title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp52

description:
LoHRp52
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp49

status: Public on May 13 2014

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description:
LoHRp49
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

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: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of longitudinal, healthy high HLA type T1D sibling (HR), healthy low HLA type T1D sibling (LR), or recent onset (RO) T1D plasma cultured with IL1RA.  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 pbmc cells

value: UPN727 PBMC cells

tag: stimulated with


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn6

description:
LoHRn6
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp40

description:
LoHRp40
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp43

description:
LoHRp43
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn2

description:
LoHRn2
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp37

description:
LoHRp37
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp34

description:
LoHRp34
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn5

description:
LoHRn5
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp46

description:
LoHRp46
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp53

description:
LoHRp53
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn8

description:
LoHRn8
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp48

description:
LoHRp48
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp54

description:
LoHRp54
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp31

description:
LoHRp31
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp41

description:
LoHRp41
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp45

description:
LoHRp45
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp47

description:
LoHRp47
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp44

description:
LoHRp44
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp42

description:
LoHRp42
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp35

description:
LoHRp35
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp38

description:
LoHRp38
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp32

description:
LoHRp32
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp51

description:
LoHRp51
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp29

description:
LoHRp29
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp50

description:
LoHRp50
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRn3

description:
LoHRn3
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp28

description:
LoHRp28
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp25

description:
LoHRp25
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp22

description:
LoHRp22
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp36

description:
LoHRp36
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp30

description:
LoHRp30
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp23

description:
LoHRp23
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp20

description:
LoHRp20
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp33

description:
LoHRp33
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp39

description:
LoHRp39
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp26

description:
LoHRp26
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp19

description:
LoHRp19
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp27

description:
LoHRp27
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp21

description:
LoHRp21
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp16

description:
LoHRp16
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp24

description:
LoHRp24
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp18

description:
LoHRp18
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp13

description:
LoHRp13
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp10

description:
LoHRp10
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp12

description:
LoHRp12
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp15

description:
LoHRp15
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp9

description:
LoHRp9
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp14

description:
LoHRp14
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp4

description:
LoHRp4
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp3

description:
LoHRp3
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp7

description:
LoHRp7
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp17

description:
LoHRp17
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp6

description:
LoHRp6
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp11

description:
LoHRp11
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp2

description:
LoHRp2
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO26

description:
LoRO26
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma

value: Longitudinal progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp5

description:
LoHRp5
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO22

description:
LoRO22
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO24

description:
LoRO24
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO25

description:
LoRO25
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO19

description:
LoRO19
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO23

description:
LoRO23
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO16

description:
LoRO16
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO18

description:
LoRO18
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO17

description:
LoRO17
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO20

description:
LoRO20
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp8

description:
LoHRp8
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO21

description:
LoRO21
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO27

description:
LoRO27
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO15

description:
LoRO15
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series  plasma LoHRp1

description:
LoHRp1
Gene expression data from UPN727 cells stimulated with auto-antibody-positive (AA+) high HLA risk sibling Longitudinal non-progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO14

description:
LoRO14
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO12

description:
LoRO12
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO9

description:
LoRO9
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO11

description:
LoRO11
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO8

description:
LoRO8
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO13

description:
LoRO13
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO10

description:
LoRO10
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO7

description:
LoRO7
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO5

description:
LoRO5
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO2

description:
LoRO2
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO4

description:
LoRO4
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO1

description:
LoRO1
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, recent onset 3045 plasma cultured with IL1RA

description:
RO3045+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO3045+IL1RA plasma

value: recent onset plasma cultured with IL1RA


title: UPN727 cells, recent onset 2991 plasma cultured with IL1RA

description:
RO2991+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2991+IL1RA plasma


title: UPN727 cells, recent onset 3139 plasma cultured with IL1RA

description:
RO3139+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO3139+IL1RA plasma


title: UPN727 cells, recent onset 3153 plasma cultured with IL1RA

description:
RO3153+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO3153+IL1RA plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO3

description:
LoRO3
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, recent onset 3052 plasma cultured with IL1RA

description:
RO3052+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO3052+IL1RA plasma


title: UPN727 cells, recent onset 3040 plasma cultured with IL1RA

description:
RO3040+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO3040+IL1RA plasma


title: UPN727 cells, recent onset 2393 plasma cultured with IL1RA

description:
RO2393+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2393+IL1RA plasma


title: UPN727 cells, recent onset 2109 plasma cultured with IL1RA

description:
RO2109+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2109+IL1RA plasma


title: UPN727 cells, recent onset 2903 plasma cultured with IL1RA

description:
RO2903+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2903+IL1RA plasma


title: UPN727 cells, recent onset 2751 plasma cultured with IL1RA

description:
RO2751+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2751+IL1RA plasma


title: UPN727 cells, recent onset 2503 plasma cultured with IL1RA

description:
RO2503+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2503+IL1RA plasma


title: UPN727 cells, recent onset 2024 plasma cultured with IL1RA

description:
RO2024+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2024+IL1RA plasma


title: UPN727 cells, recent onset 3087 plasma cultured with IL1RA

description:
RO3087+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO3087+IL1RA plasma


title: UPN727 cells, recent onset 2953 plasma cultured with IL1RA

description:
RO2953+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2953+IL1RA plasma


title: UPN727 cells, recent onset 2185 plasma cultured with IL1RA

description:
RO2185+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2185+IL1RA plasma


title: UPN727 cells, recent onset 2936 plasma cultured with IL1RA

description:
RO2936+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2936+IL1RA plasma


title: UPN727 cells, recent onset 2676 plasma cultured with IL1RA

description:
RO2676+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2676+IL1RA plasma


title: UPN727 cells, Longitudinal progressor series  plasma LoRO6

description:
LoRO6
Gene expression data from UPN727 cells stimulated with Longitudinal progressor series plasma


title: UPN727 cells, recent onset 2559 plasma cultured with IL1RA

description:
RO2559+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2559+IL1RA plasma


title: UPN727 cells, recent onset 2944 plasma cultured with IL1RA

description:
RO2944+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2944+IL1RA plasma


title: UPN727 cells, recent onset 2808 plasma cultured with IL1RA

description:
RO2808+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2808+IL1RA plasma


title: UPN727 cells, recent onset 2359 plasma cultured with IL1RA

description:
RO2359+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2359+IL1RA plasma


title: UPN727 cells, recent onset 2034 plasma cultured with IL1RA

description:
RO2034+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO2034+IL1RA plasma


title: UPN727 cells, recent onset 1997 plasma cultured with IL1RA

description:
RO1997+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1997+IL1RA plasma


title: UPN727 cells, recent onset 1707 plasma cultured with IL1RA

description:
RO1707+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1707+IL1RA plasma


title: UPN727 cells, recent onset 1939 plasma cultured with IL1RA

description:
RO1939+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1939+IL1RA plasma


title: UPN727 cells, recent onset 1442 plasma cultured with IL1RA

description:
RO1442+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1442+IL1RA plasma


title: UPN727 cells, recent onset 1437 plasma cultured with IL1RA

description:
RO1437+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1437+IL1RA plasma


title: UPN727 cells, recent onset 1012 plasma cultured with IL1RA

description:
RO1012+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1012+IL1RA plasma


title: UPN727 cells, recent onset 1225 plasma cultured with IL1RA

description:
RO1225+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1225+IL1RA plasma


title: UPN727 cells, recent onset 930 plasma cultured with IL1RA

description:
RO930+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO930+IL1RA plasma


title: WT grown in BG11C untreated rep3

city: Sevilla

first: Luis

last: Lopez Maury

address: Av Americo Vespucio 49

country: Spain

institute: IBVF

description:
WT_control_3
30 ml sample

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C US91803681).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1_105_Dec08  extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Limma

organism: Synechocystis sp. PCC 6803

source_name: WT grown in BG11C untreated

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cRNA probe preparation using 200ng of total RNA.

growth_protocol: cells were grown to exponetial phase (3-5 µg chlorophyll mL-1) in BG11C or low phosphate  BG11C (containing 30 µM phosphate)

extract_protocol: cells were resuspended in 400 µl STET and vortexedin the presence of phenol chloroform and glass beads; RNA was precipitated with ClLi traeted with Turbo DNAse (ambion) and further purified by phenol chloroform extraction.

treatment_protocol: cultures were supplemented  1mM NaAsO2 or 50mM NaHAsO3 respectively

tag: genotype/variation

value: WT

tag: growth protocol

tag: agent

value: untreated

tag: dose

value: control


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2537 plasma

description:
HR2537
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2537 plasma


title: UPN727 cells, recent onset 1057 plasma cultured with IL1RA

description:
RO1057+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1057+IL1RA plasma


title: UPN727 cells, recent onset 814 plasma cultured with IL1RA

description:
RO814+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO814+IL1RA plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2251 plasma

description:
HR2251
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2251 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2767 plasma

description:
HR2767
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2767 plasma


title: UPN727 cells, recent onset 189 plasma cultured with IL1RA

description:
RO189+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO189+IL1RA plasma


title: UPN727 cells, recent onset 253 plasma cultured with IL1RA

description:
RO253+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO253+IL1RA plasma


title: WT grown in BG11C untreated rep4

description:
WT_control_4
30 ml sample


title: UPN727 cells, recent onset 1037 plasma cultured with IL1RA

description:
RO1037+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO1037+IL1RA plasma


title: UPN727 cells, recent onset 972 plasma cultured with IL1RA

description:
RO972+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO972+IL1RA plasma


title: UPN727 cells, recent onset 159 plasma cultured with IL1RA

description:
RO159+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO159+IL1RA plasma


title: UPN727 cells, recent onset 246 plasma cultured with IL1RA

description:
RO246+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO246+IL1RA plasma


title: UPN727 cells, recent onset 355 plasma cultured with IL1RA

description:
RO355+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO355+IL1RA plasma


title: UPN727 cells, recent onset 946 plasma cultured with IL1RA

description:
RO946+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO946+IL1RA plasma


title: UPN727 cells, recent onset 62 plasma cultured with IL1RA

description:
RO62+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO62+IL1RA plasma


title: UPN727 cells, recent onset 201 plasma cultured with IL1RA

description:
RO201+IL1RA
Gene expression data from UPN727 cells stimulated with recent onset plasma cultured with IL1RA

source_name: UPN727 cells stimulated with RO201+IL1RA plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2654 plasma

description:
HR2654
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2654 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2051 plasma

description:
HR2051
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2051 plasma


title: WT grown in BG11C untreated rep2

description:
WT_control_2
30 ml sample

source_name: WT grown in BG11C untreated


title: WT grown in low phosphate BG11C untreated rep4

description:
WT_lowP_4
30 ml sample

value: low phosphate BG11C


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2339 plasma

description:
HR2339
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2339 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2684 plasma

description:
HR2684
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2684 plasma


title: WT grown in BG11C untreated rep1

description:
WT_control_1
30 ml sample


title: WT grown in low phosphate BG11C untreated rep3

description:
WT_lowP_3
30 ml sample


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2068 plasma

description:
HR2068
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2068 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 2490 plasma

description:
HR2490
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR2490 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 1710 plasma

description:
HR1710
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR1710 plasma


title: WT grown in low phosphate BG11C untreated rep2

description:
WT_lowP_2
30 ml sample


title: WT grown in low phosphate BG11C treated with 50mM arsenate for 1 h rep4

description:
WT_As5_4
30 ml sample

value: arsenate


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 1975 plasma

description:
HR1975
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR1975 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 1771 plasma

description:
HR1771
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR1771 plasma


title: WT grown in low phosphate BG11C treated with 50mM arsenate for 1 h rep3

description:
WT_As5_3
30 ml sample


title: E1_E2_CRBN_CSN_b

type: protein

city: Boston

first: Eric

middle: S

last: Fischer

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: Arrays were probed with Alexa647-Streptavidin at 1 µg/ml concentration for 45min at 4°C. Arrays were subjected to 4 washes with assay buffer followed by one wash in ddH2O and drying by centrifugation prior to feature detection.

scan_protocol: Slides were scanned using a GenePix 4200A at 450V PMT gain. Images were quantified using GenePix 5.0 feature extraction software.

data_processing: Protein arrays were normalised using the limma Bioconductor package as follows: median estimates for foreground and background intensities were imported from raw data files. Arrays were corrected using background values derived from the minimum of the backgrounds of each spot and its eight neighbours (method movingmin of the backgroundCorrect function). A small fraction of the background-corrected intensities were negative (between 0.2% and 8% of values on each array, total data ranging from -32 to 65480). To render all background-corrected intensities greater than 0, the minimum intensity minus one (-33) was subtracted and the resulting intensities log2 transformed. Log2 intensities were then quantile normalised.

molecule: protein

source_name: In vitro ubiquitylation reaction.

label_protocol: biotinylated ubiquitin was used in the ubiquitination reaction mix. Ubiquitin conjugates were probed with Alexa647 conjugated Streptavidin.

growth_protocol: In vitro ubiquitination reaction by recombinant proteins produced in insect cells.

treatment_protocol: Reaction mixture was prepared and and protoarrays immediately covered with 170 µl of reaction mixture. Arrays were incubated for 90min, subjected to 3 washes with 0.5% SDS solution and 3 washes in assay buffer before probing with Alexa647-Streptavidin.

tag: reaction mix

value: CRL4(CRBN) ubiquitin ligase reaction in presence of CSN.


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 1439 plasma

description:
HR1439
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR1439 plasma


title: WT grown in low phosphate BG11C untreated rep1

description:
WT_lowP_1
30 ml sample


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 878 plasma

description:
HR878
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR878 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 1593 plasma

description:
HR1593
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR1593 plasma


title: E1_E2_DDB2_b

value: CRL4(DDB2) ubiquitin ligase reaction


title: E1_E2_Cdt2_revlimid_b

value: CRL4(Cdt2) ubiquitin ligase reaction in presence of CRBN specific inhibitor lenalidomide.


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 1498 plasma

description:
HR1498
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR1498 plasma


title: E1_E2_Cdt2_CSN_b

value: CRL4(Cdt2) ubiquitin ligase reaction in presence of CSN


title: E1_E2_CRBN_revlimid_b

value: CRL4(CRBN) ubiquitin ligase reaction in presence of lenalidomide ligase inhibitor


title: E1_CRBN_c

value: CRL4(CRBN) ubiquitin ligase reaction.


title: WT grown in low phosphate BG11C treated with 50mM arsenate for 1 h rep2

description:
WT_As5_2
30 ml sample


title: E1_E2_Cdt2_b

value: CRL4(Cdt2) ubiquitin ligase reaction


title: WT grown in BG11C treated with 1 mM arsenite for 1 h rep4

description:
WT_As3_4
30 ml sample

value: arsenite


title: E1_E2_c

value: negative control omiting E3 ubiquitin ligase


title: E1_E2_b


title: E1_E2_CRBN_a


title: WT grown in low phosphate BG11C treated with 50mM arsenate for 1 h rep1

description:
WT_As5_1
30 ml sample


title: E1_E2_CRBN_revlimid_a


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 371 plasma

description:
HR371
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR371 plasma

value: UPN727 PBMC cells


title: E1_E2_DDB2_a


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 338 plasma

description:
HR338
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR338 plasma


title: E1_E2_a


title: E1_E2_CRBN_CSN_a


title: E1_E2_Cdt2_a


title: E1_CRBN_b


title: WT grown in BG11C treated with 1 mM arsenite for 1 h rep3

description:
WT_As3_3
30 ml sample


title: WT grown in BG11C treated with 1 mM arsenite for 1 h rep2

description:
WT_As3_2
30 ml sample


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 271 plasma

description:
HR271
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR271 plasma


title: adult-midbrain-1 vs. P0-F-2

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: See Tecan_HS4800_hybridization.txt

scan_protocol: scanning of slides using Agilent G256BA Features were extracted using Imagene software from Biodiscovery.

data_processing: [genes, no bg corr, hybset spec. dye corr]: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

organism: Mus musculus

extract_protocol: See RNA_extraction_cellLine.txt

tag: cell type

value: midbrain cells

value: mesodiencephalic dopaminergic (mdDA) neurons from Fac-sorted Pitx3gfp/+ ventral midbrains


title: WT grown in BG11C treated with 1 mM arsenite for 1 h rep1

description:
WT_As3_1
30 ml sample

value: WT


title: adult-midbrain-1 vs. EH5-sample6


title: adult-midbrain-1 vs. E15.5-F-2


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 182 plasma

description:
HR182
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR182 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 334 plasma

description:
HR334
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR334 plasma


title: adult-midbrain-1 vs. EH5-sample5


title: adult-midbrain-1 vs. EH5-sample2


title: SARS12 grown in low phosphate BG11C untreated rep2

description:
SARS12_lowP_2
30 ml sample

value: untreated


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 215 plasma

description:
HR215
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR215 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 116 plasma

description:
HR116
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR116 plasma


title: adult-midbrain-1 vs. E14.5-F-3


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 130 plasma

description:
HR130
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR130 plasma


title: SARS12 grown in low phosphate BG11C untreated rep1

description:
SARS12_lowP_1
30 ml sample

value: control


title: adult-midbrain-1 vs. P0-F-1


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 229 plasma

description:
HR229
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR229 plasma


title: SARS12 grown in low phosphate BG11C treated with 50mM arsenate for 1 h rep2

description:
SARS12_As5_2
30 ml sample

value: low phosphate BG11C


title: adult-midbrain-1 vs. E15.5-F-1


title: SARS12 grown in low phosphate BG11C treated with 50mM arsenate for 1 h rep1

description:
SARS12_As5_1
30 ml sample

value: arsenate


title: Osteoblast co-culture EtOH rep3

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

description:
OC_E_rep3
RNA of osteoblasts from co-cultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.

hyb_protocol: 1650 ng of the labeled cRNA were loaded into the array chambers and allowed to hybridize at 65⁰C for 17 hours.

scan_protocol: The arrays were scanned using an Agilent scanner (G2505C) and feature extraction was performed using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: The raw data were normalized using quantile between array normalization method in the bioconductor package, LIMMA (v.3.10.3).

label_protocol: 200 ng of total RNA was amplified and labelled using Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: LNCaP cells and osteoblasts are cultured in RPMI +10% FCS

extract_protocol: Cells were trypsinized and RNA was extracted using Trizol reagent followed by RNA clean up (Qiagen Rneasy Mini Kit)

treatment_protocol: Cells were cultured in RPMI+5% charcoal stripped serum (androgen-starved) for 48 hours prior to R1881 treatment. The treatment consists of RPMI+5% charcoal stripped and final R1881 concentration of 1 nM.

value: Osteoblast primary bone cells

tag: treated with

value: 0.008% ethanol for 48hrs (vehicle control)


title: SARSR grown in BG11C untreated rep2

description:
ARSR_control_2
30 ml sample

source_name: SARSR grown in BG11C untreated

value: SARSR


title: adult-midbrain-1 vs. E15.5-F-3


title: Osteoblast co-culture EtOH rep2

description:
OC_E_rep2
RNA of osteoblasts from co-cultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: SARSR grown in BG11C untreated rep1

description:
ARSR_control_1
30 ml sample


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 69 plasma

description:
HR69
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR69 plasma


title: adult-midbrain-1 vs. E14.5-F-1


title: adult-midbrain-1 vs. E14.5-F-2


title: Osteoblast co-culture EtOH rep1

description:
OC_E_rep1
RNA of osteoblasts from co-cultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: SARSR grown in BG11C treated with 1 mM arsenite for 1 h rep2

description:
ARSR_As3_2
30 ml sample


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 49 plasma

description:
HR49
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR49 plasma


title: SARSR grown in BG11C treated with 1 mM arsenite for 1  h rep1

description:
ARSR_As3_1
30 ml sample


title: SARSB grown in BG11C treated with 1 mM arsenite for 1 h rep2

description:
ARSB_As3_2
30 ml sample

value: SARSB


title: Osteoblast co-culture R1881 rep3

description:
OC_R1881_rep3
RNA of osteoblasts from co-cultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.

value: 1 nM R1881 for 48hrs


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 6 plasma

description:
HR6
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR6 plasma


title: SARSB grown in BG11C untreated rep1

description:
ARSB_control_1
30 ml sample

source_name: SARSB grown in BG11C untreated


title: adult-midbrain-1 vs. E13.5-F-3


title: Osteoblast monoculture EtOH rep3

description:
OM_E_rep3
RNA of osteoblasts from monocultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: Osteoblast monoculture EtOH rep2

description:
OM_E_rep2
RNA of osteoblasts from monocultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: Osteoblast co-culture R1881 rep2

description:
OC_R1881_rep2
RNA of osteoblasts from co-cultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: SARSB grown in BG11C treated with 1 mM arsenite for 1 h rep1

description:
ARSB_As3_1
30 ml sample


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2761 plasma

description:
LR2761
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2761 plasma


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 22 plasma

description:
HR22
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR22 plasma


title: SARSB grown in BG11C untreated rep2

description:
ARSB_control_2
30 ml sample


title: adult-midbrain-1 vs. E13.5-F-1


title: adult-midbrain-1 vs. E12.5-F-3


title: UPN727 cells, auto-antibody-negative (AA-) high HLA risk sibling 26 plasma

description:
HR26
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) high HLA risk sibling plasma

source_name: UPN727 cells stimulated with HR26 plasma


title: Osteoblast co-culture R1881 rep1

description:
OC_R1881_rep1
RNA of osteoblasts from co-cultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: adult-midbrain-1 vs. E12.5-F-2


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2731 plasma

description:
LR2731
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2731 plasma


title: adult-midbrain-1 vs. E12.5-F-1


title: Osteoblast monoculture EtOH rep1

description:
OM_E_rep1
RNA of osteoblasts from monocultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: adult-midbrain-1 vs. E13.5-F-2


title: EH5-sample6 vs. adult-midbrain-1


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2532 plasma

description:
LR2532
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2532 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2560 plasma

description:
LR2560
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2560 plasma


title: P0-F-1 vs. adult-midbrain-1


title: EH5-sample5 vs. adult-midbrain-1


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2707 plasma

description:
LR2707
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2707 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2683 plasma

description:
LR2683
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2683 plasma


title: Osteoblast monoculture R1881 rep3

description:
OM_R1881_rep3
RNA of osteoblasts from monocultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2696 plasma

description:
LR2696
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2696 plasma


title: LNCaP co-culture EtOH rep3

description:
LC_E_rep3
RNA of LNCaP cells from co-cultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.

tag: cell line

value: LNCaP

value: prostate cancer cells


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2549 plasma

description:
LR2549
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2549 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2379 plasma

description:
LR2379
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2379 plasma


title: E15.5-F-1 vs. adult-midbrain-1


title: P0-F-2 vs. adult-midbrain-1


title: E15.5-F-3 vs. adult-midbrain-1


title: EH5-sample2 vs. adult-midbrain-1


title: E14.5-F-2 vs. adult-midbrain-1


title: LNCaP co-culture R1881 rep2

description:
LC_R1881_rep2
RNA of LNCaP cells from co-cultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LNCaP co-culture EtOH rep2

description:
LC_E_rep2
RNA of LNCaP cells from co-cultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LNCaP co-culture R1881 rep1

description:
LC_R1881_rep1
RNA of LNCaP cells from co-cultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LNCaP co-culture R1881 rep3

description:
LC_R1881_rep3
RNA of LNCaP cells from co-cultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: E14.5-F-1 vs. adult-midbrain-1


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2215 plasma

description:
LR2215
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2215 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2477 plasma

description:
LR2477
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2477 plasma


title: Osteoblast monoculture R1881 rep1

description:
OM_R1881_rep1
RNA of osteoblasts from monocultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: E15.5-F-2 vs. adult-midbrain-1


title: E14.5-F-3 vs. adult-midbrain-1


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2489 plasma

description:
LR2489
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2489 plasma


title: LNCaP co-culture EtOH rep1

description:
LC_E_rep1
RNA of LNCaP cells from co-cultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LNCaP monoculture EtOH rep3

description:
LM_E_rep3
RNA of LNCaP cells from monocultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: Osteoblast monoculture R1881 rep2

description:
OM_R1881_rep2
RNA of osteoblasts from monocultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2091 plasma

description:
LR2091
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2091 plasma


title: E13.5-F-3 vs. adult-midbrain-1


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1940 plasma

description:
LR1940
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1940 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2138 plasma

description:
LR2138
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2138 plasma


title: E12.5-F-3 vs. adult-midbrain-1


title: LNCaP monoculture EtOH rep2

description:
LM_E_rep2
RNA of LNCaP cells from monocultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LNCaP monoculture R1881 rep3

description:
LM_R1881_rep3
RNA of LNCaP cells from monocultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1982 plasma

description:
LR1982
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1982 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1976 plasma

description:
LR1976
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1976 plasma


title: LNCaP monoculture EtOH rep1

description:
LM_E_rep1
RNA of LNCaP cells from monocultures treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LNCaP monoculture R1881 rep1

description:
LM_R1881_rep1
RNA of LNCaP cells from monocultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LNCaP monoculture R1881 rep2

description:
LM_R1881_rep2
RNA of LNCaP cells from monocultures treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1857 plasma

description:
LR1857
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1857 plasma


title: bladder biopsy during cytoscopy G168

city: Winston Salem

first: Stephen

last: Walker

address: Medical Center Blvd

institute: Wake Forest University Health Sciences

description: control

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: bladder biopsy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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-1000 Spectrophotometer.

extract_protocol: total RNA was extracted using Rneasy Minelute columns (Qiagen, Valencia CA), quantified by Nanodrop (and 260/280 ration), qualified on Agilent bioanalyzer

treatment_protocol: bladder biopsies collected during cystoscopy or at surgery (for patients undergoing cystectomy)

tag: tissue

value: bladder biopsy

tag: gender

value: female

tag: phenotype

tag: disease state


title: bladder biopsy during cytoscopy G167

description: control


title: E13.5-F-1 vs. adult-midbrain-1


title: E12.5-F-2 vs. adult-midbrain-1


title: E13.5-F-2 vs. adult-midbrain-1


title: bladder biopsy during cytoscopy G166

description: control


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1918 plasma

description:
LR1918
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1918 plasma

value: UPN727 PBMC cells


title: bladder biopsy during cytoscopy G163

description: low capacity

value: low capacity

value: Interstitial cystitis


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1700 plasma

description:
LR1700
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1700 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1592 plasma

description:
LR1592
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1592 plasma


title: bladder biopsy during cytoscopy G164

description: low capacity


title: bladder biopsy during cytoscopy G165

description: normal capactiy

value: normal capactiy


title: E12.5-F-1 vs. adult-midbrain-1

value: mesodiencephalic dopaminergic (mdDA) neurons from Fac-sorted Pitx3gfp/+ ventral midbrains

value: midbrain cells


title: bladder biopsy during cytoscopy G160

description: normal capactiy


title: bladder biopsy during cytoscopy G161

description: normal capactiy


title: bladder biopsy during cytoscopy G156

description: low capacity


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 2110 plasma

description:
LR2110
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR2110 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1226 plasma

description:
LR1226
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1226 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1497 plasma

description:
LR1497
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1497 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1922 plasma

description:
LR1922
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1922 plasma


title: bladder biopsy during cytoscopy G155

description: normal capactiy


title: bladder biopsy during cytoscopy G153

description: normal capactiy


title: bladder biopsy during cytoscopy G159

description: normal capactiy


title: bladder biopsy during cytoscopy G158

description: normal capactiy


title: GE1_107_eM3

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

description:
GE1_107_eM3
Gene expression in MCMV lung mononuclear cells

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies)

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including backgroundsubtraction), rejects outliers and calculates statistical confidences

source_name: lung mononuclear cells from MCMV infected mice

label_protocol: the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’sprotocol

extract_protocol: Digested fragments were crushed through a cell strainer using a syringe plunger, washed, red blood cells removed with lysis buffer (Qiagen) and after centrifugation,resuspended in PBS before the RNA was extracted.

treatment_protocol: Mice were 6-8 week old BALB/c females. The 4 eMCMV mice were injected intra-peritoneally with 2 x 106 plaque forming units. Control (naïve) mice were uninfected Two weeks later mice were killed by cervical dislocation, lungs were perfused with PBS, cut into pieces and digested with 0.7 mg/ml collagenase type I (Gibco) and 30 µg/ml DNase I (Sigma-Aldrich, UK) for 45 min at 37oC

tag: strain

value: BALB/c

value: lung

tag: age

value: 6-8 weeks


title: bladder biopsy during cytoscopy G154

description: low capacity


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 992 plasma

description:
LR992
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR992 plasma


title: bladder biopsy during cytoscopy G157

description: normal capactiy


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1477 plasma

description:
LR1477
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1477 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 356 plasma

description:
LR356
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR356 plasma


title: BW25113-pCA24N LB 90 min 1 mM IPTG

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: Gene expression data for IPTG induction of cells containing pCA24N (empty).

hyb_protocol: Following affymetrix protocol.  Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA.  After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours.  After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol.  After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: Data was analyzed in the Affymetrix GenomeChipOperating Software (GCOS).

organism: Escherichia coli BW25113

source_name: overexpression of empty vector (pCA24N)

label_protocol: Following affymetrix protocol.  cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

growth_protocol: Strains were grown in LBCm30 at 37°C with shaking at 250 rpm.  Overnight cultures were diluted into fresh LBCm30, grown for 2.5 h, and induced with 1 mM IPTG for 90 min (final OD600 = 1.6).

extract_protocol: Cells were lysed using a bead beater (Biospec) and mRNA was isolated using a Qiagen RNeasy mini kit (Cat# 74104).

treatment_protocol: Cells were pelleted in the presence of RNALater (Applied Biosystems) and flash frozen in ethanol-dry ice.

value: overexpression of empty vector (pCA24N)


title: GE1_107_n4

description:
GE1_107_n4
Gene expression in naïve lung mononuclear cells

source_name: lung mononuclear cells from naïve mice


title: GE1_107_eM2

description:
GE1_107_eM2
Gene expression in MCMV lung mononuclear cells


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1846 plasma

description:
LR1846
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1846 plasma


title: GE1_107_eM1

description:
GE1_107_eM1
Gene expression in MCMV lung mononuclear cells


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 890 plasma

description:
LR890
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR890 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 293 plasma

description:
LR293
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR293 plasma


title: BW25113-pCA24N_arT LB 90 min 1 mM IPTG

description: Gene expression data for IPTG induction of cells containing pCA24N_arT.

source_name: overexpression of arT (pCA24N_arT)

value: overexpression of arT (pCA24N_arT)


title: GE1_107_eM4

description:
GE1_107_eM4
Gene expression in MCMV lung mononuclear cells


title: GE1_107_n3

description:
GE1_107_n3
Gene expression in naïve lung mononuclear cells


title: 06-22-05_Krause_Eisenmann_Celegans_GC3b

city: Baltimore

first: David

last: Eisenmann

state: MD

address: 1000 Hilltop Circle

department: Biological Sciences

institute: UMBC

hyb_protocol: Standard Affymetrix protocol

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

data_processing: MAS5 data by software Partek

organism: Caenorhabditis elegans

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: Whole animals synched at L3

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

treatment_protocol: 30 minute heat shock at 30oC

tag: developmental stage

value: Young Larval Stage L3

value: control


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 342 plasma

description:
LR342
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR342 plasma

tag: responder pbmc cells


title: GE1_107_n1

description:
GE1_107_n1
Gene expression in naïve lung mononuclear cells


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 345 plasma

description:
LR345
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR345 plasma

tag: stimulated with


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 1050 plasma

description:
LR1050
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR1050 plasma


title: 06-22-05_Krause_Eisenmann_Celegans_GC1b

tag: genotype/variation


title: KO biological rep 3

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.

data_processing: The data were calculated as expression values for each gene using a robust multi-array average (RMA). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data. Probesets that had a fold change greater than 2 and an adjusted p-value less than .05 were selected.

source_name: miR-142 KO_T cells

label_protocol: Biotinylated cRNA were prepared using the WT-Ovation™ Pico System (Affymetrix), and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo(dT) and random primers for amplification at the 3’ end and throughout the whole transcriptome.

growth_protocol: Mice were housed in sterilized microisolator cages and received filtered water and normal chow. All animals were cared for under regulations reviewed and approved by the University Committee on Use and Care of Animals of the University of Michigan, based on University Laboratory Animal Medicine guidelines.

extract_protocol: The tcRNA was extracted from purified WT B6 T cells and miR-142 KO T cells with RNeasy Mini Kit (Qiagen) and the quality of the total RNA was verified by an Agilent 2100 Bioanalyzer.

treatment_protocol: T cells were isolated from individual spleen cells suspensions by negative selection

tag: strain background

value: miR-142 KO

value: male

value: 10 weeks

value: spleen

value: T cells


title: GE1_107_n2

description:
GE1_107_n2
Gene expression in naïve lung mononuclear cells

value: female


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 185 plasma

description:
LR185
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR185 plasma

value: UPN727 PBMC cells


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 135 plasma

description:
LR135
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR135 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 884 plasma

description:
LR884
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR884 plasma


title: 06-22-05_Krause_Eisenmann_Celegans_GC2b


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 140 plasma

description:
LR140
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR140 plasma


title: 06-22-05_Krause_Eisenmann_Celegans_H7_2A

value: activated beta-catenin


title: 06-22-05_Krause_Eisenmann_Celegans_H7_3A


title: KO biological rep 2


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 101 plasma

description:
LR101
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR101 plasma


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 158 plasma

description:
LR158
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR158 plasma


title: Reference pool (control) 5535696017_F

status: Public on May 12 2014

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

description: Sample name: 5535696017_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were loaded and background corrected with BeadStudio. The resulting matrix was VST transformed and RSN normalized with lumiT and lumiN functions from lumi package in R.

label: Biotin

source_name: prostate tumor/tissue

label_protocol: Amplification and Labeling was done using the Illumina TotalPrep-96 Amplification kit

extract_protocol: RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser.(I do not think we used Agilent….)

treatment_protocol: Mice were treated dailly for 5 consecutive days with the indicated drugs and prostate tumor/tissues harvested the fifth day

tag: cancer type

tag: treatment

value: Reference


title: Reference pool (control) 5535696028_F

description: Sample name: 5535696028_F


title: WT biological rep 3

source_name: WT_T cells

value: WT


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 15 plasma

description:
LR15
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR15 plasma


title: Reference pool (control) 5535696025_F

description: Sample name: 5535696025_F


title: Reference pool (control) 5512953045_B

description: Sample name: 5512953045_B


title: WT biological rep 1


title: WT biological rep 2


title: Reference pool (control) 5316830044_B

description: Sample name: 5316830044_B


title: Reference pool (control) 5312759023_E

description: Sample name: 5312759023_E


title: Reference pool (control) 5513075034_E

description: Sample name: 5513075034_E


title: Reference pool (control) 5512953041_B

description: Sample name: 5512953041_B


title: Reference pool (control) 5513075026_B

description: Sample name: 5513075026_B


title: Reference pool (control) 5312759018_E

description: Sample name: 5312759018_E


title: KO biological rep 1


title: 06-22-05_Krause_Eisenmann_Celegans_H7_1A


title: UPN727 cells, auto-antibody-negative (AA-) low HLA risk sibling 88 plasma

description:
LR88
Gene expression data from UPN727 cells stimulated with auto-antibody-negative (AA-) low HLA risk sibling plasma

source_name: UPN727 cells stimulated with LR88 plasma


title: Reference pool (control) 5502430035_E

description: Sample name: 5502430035_E


title: Reference pool (control) 5512953001_E

description: Sample name: 5512953001_E


title: Reference pool (control) 5316830041_B

description: Sample name: 5316830041_B


title: Reference pool (control) 5513075025_E

description: Sample name: 5513075025_E


title: Reference pool (control) 5316830051_B

description: Sample name: 5316830051_B


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696017_E

description: Sample name: 5535696017_E

value: ERG-P

value: Docetaxel


title: Reference pool (control) 5316830048_E

description: Sample name: 5316830048_E


title: Pb-Cre; APCflox/flox (APC mice) 5535696028_C

description: Sample name: 5535696028_C

value: Pb-Cre; APCflox/flox (APC mice)

value: APC


title: Reference pool (control) 5513075001_B

description: Sample name: 5513075001_B


title: Reference pool (control) 5312759007_B

description: Sample name: 5312759007_B


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696017_B

description: Sample name: 5535696017_B

value: Imatinib


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696025_B

description: Sample name: 5535696025_B


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696017_D

description: Sample name: 5535696017_D

value: Vehicle


title: bladder biopsy during cytoscopy G162

description: normal capactiy

source_name: bladder biopsy

value: bladder biopsy

value: normal capactiy

value: Interstitial cystitis


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696028_A

description: Sample name: 5535696028_A

value: Calcitriol


title: Nkx3.1-/- (Nkx3.1 mice) 5535696039_F

description: Sample name: 5535696039_F

value: Testosterone


title: Nkx3.1-/- (Nkx3.1 mice) 5535696012_D

description: Sample name: 5535696012_D


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696017_A

description: Sample name: 5535696017_A

value: Rapamycin


title: Reference pool (control) 5512953007_E

description: Sample name: 5512953007_E

value: control


title: Nkx3.1-/- (Nkx3.1 mice) 5535696039_B

description: Sample name: 5535696039_B


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696025_D

description: Sample name: 5535696025_D


title: Reference pool (control) 5502430025_B

description: Sample name: 5502430025_B


title: Nkx3.1-/- (Nkx3.1 mice) 5535696039_C

description: Sample name: 5535696039_C

value: Sorafenib


title: Pb-Cre; APCflox/flox (APC mice) 5535696028_E

description: Sample name: 5535696028_E


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696025_C

description: Sample name: 5535696025_C

value: Dasatinib


title: Nkx3.1-/- (Nkx3.1 mice) 5535696012_A

description: Sample name: 5535696012_A


title: Nkx3.1-/- (Nkx3.1 mice) 5535696012_F

description: Sample name: 5535696012_F


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696017_C

description: Sample name: 5535696017_C


title: Nkx3.1-/- (Nkx3.1 mice) 5535696039_A

description: Sample name: 5535696039_A


title: Nkx3.1-/- (Nkx3.1 mice) 5535696012_C

description: Sample name: 5535696012_C


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696025_A

description: Sample name: 5535696025_A


title: Pb-Cre; APCflox/flox (APC mice) 5535696028_D

description: Sample name: 5535696028_D


title: Nkx3.1-/- (Nkx3.1 mice) 5535696039_E

description: Sample name: 5535696039_E


title: Nkx3.1-/- (Nkx3.1 mice) 5535696008_E

description: Sample name: 5535696008_E


title: Nkx3.1-/- (Nkx3.1 mice) 5535696008_F

description: Sample name: 5535696008_F


title: Pb-Cre; APCflox/flox (APC mice) 5535696028_B

description: Sample name: 5535696028_B


title: Nkx3.1-/- (Nkx3.1 mice) 5535696039_D

description: Sample name: 5535696039_D


title: ARR2PB-Cre; Rosa26ERG/ERG; Ptenflox/flox (ERG-P mice) 5535696025_E

description: Sample name: 5535696025_E


title: Reference pool (control) 5316830047_E

description: Sample name: 5316830047_E

value: Reference


title: Nkx3.1-/- (Nkx3.1 mice) 5535696008_B

description: Sample name: 5535696008_B


title: Nkx3.1-/- (Nkx3.1 mice) 5535696008_A

description: Sample name: 5535696008_A


title: Nkx3.1-/- (Nkx3.1 mice) 5535696007_E

description: Sample name: 5535696007_E


title: Nkx3.1-/- (Nkx3.1 mice) 5535696007_C

description: Sample name: 5535696007_C


title: Nkx3.1-/- (Nkx3.1 mice) 5535696012_B

description: Sample name: 5535696012_B


title: Nkx3.1-/- (Nkx3.1 mice) 5535696007_B

description: Sample name: 5535696007_B


title: Nkx3.1-/- (Nkx3.1 mice) 5535696001_F

description: Sample name: 5535696001_F


title: Nkx3.1-/- (Nkx3.1 mice) 5535696001_A

description: Sample name: 5535696001_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953044_F

description: Sample name: 5512953044_F

value: NPB


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953044_D

description: Sample name: 5512953044_D


title: Nkx3.1-/- (Nkx3.1 mice) 5535696001_E

description: Sample name: 5535696001_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953007_B

description: Sample name: 5512953007_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953044_C

description: Sample name: 5512953044_C


title: Nkx3.1-/- (Nkx3.1 mice) 5535696001_C

description: Sample name: 5535696001_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953007_A

description: Sample name: 5512953007_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953007_D

description: Sample name: 5512953007_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953045_C

description: Sample name: 5512953045_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953045_D

description: Sample name: 5512953045_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953007_F

description: Sample name: 5512953007_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953007_C

description: Sample name: 5512953007_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953044_A

description: Sample name: 5512953044_A


title: Nkx3.1-/- (Nkx3.1 mice) 5535696001_D

description: Sample name: 5535696001_D


title: Nkx3.1-/- (Nkx3.1 mice) 5535696008_D

description: Sample name: 5535696008_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953045_A

description: Sample name: 5512953045_A


title: Nkx3.1-/- (Nkx3.1 mice) 5535696007_A

description: Sample name: 5535696007_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953045_E

description: Sample name: 5512953045_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953044_E

description: Sample name: 5512953044_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953044_B

description: Sample name: 5512953044_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953045_F

description: Sample name: 5512953045_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953046_B

description: Sample name: 5512953046_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953047_D

description: Sample name: 5512953047_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953047_F

description: Sample name: 5512953047_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953046_A

description: Sample name: 5512953046_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953046_E

description: Sample name: 5512953046_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953046_D

description: Sample name: 5512953046_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953047_A

description: Sample name: 5512953047_A


title: TRAMP 5512953048_F

description: Sample name: 5512953048_F

value: TRAMP


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953046_F

description: Sample name: 5512953046_F


title: TRAMP 5512953048_C

description: Sample name: 5512953048_C


title: TRAMP 5512953001_F

description: Sample name: 5512953001_F

value: Docetaxel


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953047_C

description: Sample name: 5512953047_C


title: TRAMP 5512953048_B

description: Sample name: 5512953048_B


title: TRAMP 5512953048_E

description: Sample name: 5512953048_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953046_C

description: Sample name: 5512953046_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953047_E

description: Sample name: 5512953047_E


title: TRAMP 5512953001_C

description: Sample name: 5512953001_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; BrafLSL-V600E/+ (NPB mice) 5512953047_B

description: Sample name: 5512953047_B


title: TRAMP 5512953048_D

description: Sample name: 5512953048_D


title: TRAMP 5512953001_A

description: Sample name: 5512953001_A


title: TRAMP 5512953041_C

description: Sample name: 5512953041_C


title: TRAMP 5512953048_A

description: Sample name: 5512953048_A


title: TRAMP 5512953041_E

description: Sample name: 5512953041_E


title: TRAMP 5512953001_B

description: Sample name: 5512953001_B


title: TRAMP 5512953041_D

description: Sample name: 5512953041_D


title: TRAMP 5512953038_A

description: Sample name: 5512953038_A


title: TRAMP 5512953041_F

description: Sample name: 5512953041_F


title: TRAMP 5512953038_B

description: Sample name: 5512953038_B


title: TRAMP 5512953038_D

description: Sample name: 5512953038_D


title: TRAMP 5512953038_E

description: Sample name: 5512953038_E


title: TRAMP 5512953001_D

description: Sample name: 5512953001_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075041_F

description: Sample name: 5513075041_F


title: TRAMP 5512953020_D

description: Sample name: 5512953020_D


title: TRAMP 5512953038_F

description: Sample name: 5512953038_F


title: TRAMP 5512953020_E

description: Sample name: 5512953020_E


title: TRAMP 5512953020_C

description: Sample name: 5512953020_C


title: TRAMP 5512953038_C

description: Sample name: 5512953038_C


title: TRAMP 5512953020_B

description: Sample name: 5512953020_B


title: TRAMP 5512953020_A

description: Sample name: 5512953020_A


title: TRAMP 5512953041_A

description: Sample name: 5512953041_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075041_C

description: Sample name: 5513075041_C


title: TRAMP 5512953020_F

description: Sample name: 5512953020_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075034_F

description: Sample name: 5513075034_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075041_B

description: Sample name: 5513075041_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075041_E

description: Sample name: 5513075041_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075041_A

description: Sample name: 5513075041_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075041_D

description: Sample name: 5513075041_D


title: Nkx3.1-/- (Nkx3.1 mice) 5535696007_D

description: Sample name: 5535696007_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075034_C

description: Sample name: 5513075034_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075034_D

description: Sample name: 5513075034_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075034_B

description: Sample name: 5513075034_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075005_E

description: Sample name: 5513075005_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075005_A

description: Sample name: 5513075005_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075005_C

description: Sample name: 5513075005_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075005_F

description: Sample name: 5513075005_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075005_D

description: Sample name: 5513075005_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075003_E

description: Sample name: 5513075003_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075034_A

description: Sample name: 5513075034_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075001_D

description: Sample name: 5513075001_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075005_B

description: Sample name: 5513075005_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075003_F

description: Sample name: 5513075003_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075001_C

description: Sample name: 5513075001_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075001_F

description: Sample name: 5513075001_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075003_B

description: Sample name: 5513075003_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075003_A

description: Sample name: 5513075003_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075001_E

description: Sample name: 5513075001_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075003_D

description: Sample name: 5513075003_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075003_C

description: Sample name: 5513075003_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5535696012_E

description: Sample name: 5535696012_E

value: NPK


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430035_D

description: Sample name: 5502430035_D


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430035_F

description: Sample name: 5502430035_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430035_C

description: Sample name: 5502430035_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430034_E

description: Sample name: 5502430034_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430034_F

description: Sample name: 5502430034_F


title: Nkx3.1CreERT2/+; Ptenflox/flox; p55flox/flox (NP53 mice) 5513075001_A

description: Sample name: 5513075001_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5535696001_B

description: Sample name: 5535696001_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430034_C

description: Sample name: 5502430034_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430035_B

description: Sample name: 5502430035_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430035_A

description: Sample name: 5502430035_A