title: Donor: 453; Visit Number: 40; Visit Type: QUIET

description: Donor: 453;Visit Number:40;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: YES

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

value: Moderate Persistent

tag: country


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 39

status: Public on Jul 13 2011

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

country: USA

institute: UMDNJ-SOM

hyb_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters and a pixel size of 5um.

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum (PD vs. BC) (PD vs. AD) results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.

label: Alexa Fluor 647

molecule: other

organism: Homo sapiens

label_protocol: standard Invitrogen protocol

extract_protocol: All serum (PD vs. BC) (PD vs. AD) samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

tag: age

tag: gender

value: Male

tag: mini mental state exam (mmse) score

tag: sample type

value: serum

tag: disease state

value: Alzheimer's Disease


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 34

value: Female


title: WD_replicate

status: Public on Jul 14 2011

type: RNA

city: Berlin

first: Antje

last: Ludwig

address: Ziegelstr. 5-9

department: Kardiologie

country: Germany

institute: Charité Universitätsmedizin Berlin

description: Gene expression of pooled RNA from 4 animals

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, Palo Alto, USA). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole MouseGenome Oligo Microarrays (4x44K) using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1for 1 min at room temperature followed by a second wash with preheated to 37°C the Agilent Gene Expression Wash Buffer 2 for 1 min and a final wash step with acetonitrile for 30 sec.

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

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 background subtraction), rejects outliers and calculates statistical confidences (p-values).

molecule: total RNA

organism: Mus musculus

source_name: LDLR-KO mice; Western-type diet; sham treatment

label_protocol: As starting material 1 μg of each total RNA pool was used for cDNA synthesis. Half of the reaction mixture was subsequently used for complementary RNA (cRNA) synthesis and Cy3 fluorescent labeling according to the manufacturer’s protocol. Yields of cRNA and the dye incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.).

growth_protocol: Male 10-week-old LDLR-KO mice were fed a normal chow diet (CD n=4) or a Western-type diet for 6 weeks (WD n=4 and WD+Bor n=4)

extract_protocol: RNA was isolated using Trizol with standard RNA extraction protocols. RNA samples were quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies, Palo Alto, USA). For each experiment RNA from 4 animals per group (CD, WD, WD+Bor) was pooled.

treatment_protocol: WD +Bor group received intraperitoneal injections of bortezomib (50 µg/kg body weight) twice weekly; control animals received sham-treatment with saline twice weekly .

tag: strain

tag: Sex

value: male

value: 16 weeks

tag: tissue

value: aorta


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 45


title: Donor: 673; Visit Number: 50; Visit Type: QUIET

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

description: Donor: 673;Visit Number:50;Visit Type:QUIET

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix MAS 5.0 algorithm

label: biotin

label_protocol: Affymetrix in-vitro labeling protocol

extract_protocol: RNA was extracted from human PBMCs

tag: history of acid reflux 0=no  1=yes

value: not reported

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

value: ICON-D

tag: baseline severity  nih guideline

value: Severe Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

value: W

tag: days since quiet visit

tag: visit number

value: IRL

tag: fev1 predicted

tag: leukotriene receptor antagonist use  0=no  1=yes

tag: cell type

value: PBMC


title: Donor: 653; Visit Number: 60; Visit Type: QUIET

description: Donor: 653;Visit Number:60;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: ratio of monocytes to lymphocytes  whole blood

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: country


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 7

tag: age

tag: gender

tag: mini mental state exam (mmse) score

tag: sample type

tag: disease state


title: Donor: 166; Visit Number: 20; Visit Type: QUIET

description: Donor: 166;Visit Number:20;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: NON-FASTING

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

value: AARI

tag: baseline severity  nih guideline

value: Mild Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

value: AUS

tag: fev1 predicted

tag: leukotriene receptor antagonist use  0=no  1=yes

tag: cell type


title: CD

source_name: LDLR-KO mice; chow diet; sham treatment

tag: strain

tag: Sex

tag: age

tag: tissue


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 8

tag: gender

tag: mini mental state exam (mmse) score

tag: sample type

tag: disease state


title: WD+Bor_replicate

source_name: LDLR-KO mice; Western-type diet; bortezomib treatment


title: Donor: 818; Visit Number: 60; Visit Type: QUIET

description: Donor: 818;Visit Number:60;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: initial processing lab

value: DeCODE

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: country

value: ISL


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 47

tag: age

tag: gender

value: Male

tag: mini mental state exam (mmse) score

tag: sample type

value: serum

tag: disease state

value: Alzheimer's Disease


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 4

value: Female


title: WD+Bor

tag: strain

tag: Sex

value: male

value: 16 weeks

tag: tissue

value: aorta


title: EpH4-PR cells 3

city: Bethesda

first: Erika

last: Ginsburg

state: MD

address: 37 Convent Dr.

department: NCI

institute: NIH

description: gene expression of EpH4-PR cells

hyb_protocol: Cy5/Cy3-labeled cRNA (500ng) was hybridized to the Agilent Mouse Whole Genome Oligo Microarray at 60C for 17 hours according to manufacturer's instruction, prior to washing and scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using two color scan setting for 1x44k array slides sccording to manufacturer's instructions.

data_processing: Scanned images containing approximately 41,000 unique elements were analyzed using Agilent's Feature Extraction Software.

source_name: EpH4-PR cells

label_protocol: according to Cogenic's standard published protocol

growth_protocol: EpH4-PR cells were routinely grown in DMEM media containing 10%FBS and grown to approximately 75% confluence.

extract_protocol: total RNA was extracted using Qiagen Rneasy kit accoring to manufacturer's instructions

tag: cell line

tag: cell type

value: epithelial

source_name: Stratagene mouse standard

tag: reference

value: Stratagene mouse standard


title: EpH4-PR cells 2

description: gene expression of EpH4-PR cells


title: EpH4-PR cells 1

description: gene expression of EpH4-PR cells


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 9


title: WD


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 2

value: UNK


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 3


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 48


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 5


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 1


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 6


title: Older Control serum (late stage AD vs. CO) sample 19

value: Older Control


title: Older Control serum (late stage AD vs. CO) sample 20


title: Older Control serum (late stage AD vs. CO) sample 18


title: Older Control serum (late stage AD vs. CO) sample 17


title: Alzheimer's Disease serum (late stage AD vs. CO) sample 33


title: Older Control serum (late stage AD vs. CO) sample 13


title: Older Control serum (late stage AD vs. CO) sample 12


title: Older Control serum (late stage AD vs. CO) sample 11


title: Older Control serum (late stage AD vs. CO) sample 16


title: Older Control serum (late stage AD vs. CO) sample 8


title: Older Control serum (late stage AD vs. CO) sample 14


title: Older Control serum (late stage AD vs. CO) sample 7


title: Older Control serum (late stage AD vs. CO) sample 10


title: Older Control serum (late stage AD vs. CO) sample 9


title: Older Control serum (late stage AD vs. CO) sample 2


title: Older Control serum (late stage AD vs. CO) sample 1


title: Older Control serum (late stage AD vs. CO) sample 3


title: Donor: 404; Visit Number: 50; Visit Type: QUIET

description: Donor: 404;Visit Number:50;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

value: not reported

tag: fasting status

value: YES

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: initial processing lab

value: ICON-F

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

value: Moderate Persistent

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

value: B

tag: days since quiet visit

tag: visit number

value: USA

tag: fev1 predicted

tag: leukotriene receptor antagonist use  0=no  1=yes

value: PBMC


title: Younger Control serum (late stage AD vs. NDC) sample 11

tag: age

tag: gender

tag: mini mental state exam (mmse) score

tag: sample type

value: serum

tag: disease state

value: Younger Control


title: Older Control serum (late stage AD vs. CO) sample 15

value: Male


title: Older Control serum (late stage AD vs. CO) sample 4


title: Older Control serum (late stage AD vs. CO) sample 6


title: Younger Control serum (late stage AD vs. NDC) sample 10


title: Older Control serum (late stage AD vs. NDC) sample 4


title: Older Control serum (late stage AD vs. CO) sample 5


title: Younger Control serum (late stage AD vs. NDC) sample 9


title: Younger Control serum (late stage AD vs. NDC) sample 12


title: Older Control serum (late stage AD vs. NDC) sample 2


title: Younger Control serum (late stage AD vs. NDC) sample 13


title: Older Control serum (late stage AD vs. NDC) sample 8


title: Older Control serum (late stage AD vs. NDC) sample 3


title: Younger Control serum (late stage AD vs. NDC) sample 15


title: Older Control serum (late stage AD vs. NDC) sample 5


title: Older Control serum (late stage AD vs. NDC) sample 6


title: Older Control serum (late stage AD vs. NDC) sample 7


title: Younger Control serum (late stage AD vs. NDC) sample 19

value: Female


title: Younger Control serum (late stage AD vs. NDC) sample 16


title: Younger Control serum (late stage AD vs. NDC) sample 7


title: Younger Control serum (late stage AD vs. NDC) sample 14


title: Younger Control serum (late stage AD vs. NDC) sample 20


title: Younger Control serum (late stage AD vs. NDC) sample 8


title: Older Control serum (late stage AD vs. NDC) sample 1


title: Older Control serum (late stage AD vs. NDC) sample 12


title: Older Control serum (late stage AD vs. NDC) sample 9


title: Older Control serum (late stage AD vs. NDC) sample 10


title: Older Control serum (late stage AD vs. NDC) sample 19


title: Older Control serum (late stage AD vs. NDC) sample 18


title: Younger Control serum (late stage AD vs. NDC) sample 17


title: Older Control serum (late stage AD vs. NDC) sample 17


title: Older Control serum (late stage AD vs. NDC) sample 16


title: Younger Control serum (late stage AD vs. NDC) sample 18


title: Older Control serum (late stage AD vs. NDC) sample 14


title: Older Control serum (late stage AD vs. NDC) sample 15


title: Older Control serum (late stage AD vs. NDC) sample 13


title: Younger Control serum (late stage AD vs. NDC) sample 4


title: Older Control serum (late stage AD vs. NDC) sample 20


title: Older Control serum (late stage AD vs. NDC) sample 11


title: Younger Control serum (late stage AD vs. NDC) sample 3


title: Younger Control serum (late stage AD vs. NDC) sample 1


title: Younger Control serum (late stage AD vs. NDC) sample 2


title: Younger Control serum (late stage AD vs. NDC) sample 6


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 34

value: Alzheimer's Disease


title: Younger Control serum (late stage AD vs. NDC) sample 5


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 39


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 45


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 8


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 47


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 3


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 1


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 4


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 2


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 15


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 11


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 23


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 13


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 33


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 14


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 16


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 48


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 22


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 12


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 10


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 25


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 24


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 49


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 5


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 9


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 46


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 18


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 29


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 7


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 52


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 30


title: Alzheimer's Disease serum (late stage AD vs. NDC) sample 6


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 51


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 17


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 27


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 31


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 38


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 36


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 20


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 19


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 54


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 32


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 26


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 21


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 53


title: Older Control serum (early stage AD vs. CO) sample 20


title: Older Control serum (early stage AD vs. CO) sample 18


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 28


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 50


title: Older Control serum (early stage AD vs. CO) sample 19


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 40


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 37


title: Older Control serum (early stage AD vs. CO) sample 17


title: Older Control serum (early stage AD vs. CO) sample 6


title: Older Control serum (early stage AD vs. CO) sample 15


title: Older Control serum (early stage AD vs. CO) sample 14


title: Older Control serum (early stage AD vs. CO) sample 16


title: Older Control serum (early stage AD vs. CO) sample 13


title: Alzheimer's Disease serum (early stage AD vs. CO) sample 35


title: Older Control serum (early stage AD vs. CO) sample 12


title: Older Control serum (early stage AD vs. CO) sample 11


title: Older Control serum (early stage AD vs. CO) sample 5


title: Older Control serum (early stage AD vs. CO) sample 10


title: Older Control serum (early stage AD vs. CO) sample 4


title: Older Control serum (early stage AD vs. CO) sample 7


title: Older Control serum (early stage AD vs. CO) sample 9


title: Older Control serum (early stage AD vs. CO) sample 8


title: Older Control serum (early stage AD vs. CO) sample 2


title: Younger Control serum (early stage AD vs. NDC) sample 10


title: Older Control serum (early stage AD vs. CO) sample 1


title: Younger Control serum (early stage AD vs. NDC) sample 12


title: Younger Control serum (early stage AD vs. NDC) sample 11


title: Older Control serum (early stage AD vs. NDC) sample 4


title: Younger Control serum (early stage AD vs. NDC) sample 16


title: Older Control serum (early stage AD vs. NDC) sample 1


title: Younger Control serum (early stage AD vs. NDC) sample 9


title: Older Control serum (early stage AD vs. NDC) sample 2


title: Younger Control serum (early stage AD vs. NDC) sample 15


title: Older Control serum (early stage AD vs. NDC) sample 3


title: Older Control serum (early stage AD vs. NDC) sample 7


title: Younger Control serum (early stage AD vs. NDC) sample 13


title: Older Control serum (early stage AD vs. NDC) sample 8


title: Older Control serum (early stage AD vs. CO) sample 3


title: Older Control serum (early stage AD vs. NDC) sample 6


title: Older Control serum (early stage AD vs. NDC) sample 5


title: Older Control serum (early stage AD vs. NDC) sample 12


title: Older Control serum (early stage AD vs. NDC) sample 11


title: Younger Control serum (early stage AD vs. NDC) sample 18


title: Younger Control serum (early stage AD vs. NDC) sample 8


title: Younger Control serum (early stage AD vs. NDC) sample 20


title: Older Control serum (early stage AD vs. NDC) sample 20


title: Younger Control serum (early stage AD vs. NDC) sample 19


title: Older Control serum (early stage AD vs. NDC) sample 9


title: Older Control serum (early stage AD vs. NDC) sample 19


title: Older Control serum (early stage AD vs. NDC) sample 18


title: Younger Control serum (early stage AD vs. NDC) sample 17


title: Older Control serum (early stage AD vs. NDC) sample 13


title: Older Control serum (early stage AD vs. NDC) sample 15


title: Younger Control serum (early stage AD vs. NDC) sample 3


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 16


title: Older Control serum (early stage AD vs. NDC) sample 10


title: Older Control serum (early stage AD vs. NDC) sample 14


title: Younger Control serum (early stage AD vs. NDC) sample 4


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 15


title: Younger Control serum (early stage AD vs. NDC) sample 5


title: Older Control serum (early stage AD vs. NDC) sample 17


title: Younger Control serum (early stage AD vs. NDC) sample 14


title: Younger Control serum (early stage AD vs. NDC) sample 1


title: Younger Control serum (early stage AD vs. NDC) sample 7


title: Older Control serum (early stage AD vs. NDC) sample 16


title: Younger Control serum (early stage AD vs. NDC) sample 2


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 13


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 14


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 12


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 10


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 23


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 24


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 22


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 49


title: Younger Control serum (early stage AD vs. NDC) sample 6


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 25


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 46


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 35


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 51


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 27


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 30


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 21


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 17


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 31


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 19


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 11


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 32


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 50


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 38


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 53


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 54


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 36


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 18


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 40


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 28


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 52


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 29


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 37


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 20


title: Breast Cancer serum (AD vs. BC) sample 30

value: Breast Cancer


title: Breast Cancer serum (AD vs. BC) sample 26


title: Breast Cancer serum (AD vs. BC) sample 27


title: Breast Cancer serum (AD vs. BC) sample 29


title: Alzheimer's Disease serum (early stage AD vs. NDC) sample 26


title: Breast Cancer serum (AD vs. BC) sample 24


title: Breast Cancer serum (AD vs. BC) sample 25


title: Breast Cancer serum (AD vs. BC) sample 28


title: Breast Cancer serum (AD vs. BC) sample 22


title: Breast Cancer serum (AD vs. BC) sample 16


title: Breast Cancer serum (AD vs. BC) sample 14


title: Breast Cancer serum (AD vs. BC) sample 19


title: Breast Cancer serum (AD vs. BC) sample 9


title: Breast Cancer serum (AD vs. BC) sample 7


title: Breast Cancer serum (AD vs. BC) sample 20


title: Breast Cancer serum (AD vs. BC) sample 17


title: Breast Cancer serum (AD vs. BC) sample 18


title: Breast Cancer serum (AD vs. BC) sample 13


title: Breast Cancer serum (AD vs. BC) sample 12


title: Breast Cancer serum (AD vs. BC) sample 8


title: Breast Cancer serum (AD vs. BC) sample 21


title: Breast Cancer serum (AD vs. BC) sample 15


title: Breast Cancer serum (AD vs. BC) sample 4


title: Breast Cancer serum (AD vs. BC) sample 6


title: Breast Cancer serum (AD vs. BC) sample 3


title: Breast Cancer serum (AD vs. BC) sample 5


title: Breast Cancer serum (AD vs. BC) sample 23


title: Breast Cancer serum (AD vs. BC) sample 2


title: Alzheimer's Disease serum (AD vs. BC) sample 51


title: Breast Cancer serum (AD vs. BC) sample 11


title: Alzheimer's Disease serum (AD vs. BC) sample 52


title: Alzheimer's Disease serum (AD vs. BC) sample 49


title: Breast Cancer serum (AD vs. BC) sample 1


title: Alzheimer's Disease serum (AD vs. BC) sample 47


title: Breast Cancer serum (AD vs. BC) sample 10


title: Alzheimer's Disease serum (AD vs. BC) sample 48


title: Alzheimer's Disease serum (AD vs. BC) sample 45


title: Alzheimer's Disease serum (AD vs. BC) sample 46


title: Alzheimer's Disease serum (AD vs. BC) sample 38


title: Alzheimer's Disease serum (AD vs. BC) sample 37


title: Alzheimer's Disease serum (AD vs. BC) sample 35


title: Alzheimer's Disease serum (AD vs. BC) sample 31


title: Alzheimer's Disease serum (AD vs. BC) sample 36


title: Alzheimer's Disease serum (AD vs. BC) sample 32


title: Alzheimer's Disease serum (AD vs. BC) sample 33


title: Alzheimer's Disease serum (AD vs. BC) sample 34


title: Alzheimer's Disease serum (AD vs. BC) sample 22


title: Alzheimer's Disease serum (AD vs. BC) sample 27


title: Alzheimer's Disease serum (AD vs. BC) sample 21


title: Alzheimer's Disease serum (AD vs. BC) sample 26


title: Alzheimer's Disease serum (AD vs. BC) sample 25


title: Alzheimer's Disease serum (AD vs. BC) sample 39


title: Alzheimer's Disease serum (AD vs. BC) sample 20


title: Alzheimer's Disease serum (AD vs. BC) sample 18


title: Alzheimer's Disease serum (AD vs. BC) sample 40


title: Alzheimer's Disease serum (AD vs. BC) sample 54


title: Alzheimer's Disease serum (AD vs. BC) sample 19


title: Alzheimer's Disease serum (AD vs. BC) sample 50


title: Alzheimer's Disease serum (AD vs. BC) sample 53


title: Alzheimer's Disease serum (AD vs. BC) sample 17


title: Alzheimer's Disease serum (AD vs. BC) sample 28


title: Alzheimer's Disease serum (AD vs. BC) sample 23


title: Alzheimer's Disease serum (AD vs. BC) sample 14


title: Alzheimer's Disease serum (AD vs. BC) sample 29


title: Alzheimer's Disease serum (AD vs. BC) sample 30


title: Alzheimer's Disease serum (AD vs. BC) sample 24


title: Alzheimer's Disease serum (AD vs. BC) sample 16


title: Alzheimer's Disease serum (AD vs. BC) sample 15


title: Alzheimer's Disease serum (AD vs. BC) sample 12


title: Alzheimer's Disease serum (AD vs. BC) sample 13


title: Alzheimer's Disease serum (AD vs. BC) sample 9


title: Alzheimer's Disease serum (AD vs. BC) sample 8


title: Alzheimer's Disease serum (AD vs. BC) sample 11


title: Alzheimer's Disease serum (AD vs. BC) sample 3


title: Alzheimer's Disease serum (AD vs. BC) sample 2


title: Alzheimer's Disease serum (AD vs. BC) sample 4


title: Alzheimer's Disease serum (AD vs. BC) sample 5


title: Younger Control serum (AD vs. CY) sample 20


title: Alzheimer's Disease serum (AD vs. BC) sample 1


title: Alzheimer's Disease serum (AD vs. BC) sample 6


title: Alzheimer's Disease serum (AD vs. BC) sample 7


title: Younger Control serum (AD vs. CY) sample 19


title: Younger Control serum (AD vs. CY) sample 18


title: Alzheimer's Disease serum (AD vs. BC) sample 10


title: Younger Control serum (AD vs. CY) sample 15


title: Younger Control serum (AD vs. CY) sample 16


title: Younger Control serum (AD vs. CY) sample 17


title: Younger Control serum (AD vs. CY) sample 11


title: Younger Control serum (AD vs. CY) sample 14


title: Younger Control serum (AD vs. CY) sample 4


title: Younger Control serum (AD vs. CY) sample 13


title: Younger Control serum (AD vs. CY) sample 12


title: Younger Control serum (AD vs. CY) sample 5


title: Younger Control serum (AD vs. CY) sample 9


title: Younger Control serum (AD vs. CY) sample 1


title: Alzheimer's Disease serum (AD vs. CY) sample 51


title: Younger Control serum (AD vs. CY) sample 7


title: Younger Control serum (AD vs. CY) sample 2


title: Younger Control serum (AD vs. CY) sample 10


title: Younger Control serum (AD vs. CY) sample 6


title: Younger Control serum (AD vs. CY) sample 8


title: Alzheimer's Disease serum (AD vs. CY) sample 52


title: Alzheimer's Disease serum (AD vs. CY) sample 49


title: Alzheimer's Disease serum (AD vs. CY) sample 36


title: Alzheimer's Disease serum (AD vs. CY) sample 48


title: Alzheimer's Disease serum (AD vs. CY) sample 45


title: Younger Control serum (AD vs. CY) sample 3


title: Alzheimer's Disease serum (AD vs. CY) sample 46


title: Alzheimer's Disease serum (AD vs. CY) sample 39


title: Alzheimer's Disease serum (AD vs. CY) sample 33


title: Alzheimer's Disease serum (AD vs. CY) sample 31


title: Alzheimer's Disease serum (AD vs. CY) sample 38


title: Alzheimer's Disease serum (AD vs. CY) sample 35


title: Alzheimer's Disease serum (AD vs. CY) sample 29


title: Alzheimer's Disease serum (AD vs. CY) sample 30


title: Alzheimer's Disease serum (AD vs. CY) sample 32


title: Alzheimer's Disease serum (AD vs. CY) sample 34


title: Alzheimer's Disease serum (AD vs. CY) sample 47


title: Alzheimer's Disease serum (AD vs. CY) sample 26


title: Alzheimer's Disease serum (AD vs. CY) sample 27


title: Alzheimer's Disease serum (AD vs. CY) sample 28


title: Alzheimer's Disease serum (AD vs. CY) sample 25


title: Alzheimer's Disease serum (AD vs. CY) sample 20


title: Alzheimer's Disease serum (AD vs. CY) sample 23


title: Alzheimer's Disease serum (AD vs. CY) sample 24


title: Alzheimer's Disease serum (AD vs. CY) sample 21


title: Alzheimer's Disease serum (AD vs. CY) sample 19


title: Alzheimer's Disease serum (AD vs. CY) sample 18


title: Alzheimer's Disease serum (AD vs. CY) sample 17


title: Alzheimer's Disease serum (AD vs. CY) sample 40


title: Alzheimer's Disease serum (AD vs. CY) sample 54


title: Alzheimer's Disease serum (AD vs. CY) sample 50


title: Alzheimer's Disease serum (AD vs. CY) sample 37


title: Alzheimer's Disease serum (AD vs. CY) sample 12


title: Alzheimer's Disease serum (AD vs. CY) sample 16


title: Alzheimer's Disease serum (AD vs. CY) sample 22


title: Alzheimer's Disease serum (AD vs. CY) sample 10


title: Alzheimer's Disease serum (AD vs. CY) sample 15


title: Alzheimer's Disease serum (AD vs. CY) sample 5


title: Alzheimer's Disease serum (AD vs. CY) sample 14


title: Alzheimer's Disease serum (AD vs. CY) sample 7


title: Alzheimer's Disease serum (AD vs. CY) sample 8


title: Alzheimer's Disease serum (AD vs. CY) sample 9


title: Alzheimer's Disease serum (AD vs. CY) sample 4


title: Alzheimer's Disease serum (AD vs. CY) sample 6


title: Alzheimer's Disease serum (AD vs. CY) sample 11


title: Alzheimer's Disease serum (AD vs. CY) sample 2


title: Alzheimer's Disease serum (AD vs. CY) sample 3


title: Alzheimer's Disease serum (AD vs. CY) sample 1


title: Older Control serum (AD vs. CO) sample 17


title: Older Control serum (AD vs. CO) sample 19


title: Older Control serum (AD vs. CO) sample 16


title: Older Control serum (AD vs. CO) sample 11


title: Older Control serum (AD vs. CO) sample 10


title: Alzheimer's Disease serum (AD vs. CY) sample 13


title: Older Control serum (AD vs. CO) sample 18


title: Older Control serum (AD vs. CO) sample 7


title: Older Control serum (AD vs. CO) sample 12


title: Older Control serum (AD vs. CO) sample 9


title: Older Control serum (AD vs. CO) sample 15


title: Older Control serum (AD vs. CO) sample 14


title: Older Control serum (AD vs. CO) sample 13


title: Alzheimer's Disease serum (AD vs. CY) sample 53


title: Older Control serum (AD vs. CO) sample 6


title: Older Control serum (AD vs. CO) sample 5


title: Alzheimer's Disease serum (AD vs. CO) sample 52


title: Older Control serum (AD vs. CO) sample 4


title: Alzheimer's Disease serum (AD vs. CO) sample 51


title: Alzheimer's Disease serum (AD vs. CO) sample 49


title: Older Control serum (AD vs. CO) sample 2


title: Older Control serum (AD vs. CO) sample 3


title: Older Control serum (AD vs. CO) sample 8


title: Alzheimer's Disease serum (AD vs. CO) sample 47


title: Alzheimer's Disease serum (AD vs. CO) sample 48


title: Alzheimer's Disease serum (AD vs. CO) sample 39


title: Alzheimer's Disease serum (AD vs. CO) sample 38


title: Older Control serum (AD vs. CO) sample 1


title: Alzheimer's Disease serum (AD vs. CO) sample 45


title: Alzheimer's Disease serum (AD vs. CO) sample 34


title: Alzheimer's Disease serum (AD vs. CO) sample 46


title: Alzheimer's Disease serum (AD vs. CO) sample 37


title: Alzheimer's Disease serum (AD vs. CO) sample 32


title: Alzheimer's Disease serum (AD vs. CO) sample 33


title: Alzheimer's Disease serum (AD vs. CO) sample 35


title: Alzheimer's Disease serum (AD vs. CO) sample 36


title: Alzheimer's Disease serum (AD vs. CO) sample 25


title: Alzheimer's Disease serum (AD vs. CO) sample 31


title: Alzheimer's Disease serum (AD vs. CO) sample 28


title: Alzheimer's Disease serum (AD vs. CO) sample 21


title: Alzheimer's Disease serum (AD vs. CO) sample 26


title: Alzheimer's Disease serum (AD vs. CO) sample 29


title: Alzheimer's Disease serum (AD vs. CO) sample 19


title: Alzheimer's Disease serum (AD vs. CO) sample 20


title: Alzheimer's Disease serum (AD vs. CO) sample 27


title: Alzheimer's Disease serum (AD vs. CO) sample 18


title: Alzheimer's Disease serum (AD vs. CO) sample 54


title: Alzheimer's Disease serum (AD vs. CO) sample 17


title: Alzheimer's Disease serum (AD vs. CO) sample 40


title: Alzheimer's Disease serum (AD vs. CO) sample 24


title: Alzheimer's Disease serum (AD vs. CO) sample 30


title: Alzheimer's Disease serum (AD vs. CO) sample 50


title: Alzheimer's Disease serum (AD vs. CO) sample 23


title: Alzheimer's Disease serum (AD vs. CO) sample 16


title: Alzheimer's Disease serum (AD vs. CO) sample 53


title: Alzheimer's Disease serum (AD vs. CO) sample 14


title: Alzheimer's Disease serum (AD vs. CO) sample 15


title: Alzheimer's Disease serum (AD vs. CO) sample 22


title: Alzheimer's Disease serum (AD vs. CO) sample 13


title: Alzheimer's Disease serum (AD vs. CO) sample 10


title: Alzheimer's Disease serum (AD vs. CO) sample 9


title: Alzheimer's Disease serum (AD vs. CO) sample 12


title: Alzheimer's Disease serum (AD vs. CO) sample 8


title: Alzheimer's Disease serum (AD vs. CO) sample 7


title: Alzheimer's Disease serum (AD vs. CO) sample 11


title: Alzheimer's Disease serum (AD vs. CO) sample 5


title: Alzheimer's Disease serum (AD vs. CO) sample 4


title: Alzheimer's Disease serum (AD vs. CO) sample 6


title: Alzheimer's Disease serum (AD vs. CO) sample 3


title: Alzheimer's Disease serum (AD vs. CO) sample 1


title: Alzheimer's Disease serum (AD vs. CO) sample 2


title: Older Control serum (AD vs. NDC) sample 3


title: Older Control serum (AD vs. NDC) sample 4


title: Older Control serum (AD vs. NDC) sample 2


title: Younger Control serum (AD vs. NDC) sample 12


title: Younger Control serum (AD vs. NDC) sample 10


title: Younger Control serum (AD vs. NDC) sample 11


title: Younger Control serum (AD vs. NDC) sample 9


title: Older Control serum (AD vs. NDC) sample 1


title: Older Control serum (AD vs. NDC) sample 8


title: Younger Control serum (AD vs. NDC) sample 16


title: Younger Control serum (AD vs. NDC) sample 13


title: Younger Control serum (AD vs. NDC) sample 18


title: Younger Control serum (AD vs. NDC) sample 17


title: Younger Control serum (AD vs. NDC) sample 20


title: Older Control serum (AD vs. NDC) sample 20


title: Older Control serum (AD vs. NDC) sample 5


title: Younger Control serum (AD vs. NDC) sample 8


title: Younger Control serum (AD vs. NDC) sample 14


title: Older Control serum (AD vs. NDC) sample 19


title: Younger Control serum (AD vs. NDC) sample 15


title: Older Control serum (AD vs. NDC) sample 12


title: Younger Control serum (AD vs. NDC) sample 7


title: Older Control serum (AD vs. CO) sample 20


title: Older Control serum (AD vs. NDC) sample 10


title: Older Control serum (AD vs. NDC) sample 6


title: Older Control serum (AD vs. NDC) sample 7


title: Older Control serum (AD vs. NDC) sample 9


title: Older Control serum (AD vs. NDC) sample 18


title: Older Control serum (AD vs. NDC) sample 11


title: Older Control serum (AD vs. NDC) sample 16


title: Older Control serum (AD vs. NDC) sample 15


title: Older Control serum (AD vs. NDC) sample 17


title: Younger Control serum (AD vs. NDC) sample 19


title: Younger Control serum (AD vs. NDC) sample 6


title: Alzheimer's Disease serum (AD vs. NDC) sample 48


title: Alzheimer's Disease serum (AD vs. NDC) sample 52


title: Younger Control serum (AD vs. NDC) sample 2


title: Alzheimer's Disease serum (AD vs. NDC) sample 49


title: Older Control serum (AD vs. NDC) sample 13


title: Younger Control serum (AD vs. NDC) sample 4


title: Younger Control serum (AD vs. NDC) sample 3


title: Younger Control serum (AD vs. NDC) sample 1


title: Alzheimer's Disease serum (AD vs. NDC) sample 47


title: Older Control serum (AD vs. NDC) sample 14


title: Alzheimer's Disease serum (AD vs. NDC) sample 38


title: Alzheimer's Disease serum (AD vs. NDC) sample 39


title: Alzheimer's Disease serum (AD vs. NDC) sample 51


title: Alzheimer's Disease serum (AD vs. NDC) sample 46


title: Alzheimer's Disease serum (AD vs. NDC) sample 31


title: Alzheimer's Disease serum (AD vs. NDC) sample 29


title: Alzheimer's Disease serum (AD vs. NDC) sample 45


title: Alzheimer's Disease serum (AD vs. NDC) sample 34


title: Alzheimer's Disease serum (AD vs. NDC) sample 33


title: Alzheimer's Disease serum (AD vs. NDC) sample 28


title: Alzheimer's Disease serum (AD vs. NDC) sample 35


title: Alzheimer's Disease serum (AD vs. NDC) sample 26


title: Alzheimer's Disease serum (AD vs. NDC) sample 32


title: Younger Control serum (AD vs. NDC) sample 5


title: Alzheimer's Disease serum (AD vs. NDC) sample 36


title: Alzheimer's Disease serum (AD vs. NDC) sample 25


title: Alzheimer's Disease serum (AD vs. NDC) sample 37


title: Alzheimer's Disease serum (AD vs. NDC) sample 30


title: Alzheimer's Disease serum (AD vs. NDC) sample 27


title: Alzheimer's Disease serum (AD vs. NDC) sample 19


title: Alzheimer's Disease serum (AD vs. NDC) sample 20


title: Alzheimer's Disease serum (AD vs. NDC) sample 53


title: Alzheimer's Disease serum (AD vs. NDC) sample 22


title: Alzheimer's Disease serum (AD vs. NDC) sample 54


title: Alzheimer's Disease serum (AD vs. NDC) sample 21


title: Alzheimer's Disease serum (AD vs. NDC) sample 18


title: Alzheimer's Disease serum (AD vs. NDC) sample 23


title: Alzheimer's Disease serum (AD vs. NDC) sample 24


title: Alzheimer's Disease serum (AD vs. NDC) sample 50


title: Alzheimer's Disease serum (AD vs. NDC) sample 17


title: Alzheimer's Disease serum (AD vs. NDC) sample 40


title: Alzheimer's Disease serum (AD vs. NDC) sample 15


title: Alzheimer's Disease serum (AD vs. NDC) sample 8


title: Alzheimer's Disease serum (AD vs. NDC) sample 12


title: Alzheimer's Disease serum (AD vs. NDC) sample 4


title: Alzheimer's Disease serum (AD vs. NDC) sample 11


title: Alzheimer's Disease serum (AD vs. NDC) sample 7


title: Alzheimer's Disease serum (AD vs. NDC) sample 10


title: Alzheimer's Disease serum (AD vs. NDC) sample 5


title: Alzheimer's Disease serum (AD vs. NDC) sample 14


title: Alzheimer's Disease serum (AD vs. NDC) sample 2


title: Alzheimer's Disease serum (AD vs. NDC) sample 16


title: Alzheimer's Disease serum (AD vs. NDC) sample 13


title: Alzheimer's Disease serum (AD vs. NDC) sample 3


title: Alzheimer's Disease serum (AD vs. NDC) sample 6


title: Alzheimer's Disease serum (AD vs. NDC) sample 9


title: Parkinson's Disease serum (PD vs. AD) sample 25

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum (PD vs. AD) results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.

extract_protocol: All serum (PD vs. AD) samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

value: Parkinson's Disease


title: Parkinson's Disease serum (PD vs. AD) sample 29


title: Parkinson's Disease serum (PD vs. AD) sample 28


title: Alzheimer's Disease serum (AD vs. NDC) sample 1


title: Parkinson's Disease serum (PD vs. AD) sample 23


title: Parkinson's Disease serum (PD vs. AD) sample 22


title: 12_2bATGF

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: RMA by software Partek

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: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

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

treatment_protocol: The generation of Smad3-/- mice have been described in Yang, X., et al. Targeted disruption of SMAD3 results in impaired mucosal immunity and diminished T cell responsiveness to TGF-beta. Embo J 18, 1280-1291 (1999). Mice were fed with high fat diet (55% high fat diet) and antibodies (IgG and Anti-TGF-beta) were injected through intra-peritoneal route three times in a week for 8 weeks.

tag: strain

tag: treatment

value: diet induced obese

tag: antibody

value: TGF-beta

tag: catalog#


title: Parkinson's Disease serum (PD vs. AD) sample 19


title: Parkinson's Disease serum (PD vs. AD) sample 24


title: 11_2aATGF


title: 9_1aIgG

value: IgG


title: 8-KO_HFD4b

tag: genotype

value: mixed strains of C57BL/6 and NIH Black Swiss females (Taconic)

value: high fat diet


title: 10_1bIgG


title: Parkinson's Disease serum (PD vs. AD) sample 21


title: Parkinson's Disease serum (PD vs. AD) sample 20


title: Parkinson's Disease serum (PD vs. AD) sample 27


title: 7-KO_HFD4a


title: 4-WT_HFD2b

value: WT


title: 6-KO_RD3b

value: regular diet


title: 3-WT_HFD2a


title: Parkinson's Disease serum (PD vs. AD) sample 17


title: Parkinson's Disease serum (PD vs. AD) sample 16

value: UNK


title: Parkinson's Disease serum (PD vs. AD) sample 18


title: Parkinson's Disease serum (PD vs. AD) sample 13


title: 5-KO_RD3a


title: 2-WT_RD1b


title: Parkinson's Disease serum (PD vs. AD) sample 11


title: Parkinson's Disease serum (PD vs. AD) sample 8


title: Parkinson's Disease serum (PD vs. AD) sample 15


title: Parkinson's Disease serum (PD vs. AD) sample 9


title: Parkinson's Disease serum (PD vs. AD) sample 5


title: Parkinson's Disease serum (PD vs. AD) sample 7


title: Parkinson's Disease serum (PD vs. AD) sample 6


title: Parkinson's Disease serum (PD vs. AD) sample 4


title: Parkinson's Disease serum (PD vs. AD) sample 3


title: Parkinson's Disease serum (PD vs. AD) sample 10


title: Parkinson's Disease serum (PD vs. AD) sample 14


title: Parkinson's Disease serum (PD vs. AD) sample 2


title: Gastric Tumor from patient No.72

city: Beijng

first: zheng

middle: yue

last: zhang

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

country: China

institute: Beijing Institute of Genomics

hyb_protocol: According to Illumina protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalisation with Beadstudio.

source_name: gastric tumor tissue

label_protocol: According to Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent, spectrophotometry (OD UV 260/280 ratio >1.8) and agarose gel electrophoresis.

tag: patient group

value: validation dataset patient


title: Gastric Tumor from patient No.68


title: Gastric Tumor from patient No.71


title: Parkinson's Disease serum (PD vs. AD) sample 1


title: Gastric Tumor from patient No.64


title: Alzheimer's Disease serum (PD vs. AD) sample 52


title: Gastric Tumor from patient No.63


title: Gastric Tumor from patient No.62


title: Gastric Tumor from patient No.67


title: Gastric Tumor from patient No.66


title: Gastric Tumor from patient No.70


title: Gastric Tumor from patient No.65


title: 1-WT_RD1a


title: Alzheimer's Disease serum (PD vs. AD) sample 51


title: Alzheimer's Disease serum (PD vs. AD) sample 49


title: hap43Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 6

city: San Francisco

first: Changbin

state: California

address: HSE450, 513 Parnassus Avenue

department: Department of Microbiology & Immunology

institute: University of California, San Francisco

description: Biological replicate 6 of 6. Low iron, Wt vs hap43DD

hyb_protocol: Fluorescently labeled cDNAs from mutants were directly hybridized against those from wild type grown under the same conditions; dye flip controls were included.  6 additional arrays were performed using wild type grown under iron-replete vs. iron-limiting conditions. cDNA was labeled with Cy3 and Cy5 (Amersham), and 0.5 μg of each channel was hybridized to custom Agilent C. albicans ORF arrays (15,000 spots/array, 70-mer probes) following a protocol described by Hernday et al. (Methods Enzymol. 2010;470:737-58)

scan_protocol: Arrays were scanned using a Genepix 4000A Axon scanner, and spots were filtered using GenePix Pro software.

data_processing: Data were normalized using Goulphar (LOWESS normalization) and subjected to One-class Significance Analysis of Microarrays (SAM) analysis with a median false discovery rate of 0.1%. Candidates meeting SAM criteria were also required to exhibit median 2-fold changes among 5-6 experiments.

organism: Candida albicans

source_name: Wild type grown in YEPD+BPS (low iron)

label_protocol: 10 μg of each RNA was treated with DNase I (Turbo DNA-free kit, Ambion) and reverse transcribed using aminoallyl-dUTP and Superscript II (Invitrogen) according to manufacturers’ instructions.  cDNA was labeled with Cy3 and Cy5 (Amersham)

growth_protocol: Saturated overnight cultures of sef1Δ (SN330), hap43Δ (SN694), sfu1Δ (SN515), and isogenic wild type C. albicans (SN250) were inoculated into YPD to OD600=10-4 and incubated with shaking at 30ºC.  The next morning, logarithmically growing cells were diluted to OD600 0.01 in iron-replete (wild type and sfu1Δ) or low iron (wild type, sef1Δ, and hap43Δ) medium and incubated at 30°C for 5-6 hours before harvesting at OD600=0.5-0.6.  5-6 biological replicates were performed per strain per condition.

extract_protocol: Total RNA was prepared using a hot phenol method (Miller and Johnson, 2002).

tag: genotype/variation

value: wild type

source_name: hap43Δ grown in YEPD+BPS (low iron)


title: hap43Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 4

description: Biological replicate 4 of 6. Low iron, Wt vs hap43DD


title: Parkinson's Disease serum (PD vs. AD) sample 26

value: serum


title: hap43Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 5

description: Biological replicate 5 of 6. Low iron, Wt vs hap43DD


title: Alzheimer's Disease serum (PD vs. AD) sample 48


title: hap43Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 3

description: Biological replicate 3 of 6. Low iron, Wt vs hap43DD


title: Gastric Tumor from patient No.60


title: Alzheimer's Disease serum (PD vs. AD) sample 46


title: Alzheimer's Disease serum (PD vs. AD) sample 47


title: Gastric Tumor from patient No.59


title: Alzheimer's Disease serum (PD vs. AD) sample 38


title: Alzheimer's Disease serum (PD vs. AD) sample 39


title: Alzheimer's Disease serum (PD vs. AD) sample 45


title: hap43Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 1

description: Biological replicate 1 of 6. Low iron, Wt vs hap43DD


title: Alzheimer's Disease serum (PD vs. AD) sample 36


title: Alzheimer's Disease serum (PD vs. AD) sample 35


title: Alzheimer's Disease serum (PD vs. AD) sample 37


title: Gastric Tumor from patient No.57


title: Gastric Tumor from patient No.58


title: Gastric Tumor from patient No.54


title: Gastric Tumor from patient No.55


title: hap43Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 2

description: Biological replicate 2 of 6. Low iron, Wt vs hap43DD


title: Alzheimer's Disease serum (PD vs. AD) sample 33


title: Alzheimer's Disease serum (PD vs. AD) sample 34


title: Alzheimer's Disease serum (PD vs. AD) sample 30


title: sef1Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 5

description: Biological replicate 5 of 6. Low iron, Wt vs sef1DD

source_name: sef1Δ grown in YEPD+BPS (low iron)


title: sef1Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 4

description: Biological replicate 4 of 6. Low iron, Wt vs sef1DD


title: Alzheimer's Disease serum (PD vs. AD) sample 32


title: sef1Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 6

description: Biological replicate 6 of 6. Low iron, Wt vs sef1DD


title: Alzheimer's Disease serum (PD vs. AD) sample 29


title: sef1Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 2

description: Biological replicate 2 of 6. Low iron, Wt vs sef1DD


title: Alzheimer's Disease serum (PD vs. AD) sample 28


title: Alzheimer's Disease serum (PD vs. AD) sample 27


title: Alzheimer's Disease serum (PD vs. AD) sample 31


title: Gastric Tumor from patient No.56


title: Gastric Tumor from patient No.53


title: Gastric Tumor from patient No.52


title: Gastric Tumor from patient No.50


title: Gastric Tumor from patient No.51


title: Gastric Tumor from patient No.49


title: sef1Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 3

description: Biological replicate 3 of 6. Low iron, Wt vs sef1DD


title: sfu1Δ mutant vs Wild type, in YEPD high iron medium, replicate 5

description: Biological replicate 5 of 5. High iron, Wt vs sfu1DD

source_name: Wild type grown in YEPD (high iron)

source_name: sfu1Δ grown in YEPD (high iron)


title: sfu1Δ mutant vs Wild type, in YEPD high iron medium, replicate 4

description: Biological replicate 4 of 5. High iron, Wt vs sfu1DD


title: Gastric Tumor from patient No.47


title: sef1Δ mutant vs Wild type, in YEPD+BPS  low iron medium, replicate 1

description: Biological replicate 1 of 6. Low iron, Wt vs sef1DD


title: Alzheimer's Disease serum (PD vs. AD) sample 25


title: Parkinson's Disease serum (PD vs. AD) sample 12


title: sfu1Δ mutant vs Wild type, in YEPD high iron medium, replicate 2

description: Biological replicate 2 of 5. High iron, Wt vs sfu1DD


title: sfu1Δ mutant vs Wild type, in YEPD high iron medium, replicate 3

description: Biological replicate 3 of 5. High iron, Wt vs sfu1DD


title: Alzheimer's Disease serum (PD vs. AD) sample 26


title: Alzheimer's Disease serum (PD vs. AD) sample 24


title: Alzheimer's Disease serum (PD vs. AD) sample 21


title: Alzheimer's Disease serum (PD vs. AD) sample 23


title: Alzheimer's Disease serum (PD vs. AD) sample 22


title: Wild type YEPD vs BPS, replicate 5

description: Biological replicate 5 of 6. Wild type high iron vs. low iron


title: sfu1Δ mutant vs Wild type, in YEPD high iron medium, replicate 1

description: Biological replicate 1 of 5. High iron, Wt vs sfu1DD


title: Wild type YEPD vs BPS, replicate 4

description: Biological replicate 4 of 6. Wild type high iron vs. low iron


title: Gastric Tumor from patient No.44


title: Gastric Tumor from patient No.43


title: Alzheimer's Disease serum (PD vs. AD) sample 19


title: Gastric Tumor from patient No.46


title: Alzheimer's Disease serum (PD vs. AD) sample 18


title: Gastric Tumor from patient No.45


title: Alzheimer's Disease serum (PD vs. AD) sample 20


title: Wild type YEPS vs BPS, replicate 3

description: Biological replicate 3 of 6. Wild type high iron vs. low iron


title: Alzheimer's Disease serum (PD vs. AD) sample 54


title: Wild type YEPD vs BPS, replicate 2

description: Biological replicate 2 of 6. Wild type high iron vs. low iron


title: Wild type YEPD vs BPS, replicate 1

description: Biological replicate 1 of 6. Wild type high iron vs. low iron


title: Gastric Tumor from patient No.41


title: Gastric Tumor from patient No.42


title: Gastric Tumor from patient No.39

value: training dataset patient


title: Gastric Tumor from patient No.48


title: Alzheimer's Disease serum (PD vs. AD) sample 50

value: Male


title: Alzheimer's Disease serum (PD vs. AD) sample 40


title: Alzheimer's Disease serum (PD vs. AD) sample 53


title: Gastric Tumor from patient No.40


title: Alzheimer's Disease serum (PD vs. AD) sample 17


title: Alzheimer's Disease serum (PD vs. AD) sample 13

value: Female


title: Alzheimer's Disease serum (PD vs. AD) sample 16

value: Alzheimer's Disease


title: Gastric Tumor from patient No.69


title: Gastric Tumor from patient No.37


title: Gastric Tumor from patient No.35


title: Effector memory (TEM) cells from Donor#3 [exon-level]

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TEM
Donor#3 Tem_(HuGene-1_0-st-v1).CEL

hyb_protocol: Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
In all processing steps, samples were processed at the same time as a single batch. Raw data from the generated .CEL files were imported into Partek Genomincs Suite using the RMA method.
For exon-level analysis, exons differentially expressed between groups (i.e. genes subject of alternative splicing) were identified using Partek's Alternative Splicing ANOVA (p<0.05) supported by the Benjamini-Hochberg correction method for multiple comparisons allowing for a false discovery rate of <0.05.
For gene-level analyses, probeset level data were merged into gene-level datasets based on median probeset signal level.
Differentially expressed genes (DEGs) were identified by One-Way Repeated Measures ANOVA (p<0.01) corrected by Benjamini-Hochberg's False Discovery Rate method (p<0.05), resulting in a gene list of 900 DEGs. For pair wise comparisons between all possible sample pairs (e.g. TN vs. TSCM, etc), this gene list was further filtered for between-group alpha levels of p<0.01 and a fold change criterion of >2.0. By additional filtration of the 900 significant genes, a separate list of DEGs, displaying gradually changing expression levels along with the process of memory cell differentiation, i.e. in the TN -> TSCM -> TCM -> TEM direction, direction, was also identified. Finally, a limited list of common DEGs significant when comparing T naive CD95+ cells with all three other T cell populations individually was also described using slightly modified selection criteria; One-Way Repeated Measures ANOVA (p<0.05) corrected by Benjamini-Hochberg's False Discovery Rate method (p<0.05).
Exon-level analysis_probe group file: HuGene-1_0-st-v1.r4.pgf
Transcript-level analysis_meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: CD8+ T cells

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from lymphocyte-enriched apheresis blood (provided by the NIH Blood Bank) according to standard techniques and used immediately for cell sorting. CD8+ T cells were enriched from PBMC by using the EasySep CD8+ T cell enrichment kit (Stem Cell Technologies), stained with different combinations of fluorescent-labeled monoclonal antibodies and sorted with a FACSAria (BD Biosciences) in different live (Live/Dead-; Invitrogen) CD8+ T cell subsets, as follows: TN (CD45RO-, CD45RA+, CCR7+, CD27+, CD62L+, CD11a dull, CD95-), TSCM (CD45RO-, CD45RA+, CCR7+, CD27+, CD62L+, CD11a dull, CD95+), TCM (CD45RO+, CD62L+, CCR7+) and TEM (CD45RO+, CD62L-, CCR7-), generating 12 samples total.

extract_protocol: RNEasy Micro kit (Qiagen), following manufatcturer's instructions

tag: cell type

value: CD8+ T cells

tag: cd8+ t cell subset

value: TEM

tag: donor


title: Gastric Tumor from patient No.32


title: Naïve (TN) cells from Donor#3 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TN
Donor#3 Tn_(HuGene-1_0-st-v1).CEL

value: TN


title: Gastric Tumor from patient No.38


title: Alzheimer's Disease serum (PD vs. AD) sample 14


title: Alzheimer's Disease serum (PD vs. AD) sample 15


title: Gastric Tumor from patient No.31


title: Gastric Tumor from patient No.36


title: Naïve (TN) cells from Donor#2 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TN
Donor#2 Tn_(HuGene-1_0-st-v1).CEL


title: Stem cell memory (TSCM) cells from Donor#3 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TSCM
Donor#3 Tcd95_(HuGene-1_0-st-v1).CEL

value: TSCM


title: Gastric Tumor from patient No.33


title: Central memory (TCM) cells from Donor#2 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TCM
Donor#2 Tcm_(HuGene-1_0-st-v1).CEL

value: TCM


title: Alzheimer's Disease serum (PD vs. AD) sample 12


title: Central memory (TCM) cells from Donor#3 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TCM
Donor#3 Tcm_(HuGene-1_0-st-v1).CEL


title: Alzheimer's Disease serum (PD vs. AD) sample 11


title: Hap43myc_L_ChIP1

type: genomic

description: Genomic wide Hap43 enrichment

hyb_protocol: 10 independent hybridization experiments were performed on 4 biological replicates of the untagged control and 2 biological replicates each of Sef1-Myc, Sfu1-Myc, and Hap43-Myc.  Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

data_processing: Agilent Chip Analytics software v1.2 (Agilent Technologies) was used for initial data normalization and analysis (Tuch et al., 2008), followed by visualization and additional analysis using MochiView v.1.39 (http://johnsonlab.ucsf.edu/).   High confidence regulatory events were associated with Agilent segment p-values of ≥ 4 (-log10 p-value based on the enrichment statistic for each probe in the region) and minimum 2-fold (Sef1-Myc and Hap43-Myc) or 1.5-fold (Sfu1-Myc) enrichment in both biological replicates of the epitope-tagged strains (Table S2).  Genes with enrichment peaks in untagged controls were excluded.

molecule: genomic DNA

source_name: Myc ChIP DNA from myc-tagged Hap43 strain in low iron

label_protocol: IP genomic DNA samples were labeled with Cy5 and input genomic DNA samples were labeled with Cy3. Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58)

growth_protocol: Saturated cultures of Sfu1-Myc (SN646) was inoculated into iron depleted (YEPD+BPS) liquid medium to OD600=0.05.  Cultures were incubated with shaking at 30°C until OD600 0.4.

extract_protocol: Saturated cultures of untagged wild type C. albicans (SN250), Sef1-Myc (SN423), Hap43-Myc (SN840), and Sfu1-Myc (SN646) were inoculated into low iron (untagged, Sef1-Myc, Hap43-Myc) or iron replete (untagged, Sfu1-Myc) liquid medium to OD600=0.05.  Cultures were incubated with shaking at 30°C until OD600 0.4, when formaldehyde was added to 1% final (with shaking, room temperature, 15 minutes), followed by glycine to 125mM final (with shaking, room temperature, 5 minutes).  Cells were collected by centrifugation at 4°C and washed twice with 20 mM Tris-HCl pH 7.5/150 mM NaCl, followed by freezing in liquid N2 and storage at -80°C.  Cell lysis, DNA shearing, and ChIP-Chip were performed as described (Nobile et al., 2009).

treatment_protocol: Cells were fixed, lysed, immunoprecipitated with anti-Myc antibody and genomic DNAs were sheared by sonication

value: myc-tagged Hap43 strain

tag: chip antibody

value: Anti-c-Myc 9E10

tag: antibody vendor, cat. number

value: COVANCE (MMS-150R)

source_name: Input DNA from myc-tagged Hap43 in low iron


title: Stem cell memory (TSCM) cells from Donor#2 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TSCM
Donor#2 Tcd95_(HuGene-1_0-st-v1).CEL


title: Effector memory (TEM) cells from Donor#2 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TEM
Donor#2 Tem_(HuGene-1_0-st-v1).CEL


title: Gastric Tumor from patient No.30


title: Gastric Tumor from patient No.29


title: Hap43myc_L_ChIP2

description: Genomic wide Hap43 enrichment


title: Alzheimer's Disease serum (PD vs. AD) sample 8

tag: age


title: Naïve (TN) cells from Donor#1 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TN
Donor#1 Tn_(HuGene-1_0-st-v1).CEL


title: Gastric Tumor from patient No.28


title: Alzheimer's Disease serum (PD vs. AD) sample 9

tag: gender


title: Effector memory (TEM) cells from Donor#1 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TEM
Donor#1 Tem_(HuGene-1_0-st-v1).CEL


title: Alzheimer's Disease serum (PD vs. AD) sample 10

tag: mini mental state exam (mmse) score


title: Alzheimer's Disease serum (PD vs. AD) sample 6

tag: sample type


title: Alzheimer's Disease serum (PD vs. AD) sample 7

tag: disease state


title: Sef1myc_L_ChIP2

description: Genomic wide Sef1 enrichment

source_name: Myc ChIP DNA from myc-tagged Sef1 strain in low iron

growth_protocol: Saturated cultures of Sef1-Myc (SN423) was inoculated into iron depleted (YEPD+BPS) liquid medium to OD600=0.05.  Cultures were incubated with shaking at 30°C until OD600 0.4.

tag: strain

value: myc-tagged Sef1 strain

source_name: Input DNA from myc-tagged Sef1 in low iron


title: Gastric Tumor from patient No.26


title: Sfu1myc_H_ChIP1

description: Genomic wide Sfu1 enrichment

source_name: Myc ChIP DNA from myc-tagged Sfu1 strain in high iron

growth_protocol: Saturated cultures of Sfu1-Myc (SN646) was inoculated into iron replete (YEPD) liquid medium to OD600=0.05.  Cultures were incubated with shaking at 30°C until OD600 0.4.

value: myc-tagged Sfu1 strain

source_name: Input DNA from myc-tagged Sfu1 in high iron


title: Sef1myc_L_ChIP1

description: Genomic wide Sef1 enrichment


title: Alzheimer's Disease serum (PD vs. AD) sample 5

value: UNK


title: Sfu1myc_H_ChIP2

description: Genomic wide Sfu1 enrichment


title: 016592

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description:
Patient Pec after Adalimumab treatment  vs Patient Pec before Adalimumab treatment
Date:2006/08/18

hyb_protocol: Agilent : 3000.0 ng at 60 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: standard Lowess normalization method with selection of spots presenting a signal > 3SNR

source_name: Patient Pec after Adalimumab treatment

label_protocol: Fluorescent probes were synthesized by chemical coupling of 5µgaminoallyl aRNA with cyanine 3 (Cy3) or Cy5 dyes and purified using Rneasy Mini Kit (Qiagen)

extract_protocol: Trizol

value: Patient Pec after Adalimumab treatment

value: Pec

tag: Tissue

value: mononuclear blood cells

source_name: Patient Pec before Adalimumab treatment

value: Patient Pec before Adalimumab treatment


title: Untagged Wt_L_ChIP3

description: Control for background

source_name: Myc ChIP DNA from untagged WT in low iron

growth_protocol: Saturated cultures of untagged wild type C. albicans (SN250) was inoculated into iron depleted (YEPD+BPS) liquid medium to OD600=0.05.  Cultures were incubated with shaking at 30°C until OD600 0.4.

value: wild type

source_name: Input DNA from untagged WT in low iron


title: 016593

description:
Patient Pon after Adalimumab treatment vs Patient Pon before Adalimumab treatment
Date:2006/08/18

source_name: Patient Pon after Adalimumab treatment

value: Patient Pon after Adalimumab treatment

value: Pon

source_name: Patient Pon before Adalimumab treatment

value: Patient Pon before Adalimumab treatment


title: Gastric Tumor from patient No.23

source_name: gastric tumor tissue

value: training dataset patient


title: Gastric Tumor from patient No.25


title: Central memory (TCM) cells from Donor#1 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TCM
Donor#1 Tcm_(HuGene-1_0-st-v1).CEL

value: CD8+ T cells


title: 016556

description:
Patient Bat after Adalimumab treatment  vs Patient Bat before Adalimumab treatment
Date:2006/08/31

source_name: Patient Bat after Adalimumab treatment

value: Patient Bat after Adalimumab treatment

value: Bat

source_name: Patient Bat before Adalimumab treatment

value: Patient Bat before Adalimumab treatment


title: Gastric Tumor from patient No.27


title: Gastric Tumor from patient No.24


title: Stem cell memory (TSCM) cells from Donor#1 [exon-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TSCM
Donor#1 Tcd95_(HuGene-1_0-st-v1).CEL

value: TSCM


title: Untagged Wt_L_ChIP2

description: Control for background

value: Anti-c-Myc 9E10

value: COVANCE (MMS-150R)


title: 016557

description:
Patient Sal after Etanercept treatment  vs Patient Sal before Etanercept treatment
Date:2006/08/31

source_name: Patient Sal after Etanercept treatment

value: Patient Sal after Etanercept treatment

value: Sal

source_name: Patient Sal before Etanercept treatment

value: Patient Sal before Etanercept treatment


title: Gastric Tumor from patient No.34


title: Untagged Wt_L_ChIP1

description: Control for background


title: Alzheimer's Disease serum (PD vs. AD) sample 4

value: Female

value: serum

value: Alzheimer's Disease


title: Untagged Wt_H_ChIP1

description: Control for background

source_name: Myc ChIP DNA from untagged WT in high iron

growth_protocol: Saturated cultures of untagged wild type C. albicans (SN250) was inoculated into iron replete (YEPD) liquid medium to OD600=0.05.  Cultures were incubated with shaking at 30°C until OD600 0.4.

value: wild type

source_name: Input DNA from untagged WT in high iron


title: Alzheimer's Disease serum (PD vs. AD) sample 1

value: UNK


title: Alzheimer's Disease serum (PD vs. AD) sample 2


title: 016558

description:
Patient Cal after Etanercept treatment  vs Patient Cal before Etanercept treatment
Date:2006/08/31

source_name: Patient Cal after Etanercept treatment

value: Patient Cal after Etanercept treatment

value: Cal

value: mononuclear blood cells

source_name: Patient Cal before Etanercept treatment

value: Patient Cal before Etanercept treatment


title: Alzheimer's Disease serum (PD vs. AD) sample 3

value: Male


title: 016469

description:
Patient Cov after Adalimumab treatment  vs Patient Cov before Adalimumab treatment
Date:2006/07/21

source_name: Patient Cov after Adalimumab treatment

value: Patient Cov after Adalimumab treatment

value: Cov

source_name: Patient Cov before Adalimumab treatment

value: Patient Cov before Adalimumab treatment


title: Gastric Tumor from patient No.21

value: training dataset patient


title: Gastric Tumor from patient No.22


title: Gastric Tumor from patient No.20


title: CMY_VPA_1mM_48h

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

description:
SO2005012013.CEL
Gene expression data from VPA-treated CMY cells

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to HG133A chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing:
The raw CEL files were imported into dChip and normalized with dChip.
After normalization, the model-based expression values were calculated by dChip and exported.

source_name: CMY cell line, VPA-treatment with 1mM, 48h

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

growth_protocol: CMY and CMK cells were grown in RPMI +10%FCS +1%P/S

extract_protocol: Trizol extraction of total RNA followed by cleaning up using columns from the Promega SV total RNA isolation kit.

treatment_protocol: CMY and CMK cells were treated with 1mM and 2mM VPA for 24h or 48h. Untreated cells were seeded at the same density and used as a control at the same timepoints.

value: Down Syndrome megakaryoblastic leukemia cell line

tag: treatment

value: treated with 1mM VPA for 48h


title: Gastric Tumor from patient No.18


title: 016591

description:
Patient Cer after Etanercept treatment  vs Patient Cer before Etanercept treatment
Date:2006/08/18

source_name: Patient Cer after Etanercept treatment

value: Patient Cer after Etanercept treatment

value: Cer

source_name: Patient Cer before Etanercept treatment

value: Patient Cer before Etanercept treatment


title: 016590

description:
Patient Alb after Etanercept treatment  vs Patient Alb before Etanercept treatment
Date:2006/08/18

source_name: Patient Alb after Etanercept treatment

value: Patient Alb after Etanercept treatment

value: Alb

source_name: Patient Alb before Etanercept treatment

value: Patient Alb before Etanercept treatment


title: CMK_VPA_2mM_24h

description:
SO2005012003.CEL
Gene expression data from VPA-treated CMK cells

source_name: CMK cell line, VPA-treatment with 2mM, 24h

value: treated with 2mM VPA for 24h


title: CMY_VPA_2mM_24h

description:
SO2005012006.CEL
Gene expression data from VPA-treated CMY cells

source_name: CMY cell line, VPA-treatment with 2mM, 24h


title: CMK_VPA_1mM_48h

description:
SO2005012011.CEL
Gene expression data from VPA-treated CMK cells


title: Gastric Tumor from patient No.19

source_name: gastric tumor tissue


title: CMY_VPA_1mM_24h

description:
SO2005012005.CEL
Gene expression data from VPA-treated CMY cells

source_name: CMY cell line, VPA-treatment with 1mM, 24h

value: treated with 1mM VPA for 24h


title: CMY_non-treated_control_48h

description:
SO2005012012.CEL
Gene expression data from non-treated CMY cells

source_name: CMY cell line, non-treated control, 48h

value: non-treated control, 48h


title: CMY_non-treated_control_24h

description:
SO2005012004.CEL
Gene expression data from non-treated CMY cells

source_name: CMY cell line, non-treated control, 24h

value: non-treated control, 24h


title: Gastric Tumor from patient No.14


title: Gastric Tumor from patient No.61

value: validation dataset patient


title: Gastric Tumor from patient No.17


title: CMK_non-treated_control_48h

description:
SO2005012010.CEL
Gene expression data from non-treated CMK cells

source_name: CMK cell line, non-treated control, 48h


title: Gastric Tumor from patient No.16


title: CMK_non-treated_control_24h

description:
SO2005012001.CEL
Gene expression data from non-treated CMK cells

source_name: CMK cell line, non-treated control, 24h


title: CMK_VPA_1mM_24h

description:
SO2005012002.CEL
Gene expression data from VPA-treated CMK cells

source_name: CMK cell line, VPA-treatment with 1mM, 24h


title: Gastric Tumor from patient No.15


title: Gastric Tumor from patient No.13


title: Naïve (TN) cells from Donor#3 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TN
Donor#3 Tn_(HuGene-1_0-st-v1).CEL

source_name: CD8+ T cells

value: CD8+ T cells

value: TN


title: Effector memory (TEM) cells from Donor#3 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TEM
Donor#3 Tem_(HuGene-1_0-st-v1).CEL

value: TEM


title: Gastric Tumor from patient No.12

value: training dataset patient


title: LNCaP acH2AZ ChIP-Chip

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

description: LNCaP acH2AZ ChIP-Chip on promoter array

hyb_protocol: As per standard Affymetrix protocol for the Human Promoter 1.0R tiling arrays

data_processing:
All analysis was performed with UCSC hg18 version of the human genome. The model-based analysis of tiling array (MAT) algorithm (Johnson WE et al PNAS 2006) was used with a bandwidth of 600bp to generate the bar files.
Raw data (CEL files) and 600bp smoothed IP/Input data (bar files) are provided

source_name: Lncap azH2AZ ChIP DNA

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: Cells were grown at 37ºC with 5% CO2

extract_protocol:
ChIP assays were carried out according to the manufacturer’s protocol (Upstate Biotechnology).  Briefly, ~ 1 x 106 cells, in a 10 cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 g/ml aprotinin and 1g/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice.  The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs.  The complexes were immunoprecipitated with antibodies specific for Histone H3 (Abcam #ab1791), Histone H2A (Abcam #ab18255), Histone H2AZ (Abcam #ab4174) and acetylated Histone H2AZ (Abcam #ab18262).  Ten l of antibody was used for each immunoprecipitation.  No antibody controls were also included for each ChIP assay and no precipitation was observed by quantitative Real-Time PCR (qPCR) analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by either salmon sperm DNA/protein A agarose slurry or Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times.  The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 l H2O.
Immunoprecipitated and Input DNA from ChIP was amplified with 14 cycles of whole genome amplification (WGA2 kit, Sigma) according to manufacturers instructions.

tag: antibody

value: acetylated Histone H2AZ

tag: vendor

value: Abcam

tag: catalog #

tag: tissue

value: Prostate

tag: cell line

value: LNCaP

tag: growth medium

value: T-medium w/ 10% FCS

source_name: LNCaP Input Chromatin


title: LNCaP H2AZ ChIP-Chip

description: LNCaP H2AZ ChIP-Chip on promoter array

scan_protocol: As per standard Affymetrix protocol for the Human Promoter 1.0R tiling arrays

source_name: Lncap H2AZ ChIP DNA

value: Histone H2AZ


title: LNCaP H2A ChIP-Chip

description: LNCaP H2A ChIP-Chip on promoter array

source_name: Lncap H2A ChIP DNA

value: Histone H2A


title: Central memory (TCM) cells from Donor#3 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TCM
Donor#3 Tcm_(HuGene-1_0-st-v1).CEL

tag: cell type

tag: cd8+ t cell subset

value: TCM

tag: donor


title: Gastric Tumor from patient No.11

tag: patient group


title: Naïve (TN) cells from Donor#2 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TN
Donor#2 Tn_(HuGene-1_0-st-v1).CEL


title: Gastric Tumor from patient No.9


title: Effector memory (TEM) cells from Donor#2 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TEM
Donor#2 Tem_(HuGene-1_0-st-v1).CEL


title: LNCaP H3 ChIP-Chip

description: LNCaP H3 ChIP-Chip on promoter array

source_name: Lncap H3 ChIP DNA

value: Histone H3


title: Gastric Tumor from patient No.7


title: Gastric Tumor from patient No.6


title: Gastric Tumor from patient No.10


title: PrEC acH2AZ ChIP-Chip

description: PrEC acH2AZ ChIP-Chip on promoter array

source_name: PrEC azH2AZ ChIP DNA

value: Normal cells

value: PrEGM media (Cambrex)

source_name: PrEC Input Chromatin


title: Stem cell memory (TSCM) cells from Donor#2 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TSCM
Donor#2 Tcd95_(HuGene-1_0-st-v1).CEL

value: TSCM


title: Stem cell memory (TSCM) cells from Donor#3 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#3 TSCM
Donor#3 Tcd95_(HuGene-1_0-st-v1).CEL


title: Effector memory (TEM) cells from Donor#1 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TEM
Donor#1 Tem_(HuGene-1_0-st-v1).CEL


title: Gastric Tumor from patient No.4


title: Gastric Tumor from patient No.5


title: Gastric Tumor from patient No.3


title: PrEC H2A ChIP-Chip

description: PrEC H2A ChIP-Chip on promoter array

source_name: PrEC H2A ChIP DNA


title: Naïve (TN) cells from Donor#1 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TN
Donor#1 Tn_(HuGene-1_0-st-v1).CEL


title: Gastric Tumor from patient No.8


title: Central memory (TCM) cells from Donor#2 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#2 TCM
Donor#2 Tcm_(HuGene-1_0-st-v1).CEL


title: PrEC H2AZ ChIP-Chip

description: PrEC H2AZ ChIP-Chip on promoter array

source_name: PrEC H2AZ ChIP DNA


title: PrEC H3 ChIP-Chip

description: PrEC H3 ChIP-Chip on promoter array

source_name: PrEC H3 ChIP DNA


title: Central memory (TCM) cells from Donor#1 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TCM
Donor#1 Tcm_(HuGene-1_0-st-v1).CEL


title: Stem cell memory (TSCM) cells from Donor#1 [gene-level]

description:
FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TSCM
Donor#1 Tcd95_(HuGene-1_0-st-v1).CEL


title: Gastric Tumor from patient No.1

source_name: gastric tumor tissue


title: Gastric Tumor from patient No.2


title: Bsub_AH024_LPDM_T3_rep3

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: This sample is of Bacillus subtilis strain AH024 grown in LPDM and harvested during T3 growth phase. It is the third of three AH024 biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Probes without perfect and unique matches to the latest genomic sequence (GenBank accession AL009126.3) were removed. The remaining raw data were subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185), as implemented in the BioConductor software package, version 2.6 (Gentleman et al. Genome Biology 5:R80).

organism: Bacillus subtilis

source_name: Bacillus subtilis strain AH024, LPDM, T3 growth phase

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Bacillus subtilis wild-type cells and delta-phoPR cells were grown in high and low phosphate medium at 37°C to mid-log phase (OD600 of 0.25)
Bacillus subtilis wild-type cells and delta-phoPR cells were grown in low phosphate medium at 37°C till 3 hours of phosphate limitation

extract_protocol: Total RNA was extracted using phenol and chloroform extraction and ethanol precipitaion

tag: medium

value: LPDM

tag: growth phase

tag: date

tag: experimenter

value: P+D


title: Bsub_168_LPDM_T3_rep3

description: This sample is of Bacillus subtilis strain 168 grown in LPDM and harvested during T3 growth phase. It is the third of three 168 biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis strain 168, LPDM, T3 growth phase

tag: strain


title: Persistent injury #1 [HT_MG-430B]

status: Public on Jul 12 2011

city: Boston

first: Samir

last: Parikh

address: 330 Brookline Avenue, RN280C

institute: Beth Israel Deaconess Medical Center

description: SAMPLE 10_B file

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip HT_MG-430A 24 A and B Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip HT Array Plate Scanner

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

source_name: t=42, persistent injury

growth_protocol: Standard light-dark cycle and standard ad libitum diet prior to and during experiment

treatment_protocol: injection of LPS 10 mg/kg intraperitoneally at t=0hr followed by 0.9% saline 10 ml/kg injected intraperitoneally at t=18hr

tag: gender

value: male

tag: age

value: 8 week old

tag: agent

value: LPS

tag: timepoint (hrs)

value: whole kidney

tag: renal function

value: persistent renal injury


title: Persistent injury #2 [HT_MG-430B]

description: SAMPLE 11_B file

tag: tissue


title: Early injury #2 [HT_MG-430B]

description: SAMPLE 5_B file

source_name: t=18, renal injury

value: early renal injury


title: Renal recovery #2 [HT_MG-430B]

description: SAMPLE 8_B file

source_name: t=42, recovered

value: recovered renal function


title: Bsub_168_LPDM_exp_rep2

description: This sample is of Bacillus subtilis strain 168 grown in LPDM and harvested during exponential growth phase. It is the second of three 168 biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis strain 168, LPDM, exponential growth phase

value: exp


title: Bsub_AH024_LPDM_exp_rep3

description: This sample is of Bacillus subtilis strain AH024 grown in LPDM and harvested during exponential growth phase. It is the third of three AH024 biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis strain AH024, LPDM, exponential growth phase


title: Baseline #1 [HT_MG-430B]

description: SAMPLE 1_B file

source_name: t=0, nl function

value: normal baseline renal function


title: Early Injury #1 [HT_MG-430B]

description: SAMPLE 4_B file


title: Bsub_AH024_HPDM_exp_rep3

description: This sample is of Bacillus subtilis strain AH024 grown in HPDM and harvested during exponential growth phase. It is the third of three AH024 biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis strain AH024, HPDM, exponential growth phase

value: HPDM


title: Baseline #2 [HT_MG-430B]

description: SAMPLE 2_B file


title: Baseline #3 [HT_MG-430B]

description: SAMPLE 3_B file


title: Bsub_AH024_HPDM_exp_rep1

description: This sample is of Bacillus subtilis strain AH024 grown in HPDM and harvested during exponential growth phase. It is the first of three AH024 biological replicates used in this experiment, each from separate cultures.

value: E+A


title: ALL_NDS_N59

city: Houston

first: Hon-chiu

middle: Eastwood

last: Leung

state: TX

address: 1102 Bates Street  Room C1030.09

department: Pediatrics

institute: Baylor College of Medicine

hyb_protocol: Processed DNA samples were heated at 95oC for 20 min. Upon cooling, the samples were loaded onto methylation27 chips and allowed to hybridize in RA1 buffer in a 48oC incubation oven for 16 hours. After overnight hybridization, the chips were washed and stained with XC1 to XC3 and coated with XC4.

scan_protocol: Beadarray scanner software was used and the chips were scanned using the Beadarray scanner 500GX. All parameters were in default setting.

data_processing:
IDAT files were imported into GenomeStudio software version 2009.1. Methylation modules generate the compiled project and gave out average beta value and detection p-value as output.
Average beta value is defined as the ratio of signal from a methylated probe (C not converted to T) relative to the sum of both methylated (C not converted to T) and unmethylated probes (C bisulfite-converted to T) (β value=C/[(T+C)+100]

label: Cy3 and Cy5

source_name: ALL, Non-Down syndrome

label_protocol: 500 ng of genomic DNA was bisulfite converted using the EZ-DNA methylation kit from Zymo Research. 170 ng of freshly bisulfite converted DNA was used to go through denaturation, amplification, fragmentation, and precipitation. Methylated cytidine is labeled with biotinylated guanidine whilst unmethylated cytidine becomes thymidine and is labeled with dinitrophenyl-adenine. Streptavidin-Cy3 and antiDNP-Cy5 are used to fluorescent-tag the target probes.

growth_protocol: Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with B-precursor acute lymphoblastic leukemia at diagnosis and for selected patients at a second timepoint when they were in remission

extract_protocol: Extraction of genomic DNA from Ficoll-enriched cryopreserved bone marrow samples was performed using the Allprep DNA/RNA minikit (Qiagen, Valencia, CA).

treatment_protocol: No additional treatments were performed prior to extract preparation.

value: bone marrow

value: F

tag: disease status

value: Non-Down syndrome B-precursor ALL

tag: paired sample

value: No


title: NDS_N9

source_name: remission bone marrow, Non-Down syndrome

value: UNKNOWN

value: Yes, Pair E


title: ALL_NDS_N57

value: Yes, Pair B


title: NDS_N58

value: remission bone marrow, Non-Down syndrome


title: Early injury #3 [HT_MG-430B]

description: SAMPLE 6_B file

value: male

value: 8 week old

value: LPS


title: Bsub_AH024_LPDM_T3_rep2

description: This sample is of Bacillus subtilis strain AH024 grown in LPDM and harvested during T3 growth phase. It is the second of three AH024 biological replicates used in this experiment, each from separate cultures.

value: LPDM

value: P+D


title: ALL_NDS_N23


title: Bsub_AH024_HPDM_exp_rep2

description: This sample is of Bacillus subtilis strain AH024 grown in HPDM and harvested during exponential growth phase. It is the second of three AH024 biological replicates used in this experiment, each from separate cultures.

value: exp


title: ALL_NDS_N27


title: Bsub_168_LPDM_T3_rep1

description: This sample is of Bacillus subtilis strain 168 grown in LPDM and harvested during T3 growth phase. It is the first of three 168 biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_HPDM_exp_rep3

description: This sample is of Bacillus subtilis strain 168 grown in HPDM and harvested during exponential growth phase. It is the third of three 168 biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis strain 168, HPDM, exponential growth phase


title: Bsub_168_LPDM_exp_rep3

description: This sample is of Bacillus subtilis strain 168 grown in LPDM and harvested during exponential growth phase. It is the third of three 168 biological replicates used in this experiment, each from separate cultures.


title: Bsub_168_LPDM_T3_rep2

description: This sample is of Bacillus subtilis strain 168 grown in LPDM and harvested during T3 growth phase. It is the second of three 168 biological replicates used in this experiment, each from separate cultures.


title: ALL_NDS_N10


title: Persistent injury #3 [HT_MG-430B]

description: SAMPLE 12_B file

value: whole kidney

value: persistent renal injury


title: Bsub_168_HPDM_exp_rep1

description: This sample is of Bacillus subtilis strain 168 grown in HPDM and harvested during exponential growth phase. It is the first of three 168 biological replicates used in this experiment, each from separate cultures.

value: HPDM


title: ALL_NDS_N1

value: bone marrow

value: M

value: Yes, Pair A


title: Renal recovery #1 [HT_MG-430B]

description: SAMPLE 7_B file

value: recovered renal function


title: DS_D27

source_name: remission bone marrow, Down syndrome

value: F

value: remission bone marrow, Down syndrome

value: Yes, Pair D


title: NDS_N2

value: remission bone marrow, Non-Down syndrome


title: ALL_DS_D26

source_name: ALL, Down syndrome

value: Down syndrome B-precursor ALL


title: ALL_DS_D45

value: No


title: Bsub_168_LPDM_exp_rep1

description: This sample is of Bacillus subtilis strain 168 grown in LPDM and harvested during exponential growth phase. It is the first of three 168 biological replicates used in this experiment, each from separate cultures.

value: E+A


title: Bsub_168_HPDM_exp_rep2

description: This sample is of Bacillus subtilis strain 168 grown in HPDM and harvested during exponential growth phase. It is the second of three 168 biological replicates used in this experiment, each from separate cultures.


title: ALL_DS_D13


title: Bsub_AH024_LPDM_T3_rep1

description: This sample is of Bacillus subtilis strain AH024 grown in LPDM and harvested during T3 growth phase. It is the first of three AH024 biological replicates used in this experiment, each from separate cultures.

value: LPDM


title: Bsub_AH024_LPDM_exp_rep2

description: This sample is of Bacillus subtilis strain AH024 grown in LPDM and harvested during exponential growth phase. It is the second of three AH024 biological replicates used in this experiment, each from separate cultures.


title: ALL_DS_D23


title: ALL_DS_506


title: ALL_DS_459


title: ALL_DS_542


title: ALL_DS_D17

value: Yes, Pair C


title: ALL_NDS_655

value: Non-Down syndrome B-precursor ALL


title: ALL_DS_381


title: Bsub_AH024_LPDM_exp_rep1

description: This sample is of Bacillus subtilis strain AH024 grown in LPDM and harvested during exponential growth phase. It is the first of three AH024 biological replicates used in this experiment, each from separate cultures.

value: exp

value: P+D


title: ALL_DS_92


title: ALL_DS_177


title: Renal recovery #3 [HT_MG-430B]

description: SAMPLE 9_B file

value: male

value: 8 week old

value: LPS

value: whole kidney


title: DS_D18

value: bone marrow

value: M


title: NDS ALL (4286608260_B)

description: Genomic DNA extracted from bone marrow was genotyped using the Infinium Human 3700Duo BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader 500GX (Illumina). The BeadScan Program was used to control the reader. All settings were set at default values.

data_processing: Genomic DNA extracted from bone marrow was genotyped using Infinium Human370-Duo Genotyping BeadChips (Illumina). The scanned files of the samples were loaded into GenomeStudio software 2009v1. Text files were generated using the standard report setting.

source_name: ALL, Non-Down Syndrome

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

growth_protocol: Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with B-precursor acute lymphoblastic leukemia and control patients without leukemia.

tag: raw data

tag: raw file sample id

value: ALL, Non-Down Syndrome


title: NDS ALL (4286608262_A)

value: female


title: NDS ALL (4281807491_A)


title: NDS ALL (4281807488_A)


title: NDS ALL (4286608035_B)


title: NDS ALL (4281807491_B)


title: NDS ALL (4286608035_A)


title: NDS ALL (4281807422_B)


title: NDS ALL (4286608260_A)


title: NDS ALL (4281807368_B)


title: NDS ALL (4286608048_B)


title: NDS ALL (4281807488_B)


title: NDS ALL (4281807465_B)


title: NDS ALL (4281807379_B)


title: NDS ALL (4281807370_B)


title: NDS ALL (4281807260_B)


title: NDS ALL (4281807378_A)


title: NDS ALL (4281807422_A)


title: NDS ALL (4281807342_B)


title: NDS ALL (4286608048_A)


title: NDS ALL (4281807377_B)


title: NDS ALL (4281807378_B)


title: NDS ALL (4281807415_A)


title: NDS ALL (4281807370_A)


title: NDS ALL (4281807342_A)


title: NDS ALL (4281807259_B)


title: NDS ALL (4281807377_A)


title: NDS ALL (4281807260_A)


title: NDS ALL (4281807379_A)


title: NDS ALL (4281807368_A)


title: NDS ALL (4281807254_B)


title: NDS ALL (4281807254_A)


title: NDS ALL (4281807259_A)


title: NDS (4281807793_A)

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from bone marrow was genotyped using Infinium Human370-Duo Genotyping BeadChips (Illumina). GenomeStudio v2009.1, the Genotyping Module v1.0 by Illumina Inc was used with no normalization and the following processing steps: 1) Gen Call Threshold = 0.15, 2) Import cluster from the cluster file: HumanCNV370v1_C.egt

source_name: normal, non-Downs Syndrome

value: Male

value: normal, non-Downs Syndrome


title: NDS (4281807167_A)


title: NDS (4281807875_A)

value: Female


title: NDS ALL (4281807793_B)


title: NDS (4281807626_B)


title: DS (4281807141_B)

source_name: normal, Down Syndrome

value: normal, Down Syndrome


title: NDS ALL (4281807792_A)


title: NDS ALL (4281807875_B)