title: L1_120B over L0_30A

description: Expression ratio of L1_120B and L0_30A

value: heat-treated spores 120 min after mixing with BHI

value: untreated spores 30 min after mixing with BHI


title: MCF7/shNS cells_Veh treated_rep1

status: Public on Feb 02 2016

type: RNA

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

country: USA

institute: USC

description:
8381653073_G
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF7/shNS cells

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

growth_protocol: cells were grown in phenol red free DMEM containing 10% charcoal stripped serum

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: treated with 10nM E2 or vehicle (ethanol)

tag: cell line

value: MCF7, with Control Non-specific silencing

tag: treatment

value: Veh


title: MCF7/shRx1 cells_Veh treated_rep2

description:
8381653073_B
replicate 2

source_name: MCF7/shRx1 cells

value: MCF7, with RUNX1 silencing


title: L0_30A over L1_90B

city: Ede

first: Jos

last: Boekhorst

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

description: Expression ratio of L0_30A and L1_90B

hyb_protocol: Hybridization was performed as described in van Melis et al., 2011

scan_protocol: Slides were scanned with Agilent G2505C scanner

data_processing: Microarrays were normalized using the approach reported previously (by van Melis et al 2011) for germinating spores involving the creation of so called synthetic microarrays. The background-corrected, raw signals (Cy3 and Cy5 channel) of all arrays were hierarchically clustered (Pearson correlation, complete linkage) using Genemaths XT. New synthetic arrays were defined from sample pairs showing the highest similarity in the clustering. The synthetic microarrays were Lowess normalized and all pairwise ratios were determined. The Lowess-normalized data are available on the series record in the file: cybert_ratios.xlsx.  The sample data table contains the normalized Cy5/Cy3 values that were used in the first step of the analysis.

organism: Bacillus cereus ATCC 14579

label_protocol: Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)

growth_protocol: Untreated and heat-treated (1 min 95C) B. cereus ATCC14579 spores were mixed with BHI and incubated with aeration (200rpm) at 30°C untill harvesting time (see overal design).

extract_protocol: RNA was extracted from samples in TRI-reagent by defrosting on ice, spores were mechanically disrupted by extensive bead beating in the presence of Lysing Matrix B beads. Direct-zol RNA MiniPrep was used according to the manufacturer’s instructions for on column RNA purification. Residual chromosomal DNA was removed by 30 min off column treatment of the samples with TURBO DNA-free Kit. The resulting mRNA was subsequently cleaned with RNeasy Mini Kit. The RNA quantity and quality were checked by UV spectroscopy and RNA 6000 Nanochip.

treatment_protocol: Cells were harvested at above mentioned timepoints (see overall design) by spinning down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen.

tag: strain

value: heat-treated spores 90 min after mixing with BHI


title: MCF7/shRx1 cells_E2 treated_rep2

description:
8381653073_E
replicate 2


title: L1_150A over L1_150B

description: Expression ratio of L1_150A and L1_150B

value: heat-treated spores 150 min after mixing with BHI


title: L1_90B over L1_120B

description: Expression ratio of L1_90B and L1_120B


title: MCF7/shRx1 cells_Veh treated_rep3

description:
8381653073_C
replicate 3


title: Mesothelioma sample (MARF40-III-1)

status: Public on Feb 03 2016

type: genomic

city: Honolulu

first: Michele

last: Carbone

state: HI

address: 701 Ilalo Street, Room 437

institute: University of Hawaii Cancer Center

description: Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-12v1-1 Genotyping BeadChips (Illumina).

hyb_protocol: Fragmented amplified DNA was resuspended in RA1 and hybridized to the BeadChip in PB2 at 48C for 16-24 hours.The BeadChip was washed in PB1 and then single-base extension and allele-specific staining performed.

scan_protocol: Following allele-specific staining, the BeadChip was imaged on iScan or BeadArray Reader scanners using standard Illumina protocols.

data_processing: Samples were QC checked for per-sample call-rate and then Illumina GenCall software used to cluster and produce genotype calls from the .idat files.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Whole blood

label_protocol: Genomic DNA was quantified, denatured, and then amplified at 37C for 20-24 hours. Amplified DNA was then fragmented at 37C in FMS for 1 hour.

extract_protocol: Genomic DNA was extracted from whole blood using DNeasy Blood & Tissue or QiAamp DNA Micro Kits (QIAGEN, Hilden, Germany).

tag: diagnosis

value: Mesothelioma

tag: tissue

value: whole blood


title: MCF7/shRx1 cells_E2 treated_rep3

description:
8381653073_F
replicate 3


title: MCF7/shRx1 cells_Veh treated_rep1

description:
8381653073_A
replicate 1


title: OE control, 8B

city: Toronto

first: John

middle: E

last: Dick

address: 101 College St. Toronto

country: Canada

institute: Ontario Cancer Institute

description:
8B
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Scanned with Illumina's BeadArray Reader using standard protocols.

data_processing: The data were normalised using quantile normalisation (GeneSpring GX 10.0.2).

source_name: CD34+/CD38+, miR-126 overexpression control

label_protocol: cRNA was prepared using Ambion - Illumina TotalPrep-96 RNA Amplification Kit.

extract_protocol: RNA was extracted using Trizol reagent.

treatment_protocol: miR-126 sponge or miR-126-containing viral particles (and corresponding controls).

tag: cell type

value: AML cell line

tag: cell population

value: control


title: MCF7/shRx1 cells_E2 treated_rep1

description:
8381653073_D
replicate 1


title: L1_150B over L0_50B

description: Expression ratio of L1_150B and L0_50B

value: untreated spores 50 min after mixing with BHI


title: L0_20B over L1_90B

description: Expression ratio of L0_20B and L1_90B

value: untreated spores 20 min after mixing with BHI


title: OE control, 9A

description:
9A
Replicate 3

source_name: CD34+/CD38-, miR-126 overexpression control


title: OE control, 7A

description:
7A
Replicate 1


title: L1_120B over L0_30B

description: Expression ratio of L1_120B and L0_30B


title: Mesothelioma sample (MARF2-IV-2)


title: Mesothelioma sample (MARF11-III-1)


title: L0_20B over L0_30B

description: Expression ratio of L0_20B and L0_30B


title: L0_30B over L1_120A

description: Expression ratio of L0_30B and L1_120A


title: Normal sample (UHCC4)

value: Normal sample


title: L1_120A over L1_150A

description: Expression ratio of L1_120A and L1_150A


title: L1_50B over L0_10B

description: Expression ratio of L1_50B and L0_10B

value: heat-treated spores 50 min after mixing with BHI

value: untreated spores 10 min after mixing with BHI


title: L0_20A over L1_90A

description: Expression ratio of L0_20A and L1_90A


title: L0_30A over L1_120A

description: Expression ratio of L0_30A and L1_120A


title: Normal sample (UHCC1)


title: OE control, 7B

description:
7B
Replicate 3


title: Mesothelioma sample (MARF18-III-1)


title: Normal sample (UHCC2)


title: OE control, 8D

description:
8D
Replicate 3

source_name: CD34-/CD38-, miR-126 overexpression control


title: L1_90A over L1_50A

description: Expression ratio of L1_90A and L1_50A


title: OE control, 9D

description:
9D
Replicate 2


title: OE control, 7C

description:
7C
Replicate 1

source_name: CD34-/CD38+, miR-126 overexpression control


title: KD control, 3B

description:
3B
Replicate 2

source_name: CD34+/CD38+, miR-126 knockdown control


title: KD control, 1B

description:
1B
Replicate 1


title: OE control, 7D

description:
7D
Replicate 1


title: KD control, 2B

description:
2B
Replicate 3


title: L1_50A over L1_50B

description: Expression ratio of L1_50A and L1_50B


title: OE control, 8A

description:
8A
Replicate 2


title: Normal sample (UHCC3)


title: L1_90A over L0_20B

description: Expression ratio of L1_90A and L0_20B


title: KD control, 3A

description:
3A
Replicate 3

source_name: CD34+/CD38-, miR-126 knockdown control


title: KD control, 1C

description:
1C
Replicate 3

source_name: CD34-/CD38+, miR-126 knockdown control


title: OE control, 8C

description:
8C
Replicate 2


title: KD control, 3C

description:
3C
Replicate 2


title: KD control, 2A

description:
2A
Replicate 2


title: KD control, 1A

description:
1A
Replicate 1


title: L0_10B over L0_10A

description: Expression ratio of L0_10B and L0_10A


title: OE control, 9C

description:
9C
Replicate 3


title: L0_10A over L0_20A

description: Expression ratio of L0_10A and L0_20A


title: L0_50B over L0_50A

description: Expression ratio of L0_50B and L0_50A


title: KD control, 1D

description:
1D
Replicate 3

source_name: CD34-/CD38-, miR-126 knockdown control


title: L1_90B over L0_20A

description: Expression ratio of L1_90B and L0_20A


title: 126OE, 11B

description:
11B
Replicate 3

source_name: CD34+/CD38+, miR-126 overexpression

value: miR-126-containing viral particles


title: KD control, 2C

description:
2C
Replicate 1


title: KD control, 2D

description:
2D
Replicate 1


title: 126OE, 10A

description:
10A
Replicate 3

source_name: CD34+/CD38-, miR-126 overexpression


title: SAM_EB-non_EB (Hinp1I) Rep.4

city: Quebec city

first: Habib

middle: A.

last: Shojaei Saadi

state: Quebec

address: 2440 bl hochelaga, pavillon inaf

institute: Laval University

description: Biological replicate 4 of 4. (Hinp1I)-Dye-Swap

hyb_protocol: Hybridizations were performed according to the microarray manufacturer's instructions (Agilent Technologies, Santa Clara, USA). Briefly, 1 µg of labeled sample (in 40 µL) was mixed with 158 µL of hybridization master mix containing 25 µL of bovine Cot-1 D

scan_protocol: Slides were scanned with the PowerScanner (Tecan, Männedorf, Switzerland)

data_processing: Intensity values were obtained from slide images using the Array-Pro Analyzer 6.3 software (MediaCybernetics, Bethesda, MD, USA). Raw intensities were subjected to within-array normalization(loess) followed by between-array normalization (quantile) using

organism: Bos taurus

source_name: SAM

label_protocol: Comparable DNA inputs (10 ng) were used for both embryo and sperm samples. For quality control purposes, all samples were spiked with a mixture of six synthetic DNA constructs all bearing an MseI restriction site at each end. One pair of constructs was de

growth_protocol: Bovine blastocyst production in synthetic oviduct fluid (SOF) media was performed with some modifications. Dairy cattle ovaries were collected from a commercial slaughterhouse and were transported to the laboratory in saline (0.9% NaCl) containing 1% Anti

extract_protocol: Extraction of gDNA from the collected EB embryos was carried out using the AllPrep DNA/RNA Mini Kit (Qiagen Canada Inc., Mississauga, ON, Canada) according to the manufacture manual and the samples were eluted in 37 µL for extracted DNA . The extracted gD

treatment_protocol: In order to treat the early embryos, 10 µM of S-(5?-Adenosyl)-L-methionine chloride dihydrochloride, SAM (Sigma-Aldrich, Oakville, Canada# A7007) were freshly prepared by dissolving in SOF medium for each IVF trial and were quickly aliquoted into 100 µL a

value: Expanded blastocyst

source_name: Cnt.


title: OE control, 9B

description:
9B
Replicate 2


title: KD control, 3D

description:
3D
Replicate 2


title: 126OE, 11A

description:
11A
Replicate 2


title: SAM_EB-non_EB (Aci1I) Rep.2

description: Biological replicate 2 of 4. (Aci1I)-Dye-Swap


title: 126OE, 10B

description:
10B
Replicate 1


title: SAM_EB-non_EB (Hinp1I) Rep.3

description: Biological replicate 3 of 4. (Hinp1I)-Dye-Swap


title: SAM_EB-non_EB (Hinp1I) Rep.1

description: Biological replicate 2 of 4. (Hinp1I)-Dye-Swap


title: SAM_EB-non_EB (Hinp1I) Rep.2

description: Biological replicate 1 of 4. (Hinp1I)-Dye-Swap


title: SAM_EB-non_EB (HpaII) Rep.4

description: Biological replicate 4 of 4. (HpaII)-Dye-Swap


title: SAM_EB-non_EB (Aci1I) Rep.4

description: Biological replicate 4 of 4. (Aci1I)-Dye-Swap


title: 126OE, 12A

description:
12A
Replicate 1


title: SAM_EB-non_EB (Aci1I) Rep.1

description: Biological replicate 1 of 4. (Aci1I)-Dye-Swap


title: 126OE, 12C

description:
12C
Replicate 3

source_name: CD34-/CD38+, miR-126 overexpression


title: SAM_EB-non_EB (HpaII) Rep.3

description: Biological replicate 3 of 4. (HpaII)-Dye-Swap


title: 126OE, 11C

description:
11C
Replicate 2


title: 126OE, 10C

description:
10C
Replicate 1


title: MEP rep4

city: Fukuoka

first: Kohta

last: Miyawaki

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

description: Gene expression of Megakaryocyte Erythrocyte Progenitor from bone marrow of healthy donor

hyb_protocol: cRNA (800 ng) was hybridized to the microarray chip (SurePrint G3 Human Gene Expression 8x60K v2, Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT sensitivity is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw expression data was imported and normalized by using GeneSpring GX software (Agilent Technologies)

source_name: Bone Marrow, MEP, replicate 4

label_protocol: Cyanine3-labeled cRNA from each sample was prepared to mRNA amplification by using Low Input Quick Amp Labeling Kit (one-color) (Agilent Technologies) according to the manufacture's instruction.

extract_protocol: Target populations ranging in number from 5000 cells were double-sorted directly to Trizol reagent (Life Technologies). Total RNA extracted in accordance with the manufacture's instruction.

value: Bone Marrow

tag: gender

value: Male


title: GMP rep4

description: Gene expression of Granulocyte Monocyte Progenitor from bone marrow of healthy donor

source_name: Bone Marrow, GMP, replicate 4


title: MEP rep5

source_name: Bone Marrow, MEP, replicate 5


title: SAM-treated Expnaded Blastocysts-non-treated Expanded Blastocysts (HpaII) Rep.1

description: Biological replicate 1 of 4. (HpaII)-Dye-Swap


title: SAM_EB-non_EB (HpaII) Rep.2

description: Biological replicate 2 of 4. (HpaII)-Dye-Swap


title: SAM_EB-non_EB (Aci1I) Rep.3

description: Biological replicate 3 of 4. (Aci1I)-Dye-Swap


title: MegP rep4

description: Gene expression of Megakaryocyte Progenitor from bone marrow of healthy donor

source_name: Bone Marrow, MegP, replicate 4


title: 126KD, 4B

description:
4B
Replicate 3

source_name: CD34+/CD38+, miR-126 knockdown

value: miR-126 sponge


title: 126OE, 11D

description:
11D
Replicate 1

source_name: CD34-/CD38-, miR-126 overexpression


title: HSC rep4

description: Gene expression of HSC from bone marrow of healthy donor

source_name: Bone Marrow, HSC, replicate 4


title: CMP rep4

description: Gene expression of Common Myeloid Progenitor from bone marrow of healthy donor

source_name: Bone Marrow, CMP, replicate 4


title: MEP rep3

source_name: Bone Marrow, MEP, replicate 3


title: GMP rep3

source_name: Bone Marrow, GMP, replicate 3


title: 126OE, 10D

description:
10D
Replicate 2


title: 126KD, 6B

description:
6B
Replicate 2


title: L0_50A over L0_30A

description: Expression ratio of L0_50A and L0_30A

value: untreated spores 30 min after mixing with BHI


title: CMP rep3

source_name: Bone Marrow, CMP, replicate 3


title: 126KD, 4A

description:
4A
Replicate 3

source_name: CD34+/CD38-, miR-126 knockdown


title: MegP rep3

source_name: Bone Marrow, MegP, replicate 3


title: 126OE, 12D

description:
12D
Replicate 3


title: HSC rep3

source_name: Bone Marrow, HSC, replicate 3


title: 126KD, 5B

description:
5B
Replicate 1


title: 126KD, 6A

description:
6A
Replicate 1


title: 126KD, 5A

description:
5A
Replicate 2


title: HSC rep2

source_name: Bone Marrow, HSC, replicate 2


title: MegP rep2

source_name: Bone Marrow, MegP, replicate 2


title: GMP rep2

source_name: Bone Marrow, GMP, replicate 2


title: CMP rep2

source_name: Bone Marrow, CMP, replicate 2


title: 126KD, 5C

description:
5C
Replicate 3

source_name: CD34-/CD38+, miR-126 knockdown


title: 126KD, 4C

description:
4C
Replicate 1


title: MEP rep2

source_name: Bone Marrow, MEP, replicate 2


title: GMP rep1

source_name: Bone Marrow, GMP, replicate 1


title: piNC

city: guangzhou

first: xue

last: zhang

state: guangdong

address: 74 zhongshan 2 Rd

country: China

institute: sun yat sen university

description: Gene expression data from dendritic cells transfected with piNC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: dendritic cells from healthy donor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: PBMCs were isolated from healthy human donors through Ficoll gradient centrifugation and then CD14+ monocytes were isolated with BD IMagTM anti-human CD14 magnetic particles. The cells were cultured in the RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), 100 U/ml of penicillin, and 100 U/ml of streptomycin (Hyclone). GM-CSF (1000 U/ml), and IL-4 (500 U/ml) were used to induce the differentiation of monocytes into DCs

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

treatment_protocol: The DCs were transfected with piNC or td-piR(Glu) with lipofectamine RNAiMAX during the differentiation from monocytes.

value: dendritic cells

tag: transfection

value: piNC


title: MegP rep1

source_name: Bone Marrow, MegP, replicate 1


title: BT-474 cell line_HER2 siRNA siRNA_10 nM Estrogen_4 hrs_Replica 3.

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing: Expressions estimated using BRB Array Tools software, RMA signal method

source_name: BT-474_HER2 siRNA siRNA_10 nM Estrogen_24 hrs

label_protocol: 3' IVT express

treatment_protocol: BT-474 cell line.

tag: genotype/variation

value: HER-2 siRNA knockdown

tag: treated with

value: 10 nM Estrogen

tag: treatment duration

value: 4 hours


title: BT-474 cell line_HER2 siRNA siRNA_10 nM Estrogen_4 hrs_Replica 2.

source_name: BT-474_HER2 siRNA siRNA_10 nM Estrogen_4 hrs


title: td-piR(Glu)

description: Gene expression data from dendritic cells transfected with td-piR(Glu)

value: td-piR(Glu)


title: MEP rep1

source_name: Bone Marrow, MEP, replicate 1


title: BT-474 cell line_HER2 siRNA_Vehicle (0.001% Ethanol)_4 hrs_Replica 3.

source_name: BT-474_HER2 siRNA_Vehicle (0.001% Ethanol)_4 hrs

value: 0.001% Ethanol (vehicle)


title: CMP rep1

source_name: Bone Marrow, CMP, replicate 1


title: 126KD, 5D

description:
5D
Replicate 3

source_name: CD34-/CD38-, miR-126 knockdown

value: AML cell line


title: BT-474 cell line_HER2 siRNA_Vehicle (0.001% Ethanol)_4 hrs_Replica 1.


title: BT-474 cell line_Control siRNA_10 nM Estrogen_4 hrs_Replica 1.

source_name: BT-474_Control siRNA_10 nM Estrogen_4 hrs

value: Control siRNA


title: 126KD, 6C

description:
6C
Replicate 2


title: BT-474 cell line_HER2 siRNA siRNA_10 nM Estrogen_24 hrs_Replica 2.

value: 24 hours


title: BT-474 cell line_Control siRNA_Vehicle (0.001% Ethanol)_4 hrs_Replica 3.

source_name: BT-474_Control siRNA_Vehicle (0.001% Ethanol)_4 hrs


title: BT-474 cell line_HER2 siRNA siRNA_10 nM Estrogen_24 hrs_Replica 1.


title: BT-474 cell line_HER2 siRNA siRNA_10 nM Estrogen_24 hrs_Replica 3.


title: 126KD, 6D

description:
6D
Replicate 1


title: 126OE, 12B

description:
12B
Replicate 2

source_name: CD34+/CD38+, miR-126 overexpression


title: BT-474 cell line_HER2 siRNA_Vehicle (0.001% Ethanol)_4 hrs_Replica 2.


title: BT-474 cell line_Control siRNA_10 nM Estrogen_4 hrs_Replica 3


title: BT-474 cell line_HER2 siRNA_Vehicle (0.001% Ethanol)_24 hrs_Replica 1.

source_name: BT-474_HER2 siRNA_Vehicle (0.001% Ethanol)_24 hrs


title: HSC rep1

source_name: Bone Marrow, HSC, replicate 1


title: BT-474 cell line_Control siRNA_Vehicle (0.001% Ethanol)_4 hrs_Replica 1.


title: BT-474 cell line_HER2 siRNA_Vehicle (0.001% Ethanol)_24 hrs_Replica 3.


title: BT-474 cell line_HER2 siRNA_Vehicle (0.001% Ethanol)_24 hrs_Replica 2.


title: BT-474 cell line_Control siRNA_10 nM Estrogen_24 hrs_Replica 2.

source_name: BT-474_Control siRNA_10 nM Estrogen_24 hrs


title: Colorectal Tissue-112911-01TB

city: Riyadh

first: Musa

last: Gabere

address: Kashmalaan

department: Bioinformatics

country: Saudi Arabia

institute: King Abdullah International Medical Research Center,  NGHA

description: Colorectal Normal Tissue-112911-01TB-Affymetrix Human Exon 1.0 ST.CEL

hyb_protocol: GeneChip Hybridization Wash and Stain Kit (cat # 900720) was procured from Affymetrix and used according the manufacturers protocol.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations

data_processing:
Data Processing using Expression console Software (v.1.4.1). The default recommended settings by Expression console was used to analyze the data; RMA for quantile normalization and log2-transformation.
probe group file: HuEx-1_0-st-v2.r2.pgf

label: Standard Affymetrix protocol

source_name: Colorectal Tumor Tissue

label_protocol: Gene Chip WT Terminal Labelling and Controls Kit (cat # 951024) was procured from Affymetrix and used according the manufacturers protocol.

growth_protocol: NONE; Tissue samples were used

extract_protocol: RNA was isolated from <30mg of biopsy and surgery derived tissues using Macherey Nagel (Germany) Trio Kit. Both DNA and RNA were extracted in the same protocol accoding to manufacturers protocol

tag: subject status

value: colorectal cancer (CRC) patient

tag: subject/sample id

value: Female

tag: age (yrs)

value: Descending colon (sigmoid)

tag: tnm classification

value: Tumor


title: Colorectal Tissue-121613-01NB

description: Colorectal Normal Tissue-121613-01NB-Affymetrix Human Exon 1.0 ST.CEL

source_name: Colorectal Normal Tissue

value: Male

value: Sigmoid

value: Adjacent Normal


title: BT-474 cell line_Control siRNA_10 nM Estrogen_24 hrs_Replica 1.


title: Colorectal Tissue-112911-01NB

description: Colorectal Normal Tissue-112911-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-112611-03TB

description: Colorectal Normal Tissue-112611-03TB-Affymetrix Human Exon 1.0 ST.CEL

value: Descending colon


title: BT-474 cell line_Control siRNA_Vehicle (0.001% Ethanol)_24 hrs_Replica 1.

source_name: BT-474_Control siRNA_Vehicle (0.001% Ethanol)_24 hrs


title: BT-474 cell line_Control siRNA_Vehicle (0.001% Ethanol)_24 hrs_Replica 2.


title: Colorectal Tissue-112611-02TB

description: Colorectal Normal Tissue-112611-02TB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-121613-01TB

description: Colorectal Normal Tissue-121613-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-092511-01TB

description: Colorectal Normal Tissue-092511-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: Ascending (hepatic flexure)


title: Colorectal Tissue-112611-03NB

description: Colorectal Normal Tissue-112611-03NB-Affymetrix Human Exon 1.0 ST.CEL


title: BT-474 cell line_Control siRNA_Vehicle (0.001% Ethanol)_4 hrs_Replica 2.


title: Colorectal Tissue-100311-01TB

description: Colorectal Normal Tissue-100311-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: transverse (Hepatic flexure)


title: Colorectal Tissue-100311-01NB

description: Colorectal Normal Tissue-100311-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-082812-01TB

description: Colorectal Normal Tissue-082812-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-092511-01NB

description: Colorectal Normal Tissue-092511-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: BT-474 cell line_Control siRNA_Vehicle (0.001% Ethanol)_24 hrs_Replica 3.


title: Colorectal Tissue-112611-01NB

description: Colorectal Normal Tissue-112611-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-092711-01TB

description: Colorectal Normal Tissue-092711-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: sigmoid


title: BT-474 cell line_Control siRNA_10 nM Estrogen_24 hrs_Replica 3

value: 10 nM Estrogen


title: Colorectal Tissue-082812-01NB

description: Colorectal Normal Tissue-082812-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-072711-01NB

description: Colorectal Normal Tissue-072711-01NB-Affymetrix Human Exon 1.0 ST.CEL

value: Ascending colon (cecal)


title: Colorectal Tissue-073011-02NB

description: Colorectal Normal Tissue-073011-02NB-Affymetrix Human Exon 1.0 ST.CEL

value: Right colon (cecum)


title: 126KD, 4D

description:
4D
Replicate 2

value: AML cell line

value: miR-126 sponge


title: Colorectal Tissue-070911-01NB

description: Colorectal Normal Tissue-070911-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-052311-01TB

description: Colorectal Normal Tissue-052311-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-061013-01TB

description: Colorectal Normal Tissue-061013-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-042413-01TB

description: Colorectal Normal Tissue-042413-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: Rectal


title: Colorectal Tissue-073011-01TB

description: Colorectal Normal Tissue-073011-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: colorectal cancer (CRC) patient


title: Colorectal Tissue-052811-01TB

description: Colorectal Normal Tissue-052811-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: Female

value: rectosigmoid


title: Colorectal Tissue-052811-01NB

description: Colorectal Normal Tissue-052811-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-012214-01NB

description: Colorectal Normal Tissue-012214-01NB-Affymetrix Human Exon 1.0 ST.CEL

value: transverse colon


title: Colorectal Tissue-010714-01NB

description: Colorectal Normal Tissue-010714-01NB-Affymetrix Human Exon 1.0 ST.CEL

value: Desending colon


title: Colorectal Tissue-012114-01NB

description: Colorectal Normal Tissue-012114-01NB-Affymetrix Human Exon 1.0 ST.CEL

value: Male


title: Colorectal Tissue-012014-01TB

description: Colorectal Normal Tissue-012014-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: Tumor


title: lin-CB 3 CD34-CD38+

description: CB 27G

hyb_protocol: microRNA hybridization was performed according to Lu et al. Nature 2005, PubMed 15944708

data_processing:
Data processing was performed according to Lu et al. Nature 2005, PubMed 15944708
Raw data were log2 transformed and thresholded at 4

label: Biotin

source_name: Peripheral Blood/AML

label_protocol: microRNA labeling was performed according to Lu et al. Dev Cell 2008, PubMed 18539114.

growth_protocol: White blood cells from the peripheral blood of AML patients were enriched by Ficoll gradient centrifugation and viably frozen

extract_protocol: Total RNA was recovered from each cell population by standard Trizol purification

treatment_protocol: AML patient samples were thawed, stained for CD34 and CD38 cell surface marker expression and flow sorted in to 4 populations (CD34+/CD38-, CD34+/CD38+, CD34-/CD38+. and CD34-/CD38-).  Each population was xenotransplanted to assess Leukemia initiating capacity


title: Colorectal Tissue-012114-01TB

description: Colorectal Normal Tissue-012114-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: lin-CB 3 CD34+CD38-

description: CB 27A

scan_protocol: microRNA hybridization was performed according to Lu et al. Nature 2005, PubMed 15944708


title: CD34-CD38

description: 8227 E

source_name: AML cell line


title: BT-474 cell line_HER2 siRNA siRNA_10 nM Estrogen_4 hrs_Replica 1.

value: HER-2 siRNA knockdown

value: 4 hours


title: lin-CB 2 CD34+CD38-

description: CB 26A


title: lin-CB 1 CD34-CD38+

description: CB 25G


title: lin-CB 2 CD34+CD38lo

description: CB 26C


title: lin-CB 3 CD34+CD38lo

description: CB 27C


title: Colorectal Tissue-062011-01TB

description: Colorectal Normal Tissue-062011-01TB-Affymetrix Human Exon 1.0 ST.CEL

value: Proximal sigmoid


title: CD34+CD38-

description: 8227 A


title: Colorectal Tissue-012214-01TB

description: Colorectal Normal Tissue-012214-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-070113-01NB

description: Colorectal Normal Tissue-070113-01NB-Affymetrix Human Exon 1.0 ST.CEL

value: Adjacent Normal


title: Colorectal Tissue-033114-01NB

description: Colorectal Normal Tissue-033114-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-051611-01NB

description: Colorectal Normal Tissue-051611-01NB-Affymetrix Human Exon 1.0 ST.CEL

value: sigmoid


title: Colorectal Tissue-052311-01NB

description: Colorectal Normal Tissue-052311-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-070113-01TB

description: Colorectal Normal Tissue-070113-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: lin-CB 1 CD34+CD38lo

description: CB 25C


title: CD34-CD38-

description: 8227 G


title: Colorectal Tissue-010714-01TB

description: Colorectal Normal Tissue-010714-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-012014-01NB

description: Colorectal Normal Tissue-012014-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: Colorectal Tissue-033114-01TB

description: Colorectal Normal Tissue-033114-01TB-Affymetrix Human Exon 1.0 ST.CEL


title: lin-CB 1 CD34+CD38+

description: CB 25E


title: Colorectal Tissue-061013-01NB

description: Colorectal Normal Tissue-061013-01NB-Affymetrix Human Exon 1.0 ST.CEL


title: aml 24 CD34+CD38+

description: aml 24C

tag: in vivo leukemia initiating capacity

value: Not Tested


title: aml 24 CD34+CD38-

description: aml 24A


title: lin-CB 1 bulk cells

description: CB 25J

value: bulk cells


title: aml 24 bulk blasts

description: aml 24H

value: bulk blasts


title: lin-CB 1 CD34+CD38-

description: CB 25A


title: aml 24 CD34-CD38+

description: aml 24E


title: lin-CB 1 CD34-CD38-

description: CB 25H


title: aml 24 CD34-CD38-

description: aml 24G


title: aml 22 CD34-CD38+

description: aml 22E


title: Colorectal Tissue-100311-03NB

description: Colorectal Normal Tissue-100311-03NB-Affymetrix Human Exon 1.0 ST.CEL

value: transverse (Hepatic flexure)


title: aml 23 bulk blasts

description: aml 23H


title: aml 23 CD34+CD38+

description: aml 23C


title: aml 22 bulk blasts

description: aml 22H


title: aml 23 CD34-CD38+

description: aml 23E


title: BT-474 cell line_Control siRNA_10 nM Estrogen_4 hrs_Replica 2.

tag: cell line

value: Control siRNA

value: 10 nM Estrogen


title: aml 22 CD34+CD38+

description: aml 22C


title: aml 21 CD34-CD38+

description: aml 21E


title: aml 22 CD34+CD38-

description: aml 22A


title: aml 23 CD34+CD38-

description: aml 23A


title: aml 21 CD34+CD38-

description: aml 21A


title: aml 20 CD34-CD38-

description: aml 20G


title: VUB31_D_27

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829070B_bottom_Cy3_female_fused.txt, sample_vs_male_reference:131206-829070B_bottom_Cy3_male_fused.txt

hyb_protocol: After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files

data_processing: .TIFF files were imported in, and processed by, BlueFuse Multi 3.1.

source_name: hESC culture

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.

tag: sample

value: Single hESC

tag: assayed molecule

value: Amplified DNA

tag: density group

value: high

source_name: female/male reference

value: reference


title: VUB31_D_30

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140424-829012B_top_female_fused2.txt, sample_vs_male_reference:140424-829012B_top_male_fused2.txt


title: VUB31_D_28

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829070B_bottom_Cy5_female_fused.txt, sample_vs_male_reference:131206-829070B_bottom_Cy5_male_fused.txt


title: aml 22 CD34-CD38-

description: aml 22G


title: aml 20 CD34-CD38+

description: aml 20E


title: aml 20 CD34+CD38+

description: aml 20C


title: aml 19 bulk blasts

description: aml 19H


title: aml 20 CD34+CD38-

description: aml 20A


title: aml 21 CD34+CD38+

description: aml 21C


title: aml 19 CD34-CD38-

description: aml 19G

value: Engrafting


title: VUB31_D_29

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140424-829012B_top_female_fused.txt, sample_vs_male_reference:140424-829012B_top_male_fused.txt


title: VUB31_D_24

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140424-829011B_bottom_female_fused.txt, sample_vs_male_reference:140424-829011B_bottom_male_fused.txt


title: aml 19 CD34+CD38+

description: aml 19C


title: aml 19 CD34-CD38+

description: aml 19E


title: aml 18 bulk blasts

description: aml 18H


title: VUB31_D_21

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829068B_top_Cy5_female_fused.txt, sample_vs_male_reference:131206-829068B_top_Cy5_male_fused.txt


title: aml 19 CD34+CD38-

description: aml 19A


title: VUB31_D_26

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829070B_top_Cy5_female_fused.txt, sample_vs_male_reference:131206-829070B_top_Cy5_male_fused.txt


title: VUB31_D_22

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829069B_top_Cy3_female_fused.txt, sample_vs_male_reference:131206-829069B_top_Cy3_male_fused.txt


title: aml 18 CD34-CD38-

description: aml 18G


title: VUB31_D_25

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829070B_top_Cy3_female_fused.txt, sample_vs_male_reference:131206-829070B_top_Cy3_male_fused.txt


title: aml 18 CD34-CD38+

description: aml 18E

value: Non-Engrafting


title: VUB31_D_20

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829068B_top_Cy3_female_fused.txt, sample_vs_male_reference:131206-829068B_top_Cy3_male_fused.txt


title: VUB31_D_17

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130805-829051B_top_Cy3_female_fused.txt, sample_vs_male_reference:130805-829051B_top_Cy3_male_fused.txt


title: VUB31_D_19

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130805-829051B_bottom_Cy5_female_fused.txt, sample_vs_male_reference:130805-829051B_bottom_Cy5_male_fused.txt


title: VUB31_D_15

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130805-829050B_top_Cy5_female_fused.txt, sample_vs_male_reference:130805-829050B_top_Cy5_male_fused.txt


title: VUB31_D_16

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130805-829050B_bottom_Cy3_female_fused.txt, sample_vs_male_reference:130805-829050B_bottom_Cy3_male_fused.txt


title: VUB31_D_14

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130805-829050B_top_Cy3_female_fused.txt, sample_vs_male_reference:130805-829050B_top_Cy3_male_fused.txt


title: VUB31_D_18

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130805-829051B_top_Cy5_female_fused.txt, sample_vs_male_reference:130805-829051B_top_Cy5_male_fused.txt


title: aml 18 CD34+CD38+

description: aml 18C


title: aml 18 CD34+CD38-

description: aml 18A


title: VUB31_D_13

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130805-829048B_top_Cy5_female_fused.txt, sample_vs_male_reference:130805-829048B_top_Cy5_male_fused.txt


title: VUB31_D_23

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 131206-829069B_top_Cy5_female_fused.txt, sample_vs_male_reference:131206-829069B_top_Cy5_male_fused.txt


title: aml 17 CD34-CD38-

description: aml 17G


title: aml 17 bulk blasts

description: aml 17H


title: aml 17 CD34-CD38+

description: aml 17E


title: aml 17 CD34+CD38-

description: aml 17A


title: aml 16 bulk blasts

description: aml 16H


title: VUB31_D_12

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829046B_bottom_Cy5_female_fused.txt, sample_vs_male_reference:130724-829046B_bottom_Cy5_male_fused.txt


title: aml 16 CD34-CD38+

description: aml 16E


title: VUB31_D_11

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829046B_bottom_Cy3_female_fused.txt, sample_vs_male_reference:130724-829046B_bottom_Cy3_male_fused.txt


title: VUB31_D_10

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829046B_top_Cy5_female_fused.txt, sample_vs_male_reference:130724-829046B_top_Cy5_male_fused.txt


title: VUB31_D_09

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829046B_top_Cy3_female_fused.txt, sample_vs_male_reference:130724-829046B_top_Cy3_male_fused.txt


title: aml 16 CD34+CD38+

description: aml 16C


title: aml 16 CD34-CD38-

description: aml 16G


title: aml 15 bulk blasts

description: aml 15H


title: VUB31_D_03

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130528-376010B_top_Cy3_female_fused.txt, sample_vs_male_reference:130528-376010B_top_Cy3_male_fused.txt


title: aml 16 CD34+CD38-

description: aml 16A


title: VUB31_D_04

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130528-376010B_top_Cy5_female_fused.txt, sample_vs_male_reference:130528-376010B_top_Cy5_male_fused.txt


title: VUB31_D_05

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130528-376010B_bottom_Cy3_female_fused.txt, sample_vs_male_reference:130528-376010B_bottom_Cy3_male_fused.txt


title: VUB31_D_06

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130528-376010B_bottom_Cy5_female_fused.txt, sample_vs_male_reference:130528-376010B_bottom_Cy5_male_fused.txt


title: VUB31_D_07

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829045B_bottom_Cy3_female_fused.txt, sample_vs_male_reference:130724-829045B_bottom_Cy3_male_fused.txt


title: VUB31_D_08

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829045B_bottom_Cy5_female_fused.txt, sample_vs_male_reference:130724-829045B_bottom_Cy5_male_fused.txt


title: aml 15 CD34-CD38+

description: aml 15E


title: aml 15 CD34+CD38+

description: aml 15C


title: aml 15 CD34-CD38-

description: aml 15G


title: VUB31_A_29

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829034B_top_female_fused2.txt, sample_vs_male_reference:140513-829034B_top_male_fused2.txt

value: low


title: VUB31_A_28

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829034B_top_female_fused.txt, sample_vs_male_reference:140513-829034B_top_male_fused.txt


title: VUB31_D_01

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829045B_top_Cy3_female_fused.txt, sample_vs_male_reference:130724-829045B_top_Cy3_male_fused.txt


title: VUB31_A_27

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829033B_bottom_female_fused2.txt, sample_vs_male_reference:140513-829033B_bottom_male_fused2.txt


title: VUB31_D_02

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829045B_top_Cy5_female_fused.txt, sample_vs_male_reference:130724-829045B_top_Cy5_male_fused.txt


title: aml 17 CD34+CD38+

description: aml 17C


title: VUB31_A_26

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829033B_bottom_female_fused.txt, sample_vs_male_reference:140513-829033B_bottom_male_fused.txt


title: aml 14 CD34-CD38-

description: aml 14G


title: aml 15 CD34+CD38-

description: aml 15A


title: aml 13 bulk blasts

description: aml 13H


title: aml 14 CD34+CD38+

description: aml 14C


title: aml 14 CD34-CD38+

description: aml 14E


title: mouse_#5_P21_control

city: Tempe

first: Jason

middle: M

last: Newbern

state: AZ

department: School of Life Sciences

institute: Arizona State University

hyb_protocol: According to manufactory protocol (Affymatrix) conducted by UNC functional genomics core facility

data_processing: Data were analyzed using Partek Genomics Suite Version 6

organism: Mus musculus

source_name: sensoricortex

extract_protocol: According to manufactory protocol (Qiagen miRNeasy kit)

tag: tissue

value: sensoricortex

value: control (gain of function)

tag: age

value: Postnatal day 21


title: aml 13 CD34-CD38-

description: aml 13G

tag: cell population


title: aml 14 CD34+CD38-

description: aml 14A


title: mouse_#6_P21_mutant

scan_protocol: According to manufactory protocol (Affymatrix) conducted by UNC functional genomics core facility

value: mutant (gain of function)


title: mouse_#3_P21_mutant

label_protocol: According to manufactory protocol (Affymatrix) conducted by UNC functional genomics core facility


title: aml 13 CD34-CD38+

description: aml 13E

value: Not Tested


title: mouse_#4_P21_control


title: mouse_#2_P21_control


title: mouse_#1_P21_mutant


title: aml 13 CD34+CD38-

description: aml 13A


title: VUB31_A_23

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829014B_top_female_fused2.txt, sample_vs_male_reference:140513-829014B_top_male_fused2.txt


title: aml 13 CD34+CD38+

description: aml 13C


title: VUB31_A_22

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829014B_top_female_fused.txt, sample_vs_male_reference:140513-829014B_top_male_fused.txt


title: VUB31_A_17

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829018B_top_female_fused2.txt, sample_vs_male_reference:140422-829018B_top_male_fused2.txt


title: VUB31_A_19

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829018B_bottom_female_fused2.txt, sample_vs_male_reference:140422-829018B_bottom_male_fused2.txt


title: VUB31_A_20

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829013B_bottom_female_fused.txt, sample_vs_male_reference:140513-829013B_bottom_male_fused.txt


title: VUB31_A_18

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829018B_bottom_female_fused.txt, sample_vs_male_reference:140422-829018B_bottom_male_fused.txt


title: VUB31_A_16

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829034B_bottom_Cy5_female_fused.txt, sample_vs_male_reference:140513-829034B_bottom_Cy5_male_fused.txt


title: VUB31_A_24

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829033B_top_female_fused.txt, sample_vs_male_reference:140513-829033B_top_male_fused.txt


title: VUB31_A_15

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829017B_bottom_female_fused2.txt, sample_vs_male_reference:140422-829017B_bottom_male_fused2.txt


title: VUB31_A_21

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829013B_bottom_female_fused2.txt, sample_vs_male_reference:140513-829013B_bottom_male_fused2.txt


title: aml 12 CD34-CD38+

description: aml 12E


title: VUB31_A_12

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829017B_top_female_fused.txt, sample_vs_male_reference:140422-829017B_top_male_fused.txt


title: aml 12 CD34+CD38-

description: aml 12A


title: VUB31_A_14

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829017B_bottom_female_fused.txt, sample_vs_male_reference:140422-829017B_bottom_male_fused.txt


title: aml 11 CD34-CD38-

description: aml 11G


title: VUB31_A_13

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829017B_top_female_fused2.txt, sample_vs_male_reference:140422-829017B_top_male_fused2.txt


title: VUB31_A_11

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829016B_bottom_female_fused2.txt, sample_vs_male_reference:140422-829016B_bottom_male_fused2.txt


title: aml 11 CD34-CD38+

description: aml 11E


title: VUB31_A_10

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829016B_bottom_female_fused.txt, sample_vs_male_reference:140422-829016B_bottom_male_fused.txt


title: aml 11 CD34+CD38+

description: aml 11C


title: VUB31_A_09

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829016B_top_female_fused2.txt, sample_vs_male_reference:140422-829016B_top_male_fused2.txt


title: aml 12 bulk blasts

description: aml 12H


title: aml 11 CD34+CD38-

description: aml 11A


title: VUB31_A_25

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140513-829033B_top_female_fused2.txt, sample_vs_male_reference:140513-829033B_top_male_fused2.txt


title: aml 10 bulk blasts

description: aml 10H


title: aml 12 CD34-CD38-

description: aml 12G


title: aml 10 CD34+CD38+

description: aml 10C


title: aml 12 CD34+CD38+

description: aml 12C


title: VUB31_A_08

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829016B_top_female_fused.txt, sample_vs_male_reference:140422-829016B_top_male_fused.txt


title: aml 10 CD34-CD38+

description: aml 10E


title: aml 11 bulk blasts

description: aml 11H


title: aml 9 bulk blasts

description: aml 9H


title: aml 9 CD34-CD38-

description: aml 9G


title: VUB31_A_06

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829015B_bottom_female_fused.txt, sample_vs_male_reference:140422-829015B_bottom_male_fused.txt


title: VUB31_A_07

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829015B_bottom_female_fused2.txt, sample_vs_male_reference:140422-829015B_bottom_male_fused2.txt


title: aml 9 CD34+CD38+

description: aml 9C


title: VUB31_A_05

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829015B_top_female_fused2.txt, sample_vs_male_reference:140422-829015B_top_male_fused2.txt


title: aml 9 CD34+CD38-

description: aml 9A


title: VUB31_A_01

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829025B_bottom_female_fused.txt, sample_vs_male_reference:140422-829025B_bottom_male_fused.txt


title: VUB31_A_03

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829026B_top_female_fused.txt, sample_vs_male_reference:140422-829026B_top_male_fused.txt


title: aml 8 bulk blasts

description: aml 8H


title: aml 8 CD34-CD38-

description: aml 8G


title: aml 8 CD34+CD38+

description: aml 8C


title: aml 8 CD34+CD38-

description: aml 8A


title: VUB31_A_04

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829015B_top_female_fused.txt, sample_vs_male_reference:140422-829015B_top_male_fused.txt


title: aml 7 CD34-CD38-

description: aml 7G


title: aml 9 CD34-CD38+

description: aml 9E


title: VUB31_A_02

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 140422-829025B_bottom_female_fused2.txt, sample_vs_male_reference:140422-829025B_bottom_male_fused2.txt


title: aml 7 CD34+CD38+

description: aml 7C


title: aml 7 CD34-CD38+

description: aml 7E


title: shoot_9day_rep3

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.

organism: Arabidopsis thaliana

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: Seeds of Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 9 days. Plantlets were then transferred to ceramics granular soil (size 2.5L, Sakatanotane, Japan) and grown for 8 days at 22°C.

extract_protocol: RNA was extracted from at least three biological replicates with the mirVana miRNA Isolation Kit (Ambion, USA) according to the manufacturer’s instructions

treatment_protocol: The drought treatment was commenced by removing excess water from the trays and ceasing any subsequent watering. Roots and shoots were harvested separately at 0, 1, 3, 5, 7 and 9 days after the onset of drought treatment.

value: shoot

tag: treatment

value: drought stress 9 day

tag: ecotype


title: shoot_7day_rep3

value: drought stress 7 day


title: shoot_9day_rep1


title: aml 7 CD34+CD38-

description: aml 7A


title: shoot_7day_rep1


title: shoot_7day_rep2


title: shoot_9day_rep2


title: aml 6 bulk blasts

description: aml 6H

value: bulk blasts


title: shoot_5day_rep3

value: drought stress 5 day


title: aml 7 bulk blasts

description: aml 7H


title: Phgdh KO-MEF_–Ser_1

first: Shigeki

last: Furuya

address: 6-10-1, Hakozaki, Higashi-ku

hyb_protocol: The biotin-labeled amplified cDNA was fragmented and hybridized to the Mouse Genome 430 2.0 GeneChip array (Affymetrix) for 16 h at 45°C.

scan_protocol: After washing, the arrays were scanned by a GeneChipScanner (Affymetrix), and the scans were processed using the GeneSuite software (Affymetrix).

data_processing: The raw data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Phgdh KO-MEF_L-Ser-depleted

label_protocol: Total RNA (250 ng) was used to generate biotin-labeled cDNA using the GeneChip 3′ IVT Express Kit (Affymetrix).

growth_protocol: KO-MEFs were cultured in commercially available medium DMEM supplemented with 10% FBS overnight (12–24 h).

extract_protocol: RNA was extracted and purified using the RiboPure kit (Life Technologies) according to the manufacturer's instructions.

treatment_protocol: Then medium was changed to L-Ser-depleted or -supplemented media, and cells were incubated for 6 h.

tag: genotype/variation

value: Phgdh KO

tag: tissue source

value: E13.5 embryo

value: Spontaneously immortalized mouse embyonic fibroblasts (MEFs)

tag: cultured in

value: L-Ser-depleted medium for 6 h.


title: Phgdh KO-MEF_–Ser_2


title: shoot_3day_rep4

value: drought stress 3 day


title: shoot_5day_rep2


title: Phgdh KO-MEF_+Ser_3

source_name: Phgdh KO-MEF_L-Ser-supplemented

value: L-Ser-supplemented medium for 6 h.


title: Phgdh KO-MEF_+Ser_2


title: shoot_3day_rep2


title: Phgdh KO-MEF_–Ser_3


title: shoot_5day_rep1


title: shoot_3day_rep3


title: aml 6 CD34-CD38-

description: aml 6G

value: Non-Engrafting


title: Phgdh KO-MEF_+Ser_1


title: shoot_3day_rep1


title: aml 6 CD34+CD38+

description: aml 6C

value: Engrafting


title: mCD4_0min_PMA_rep2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

hyb_protocol: Hybridisation samples were prepared for a 8-pack microarray using 600 ng cRNA each according to the hybridisation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), loaded onto the 8-pack array slide and hybridised at 65 °C overnight

scan_protocol: After washing the microarray was scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays (Dye channel: Green; Scan region: Scan Area (61 x 21.6 mm); Scan resolution (μm): 3; Tiff: 20 bit)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) (protocol GE1_107_Sep09, Grid: 028005_D_GeneList_20131202 and platform Agilent SurePrint G3 Mouse GE 8x60K). The raw data output by Feature Extraction Software was analysed using the LIMMA R package with quantile normalisation and background subtraction.

source_name: Memory splenic CD4+ T-cells

label_protocol: 25 ng RNA was labelled with Cyanine 3-CTP according to the sample preparation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling). Amplified labelled RNA samples were purified by using Qiagen's RNeasy mini spin columns and cRNA quantified by using a Nanodrop

growth_protocol: CD4 and CD8 single positive naive T cells were isolated from the spleens of C42 transgenic mice using MACS CD4 and CD8 T cell Isolation kits followed by enrichment for naive cells using MACS CD62L+ microbeads according to the manufacturer’s instructions (Miltenyi Biotec, Auburn, CA). CD4 and CD8 T-blast cells were generated from purified splenic cells cultured under activating conditions. CD4 or CD8 single positive T cells were isolated using MACS CD4 (L3T4) or CD8a (Ly2) microbeads. Cells were cultured at 5x105 cells/ml in IMDM and activated with 2g/ml Concanavalin A for 40 hours. Cells were then maintained at 5x105 cells/ml in 50U/ml IL-2 (Peprotech) for an additional 2-3 days before harvesting. CD4 memory T cells were purified from splenocytes using the Easy Sep mouse memory CD4 T cell Isolation Kit according to the manufacturer’s instructions (Stem Cell Technologies).

extract_protocol: RNA was extracted from cells using TRIzol® (Invitrogen) according to manufacturers instruction. First strand cDNA synthesis was carried out using M-MLV reverse transcriptase (Invitrogen) according to manufacturers instructions using 1-2 μg of RNA.

treatment_protocol: Cells were stimulated with 20ng/ml phorbol myristate acetate (PMA) and 2uM Calcium Ionophore (CaI) in IMDM supplemented with 50U/ml IL-2 at a concentration of 1x106 cells/ml for up to 4 hours.

tag: pma treatment

value: 0 min

tag: cell type

value: Memory splenic CD4+ T-cells


title: mCD4_120min_PMA_rep2

value: 120 min


title: aml 6 CD34-CD38+

description: aml 6E


title: aml 5 bulk blasts

description: aml 5H


title: aml 6 CD34+CD38-

description: aml 6A


title: aml 5 CD34-CD38+

description: aml 5E


title: aml 5 CD34+CD38+

description: aml 5C


title: aml 5 CD34+CD38-

description: aml 5A


title: shoot_1day_rep4

value: drought stress 1 day


title: aml 4 bulk blasts

description: aml 4H


title: mCD4_0min_PMA_rep1


title: bCD4_120min_PMA_rep2

source_name: Blast-cultured splenic CD4+ T-cells

value: Blast-cultured splenic CD4+ T-cells


title: aml 4 CD34-CD3-

description: aml 4G

value: Not Tested


title: shoot_1day_rep2

value: shoot


title: shoot_1day_rep1


title: shoot_0day_rep3

value: unstress condition


title: root_9day_rep4

value: root

value: drought stress 9 day


title: shoot_0day_rep2


title: root_9day_rep1


title: root_9day_rep3


title: bCD4_120min_PMA_rep1


title: bCD4_0min_PMA_rep2


title: bCD4_0min_PMA_rep1


title: nCD4_120min_PMA_rep2

source_name: Naïve splenic CD4+ T-cells

value: Naive splenic CD4+ T-cells


title: bCD8_0min_PMA_rep1

source_name: Blast-cultured splenic CD8+ T-cells

value: Blast-cultured splenic CD8+ T-cells


title: aml 4 CD34+CD38+

description: aml 4C


title: aml 4 CD34-CD38+

description: aml 4E


title: shoot_0day_rep1


title: bCD8_120min_PMA_rep1


title: nCD4_0min_PMA_rep2


title: aml 3 bulk blasts

description: aml 3H

value: bulk blasts


title: nCD4_0min_PMA_rep1


title: nCD4_120min_PMA_rep1


title: root_9day_rep2


title: aml 3 CD34-CD38+

description: aml 3E


title: aml 3 CD34-CD38-

description: aml 3G


title: aml 3 CD34+CD38+

description: aml 3C


title: aml 3 CD34+CD38-

description: aml 3A


title: aml 2 bulk blasts

description: aml 2H


title: aml 2 CD34-CD38+

description: aml 2E


title: aml 2 CD34+CD38+

description: aml 2C


title: mCD4_120min_PMA_rep1


title: nCD8_0min_PMA_rep1

source_name: Naïve splenic CD8+ T-cells

value: Naive splenic CD8+ T-cells


title: aml 2 CD34-CD38-

description: aml 2G


title: root_7day_rep4

value: drought stress 7 day


title: root_7day_rep2


title: root_5day_rep2

value: drought stress 5 day


title: aml 2 CD34+CD38-

description: aml 2A

value: Engrafting


title: nCD8_120min_PMA_rep1


title: aml 1 CD34+CD38+

description: aml 1C


title: root_7day_rep1


title: aml 1 CD34-CD38+

description: aml 1E

value: Non-Engrafting


title: root_5day_rep3


title: root_7day_rep3


title: aml 1 CD34-CD38-

description: aml 1G


title: HCC 4

status: Public on Feb 01 2016

city: Guangzhou

first: Xue-Jia

last: Lin

state: Guangdong

address: Xin Gang Xi Road 135#

institute: Sun Yat-sen University

description: Test

data_processing:
Cycle threshold (Ct) values were processed and exported using SDS v2.4 software (Applied Biosystems, Foster City, CA). MiRNAs with Ct>35 across all samples were removed from subsequent analysis. The data from different plates were calibrated as follows: plate A and plate B were calibrated to each other according to the average Ct value of U6 snRNA with four replicates in each plate. Four methods, including NormFinder, geNorm, limma quantile and mean-centering restricted (MCR), were used for data normalization.
Matrix normalized worksheets report normalized signal according to the corresponding normalization methods. Fold Change worksheet reports HCC_average/CHB_average ratios.

label: FAM

source_name: Serum

label_protocol: TaqMan Megaplex RT and pre-amplification reactions (Applied Biosystems, Foster City, CA) were performed using equal volumes of input RNA. QPCR on 754 human miRNAs was then conducted in the Applied Biosystems 7900HT Real-Time PCR System using the TaqMan Array Human MicroRNA A+B Cards Set v3.0 (Applied Biosystems, Foster City, CA).

extract_protocol: For serum preparation, peripheral blood was subjected to centrifugation at 400×g for 10 min. The supernatant was transferred into 1.5 ml tubes and centrifuged at 1,800×g for 10 min to remove any remaining cellular debris. Total RNA from 200 μl sera was extracted using mirVana miRNA Isolation Kit (Cat No. AM1560, Ambion/Applied Biosystems, Foster City, CA) according to the manufacturer’s protocol.

tag: diagnosis

value: hepatocellular carcinoma (HCC)

tag: gender

value: Male


title: HCC 6

description: Test


title: aml 1 CD34+CD38-

description: aml 1A

tag: in vivo leukemia initiating capacity


title: HCC 3

description: Test


title: CHB 8

description: Control

value: Chronic hepatitis B (CHB)


title: CHB 7

description: Control


title: HCC 1

description: Test


title: HCC 5

description: Test


title: root_3day_rep2

value: drought stress 3 day


title: HCC 2

description: Test


title: root_5day_rep1


title: root_1day_rep1

value: drought stress 1 day


title: root_1day_rep3


title: AV234

city: Liverpool

first: Liyi

last: Wang

state: Merseyside

address: Crown Street

department: Department of Physiology

country: United Kingdom

institute: University of Liverpool

description:
Slide 22
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171963_S01.txt
Cy5 File: 0_Exiqon_14171963_S01.txt

hyb_protocol: The Hy3TM labelled samples and Hy5TM labelled reference RNA samples were mixed pairwise and hybridised to the miRCURY TM LNA Array ver5 that contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBase version 14.0

scan_protocol: Microarrays were scanned using an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA). Image analysis was carried out using ImaGene 8.0 software (BioDiscovery, Hawthorne, CA, USA).

data_processing:
Log2 transformed median Hy3/Hy5 ratios were calculated using median signals on capture probe replicates and the average log2 median ratios across samples taken. The difference in log2 median ratio (LMR) between sample groups was calculated and subjected to Student t-test (two tailed) or ANOVA using Bonferroni correction. The miRNA data resource was accessed at www.mirbase.org. Principal component analysis (PCA) and hierarchical clustering were performed using DNA Chip Analyser (dChip0 software, www.dchip.org). Validated target miRNAs were obtained from TarBase (Vergoulis T et al.,; Nucleic acids research 40: D222-229, 2012), miRecords (Xiao F et al.,; Nucleic acids research 37: D105-110, 2009) and MetaCore databases (GeneGo, ST Joseph, MI, USA). Network enrichment analysis of miRNA targets was performed using MetaCore and statistically significant networks and pathways were identified at p<0.05 with 5% FDR.  Predicted targets of miR-181d were retrieved from TargetScan release 5.1 (Friedman RC et al.,; Genome Res 19: 92-105, 2009) using a context score below -0.2 for high efficacy targets. Gene expression profiles of gastric myofibroblasts, previously carried out using GeneChip Human Genome U133 Plus 2.0 array and deposited at  http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44740 (Balabanova S et al., Carcinogenesis 35: 1798-1806, 2014) were used to determine the abundance of potential miRNA regulators and target transcripts.
Signals were background corrected (i.e. Normexp with offset value 10) and normalised using the globally weighted scatterplot smoothing (LOWESS) regression algorithm.

source_name: Reference sample

label_protocol: Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark).

growth_protocol: Human primary CAMs and ATMs had previously been generated from patients undergoing surgery for gastric or esophagal cancer.  Normal myofibroblasts from both parts (antrum, corpus) of healthy stomach and esophagus had been generated from deceased transplant donors. The patients, and the myofibroblasts obtained from them have previously been reported (Czepan M et al., Pflugers Archiv : European journal of physiology 463: 459-475, 2012;  Holmberg C et al., Carcinogenesis 33: 1553-1562, 2012). This work had been approved by the Ethics Committee of the University of Szeged, Hungary. Myofibroblasts were cultured as previously described and were used between passages 3 and 10 (Holmberg C et al., Carcinogenesis 33: 1553-1562, 2012). Tumor and adjacent tissues were characterized using the TNM classification (Supplementary Methods, available at Carcinogenesis Online -Holmberg. C., et al. Carcinogenesis ; 33(8): 1553–1562, 2012) for gastric cancer (Sobin L.H., et al. Wiley-Blackwell; Chichester,2009).

extract_protocol: Myofibroblasts (1.5 million) were cultured overnight in 75cm dishes and total RNA was extracted using miRNeasy according the manufacturer’s instructions (Qiagen, Crawley, UK)

tag: type

value: Reference sample

source_name: Oesophagus

value: OMT


title: AV268

description:
Slide 19
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171960_S01.txt
Cy5 File: 0_Exiqon_14171960_S01.txt

value: NTM


title: AV287

description:
Slide 21
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171962_S01.txt
Cy5 File: 0_Exiqon_14171962_S01.txt


title: root_1day_rep2

value: root


title: root_0day_rep2

value: unstress condition


title: AV267

description:
Slide 18
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171959_S01.txt
Cy5 File: 0_Exiqon_14171959_S01.txt


title: root_0day_rep1


title: AV278

description:
Slide 16
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171957_S01.txt
Cy5 File: 0_Exiqon_14171957_S01.txt


title: AV284

description:
Slide 20
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171961_S01.txt
Cy5 File: 0_Exiqon_14171961_S01.txt


title: AV254

description:
Slide 15
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171956_S01.txt
Cy5 File: 0_Exiqon_14171956_S01.txt

value: CAM-AC


title: AV242

description:
Slide 17
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171958_S01.txt
Cy5 File: 0_Exiqon_14171958_S01.txt


title: root_3day_rep1


title: root_3day_rep3


title: CHB 5

description: Control


title: CHB 1

description: Control


title: CHB 3

description: Control


title: root_0day_rep3


title: AV245

description:
Slide 9
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172345_S01.txt
Cy5 File: 0_Exiqon_14172345_S01.txt


title: AV246

description:
Slide 10
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172346_S01.txt
Cy5 File: 0_Exiqon_14172346_S01.txt

value: ATM-AC


title: CHB 4

description: Control


title: shoot_1day_rep3

value: shoot


title: AV260

description:
Slide 12
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171953_S01.txt
Cy5 File: 0_Exiqon_14171953_S01.txt


title: AV247

description:
Slide 14
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171955_S01.txt
Cy5 File: 0_Exiqon_14171955_S01.txt


title: AV233

description:
Slide 47
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172281_S01.txt
Cy5 File: 0_Exiqon_14172281_S01.txt

source_name: Gastric

value: OTM


title: AV269

description:
Slide 5
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172344_S01.txt
Cy5 File: 0_Exiqon_14172344_S01.txt

value: CAM-SC


title: AV272

description:
Slide 46
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172280_S01.txt
Cy5 File: 0_Exiqon_14172280_S01.txt

value: PAM-A


title: AV236

description:
Slide 48
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172282_S01.txt
Cy5 File: 0_Exiqon_14172282_S01.txt


title: AV220

description:
Slide 49
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172177_S01.txt
Cy5 File: 0_Exiqon_14172177_S01.txt


title: AV243

description:
Slide 2
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171930_S01.txt
Cy5 File: 0_Exiqon_14171930_S01.txt


title: AV292

description:
Slide 4
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172343_S01.txt
Cy5 File: 0_Exiqon_14172343_S01.txt


title: AV244

description:
Slide 3
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171934_S01.txt
Cy5 File: 0_Exiqon_14171934_S01.txt

value: ATM-SC


title: AV240

description:
Slide 1
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171928_S01.txt
Cy5 File: 0_Exiqon_14171928_S01.txt


title: AV288

description:
Slide 45
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172279_S01.txt
Cy5 File: 0_Exiqon_14172279_S01.txt


title: AV291

description:
Slide 8
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171941_S01.txt
Cy5 File: 0_Exiqon_14171941_S01.txt


title: AV280

description:
Slide 42
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172289_S01.txt
Cy5 File: 0_Exiqon_14172289_S01.txt

value: NTM-A


title: AV276

description:
Slide 6
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171938_S01.txt
Cy5 File: 0_Exiqon_14171938_S01.txt


title: AV248

description:
Slide 7
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171939_S01.txt
Cy5 File: 0_Exiqon_14171939_S01.txt


title: AV273

description:
Slide 40
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172287_S01.txt
Cy5 File: 0_Exiqon_14172287_S01.txt


title: AV265

description:
Slide 11
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171952_S01.txt
Cy5 File: 0_Exiqon_14171952_S01.txt


title: AV282

description:
Slide 38
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172284_S01.txt
Cy5 File: 0_Exiqon_14172284_S01.txt


title: AV275

description:
Slide 43
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172277_S01.txt
Cy5 File: 0_Exiqon_14172277_S01.txt

value: NTM-C


title: AV277

description:
Slide 39
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172286_S01.txt
Cy5 File: 0_Exiqon_14172286_S01.txt


title: AV279

description:
Slide 37
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172283_S01.txt
Cy5 File: 0_Exiqon_14172283_S01.txt

value: NTN-C


title: AV219

description:
Slide 44
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172278_S01.txt
Cy5 File: 0_Exiqon_14172278_S01.txt


title: AV274

description:
Slide 41
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172288_S01.txt
Cy5 File: 0_Exiqon_14172288_S01.txt


title: AV283

description:
Slide 36
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172276_S01.txt
Cy5 File: 0_Exiqon_14172276_S01.txt


title: AV290

description:
Slide 35
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172275_S01.txt
Cy5 File: 0_Exiqon_14172275_S01.txt


title: AV286

description:
Slide 32
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172272_S01.txt
Cy5 File: 0_Exiqon_14172272_S01.txt


title: AV218

description:
Slide 28
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172267_S01.txt
Cy5 File: 0_Exiqon_14172267_S01.txt

value: ATM


title: AV295

description:
Slide 29
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172269_S01.txt
Cy5 File: 0_Exiqon_14172269_S01.txt


title: AV270

description:
Slide 26
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172266_S01.txt
Cy5 File: 0_Exiqon_14172266_S01.txt

value: CAM


title: AV239

description:
Slide 22
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172262_S01.txt
Cy5 File: 0_Exiqon_14172262_S01.txt

value: Reference sample


title: AV285

description:
Slide 20
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172260_S01.txt
Cy5 File: 0_Exiqon_14172260_S01.txt


title: AV264

description:
Slide 31
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172271_S01.txt
Cy5 File: 0_Exiqon_14172271_S01.txt


title: AV255

description:
Slide 11
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172250_S01.txt
Cy5 File: 0_Exiqon_14172250_S01.txt


title: AV289

description:
Slide 33
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172273_S01.txt
Cy5 File: 0_Exiqon_14172273_S01.txt


title: AV229

description:
Slide 9
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172248_S01.txt
Cy5 File: 0_Exiqon_14172248_S01.txt


title: AV293

description:
Slide 19
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172259_S01.txt
Cy5 File: 0_Exiqon_14172259_S01.txt


title: AV253

description:
Slide 21
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172261_S01.txt
Cy5 File: 0_Exiqon_14172261_S01.txt


title: AV257

description:
Slide 13
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172252_S01.txt
Cy5 File: 0_Exiqon_14172252_S01.txt


title: AV226

description:
Slide 17
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172257_S01.txt
Cy5 File: 0_Exiqon_14172257_S01.txt


title: AV252

description:
Slide 24
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172264_S01.txt
Cy5 File: 0_Exiqon_14172264_S01.txt


title: AV241

description:
Slide 25
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172265_S01.txt
Cy5 File: 0_Exiqon_14172265_S01.txt


title: AV271

description:
Slide 27
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172268_S01.txt
Cy5 File: 0_Exiqon_14172268_S01.txt


title: AV258

description:
Slide 14
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172253_S01.txt
Cy5 File: 0_Exiqon_14172253_S01.txt


title: AV294

description:
Slide 18
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172258_S01.txt
Cy5 File: 0_Exiqon_14172258_S01.txt


title: AV256

description:
Slide 12
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172251_S01.txt
Cy5 File: 0_Exiqon_14172251_S01.txt


title: AV235

description:
Slide 15
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172254_S01.txt
Cy5 File: 0_Exiqon_14172254_S01.txt


title: AV259

description:
Slide 30
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172270_S01.txt
Cy5 File: 0_Exiqon_14172270_S01.txt


title: AV266

description:
Slide 23
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172263_S01.txt
Cy5 File: 0_Exiqon_14172263_S01.txt


title: AV225

description:
Slide 16
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172256_S01.txt
Cy5 File: 0_Exiqon_14172256_S01.txt


title: AV228

description:
Slide 8
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172247_S01.txt
Cy5 File: 0_Exiqon_14172247_S01.txt


title: AV263

description:
Slide 6
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172245_S01.txt
Cy5 File: 0_Exiqon_14172245_S01.txt


title: AV224

description:
Slide 4
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172243_S01.txt
Cy5 File: 0_Exiqon_14172243_S01.txt


title: AV230

description:
Slide 10
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172249_S01.txt
Cy5 File: 0_Exiqon_14172249_S01.txt


title: AV227

description:
Slide 7
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172246_S01.txt
Cy5 File: 0_Exiqon_14172246_S01.txt


title: AV262

description:
Slide 5
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172244_S01.txt
Cy5 File: 0_Exiqon_14172244_S01.txt


title: AV281

description:
Slide 34
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172274_S01.txt
Cy5 File: 0_Exiqon_14172274_S01.txt


title: AV223

description:
Slide 3
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172242_S01.txt
Cy5 File: 0_Exiqon_14172242_S01.txt


title: AV222

description:
Slide 2
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172241_S01.txt
Cy5 File: 0_Exiqon_14172241_S01.txt


title: AV221

description:
Slide 1
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14172240_S01.txt
Cy5 File: 0_Exiqon_14172240_S01.txt


title: CHB 2

description: Control

value: Chronic hepatitis B (CHB)

value: Male


title: CTRL13

type: protein

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

hyb_protocol: Serum samples were diluted 1:200 in Protein Array Blocking buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5α E. coli lysate (MCLAB, San Francisco, CA) and incubated on arrays over night at 4°C. Microarray slides were incubated in biotin-conjugated anti-IgG Fc fragment secondary antibody (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer, and detected by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Columbia, MD). The slides were washed and air-dried by brief centrifugation.

scan_protocol: Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to Pf or Pv proteins on the microarray, the following steps were taken: i) the median background signal of antibody binding to 24 spots of IVTT reaction without DNA template (no template control, NTC) was calculated for each individual sample; ii) the raw values of antibody binding to Pf and Pv polypeptides were divided by their corresponding median NTC value, generating fold-over-control (FOC) values; iii) FOC values were log2-transformed for data normalization (data presented in Sample data tables).

molecule: protein

source_name: plasma, unexposed, naive

value: plasma

tag: sample collection time

tag: sample collection site

value: Irvine, California, USA

tag: sample source

value: healthy blood donor at UCI

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: unexposed

tag: symptomatic or asymptomatic at sample collection

value: naive

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: CTRL12

tag: tissue


title: CTRL15


title: CTRL10


title: CTRL11


title: PCD81

source_name: plasma, exposed, non-malaria fever

value: March 2013

value: Mae Tan, Tak, Thailand

value: hospital outpatient (PCD)

value: exposed

value: non-malaria fever

value: negative


title: CTRL3


title: CTRL2


title: PCD79

source_name: plasma, exposed, fever malaria

value: January 2014

value: fever malaria

value: positive

value: P. falciparum, P. vivax


title: CTRL4


title: PCD82


title: CTRL6


title: CTRL16


title: PCD83


title: CTRL1


title: CTRL14


title: PCD77

value: August 2013


title: CHB 6

description: Control

value: Chronic hepatitis B (CHB)

value: Male

tag: age


title: CTRL8

value: plasma

value: Irvine, California, USA


title: PCD76


title: AV261

description:
Slide 13
Total RNA and reference samples were labelled with Hy3TM and Hy5TM fluorescence labels respectively (Exiqon Services, Vedbaek, Denmark)
Cy3 File: 1_Exiqon_14171954_S01.txt
Cy5 File: 0_Exiqon_14171954_S01.txt

value: Reference sample

value: CAM-AC


title: CTRL7

value: healthy blood donor at UCI

value: unexposed

value: naive


title: PCD78

value: Mae Tan, Tak, Thailand

value: hospital outpatient (PCD)

value: exposed


title: CTRL5


title: CTRL9


title: PCD80

value: January 2014


title: PCD73

value: non-malaria fever

value: negative


title: PCD74


title: PCD61

value: March 2013

value: fever malaria

value: positive

value: P. falciparum, P. vivax


title: PCD70

value: plasma

value: August 2013


title: PCD55


title: PCD62


title: PCD64


title: PCD71


title: PCD57


title: PCD75

value: P. falciparum


title: PCD54


title: PCD60


title: PCD72

value: P. vivax


title: PCD59


title: PCD58


title: PCD56


title: PCD69


title: PCD63


title: PCD66


title: PCD65


title: PCD68


title: PCD67


title: PCD53


title: PCD52


title: PCD51


title: PCD50


title: PCD48

value: P. malariae


title: PCD46


title: PCD49


title: PCD47


title: PCD45


title: PCD44


title: PCD43


title: PCD41


title: PCD38


title: PCD34


title: PCD42


title: PCD37


title: PCD39


title: PCD28


title: PCD29


title: PCD33


title: PCD26


title: PCD32


title: PCD27


title: PCD30


title: PCD35


title: PCD40


title: PCD21


title: PCD17


title: PCD20


title: PCD31


title: PCD36


title: PCD18


title: PCD23


title: PCD24


title: PCD25


title: PCD16


title: PCD19


title: PCD22


title: PCD14


title: PCD15


title: PCD13


title: PCD9


title: PCD7


title: PCD10


title: PCD6


title: PCD8


title: PCD11


title: MBS298

source_name: plasma, exposed, asymptomatic

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)

value: asymptomatic


title: MBS297


title: MBS292

source_name: plasma, exposed, healthy

value: healthy


title: MBS293

value: exposed


title: MBS294


title: MBS296

value: January 2014


title: MBS290


title: MBS289


title: MBS291


title: MBS288


title: MBS286


title: MBS287


title: PCD4

value: Mae Tan, Tak, Thailand

value: hospital outpatient (PCD)

value: non-malaria fever


title: PCD12

value: negative


title: MBS285

value: March 2013


title: MBS284


title: PCD1

value: fever malaria

value: positive

value: P. falciparum, P. vivax


title: MBS295

value: plasma


title: PCD5


title: PCD2


title: MBS282


title: MBS283


title: MBS280


title: PD1 Cerebellum to frontal cortex, both extracted with Puregene

city: London

first: Christos

last: Proukakis

address: Rowland Hill Street

department: Clinical Neuroscience

institute: UCL Institute of Neurology

description: PD1 CER/FC pure 1288

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed and

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
normalized log10 ratio (Cy5/Cy3) representing test/reference

source_name: PD1 cerebellum

label_protocol: 500ng of DNA was used, with hybridisation performed according to manufacturer protocol. DNA was digested with AluI and RsaI for 2 h at 37 °C. Genomic DNA was fluorescently labelled with the SureTag DNA Labelling Kit (Agilent).

extract_protocol: Qiagen Dneasy spin columns, or Qiagen Puregene, as specified. In spin columns, 25mg or 5 mg tissue starting amount was used as stated; proteinase K treatment in spin columns was 2 hours unless stated. Puregene extractions were done according to manufacturer protocol with 50mg starting material.

tag: extraction protocol

value: Puregene extraction

source_name: PD1 frontal cortex


title: MBS276


title: PD3 cerebellum, 5 mg spin column overnight to Puregene extracted DNA

description: PD3 CER 5:Pure 1285

source_name: PD3 cerebellum

value: spin column extraction overnight with 5mg starting material


title: MBS278

value: Mae Salid Noi, Tak, Thailand


title: MBS277

value: community mass blood survey (ACD)


title: PD4 cerebellum, 25 mg spin column overnight to Puregene extracted DNA

description: PD4 CER 25mg:Pure 1287

source_name: PD4 cerebellum

value: spin column extraction overnight with 25mg starting material


title: PD3 cerebellum, 25 mg spin column overnight to Puregene extracted DNA

description: PD3 CER 25mg:Pure 1284


title: MBS275

value: asymptomatic

value: P. vivax


title: MBS273

value: January 2014

value: exposed

value: healthy


title: PCD3

value: Mae Tan, Tak, Thailand

value: hospital outpatient (PCD)

value: non-malaria fever


title: MBS274

value: negative


title: MBS269

value: March 2013


title: PD2 frontal cortex to cerebellum

description: Case_1197_PD2 FC/CER

source_name: PD2 frontal cortex

value: 25mg spin column extraction

source_name: PD cerebellum


title: MBS270

value: plasma

value: August 2013


title: MBS272


title: MBS271


title: MBS268

source_name: plasma, exposed, fever at 4mo

value: fever at 4mo

value: positive

value: P. falciparum, P. ovale


title: PD2 cerebellum to frontal cortex

description: PD2 CER/FC Case_1189_

source_name: PD2 cerebellum


title: MBS281

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)


title: MBS267


title: MBS279


title: PD1 cerebellum to frontal cortex

description: PD1 CER/FC Case_1183_


title: Male to Female Agilent reference DNA

source_name: Agilent male reference DNA

tag: sample dna

value: Agilent male reference DNA

source_name: Agilent female reference DNA

tag: reference

value: Agilent female reference DNA


title: C4 frontal cortex

description: C4 FC Case_1100_

source_name: control 4 frontal cortex


title: MBS265

value: exposed


title: MBS266

value: healthy


title: C2 frontal cortex

description: C2 FC Case_1095_

source_name: control 2 frontal cortex


title: MBS264


title: C1 frontal cortex

description: C1 FC Case_1117_

source_name: control 1 frontal cortex


title: PD4 cerebellum to frontal cortex

description: PD4 CER/FC Case_1188_

source_name: PD4 frontal cortex


title: C3 frontal cortex

description: C3 FC Case_1097_

source_name: control 3 frontal cortex


title: PD1 frontal cortex

description: PD1 FC Case_1155_


title: PD2 frontal cortex

description: PD2 FC Case_1157_


title: MBS263


title: MBS260


title: C3 cerebellum

description: C3 CER Case_1076_

source_name: control 3 cerebellum


title: C4 cerebellum

description: C4 CER Case_1084_

source_name: control 4 cerebellum


title: MBS262

source_name: plasma, exposed, healthy


title: MBS261


title: MBS257


title: MBS259


title: C2 cerebellum

description: C2 CER Case_1074_

source_name: control 2 cerebellum


title: MBS255


title: MBS254


title: MBS256


title: C1 cerebellum

description: C1 CER Case_1109_

source_name: control 1 cerebellum


title: PD3 cerebellum

description: PD3 CER Case_1153_

source_name: PD3 cerebellum


title: PD4 cerebellum

description: PD4 CER Case_1105_

source_name: PD4 cerebellum


title: PD2 cerebellum

description: PD2 CER Case_1075_


title: PD4 frontal cortex

description: PD4 FC Case_1158_


title: PD3 frontal cortex

description: PD3 FC Case_1148_

source_name: PD3 frontal cortex


title: MBS253


title: PD1 cerebellum

description: PD1 CER Case_1072_

source_name: PD1 cerebellum


title: MBS252

value: January 2014


title: MBS251


title: MBS249


title: MBS250


title: MBS248


title: MBS247


title: MBS239


title: MBS242


title: MBS246

source_name: plasma, exposed, fever

value: fever

value: P. vivax


title: MBS245

value: negative


title: MBS244

source_name: plasma, exposed, asymptomatic

value: asymptomatic


title: MBS238

value: March 2013


title: MBS240

value: plasma

value: P. falciparum


title: MBS241


title: MBS243