breast carcinoma
064KK-UM-IU

hyb_protocol: starndard protocol

scan_protocol: The majority of genotyping experiments were conducted at the SNP&SEQ Technology Platform in Uppsala by using four similar in SNP-density Illumina platforms (Human 660W-Quad, Human1M-Duo, HumanOmniExpress and HumanOmniExpressExome beadchips), according to the recommendations of the manufacturer.

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility  “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

molecule: genomic DNA

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

label_protocol: starndard protocol

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).

tag: gender

value: female

tag: age at cancer diagnosis (yrs)

tag: tumor grade

value: Luminal B, HER2-

tag: tumor focality

value: multifocal


title: 064KK-VB_788

description:
uninvolved margin in the immediate vicinity of the mammilla
064KK-VB


title: RH117A3_132

description:
TUMORS4: 29_primaryTumors_GPL6984.txt
Genotyping on DNA extracted from a primary tumor

hyb_protocol: standard protocol

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

source_name: DNA extracted from primary tumor

label_protocol: standard protocol

tag: age at cancer diagnosis

value: unifocal

tag: tissue

value: primary tumor


title: 064KK-UM-IL_786

description:
uninvolved margin of breast carcinoma
064KK-UM-IL


title: PM102A2_131

value: Triple negative


title: 064KK-UM-EU_785

description:
uninvolved margin of breast carcinoma
064KK-UM-EU


title: 064KK-UM-EL_784

description:
uninvolved margin of breast carcinoma
064KK-UM-EL


title: PI33A_130


title: MH016_PT2_128

value: Luminal B, HER2+


title: Treg.CD45RO+.CD71+.rep2


title: 063JB-VB_783

description:
uninvolved margin in the immediate vicinity of the mammilla
063JB-VB


title: 063JB-UM-IU_782

description:
uninvolved margin of breast carcinoma
063JB-UM-IU


title: MH016_PT1_127


title: 063JB-UM-IL_781

description:
uninvolved margin of breast carcinoma
063JB-UM-IL


title: Treg.CD45RO+.CD71-.rep2

value: Treg CD45RO+ CD71-


title: Treg.CD45RO+.CD71+.rep1

value: Treg CD45RO+ CD71+


title: UPN727 cells, TN14 PL09 at baseline

source_name: UPN727 cells stimulated with TN14_PL09_BL serum


title: ME114A2_126


title: UPN727 cells, TN14 PL08 at 12 month

source_name: UPN727 cells stimulated with TN14_PL08_M12 serum


title: UPN727 cells, TN14 PL08 at 9 month

source_name: UPN727 cells stimulated with TN14_PL08_M9 serum


title: UPN727 cells, TN14 PL08 at baseline

source_name: UPN727 cells stimulated with TN14_PL08_BL serum


title: UPN727 cells, TN14 PL07 at 12 month

source_name: UPN727 cells stimulated with TN14_PL07_M12 serum


title: LK003_PT2_125

value: Luminal A


title: Treg.CD45RO+.CD39+.CD26+.rep1

value: Treg CD45RO+ CD39+ CD26+

value: Sorted ex vivo Treg subset


title: MK120A2_129


title: LK003_PT1_124


title: 063JB-UM-EL_779

description:
uninvolved margin of breast carcinoma
063JB-UM-EL


title: Treg.CD45RO+.CD39+.CD26+.rep3


title: Treg.CD45RO+.CD39+.CD26+.rep2


title: Treg.CD45RO+.CD71-.rep1


title: UPN727 cells, TN14 PL07 at baseline

source_name: UPN727 cells stimulated with TN14_PL07_BL serum


title: Treg.CD45RO+.CD39+.CD26-.rep3

value: Treg CD45RO+ CD39+ CD26-


title: UPN727 cells, TN14 PL06 at 12 month

source_name: UPN727 cells stimulated with TN14_PL06_M12 serum

value: UPN727 cells


title: UPN727 cells, TN14 PL07 at 9 month

source_name: UPN727 cells stimulated with TN14_PL07_M9 serum

value: 9 month into treatment


title: 062BI-VB_776

description:
uninvolved margin in the immediate vicinity of the mammilla
062BI-VB


title: KS141A3_123


title: Treg.CD45RO+.CD71-.rep3

source_name: Human Treg subsets from peripheral blood


title: 062BI-UM-IL_775

description:
uninvolved margin of breast carcinoma
062BI-UM-IL


title: KK123A3_122


title: UPN727 cells, TN14 PL06 at 9 month

source_name: UPN727 cells stimulated with TN14_PL06_M9 serum


title: 062BI-UM-EU_774

description:
uninvolved margin of breast carcinoma
062BI-UM-EU


title: 063JB-UM-EU_780

description:
uninvolved margin of breast carcinoma
063JB-UM-EU


title: KB132A2_121


title: Treg.CD45RO+.CD39+.CD26-.rep2


title: UPN727 cells, TN14 PL06 at baseline

source_name: UPN727 cells stimulated with TN14_PL06_BL serum

value: at baseline


title: 062BI-UM-EL_773

description:
uninvolved margin of breast carcinoma
062BI-UM-EL


title: UPN727 cells, TN14 PL05 at 12 month

source_name: UPN727 cells stimulated with TN14_PL05_M12 serum

value: 12 month into treatment


title: JU32A1_120

value: female


title: IMH013_PT2_119


title: UPN727 cells, TN14 PL05 at 9 month

source_name: UPN727 cells stimulated with TN14_PL05_M9 serum


title: UPN727 cells, TN14 PL05 at baseline

source_name: UPN727 cells stimulated with TN14_PL05_BL serum


title: 061AS-VB_770

description:
uninvolved margin in the immediate vicinity of the mammilla
061AS-VB


title: Treg.CD45RO+.CD39+.CD26-.rep1

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name


title: Treg.CD45RO+.CD39-.CD26+.rep3

value: Treg CD45RO+ CD39- CD26+


title: 061AS-UM-IL_768

description:
uninvolved margin of breast carcinoma
061AS-UM-IL


title: DM138A2_117


title: IMH013_PT1_118

value: multifocal


title: 061AS-UM-IU_769

description:
uninvolved margin of breast carcinoma
061AS-UM-IU

value: unifocal


title: 061AS-UM-EU_767

description:
uninvolved margin of breast carcinoma
061AS-UM-EU


title: 061AS-UM-EL_766

description:
uninvolved margin of breast carcinoma
061AS-UM-EL


title: DH74A1_116

description:
TUMORS4: 29_primaryTumors_GPL6984.txt
Genotyping on DNA extracted from a primary tumor

value: primary tumor


title: Treg.CD45RO+.CD39-.CD26+.rep2


title: CJ112A3_115

value: Triple negative


title: 060HP-VB_763

description:
uninvolved margin in the immediate vicinity of the mammilla
060HP-VB

value: Luminal B, HER2-


title: Treg.CD45RO+.CD39-.CD26+.rep1


title: CG010_PT1_114


title: Treg.CD45RO+.CD39-.CD26-.rep2

value: Treg CD45RO+ CD39- CD26-


title: 060HP-UM-IU_762

description:
uninvolved margin of breast carcinoma
060HP-UM-IU


title: UPN727 cells, TN14 PL04 at 12 month

source_name: UPN727 cells stimulated with TN14_PL04_M12 serum


title: BU97A1_113


title: Treg.CD45RO+.CD39-.CD26-.rep1


title: Treg.CD45RO+.CD38+.rep3

value: Treg CD45RO+ CD38+


title: UPN727 cells, TN14 PL04 at baseline

source_name: UPN727 cells stimulated with TN14_PL04_BL serum


title: BMK015_PT2_112

source_name: DNA extracted from primary tumor

value: Luminal A


title: UPN727 cells, TN14 PL04 at 9 month

source_name: UPN727 cells stimulated with TN14_PL04_M9 serum


title: 060HP-UM-IL_761

description:
uninvolved margin of breast carcinoma
060HP-UM-IL

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: UPN727 cells, TN14 PL03 at baseline

source_name: UPN727 cells stimulated with TN14_PL03_BL serum


title: Treg.CD45RO+.CD38+.rep2


title: UPN727 cells, TN14 PL03 at 12 month

source_name: UPN727 cells stimulated with TN14_PL03_M12 serum


title: 060HP-UM-EU_760

description:
uninvolved margin of breast carcinoma
060HP-UM-EU


title: UPN727 cells, TN14 PL03 at 9 month

source_name: UPN727 cells stimulated with TN14_PL03_M9 serum


title: Treg.CD45RO+.CD38+.rep1


title: Treg.CD45RO+.CD39-.CD26-.rep3


title: UPN727 cells, TN14 PL02 at 12 month

source_name: UPN727 cells stimulated with TN14_PL02_M12 serum


title: BMK015_PT1_111


title: 060HP-UM-EL_759

description:
uninvolved margin of breast carcinoma
060HP-UM-EL


title: BMF005_PT2_110


title: Treg.CD45RO+.CD38-.rep2

value: Treg CD45RO+ CD38-


title: UPN727 cells, TN14 PL02 at baseline

source_name: UPN727 cells stimulated with TN14_PL02_BL serum


title: BK152A_108

value: Luminal B, HER2+


title: 059HS-VB_758

description:
uninvolved margin in the immediate vicinity of the mammilla
059HS-VB


title: AL002_PT3_107


title: 059HS-UM-IL_756

description:
uninvolved margin of breast carcinoma
059HS-UM-IL


title: AL002_PT1_105


title: Treg.CD45RO+.CD38-.rep1

value: Sorted ex vivo Treg subset


title: 059HS-UM-EU_755

description:
uninvolved margin of breast carcinoma
059HS-UM-EU


title: Treg.CD45RO+.CD279+.rep2

value: Treg CD45RO+ CD279+


title: 058ZA-VB_754

description:
uninvolved margin in the immediate vicinity of the mammilla
058ZA-VB


title: 059HS-UM-IU_757

description:
uninvolved margin of breast carcinoma
059HS-UM-IU


title: SE135K_108

description:
CONTROLS4: 23_controls_GPL6984.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

source_name: DNA extracted from whole blood

value: whole blood


title: UPN727 cells, TN14 PL02 at 9 month

source_name: UPN727 cells stimulated with TN14_PL02_M9 serum

value: UPN727 cells

value: 9 month into treatment


title: BMF005_PT1_109

value: female


title: Treg.CD45RO+.CD279-.rep3

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

source_name: Human Treg subsets from peripheral blood

value: Treg CD45RO+ CD279-


title: UPN727 cells, TN14 PL01 at 9 month

source_name: UPN727 cells stimulated with TN14_PL01_M9 serum


title: Treg.CD45RO+.CD279-.rep2


title: UPN727 cells, TN14 PL01 at baseline

source_name: UPN727 cells stimulated with TN14_PL01_BL serum

value: at baseline


title: UPN727 cells, TN14 CA43 at baseline

source_name: UPN727 cells stimulated with TN14_CA43_BL serum


title: 058ZA-UM-IL_752

description:
uninvolved margin of breast carcinoma
058ZA-UM-IL

value: unifocal


title: UPN727 cells, TN14 CA43 at 12 month

source_name: UPN727 cells stimulated with TN14_CA43_M12 serum

value: 12 month into treatment


title: RH117K_107


title: Treg.CD45RO+.CD279-.rep1


title: UPN727 cells, TN14 CA42 at 12 month

source_name: UPN727 cells stimulated with TN14_CA42_M12 serum


title: UPN727 cells, TN14 PL10 at 12 month

source_name: UPN727 cells stimulated with TN14_PL10_M12 serum


title: Treg.CD45RO+.CD279+.rep1


title: Treg.CD45RO+.CD279+.rep3


title: Treg.CD45RO+.CD38-.rep3


title: UPN727 cells, TN14 PL01 at 12 month

source_name: UPN727 cells stimulated with TN14_PL01_M12 serum


title: AL002_PT2_106

source_name: DNA extracted from primary tumor

value: multifocal

value: primary tumor


title: 058ZA-UM-IU_753

description:
uninvolved margin of breast carcinoma
058ZA-UM-IU

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: Luminal B, HER2-


title: 058ZA-UM-EU_751

description:
uninvolved margin of breast carcinoma
058ZA-UM-EU


title: PM102K_106

value: Triple negative


title: 058ZA-UM-EL_750

description:
uninvolved margin of breast carcinoma
058ZA-UM-EL


title: 057GS-VB_749

description:
uninvolved margin in the immediate vicinity of the mammilla
057GS-VB


title: UPN727 cells, TN14 CA43 at 9 month

source_name: UPN727 cells stimulated with TN14_CA43_M9 serum


title: PI33K_105


title: UPN727 cells, TN14 CA42 at 9 month

source_name: UPN727 cells stimulated with TN14_CA42_M9 serum


title: 057GS-UM-IL_747

description:
uninvolved margin of breast carcinoma
057GS-UM-IL


title: Treg.CD45RO+.CD272+.rep1

value: Treg CD45RO+ CD272+


title: Treg.CD45RO+.CD272+.rep3


title: MK120K_104

value: Luminal A


title: Treg.CD45RO+.CD272+.rep2


title: Treg.CD45RO+.CD272-.rep3

value: Treg CD45RO+ CD272-


title: UPN727 cells, TN14 CA41 at 12 month

source_name: UPN727 cells stimulated with TN14_CA41_M12 serum


title: UPN727 cells, TN14 CA42 at baseline

source_name: UPN727 cells stimulated with TN14_CA42_BL serum


title: LK003_SK_101

description:
CONTROLS4: 23_controls_GPL6984.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy

source_name: DNA extracted from skin biopsy

value: skin biopsy


title: MH016_SK_103

value: Luminal B, HER2+


title: 057GS-UM-EU_746

description:
uninvolved margin of breast carcinoma
057GS-UM-EU


title: Treg.CD45RO+.CD272-.rep2

value: Sorted ex vivo Treg subset


title: UPN727 cells, TN14 CA41 at 9 month

source_name: UPN727 cells stimulated with TN14_CA41_M9 serum

value: UPN727 cells


title: 056AKP-VB_744

description:
uninvolved margin in the immediate vicinity of the mammilla
056AKP-VB


title: 057GS-UM-EL_745

description:
uninvolved margin of breast carcinoma
057GS-UM-EL


title: 057GS-UM-IU_748

description:
uninvolved margin of breast carcinoma
057GS-UM-IU


title: KZ54K_100

source_name: DNA extracted from whole blood

value: whole blood


title: KS141K_99

value: female


title: Treg.CD45RO+.CD200+.rep3

source_name: Human Treg subsets from peripheral blood

value: Treg CD45RO+ CD200+


title: UPN727 cells, TN14 CA40 at 9 month

source_name: UPN727 cells stimulated with TN14_CA40_M9 serum

value: 9 month into treatment


title: 056AKP-UM-IU_743

description:
uninvolved margin of breast carcinoma
056AKP-UM-IU

value: unifocal


title: UPN727 cells, TN14 CA41 at baseline

source_name: UPN727 cells stimulated with TN14_CA41_BL serum

value: at baseline


title: ME114K_102


title: UPN727 cells, TN14 CA40 at 12 month

source_name: UPN727 cells stimulated with TN14_CA40_M12 serum

value: 12 month into treatment


title: KB132K_97

value: multifocal


title: Treg.CD45RO+.CD272-.rep1


title: 056AKP-UM-IL_742

description:
uninvolved margin of breast carcinoma
056AKP-UM-IL


title: KK123K_98


title: Treg.CD45RO+.CD200-.rep3

value: Treg CD45RO+ CD200-


title: 056AKP-UM-EU_741

description:
uninvolved margin of breast carcinoma
056AKP-UM-EU


title: UPN727 cells, TN14 CA40 at baseline

source_name: UPN727 cells stimulated with TN14_CA40_BL serum


title: JU32K_96


title: Treg.CD45RO+.CD200+.rep2


title: Treg.CD45RO+.CD200+.rep1


title: UPN727 cells, TN14 CA39 at 9 month

source_name: UPN727 cells stimulated with TN14_CA39_M9 serum


title: 056AKP-UM-EL_740

description:
uninvolved margin of breast carcinoma
056AKP-UM-EL


title: Treg.CD45RO+.CD200-.rep2


title: UPN727 cells, TN14 CA38 at 12 month

source_name: UPN727 cells stimulated with TN14_CA38_M12 serum


title: 055GG-UM-IL_737

description:
uninvolved margin of breast carcinoma
055GG-UM-IL

value: Luminal B, HER2-


title: DM138K_94

description:
CONTROLS4: 23_controls_GPL6984.txt
Control experiment, DNA genotyping on DNA extracted from whole blood


title: Treg.CD45RO+.CD200-.rep1

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name


title: UPN727 cells, TN14 CA39 at baseline

source_name: UPN727 cells stimulated with TN14_CA39_BL serum


title: CJ112K_92

value: Triple negative


title: UPN727 cells, TN14 CA38 at 9 month

source_name: UPN727 cells stimulated with TN14_CA38_M9 serum


title: 055GG-UM-EU_736

description:
uninvolved margin of breast carcinoma
055GG-UM-EU

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: Treg.CD45RO+.CD195+.rep1

value: Treg CD45RO+ CD195+


title: 055GG-VB_739

description:
uninvolved margin in the immediate vicinity of the mammilla
055GG-VB


title: Treg.CD45RO+.CD195+.rep2


title: CG010_SK_91


title: 055GG-UM-EL_735

description:
uninvolved margin of breast carcinoma
055GG-UM-EL


title: BU97K_90


title: BMK015_SK_89

value: Luminal A


title: Treg.CD45RO+.CD195-.rep1

value: Treg CD45RO+ CD195-


title: IMH013_SK_95

value: skin biopsy


title: UPN727 cells, TN14 CA37 at 12 month

source_name: UPN727 cells stimulated with TN14_CA37_M12 serum


title: Treg.CD45RO+.CD161+.rep2

value: Treg CD45RO+ CD161+

value: Sorted ex vivo Treg subset


title: 055GG-UM-IU_738

description:
uninvolved margin of breast carcinoma
055GG-UM-IU


title: Treg.CD45RO+.CD195-.rep2


title: UPN727 cells, TN14 CA37 at 9 month

source_name: UPN727 cells stimulated with TN14_CA37_M9 serum

value: UPN727 cells


title: DH74K_93

value: female

value: whole blood


title: 053KS-VB_730

description:
uninvolved margin in the immediate vicinity of the mammilla
053KS-VB

value: ductal ca. in situ + Paget's ca.

value: multifocal ductal ca. in situ


title: 054MJ-VB_734

description:
uninvolved margin in the immediate vicinity of the mammilla
054MJ-VB

value: unifocal


title: BK152K_87

value: Luminal B, HER2+


title: UPN727 cells, TN14 CA39 at 12 month

source_name: UPN727 cells stimulated with TN14_CA39_M12 serum

value: 12 month into treatment


title: Treg.CD45RO+.CD161+.rep1


title: Treg.CD45RO+.CD161-.rep3

value: Treg CD45RO+ CD161-


title: UPN727 cells, TN14 CA38 at baseline

source_name: UPN727 cells stimulated with TN14_CA38_BL serum

value: at baseline


title: UPN727 cells, TN14 CA36 at 12 month

source_name: UPN727 cells stimulated with TN14_CA36_M12 serum


title: 054MJ-UM_733

description:
uninvolved margin of breast carcinoma
054MJ-UM

value: Luminal B, HER2-


title: UPN727 cells, TN14 CA36 at baseline

source_name: UPN727 cells stimulated with TN14_CA36_BL serum


title: BMF005_SK_88

description:
CONTROLS4: 23_controls_GPL6984.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy

source_name: DNA extracted from skin biopsy

value: multifocal


title: 053KS-UM-IU_729

description:
uninvolved margin of breast carcinoma
053KS-UM-IU


title: UPN727 cells, TN14 CA36 at 9 month

source_name: UPN727 cells stimulated with TN14_CA36_M9 serum

value: 9 month into treatment


title: Treg.CD45RO+.CD161-.rep2

source_name: Human Treg subsets from peripheral blood


title: AL002_SK_86


title: 053KS-UM-IL_728

description:
uninvolved margin of breast carcinoma
053KS-UM-IL


title: SJ88B_591

description:
uninvolved margin of breast carcinoma
SJ88B


title: UPN727 cells, TN14 CA37 at baseline

source_name: UPN727 cells stimulated with TN14_CA37_BL serum


title: 053KS-UM-EU_727

description: uninvolved margin of breast carcinoma


title: SE135B_588

description:
uninvolved margin of breast carcinoma
SE135B


title: Treg.CD45RO+.CD109+.rep3

value: Treg CD45RO+ CD109+


title: 053KS-UM-EL_726

description: uninvolved margin of breast carcinoma


title: RB84B_576

description:
uninvolved margin of breast carcinoma
RB84B


title: 052JW-VB_723

description: uninvolved margin in the immediate vicinity of the mammilla

value: Triple negative


title: UPN727 cells, TN14 CA35 at 9 month

source_name: UPN727 cells stimulated with TN14_CA35_M9 serum


title: PM102B_572

description:
uninvolved margin of breast carcinoma
PM102B


title: 052JW-UM-IL_722

description: uninvolved margin of breast carcinoma


title: Treg.CD45RO+.CD109+.rep1


title: Treg.CD45RO+.CD109+.rep2


title: Treg.CD45RO+.CD161-.rep1


title: PJ133B_565

description:
uninvolved margin of breast carcinoma
PJ133B

value: Luminal A


title: Treg.CD45RO+.CD109-.rep3

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

value: Treg CD45RO+ CD109-

value: Sorted ex vivo Treg subset


title: 052JW-UM-EU_721

description: uninvolved margin of breast carcinoma

value: female


title: 052JW-UM-EL_720

description: uninvolved margin of breast carcinoma


title: PI33B_560

description:
uninvolved margin of breast carcinoma
PI33B


title: PJ121B_563

description:
uninvolved margin of breast carcinoma
PJ121B


title: UPN727 cells, TN14 CA34 at 9 month

source_name: UPN727 cells stimulated with TN14_CA34_M9 serum

value: UPN727 cells


title: Treg.CD45RO+.CD109-.rep1


title: UPN727 cells, TN14 CA35 at 12 month

source_name: UPN727 cells stimulated with TN14_CA35_M12 serum


title: UPN727 cells, TN14 CA34 at baseline

source_name: UPN727 cells stimulated with TN14_CA34_BL serum


title: PE103B_548

description:
uninvolved margin of breast carcinoma
PE103B


title: 051AZ-VB_copy_719


title: UPN727 cells, TN14 CA34 at 12 month

source_name: UPN727 cells stimulated with TN14_CA34_M12 serum


title: UPN727 cells, TN14 CA33 at 12 month

source_name: UPN727 cells stimulated with TN14_CA33_M12 serum


title: Treg.CD45RO+.CD109-.rep2


title: UPN727 cells, TN14 CA35 at baseline

source_name: UPN727 cells stimulated with TN14_CA35_BL serum


title: 051AZ-VB_718

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: OG93B_544

description:
uninvolved margin of breast carcinoma
OG93B


title: Treg.CD45RO+.CD101+.rep4

value: Treg CD45RO+ CD101+


title: UPN727 cells, TN14 CA33 at 9 month

source_name: UPN727 cells stimulated with TN14_CA33_M9 serum


title: NJ111B_535

description:
uninvolved margin of breast carcinoma
NJ111B


title: 051AZ-UM-IU_717

description: uninvolved margin of breast carcinoma


title: 051AZ-UM-IL_716

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA32 at 12 month

source_name: UPN727 cells stimulated with TN14_CA32_M12 serum


title: Treg.CD45RO+.CD101-.rep4

value: Treg CD45RO+ CD101-


title: OB125B_542

description:
uninvolved margin of breast carcinoma
OB125B

value: unifocal


title: 051AZ-UM-EU_715

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA33 at baseline

source_name: UPN727 cells stimulated with TN14_CA33_BL serum


title: UPN727 cells, TN14 CA32 at baseline

source_name: UPN727 cells stimulated with TN14_CA32_BL serum


title: UPN727 cells, TN14 CA32 at 9 month

source_name: UPN727 cells stimulated with TN14_CA32_M9 serum


title: MU154B1_531

description:
uninvolved margin of breast carcinoma
MU154B1


title: Treg.CD45RO+.CD101-.rep3


title: Treg.CD45RO+.CD101+.rep3


title: MM69B_528

description:
uninvolved margin of breast carcinoma
MM69B


title: MM115B_524

description:
uninvolved margin of breast carcinoma
MM115B


title: Treg.CD45RO+.CD101-.rep1


title: Treg.CD45RO+.CD101+.rep2


title: UPN727 cells, TN14 CA31 at 12 month

source_name: UPN727 cells stimulated with TN14_CA31_M12 serum


title: UPN727 cells, TN14 CA31 at 9 month

source_name: UPN727 cells stimulated with TN14_CA31_M9 serum


title: UPN727 cells, TN14 CA31 at baseline

source_name: UPN727 cells stimulated with TN14_CA31_BL serum


title: 050RW-VB_713

value: multifocal?


title: 050RW-UM-IL_711

description: uninvolved margin of breast carcinoma


title: 050RW-UM-IU_712

description: uninvolved margin of breast carcinoma


title: ML36B3_522

description:
uninvolved margin of breast carcinoma
ML36B3


title: 051AZ-UM-EL_714

description: uninvolved margin of breast carcinoma


title: Treg.CD45RO+.CCR7+.CCR6+.rep3

source_name: Human Treg subsets from peripheral blood

value: Treg CD45RO+ CCR7+ CCR6+


title: Treg.CD45RO+.CD101-.rep2


title: Treg.CD45RO+.CCR7+.CCR6+.rep2


title: ML36B2_521

description:
uninvolved margin of breast carcinoma
ML36B2


title: 050RW-UM-EL_copy_709

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA30 at 9 month

source_name: UPN727 cells stimulated with TN14_CA30_M9 serum


title: UPN727 cells, TN14 CA30 at 12 month

source_name: UPN727 cells stimulated with TN14_CA30_M12 serum

value: 12 month into treatment


title: MK120B_505

description:
uninvolved margin of breast carcinoma
MK120B


title: 050RW-UM-EL_708

description: uninvolved margin of breast carcinoma


title: MH016_UM99_503

description:
uninvolved margin of breast carcinoma
MH016_UM99

value: Luminal B, HER2+


title: UPN727 cells, TN14 CA30 at baseline

source_name: UPN727 cells stimulated with TN14_CA30_BL serum

value: at baseline


title: 049ASZ-VB_707

description: uninvolved margin in the immediate vicinity of the mammilla


title: MH016_UM98_502

description:
uninvolved margin of breast carcinoma
MH016_UM98

value: multifocal


title: 049ASZ-UM-IU_706

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA29 at 12 month

source_name: UPN727 cells stimulated with TN14_CA29_M12 serum


title: MH016_UM4_501

description:
uninvolved margin of breast carcinoma
MH016_UM4


title: Treg.CD45RO+.CCR7+.CCR6-.rep3

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

value: Treg CD45RO+ CCR7+ CCR6-


title: MH016_UM3_500

description:
uninvolved margin of breast carcinoma
MH016_UM3


title: 049ASZ-UM-EU_704

description: uninvolved margin of breast carcinoma


title: MH016_UM2_499

description:
uninvolved margin of breast carcinoma
MH016_UM2


title: MH016_UM1_498

description:
uninvolved margin of breast carcinoma
MH016_UM1


title: 048EB-VB_700

value: Luminal B, HER2-


title: Treg.CD45RO+.CCR7-.CCR6+.rep3

value: Treg CD45RO+ CCR7- CCR6+


title: MG124B_493

description:
uninvolved margin of breast carcinoma
MG124B

value: Triple negative


title: Treg.CD45RO+.CCR7+.CCR6+.rep1


title: Treg.CD45RO+.CCR7+.CCR6-.rep1


title: Treg.CD45RO+.CCR7+.CCR6-.rep2


title: 048EB-UM-IU_699

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA29 at baseline

source_name: UPN727 cells stimulated with TN14_CA29_BL serum


title: UPN727 cells, TN14 CA28 at 9 month

source_name: UPN727 cells stimulated with TN14_CA28_M9 serum

value: 9 month into treatment


title: ME114B_490

description:
uninvolved margin of breast carcinoma
ME114B


title: 049ASZ-UM-IL_705

description: uninvolved margin of breast carcinoma

value: Luminal A


title: UPN727 cells, TN14 CA29 at 9 month

source_name: UPN727 cells stimulated with TN14_CA29_M9 serum


title: UPN727 cells, TN14 CA27 at 12 month

source_name: UPN727 cells stimulated with TN14_CA27_M12 serum


title: UPN727 cells, TN14 CA28 at baseline

source_name: UPN727 cells stimulated with TN14_CA28_BL serum


title: UPN727 cells, TN14 CA28 at 12 month

source_name: UPN727 cells stimulated with TN14_CA28_M12 serum


title: Treg.CD45RO+.CCR7-.CCR6+.rep1

value: Sorted ex vivo Treg subset


title: 048EB-UM-IL_698

description: uninvolved margin of breast carcinoma

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: female


title: MDAMB231-mir184_mimic-rep4

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

description: MDA-MB-231 cells, mir-184 mimic, 48 hours

hyb_protocol: Labeled, fragmented cDNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalised using NormalizeAffymetrixST GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

label_protocol: RNA samples were reverse transcribed into biotinylated cRNA at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

growth_protocol: MDA-MB-231 cells were cultured in RPMI 1640 media supplemented with 10% FCS at 37°C, 5% CO2. Cells were subcultured every 3 to 4 days.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) using the manufacturers protocol and further ethanol precipitated to remove salt contaminants. The RNA was quantified using the Nanodrop 1000 spectrophotometre and the integrity of the RNA was determined using the Agilent  2100 bioanalyser. (Agilent Technologies, Santa Clara, CA)

treatment_protocol: MDA-MB-231 cells were seeded in 6 well plates at a cell density of 1.8 x 105 cells/ well. The next day, miRIDIAN miRNA mimics (Dharmacon) were transfected into cells using Lipofectamine 2000 (Invitrogen) according to the manufacturers protocol for transfecting siRNA. Mimics (Final concentration of 50nm) was mixed with 1% lipofectamine 2000 (v/v) diluted in Opti-MEM transfection medium (Invitrogen) and incubated for 20 minutes. The mimics were added dropwise onto cells in growth medium at a final concentration of 50nm. Fresh medium was replaced 24hours post transfection.

tag: cell line

value: breast

tag: transfection

value: mir-184 mimic, 48 hours


title: MDAMB231-mir184_mimic-rep3

source_name: MDA-MB-231 cells, mir-184 mimic, 48 hours


title: Treg.CD45RO+.CCR7-.CCR6+.rep2


title: 049ASZ-UM-EL_703

description: uninvolved margin of breast carcinoma

value: unifocal


title: UPN727 cells, TN14 CA27 at baseline

source_name: UPN727 cells stimulated with TN14_CA27_BL serum

value: UPN727 cells


title: UPN727 cells, TN14 CA26 at 12 month

source_name: UPN727 cells stimulated with TN14_CA26_M12 serum


title: MDAMB231-mir184_mimic-rep2


title: MC109B_482

description:
uninvolved margin of breast carcinoma
MC109B


title: MD86B_486

description:
uninvolved margin of breast carcinoma
MD86B


title: 048EB-UM-EU_697

description: uninvolved margin of breast carcinoma


title: MD106B_484

description:
uninvolved margin of breast carcinoma
MD106B


title: UPN727 cells, TN14 CA27 at 9 month

source_name: UPN727 cells stimulated with TN14_CA27_M9 serum


title: MB101B_480

description:
uninvolved margin of breast carcinoma
MB101B


title: 048EB-UM-EL_696

description: uninvolved margin of breast carcinoma


title: 047MS-UM-IL_693

description: uninvolved margin of breast carcinoma


title: 047MS-UM-IU_694

description: uninvolved margin of breast carcinoma


title: 047MS-VB_695


title: LK003_UM3_478

description:
uninvolved margin of breast carcinoma
LK003_UM3


title: LK003_UM99_479

description:
uninvolved margin of breast carcinoma
LK003_UM99


title: LK003_UM2_477

description:
uninvolved margin of breast carcinoma
LK003_UM2


title: 047MS-UM-EL_691

description: uninvolved margin of breast carcinoma


title: LK003_UM1_476

description:
uninvolved margin of breast carcinoma
LK003_UM1


title: MDAMB231-mir184_mimic-rep1


title: 046MU-VB_690

description: uninvolved margin in the immediate vicinity of the mammilla


title: LEB004_UM99_472

description:
uninvolved margin of breast carcinoma
LEB004_UM99


title: MDAMB231-negative_control-rep3

description: MDA-MB-231 cells, mir-184 mimic negative control, 48 hours


title: MDAMB231-negative_control-rep2

source_name: MDA-MB-231 cells, mir-184 mimic negative control, 48 hours


title: UPN727 cells, TN14 CA26 at 9 month

source_name: UPN727 cells stimulated with TN14_CA26_M9 serum


title: 046MU-UM-IU_689

description: uninvolved margin of breast carcinoma


title: LEB004_UM4_471

description:
uninvolved margin of breast carcinoma
LEB004_UM4


title: MDAMB231-negative_control-rep1

value: mir-184 mimic negative control, 48 hours


title: UPN727 cells, TN14 CA25 at 12 month

source_name: UPN727 cells stimulated with TN14_CA25_M12 serum

value: 12 month into treatment


title: UPN727 cells, TN14 CA25 at baseline

source_name: UPN727 cells stimulated with TN14_CA25_BL serum


title: KRAS-mutant lung adenocarcinoma  B2-130

city: Houston

first: Lixia

last: Diao

state: TX

address: 1400 Pressler Steet

department: Bioinfomatics and Computational Biology

institute: University of Texa MD Anderson

description: KRAS-mutant lung adenocarcinoma from the BATTLE-2 trial

hyb_protocol: Samples (fragmented and labeled sscDNA (2ug)) were hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays for 17hrs at 45 C/60rpm in a GeneChip Affymetrix Hybridization Oven 645. The GeneChips were washed and stained using the Affymetrix Fluidics station 450 controlled by Affymetrix GeneChip Command Console (AGCC) Software, v4.0

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000, 7G controlled by AGCC Software.

data_processing: The arrays were analyzed with Robust Multi-Array Average ( RMA)  gene analysis using Affymetrix default analysis settings.Starting with the probe-level data from a set of Gene Chips, the perfect-match (PM) values were background-corrected, normalized and finally summarized resulting in a set of expression measures.

source_name: KRAS mutant, lung adenocarcinoma

label_protocol: Samples were enzymatically fragmented and labelled using the EncoreTM Biotin Module (NuGEN Technologies)

growth_protocol: KRAS-mutant lung adenocarcinomas from the BATTLE-2 trial

extract_protocol: Fresh frozen needle biopsy samples were embedded in OCT and stored at -80oC. OCT was removed and tissue shavings collected. RNA was extracted using the RNAqueous®-Micro Total RNA Isolation Kit (Life Technologies, AM1931). cDNA synthesis and amplification were performed using the Ovation®Pico WTA System V2 (NuGEN). Purification of SPIA  cDNA was performed using the QIAGEN QIAquick PCR Purification Kit.

tag: age

value: Not applicable

value: Lung Adenocarcinoma

tag: genotype

value: KRAS-mutant


title: UPN727 cells, TN14 CA26 at baseline

source_name: UPN727 cells stimulated with TN14_CA26_BL serum

value: at baseline


title: UPN727 cells, TN14 CA25 at 9 month

source_name: UPN727 cells stimulated with TN14_CA25_M9 serum


title: 046MU-UM-IL_688

description: uninvolved margin of breast carcinoma


title: KRAS-mutant lung adenocarcinoma  B2-121


title: UPN727 cells, TN14 CA24 at 9 month

source_name: UPN727 cells stimulated with TN14_CA24_M9 serum


title: KRAS-mutant lung adenocarcinoma  B2-160


title: 047MS-UM-EU_692

description: uninvolved margin of breast carcinoma


title: LEB004_UM3_470

description:
uninvolved margin of breast carcinoma
LEB004_UM3

value: multifocal


title: UPN727 cells, TN14 CA24 at baseline

source_name: UPN727 cells stimulated with TN14_CA24_BL serum


title: KRAS-mutant lung adenocarcinoma  B2-172


title: MDAMB231-negative_control-rep4


title: UPN727 cells, TN14 CA23 at 12 month

source_name: UPN727 cells stimulated with TN14_CA23_M12 serum


title: UPN727 cells, TN14 CA24 at 12 month

source_name: UPN727 cells stimulated with TN14_CA24_M12 serum


title: KRAS-mutant lung adenocarcinoma  B2-089


title: 046MU-UM-EU_687

description: uninvolved margin of breast carcinoma


title: LEB004_UM1_468

description:
uninvolved margin of breast carcinoma
LEB004_UM1


title: 046MU-UM-EL_686

description: uninvolved margin of breast carcinoma


title: 045EK-VB_685


title: UPN727 cells, TN14 CA23 at 9 month

source_name: UPN727 cells stimulated with TN14_CA23_M9 serum


title: KZ54B_463

description:
uninvolved margin of breast carcinoma
KZ54B

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: Luminal B, HER2+


title: UPN727 cells, TN14 CA23 at baseline

source_name: UPN727 cells stimulated with TN14_CA23_BL serum


title: KM19B_450

description:
uninvolved margin of breast carcinoma
KM19B


title: 045EK-UM-IU_684

description: uninvolved margin of breast carcinoma

value: Triple negative


title: KM143B_448

description:
uninvolved margin of breast carcinoma
KM143B


title: 045EK-UM-IL_683

description: uninvolved margin of breast carcinoma


title: 045EK-UM-EU_682

description: uninvolved margin of breast carcinoma


title: LEB004_UM2_469

description:
uninvolved margin of breast carcinoma
LEB004_UM2


title: 045EK-UM-EL_681

description: uninvolved margin of breast carcinoma


title: KM136B_446

description:
uninvolved margin of breast carcinoma
KM136B

value: Luminal B, HER2-


title: Treg.CD45RO+.CD101+.rep1

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

source_name: Human Treg subsets from peripheral blood

value: Treg CD45RO+ CD101+


title: KRAS-mutant lung adenocarcinoma  B2-108


title: KK123B_443

description:
uninvolved margin of breast carcinoma
KK123B

value: Luminal A


title: KRAS-mutant lung adenocarcinoma  B2-083


title: UPN727 cells, TN14 CA22 at 12 month

source_name: UPN727 cells stimulated with TN14_CA22_M12 serum


title: KRAS-mutant lung adenocarcinoma  B2-062


title: 044JD-VB_680

value: female


title: UPN727 cells, TN14 CA22 at baseline

source_name: UPN727 cells stimulated with TN14_CA22_BL serum


title: KJ142B_437

description:
uninvolved margin of breast carcinoma
KJ142B


title: KE53B_429

description:
uninvolved margin of breast carcinoma
KE53B


title: KRAS-mutant lung adenocarcinoma  B2-281


title: KE127B_427

description:
uninvolved margin of breast carcinoma
KE127B


title: 044JD-UM-IL_678

description: uninvolved margin of breast carcinoma


title: KRAS-mutant lung adenocarcinoma  B2-116


title: UPN727 cells, TN14 CA22 at 9 month

source_name: UPN727 cells stimulated with TN14_CA22_M9 serum

value: 9 month into treatment


title: UPN727 cells, TN14 CA21 at 12 month

source_name: UPN727 cells stimulated with TN14_CA21_M12 serum


title: KRAS-mutant lung adenocarcinoma  B2-255


title: KRAS-mutant lung adenocarcinoma  B2-047


title: KRAS-mutant lung adenocarcinoma  B2-058


title: KRAS-mutant lung adenocarcinoma  B2-037


title: UPN727 cells, TN14 CA20 at 12 month

source_name: UPN727 cells stimulated with TN14_CA20_M12 serum


title: UPN727 cells, TN14 CA20 at 9 month

source_name: UPN727 cells stimulated with TN14_CA20_M9 serum


title: UPN727 cells, TN14 CA21 at 9 month

source_name: UPN727 cells stimulated with TN14_CA21_M9 serum


title: 043WB-VB_676

description: uninvolved margin in the immediate vicinity of the mammilla


title: KB132B_423

description:
uninvolved margin of breast carcinoma
KB132B


title: KB80B_425

description:
uninvolved margin of breast carcinoma
KB80B


title: 043WB-UM-IU_675

description: uninvolved margin of breast carcinoma


title: KRAS-mutant lung adenocarcinoma  B2-093

source_name: KRAS mutant, lung adenocarcinoma


title: UPN727 cells, TN14 CA19 at 12 month

source_name: UPN727 cells stimulated with TN14_CA19_M12 serum


title: 044JD-UM-IU_679

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA21 at baseline

source_name: UPN727 cells stimulated with TN14_CA21_BL serum


title: KA15B_420

description:
uninvolved margin of breast carcinoma
KA15B


title: KRAS-mutant lung adenocarcinoma  B2-203

description: KRAS-mutant lung adenocarcinoma from the BATTLE-2 trial


title: KRAS-mutant lung adenocarcinoma  B2-010


title: JU32B_417

description:
uninvolved margin of breast carcinoma
JU32B


title: 043WB-UM-IL_674

description: uninvolved margin of breast carcinoma


title: 044JD-UM-EL_677

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA20 at baseline

source_name: UPN727 cells stimulated with TN14_CA20_BL serum


title: KRAS-mutant lung adenocarcinoma  B2-016


title: JJ144B_410

description:
uninvolved margin of breast carcinoma
JJ144B


title: 043WB-UM-EL_672

description: uninvolved margin of breast carcinoma


title: KRAS-mutant lung adenocarcinoma  B2-185


title: JB11B_406

description:
uninvolved margin of breast carcinoma
JB11B


title: UPN727 cells, TN14 CA19 at 9 month

source_name: UPN727 cells stimulated with TN14_CA19_M9 serum


title: UPN727 cells, TN14 CA18 at 12 month

source_name: UPN727 cells stimulated with TN14_CA18_M12 serum


title: KRAS-mutant lung adenocarcinoma  B2-236


title: 042JL-VB_669


title: IMH013_UM99_401

description:
uninvolved margin of breast carcinoma
IMH013_UM99


title: UPN727 cells, TN14 CA19 at baseline

source_name: UPN727 cells stimulated with TN14_CA19_BL serum


title: 042JL-UM-IU_668

description: uninvolved margin of breast carcinoma

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: IMH013_UM98_400

description:
uninvolved margin of breast carcinoma
IMH013_UM98


title: 042JL-UM-IL_667

description: uninvolved margin of breast carcinoma


title: IMH013_UM4_399

description:
uninvolved margin of breast carcinoma
IMH013_UM4


title: KRAS-mutant lung adenocarcinoma  B2-098


title: IMH013_UM1_398

description:
uninvolved margin of breast carcinoma
IMH013_UM1


title: 041JS-VB_664


title: KRAS-mutant lung adenocarcinoma  B2-111


title: KRAS-mutant lung adenocarcinoma  B2-120


title: 042JL-UM-EL_665

description: uninvolved margin of breast carcinoma


title: GW39B_389

description:
uninvolved margin of breast carcinoma
GW39B


title: UPN727 cells, TN14 CA17 at 12 month

source_name: UPN727 cells stimulated with TN14_CA17_M12 serum


title: HW82B_394

description:
uninvolved margin of breast carcinoma
HW82B


title: UPN727 cells, TN14 CA17 at 9 month

source_name: UPN727 cells stimulated with TN14_CA17_M9 serum


title: KRAS-mutant lung adenocarcinoma  B2-075


title: KRAS-mutant lung adenocarcinoma  B2-070


title: 041JS-UM-IU_663

description: uninvolved margin of breast carcinoma


title: DM138B_378

description:
uninvolved margin of breast carcinoma
DM138B


title: UPN727 cells, TN14 CA17 at baseline

source_name: UPN727 cells stimulated with TN14_CA17_BL serum


title: 042JL-UM-EU_666

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA18 at 9 month

source_name: UPN727 cells stimulated with TN14_CA18_M9 serum


title: UPN727 cells, TN14 CA16 at 12 month

source_name: UPN727 cells stimulated with TN14_CA16_M12 serum


title: DH74B_373

description:
uninvolved margin of breast carcinoma
DH74B


title: KRAS-mutant lung adenocarcinoma  B2-003


title: UPN727 cells, TN14 CA18 at baseline

source_name: UPN727 cells stimulated with TN14_CA18_BL serum


title: UPN727 cells, TN14 CA16 at 9 month

source_name: UPN727 cells stimulated with TN14_CA16_M9 serum


title: KRAS-mutant lung adenocarcinoma  B2-019


title: KRAS-mutant lung adenocarcinoma  B2-072


title: UPN727 cells, TN14 CA15 at 12 month

source_name: UPN727 cells stimulated with TN14_CA15_M12 serum


title: KRAS-mutant lung adenocarcinoma  B2-139


title: KRAS-mutant lung adenocarcinoma  B2-162


title: UPN727 cells, TN14 CA16 at baseline

source_name: UPN727 cells stimulated with TN14_CA16_BL serum


title: UPN727 cells, TN14 CA15 at 9 month

source_name: UPN727 cells stimulated with TN14_CA15_M9 serum


title: 041JS-UM-EU_661

description: uninvolved margin of breast carcinoma


title: DE137B_366

description:
uninvolved margin of breast carcinoma
DE137B


title: 041JS-UM-EL_660

description: uninvolved margin of breast carcinoma


title: DE108B_364

description:
uninvolved margin of breast carcinoma
DE108B


title: 041JS-UM-IL_662

description: uninvolved margin of breast carcinoma


title: DA83B_362

description:
uninvolved margin of breast carcinoma
DA83B


title: 040HM-VB_659

description: uninvolved margin in the immediate vicinity of the mammilla


title: 040HM-UM-IU_658

description: uninvolved margin of breast carcinoma


title: CM155B_360

description:
uninvolved margin of breast carcinoma
CM155B


title: UPN727 cells, TN14 CA15 at baseline

source_name: UPN727 cells stimulated with TN14_CA15_BL serum


title: KRAS-mutant lung adenocarcinoma  B2-117

description: KRAS-mutant lung adenocarcinoma from the BATTLE-2 trial

source_name: KRAS mutant, lung adenocarcinoma


title: 040HM-UM-IL_657

description: uninvolved margin of breast carcinoma


title: CJ112B_358

description:
uninvolved margin of breast carcinoma
CJ112B


title: 040HM-UM-EU_656

description: uninvolved margin of breast carcinoma


title: CG010_UM99_356

description:
uninvolved margin of breast carcinoma
CG010_UM99


title: 040HM-UM-EL_655

description: uninvolved margin of breast carcinoma


title: CG010_UM4_355

description:
uninvolved margin of breast carcinoma
CG010_UM4


title: CG010_UM2_354

description:
uninvolved margin of breast carcinoma
CG010_UM2


title: 039BW-VB_654


title: KRAS-mutant lung adenocarcinoma  B2-209


title: 039BW-UM-IL_653

description: uninvolved margin of breast carcinoma


title: CB110B_350

description:
uninvolved margin of breast carcinoma
CB110B


title: KRAS-mutant lung adenocarcinoma  B2-197


title: BU97B_348

description:
uninvolved margin of breast carcinoma
BU97B


title: KRAS-mutant lung adenocarcinoma  B2-241


title: UPN727 cells, TN14 CA13 at 12 month

source_name: UPN727 cells stimulated with TN14_CA13_M12 serum


title: 039BW-UM-EL_651

description: uninvolved margin of breast carcinoma


title: KRAS-mutant lung adenocarcinoma  B2-249


title: UPN727 cells, TN14 CA14 at baseline

source_name: UPN727 cells stimulated with TN14_CA14_BL serum


title: UPN727 cells, TN14 CA13 at baseline

source_name: UPN727 cells stimulated with TN14_CA13_BL serum


title: UPN727 cells, TN14 CA13 at 9 month

source_name: UPN727 cells stimulated with TN14_CA13_M9 serum


title: UPN727 cells, TN14 CA14 at 9 month

source_name: UPN727 cells stimulated with TN14_CA14_M9 serum


title: 038ALZ-VB_648

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: BMK015_UM99_346

description:
uninvolved margin of breast carcinoma
BMK015_UM99


title: UPN727 cells, TN14 CA14 at 12 month

source_name: UPN727 cells stimulated with TN14_CA14_M12 serum


title: UPN727 cells, TN14 CA12 at 12 month

source_name: UPN727 cells stimulated with TN14_CA12_M12 serum


title: KRAS-mutant lung adenocarcinoma  B2-254


title: CV-HCV NK cells_repeat 8_mAdbID:125368

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 125368

hyb_protocol: Affymetrix Hybridization Protocol RNA quality and quantity was estimated using Nanodrop (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). First- and second-strand cDNA were synthesized from 10 ng of total RNA according to manufacturer's instructions (Nugen Ovation Pico WTA System V2). cDNAs were fragmented, biotinylated (Nugen Encore Biotin Module), and hybridized to the GeneChip Human Gene 1.0 ST Arrays (Affymetrix WT Terminal Labeling Kit).

scan_protocol: Affymetrix Scanning Protocol The arrays were washed and stained on a GeneChip Fluidics Station 450 (Affymetrix) and scanned by GeneChip Scanner 3000.

data_processing:
Affymetrix RMA Data Processing
Calculation Method: After Robust Multichip Average (RMA) normalization, the statistically significant gene expression changes were functionally analyzed using Partek Genomic Suite (St. Louis, MO).

source_name: Chronically Viraemic HCV-infected (CV-HCV) NK cells

label_protocol: Nugen Encore Biotin Module according to manufacturer's protocol

extract_protocol:
miRNeasy Minikit
Total RNA from purified NK cells derived from HD, SVR, NR, SR and CH-HCV individuals were extracted using miRNeasy minikit (Qiagen) according to the manufacture's protocol.

value: Blood

value: Natural Killer (NK) cells purified from PBMC's

tag: disease state

value: Hepatitis C virus (HCV) infection


title: 039BW-UM-EU_652

description: uninvolved margin of breast carcinoma

value: unifocal


title: BMK015_UM98_345

description:
uninvolved margin of breast carcinoma
BMK015_UM98


title: UPN727 cells, TN14 CA12 at 9 month

source_name: UPN727 cells stimulated with TN14_CA12_M9 serum

value: UPN727 cells


title: UPN727 cells, TN14 CA12 at baseline

source_name: UPN727 cells stimulated with TN14_CA12_BL serum


title: 038ALZ-UM-IU_647

description: uninvolved margin of breast carcinoma


title: BMK015_UM3_344

description:
uninvolved margin of breast carcinoma
BMK015_UM3


title: SR NK cells_repeat 5_mAdbID:125366

description: mAdb experiment ID: 125366

source_name: Spontaneously Recovered (SR) NK cells

tag: cell type

tag: patient group

value: spontaneously recovered (SR)


title: UPN727 cells, TN14 CA11 at 12 month

source_name: UPN727 cells stimulated with TN14_CA11_M12 serum

value: 12 month into treatment


title: 038ALZ-UM-IL_646

description: uninvolved margin of breast carcinoma


title: BMK015_UM2_343

description:
uninvolved margin of breast carcinoma
BMK015_UM2


title: SVR NK cells_repeat 9_mAdbID:125369

description: mAdb experiment ID: 125369

source_name: Sustained Virologic Response (SVR) NK cells

value: sustained virologic responder (SVR)


title: CV-HCV NK cells_repeat 1_mAdbID:125364

description: mAdb experiment ID: 125364


title: 038ALZ-UM-EU_645

description: uninvolved margin of breast carcinoma


title: BMK015_UM1_342

description:
uninvolved margin of breast carcinoma
BMK015_UM1


title: UPN727 cells, TN14 CA11 at 9 month

source_name: UPN727 cells stimulated with TN14_CA11_M9 serum


title: CV-HCV NK cells_repeat 7_mAdbID:125363

description: mAdb experiment ID: 125363


title: SR NK cells_repeat 4_mAdbID:125365

description: mAdb experiment ID: 125365


title: SR NK cells_repeat 6_mAdbID:125367

description: mAdb experiment ID: 125367


title: 038ALZ-UM-EL_644

description: uninvolved margin of breast carcinoma


title: BMF005_UM99_338

description:
uninvolved margin of breast carcinoma
BMF005_UM99


title: UPN727 cells, TN14 CA11 at baseline

source_name: UPN727 cells stimulated with TN14_CA11_BL serum

value: at baseline


title: 036CS-VB_641


title: BMF005_UM5_337

description:
uninvolved margin of breast carcinoma
BMF005_UM5

value: multifocal


title: UPN727 cells, TN14 CA10 at 12 month

source_name: UPN727 cells stimulated with TN14_CA10_M12 serum


title: UPN727 cells, TN14 CA10 at 9 month

source_name: UPN727 cells stimulated with TN14_CA10_M9 serum


title: BMF005_UM4_336

description:
uninvolved margin of breast carcinoma
BMF005_UM4


title: 036CS-UM-IU_640

description: uninvolved margin of breast carcinoma


title: 036CS-UM-IL_639

description: uninvolved margin of breast carcinoma


title: BMF005_UM3_335

description:
uninvolved margin of breast carcinoma
BMF005_UM3


title: 029LN-VB_638

description: uninvolved margin in the immediate vicinity of the mammilla


title: BMF005_UM1_334

description:
uninvolved margin of breast carcinoma
BMF005_UM1


title: 029LN-UM-IL_637

description: uninvolved margin of breast carcinoma


title: BM50B_329

description:
uninvolved margin of breast carcinoma
BM50B


title: 043WB-UM-EU_673

description: uninvolved margin of breast carcinoma


title: 029LN-UM-EU_636

description: uninvolved margin of breast carcinoma


title: BL87B_327

description:
uninvolved margin of breast carcinoma
BL87B


title: CV-HCV NK cells_repeat 6_mAdbID:125361

description: mAdb experiment ID: 125361


title: 029LN-UM-EL_635

description: uninvolved margin of breast carcinoma


title: CV-HCV NK cells_repeat 5_mAdbID:125358

description: mAdb experiment ID: 125358


title: HD NK cells_repeat 7_mAdbID:125357

description: mAdb experiment ID: 125357

source_name: Healthy Donor (HD) NK cells


title: BK152B_322

description:
uninvolved margin of breast carcinoma
BK152B

value: Luminal B, HER2+


title: SR NK cells_repeat 2_mAdbID:125360

description: mAdb experiment ID: 125360


title: UPN727 cells, TN14 CA09 at 9 month

source_name: UPN727 cells stimulated with TN14_CA09_M9 serum


title: UPN727 cells, TN14 CA10 at baseline

source_name: UPN727 cells stimulated with TN14_CA10_BL serum


title: SR NK cells_repeat 1_mAdbID:125359

description: mAdb experiment ID: 125359


title: SR NK cells_repeat 3_mAdbID:125362

description: mAdb experiment ID: 125362


title: UPN727 cells, TN14 CA09 at 12 month

source_name: UPN727 cells stimulated with TN14_CA09_M12 serum


title: UPN727 cells, TN14 CA08 at 12 month

source_name: UPN727 cells stimulated with TN14_CA08_M12 serum


title: 017KM-UM-IU_625

description: uninvolved margin of breast carcinoma

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: UPN727 cells, TN14 CA08 at baseline

source_name: UPN727 cells stimulated with TN14_CA08_BL serum


title: HD NK cells_repeat 5_mAdbID:125355

description: mAdb experiment ID: 125355


title: AL002_UM99_315

description:
uninvolved margin of breast carcinoma
AL002_UM99


title: HD NK cells_repeat 3_mAdbID:125353

description: mAdb experiment ID: 125353


title: HD NK cells_repeat 6_mAdbID:125356

description: mAdb experiment ID: 125356


title: UPN727 cells, TN14 CA09 at baseline

source_name: UPN727 cells stimulated with TN14_CA09_BL serum


title: UPN727 cells, TN14 CA07 at 12 month

source_name: UPN727 cells stimulated with TN14_CA07_M12 serum


title: UPN727 cells, TN14 CA08 at 9 month

source_name: UPN727 cells stimulated with TN14_CA08_M9 serum


title: HD NK cells_repeat 4_mAdbID:125354

description: mAdb experiment ID: 125354


title: 017KM-UM-IL_624

description: uninvolved margin of breast carcinoma


title: AL002_UM2_313

description:
uninvolved margin of breast carcinoma
AL002_UM2


title: 017KM-VB_626


title: HD NK cells_repeat 1_mAdbID:125351

description: mAdb experiment ID: 125351


title: UPN727 cells, TN14 CA07 at baseline

source_name: UPN727 cells stimulated with TN14_CA07_BL serum


title: 017KM-UM-EL_622

description: uninvolved margin of breast carcinoma


title: AL002_UM1_312

description:
uninvolved margin of breast carcinoma
AL002_UM1


title: 015SK-VB_617


title: AB007_UM3_305

description:
uninvolved margin of breast carcinoma
AB007_UM3


title: AB007_UM99_307

description:
uninvolved margin of breast carcinoma
AB007_UM99


title: AL002_UM3_314

description:
uninvolved margin of breast carcinoma
AL002_UM3


title: CV-HCV NK cells_repeat 2_mAdbID:125348

description: mAdb experiment ID: 125348

source_name: Chronically Viraemic HCV-infected (CV-HCV) NK cells


title: HD NK cells_repeat 2_mAdbID:125352

description: mAdb experiment ID: 125352


title: 017KM-UM-EU_623

description: uninvolved margin of breast carcinoma


title: CV-HCV NK cells_repeat 3_mAdbID:125349

description: mAdb experiment ID: 125349


title: UPN727 cells, TN14 CA07 at 9 month

source_name: UPN727 cells stimulated with TN14_CA07_M9 serum


title: UPN727 cells, TN14 CA06 at baseline

source_name: UPN727 cells stimulated with TN14_CA06_BL serum


title: UPN727 cells, TN14 CA06 at 12 month

source_name: UPN727 cells stimulated with TN14_CA06_M12 serum


title: CV-HCV NK cells_repeat 4_mAdbID:125350

description: mAdb experiment ID: 125350


title: UPN727 cells, TN14 CA06 at 9 month

source_name: UPN727 cells stimulated with TN14_CA06_M9 serum


title: 015SK-UM-IU_616

description: uninvolved margin of breast carcinoma


title: UPN727 cells, TN14 CA05 at 12 month

source_name: UPN727 cells stimulated with TN14_CA05_M12 serum


title: AB007_UM2_304

description:
uninvolved margin of breast carcinoma
AB007_UM2


title: AB007_UM4_306

description:
uninvolved margin of breast carcinoma
AB007_UM4


title: 015SK-UM-IL_615

description: uninvolved margin of breast carcinoma


title: 015SK-UM-EU_614

description: uninvolved margin of breast carcinoma


title: 015SK-UM-EL_613

description: uninvolved margin of breast carcinoma


title: 006MK-VB_606


title: NR NK cells_repeat 10_mAdbID:125347

description: mAdb experiment ID: 125347

source_name: Non-responder (NR) NK cells

value: non-responder (NR)


title: UPN727 cells, TN14 CA04 at 12 month

source_name: UPN727 cells stimulated with TN14_CA04_M12 serum


title: NR NK cells_repeat 8_mAdbID:125345

description: mAdb experiment ID: 125345


title: 006MK-UM-IU_605

description: uninvolved margin of breast carcinoma

value: Luminal B, HER2-


title: NR NK cells_repeat 9_mAdbID:125346

description: mAdb experiment ID: 125346


title: UPN727 cells, TN14 CA04 at 9 month

source_name: UPN727 cells stimulated with TN14_CA04_M9 serum


title: UPN727 cells, TN14 CA05 at baseline

source_name: UPN727 cells stimulated with TN14_CA05_BL serum


title: UPN727 cells, TN14 CA05 at 9 month

source_name: UPN727 cells stimulated with TN14_CA05_M9 serum


title: UPN727 cells, TN14 CA04 at baseline

source_name: UPN727 cells stimulated with TN14_CA04_BL serum


title: NR NK cells_repeat 6_mAdbID:125343

description: mAdb experiment ID: 125343


title: 006MK-UM-IL_604

description: uninvolved margin of breast carcinoma

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: 004JJ-UM-IL_598

description: uninvolved margin of breast carcinoma


title: 006MK-UM-EL_603

description: uninvolved margin of breast carcinoma


title: NR NK cells_repeat 7_mAdbID:125344

description: mAdb experiment ID: 125344


title: 004JJ-VB_600


title: NR NK cells_repeat 5_mAdbID:125342

description: mAdb experiment ID: 125342


title: UPN727 cells, TN14 CA03 at baseline

source_name: UPN727 cells stimulated with TN14_CA03_BL serum


title: UPN727 cells, TN14 CA03 at 12 month

source_name: UPN727 cells stimulated with TN14_CA03_M12 serum


title: SVR NK cells_repeat 7_mAdbID:125338

description: mAdb experiment ID: 125338

source_name: Sustained Virologic Response (SVR) NK cells


title: SVR NK cells_repeat 8_mAdbID:125339

description: mAdb experiment ID: 125339


title: 004JJ-UM-IU_599

description: uninvolved margin of breast carcinoma


title: 004JJ-UM-EU_597

description: uninvolved margin of breast carcinoma


title: NR NK cells_repeat 4_mAdbID:125341

description: mAdb experiment ID: 125341


title: UPN727 cells, TN14 CA02 at 12 month

source_name: UPN727 cells stimulated with TN14_CA02_M12 serum


title: SVR NK cells_repeat 6_mAdbID:125337

description: mAdb experiment ID: 125337


title: NR NK cells_repeat 3_mAdbID:125340

description: mAdb experiment ID: 125340


title: ZL152-PT_104

description:
TUMORS3: 98_primaryTumors_18224.txt
Genotyping on DNA extracted from a primary tumor

source_name: DNA extracted from primary tumor

value: primary tumor


title: UPN727 cells, TN14 CA01 at 12 month

source_name: UPN727 cells stimulated with TN14_CA01_M12 serum


title: SVR NK cells_repeat 4_mAdbID:125335

description: mAdb experiment ID: 125335


title: UPN727 cells, TN14 CA02 at 9 month

source_name: UPN727 cells stimulated with TN14_CA02_M9 serum


title: UV023-PT2_103

value: Luminal A


title: UPN727 cells, TN14 CA02 at baseline

source_name: UPN727 cells stimulated with TN14_CA02_BL serum


title: SVR NK cells_repeat 5_mAdbID:125336

description: mAdb experiment ID: 125336


title: UPN727 cells, TN14 CA03 at 9 month

source_name: UPN727 cells stimulated with TN14_CA03_M9 serum


title: UV023-PT1_102

value: female


title: NR NK cells_repeat 2_mAdbID:125333

description: mAdb experiment ID: 125333


title: TP169-PT_101


title: NR NK cells_repeat 1_mAdbID:125332

description: mAdb experiment ID: 125332


title: D431 T-BMP7: GSC resistant to 500 uM TMZ treated with BMP7

city: Los Angeles

first: Cho-Lea

last: Tso

state: CA

address: 10833 Le Conte Avenue

department: Surgery

institute: University of California, Los Angeles

description:
Human/patient (brain tumor)
D431 T-BMP7: D431 GSC resistant to 500 uM TMZ treated with BMP7

hyb_protocol: hybridized on Affymetrix GeneChip U133 Plus 2.0 Array

scan_protocol: GeneArray scanner (Affymetrix).

data_processing: The CEL files generated by the Affymetrix Microarray Suite version 5.0 were converted into DCP files using the DNA-Chip Analyzer (dChip 1.3; http://biosun1.harvard.edu/complab/dchip/).

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

growth_protocol: GSC cultures in stem cell growth media

extract_protocol: Total RNA was extracted from untreated and BMP7 treated D431-parental GSC and D431-500uM TMZ GSC (resistance to 500 uM TMZ)

treatment_protocol: untreated or treated with BMP7 (100ng/ml)

value: glioblastoma stem cells

tag: treatment


title: SVR NK cells_repeat 3_mAdbID:125334

description: mAdb experiment ID: 125334

value: Blood


title: BH81B_318

description:
uninvolved margin of breast carcinoma
BH81B


title: SVR NK cells_repeat 2_mAdbID:125331

description: mAdb experiment ID: 125331

value: Natural Killer (NK) cells purified from PBMC's


title: UPN727 cells, TN14 CA01 at baseline

source_name: UPN727 cells stimulated with TN14_CA01_BL serum

tag: responder cells


title: D431 T-Control: GSC resistant to 500 uM TMZ (no BMP7 treatment)

description:
Human/patient (brain tumor)
D431 T-Control: D431 GSC resistant to 500 uM TMZ (no BMP7 treatment)


title: UPN727 cells, TN14 CA01 at 9 month

source_name: UPN727 cells stimulated with TN14_CA01_M9 serum

tag: patient

value: 9 month into treatment


title: SK056-PT2_99

value: Triple negative


title: Blood [14P1201030]

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

country: China

institute: The Chinese University of Hong Kong

hyb_protocol: Illumina standard protocol for CytoSNP 12 chips (GPL16483), using automation with the Tecan Evo robot.

data_processing: Genomic DNA was genotyped using KaryoStudio V 1.3.11 and GenomeStudio V2011.1 (Illumina) based on hg19.

label: C-Bio and A-DNP

growth_protocol: Uncultured samples of chorionic villus sampling, amniotic fluid,  placental tissue and blood were used for direct DNA extraction

extract_protocol: Genomic DNA extraction done by Qiagen DNeasy® Blood & Tissue Kit following manufacturer's instructions

treatment_protocol: Samples were untreated

tag: sample origin

value: Postnatal

tag: clinical indication

value: CHD; positive Down screening risk:1/260


title: AF [14P1201033]

scan_protocol: Illumina standard protocol for CytoSNP 12 chips (GPL16483), using automation with the Tecan Evo robot.

source_name: Prenatal diagnosis_AF

value: Prenatal diagnosis

value: positive Down screening risk:1/10

value: Amniotic fluid


title: SD164-PT_97

tag: gender

value: unifocal


title: AF [14P1201034]

label_protocol: Illumina standard protocol for CytoSNP 12 chips (GPL16483), using automation with the Tecan Evo robot.

value: Ultrasound abnormality:NT2.9MM, bilateral fetal choroid plexus cysts.


title: SVR NK cells_repeat 1_mAdbID:125330

description: mAdb experiment ID: 125330

value: Hepatitis C virus (HCV) infection

value: sustained virologic responder (SVR)


title: D431 P-BMP7: parental GSC treated with BMP7

description:
Human/patient (brain tumor)
D431 P-BMP7: parental D431 GSC treated with BMP7


title: SK056-PT1_98

tag: tumor grade

value: multifocal

value: primary tumor


title: MW158-PT_96

value: female

value: Luminal B, HER2-

tag: tumor focality


title: AF [12ZS122525]

value: positive Down screening risk:1/150


title: D431 P-Control: parental GSC (no BMP7 treatment)

description:
Human/patient (brain tumor)
D431 P-Control: parental D431GSC (no BMP7 treatment)

value: glioblastoma stem cells


title: E445-TMZ500-C2: GSC survived in two cycle treatment of 500uM TMZ

description:
Human/patient (brain tumor)
survival clones selected by 500uM TMZ (2 cycle)

source_name: E445-TMZ500-C2: GSC survived in two cycle treatment with 500uM TMZ

extract_protocol: Total RNA was extracted from untreated, parental GSC  or treatment resistant GSC clones survived 500uM TMZ treatment, using an RNeasy kit (QIAGEN)

treatment_protocol: untreated or treated with 500uM TMZ


title: AF [12ZS120626]

value: positive Down screening risk:1/200


title: NCI-H520_anti-CNOT6-shRNA_rep1

city: Larissa

first: Nikolaos

last: Balatsos

state: Thessaly

address: Ploutonos 26 & Aiolou str

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 60K Microarray (028004) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color (Cy3) scan setting for expression array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NCI-H520 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: NCI-H520 cell line was routinely maintained in RPMI-1640 (Biosera), supplemented with 10% Fetal Bovine Serum (FBS, Biosera) in a humidified atmosphere of 5% CO2 at 37ºC

extract_protocol: Total RNA was extracted using the TRI Reagent® Protocol (Sigma), following the manufacturer's recommendations

treatment_protocol: NCI-H520 cells grown into 6-well plates, were transfected with 6μg plasmid DNA containing shRNAs sequences (pLKO.1) designed to silence the selected deadenylase, using cationic liposomes (X-fect, Clontech) according to manufacturer’s instructions. Wild type cells, cells transfected with empty vector or shRNA with no homology to known gene sequences were used as controls. The following shDNA plasmids (MISSION® shRNA, SIGMA) were used to silence the respective deadenylases: PARN (NM_002582), CNOT6 (NM_15455), CNOT6L (NM_012118), CNOT7 (NM_013354), Nocturnin (NM_012118), and non-targeting controls (SHC001 and SHC016). Puromycin selection (6μg/mL) was performed 12h after transfection according to the manufacturer. Cells were harvested 72h upon transfection.

value: human cancer cells

tag: transfected with


title: E445-TMZ500-C1: GSC survived in one cycle treatment of 500uM TMZ

description:
Human/patient (brain tumor)
survival clones selected by 500uM TMZ(1 cycle)

source_name: E445-TMZ500-C1: GSC survived in one cycle treatment with 500uM TMZ


title: NCI-H520_anti-CNOT7-shRNA_rep1


title: NCI-H520_anti-NOC-shRNA_rep1

value: anti-NOC-shRNA


title: AF [12ZS082312]

value: positive Down screening risk:1/20

tag: tissue


title: MS168-PT_95

tag: age at cancer diagnosis


title: SK056-PT3_100

value: Triple negative


title: MN036-PT3_94

value: Luminal B, HER2+


title: NCI-H520_anti-PARN-shRNA_rep1

tag: cell line

value: anti-PARN-shRNA


title: MN036-PT2_93


title: MN036-PT1_92


title: ML012-PT_91

value: Luminal A


title: S496-TMZ500-C1: GSC survived in one cycle treatment of 500uM TMZ

description:
Human/patient (brain tumor)
survival clones selected by 500uM TMZ (1 cycle)

source_name: S496-TMZ500-C1: GSC survived in one cycle treatment with 500uM TMZ


title: AF [12ZS232605]

value: Prenatal diagnosis

value: Ultrasound abnormality:Ventricular has strong echo.

value: Amniotic fluid


title: MH047-PT2_90

value: unifocal


title: NCI-H520_empty-vector_rep1

value: empty-vector


title: Blood [12ZS260804]

value: Postnatal

value: Autism

value: Blood


title: AF [12ZS071303]

value: Ultrasound abnormality:Fetal brain cavity effusion


title: NCI-H520_non-target-vector_rep1

value: non-target-vector


title: MH047-PT1_89

value: female

value: primary tumor


title: D431-TMZ500-C2: GSC survived in two cycle treatment of 500uM TMZ

source_name: D431-TMZ500-C2: GSC survived in two cycle treatment with 500uM TMZ

value: glioblastoma stem cells

value: survival clones selected by 500uM TMZ (2 cycle)


title: AF [12ZS261206]

value: Inversion of chromosome 9 (hyperbilirubinemia, impetigo found when birth)


title: AF [12ZS032412]

value: Ultrasound abnormality:polyhydramnios


title: AF [12ZS262500]

value: positive Down screening risk:1/180


title: Blood [12ZS102508]

value: Previous pregnancy with stillbirth indicated as 10q11.22 1.2Mx3


title: AF [12ZS071200]

value: Prenatal diagnosis

value: positive Down screening risk:1/270


title: MD052-PT1_86

value: Luminal B, HER2-

value: multifocal


title: Blood [12ZS121913]

value: Postnatal

value: DiGeorge syndrome, CHD, her father diagnosed to carry a translocation in 22q


title: D431-TMZ500-C1: GSC survived in one cycle treatment of 500uM TMZ

source_name: D431-TMZ500-C1: GSC survived in one cycle treatment with 500uM TMZ

value: survival clones selected by 500uM TMZ (1 cycle)


title: NCI-H520_anti-CNOT6L-shRNA_rep1

value: human cancer cells


title: ME029-PT1_87


title: MD006-PT1_85


title: S496-TMZ500-C2: GSC survived in two cycle treatment of 500uM TMZ

description:
Human/patient (brain tumor)
survival clones selcted by 500uM TMZ (2 cycle)

source_name: S496-TMZ500-C2: GSC survived in two cycle treatment with 500uM TMZ


title: MB032-PT3_83


title: D431-2: parental GSC, untreated

description:
Human/patient (brain tumor)
untreated, parental GSC

source_name: D431-2: parental GSC, untreated

value: untreated, parental GSC


title: Blood [12ZS262505]

value: epilepsy, encephalodysplasia, Inversion found in chromosome 9

value: Blood


title: D431-1: parental GSC, untreated

source_name: D431-1: parental GSC, untreated

value: glioblastoma stem cells


title: UPN727 cells, AIDA PL25 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL25 6 month into treatment

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensities.  Each sample was independently analyzed (5 arrays per patient, at baseline, 1, 3, 6, and 9 months into treatment, 235 arrays in total).  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA as a statistic analysis method in Partek GS.

source_name: UPN727 cells stimulated with AIDA_PL25_M6 serum

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% serum from recent-onset (RO) T1D patients that were given Placebo or Anakinra at their respective time points.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

value: UPN727 cells

tag: timepoint

value: 6 month into treatment


title: UPN727 cells, AIDA PL25 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL25 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL25_M9 serum

value: 9 month into treatment


title: MB032-PT4_84

source_name: DNA extracted from primary tumor

value: female

value: primary tumor


title: UPN727 cells, AIDA PL25 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL25 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL25_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA PL25 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL25 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL25_M3 serum

value: 3 month into treatment


title: MB032-PT1_81

value: Luminal B, HER2-


title: ME029-PT2_88

value: multifocal


title: MA018-PT2_80


title: AF [12ZS032519]

value: Prenatal diagnosis

value: adv mat age

value: Amniotic fluid


title: UPN727 cells, AIDA PL25 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL25 at baseline

source_name: UPN727 cells stimulated with AIDA_PL25_BL serum

value: at baseline


title: MB032-PT2_82


title: UPN727 cells, AIDA PL24 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL24 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL24_M9 serum


title: UPN727 cells, AIDA PL24 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL24 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL24_M6 serum


title: AF [12ZS030824]

source_name: Prenatal diagnosis_AF

value: Ultrasound abnormality:obstruction of duodenum


title: Placenta [14S0894237]

source_name: Induced abortion_Placenta

value: Induced abortion

value: Ultrasound abnormality:NT8.8; hydroderma; thoracoceloschisis

value: Placental tissue


title: Placenta [14S0718638]

value: Ultrasound abnormality:multiple abnormality; deroncus


title: MA018-PT1_79

description:
TUMORS3: 98_primaryTumors_18224.txt
Genotyping on DNA extracted from a primary tumor


title: Placenta [14S0026995]

value: Ultrasound abnormality:agenesis of left arm; developmental retardation of the fingers of right hand;


title: CVS [14S0014271]

value: Miscarriage

value: chorionic villus sampling


title: LH045-PT1_77

value: female

value: Luminal A

value: primary tumor


title: UPN727 cells, AIDA PL24 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL24 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL24_M3 serum

value: UPN727 cells

value: 3 month into treatment


title: LF042-PT2_76

value: multifocal


title: LF042-PT1_75


title: KS150-PT_74

value: Luminal B, HER2-

value: unifocal


title: CVS [14S0894218]


title: CVS [14S0026197]


title: UPN727 cells, AIDA PL24 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL24 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL24_M1 serum

value: 1 month into treatment


title: CVS [14S0026927]


title: KM159-PT_73


title: UPN727 cells, AIDA PL24 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL24 at baseline

source_name: UPN727 cells stimulated with AIDA_PL24_BL serum

value: at baseline


title: Cord_blood [14B0002792]

source_name: Prenatal diagnosis_Cord_blood

value: Prenatal diagnosis

value: Ultrasound abnormality:thighbone inconsistent size; left thighbone is longer than the right one

value: Cord Blood


title: UPN727 cells, AIDA PL23 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL23 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL23_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA PL23 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL23 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL23_M6 serum

value: 6 month into treatment


title: KK151-PT_72

value: Luminal B, HER2+


title: Blood [IMS13S0009]

value: Postnatal

value: MR, blepharoptosis; karyotyping abnormal:46,XY,15p+

value: Blood


title: UPN727 cells, AIDA PL23 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL23 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL23_M3 serum


title: AF [IMS12S00104]

value: Ultrasound abnormality:fetal cerebral ventriculomegaly; previous pregnancy with hydrocephalus

value: Amniotic fluid


title: JP149-PT_71

value: female

value: Triple negative

value: primary tumor


title: IP008-PT_70

value: Luminal A

value: multifocal


title: AF [IMS13S0003]

value: Ultrasound abnormality:IUGR; previous family abnormal pregnancy


title: UPN727 cells, AIDA PL23 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL23 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL23_M1 serum

value: UPN727 cells

value: 1 month into treatment


title: AF [IMS12S00105]

value: Prenatal diagnosis

value: positive Down screening risk; karyotyping abnormal:46,XY,15p+


title: Blood [IMS13S0007]

value: Facial anomalies, fifth finger bending, hypospadia, small and short penis.


title: HZK162-PT_69

value: Luminal B, HER2-

value: unifocal


title: UPN727 cells, AIDA PL23 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL23 at baseline

source_name: UPN727 cells stimulated with AIDA_PL23_BL serum

value: at baseline


title: AF [IMS13S0008]

value: Ultrasound abnormality:CHD; ad mat age; karyotyping abnormal:46,XX,5p-


title: HS006-PT_68

source_name: DNA extracted from primary tumor


title: GS166-PT_67


title: UPN727 cells, AIDA PL22 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL22 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL22_M9 serum

value: 9 month into treatment


title: LH045-PT2_78


title: GS011-PT_66


title: UPN727 cells, AIDA PL22 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL22 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL22_M6 serum

value: 6 month into treatment


title: AF [12DNJ057]

value: Familial Defect:previous pregnancy with multiple-anomalies

value: Amniotic fluid


title: UPN727 cells, AIDA PL22 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL22 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL22_M3 serum

value: 3 month into treatment


title: GGB040-PT3_65

value: female

value: primary tumor


title: AF [12DNJ056]

value: Ultrasound abnormality:CHD


title: GGB040-PT2_64

value: multifocal


title: UPN727 cells, AIDA PL22 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL22 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL22_M1 serum

value: UPN727 cells

value: 1 month into treatment


title: GGB040-PT1_63


title: GC147-PT_62

value: Luminal A


title: UPN727 cells, AIDA PL21 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL21 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL21_M9 serum


title: UPN727 cells, AIDA PL21 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL21 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL21_M3 serum


title: UPN727 cells, AIDA PL21 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL21 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL21_M6 serum


title: UPN727 cells, AIDA PL22 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL22 at baseline

source_name: UPN727 cells stimulated with AIDA_PL22_BL serum


title: EW155-PT_61

description:
TUMORS3: 98_primaryTumors_18224.txt
Genotyping on DNA extracted from a primary tumor


title: AF [12DNJ045]

source_name: Prenatal diagnosis_AF

value: Prenatal diagnosis

value: Ultrasound abnormality:CHD (Ventriculap Septal Defect)


title: EJ001-PT1_60

value: Triple negative

value: unifocal


title: UPN727 cells, AIDA PL21 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL21 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL21_M1 serum


title: Blood [12DNJ041]

value: Postnatal

value: DD, hypotonia, facial anomalies.

value: Blood


title: UPN727 cells, AIDA PL20 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL20 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL20_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA PL21 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL21 at baseline

source_name: UPN727 cells stimulated with AIDA_PL21_BL serum

value: at baseline


title: EG163-PT_59


title: UPN727 cells, AIDA PL20 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL20 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL20_M6 serum

value: 6 month into treatment


title: AF [12DNJ032]

value: Ultrasound abnormality:CHD (Hypoplastic right heart, PAS)

value: Amniotic fluid


title: BK008-PT1_58

value: female

value: Luminal B, HER2+

value: primary tumor


title: KO-BL, rep 2

first: Frank

last: McKeon

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: Gene expression data from stem cells

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing:
Expression console, Partek Genome Suite 6.6
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

organism: Mus musculus

source_name: p63 KO bladder epithelial stem cell culture

label_protocol: Encore® Biotin Module (Nugen)

extract_protocol: PicoPure® RNA Isolation Kit (life technologies), RNeasy Mini Kit (Qiagen)

tag: strain

value: bladder

value: bladder epithelial stem cell culture

tag: genotype/variation

value: p63 knockout


title: AF [12DNJ054]

value: Prenatal diagnosis

value: Ultrasound abnormality:Fetal jugular Lymphatic hydrocele.


title: BD038-PT1_56

value: Luminal A

value: multifocal


title: WT-BL, rep 1

description: Gene expression data from stem cells

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

source_name: Wild type bladder epithelial stem cell culture

tag: cell type

value: Wild type


title: BD038-PT2_57


title: AF [12DNJ040]


title: Blood [12DNJ038]

value: Postnatal

value: intellectual disability, developmental languague disorder

value: Blood


title: Blood [12DNJ025]

value: MR, dwarf, corpulent, enorchia.


title: AF [IMS12S00102]

value: Familial Chr. Defect:Mat balanced translocation, previous livebirth with autism


title: UPN727 cells, AIDA PL20 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL20 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL20_M1 serum

value: UPN727 cells

value: 1 month into treatment


title: AW020-PT3_55

source_name: DNA extracted from primary tumor

value: female

value: Luminal B, HER2+


title: UPN727 cells, AIDA PL20 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL20 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL20_M3 serum

value: 3 month into treatment


title: UPN727 cells, AIDA PL19 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL19 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL19_M9 serum

value: 9 month into treatment


title: Hi-Myc enzalutamide rep3

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was log2 transformed and quantile normalized using Partek Genomics suite

source_name: Mouse Prostate, enzalutamide (30 mg/kg) oral gavage x 3 days

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

growth_protocol: Hi-Myc transgenic mice were fed ad lib

extract_protocol: Tissue was ground in Trizol using tissue grinder and then purified using Qiagen RNAEasy column

treatment_protocol: Mice underwent surgical castration or drug treat via oral gavage

value: Hi-Myc

tag: tissue type

value: prostate tumor


title: AW020-PT2_54

value: primary tumor


title: AW020-PT1_53


title: AH028-PT3_52

value: Luminal B, HER2-


title: AF [12DNJ037]

value: Prenatal diagnosis

value: positive Down screening risk:1/220; IUGR

value: Amniotic fluid


title: UPN727 cells, AIDA PL19 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL19 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL19_M6 serum

value: 6 month into treatment


title: WT-BL, rep 2

description: Gene expression data from stem cells

value: bladder

value: bladder epithelial stem cell culture

value: Wild type


title: AF [12DNJ016]

value: positive Down screening risk:1/117; ad mat age; karyotyping abnormal:46,XY,15p+


title: AF [12DNJ017]

value: adv mat age


title: AF [12DNJ013]

value: Ultrasound abnormality:severse IUGR, CHD, facial anomalies (Low-set ears, a small jaw)


title: AH028-PT2_51

value: female

value: multifocal


title: AH028-PT1_50


title: Hi-Myc bicalutamide rep3

description: replicate 3

source_name: Mouse Prostate, bicalutamide (30 mg/kg) oral gavage x 3 days


title: Hi-Myc enzalutamide rep2

description: replicate 2


title: UPN727 cells, AIDA PL20 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL20 at baseline

source_name: UPN727 cells stimulated with AIDA_PL20_BL serum

value: UPN727 cells

value: at baseline


title: UPN727 cells, AIDA PL19 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL19 at baseline

source_name: UPN727 cells stimulated with AIDA_PL19_BL serum


title: Hi-Myc enzalutamide rep1

description: replicate 1

value: Hi-Myc

value: prostate tumor


title: AF [12DNJ014]

value: positive Down screening risk:1/55


title: AF [12DNJ007]

value: Prenatal diagnosis

value: holoprosencephaly, facial deformity (cyclopia,beak nose)


title: UPN727 cells, AIDA PL19 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL19 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL19_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA PL18 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL18 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL18_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA PL19 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL19 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL19_M3 serum

value: 3 month into treatment


title: Hi-Myc bicalutamide rep2

description: replicate 2


title: Hi-Myc bicalutamide rep1

description: replicate 1


title: ACV037-PT1_47

value: Luminal B, HER2+

value: primary tumor


title: Hi-Myc castrate rep3

description: replicate 3

source_name: Mouse Prostate, Castration 3 days prior


title: AF [12DNJ008]

source_name: Prenatal diagnosis_AF

value: IUGR (intrauterine growth retardation), Fetal cerebral ventriculomegaly

value: Amniotic fluid


title: 143DMG-PT_46

value: Luminal B, HER2-

value: unifocal


title: UPN727 cells, AIDA PL18 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL18 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL18_M9 serum

value: 9 month into treatment


title: Blood [12DNJ005]

value: Postnatal

value: maternal karyotyping abnormal

value: Blood


title: 142AK-PT_45

value: female


title: AF [12DNJ006]

value: Familial Chr. Defect:Mat 46XX, t(3;14)(q21;p13), previous two pregnancies with cyst of cord and stillbirth, respectively; karyotyping abnormal:46,XX,-14,+der(14)t(3;14)(q21;p13)


title: AF [12DNJ030]

value: Prenatal diagnosis

value: IUGR


title: Hi-Myc rep3

description: replicate 3

source_name: Mouse Prostate, Vehicle x 3 days

value: Hi-Myc

value: prostate tumor


title: 139MD-PT_43


title: Blood [12DNJ043]

value: intellectual disability, developmental languague disorder


title: 141BB-PT_44


title: 133ML-PT_41


title: Hi-Myc rep2

description: replicate 2


title: 131SD-PT_40

value: Luminal A


title: AE031-PT2_49

value: multifocal

value: primary tumor


title: UPN727 cells, AIDA PL17 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL17 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL17_M6 serum

value: UPN727 cells

value: 6 month into treatment


title: UPN727 cells, AIDA PL17 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL17 at baseline

source_name: UPN727 cells stimulated with AIDA_PL17_BL serum

value: at baseline


title: UPN727 cells, AIDA PL18 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL18 at baseline

source_name: UPN727 cells stimulated with AIDA_PL18_BL serum


title: UPN727 cells, AIDA PL17 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL17 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL17_M9 serum

value: 9 month into treatment


title: AE031-PT1_48

description:
TUMORS3: 98_primaryTumors_18224.txt
Genotyping on DNA extracted from a primary tumor

source_name: DNA extracted from primary tumor


title: UPN727 cells, AIDA PL17 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL17 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL17_M3 serum

value: 3 month into treatment


title: UPN727 cells, AIDA PL16 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL16 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL16_M9 serum