title: Adults B-cell ALL Bone marrow, sample 193

source_name: Bone marrow cells (test)

value: PETHEMA LAL-AR/2011

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Adults B-cell ALL Peripheral blood, sample 200

status: Public on May 03 2016

type: genomic

city: Salamanca

first: Jesús

middle: Maria

last: Hernández-Rivas

state: Salamanca

address: Paseo San Vicente, 88-182

department: Hematology

country: Spain

institute: Hospital Universitario de Salamanca, Universidad de Salamanca-CSIC

hyb_protocol: Hybridization was performed according to the instructions in the NimbleGen Array User Guide

scan_protocol: Scanning was performed according to the instructions in the NimbleGen Array User Guide

data_processing: Arrays were processed using Nimblegen's standard protocol and segmented using the CGHweb tool.

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood cells (test)

label_protocol: Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA)

extract_protocol: The genomic DNA was extracted from frozen bone marrow or fixed peripheral blood cell samples with QIAmp DNA Mini Kit (Qiagen,  16 Valencia, CA, USA) following the manufacturer’s instructions

tag: cell type

value: Peripheral blood cells

tag: gender

value: Female

tag: disease state

value: B-cell acute lymphoblastic leukemia

tag: age group

value: Adults ≥18 years

tag: genetic subtype

value: Normal

tag: treatment

value: PETHEMA LAL-AR/2003

source_name: control

value: Not applicable

tag: reference composition


title: Adults B-cell ALL Peripheral blood, sample 190

value: Male

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Adults B-cell ALL Peripheral blood, sample 196


title: Adults B-cell ALL Bone marrow, sample 203

value: Bone marrow cells


title: Normal Control Donor serum sample 39

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

country: USA

institute: UMDNJ-SOM

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters, PMT of 600, and a pixel size of 5um.

data_processing:
The GPR files were imported into Invitrogen's Prospector v5.2.1 microarray analysis software.  Individual serum results were linearly normalized via internal reference features into diagnostically appropriate disease or control groups  using the "Group Characterization" function.  Group characterized samples were then compared to identify the differential expression of autoantibodies using the "Two Groups Comparison" feature.   More information about this process, and the exact differentiating power being addressed with each comparison, can be found in the accompanying manuscript.  Selected biomarker potential, power, and efficacy was further evaluated using Random Forest (RF) Training and Testing Set analysis and decision-tree logic.
Normalized fluorescence intensities are presented in Relative Fluorescent Units (RFUs).
The RFU values for individual proteins in a sample.  These values are reported for every sample used in any comparison and are subject to a degree of normalized variation depending on group characterization and the exact diagnostic comparison rendered.

label: Alexa Fluor 647

molecule: other

source_name: Normal Control Donor serum sample 39

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

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

tag: age


title: Adults B-cell ALL Bone marrow, sample 192


title: Adults B-cell ALL Bone marrow, sample 204

value: UNKN


title: Adults B-cell ALL Bone marrow, sample 197


title: Normal Control Donor serum sample 41

source_name: Normal Control Donor serum sample 41


title: Adults B-cell ALL Bone marrow, sample 205

value: PETHEMA LAL-AR/93


title: Normal Control Donor serum sample 40

source_name: Normal Control Donor serum sample 40


title: Adults B-cell ALL Bone marrow, sample 194


title: Normal Control Donor serum sample 37

source_name: Normal Control Donor serum sample 37


title: Adults B-cell ALL Bone marrow, sample 189


title: Adults B-cell ALL Bone marrow, sample 191

value: FLAG-IDA


title: Normal Control Donor serum sample 36

source_name: Normal Control Donor serum sample 36

value: MALE


title: Normal Control Donor serum sample 34

source_name: Normal Control Donor serum sample 34


title: Normal Control Donor serum sample 35

source_name: Normal Control Donor serum sample 35

value: FEMALE


title: Normal Control Donor serum sample 38

source_name: Normal Control Donor serum sample 38


title: Adults B-cell ALL Bone marrow, sample 186

value: PETHEMA LAL-RI/2008


title: Children T-cell ALL Peripheral blood, sample 216

value: T-cell acute lymphoblastic leukemia

value: Children <18 years


title: Adults B-cell ALL Bone marrow, sample 178

value: Female

value: Others

value: PETHEMA LAL-AR/2011

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Normal Control Donor serum sample 33

source_name: Normal Control Donor serum sample 33


title: Adults B-cell ALL Bone marrow, sample 181

value: B-cell acute lymphoblastic leukemia

value: Adults ≥18 years

value: No therapy


title: Adults B-cell ALL Bone marrow, sample 188

value: Male

value: Normal

value: Not applicable

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 183

value: Bone marrow cells

value: NHL 2002 GMALL


title: Adults B-cell ALL Bone marrow, sample 180

value: PETHEMA LAL-AR/2003


title: Adults B-cell ALL Bone marrow, sample 179

value: PETHEMA LAL-AR/93


title: Adults B-cell ALL Bone marrow, sample 187

value: UNKN


title: Adults B-cell ALL Bone marrow, sample 184


title: Normal Control Donor serum sample 31

source_name: Normal Control Donor serum sample 31

value: FEMALE


title: Adults B-cell ALL Bone marrow, sample 176

value: Female


title: Normal Control Donor serum sample 32

source_name: Normal Control Donor serum sample 32


title: Normal Control Donor serum sample 30

source_name: Normal Control Donor serum sample 30

value: MALE


title: Adults B-cell ALL Bone marrow, sample 177

value: Others

value: ALL Adult protocol-Adaptation of GMALL05/93 protocol


title: Adults B-cell ALL Bone marrow, sample 172

value: B-cell acute lymphoblastic leukemia

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Normal Control Donor serum sample 29

source_name: Normal Control Donor serum sample 29


title: Adults B-cell ALL Bone marrow, sample 173

value: Adults ≥18 years


title: Adults B-cell ALL Bone marrow, sample 170

value: Male

value: Hyper (>50)


title: Adults B-cell ALL Bone marrow, sample 175

value: PETHEMA LAL-RI/96

value: Not applicable


title: Adults B-cell ALL Bone marrow, sample 174

value: Bone marrow cells

value: PETHEMA LAL-AR 2011


title: Adults B-cell ALL Bone marrow, sample 169

value: PETHEMA Burkimab-08


title: Normal Control Donor serum sample 28

source_name: Normal Control Donor serum sample 28


title: Adults B-cell ALL Bone marrow, sample 166

source_name: Bone marrow cells (test)

value: PETHEMA LAL-RI/2008

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 167

value: UNKN


title: Adults B-cell ALL Bone marrow, sample 164

value: Female


title: Normal Control Donor serum sample 26

source_name: Normal Control Donor serum sample 26

value: MALE


title: Adults B-cell ALL Bone marrow, sample 171

source_name: control


title: Adults B-cell ALL Bone marrow, sample 165

value: PETHEMA LAL/89


title: Normal Control Donor serum sample 25

source_name: Normal Control Donor serum sample 25


title: Normal Control Donor serum sample 24

source_name: Normal Control Donor serum sample 24


title: Normal Control Donor serum sample 23

source_name: Normal Control Donor serum sample 23


title: Normal Control Donor serum sample 22

source_name: Normal Control Donor serum sample 22


title: Adults B-cell ALL Bone marrow, sample 161


title: Adults B-cell ALL Bone marrow, sample 160

value: PETHEMA LAL-IR/2011


title: Adults B-cell ALL Bone marrow, sample 158

value: B-cell acute lymphoblastic leukemia

value: PETHEMA LAL-07OLD


title: Adults B-cell ALL Bone marrow, sample 163

value: Adults ≥18 years

value: PETHEMA LAL-AR/93


title: Adults B-cell ALL Bone marrow, sample 156

value: Male

value: PETHEMA LAL-AR/2003


title: Normal Control Donor serum sample 20

source_name: Normal Control Donor serum sample 20

value: FEMALE


title: Adults B-cell ALL Bone marrow, sample 154

value: Bone marrow cells

value: Not applicable

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 144

value: No therapy


title: Adults B-cell ALL Bone marrow, sample 155

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Normal Control Donor serum sample 21

source_name: Normal Control Donor serum sample 21


title: Normal Control Donor serum sample 19

source_name: Normal Control Donor serum sample 19


title: Adults B-cell ALL Peripheral blood, sample 150

source_name: Peripheral blood cells (test)

value: Peripheral blood cells

value: GMALL


title: Adults B-cell ALL Bone marrow, sample 148

value: UNKN


title: Adults B-cell ALL Bone marrow, sample 159

value: Female

value: PETHEMA LAL/OLD-FRA


title: Adults B-cell ALL Bone marrow, sample 149

value: B-cell acute lymphoblastic leukemia


title: Adults B-cell ALL Bone marrow, sample 151


title: Adults B-cell ALL Bone marrow, sample 146

value: PETHEMA LAL-07FRAIL/EWALL-PH-01


title: Normal Control Donor serum sample 18

source_name: Normal Control Donor serum sample 18


title: Adults B-cell ALL Bone marrow, sample 153

value: Adults ≥18 years

value: PETHEMA LAL Ph/2008


title: Normal Control Donor serum sample 17

source_name: Normal Control Donor serum sample 17


title: Adults B-cell ALL Bone marrow, sample 145


title: Normal Control Donor serum sample 16

source_name: Normal Control Donor serum sample 16


title: Adults B-cell ALL Bone marrow, sample 157


title: Adults B-cell ALL Bone marrow, sample 142

value: Male


title: Adults B-cell ALL Bone marrow, sample 139

value: PETHEMA LAL-Ph/2000/Imatinib


title: Adults B-cell ALL Bone marrow, sample 147


title: Adults B-cell ALL Bone marrow, sample 138


title: Adults B-cell ALL Bone marrow, sample 141

value: PETHEMA LAL-RI/96 with Glivec


title: Normal Control Donor serum sample 15

source_name: Normal Control Donor serum sample 15

value: FEMALE


title: Normal Control Donor serum sample 14

source_name: Normal Control Donor serum sample 14


title: Adults B-cell ALL Bone marrow, sample 137

value: Bone marrow cells

value: Not applicable


title: Adults B-cell ALL Bone marrow, sample 143

value: PETHEMA LAL-AR/89


title: Normal Control Donor serum sample 12

source_name: Normal Control Donor serum sample 12


title: Normal Control Donor serum sample 11

source_name: Normal Control Donor serum sample 11


title: Normal Control Donor serum sample 13

source_name: Normal Control Donor serum sample 13

value: MALE


title: Normal Control Donor serum sample 27

source_name: Normal Control Donor serum sample 27


title: Normal Control Donor serum sample 10

source_name: Normal Control Donor serum sample 10


title: Adults B-cell ALL Peripheral blood, sample 136

value: Peripheral blood cells

source_name: control

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 134

source_name: Bone marrow cells (test)

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 135

value: PETHEMA LAL-07OLD


title: Normal Control Donor serum sample 9

source_name: Normal Control Donor serum sample 9


title: Adults B-cell ALL Bone marrow, sample 133

value: Female

value: PETHEMA LAL Ph-2007/ PETHEMA LAL Ph-2008


title: Adults B-cell ALL Bone marrow, sample 140

value: B-cell acute lymphoblastic leukemia

value: PETHEMA LAL-Ph/2000


title: GFP-overexpression rep1

type: RNA

city: Shanghai

first: Gang

last: Liu

address: 320 Yueyang Rd, Shanghai

country: China

institute: Shanghai Institutes for Biological Sciences

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: The raw data were normalized with GeneSpring Software GX 12.6.1 using quartile

molecule: total RNA

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: HCC cell line MHCCLM3 were over expressed with DMGDH and GFP

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

value: Human Hepatocellular Carcinoma (HCC) cell line

tag: genotype/variation

value: GFP-overexpression


title: Adults B-cell ALL Bone marrow, sample 128

value: Male

value: Adults ≥18 years

value: Second-generation TKI


title: Adults B-cell ALL Bone marrow, sample 126

value: Bone marrow cells

value: PETHEMA LAL-AR/93


title: Adults B-cell ALL Bone marrow, sample 124

value: PETHEMA LAL-Ph/2000/Imatinib

value: Not applicable


title: Adults B-cell ALL Bone marrow, sample 122

value: PETHEMA LAL Ph/2008


title: DMGDH-overexpression rep2

value: DMGDH-overexpression


title: GFP-overexpression rep2


title: Adults B-cell ALL Bone marrow, sample 185

value: Normal

value: PETHEMA LAL-AR/2003

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 125


title: Adults B-cell ALL Bone marrow, sample 127


title: Adults B-cell ALL Bone marrow, sample 123

value: PETHEMA LAL Ph-2008/Clinical Trial CSTI571BES02


title: Adults B-cell ALL Bone marrow, sample 130

value: B-cell acute lymphoblastic leukemia


title: Adults B-cell ALL Bone marrow, sample 120


title: Adults B-cell ALL Bone marrow, sample 131


title: GFP-overexpression rep3


title: DMGDH-overexpression rep3


title: Normal Control Donor serum sample 8

source_name: Normal Control Donor serum sample 8


title: Adults B-cell ALL Bone marrow, sample 132


title: Adults B-cell ALL Bone marrow, sample 121


title: Intestine_Adenoma-3

city: Kyoto

first: Yoshihisa

last: Okuchi

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Pathology and Biology of Diseases

country: Japan

institute: Kyoto university

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST arrays (Affymetrix).

scan_protocol: Hybridized arrays were scanned using an Affymetrix GeneChip Scanner (Affymetrix).

data_processing: The obtained data were analyzed by using GeneChip Command Console, Expression Console, and Transcriptome Analysis Console software (Affymetrix).

label: biotin

source_name: intestinal adenomas

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Adenomas, the surrounding normal mucosae (within 5 mm from the adenomas), and the mucosae located more than 2 cm away from the adenomas were collected from human colorectal specimens that were resected from four FAP patients during total or subtotal colectomy.

extract_protocol: RNA was extracte from each human sample with the RNeasy Mini Kit (QIAGEN), according to the manufacturer’s instructions.

tag: tissue

value: Large intestine

value: adenoma


title: Intestine_Adenoma-2


title: Normal Control Donor serum sample 7

source_name: Normal Control Donor serum sample 7


title: Adults B-cell ALL Bone marrow, sample 118

value: Female

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Adults B-cell ALL Peripheral blood, sample 119

source_name: Peripheral blood cells (test)

value: Peripheral blood cells

value: Male

value: Adults ≥18 years

value: UNKN


title: Normal Control Donor serum sample 5

source_name: Normal Control Donor serum sample 5


title: Normal Control Donor serum sample 6

source_name: Normal Control Donor serum sample 6


title: Intestine_Mucosa adjacent to adenoma-3

source_name: normal intestinal epithelial cells adjacent to adenomas

value: normal epithelial cells


title: Intestine_Adenoma-1


title: Adults B-cell ALL Bone marrow, sample 117

value: Bone marrow cells

value: Not applicable


title: Adults B-cell ALL Bone marrow, sample 116

value: PETHEMA LAL Ph/2008


title: Normal Control Donor serum sample 4

source_name: Normal Control Donor serum sample 4


title: Intestine_Mucosa adjacent to adenoma-2


title: Children B-cell ALL Bone marrow, sample 114

value: Children <18 years

value: Normal

value: PETHEMA LAL-AR/93


title: Adults B-cell ALL Bone marrow, sample 129


title: Intestine_Mucosa apart from adenoma-3

source_name: normal intestinal epithelial cells apart from adenomas


title: Intestine_Mucosa adjacent to adenoma-1


title: Children B-cell ALL Bone marrow, sample 113

value: PETHEMA LAL-RI/2008

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Normal Control Donor serum sample 3

source_name: Normal Control Donor serum sample 3


title: Normal Control Donor serum sample 1

source_name: Normal Control Donor serum sample 1


title: Normal Control Donor serum sample 2

source_name: Normal Control Donor serum sample 2


title: Children B-cell ALL Bone marrow, sample 115

value: B-cell acute lymphoblastic leukemia

value: PETHEMA LAL-RI/1995


title: Children B-cell ALL Bone marrow, sample 111


title: Children B-cell ALL Bone marrow, sample 107

value: Female

value: LAL/SEHOP-PETHEMA 2013


title: Children B-cell ALL Bone marrow, sample 108

value: PETHEMA LAL-RI/96


title: Children B-cell ALL Bone marrow, sample 110

value: PETHEMA LAL-AR/2003

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 109

value: Male

value: UNKN


title: Early-Stage Parkinson's Disease serum sample 24


title: Children B-cell ALL Bone marrow, sample 106

value: Bone marrow cells


title: Early-Stage Parkinson's Disease serum sample 23


title: Early-Stage Parkinson's Disease serum sample 21


title: Early-Stage Parkinson's Disease serum sample 25


title: Early-Stage Parkinson's Disease serum sample 20


title: Early-Stage Parkinson's Disease serum sample 22


title: Early-Stage Parkinson's Disease serum sample 19


title: Early-Stage Parkinson's Disease serum sample 17


title: Early-Stage Parkinson's Disease serum sample 18


title: Children B-cell ALL Bone marrow, sample 112

value: Not applicable


title: Children B-cell ALL Bone marrow, sample 105


title: Adipocyte

city: Sydney

first: Ashwin

last: Unnikrishnan

state: NSW

address: Room 217, Level 2, Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales

department: Lowy Cancer Research Centre

country: Australia

institute: University of New South Wales

description: SAMPLE 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalized using quantile normalization in GenePattern.

label: Biotin

organism: Mus musculus

source_name: mouse adult bone marrow mesenchymal stem cells

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

extract_protocol: Total RNA was extracted using Qiagen's RNeasy kit following manufacturer's standard recommendation.

tag: strain

value: Differentiated adipocytes


title: MSC-2

description: SAMPLE 5

value: Undifferentiated MSCs


title: oCFU-F

description: SAMPLE 10

value: Reprogrammed osteocytes


title: aCFU-F

description: SAMPLE 7

value: Reprogrammed adipocytes


title: DMGDH-overexpression rep1

value: Human Hepatocellular Carcinoma (HCC) cell line

value: DMGDH-overexpression


title: Children B-cell ALL Bone marrow, sample 93

value: B-cell acute lymphoblastic leukemia

value: Children <18 years

value: Normal

value: PETHEMA LAL/89


title: Children B-cell ALL Bone marrow, sample 95

value: Female

value: PETHEMA LAL-RI/96


title: cCFU-F

description: SAMPLE 8

value: Reprogrammed chondrocytes


title: Children B-cell ALL Bone marrow, sample 101

value: Male

value: PETHEMA LAL-AR/2005

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Early-Stage Parkinson's Disease serum sample 16


title: Intestine_Mucosa apart from adenoma-1

value: Large intestine

value: normal epithelial cells


title: Children B-cell ALL Bone marrow, sample 94

value: Bone marrow cells

value: Not applicable


title: Osteocyte

description: SAMPLE 9

value: Differentiated osteocytes


title: Intestine_Mucosa apart from adenoma-2


title: Osteocyte_Treated

description: SAMPLE 6

value: Treated in vivo derived osteocytes


title: Children B-cell ALL Bone marrow, sample 102


title: Children B-cell ALL Bone marrow, sample 100

value: PETHEMA LAL-Ph/2000

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Osteocyte_in vivo

description: SAMPLE 4

value: In vivo derived osteocytes


title: 795-Preleukemia-GFP-

city: Stanford

first: Jesus

last: Duque-Afonso

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: The array was placed in 45°C hybridization oven, at 60 rpm, and incubated for 17 hours ± 1 hour. Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the Stanford PAN Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). Affymetrix GeneChip Scanner 3000 7G was used for scanning. It takes approximately 10 minutes to scan each Gene Array.

data_processing:
Raw data were processed with Affymetrix GeneChip Expression Console and Affymetrix GeneChip Command Console  for background correction and normalization. Data analysis and statistical evaluations were performed with Nexus Expression (Biodiscover, Hawthorne, CA, USA). We defined a probeset as present when it had a p-value < 0.05 and fold differential expression >1.2 between groups.
RMA

source_name: healthy preleukemia

label_protocol: The Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay is  designed to generate amplified and biotinylated sense-strand DNA targets

growth_protocol: Bone marrow cells were isolated from sacrificed mice and sorted for Lin-CD19+CD43+ progenitor B-cells

extract_protocol: RNA extraction by RNeasy plus mini kit

tag: Sex

value: Sorted B-cell progenitors GFP -


title: Early-Stage Parkinson's Disease serum sample 15


title: Chondrocyte

description: SAMPLE 3

value: Differentiated chondrocytes


title: Children B-cell ALL Bone marrow, sample 99

value: B-cell acute lymphoblastic leukemia

value: Children <18 years

value: Normal

value: UNKN

source_name: control


title: Children B-cell ALL Bone marrow, sample 96

source_name: Bone marrow cells (test)

value: Female

value: PETHEMA LAL-RI/96


title: Early-Stage Parkinson's Disease serum sample 14


title: Children B-cell ALL Bone marrow, sample 103

value: BFM


title: Children B-cell ALL Bone marrow, sample 97


title: Children B-cell ALL Bone marrow, sample 104

value: Male

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 98

value: Bone marrow cells

value: Not applicable


title: Early-Stage Parkinson's Disease serum sample 11


title: Early-Stage Parkinson's Disease serum sample 12


title: Early-Stage Parkinson's Disease serum sample 13


title: MSC-1

description: SAMPLE 1

value: Undifferentiated MSCs


title: Early-Stage Parkinson's Disease serum sample 8


title: Early-Stage Parkinson's Disease serum sample 9


title: Early-Stage Parkinson's Disease serum sample 10


title: Early-Stage Parkinson's Disease serum sample 7


title: Early-Stage Parkinson's Disease serum sample 6


title: Early-Stage Parkinson's Disease serum sample 5


title: 789-Preleukemia-GFP-


title: 409-WT

source_name: wild-type

value: Sorted B-cell progenitors


title: 795-Preleukemia-GFP+

value: Sorted B-cell progenitors GFP +


title: Children B-cell ALL Bone marrow, sample 91


title: 788-Preleukemia-GFP-


title: 789-Preleukemia-GFP+


title: EAE dLN mem-3

city: Atlanta

first: Kareem

last: Graham

state: GA

address: 615 Michael Street, Room 601

department: Physiology

institute: Emory University

hyb_protocol: The fragmented and labeled targets were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays per standard    Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at  60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: GeneSpring GX 12.6 was used for processing and analyzing the data. Genespring preprocessing and default normalization (RMA-16) was applied to each dataset

source_name: draining (inguinal) lymph node, acute clinical EAE

label_protocol: Affymetrix GeneChip Expression 3'-amplification two-Cycle cDNA Synthesis Kit was used to generate biotin-labeled cRNA targets from 1ng of total RNA

extract_protocol: RNeasy mini kit (Qiagen) according to manufacturer's instruction

value: lymph node

value: memory phenotype CD4+ T cells

value: 8-10 weeks

tag: strain/phenotype

value: C57BL/6, MOG35-55-induced EAE

value: female


title: Children B-cell ALL Bone marrow, sample 86

value: B-cell acute lymphoblastic leukemia

value: Children <18 years

value: Normal


title: 410-WT

value: Female


title: Children B-cell ALL Bone marrow, sample 85

value: PETHEMA LAL-RI/96

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: 788-Preleukemia-GFP+

value: Male


title: 407-WT


title: Early-Stage Parkinson's Disease serum sample 4


title: Children B-cell ALL Bone marrow, sample 92

value: Bone marrow cells

value: PETHEMA LAL-BR-01


title: EAE dLN mem-2


title: 404-WT


title: Children B-cell ALL Bone marrow, sample 87

value: Not applicable

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: 411-WT

value: Sorted B-cell progenitors


title: EAE dLN mem-1

value: lymph node


title: Children B-cell ALL Bone marrow, sample 88


title: 2113-WT


title: Children B-cell ALL Bone marrow, sample 84


title: Children B-cell ALL Bone marrow, sample 89


title: 405-WT


title: Children B-cell ALL Bone marrow, sample 90

value: LAL/SEHOP-PETHEMA IR 2012


title: Early-Stage Parkinson's Disease serum sample 2


title: Children B-cell ALL Bone marrow, sample 82

value: UNKN


title: Early-Stage Parkinson's Disease serum sample 1


title: Breast Cancer serum sample 11

source_name: Breast Cancer serum sample 11


title: Early-Stage Parkinson's Disease serum sample 3


title: EAE CNS mem-3

source_name: spinal cord, acute clinical EAE

value: spinal cord

value: memory phenotype CD4+ T cells

value: 8-10 weeks

value: C57BL/6, MOG35-55-induced EAE


title: Breast Cancer serum sample 10

source_name: Breast Cancer serum sample 10


title: Children B-cell ALL Bone marrow, sample 83

value: B-cell acute lymphoblastic leukemia

value: Children <18 years

value: Normal


title: EAE CNS mem-2

value: female


title: 1012-Leukemia

source_name: Leukemia

value: Female

value: Total bone marrow


title: Breast Cancer serum sample 7

source_name: Breast Cancer serum sample 7


title: 406-WT


title: 952-Leukemia


title: 951-Leukemia


title: Lung of uninfected mice, biological rep4

city: Beijing

first: Yang

last: Hu

address: No. 8 GongTi Southern Road, Chao Yang District

department: Department of Respiratory Medicine and Critical Care Medicine

institute: Beijing Chao-Yang Hospital Affiliated to Capital Medical University

description: Gene expression data from left lung of uninfected mice.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix® GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix® microarray data were collected with Affymetrix® GeneChip® Command Console® Software. Probe values were corrected for background and normalized via quantile normalized by Robust Multichip Average (RMA) of the Bioconductor 'affy' package.In the detection column, calls include P for Present, A for Absent, and M for Marginal.

source_name: left lung of uninfected wild-type mice

label_protocol: 100ng RNA was amplified and labeled using the MessageAmp™ Premier RNA Amplification Kit (Ambion, AM1792) according to the manufacturer's instructions..

growth_protocol: After euthanasia, the left lobe of mice lung was excised and then frozen in liquid nitrogen quickly. The tissuse was then transferrd to a -80℃ freezer.

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

treatment_protocol: 14 days before Pneumocystis infection, the group of dexamethasone-treated PCP mice were given 4mg/l dexamethasone and 1 mg/ml tetracycline in drinking water consecutively until euthanasia. Both dexamethasone-treated and wild-type PCP mice were inoculated intratracheally with 1 × 10^6 Pneumocystis nuclei and control mice were given lung homogenate from uninfected scid mice. 14 days after infection, mice were sacrified and the left lung was excised.

value: left lung

value: male

value: 8 weeks


title: EAE CNS mem-1


title: Lung of uninfected mice, biological rep2


title: Lung of Pneumocystis infected dexamethasone-treated mice,biological rep4

description: Gene expression data from lung of dexamethasone-treated mice 14d post Pneumocystis infection. The dexamethasone was given 14d prior to infection until euthanasia.

source_name: left lung of dexamethasone-treated mice with Pneumocystis infection


title: 541-Leukemia


title: 624-Leukemia

value: Male


title: 408-WT

value: Sorted B-cell progenitors


title: Breast Cancer serum sample 8

source_name: Breast Cancer serum sample 8


title: Children B-cell ALL Peripheral blood, sample 81

source_name: Peripheral blood cells (test)

value: Peripheral blood cells

value: Not applicable

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 77

value: Bone marrow cells

value: PETHEMA LAL-BR-01

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 79

value: B-cell acute lymphoblastic leukemia


title: Children B-cell ALL Bone marrow, sample 80

value: Children <18 years

value: PETHEMA LAL-RI/96


title: Children B-cell ALL Bone marrow, sample 75

value: Normal


title: Lung of uninfected mice, biological rep3


title: 950-Leukemia

value: Female


title: Children B-cell ALL Bone marrow, sample 78


title: Lung of uninfected mice, biological rep1


title: Lung of Pneumocystis infected dexamethasone-treated mice,biological rep5


title: Breast Cancer serum sample 6

source_name: Breast Cancer serum sample 6


title: Lung of Pneumocystis infected dexamethasone-treated mice,biological rep3


title: Breast Cancer serum sample 4

source_name: Breast Cancer serum sample 4


title: Children B-cell ALL Bone marrow, sample 76


title: Breast Cancer serum sample 9

source_name: Breast Cancer serum sample 9


title: Breast Cancer serum sample 5

source_name: Breast Cancer serum sample 5


title: Breast Cancer serum sample 3

source_name: Breast Cancer serum sample 3


title: Breast Cancer serum sample 2

source_name: Breast Cancer serum sample 2


title: 1035-Leukemia

value: Total bone marrow


title: Breast Cancer serum sample 1

source_name: Breast Cancer serum sample 1


title: Alzheimer's Disease serum sample 50

source_name: Alzheimer's Disease serum sample 50


title: Lung of Pneumocystis infected dexamethasone-treated mice,biological rep2

value: left lung


title: Lung of Pneumocystis infected dexamethasone-treated mice,biological rep1

value: male


title: 906-Leukemia


title: Children B-cell ALL Bone marrow, sample 74

source_name: Bone marrow cells (test)

value: BFM

source_name: control


title: 650-Leukemia


title: Children B-cell ALL Bone marrow, sample 73

value: Male


title: Alzheimer's Disease serum sample 49

source_name: Alzheimer's Disease serum sample 49


title: Alzheimer's Disease serum sample 48

source_name: Alzheimer's Disease serum sample 48


title: 341-Leukemia

source_name: Leukemia


title: Children B-cell ALL Bone marrow, sample 69


title: Children B-cell ALL Bone marrow, sample 72

value: PETHEMA LAL/89


title: Children B-cell ALL Bone marrow, sample 68


title: Lung of Pneumocystis infected mice,biological rep4

description: Gene expression data from lung of wild-type mice 14d post Pneumocystis infection.

source_name: left lung of wild-type mice with Pneumocystis infection

value: 8 weeks


title: Children B-cell ALL Peripheral blood, sample 71

value: Peripheral blood cells

value: UNKN

value: Not applicable


title: 475-Leukemia


title: 350-Leukemia


title: 440-Leukemia


title: Lung of Pneumocystis infected mice,biological rep1


title: Lung of Pneumocystis infected mice,biological rep2


title: Alzheimer's Disease serum sample 45

source_name: Alzheimer's Disease serum sample 45

value: Unknown


title: Alzheimer's Disease serum sample 46

source_name: Alzheimer's Disease serum sample 46


title: 864-Leukemia


title: Lung of Pneumocystis infected mice,biological rep3


title: Children B-cell ALL Bone marrow, sample 67

value: Bone marrow cells

value: LAL/SEHOP-PETHEMA 2013

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Alzheimer's Disease serum sample 47

source_name: Alzheimer's Disease serum sample 47


title: Children B-cell ALL Bone marrow, sample 66

value: B-cell acute lymphoblastic leukemia

value: Children <18 years

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: 681-Leukemia

value: Female

value: Total bone marrow


title: Alzheimer's Disease serum sample 44

source_name: Alzheimer's Disease serum sample 44


title: Alzheimer's Disease serum sample 42

source_name: Alzheimer's Disease serum sample 42


title: Alzheimer's Disease serum sample 43

source_name: Alzheimer's Disease serum sample 43


title: 965-Leukemia


title: 517-Leukemia


title: Children B-cell ALL Bone marrow, sample 65

value: Normal

value: PETHEMA LAL-AR/93


title: 1162-Leukemia


title: Intestine_Adenoma2

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).

source_name: intestinal adenomas

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the Ovation One-Direct System (NuGEN) and then fragmented and labeled with the Encore Biotin Module (NuGEN).

growth_protocol: Crypts were collected by using 40 μm-diameter glass capillary pipettes.

extract_protocol: RNA was extracte from each isolated crypt with the NucleoSpin RNA XS (TaKaRa), according to the manufacturer’s instructions. The quality of RNA was examined with an Agilent 2100 bioanalyzer and RNA Pico LabChip kits (Agilent Technologies).

value: small intestine

value: adenoma

value: Apc mutant mice crossed with trangenic mice expressing FPs


title: Intestine_Adenoma3


title: Alzheimer's Disease serum sample 41

source_name: Alzheimer's Disease serum sample 41


title: Children B-cell ALL Bone marrow, sample 63

value: Others

value: Hoelzer protocol


title: Alzheimer's Disease serum sample 40

source_name: Alzheimer's Disease serum sample 40


title: Children B-cell ALL Bone marrow, sample 64

value: Not applicable


title: Children B-cell ALL Bone marrow, sample 61

value: PETHEMA LAL-RI/96


title: Alzheimer's Disease serum sample 39

source_name: Alzheimer's Disease serum sample 39


title: Alzheimer's Disease serum sample 38

source_name: Alzheimer's Disease serum sample 38


title: Children B-cell ALL Bone marrow, sample 62

source_name: Bone marrow cells (test)

value: Bone marrow cells


title: Alzheimer's Disease serum sample 37

source_name: Alzheimer's Disease serum sample 37


title: Intestine_Adenoma1


title: Intestine_FP_lo-6

source_name: normal intestinal epithelial cells adjacent to adenomas

value: normal epithelial cells


title: Intestine_FP_lo-5


title: Intestine_FP_lo-4


title: Intestine_FP_lo-2


title: Alzheimer's Disease serum sample 35

source_name: Alzheimer's Disease serum sample 35

value: Male


title: Alzheimer's Disease serum sample 34

source_name: Alzheimer's Disease serum sample 34


title: Children B-cell ALL Bone marrow, sample 59

value: B-cell acute lymphoblastic leukemia

value: BFM 95

source_name: control


title: Alzheimer's Disease serum sample 36

source_name: Alzheimer's Disease serum sample 36


title: Intestine_FP_hi-2


title: Intestine_FP_hi-3


title: Children B-cell ALL Bone marrow, sample 60

value: Children <18 years

value: PETHEMA LAL-BR-01

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 57

value: Female


title: Intestine_FP_hi-4


title: Alzheimer's Disease serum sample 32

source_name: Alzheimer's Disease serum sample 32

value: Unknown


title: Intestine_FP_lo-1

value: small intestine


title: Children B-cell ALL Bone marrow, sample 58

value: UNKN

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 50


title: Children B-cell ALL Bone marrow, sample 52


title: Intestine_FP_lo-3

value: Apc mutant mice crossed with trangenic mice expressing FPs


title: Children B-cell ALL Bone marrow, sample 54


title: Children B-cell ALL Peripheral blood, sample 53

source_name: Peripheral blood cells (test)

value: Peripheral blood cells

value: PETHEMA LAL-AR/2003


title: Alzheimer's Disease serum sample 33

source_name: Alzheimer's Disease serum sample 33


title: Children B-cell ALL Bone marrow, sample 55

value: Others

value: PETHEMA LAL-RI/96

value: Not applicable


title: Children B-cell ALL Bone marrow, sample 56

value: Bone marrow cells

value: Male


title: Children B-cell ALL Bone marrow, sample 51

value: B-cell acute lymphoblastic leukemia

value: PETHEMA LAL-AR/2011


title: Alzheimer's Disease serum sample 31

source_name: Alzheimer's Disease serum sample 31


title: Alzheimer's Disease serum sample 29

source_name: Alzheimer's Disease serum sample 29


title: Alzheimer's Disease serum sample 28

source_name: Alzheimer's Disease serum sample 28


title: Alzheimer's Disease serum sample 27

source_name: Alzheimer's Disease serum sample 27


city: Stockholm

first: Hiromasa

last: Morikawa

state: Stockholms

address: Karolinska University Hospital, L8:05

department: Medicine

country: Sweden

institute: Karolinska Institutet

description:
Gene expression data from macrophage-associated marker F4/80+ cells from tumors implanted in St2-/-, rep3
YY6_ko3

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalization are performed using robust multi-array analysis (RMA)

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA samples  were prepared using an RNAeasy kit (Qiagen) and hybridized using Affymetrix 1.0 ST Gene arrays.

tag: protocol

value: tumors implanted in St2-/- mouse

value: F4/80+ cells isolated from tumors


description:
Gene expression data from macrophage-associated marker F4/80+ cells from tumors implanted in St2-/-, rep2
YY5_ko2


title: Alzheimer's Disease serum sample 30

source_name: Alzheimer's Disease serum sample 30


title: Children B-cell ALL Bone marrow, sample 49

value: Female

value: Children <18 years

value: BFM

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 48

value: PETHEMA LAL-AR/2005


title: Alzheimer's Disease serum sample 26

source_name: Alzheimer's Disease serum sample 26

value: Unknown


title: Children B-cell ALL Bone marrow, sample 70

value: Normal


title: Alzheimer's Disease serum sample 24

source_name: Alzheimer's Disease serum sample 24


title: Lung of Pneumocystis infected mice,biological rep5

source_name: left lung of wild-type mice with Pneumocystis infection

value: left lung

value: male

value: 8 weeks


description:
Gene expression data from macrophage-associated marker F4/80+ cells from tumors implanted in wild, rep2
YY2_wt2

value: wild type

value: tumors implanted in wild type mouse


description:
Gene expression data from macrophage-associated marker F4/80+ cells from tumors implanted in wild, rep3
YY3_wt3


title: Alzheimer's Disease serum sample 22

source_name: Alzheimer's Disease serum sample 22

value: Male


description:
Gene expression data from macrophage-associated marker F4/80+ cells from tumors implanted in wild, rep1
YY1_wt1


description:
Gene expression data from macrophage-associated marker F4/80+ cells from tumors implanted in St2-/-, rep1
YY4_ko1


title: Children B-cell ALL Bone marrow, sample 46

source_name: Bone marrow cells (test)

value: Bone marrow cells

value: B-cell acute lymphoblastic leukemia

value: Not applicable


title: Alzheimer's Disease serum sample 21

source_name: Alzheimer's Disease serum sample 21


title: Children B-cell ALL Bone marrow, sample 43

value: ETV6-RUNX1 (TEL-AML1)


title: Children B-cell ALL Bone marrow, sample 44

value: Female

value: PETHEMA LAL-AR/2003 with Imatinib


title: Alzheimer's Disease serum sample 20

source_name: Alzheimer's Disease serum sample 20


title: Children B-cell ALL Bone marrow, sample 45

value: Children <18 years

value: European Pediatric Protocol/ALL-Ph+

source_name: control


title: Alzheimer's Disease serum sample 23

source_name: Alzheimer's Disease serum sample 23


title: Alzheimer's Disease serum sample 25

source_name: Alzheimer's Disease serum sample 25


title: Children B-cell ALL Bone marrow, sample 42

value: BFM

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Children B-cell ALL Bone marrow, sample 47

value: PETHEMA LAL-AR/2005

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Alzheimer's Disease serum sample 19

source_name: Alzheimer's Disease serum sample 19


title: Intestine_FP_hi-1

source_name: normal intestinal epithelial cells adjacent to adenomas

value: small intestine

value: normal epithelial cells

value: Apc mutant mice crossed with trangenic mice expressing FPs


title: Children B-cell ALL Bone marrow, sample 38


title: WERI Mock-infected 24 hours rep 2

city: Subiaco

first: Genevieve

last: Syn

state: Western Australia

address: 100 Roberts Road

institute: Telethon Kids Institute

description: Mock-infected WERI cells

hyb_protocol: Outsourced to Australian Genome Research Facility (Melbourne Node)

data_processing: All data analysis was done in R Version 3.1.3 using R package Lumi to read in raw expression values, perform QC background correction and normalisation of data. Differential expression analysis was carried out using t\he R package Limma

growth_protocol: Cells were grown in RPMI-1640 medium (Gibco) supplemented with 100U/ml Penicillin/100ug ug/ml Streptomycin (Gibco), 2mM Glutamax supplement (Gibco) and 10% heat-inactivated fetal calf serum.

extract_protocol: Cells were harvested using Tri-reagent (Sigma Aldrich) and total RNA was extracted using Direct-Zol RNA Miniprep kit (Zymo research) following manufacturer's instructions

treatment_protocol: 1 X 10^6 WERI cells were infected with Toxoplasma gondii RH (Type I) strain at a multiplicity of infection of 10 for 2 hours, 6 hours and 24 hours. 1 X 10^6 mock-infected cells were treated exactly the same as infected cells but with the absence of Toxoplasma.

value: Mock-infected

tag: time of infection

value: 24 hours

value: Retinoblastoma

tag: sample type

value: Cell line


title: Children B-cell ALL Bone marrow, sample 39

tag: cell type

value: Bone marrow cells

value: B-cell acute lymphoblastic leukemia

value: Not applicable


title: WERI Infected 24 hours rep 2

description: T. gondii infected WERI cells

scan_protocol: Outsourced to Australian Genome Research Facility (Melbourne Node)

value: Infected with Toxoplasma


title: Alzheimer's Disease serum sample 17

source_name: Alzheimer's Disease serum sample 17

tag: gender

value: Male


title: Alzheimer's Disease serum sample 16

source_name: Alzheimer's Disease serum sample 16


title: Children B-cell ALL Bone marrow, sample 41

value: Female

tag: disease state

value: Children <18 years

value: ETV6-RUNX1 (TEL-AML1)

value: UNKN


title: WERI Mock-infected 24 hours rep 1

description: Mock-infected WERI cells

label_protocol: Outsourced to Australian Genome Research Facility (Melbourne Node)


title: Alzheimer's Disease serum sample 15

source_name: Alzheimer's Disease serum sample 15


title: Children B-cell ALL Bone marrow, sample 37

tag: age group

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: WERI Mock-infected 6 hours rep 2

description: Mock-infected WERI cells

value: 6 hours


title: Alzheimer's Disease serum sample 14

source_name: Alzheimer's Disease serum sample 14


title: WERI Infected 6 hours rep 2

description: T. gondii infected WERI cells


title: Children B-cell ALL Bone marrow, sample 40

tag: genetic subtype

value: PETHEMA LAL-RI/96


title: WERI Mock-infected 6 hours rep 1

description: Mock-infected WERI cells

tag: treatment


title: Alzheimer's Disease serum sample 13

source_name: Alzheimer's Disease serum sample 13


title: Alzheimer's Disease serum sample 18

source_name: Alzheimer's Disease serum sample 18


title: WERI Infected 6 hours rep 1

description: T. gondii infected WERI cells


title: WERI Mock-infected 2 hours rep 2

description: Mock-infected WERI cells

value: 2 hours


title: Children B-cell ALL Bone marrow, sample 34

value: BFM 95

tag: reference composition

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Alzheimer's Disease serum sample 12

source_name: Alzheimer's Disease serum sample 12

tag: age


title: Alzheimer's Disease serum sample 11

source_name: Alzheimer's Disease serum sample 11


title: Children B-cell ALL Bone marrow, sample 36

value: PETHEMA LAL/89


title: Children B-cell ALL Bone marrow, sample 35

value: LAL/SEHOP-PETHEMA 2013


title: WERI Infected 24 hours rep 1

description: T. gondii infected WERI cells

value: 24 hours

value: Retinoblastoma

value: Cell line


title: WERI Infected 2hours rep 1

description: T. gondii infected WERI cells

value: Infected with Toxoplasma


title: WERI Infected 2hours rep 2

description: T. gondii infected WERI cells


title: Alzheimer's Disease serum sample 10

source_name: Alzheimer's Disease serum sample 10

value: Male


title: Children B-cell ALL Bone marrow, sample 32

source_name: Bone marrow cells (test)

value: Bone marrow cells

value: B-cell acute lymphoblastic leukemia

value: PETHEMA LAL-BR-01

value: Not applicable


title: Children B-cell ALL Bone marrow, sample 30

value: Female

value: Children <18 years

value: ETV6-RUNX1 (TEL-AML1)


title: Children B-cell ALL Bone marrow, sample 33

value: PETHEMA LAL/89


title: Alzheimer's Disease serum sample 8

source_name: Alzheimer's Disease serum sample 8


title: Alzheimer's Disease serum sample 9

source_name: Alzheimer's Disease serum sample 9


title: Alzheimer's Disease serum sample 6

source_name: Alzheimer's Disease serum sample 6


title: Alzheimer's Disease serum sample 4

source_name: Alzheimer's Disease serum sample 4


title: Alzheimer's Disease serum sample 7

source_name: Alzheimer's Disease serum sample 7


title: Alzheimer's Disease serum sample 2

source_name: Alzheimer's Disease serum sample 2


title: Alzheimer's Disease serum sample 3

source_name: Alzheimer's Disease serum sample 3


title: Alzheimer's Disease serum sample 1

source_name: Alzheimer's Disease serum sample 1


title: Alzheimer's Disease serum sample 5

source_name: Alzheimer's Disease serum sample 5


title: Mild Cognitive Impairment Sample LMCI 18


title: Children B-cell ALL Bone marrow, sample 28

value: PETHEMA LAL-RI/96

source_name: control


title: Children B-cell ALL Bone marrow, sample 27

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: WERI Mock-infected 2 hours rep 1

description: Mock-infected WERI cells

value: Mock-infected

value: 2 hours


title: Children B-cell ALL Peripheral blood, sample 29

source_name: Peripheral blood cells (test)

value: Peripheral blood cells

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Mild Cognitive Impairment Sample LMCI 17


title: Mild Cognitive Impairment Sample LMCI 16


title: Children B-cell ALL Bone marrow, sample 26


title: Children B-cell ALL Bone marrow, sample 24


title: Children B-cell ALL Bone marrow, sample 25

value: PETHEMA LAL-AR/2005


title: Mild Cognitive Impairment Sample LMCI 15


title: Children B-cell ALL Bone marrow, sample 22


title: Mild Cognitive Impairment Sample LMCI 14


title: Children B-cell ALL Bone marrow, sample 21


title: Mild Cognitive Impairment Sample LMCI 12


title: Mild Cognitive Impairment Sample LMCI 11


title: Mild Cognitive Impairment Sample LMCI 10


title: Children B-cell ALL Bone marrow, sample 20


title: Children B-cell ALL Bone marrow, sample 18


title: Children B-cell ALL Bone marrow, sample 19

value: LAL/SEHOP-PETHEMA 2013


title: Children B-cell ALL Peripheral blood, sample 23

value: Male

value: UNKN


title: Mild Cognitive Impairment Sample LMCI 9

source_name: Mild Cognitive Impairment Sample LMCI 9


title: Mild Cognitive Impairment Sample LMCI 13


title: Mild Cognitive Impairment Sample LMCI 7

source_name: Mild Cognitive Impairment Sample LMCI 7


title: Children B-cell ALL Bone marrow, sample 15

value: Bone marrow cells

value: B-cell acute lymphoblastic leukemia

value: Hyper (>50)

value: PETHEMA ALL/IR-HR


title: Mild Cognitive Impairment Sample LMCI 6

source_name: Mild Cognitive Impairment Sample LMCI 6


title: Mild Cognitive Impairment Sample LMCI 8

source_name: Mild Cognitive Impairment Sample LMCI 8


title: Children B-cell ALL Bone marrow, sample 16

value: Children <18 years

value: BFM

value: Not applicable


title: Mild Cognitive Impairment Sample LMCI 5

source_name: Mild Cognitive Impairment Sample LMCI 5


title: Children B-cell ALL Bone marrow, sample 14

source_name: Bone marrow cells (test)

value: Female

value: PETHEMA LAL-RI/96


title: Mild Cognitive Impairment Sample LMCI 4

source_name: Mild Cognitive Impairment Sample LMCI 4


title: Children B-cell ALL Bone marrow, sample 12


title: VCaPexosomes_TotalRNA

first: Nham

last: Tran

address: Jones

department: CHT/FEIT

institute: UTS

description: VCaPE; lncRNA expression in exosomes

hyb_protocol: 2 × GE Hybridization buffer

scan_protocol: The Arraystar Human LncRNA Array v2.0 were scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Raw mRNA data normalization and low intensity filtering: Raw signal intensities were first normalized in quantile method by GeneSpring GX v11.5.1, low intensity mNAs were filtered (mRNAs that at least 6 out of 10 samples have flags in Present or Marginal were chosen for further analysis, the normalized signals were adjusted by Combat program to remove batch effects.

source_name: Human Prostate Cencer cell lines_exosomes

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

growth_protocol: The prostate cancer cell lines, LNCaP, PC3, and DU145 were grown in RPMI, whereas VCaP cells were grown in F12:DMEM and PNT2 in defined KSFM (Invitrogen, USA). All cells were incubated at 370C in 5% CO2, and supplemented with 1% v/v penicillin, streptomycin, glutamine (PSG) and 10% v/v fetal calf serum (FCS).

extract_protocol: Cell lines were harvested usinh standard tissue culture conditions. Exosomes were isolated using ultracentrifugation. RNAzol RT (Molecular Research Center, USA) was used to extract total RNA from both cellular and exosomal sources.

treatment_protocol: No treatment

tag: cell line

value: VCaP

value: Human Prostate Cencer cell lines

tag: cell line info.

value: Prostate adenocarcinoma isolated from metastatic deposit in lumbar vertebrae

value: exosomes


title: Children B-cell ALL Bone marrow, sample 13

value: PETHEMA LAL-BR-01

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Mild Cognitive Impairment Sample LMCI 2

source_name: Mild Cognitive Impairment Sample LMCI 2

value: Male


title: Children B-cell ALL Bone marrow, sample 10

value: PETHEMA-SEHOP/LAL/IR

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: PC3cells_TotalRNA

description: PCC; lncRNA expression in cells

source_name: Human Prostate Cencer cell lines_cells

value: Prostate adenocarcinoma isolated from metastatic deposit in bone

value: parent cell line


title: PC3exosomes_TotalRNA

description: PCE; lncRNA expression in exosomes


title: Mild Cognitive Impairment Sample LMCI 1

source_name: Mild Cognitive Impairment Sample LMCI 1


title: Mild Cognitive Impairment Sample EMCI 32


title: Children B-cell ALL Bone marrow, sample 9

value: Bone marrow cells

value: B-cell acute lymphoblastic leukemia

value: Hyper (>50)


title: Children B-cell ALL Bone marrow, sample 5

value: Children <18 years

value: Not applicable


title: PNT2cells_TotalRNA

description: NTC; lncRNA expression in cells

source_name: Human Normal Prostate  cell lines_cells

value: Human Normal Prostate  cell lines

value: Normal Prostate epithelium immortalised with SV40


title: Children B-cell ALL Bone marrow, sample 17

value: Female

value: LAL/SEHOP-PETHEMA 2013


title: VCaPcells_TotalRNA

description: VCaPC; lncRNA expression in cells

value: VCaP

value: Human Prostate Cencer cell lines

value: Prostate adenocarcinoma isolated from metastatic deposit in lumbar vertebrae


title: Mild Cognitive Impairment Sample EMCI 30

value: Male


title: Children B-cell ALL Bone marrow, sample 8


title: Children B-cell ALL Bone marrow, sample 2

value: PETHEMA LAL-RI/96

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Mild Cognitive Impairment Sample LMCI 3

source_name: Mild Cognitive Impairment Sample LMCI 3


title: PNT2exosomes_TotalRNA

description: NTE; lncRNA expression in exosomes

source_name: Human Normal Prostate  cell lines_exosomes

value: exosomes


title: DU145cells_TotalRNA

description: DUC; lncRNA expression in cells

value: Prostate adenocarcinoma derived from metastatic deposit in brain

value: parent cell line


title: DU145exosomes_TotalRNA

description: DUE; lncRNA expression in exosomes


title: Children B-cell ALL Bone marrow, sample 6

value: Bone marrow cells

value: B-cell acute lymphoblastic leukemia

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Mild Cognitive Impairment Sample EMCI 31


title: Mild Cognitive Impairment Sample EMCI 28


title: Children B-cell ALL Bone marrow, sample 11

value: Children <18 years

value: Hyper (>50)

value: Not applicable


title: Children B-cell ALL Bone marrow, sample 7

value: Female

value: UNKN


title: Mild Cognitive Impairment Sample EMCI 27


title: Children B-cell ALL Peripheral blood, sample 3

value: Peripheral blood cells

value: LAL/SEHOP-PETHEMA 2013


title: Children B-cell ALL Peripheral blood, sample 4


title: Mild Cognitive Impairment Sample EMCI 26


title: Children B-cell ALL Bone marrow, sample 1


title: Mild Cognitive Impairment Sample EMCI 24


title: Mild Cognitive Impairment Sample EMCI 22


title: Mild Cognitive Impairment Sample EMCI 29


title: Mild Cognitive Impairment Sample EMCI 23


title: Mild Cognitive Impairment Sample EMCI 25


title: Mild Cognitive Impairment Sample EMCI 20


title: Mild Cognitive Impairment Sample EMCI 18


title: Mild Cognitive Impairment Sample EMCI 19


title: Mild Cognitive Impairment Sample EMCI 17


title: Mild Cognitive Impairment Sample EMCI 16


title: Mild Cognitive Impairment Sample EMCI 15


title: Mild Cognitive Impairment Sample EMCI 21


title: P28_BDS sample #21

city: New Haven

first: Arie

last: Kaffman

state: Connecticut

address: 300 George St. Suite 901

department: Psychiatry

institute: Yale University

hyb_protocol: Samples were processed for hybridization using automated nCounter Prep Station.

scan_protocol: Hybridized complexes were scanned in the nCounter Digital analyzer.

data_processing: Counts were normalized to positive controls and 5 housekeeping genes (e.g. Alas1, Gapdh, Oaz1, Polr1b, Sdha, Tbp) that were not affected by either BDS or age and showed a coefficient of variation of less than 20%. Genes were considered “present” if at least 40% of the samples showed hybridization signal that was 2 s.d. above the mean value for the negative control probes.

label: nanostring fluorescence barcode

source_name: Hippocampal microgila PND28-BDS

label_protocol: Two ng of RNA were converted to cDNA using Superscript Vilo (Cat# 11754, Life Technologies), amplified with 5 rounds of PCR according to the nCounter single cell gene expression protocol and hybridized to the mouse immune panel (Cat# 150761, NanoString Technologies).

extract_protocol: microglial were acutely isolated from the hippocampus using Percoll gradient followed by FACS analysis. RNA was harvested using the he mirVana mirRNA isolation kit (Cat # AM 1560, Life technologies) and was then concentrated and Dnase treated on column using the RNA clean and contractor-5 kit (Cat# R1015, Zymo Research).

treatment_protocol: Mice were exposed to brief daily separation as described previously (Wei L. et al. Developmental neuroscience, 2015). In brief, pups are separated from their mother daily for 15min from postnatal day 1-21.

tag: tissue

value: hippocampus

value: microglia

value: male

value: Balbc


title: Mild Cognitive Impairment Sample EMCI 14


title: P28_BDS sample #43

tag: strain


title: P28_control sample #54

source_name: Hippocampal microgila PND28-control


title: P28_BDS sample #35


title: P28_BDS sample #7


title: P28_control sample # 44


title: P28_BDS sample #25


title: P28_BDS sample #55


title: LNCaPcells_TotalRNA

description: LNC; lncRNA expression in cells

value: LNCaP

value: Human Prostate Cencer cell lines

value: Prostate adenocarcinoma isolated from metastatic deposit in lymph node


title: Mild Cognitive Impairment Sample EMCI 13

value: Male


title: Mild Cognitive Impairment Sample EMCI 12


title: P28_control sample #27


title: Mild Cognitive Impairment Sample EMCI 10


title: P28_control sample # 13


title: P28_control smaple #9


title: P28_control sample #5


title: Mild Cognitive Impairment Sample EMCI 9

source_name: Mild Cognitive Impairment Sample EMCI 9


title: Mild Cognitive Impairment Sample EMCI 11


title: nuoG d1 p.i. (252800518544_1_3)

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.6µg labeled samples were hybridized to Agilent-028005 arrays according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution and 20 bit image depth using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent Technologies). The extracted txt files were further analyzed with GeneSpring 12.6 GX (Agilent Technologies).

source_name: lymph node, BCG Berlin ΔureC:: hly ΔnuoG , d1 p.i.

label_protocol: Total RNA labeling was performed with the single color Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: All BCG strains were grown in Middlebrook 7H9 broth (Becton Dickinson) supplemented with albumin-dextrose-catalase enrichment (Becton Dickinson), 0.2% glycerol, 0.05% Tween 80 in 1 L roller bottles (450 cm2) at 37°C and 2 rpm to mid log growth or on Middlebrook 7H11 agar (Becton Dickinson) containing 10% v/v oleic acid-albumin-dextrose-catalase enrichment (Becton Dickinson) and 0.2% glycerol.

extract_protocol: Draining lymph nodes were collected and placed immediately into RNAlater (Qiagen). Total RNA was isolated with TRIzol (Life Technologies) according to the supplier's protocol using Glycogen as carrier.

treatment_protocol: Mice were vaccinated subcutaneously at the tail base with 10e6 CFUs of BCG strains in 100 µl PBS.

tag: strain/background

value: lymph node

tag: infection

value: BCG Berlin delta-ureC::hly delta-nuoG

tag: time point (post-infection)

value: day 1


title: SSI d1 p.i. (252800518544_1_1)

source_name: lymph node, BCG SSI, d1 p.i.

value: BCG SSI


title: P14_BDS sample #59

source_name: Hippocampal microgila PND14-BDS

extract_protocol: microglia  were acutely isolated from the hippocampus using Percoll gradient followed by FACS analysis. RNA was harvested using the he mirVana mirRNA isolation kit (Cat # AM 1560, Life technologies) and was then concentrated and Dnase treated on column using the RNA clean and contractor-5 kit (Cat# R1015, Zymo Research).


title: Hlys d1 p.i. (252800518544_1_2)

source_name: lymph node, BCG Berlin ΔureC:: hly, d1 p.i.

value: BCG Berlin delta-ureC::hly


title: Mild Cognitive Impairment Sample EMCI 8

source_name: Mild Cognitive Impairment Sample EMCI 8


title: Hlys d7 p.i. (252800518563_2_2)

source_name: lymph node, BCG Berlin ΔureC:: hly, d7 p.i.

value: day 7


title: SSI d7 p.i. (252800518563_2_1)

source_name: lymph node, BCG SSI, d7 p.i.


title: none d0 p.i. (252800518563_2_4)

source_name: lymph node, no BCG, d0 p.i.

value: day 0


title: nuoG d7 p.i. (252800518563_2_3)

source_name: lymph node, BCG Berlin ΔureC:: hly ΔnuoG , d7 p.i.


title: Hlys d7 p.i. (252800518544_2_4)


title: P14_BDS sample #38


title: Mild Cognitive Impairment Sample EMCI 7

source_name: Mild Cognitive Impairment Sample EMCI 7


title: nuoG d1 p.i. (252800518563_1_1)


title: SSI d3 p.i. (252800518563_1_2)

source_name: lymph node, BCG SSI, d3 p.i.

value: day 3


title: nuoG d3 p.i. (252800518563_1_4)

source_name: lymph node, BCG Berlin ΔureC:: hly ΔnuoG , d3 p.i.


title: Hlys d3 p.i. (252800518563_1_3)

source_name: lymph node, BCG Berlin ΔureC:: hly, d3 p.i.


title: nuoG d3 p.i. (252800518544_2_2)


title: Hlys d3 p.i. (252800518544_2_1)


title: SSI d1 p.i. (252800518562_2_3)


title: none d0 p.i. (252800518562_2_2)


title: P14_BDS sample #24


title: Mild Cognitive Impairment Sample EMCI 6

source_name: Mild Cognitive Impairment Sample EMCI 6


title: Hlys d7 p.i. (252800518562_1_4)


title: SSI d7 p.i. (252800518562_1_3)


title: Mild Cognitive Impairment Sample EMCI 5

source_name: Mild Cognitive Impairment Sample EMCI 5

value: Female


title: SSI d3 p.i. (252800518544_1_4)


title: Hlys d1 p.i. (252800518562_2_4)


title: nuoG d7 p.i. (252800518562_2_1)


title: P14_BDS sample #17

value: hippocampus


title: Mild Cognitive Impairment Sample EMCI 4

source_name: Mild Cognitive Impairment Sample EMCI 4


title: nuoG d3 p.i. (252800518562_1_2)


title: Mild Cognitive Impairment Sample EMCI 2

source_name: Mild Cognitive Impairment Sample EMCI 2


title: LNCaPexosomes_TotalRNA

description: LNE; lncRNA expression in exosomes

source_name: Human Prostate Cencer cell lines_exosomes

value: exosomes


title: Mild Cognitive Impairment Sample EMCI 3

source_name: Mild Cognitive Impairment Sample EMCI 3


title: P14_control sample # 69

source_name: Hippocampal microgila PND14-control

value: microglia

value: male


title: P14_control sample #52

value: Balbc


title: P14_BDS sample #11

source_name: Hippocampal microgila PND14-BDS


title: Mild Cognitive Impairment Sample EMCI 1

source_name: Mild Cognitive Impairment Sample EMCI 1


title: P14_control smaple #18


title: P14_control sample # 40


title: control P28 sample #138

source_name: Hippocampal microgila PND28-control

extract_protocol: microglia were acutely isolated from the hippocampus using Percoll gradient followed by FACS analysis. RNA was harvested using the he mirVana mirRNA isolation kit (Cat # AM 1560, Life technologies) and was then concentrated and Dnase treated on column using the RNA clean and contractor-5 kit (Cat# R1015, Zymo Research).

treatment_protocol: Mice were raised under control condition as described previously (Wei L. et al. Developmental neuroscience, 2015).


title: SSI d3 p.i. (252800518547_2_4)


title: control P28 sample #137


title: P14_control sample #1


title: control P28 sample #119


title: nuoG d7 p.i. (252800518547_1_3)


title: nuoG d1 p.i. (252800518547_2_3)

source_name: lymph node, BCG Berlin ΔureC:: hly ΔnuoG , d1 p.i.


title: control P28 sample #134


title: control P28 sample #135


title: none d0 p.i. (252800518547_1_4)

source_name: lymph node, no BCG, d0 p.i.


title: Hlys d1 p.i. (252800518547_2_2)

source_name: lymph node, BCG Berlin ΔureC:: hly, d1 p.i.


title: SSI d7 p.i. (252800518547_1_1)

source_name: lymph node, BCG SSI, d7 p.i.


title: nuoG d3 p.i. (252800518546_2_4)


title: SSI d1 p.i. (252800518547_2_1)

source_name: lymph node, BCG SSI, d1 p.i.


title: Adults B-cell ALL Bone marrow, sample 198

source_name: Bone marrow cells (test)

value: Bone marrow cells

value: B-cell acute lymphoblastic leukemia

value: Adults ≥18 years

value: Normal

value: PETHEMA LAL-AR/2003

source_name: control

value: Not applicable

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: SSI d7 p.i. (252800518544_2_3)

value: lymph node

value: BCG SSI


title: Hippocampus_saline_24h_replicate_2

city: Trento

first: Yuri

last: Bozzi

address: via Sommarive 9

department: CIBIO - Centre for Integrative Biology

country: Italy

institute: University of Trento

description: mRNA expression  profile of the mouse epileptic hippocampus, 24 hours after saline treatment (replicate 2)

hyb_protocol: According to manufacturer's instructions for Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F.

scan_protocol: Slides were scanned immediately after washing using a Agilent High-Resolution C Scanner with one color scan setting for 4x44k array slides, according to manufacture's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Intensity values were processed with GeneSpring GX software (Agilent) using default parameters to remove low-quality probes (Sgado` et al., 2013). Signals were then normalized by means of the quantile normalization method, and data were statistically filtered by two-way ANOVA imposing a fold change 2 for each gene in at least one of the four experimental data groups. Differentially expressed genes were classified by DAVID software, applying Benjamini-corrected p value cutoff of 0.05. Data are reported as mean values of normalized signal intensity values  (n=3 per group).

source_name: epileptic hippocampus, 24h after saline

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent 5190-0442) according to the manufacturer's instructions.

growth_protocol: not applicable

extract_protocol: RNAs from dissected hippocampi (n=3 per experimental group) were purified using standard column purification according to the manufacturer’s protocol (RNAeasy Mini Kit, QIAGEN). RNA quality was analyzed by microfluidic gel electrophoresis on RNA 6000 NanoChips using the Agilent 2100 Bioanalyzer. Only RNA with a high ( 9) RNA integrity number was selected and used for subsequent retrotranscription, labeling, and array hybridization according to Agilent protocols.

treatment_protocol: Mice were unilaterally injected with 50 nl of a 20mM solution of KA in PBS into the left dorsal hippocampus under Hypnorm/Hypnovel anesthesia. Three weeks later, after developing chronic recurrent seizures, animal received a single intraperitoneal injection of LPS or saline solution. Hippocampi were freshly dissected 4 and 24 hours after LPS/saline injection.

value: whole hippocampus

value: 12 weeks


title: Hlys d7 p.i. (252800518547_1_2)

source_name: lymph node, BCG Berlin ΔureC:: hly, d7 p.i.

value: BCG Berlin delta-ureC::hly

value: day 7


title: control P28 sample #118

value: hippocampus


title: Hippocampus_saline_24h_replicate_3

description: mRNA expression  profile of the mouse epileptic hippocampus, 24 hours after saline treatment (replicate 3)


title: Hippocampus_LPS_24h_replicate_3

description: mRNA expression  profile of the mouse epileptic hippocampus, 24 hours after LPS treatment (replicate 3)

source_name: epileptic hippocampus, 24h after LPS


title: Hlys d3 p.i. (252800518546_2_3)

source_name: lymph node, BCG Berlin ΔureC:: hly, d3 p.i.

value: day 3


title: nuoG d1 p.i. (252800518546_2_1)

value: BCG Berlin delta-ureC::hly delta-nuoG

value: day 1


title: Adults B-cell ALL Bone marrow, sample 182

extract_protocol: The genomic DNA was extracted from frozen bone marrow or fixed peripheral blood cell samples with QIAmp DNA Mini Kit (Qiagen,  16 Valencia, CA, USA) following the manufacturer’s instructions

value: Bone marrow cells

value: Female

value: Others

value: PETHEMA LAL-RI/2008

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Hippocampus_saline_24h_replicate_1

description: mRNA expression  profile of the mouse epileptic hippocampus, 24 hours after saline treatment (replicate 1)

value: male


title: SSI d3 p.i. (252800518546_2_2)

source_name: lymph node, BCG SSI, d3 p.i.


title: Hippocampus_LPS_24h_replicate_2

description: mRNA expression  profile of the mouse epileptic hippocampus, 24 hours after LPS treatment (replicate 2)


title: Hippocampus_LPS_4h_replicate_3

description: mRNA expression  profile of the mouse epileptic hippocampus, 4 hours after LPS treatment (replicate 3)

source_name: epileptic hippocampus, 4h after LPS


title: control P14 sample #81

source_name: Hippocampal microgila PND14-control

value: microglia

value: Balbc


title: Hlys d1 p.i. (252800518546_1_4)

value: lymph node


title: control P14 sample # 16


title: Hippocampus_LPS_24h_replicate_1

description: mRNA expression  profile of the mouse epileptic hippocampus, 24 hours after LPS treatment (replicate 1)

value: whole hippocampus


title: none d0 p.i. (252800518546_1_2)

value: day 0


title: Hippocampus_LPS_4h_replicate_1

description: mRNA expression  profile of the mouse epileptic hippocampus, 4 hours after LPS treatment (replicate 1)

value: 12 weeks


title: control P14 smaple #5


title: Adults B-cell ALL Bone marrow, sample 152

value: B-cell acute lymphoblastic leukemia

value: Adults ≥18 years

value: PETHEMA LAL-AR/2003

value: Not applicable


title: Hippocampus_LPS_4h_replicate_2

description: mRNA expression  profile of the mouse epileptic hippocampus, 4 hours after LPS treatment (replicate 2)


title: Hippocampus_saline_4h_replicate_1

description: mRNA expression  profile of the mouse epileptic hippocampus, 4 hours after saline treatment (replicate 1)

source_name: epileptic hippocampus, 4h after saline


title: PB_Control_4

city: Darlinghurst

first: Tim

last: Molloy

address: Level 8, 405 Liverpool St

department: Haematology

institute: St Vincent's Centre for Applied Medical Research

hyb_protocol: GeneChip hybridisation oven 640 at a final concentration of 23 ng/µL using a GeneChip Hybridization, Wash and Stain Kit (both Affymetrix) in accordance with manufacturer’s instructions.

scan_protocol: Arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip 3000 7G+ scanner and using GeneChip Command Console Software (all Affymetrix), following manufacturer’s instructions.

data_processing: Microarray data were pre-processed using the robust multi-array average (RMA) algorithm, background correction, quartile normalisation and gene-level probe set summation19. Genes differentially expressed between the two groups were identified by Significance Analysis of Microarrays (SAM) analysis with a false discovery rate (FDR) of 0.1 using BRBArrayTools Version 4.4 software Gene networks were generated by Ingenuity Pathway Analysis (IPA) software (Qiagen, Redwood City, CA).

organism: Ovis aries

source_name: Peripheral blood, control

label_protocol: WTPlus Kit (Affymetrix)

growth_protocol: Ovis arise (merino cross) singleton fetuses at 95d gestational age

extract_protocol: PaxGene RNA blood tubes with extraction according to manufacturer's instructions

treatment_protocol: chronic catheterisation followed by intraamniotic exposure of 10mg E.coli lipopolysaccharides (intervention) or sterile saline (control)

value: Control


title: Hippocampus_saline_4h_replicate_2

description: mRNA expression  profile of the mouse epileptic hippocampus, 4 hours after saline treatment (replicate 2)


title: Hippocampus_saline_4h_replicate_3

description: mRNA expression  profile of the mouse epileptic hippocampus, 4 hours after saline treatment (replicate 3)


title: Children B-cell ALL Bone marrow, sample 31

value: Bone marrow cells

value: Male

value: Children <18 years

value: ETV6-RUNX1 (TEL-AML1)

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: SSI d1 p.i. (252800518546_1_3)

value: BCG SSI

value: day 1


title: nuoG d7 p.i. (252800518546_1_1)

source_name: lymph node, BCG Berlin ΔureC:: hly ΔnuoG , d7 p.i.

value: BCG Berlin delta-ureC::hly delta-nuoG

value: day 7


title: Hlys d7 p.i. (252800518545_2_4)

value: lymph node

value: BCG Berlin delta-ureC::hly


title: control P14 sample #4

value: hippocampus

value: microglia

value: male

value: Balbc


title: Adults B-cell ALL Bone marrow, sample 162

value: B-cell acute lymphoblastic leukemia

value: Adults ≥18 years

value: PETHEMA LAL-AR/2003

value: Not applicable


title: control P14 sample #25


title: PB_Control_3

value: Control


title: SSI d7 p.i. (252800518545_2_3)


title: nuoG d3 p.i. (252800518545_2_2)

source_name: lymph node, BCG Berlin ΔureC:: hly ΔnuoG , d3 p.i.

value: day 3


title: PB_Control_2


title: PB_Intervention_4

source_name: Peripheral blood, intervention

value: Intervention


title: PB_Intervention_3


title: NP, Pax6 Null (Sey)

status: Public on May 02 2016

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

description:
Rep1 = sch20090224mg10_16_SeyCAday8_282_(MoGene-1_0-st-v1).CEL
Rep2 = sch20090224mg10_17_SeyCAday8_282_(MoGene-1_0-st-v1).CEL
Rep3 = sch20090224mg10_18_SeyCAday8_282_(MoGene-1_0-st-v1).CEL

hyb_protocol: hybridization was performed according to standard Affymetrix procedure

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: probesets were summarized and probeset-level values normalized with rma(target=core) function from R/Bioconductor package oligo (version 1.14.0). Normalized data file is available on the series record and contains the RMA signal summarized across the replicates.

source_name: Sey mutant neural progenenitors

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

growth_protocol: For neuronal progenitor transcriptome analysis, wild type and Sey cells were differentiated as previously described (Bibel et al. 2004; Plachta et al. 2004; Bibel et al. 2007)

extract_protocol: RNA was extracted using RNeasy kit (Qiagen)

value: Brain

tag: genotype

value: Sey

value: neural progenitors


title: PB_Intervention_2


title: NP, WT

description:
Rep1 = sch20090224mg10_13_WTCAday8_282_(MoGene-1_0-st-v1).CEL
Rep2 = sch20090224mg10_14_WTCAday8_282_(MoGene-1_0-st-v1).CEL
Rep3 = sch20090224mg10_15_WTCAday8_282_(MoGene-1_0-st-v1).CEL

source_name: Wild type neural progenitors

value: WT


title: nuoG d1 p.i. (252800518545_1_3)

source_name: lymph node, BCG Berlin ΔureC:: hly ΔnuoG , d1 p.i.

value: lymph node

value: BCG Berlin delta-ureC::hly delta-nuoG

value: day 1


title: Hlys d3 p.i. (252800518562_1_1)

value: BCG Berlin delta-ureC::hly


title: nf_2877

city: St. John's

first: Guangju

last: Zhai

state: NL

address: 300 Prince Philip Drive

department: Genetics, Medicine

country: Canada

institute: Memorial University of Newfoundland

description: Hybridized to customized Axiom array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

source_name: peripheral blood sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: sample

tag: population

value: Newfoundland and Labrador

tag: disease status

value: Healthy

tag: inferred gender

value: Male


title: nf_1502

description: Hybridized to customized Axiom array

value: Female


title: SSI d3 p.i. (252800518545_1_4)

value: BCG SSI


title: Hlys d1 p.i. (252800518545_1_2)

source_name: lymph node, BCG Berlin ΔureC:: hly, d1 p.i.


title: nf_2908

description: Hybridized to customized Axiom array


title: nf_2882

description: Hybridized to customized Axiom array


title: nf_2982

description: Hybridized to customized Axiom array


title: nf_2770

description: Hybridized to customized Axiom array


title: nf_1761

description: Hybridized to customized Axiom array


title: PB_Intervention_1


title: nf_1921

description: Hybridized to customized Axiom array


title: nf_1453

description: Hybridized to customized Axiom array


title: nf_1342

description: Hybridized to customized Axiom array


title: SSI d1 p.i. (252800518545_1_1)

source_name: lymph node, BCG SSI, d1 p.i.


title: nf_1514

description: Hybridized to customized Axiom array


title: nf_1857

description: Hybridized to customized Axiom array


title: SPAT2

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description: Replicate 2 of 3, SPA vs HOM

hyb_protocol: Cy3- and Cy5-labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65 °C; Slides were washed using the Gene Expression Wash Buffer Kit (also provided by Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: raw data files were transferred to limma for further processing and final statistical analysis. Pre-processing: background correction (normexp), followed by within- (global loess) and between-array (Aquantile) normalization. Linear modelling was performed with incorporation of intraspot-correlations.

organism: Tetranychus urticae

source_name: LS-VL, SPA, whole organism

label_protocol: 100 ng of total RNA (+ RNA-Spike-In control) was used to generate Cy3- or Cy5-labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)

growth_protocol: Spider mites were reared on bean, Phaseolus vulgaris cv Prelude under controlled conditions (23°C, 16:8 LD photoperiod)

extract_protocol: Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion). RNA was extracted from 50 1-2-day old adult female mites in 3 biological replicates from each regime (HOM, SPA and TEM).

treatment_protocol: Three selection regimes were installed and maintained for over 30 generations. First, a patchy metapopulation consisting of nine patches weekly refreshed with a leaf of 20cm², a classical metapopulation consisting of nine patches with temporally changing levels of resources (HOM). Second, a mainland-island metapopulation consisting of 3 patches of standard leaf size (20cm²) and another three of double size (SPA). Third, a classical metapopulation in which the same amount of resources was assigned randomly to nine patches. Here patch sizes and local carrying capacities fluctuated strongly over time, but total metapopulation carrying capacity (9 x 20cm²) remained constant over time (TEM).

tag: stress

value: spatially-stressed mites

tag: development stage

value: adult

tag: gender

value: female

source_name: LS-VL, HOM, whole organism

value: none (control)


title: nf_1671

description: Hybridized to customized Axiom array


title: nf_2768

description: Hybridized to customized Axiom array


title: TEMP2

description: Replicate 2 of 3, TEM vs HOM

source_name: LS-VL, TEM, whole organism

value: tempospatially-stressed


title: nf_1447

description: Hybridized to customized Axiom array


title: nf_1858

description: Hybridized to customized Axiom array


title: SPAT3

description: Replicate 3 of 3, SPA vs HOM


title: TEMP1

description: Replicate 1 of 3, TEM vs HOM


title: nf_2975

description: Hybridized to customized Axiom array


title: SPAT1

description: Replicate 1 of 3, SPA vs HOM


title: TEMP3

description: Replicate 3 of 3, TEM vs HOM


title: nf_1709

description: Hybridized to customized Axiom array


title: control P14 sample # 61

value: hippocampus

tag: cell type

value: microglia

value: male

value: Balbc


title: nf_2892

description: Hybridized to customized Axiom array


title: nf_1651

description: Hybridized to customized Axiom array


title: nf_1777

description: Hybridized to customized Axiom array


title: nf_1943

description: Hybridized to customized Axiom array


title: nf_2884

description: Hybridized to customized Axiom array


title: nf_2793

description: Hybridized to customized Axiom array


title: nf_2860

description: Hybridized to customized Axiom array


title: nf_2881

description: Hybridized to customized Axiom array


title: nf_3163

description: Hybridized to customized Axiom array


title: nf_2850

description: Hybridized to customized Axiom array


title: nf_2984

description: Hybridized to customized Axiom array


title: nf_1700

description: Hybridized to customized Axiom array


title: nf_2796

description: Hybridized to customized Axiom array


title: nf_2823

description: Hybridized to customized Axiom array


title: nf_2944

description: Hybridized to customized Axiom array


title: nf_1480

description: Hybridized to customized Axiom array


title: nf_1431

description: Hybridized to customized Axiom array


title: nf_1746

description: Hybridized to customized Axiom array


title: nf_1764

description: Hybridized to customized Axiom array


title: nf_1880

description: Hybridized to customized Axiom array


title: nf_1710

description: Hybridized to customized Axiom array


title: nf_1614

description: Hybridized to customized Axiom array


title: nf_2202

description: Hybridized to customized Axiom array


title: nf_1462

description: Hybridized to customized Axiom array


title: nf_2856

description: Hybridized to customized Axiom array


title: nf_1504

description: Hybridized to customized Axiom array


title: nf_2166

description: Hybridized to customized Axiom array


title: nf_1924

description: Hybridized to customized Axiom array


title: nf_1509

description: Hybridized to customized Axiom array


title: nf_1507

description: Hybridized to customized Axiom array


title: nf_1896

description: Hybridized to customized Axiom array


title: nf_2872

description: Hybridized to customized Axiom array


title: nf_2109

description: Hybridized to customized Axiom array


title: nf_1728

description: Hybridized to customized Axiom array


title: nf_2585

description: Hybridized to customized Axiom array


title: nf_1371

description: Hybridized to customized Axiom array


title: nf_2949

description: Hybridized to customized Axiom array


title: nf_2599

description: Hybridized to customized Axiom array


title: nf_2259

description: Hybridized to customized Axiom array


title: nf_1464

description: Hybridized to customized Axiom array


title: nf_2969

description: Hybridized to customized Axiom array


title: nf_1951

description: Hybridized to customized Axiom array


title: nf_1923

description: Hybridized to customized Axiom array


title: nf_1546

description: Hybridized to customized Axiom array


title: nf_2177

description: Hybridized to customized Axiom array


title: nf_1763

description: Hybridized to customized Axiom array


title: nf_1958

description: Hybridized to customized Axiom array


title: nf_1853

description: Hybridized to customized Axiom array


title: nf_1609

description: Hybridized to customized Axiom array


title: nf_2815

description: Hybridized to customized Axiom array


title: nf_2871

description: Hybridized to customized Axiom array


title: nf_2143

description: Hybridized to customized Axiom array


title: nf_2861

description: Hybridized to customized Axiom array


title: nf_1990

description: Hybridized to customized Axiom array


title: nf_1486

description: Hybridized to customized Axiom array


title: nf_2911

description: Hybridized to customized Axiom array


title: nf_2880

description: Hybridized to customized Axiom array


title: nf_2142

description: Hybridized to customized Axiom array


title: nf_2705

description: Hybridized to customized Axiom array


title: nf_1481

description: Hybridized to customized Axiom array


title: nf_2930

description: Hybridized to customized Axiom array


title: nf_1365

description: Hybridized to customized Axiom array


title: nf_2934

description: Hybridized to customized Axiom array


title: nf_2986

description: Hybridized to customized Axiom array


title: nf_2157

description: Hybridized to customized Axiom array


title: nf_2862

description: Hybridized to customized Axiom array


title: nf_1472

description: Hybridized to customized Axiom array


title: nf_2826

description: Hybridized to customized Axiom array


title: nf_1752

description: Hybridized to customized Axiom array


title: nf_2020

description: Hybridized to customized Axiom array


title: nf_1675

description: Hybridized to customized Axiom array


title: nf_1497

description: Hybridized to customized Axiom array


title: nf_1989

description: Hybridized to customized Axiom array


title: nf_2589

description: Hybridized to customized Axiom array


title: nf_1455

description: Hybridized to customized Axiom array


title: nf_1673

description: Hybridized to customized Axiom array


title: nf_2108

description: Hybridized to customized Axiom array


title: nf_1501

description: Hybridized to customized Axiom array


title: nf_1575

description: Hybridized to customized Axiom array


title: nf_1510

description: Hybridized to customized Axiom array


title: nf_2754

description: Hybridized to customized Axiom array


title: nf_2018

description: Hybridized to customized Axiom array


title: nf_1918

description: Hybridized to customized Axiom array


title: nf_1875

description: Hybridized to customized Axiom array


title: nf_1543

description: Hybridized to customized Axiom array


title: nf_2045

description: Hybridized to customized Axiom array


title: nf_1476

description: Hybridized to customized Axiom array


title: nf_1379

description: Hybridized to customized Axiom array


title: nf_2707

description: Hybridized to customized Axiom array


title: nf_1925

description: Hybridized to customized Axiom array


title: nf_1748

description: Hybridized to customized Axiom array


title: nf_1745

description: Hybridized to customized Axiom array


title: nf_2948

description: Hybridized to customized Axiom array


title: nf_1770

description: Hybridized to customized Axiom array


title: nf_1382

description: Hybridized to customized Axiom array


title: nf_3614

description: Hybridized to customized Axiom array


title: nf_2808

description: Hybridized to customized Axiom array


title: nf_1997

description: Hybridized to customized Axiom array


title: nf_1508

description: Hybridized to customized Axiom array


title: nf_1840

description: Hybridized to customized Axiom array


title: nf_2014

description: Hybridized to customized Axiom array


title: nf_2859

description: Hybridized to customized Axiom array


title: nf_2843

description: Hybridized to customized Axiom array


title: nf_1736

description: Hybridized to customized Axiom array


title: nf_2036

description: Hybridized to customized Axiom array


title: nf_2817

description: Hybridized to customized Axiom array


title: nf_2677

description: Hybridized to customized Axiom array


title: nf_1544

description: Hybridized to customized Axiom array


title: nf_1489

description: Hybridized to customized Axiom array


title: nf_1827

description: Hybridized to customized Axiom array


title: nf_1859

description: Hybridized to customized Axiom array


title: nf_2537

description: Hybridized to customized Axiom array


title: nf_2795

description: Hybridized to customized Axiom array


title: nf_2819

description: Hybridized to customized Axiom array


title: nf_1548

description: Hybridized to customized Axiom array


title: nf_1339

description: Hybridized to customized Axiom array


title: nf_2685

description: Hybridized to customized Axiom array


title: nf_1547

description: Hybridized to customized Axiom array


title: nf_2037

description: Hybridized to customized Axiom array


title: nf_1945

description: Hybridized to customized Axiom array


title: nf_1637

description: Hybridized to customized Axiom array


title: nf_1552

description: Hybridized to customized Axiom array


title: nf_3118

description: Hybridized to customized Axiom array


title: nf_1469

description: Hybridized to customized Axiom array


title: nf_1474

description: Hybridized to customized Axiom array


title: nf_1765

description: Hybridized to customized Axiom array


title: nf_2121

description: Hybridized to customized Axiom array


title: nf_1759

description: Hybridized to customized Axiom array


title: nf_2049

description: Hybridized to customized Axiom array


title: nf_1516

description: Hybridized to customized Axiom array


title: nf_2270

description: Hybridized to customized Axiom array


title: Adults B-cell ALL Bone marrow, sample 168

city: Salamanca

first: Jesús

last: Hernández-Rivas

address: Paseo San Vicente, 88-182

institute: Hospital Universitario de Salamanca, Universidad de Salamanca-CSIC

hyb_protocol: Hybridization was performed according to the instructions in the NimbleGen Array User Guide

scan_protocol: Scanning was performed according to the instructions in the NimbleGen Array User Guide

data_processing: Arrays were processed using Nimblegen's standard protocol and segmented using the CGHweb tool.

source_name: Bone marrow cells (test)

label_protocol: Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA)

value: Bone marrow cells

tag: disease state

value: B-cell acute lymphoblastic leukemia

tag: age group

value: Adults ≥18 years

tag: genetic subtype

value: Hyper (>50)

tag: treatment

value: UNKN

source_name: control

value: Not applicable

tag: reference composition

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: nf_2801

description: Hybridized to customized Axiom array

value: Newfoundland and Labrador

value: Healthy

value: Female


title: nf_1561

description: Hybridized to customized Axiom array

value: Male


title: nf_2349

description: Hybridized to customized Axiom array


title: nf_1934

description: Hybridized to customized Axiom array


title: nf_1773

description: Hybridized to customized Axiom array


title: nf_1767

description: Hybridized to customized Axiom array


title: nf_2338

description: Hybridized to customized Axiom array


title: nf_1590

description: Hybridized to customized Axiom array


title: nf_2009

description: Hybridized to customized Axiom array


title: nf_3132

description: Hybridized to customized Axiom array


title: nf_1562

description: Hybridized to customized Axiom array


title: nf_3147

description: Hybridized to customized Axiom array


title: nf_3142

description: Hybridized to customized Axiom array


title: nf_1936

description: Hybridized to customized Axiom array


title: nf_1550

description: Hybridized to customized Axiom array


title: nf_2002

description: Hybridized to customized Axiom array


title: nf_1482

description: Hybridized to customized Axiom array


title: nf_3563

description: Hybridized to customized Axiom array


title: nf_1435

description: Hybridized to customized Axiom array


title: nf_3606

description: Hybridized to customized Axiom array


title: nf_2161

description: Hybridized to customized Axiom array


title: nf_3065

description: Hybridized to customized Axiom array


title: nf_3562

description: Hybridized to customized Axiom array


title: nf_1729

description: Hybridized to customized Axiom array


title: nf_3141

description: Hybridized to customized Axiom array


title: nf_3603

description: Hybridized to customized Axiom array


title: nf_3005

description: Hybridized to customized Axiom array


title: nf_3136

description: Hybridized to customized Axiom array


title: nf_2173

description: Hybridized to customized Axiom array


title: nf_3115

description: Hybridized to customized Axiom array


title: nf_1956

description: Hybridized to customized Axiom array


title: nf_1588

description: Hybridized to customized Axiom array


title: nf_1595

description: Hybridized to customized Axiom array


title: nf_2991

description: Hybridized to customized Axiom array


title: nf_3114

description: Hybridized to customized Axiom array


title: nf_1965

description: Hybridized to customized Axiom array


title: nf_1589

description: Hybridized to customized Axiom array


title: nf_1564

description: Hybridized to customized Axiom array


title: nf_1493

description: Hybridized to customized Axiom array


title: nf_3022

description: Hybridized to customized Axiom array


title: nf_3081

description: Hybridized to customized Axiom array


title: nf_1649

description: Hybridized to customized Axiom array


title: nf_3053

description: Hybridized to customized Axiom array


title: nf_1612

description: Hybridized to customized Axiom array


title: nf_1598

description: Hybridized to customized Axiom array


title: nf_3021

description: Hybridized to customized Axiom array


title: nf_3605

description: Hybridized to customized Axiom array


title: nf_1929

description: Hybridized to customized Axiom array


title: nf_3062

description: Hybridized to customized Axiom array


title: nf_3061

description: Hybridized to customized Axiom array


title: nf_3046

description: Hybridized to customized Axiom array


title: nf_2989

description: Hybridized to customized Axiom array


title: nf_3043

description: Hybridized to customized Axiom array


title: nf_3149

description: Hybridized to customized Axiom array


title: nf_1376

description: Hybridized to customized Axiom array


title: nf_3636

description: Hybridized to customized Axiom array


title: nf_2996

description: Hybridized to customized Axiom array


title: nf_3653

description: Hybridized to customized Axiom array


title: nf_3607

description: Hybridized to customized Axiom array


title: nf_3012

description: Hybridized to customized Axiom array


title: nf_1954

description: Hybridized to customized Axiom array


title: nf_3157

description: Hybridized to customized Axiom array


title: nf_3646

description: Hybridized to customized Axiom array


title: nf_3067

description: Hybridized to customized Axiom array


title: nf_3159

description: Hybridized to customized Axiom array


title: nf_3045

description: Hybridized to customized Axiom array


title: nf_1674

description: Hybridized to customized Axiom array


title: nf_1540

description: Hybridized to customized Axiom array


title: nf_2224

description: Hybridized to customized Axiom array


title: nf_2118

description: Hybridized to customized Axiom array


title: nf_2943

description: Hybridized to customized Axiom array


title: nf_1519

description: Hybridized to customized Axiom array


title: nf_1554

description: Hybridized to customized Axiom array


title: nf_2044

description: Hybridized to customized Axiom array


title: nf_2591

description: Hybridized to customized Axiom array