title: Oxydative bisulfite treated genomic DNA from Down syndrome Cerebellum  3

description:
Down syndrome  Adult Cerebellum of patient 1391 with oxidative bisulfite treatment for 5mC assessment
tb8491_OXBS

source_name: Oxydative bisulfite treated  Down syndrome Cerebellum 3


title: Oxydative bisulfite treated  genomic DNA from Down syndrome Cerebellum  2

status: Public on Oct 30 2015

type: genomic

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

country: USA

institute: HUMC

description:
Down syndrome  Adult Cerebellum of patient 482 with oxidative bisulfite treatment for 5mC assessment
tb8490_OXBS

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol. To distinguish 5mc from 5hmC in a subset of Down syndrome and control cerebellar cortices, bisulfite converted DNA and oxidative bisulfite converted DNA according to TrueMethylTM6 kit (CEGX) protocol was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip, in parallel.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
Genome Studio software
For DS_processed_norm_no_batch_correction_no_filtering_matrix_1: normalized average beta values after background correction and normalization to internal controls (before ComBat batch adjustment and with no filtering)
For DS_processed_norm_batch_corrected_filtered_matrix_2: normalized average beta values after background correction and normalization to internal controls. In addition all probes mapping on the X or Y chromosome were removed along with those probes querying CpGs that overlapped common simple nucleotide polymorphisms (SNPs with minor allele frequency>1% in dbSNP build 138). Poorly performing probes with missing values (AVG_Beta detection p-value>.05) in more than 10% of the samples per subgroup were filtered out. We corrected for batch effect in the filtered probe sets using the ComBat R package including disease status in the adjustment model as an explanatory covariate, separately by tissue and cell type.  ComBat adjustment requires at least 2 samples per batch. For each batch and tissue, probes with non missing values in less than 2 samples from the same subgroup were filtered out. These processed data correspond to the supplementary tables S3-S7 of the published manuscript.
For DS_OXBS_processed_matrix_3: BS values correspond to  normalized average beta values (background correction and normalization to internal controls) after bisulfite treatment and OXBS values correspond to  normalized average beta values after oxidative bisulfite treatment. In the manuscript, probes with detection p-values>0.005 in more than 1 sample were filtered out. These processed data correspond to the supplementary table S8 of the published manuscript.
For DS_raw_signal_matrix_1: unmethylated and methylated signal intensities without background correction and normalization to internal controls
For DS_OXBS_raw_signal_matrix_2: unmethylated and methylated signal intensities without background correction and normalization to internal controls.  BS values correspond to intenstities in bisulifte treated DNA samples, OXBS values correspond to intenstities in oxidative bisulfite treated DNA samples.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Oxydative bisulfite treated  Down syndrome Cerebellum 2

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

tag: gender

value: Male

tag: developmental stage

value: Adult

tag: tissue

value: Cerebellar cortex

tag: cell type

value: Whole grey matter

tag: disease state

value: Down syndrome


title: Bisulfite treated genomic DNA from Control Cerebellum  2

description:
Control  Adult Cerebellum of patient 252 with bisulfite treatment for 5hmC and 5mC assessment
tb8487_BS

source_name: Bisulfite treated  Control Cerebellum 2

value: Female

value: Normal


title: genomic DNA from Control Fetal cerebrum  5

description:
Control Fetal cerebrum of patient 12-BR-127
tb7038

source_name: Control Fetal cerebrum 5

value: Fetus

value: Cerebrum

value: Whole Cerebrum


title: genomic DNA from Control Fetal cerebrum  3

description:
Control Fetal cerebrum of patient 6-BR-132
tb7032

source_name: Control Fetal cerebrum 3


title: Blantyre Malaria Project_PID_3071

type: RNA

city: Bronx

first: Johanna

middle: Patricia

last: Daily

state: NY

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

institute: Albert Einstein College of Medicine

description: Patients with Cerebral Malaria were enrolled in the Blantyre Malaria project. 3 mL of whole blood in EDTA was collected at admission and added to Tri-reagent BD (Molecular Research Center) and frozen at -80oC

hyb_protocol: Following fragmentation, 5.5ug of sscDNA were hybridized for 17 hours at 45C on GeneChip Human Gene 1.0 ST Array, GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G7

data_processing:
CEL files were analyzed using GenePattern; Robust Multi-Array Average (RMA) procedure was used, and the data was quantile normalized and background corrected. There are 32,322 probes
We collapsed the probes to 24,891 genes and removed unannotated genes

label: biotin

molecule: total RNA

source_name: Human whole blood_Cerebral malaria_3071

label_protocol: Biotinylated sscDNA were prepared according to the standard Ambion and Afymetrix protocols from 5.5ug total sscDNA (The Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript (WT)

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

tag: retinopathy

value: Ret+

tag: parasitemia

value: blood


title: genomic DNA from Control Fetal cerebrum  2

description:
Control Fetal cerebrum of patient 2-BR-92
tb7028

source_name: Control Fetal cerebrum 2


title: genomic DNA from Control Fetal cerebrum  4

description:
Control Fetal cerebrum of patient 8-BR-134
tb7034

source_name: Control Fetal cerebrum 4


title: Blantyre Malaria Project_PID_3055

source_name: Human whole blood_Cerebral malaria_3055


title: Oxydative bisulfite treated  genomic DNA from Control Cerebellum  3

description:
Control  Adult Cerebellum of patient 255 with oxidative bisulfite treatment for 5mC assessment
tb8488_OXBS

source_name: Oxydative bisulfite treated  Control Cerebellum 3


title: Blantyre Malaria Project_PID_3067

source_name: Human whole blood_Cerebral malaria_3067

value: Ret-


title: Blantyre Malaria Project_PID_3061

source_name: Human whole blood_Cerebral malaria_3061


title: Blantyre Malaria Project_PID_3063

source_name: Human whole blood_Cerebral malaria_3063


title: Blantyre Malaria Project_PID_3050

source_name: Human whole blood_Cerebral malaria_3050


title: genomic DNA from Down syndrome Fetal cerebrum  8

description:
Down syndrome Fetal cerebrum of patient 15-BR-74
tb7041

source_name: Down syndrome Fetal cerebrum 8


title: Blantyre Malaria Project_PID_3048

source_name: Human whole blood_Cerebral malaria_3048


title: Blantyre Malaria Project_PID_3052

source_name: Human whole blood_Cerebral malaria_3052


title: Blantyre Malaria Project_PID_3044

source_name: Human whole blood_Cerebral malaria_3044


title: Blantyre Malaria Project_PID_3042

source_name: Human whole blood_Cerebral malaria_3042


title: genomic DNA from Down syndrome Fetal cerebrum  6

description:
Down syndrome Fetal cerebrum of patient 7-BR-13
tb7033

source_name: Down syndrome Fetal cerebrum 6


title: Blantyre Malaria Project_PID_3038

source_name: Human whole blood_Cerebral malaria_3038


title: genomic DNA from Down syndrome Fetal cerebrum  3

description:
Down syndrome Fetal cerebrum of patient 13-BR-60
tb7039

source_name: Down syndrome Fetal cerebrum 3


title: Blantyre Malaria Project_PID_3032

source_name: Human whole blood_Cerebral malaria_3032


title: genomic DNA from Control Fetal cerebrum  1

description:
Control Fetal cerebrum of patient 10-BR-107
tb7036

source_name: Control Fetal cerebrum 1


title: Blantyre Malaria Project_PID_3024

source_name: Human whole blood_Cerebral malaria_3024


title: Blantyre Malaria Project_PID_3030

source_name: Human whole blood_Cerebral malaria_3030


title: Blantyre Malaria Project_PID_3023

source_name: Human whole blood_Cerebral malaria_3023


title: genomic DNA from Down syndrome Fetal cerebrum  2

description:
Down syndrome Fetal cerebrum of patient 9-BR-37
tb7035

source_name: Down syndrome Fetal cerebrum 2


title: Blantyre Malaria Project_PID_3020

source_name: Human whole blood_Cerebral malaria_3020


title: genomic DNA from Down syndrome Fetal cerebrum  1

description:
Down syndrome Fetal cerebrum of patient 3-BR-20
tb7029

source_name: Down syndrome Fetal cerebrum 1


title: genomic DNA from Down syndrome Fetal cerebrum  4

description:
Down syndrome Fetal cerebrum of patient 1-BR-1
tb7027

source_name: Down syndrome Fetal cerebrum 4


title: genomic DNA from Control T cells 9

description:
Control Adult T cells
tb7244

source_name: Control T cells 9

value: Blood

value: T cells


title: Blantyre Malaria Project_PID_3013

source_name: Human whole blood_Cerebral malaria_3013


title: Blantyre Malaria Project_PID_3031

source_name: Human whole blood_Cerebral malaria_3031


title: Blantyre Malaria Project_PID_3015

source_name: Human whole blood_Cerebral malaria_3015


title: genomic DNA from Control T cells 5

description:
Control Adult T cells
tb6539

source_name: Control T cells 5


title: genomic DNA from Control T cells 10

description:
Control Adult T cells
tb7764

source_name: Control T cells 10


title: Blantyre Malaria Project_PID_3009

source_name: Human whole blood_Cerebral malaria_3009


title: genomic DNA from Control T cells 6

description:
Control Adult T cells
tb6538

source_name: Control T cells 6


title: genomic DNA from Control T cells 4

description:
Control Adult T cells
tb6354

source_name: Control T cells 4


title: genomic DNA from Control T cells 3

description:
Control Adult T cells
tb6353

source_name: Control T cells 3


title: Blantyre Malaria Project_PID_3008

source_name: Human whole blood_Cerebral malaria_3008


title: genomic DNA from Down syndrome Fetal cerebrum  5

description:
Down syndrome Fetal cerebrum of patient 5-BR-28
tb7031

source_name: Down syndrome Fetal cerebrum 5


title: genomic DNA from Control T cells 7

description:
Control Adult T cells
tb6788

source_name: Control T cells 7


title: Blantyre Malaria Project_PID_2824

source_name: Human whole blood_Cerebral malaria_2824


title: Blantyre Malaria Project_PID_2830

source_name: Human whole blood_Cerebral malaria_2830


title: genomic DNA from Control T cells 8

description:
Control Adult T cells
tb7216

source_name: Control T cells 8


title: Blantyre Malaria Project_PID_2822

source_name: Human whole blood_Cerebral malaria_2822


title: Blantyre Malaria Project_PID_3029

source_name: Human whole blood_Cerebral malaria_3029


title: genomic DNA from Down syndrome T cells 9

description:
Down syndrome Adult T cells
ds847

source_name: Down syndrome T cells 9


title: genomic DNA from Down syndrome T cells 10

description:
Down syndrome Adult T cells
ds915

source_name: Down syndrome T cells 10


title: Blantyre Malaria Project_PID_2826

source_name: Human whole blood_Cerebral malaria_2826


title: Blantyre Malaria Project_PID_2818

source_name: Human whole blood_Cerebral malaria_2818


title: genomic DNA from Control T cells 1

description:
Control Adult T cells
tb6351

source_name: Control T cells 1


title: genomic DNA from Down syndrome T cells 8

description:
Down syndrome Adult T cells
ds845

source_name: Down syndrome T cells 8


title: genomic DNA from Down syndrome T cells 7

description:
Down syndrome Adult T cells
ds851

source_name: Down syndrome T cells 7


title: genomic DNA from Down syndrome T cells 11

description:
Down syndrome Adult T cells
ds925

source_name: Down syndrome T cells 11


title: 138-Metastases

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

hyb_protocol: 10 ug of purified unfragmented target cRNA was hybridized on each chip.

scan_protocol: The microarrays were hybridized, washed, and processed using a direct detection method of the biotin-containing transcripts by a Streptavidin-Alexa647 conjugate (Invitrogen, Carlsbad, CA).  Scanned images were analyzed using the Genepix 6.0 software (Axon Instruments, Sunnyvale, CA).

data_processing:
The chip was annotated using AnnBuilder Package available for the R software starting from the GeneBank accession numbers made available through Compugen/Sigma-Genosys.
The median signal subtracted for the background was normalized using a variance-stabilizing transformation stratifying the spots by grid (Huber W, von Heydebreck A, Sultmann H, et al: Bioinformatics 18:S96-S104, 2002 [suppl 1]) as implemented in the vsn package.

source_name: Metastases

label_protocol: For target preparation, 5 μg of total RNA were reverse transcribed using SuperscriptT-II/RNaseH-priming with T7-(dT)24 oligonucleotides and the second-strand cDNA synthesized using E coli DNA polymerase I. Biotinylated cRNA was generated using T7 RNA polymerase and Biotin 11-UTP.

extract_protocol: total RNA from snap frozen tissue using 4M guanidine thiocyanate containing 0.1M 2-mercaptoethanol and centrifuged through a CsCl2 gradient. RNA quality and concentration were assesed using Agilent 2100 Bioanalyzer.

value: metastases from pancreatic neuroendocrine tumours


title: Blantyre Malaria Project_PID_2808

source_name: Human whole blood_Cerebral malaria_2808


title: genomic DNA from Down syndrome T cells 5

description:
Down syndrome Adult T cells
ds822

source_name: Down syndrome T cells 5


title: Blantyre Malaria Project_PID_2812

source_name: Human whole blood_Cerebral malaria_2812


title: genomic DNA from Control T cells 2

description:
Control Adult T cells
tb6352

source_name: Control T cells 2


title: genomic DNA from Down syndrome T cells 6

description:
Down syndrome Adult T cells
ds831

source_name: Down syndrome T cells 6


title: Blantyre Malaria Project_PID_2821

source_name: Human whole blood_Cerebral malaria_2821


title: 137-Metastases


title: genomic DNA from Control Frontal Cortex  8

description:
Control  Adult Frontal Cortex of patient 590
tb7081

source_name: Control Frontal Cortex  8

value: Frontal Cortex


title: Blantyre Malaria Project_PID_2811

source_name: Human whole blood_Cerebral malaria_2811


title: genomic DNA from Down syndrome T cells 1

description:
Down syndrome Adult T cells
ds842

source_name: Down syndrome T cells 1

value: Male


title: 136-Metastases


title: 135-Metastases


title: genomic DNA from Down syndrome T cells 2

description:
Down syndrome Adult T cells
ds790

source_name: Down syndrome T cells 2

value: Adult


title: Blantyre Malaria Project_PID_2807

source_name: Human whole blood_Cerebral malaria_2807


title: genomic DNA from Control Frontal Cortex  7

description:
Control  Adult Frontal Cortex of patient 580
tb7080

source_name: Control Frontal Cortex  7


title: Blantyre Malaria Project_PID_2806

source_name: Human whole blood_Cerebral malaria_2806


title: Blantyre Malaria Project_PID_2802

source_name: Human whole blood_Cerebral malaria_2802


title: genomic DNA from Control Frontal Cortex  5

description:
Control  Adult Frontal Cortex of patient 256
tb5985

source_name: Control Frontal Cortex  5


title: 134-Metastases


title: genomic DNA from Down syndrome T cells 3

description:
Down syndrome Adult T cells
ds813

source_name: Down syndrome T cells 3


title: 133-Non-functional PanNET

source_name: Non-functional PanNET

value: pancreatic neuroendocrine tumours


title: 132-Metastases

source_name: Metastases


title: genomic DNA from Down syndrome Fetal cerebrum  7

description:
Down syndrome Fetal cerebrum of patient 11-BR-45
tb7037

source_name: Down syndrome Fetal cerebrum 7


title: Blantyre Malaria Project_PID_2800

source_name: Human whole blood_Cerebral malaria_2800


title: genomic DNA from Control Frontal Cortex  3

description:
Control  Adult Frontal Cortex of patient 252
tb5983

source_name: Control Frontal Cortex  3

value: Whole grey matter


title: genomic DNA from Control Frontal Cortex  4

description:
Control  Adult Frontal Cortex of patient 255
tb5984

source_name: Control Frontal Cortex  4


title: 129-Non-functional PanNET


title: 130-Non-functional PanNET


title: Blantyre Malaria Project_PID_2801

description: Patients with Cerebral Malaria were enrolled in the Blantyre Malaria project. 3 mL of whole blood in EDTA was collected at admission and added to Tri-reagent BD (Molecular Research Center) and frozen at -80oC

source_name: Human whole blood_Cerebral malaria_2801


title: Blantyre Malaria Project_PID_2817

source_name: Human whole blood_Cerebral malaria_2817


title: Blantyre Malaria Project_PID_2795

source_name: Human whole blood_Cerebral malaria_2795


title: genomic DNA from Control Frontal Cortex  6

description:
Control  Adult Frontal Cortex of patient 1169
tb5986

source_name: Control Frontal Cortex  6


title: 128-Non-functional PanNET


title: genomic DNA from Control Frontal Cortex  2

description:
Control  Adult Frontal Cortex of patient 248
tb5982

source_name: Control Frontal Cortex  2


title: 127-Insulinoma

source_name: Insulinoma


title: Blantyre Malaria Project_PID_2797

source_name: Human whole blood_Cerebral malaria_2797


title: genomic DNA from Down syndrome Frontal Cortex  14

description:
Down syndrome  Adult Frontal Cortex of patient 1391
tb5979

source_name: Down syndrome Frontal Cortex  14

value: Down syndrome


title: 126-Non-functional PanNET


title: genomic DNA from Control Frontal Cortex  1

description:
Control  Adult Frontal Cortex of patient 247
tb5981

source_name: Control Frontal Cortex  1


title: genomic DNA from Down syndrome Frontal Cortex  13

description:
Down syndrome  Adult Frontal Cortex of patient 1343
tb5977

source_name: Down syndrome Frontal Cortex  13

value: Female


title: Blantyre Malaria Project_PID_2791

source_name: Human whole blood_Cerebral malaria_2791


title: genomic DNA from Down syndrome Frontal Cortex  12

description:
Down syndrome  Adult Frontal Cortex of patient 1342
tb5976

source_name: Down syndrome Frontal Cortex  12


title: genomic DNA from Down syndrome T cells 4

description:
Down syndrome Adult T cells
ds823

source_name: Down syndrome T cells 4


title: Blantyre Malaria Project_PID_2789

source_name: Human whole blood_Cerebral malaria_2789


title: Blantyre Malaria Project_PID_2793

source_name: Human whole blood_Cerebral malaria_2793


title: 124-Non-functional PanNET

source_name: Non-functional PanNET


title: 125-Insulinoma


title: genomic DNA from Down syndrome Frontal Cortex  11

description:
Down syndrome  Adult Frontal Cortex of patient 1335
tb5975

source_name: Down syndrome Frontal Cortex  11


title: genomic DNA from Down syndrome Frontal Cortex  10

description:
Down syndrome  Adult Frontal Cortex of patient 1330
tb5974

source_name: Down syndrome Frontal Cortex  10


title: 123-Insulinoma


title: Blantyre Malaria Project_PID_2784

source_name: Human whole blood_Cerebral malaria_2784


title: genomic DNA from Down syndrome Frontal Cortex  9

description:
Down syndrome  Adult Frontal Cortex of patient 1322
tb5973

source_name: Down syndrome Frontal Cortex  9


title: Blantyre Malaria Project_PID_2798

source_name: Human whole blood_Cerebral malaria_2798


title: Blantyre Malaria Project_PID_2786

source_name: Human whole blood_Cerebral malaria_2786


title: Blantyre Malaria Project_PID_2785

source_name: Human whole blood_Cerebral malaria_2785


title: Blantyre Malaria Project_PID_2790

source_name: Human whole blood_Cerebral malaria_2790


title: 122-Non-functional PanNET


title: 131-Metastases

source_name: Metastases


title: genomic DNA from Down syndrome Frontal Cortex  7

description:
Down syndrome  Adult Frontal Cortex of patient 1280
tb5970

source_name: Down syndrome Frontal Cortex  7


title: 120-Non-functional PanNET


title: 121-Insulinoma

source_name: Insulinoma


title: genomic DNA from Down syndrome Frontal Cortex  8

description:
Down syndrome  Adult Frontal Cortex of patient 1308
tb5972

source_name: Down syndrome Frontal Cortex  8


title: 119-Functional

source_name: Functional


title: Blantyre Malaria Project_PID_2777

source_name: Human whole blood_Cerebral malaria_2777


title: Blantyre Malaria Project_PID_2783

source_name: Human whole blood_Cerebral malaria_2783


title: Blantyre Malaria Project_PID_2779

source_name: Human whole blood_Cerebral malaria_2779


title: 118-Insulinoma


title: Blantyre Malaria Project_PID_2776

source_name: Human whole blood_Cerebral malaria_2776


title: genomic DNA from Down syndrome Frontal Cortex  4

description:
Down syndrome  Adult Frontal Cortex of patient 1139
tb5967

source_name: Down syndrome Frontal Cortex  4


title: Blantyre Malaria Project_PID_2773

source_name: Human whole blood_Cerebral malaria_2773


title: Blantyre Malaria Project_PID_2769

source_name: Human whole blood_Cerebral malaria_2769


title: genomic DNA from Down syndrome Frontal Cortex  2

description:
Down syndrome  Adult Frontal Cortex of patient 482
tb5965

source_name: Down syndrome Frontal Cortex  2


title: genomic DNA from Down syndrome Frontal Cortex  6

description:
Down syndrome  Adult Frontal Cortex of patient 1238
tb5969

source_name: Down syndrome Frontal Cortex  6


title: 115-Non-functional PanNET

source_name: Non-functional PanNET


title: 114-Non-functional PanNET


title: 113-Non-functional PanNET

description:
113 (replicate of 112)
Q1-Ac


title: genomic DNA from Down syndrome Frontal Cortex  3

description:
Down syndrome  Adult Frontal Cortex of patient 712
tb5966

source_name: Down syndrome Frontal Cortex  3


title: Blantyre Malaria Project_PID_2763

source_name: Human whole blood_Cerebral malaria_2763


title: Blantyre Malaria Project_PID_2767

source_name: Human whole blood_Cerebral malaria_2767


title: 112-Non-functional PanNET


title: Blantyre Malaria Project_PID_2775

source_name: Human whole blood_Cerebral malaria_2775


title: genomic DNA from Down syndrome Frontal Cortex  1

description:
Down syndrome  Adult Frontal Cortex of patient 375
tb5964

source_name: Down syndrome Frontal Cortex  1


title: genomic DNA from Control neuron Frontal Cortex neurons 10

description:
Control neuron Adult Frontal Cortex of patient NYBB3966
tb6573

value: Fluorescence-activated nuclei sorted neurons

value: Normal


title: Blantyre Malaria Project_PID_2760

description: Patients with Cerebral Malaria were enrolled in the Blantyre Malaria project. 3 mL of whole blood in EDTA was collected at admission and added to Tri-reagent BD (Molecular Research Center) and frozen at -80oC

source_name: Human whole blood_Cerebral malaria_2760


title: 109-Normal pancreas islet

source_name: Normal pancreas islet

value: normal pancreas islet


title: 108-Normal pancreas islet


title: 110-Normal pancreas islet


title: genomic DNA from Control neuron Frontal Cortex neurons 7

description:
Control neuron Adult Frontal Cortex of patient 580
tb7185

source_name: Control neuron Frontal Cortex neurons 7


title: Blantyre Malaria Project_PID_2754

source_name: Human whole blood_Cerebral malaria_2754


title: genomic DNA from Control neuron Frontal Cortex neurons 11

description:
Control neuron Adult Frontal Cortex of patient NYBB3988
tb6576


title: Blantyre Malaria Project_PID_2761

source_name: Human whole blood_Cerebral malaria_2761


title: 106-Normal pancreas

source_name: Normal pancreas

value: normal pancreas


title: 117-Non-functional PanNET


title: Blantyre Malaria Project_PID_2759

source_name: Human whole blood_Cerebral malaria_2759

value: Ret+


title: Blantyre Malaria Project_PID_2753

source_name: Human whole blood_Cerebral malaria_2753

value: blood


title: 107-Normal pancreas

description:
107 (replicate of 106)
N2-Ac


title: genomic DNA from Control neuron Frontal Cortex neurons 2

description:
Control neuron Adult Frontal Cortex of patient 248
tb6627

source_name: Control neuron Frontal Cortex neurons 2


title: 116-Non-functional PanNET


title: 105-Normal pancreas

description:
105 (replicate of 104)
N1-Ac


title: Blantyre Malaria Project_PID_2752

source_name: Human whole blood_Cerebral malaria_2752


title: 104-Normal pancreas


title: genomic DNA from Control neuron Frontal Cortex neurons 6

description:
Control neuron Adult Frontal Cortex of patient 1169
tb6970

source_name: Control neuron Frontal Cortex neurons 6


title: genomic DNA from Control neuron Frontal Cortex neurons 3

description:
Control neuron Adult Frontal Cortex of patient 252
tb6628

source_name: Control neuron Frontal Cortex neurons 3


title: Blantyre Malaria Project_PID_2744

source_name: Human whole blood_Cerebral malaria_2744

value: Ret-


title: genomic DNA from Control neuron Frontal Cortex neurons 8

description:
Control neuron Adult Frontal Cortex of patient NYBB336
tb6571

source_name: Control neuron Frontal Cortex neurons 8


title: genomic DNA from Control neuron Frontal Cortex neurons 4

description:
Control neuron Adult Frontal Cortex of patient 247
tb6629

source_name: Control neuron Frontal Cortex neurons 4


title: Blantyre Malaria Project_PID_2745

source_name: Human whole blood_Cerebral malaria_2745


title: Blantyre Malaria Project_PID_2739

source_name: Human whole blood_Cerebral malaria_2739


title: 101-Normal pancreas islet


title: genomic DNA from Down syndrome Frontal Cortex  5

description:
Down syndrome  Adult Frontal Cortex of patient 1151
tb5968

source_name: Down syndrome Frontal Cortex  5


title: genomic DNA from Control neuron Frontal Cortex neurons 5

description:
Control neuron Adult Frontal Cortex of patient 256
tb6969

source_name: Control neuron Frontal Cortex neurons 5


title: 103-Non-functional PanNET

description:
103 (replicate of 102)
K9-Ac

source_name: Non-functional PanNET


title: 102-Non-functional PanNET


title: 100-Insulinoma

source_name: Insulinoma


title: Blantyre Malaria Project_PID_2738

source_name: Human whole blood_Cerebral malaria_2738


title: 98-Non-functional PanNET


title: Blantyre Malaria Project_PID_2736

source_name: Human whole blood_Cerebral malaria_2736


title: genomic DNA from Down syndrome Frontal Cortex neurons 6

description:
Down syndrome neuron Adult Frontal Cortex of patient 1343
tb6625

source_name: Down syndrome Frontal Cortex neurons 6


title: Blantyre Malaria Project_PID_2737

source_name: Human whole blood_Cerebral malaria_2737


title: genomic DNA from Down syndrome Frontal Cortex neurons 8

description:
Down syndrome neuron Adult Frontal Cortex of patient 1378
tb7181

source_name: Down syndrome Frontal Cortex neurons 8


title: genomic DNA from Down syndrome Frontal Cortex neurons 9

description:
Down syndrome neuron Adult Frontal Cortex of patient 1335
tb7179

source_name: Down syndrome Frontal Cortex neurons 9


title: genomic DNA from Down syndrome Frontal Cortex neurons 3

description:
Down syndrome neuron Adult Frontal Cortex of patient 482
tb6622

source_name: Down syndrome Frontal Cortex neurons 3


title: genomic DNA from Down syndrome Frontal Cortex neurons 7

description:
Down syndrome neuron Adult Frontal Cortex of patient 1391
tb6648

source_name: Down syndrome Frontal Cortex neurons 7


title: genomic DNA from Control neuron Frontal Cortex neurons 1

description:
Control neuron Adult Frontal Cortex of patient 255
tb6626

source_name: Control neuron Frontal Cortex neurons 1


title: Blantyre Malaria Project_PID_2735

source_name: Human whole blood_Cerebral malaria_2735


title: genomic DNA from Down syndrome Frontal Cortex neurons 5

description:
Down syndrome neuron Adult Frontal Cortex of patient 1342
tb6624

source_name: Down syndrome Frontal Cortex neurons 5


title: genomic DNA from Down syndrome Frontal Cortex neurons 1

description:
Down syndrome neuron Adult Frontal Cortex of patient 712
tb6620

source_name: Down syndrome Frontal Cortex neurons 1


title: 97-Non-functional PanNET


title: 96-Non-functional PanNET


title: Blantyre Malaria Project_PID_2734

description: Patients with Cerebral Malaria were enrolled in the Blantyre Malaria project. 3 mL of whole blood in EDTA was collected at admission and added to Tri-reagent BD (Molecular Research Center) and frozen at -80oC

source_name: Human whole blood_Cerebral malaria_2734


title: 95-Non-functional PanNET


title: genomic DNA from Down syndrome Frontal Cortex neurons 2

description:
Down syndrome neuron Adult Frontal Cortex of patient 1308
tb6621

source_name: Down syndrome Frontal Cortex neurons 2


title: Blantyre Malaria Project_PID_2729

source_name: Human whole blood_Cerebral malaria_2729


title: 99-Non-functional PanNET

source_name: Non-functional PanNET


title: 93-Non-functional PanNET


title: 94-Insulinoma

source_name: Insulinoma


title: Blantyre Malaria Project_PID_2727

source_name: Human whole blood_Cerebral malaria_2727


title: Blantyre Malaria Project_PID_2723

source_name: Human whole blood_Cerebral malaria_2723


title: Blantyre Malaria Project_PID_2724

source_name: Human whole blood_Cerebral malaria_2724


title: 92-Insulinoma


title: 90-Non-functional PanNET


title: genomic DNA from Alzheimer's disease Frontal Cortex neurons 2

description:
Alzheimer's disease neuron Adult Frontal Cortex of patient NYBB4135
tb6569

value: Alzheimer's disease


title: Blantyre Malaria Project_PID_2720

source_name: Human whole blood_Cerebral malaria_2720


title: genomic DNA from Down syndrome Frontal Cortex neurons 4

description:
Down syndrome neuron Adult Frontal Cortex of patient 1139
tb6623

source_name: Down syndrome Frontal Cortex neurons 4


title: Blantyre Malaria Project_PID_2741

source_name: Human whole blood_Cerebral malaria_2741


title: 91-Non-functional PanNET

description:
91 (replicate of 90)
K65-Ac


title: genomic DNA from Control neuron Frontal Cortex neurons 9

description:
Control neuron Adult Frontal Cortex of patient NYBB3967
tb6572

source_name: Control neuron Frontal Cortex neurons 9


title: Blantyre Malaria Project_PID_2721

source_name: Human whole blood_Cerebral malaria_2721


title: genomic DNA from Alzheimer's disease Frontal Cortex neurons 3

description:
Alzheimer's disease neuron Adult Frontal Cortex of patient NYBB4118
tb6568


title: Blantyre Malaria Project_PID_2717

source_name: Human whole blood_Cerebral malaria_2717


title: genomic DNA from Alzheimer's disease Frontal Cortex neurons 1

description:
Alzheimer's disease neuron Adult Frontal Cortex of patient NYBB4099
tb6567


title: genomic DNA from Control Frontal Cortex glia 5

description:
Control glia Adult Frontal Cortex of patient 252
tb6680

source_name: Control Frontal Cortex glia 5

value: Fluorescence-activated nuclei sorted glia


title: 88-Non-functional PanNET

description:
88 (replicate of 87)
K63-Ac


title: Blantyre Malaria Project_PID_2714

source_name: Human whole blood_Cerebral malaria_2714


title: Blantyre Malaria Project_PID_2712

source_name: Human whole blood_Cerebral malaria_2712


title: Blantyre Malaria Project_PID_2764

source_name: Human whole blood_Cerebral malaria_2764


title: genomic DNA from Control Frontal Cortex glia 6

description:
Control glia Adult Frontal Cortex of patient 247
tb6681

source_name: Control Frontal Cortex glia 6


title: 84-Non-functional PanNET


title: 86-Non-functional PanNET


title: 87-Non-functional PanNET


title: 76-Normal pancreas

source_name: Normal pancreas


title: Blantyre Malaria Project_PID_2707

source_name: Human whole blood_Cerebral malaria_2707


title: Blantyre Malaria Project_PID_2711

source_name: Human whole blood_Cerebral malaria_2711


title: 75-Non-functional PanNET

source_name: Non-functional PanNET


title: Blantyre Malaria Project_PID_2708

source_name: Human whole blood_Cerebral malaria_2708


title: genomic DNA from Control Frontal Cortex glia 7

description:
Control glia Adult Frontal Cortex of patient 580
tb7186

source_name: Control Frontal Cortex glia 7


title: genomic DNA from Control Frontal Cortex glia 1

description:
Control glia Adult Frontal Cortex of patient 256
tb6973

source_name: Control Frontal Cortex glia 1


title: 74-Non-functional PanNET


title: genomic DNA from Control Frontal Cortex glia 4

description:
Control glia Adult Frontal Cortex of patient 248
tb6679

source_name: Control Frontal Cortex glia 4


title: Blantyre Malaria Project_PID_2706

source_name: Human whole blood_Cerebral malaria_2706


title: genomic DNA from Down syndrome Frontal Cortex glia 8

description:
Down syndrome glia Adult Frontal Cortex of patient 1335
tb7180

source_name: Down syndrome Frontal Cortex glia 8


title: genomic DNA from Down syndrome Frontal Cortex glia 7

description:
Down syndrome glia Adult Frontal Cortex of patient 1391
tb6675

source_name: Down syndrome Frontal Cortex glia 7


title: Healthy individuals non-contactants of leprosy patients P12-132

city: Belo Horizonte

first: Alex

middle: FIORINI

last: Carvalho

state: MG

address: Avenida Antonio Carlos 6627

department: DMVP

country: Brazil

institute: UFMG

description: leprosy patients had never taken any specific leprosy treatment (MDT) or were under any other medication at the time of diagnosis and did not present other diseases

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

scan_protocol: Scanned on an Agilent G2565BA scanner. scan protocol

data_processing: Agilent Feature Extraction Software (v10.1) was used for background subtraction and LOWESS normalization. data processing

source_name: healthy individuals

label_protocol: 200 ng of total RNA and the Agilent RNA Spike-in for two color (Agilent Technologies, Santa Clara, USA) were reverse-transcribed into double-stranded cDNA with the MMLV reverse transcriptase enzyme and primed with the oligo-dT-T7 polymerase promoter sequence. The Cy3-labeled cRNA obtained from cell culture pools, and Cy5-labeled cRNA obtained from leprosy biopsy were then transcribed in vitro by T7 RNA Polymerase. The quantity and efficiency of the labeled amplified Cy3-cRNA and Cy5-cRNA were determined with a NanoDrop™ ND-1000 (Thermo Scientific, Wilmington, Delaware, USA). Labeled cRNAs were hybridized to the Agilent G4851A SurePrint G3 Human GE 8x60k Microarray Kit (Agilent, Santa Clara, USA). label protocol

growth_protocol: growth protocol

extract_protocol:
extract protocol
Total RNA extracted using QIAGEN miRNeasy mini kit following manufacturer's instructions extract protocol

value: Skin biopsy

source_name: Reference RNA

tag: sample type

value: pooled RNA samles from cell lines (DAUDI, DLD1, DU145, FADU, GM637, H146,H1080, HB4a, HEK 293, jukart, SAOS-2, SKBR3, SK-MEL-28, T24 AND T98G)


title: Healthy individuals non-contactants of leprosy patients P12-134


title: 73-Non-functional PanNET


title: genomic DNA from Down syndrome Frontal Cortex glia 9

description:
Down syndrome glia Adult Frontal Cortex of patient 1378
tb7182

source_name: Down syndrome Frontal Cortex glia 9

value: Male

value: Frontal Cortex


title: 72-Non-functional PanNET

value: pancreatic neuroendocrine tumours


title: genomic DNA from Control Frontal Cortex glia 2

description:
Control glia Adult Frontal Cortex of patient 1169
tb6974

source_name: Control Frontal Cortex glia 2

value: Adult


title: 70-Non-functional PanNET


title: 89-Non-functional PanNET


title: Healthy individuals non-contactants of leprosy patients P12-130


title: 71-Insulinoma

source_name: Insulinoma


title: genomic DNA from Down syndrome Frontal Cortex glia 6

description:
Down syndrome glia Adult Frontal Cortex of patient 1343
tb6674

source_name: Down syndrome Frontal Cortex glia 6

value: Down syndrome


title: Healthy individuals non-contactants of leprosy patients P12-127


title: genomic DNA from Down syndrome Frontal Cortex glia 5

description:
Down syndrome glia Adult Frontal Cortex of patient 1342
tb6673

source_name: Down syndrome Frontal Cortex glia 5


title: 68-Non-functional PanNET


title: genomic DNA from Control Frontal Cortex glia 3

description:
Control glia Adult Frontal Cortex of patient 255
tb6976

source_name: Control Frontal Cortex glia 3

value: Female


title: 67-Non-functional PanNET


title: 69-Non-functional PanNET


title: Healthy individuals non-contactants of leprosy patients P12-140


title: genomic DNA from Down syndrome Frontal Cortex glia 1

description:
Down syndrome glia Adult Frontal Cortex of patient 712
tb6669

source_name: Down syndrome Frontal Cortex glia 1


title: Borderline Lepromatous leprosy form - BL RO234

source_name: leprosy patients


title: genomic DNA from Down syndrome Frontal Cortex glia 4

description:
Down syndrome glia Adult Frontal Cortex of patient 1139
tb6672

source_name: Down syndrome Frontal Cortex glia 4


title: Healthy individuals non-contactants of leprosy patients P12-136


title: 66-Non-functional PanNET

source_name: Non-functional PanNET


title: Type 2 Reaction - R2 P12-6ENH


title: genomic DNA from Down syndrome Frontal Cortex glia 2

description:
Down syndrome glia Adult Frontal Cortex of patient 1308
tb6670

source_name: Down syndrome Frontal Cortex glia 2


title: genomic DNA from Down syndrome Frontal Cortex glia 3

description:
Down syndrome glia Adult Frontal Cortex of patient 482
tb6671

source_name: Down syndrome Frontal Cortex glia 3


title: Lepromatous leprosy form - LL RO235


title: Healthy individuals non-contactants of leprosy patients P12-131


title: genomic DNA from Control Cerebellum  9

description:
Control  Adult Cerebellum of patient 220
tb8929

source_name: Control Cerebellum 9

value: Cerebellar cortex

value: Whole grey matter


title: genomic DNA from Control Cerebellum  7

description:
Control  Adult Cerebellum of patient 164
tb8927

source_name: Control Cerebellum 7

value: Normal


title: genomic DNA from Control Cerebellum  5

description:
Control  Adult Cerebellum of patient 256
tb6341

source_name: Control Cerebellum 5


title: 65-Non-functional PanNET


title: 62-Non-functional PanNET


title: 61-Insulinoma


title: genomic DNA from Control Cerebellum  4

description:
Control  Adult Cerebellum of patient 255
tb6340

source_name: Control Cerebellum 4


title: Type 1 Reaction - R1 41B

description: reactional patients under specific leprosy treatment (MDT)

source_name: Reference RNA


title: 63-Non-functional PanNET


title: genomic DNA from Control Cerebellum  6

description:
Control  Adult Cerebellum of patient 1169
tb6342

source_name: Control Cerebellum 6


title: genomic DNA from Control Cerebellum  8

description:
Control  Adult Cerebellum of patient 180
tb8928

source_name: Control Cerebellum 8


title: Borderline Borderline leprosy form - BB 5P

description: leprosy patients had never taken any specific leprosy treatment (MDT) or were under any other medication at the time of diagnosis and did not present other diseases


title: 60-Non-functional PanNET


title: 59-Insulinoma

source_name: Insulinoma


title: Lepromatous leprosy form - LL RO186


title: Healthy individuals non-contactants of leprosy patients C1

source_name: healthy individuals


title: genomic DNA from Control Cerebellum  3

description:
Control  Adult Cerebellum of patient 252
tb6339

source_name: Control Cerebellum 3


title: genomic DNA from Control Cerebellum  2

description:
Control  Adult Cerebellum of patient 248
tb6338

source_name: Control Cerebellum 2


title: Type 1 Reaction - R1 37B


title: 64-Non-functional PanNET


title: 58-Non-functional PanNET


title: Type 1 Reaction - R1 19P


title: 57-Non-functional PanNET


title: Type 1 Reaction - R1 29B


title: 56-Non-functional PanNET


title: Type 1 Reaction - R1 13R


title: Healthy individuals non-contactants of leprosy patients C2


title: 54-Non-functional PanNET


title: genomic DNA from Down syndrome Cerebellum  13

description:
Down syndrome  Adult Cerebellum of patient 1449
tb6336

source_name: Down syndrome Cerebellum 13


title: genomic DNA from Down syndrome Cerebellum  12

description:
Down syndrome  Adult Cerebellum of patient 1391
tb6335

source_name: Down syndrome Cerebellum 12


title: 53-Non-functional PanNET


title: Borderline Lepromatous leprosy form - BL RO178

source_name: leprosy patients


title: genomic DNA from Control Cerebellum  1

description:
Control  Adult Cerebellum of patient 247
tb6337

source_name: Control Cerebellum 1


title: Borderline Borderline leprosy form - BB 101R


title: 52-Non-functional PanNET

source_name: Non-functional PanNET


title: 50-Non-functional PanNET


title: genomic DNA from Down syndrome Cerebellum  8

description:
Down syndrome  Adult Cerebellum of patient 1335
tb6331

source_name: Down syndrome Cerebellum 8


title: 51-Non-functional PanNET


title: Borderline-Tuberculoid leprosy form - BT 13P


title: genomic DNA from Down syndrome Cerebellum  9

description:
Down syndrome  Adult Cerebellum of patient 1342
tb6332

source_name: Down syndrome Cerebellum 9


title: 49-Non-functional PanNET


title: genomic DNA from Down syndrome Cerebellum  10

description:
Down syndrome  Adult Cerebellum of patient 1343
tb6333

source_name: Down syndrome Cerebellum 10


title: Borderline Borderline leprosy form - BB 17R


title: Borderline-Tuberculoid leprosy form - BT 11P


title: genomic DNA from Down syndrome Cerebellum  7

description:
Down syndrome  Adult Cerebellum of patient 1283
tb6330

source_name: Down syndrome Cerebellum 7


title: 48-Non-functional PanNET


title: genomic DNA from Down syndrome Cerebellum  11

description:
Down syndrome  Adult Cerebellum of patient 1378
tb6334

source_name: Down syndrome Cerebellum 11


title: Borderline-Tuberculoid leprosy form - BT 115R

source_name: Reference RNA


title: 47-Insulinoma


title: 46-Non-functional PanNET


title: genomic DNA from Down syndrome Cerebellum  6

description:
Down syndrome  Adult Cerebellum of patient 1280
tb6329

source_name: Down syndrome Cerebellum 6


title: 45-Non-functional PanNET

description:
45 (replicate of 44)
K19-Ac


title: Borderline Borderline leprosy form - BB 98R


title: Tuberculoid leprosy form - TT 3P


title: 55-Insulinoma


title: genomic DNA from Down syndrome Cerebellum  3

description:
Down syndrome  Adult Cerebellum of patient 712
tb6326

source_name: Down syndrome Cerebellum 3


title: genomic DNA from Down syndrome Cerebellum  2

description:
Down syndrome  Adult Cerebellum of patient 482
tb6325

source_name: Down syndrome Cerebellum 2


title: genomic DNA from Down syndrome Cerebellum  5

description:
Down syndrome  Adult Cerebellum of patient 1238
tb6328

source_name: Down syndrome Cerebellum 5


title: Type 1 Reaction - R1 19B

description: reactional patients under specific leprosy treatment (MDT)


title: genomic DNA from Down syndrome Cerebellum  1

description:
Down syndrome  Adult Cerebellum of patient 311
tb6324

source_name: Down syndrome Cerebellum 1


title: Tuberculoid leprosy form - TT 112R

description: leprosy patients had never taken any specific leprosy treatment (MDT) or were under any other medication at the time of diagnosis and did not present other diseases


title: Tuberculoid leprosy form - TT 6P


title: genomic DNA from Down syndrome Cerebellum  4

description:
Down syndrome  Adult Cerebellum of patient 1139
tb6327

source_name: Down syndrome Cerebellum 4


title: genomic DNA from Control Cerebellum  10

description:
Control  Adult Cerebellum of patient 4518
tb8930

source_name: Control Cerebellum 10


title: 44-Non-functional PanNET


title: 43-Insulinoma

description:
43 (replicate of 42)
K18-Ac

source_name: Insulinoma


title: 42-Insulinoma


title: Type 1 Reaction - R1 50R

source_name: leprosy patients


title: Type 2 Reaction - R2 44B


title: 40-Non-functional PanNET


title: 41-Insulinoma


title: Borderline Lepromatous leprosy form - BL RO118


title: Borderline Lepromatous leprosy form - BL RO143


title: 39-Non-functional PanNET


title: 37-Non-functional PanNET


title: 38-Non-functional PanNET


title: Type 1 Reaction - R1 31B


title: Borderline-Tuberculoid leprosy form - BT 12P


title: 36-Non-functional PanNET


title: 35-Insulinoma


title: Tuberculoid leprosy form - TT 37R


title: 33-Non-functional PanNET


title: 34-Non-functional PanNET


title: Type 2 Reaction - R2 43B


title: Borderline Borderline leprosy form - BB 42B


title: Type 2 Reaction - R2 36B


title: genomic DNA from in vitro activated naive B cells [BN280_P1]

city: Rennes

first: Gilles

last: Salbert

address: Avenue du Général Leclerc

department: Biology

country: France

institute: University of Rennes 1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using the standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan reader using standard recommended Illumina scanner setting

data_processing: Using the minfi R package available through Bioconductor

source_name: in vitro activation of naive B cell from normal blood

growth_protocol: Naive B cells from healthy donors were purified using magnetic cell separation (Miltenyi Biotech), CFSE-labeled and cultured at 7.5.105 cells/ml for 4 days with cocktail 1. Activated B cells were then washed and further cultured at 4.105 with cocktail 2 (Le Gallou et al., 2012)

extract_protocol: DNA extracted using the DNA/RNA minikit (Qiagen) after cell sorting (FACS Aria, BD Biosciences)

treatment_protocol: Stimulation cocktail 1 (2,6 µg/ml Fab'2 anti-Ig, 100 ng/ml CD40 Ligand, 1 µg/ml CpG ODN 2006 and 50 U/ml IL2) for 4 days then differentiation cocktail 2 (50 U/ml IL2, 5 ng/ml IL4, 10 ng/ml IL10) for 2 days (Le Gallou et al., 2012)

tag: patient id

tag: subpopulation labeling

value: DAPI neg CFSE low CD38 high

tag: day of isolation


title: genomic DNA from in vitro activated naive B cells [BN287_D4_CFSEloHneg]

value: DAPI neg CFSE low Hoescht - (G1)


title: Type 2 Reaction - R2 2B


title: genomic DNA from in vitro activated naive B cells [BN287_D4CFSEloH+pos]

value: DAPI neg CFSE low Hoescht + (S/G2/M)


title: genomic DNA from in vitro activated naive B cells [BN287_P2_Hpos]

value: DAPI neg CFSE low CD38 low Hoescht + (S/G2/M)


title: genomic DNA from in vitro activated naive B cells [BN287_P1]


title: Type 1 Reaction - R1 45B


title: genomic DNA from in vitro activated naive B cells [BN287_P3]

value: DAPI neg CFSE high CD38 low


title: Q6

description: functional pancreatic neuroendocrine tumours

hyb_protocol: Hybridization signals were detected with Streptavidin-Alexa647 conjugate.

scan_protocol: Scanned images (Axon 4000B) were quantified using the Genepix 6.0 software (Axon Instruments, Sunnyvale, CA).

data_processing:
Most of the analysis and graphics were generated using R software version 2.0.1 and Bioconductor version 1.625 packages.
Sequentially, the blank and probe controls spots were removed from the data set of the 56 microRNA microarrays, and the local background was then subtracted from the median signal. Next, the data were normalized using a variance-stabilizing transformation stratified, within each array, by grid using the vsn package. The data resulting from this transformation can be considered as equivalent to logarithmic transformed data.

label_protocol: Five micrograms of total RNA were separately added to reaction mix in a final volume of 12 μl, containing 1 μg of [3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl of 0.1 M DTT, 1 μl of 10 mM dNTP mix, and 1 μl of SuperScript II RNaseH- reverse transcriptase (200 units/μl) was added to a final volume of 20 μl, and the mixture was incubated for 90 min in a 37°C water bath. After incubation for first-strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first-strand reaction mix and incubated at 65°C for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then, 5 μl of 1 M Tris·HCI (pH 7.6, Sigma) was added to neutralize the reaction mix, and labeled targets were stored in 28.5 μl at -80°C until chip hybridization.

extract_protocol: A neoplastic cellularity higher than 90% was obtained by cryostat enrichment. RNA was extracted with Trizol (Invitrogen, Carlsbad, CA) from 10 20-μm thick cryostat sections, checking the cell composition of the sample every five sections. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: tumor type


title: Q5

description: Non-functional pancreatic neuroendocrine tumours


title: genomic DNA from in vitro activated naive B cells [BN287_P2_Hneg]

value: DAPI neg CFSE low CD38 low Hoescht - (G1)


title: Q4

source_name: functional pancreatic neuroendocrine tumours


title: Borderline-Tuberculoid leprosy form - BT 8P

value: Skin biopsy


title: Type 1 Reaction - R1 32B

value: pooled RNA samles from cell lines (DAUDI, DLD1, DU145, FADU, GM637, H146,H1080, HB4a, HEK 293, jukart, SAOS-2, SKBR3, SK-MEL-28, T24 AND T98G)


title: Borderline Lepromatous leprosy form - BL 17P


title: genomic DNA from in vitro activated naive B cells [BN280_P2_Hneg]


title: Borderline Lepromatous leprosy form - BL 16P


title: Q13

source_name: Non-functional pancreatic neuroendocrine tumours


title: Borderline Borderline leprosy form - BB 09R


title: Q12

value: Non-functional pancreatic neuroendocrine tumours


title: genomic DNA from in vitro activated naive B cells [BN280_P2_Hpos]


title: genomic DNA from in vitro activated naive B cells [BN287_D4_CFSEhi]

value: DAPI neg CFSE high


title: genomic DNA from in vitro activated naive B cells [BN280_D4_CFSEloHneg]


title: genomic DNA from in vitro activated naive B cells [BN278_P3]


title: Borderline Borderline leprosy form - BB 107R


title: K9


title: K8


title: genomic DNA from in vitro activated naive B cells [BN280_P3]


title: genomic DNA from in vitro activated naive B cells [BN280_D4CFSEloHpos]


title: genomic DNA from in vitro activated naive B cells [BN280_D4_CFSEhi]


title: Tuberculoid leprosy form - TT 52R


title: Q2

value: functional pancreatic neuroendocrine tumours


title: RNA-P3 subpopulation [BN152_P3]

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized on HG-U219 arrays in 120ul volume/well. The GeneTitan Hybridization, Wash and Stain kit (Affymetrix) was used for preparing hybridization mixes and automated processing of 96-array plates on the GeneTitan Instrument (Affymetrix)

scan_protocol: HG-U219 Array Plates were scanned on the GeneTitan instrument (Affymetrix) imaging device according to manufacturer's instructions

data_processing: Raw data were normalized with the Robust Multichip Analysis (RMA) algorithm using BioConductor Affy Package

label_protocol: 150ng of each of the samples with RIN value >7 were converted to biotinylated cRNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) using a standard T7-based amplification protocol

extract_protocol: RNA was extracted using the AllPrep DNA/RNA mini kit (Qiagen) after cell-sorting of the different subpopulations (FACS Aria, BD Biosciences).


title: genomic DNA from in vitro activated naive B cells [BN278_P1]


title: K76


title: Q14


title: Borderline-Tuberculoid leprosy form - BT 59B


title: K80


title: K75


title: genomic DNA from in vitro activated naive B cells [BN278_D4_CFSEhi]


title: RNA-P2 subpopulation [BN152_P2]

value: DAPI neg CFSE low CD38 low


title: K7


title: K69


title: Type 2 Reaction - R2 47B


title: Tuberculoid leprosy form - TT 29R


title: Borderline Borderline leprosy form - BB 01R


title: Type 2 Reaction - R2 33B


title: genomic DNA from in vitro activated naive B cells [BN278_P2_Hpos]


title: RNA-P1 subpopulation [BN152_P1]


title: genomic DNA from in vitro activated naive B cells [BN278_D4_CFSEloHpos]


title: RNA-D4_CFSEhi subpopulation [BN152_D4 CFSEhi]

description: BN152_D4 CFSEhi.CEL


title: genomic DNA from in vitro activated naive B cells [BN278_D4_CFSEloHneg]


title: Type 1 Reaction - R1 40B


title: K63


title: Borderline-Tuberculoid leprosy form - BT 39R


title: K66


title: genomic DNA from in vitro activated naive B cells [BN119-120-121_P1]


title: genomic DNA from in vitro activated naive B cells [BN148_P1]


title: RNA-D4_CFSElo subpopulation [BN152_D4 CFSElo]

description: BN152_D4 CFSElo.CEL

value: DAPI neg CFSE low


title: genomic DNA from in vitro activated naive B cells [BN278_P2_Hneg]


title: RNA-P2 subpopulation [BN151_P2]


title: K60

description: Acinar cell carcinoma

source_name: Acinar cell carcinoma

value: Acinar cell carcinoma


title: genomic DNA from in vitro activated naive B cells [BN151_P1]


title: RNA-P1 subpopulation [BN151_P1]


title: Type 1 Reaction - R1 10B


title: genomic DNA from in vitro activated naive B cells [BN152_P1]


title: RNA-D4_CFSElo subpopulation [BN151_D4 CFSElo]

description: BN151_D4 CFSElo.CEL


title: K6


title: K58

description: Acinar cell carcinoma


title: Borderline Lepromatous leprosy form - BL 99R


title: K54

description: Acinar cell carcinoma


title: RNA-P3 subpopulation [BN151_P3]


title: K53

description: Acinar cell carcinoma


title: K47


title: Borderline Lepromatous leprosy form - BL 97R


title: RNA-P3 subpopulation [BN148_P3]


title: RNA-D4_CFSEhi subpopulation [BN151_D4 CFSEhi]

description: BN151_D4 CFSEhi.CEL


title: Type 2 Reaction - R2 68B


title: Type 1 Reaction - R1 56B


title: Lepromatous leprosy form - LL 111R


title: RNA-P1 subpopulation [BN148_P1]


title: K43


title: RNA-P2 subpopulation [BN148_P2]


title: K42


title: RNA-D4_CFSEhi subpopulation [BN148_D4 CFSEhi]

description: BN148_D4 CFSEhi.CEL


title: RNA-D4_CFSElo subpopulation [BN148_D4 CFSElo]

description: BN148_D4 CFSElo.CEL


title: RNA-P1 subpopulation [BN123_P1]


title: K37


title: K41


title: genomic DNA from in vitro activated naive B cells [BN123_P1]


title: Borderline Lepromatous leprosy form - BL 15P


title: K36


title: Borderline-Tuberculoid leprosy form - BT 44R


title: Borderline Borderline leprosy form - BB 14P


title: K35


title: K32


title: Borderline-Tuberculoid leprosy form - BT 41R


title: K3


title: K31


title: K25


title: K24


title: K29


title: Tuberculoid leprosy form - TT 12B


title: K20


title: K19


title: Type 2 Reaction - R2 11B


title: Tuberculoid leprosy form - TT 36R


title: K2


title: K15


title: K16


title: K14


title: K23


title: K13


title: Borderline Borderline leprosy form - BB 94R


title: Borderline-Tuberculoid leprosy form - BT 114R


title: K11


title: Type 1 Reaction - R1 32R


title: Borderline Lepromatous leprosy form - BL 66B


title: Tuberculoid leprosy form - TT 45R


title: A-T case, rep 2

city: Piscataway

first: Ronald

middle: P.

last: Hart

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
Total cellular RNA
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Output from Illumina GenomeStudio was loaded into R using limma, normalized with the neqc function (background correction followed by quantile normalization), and then modeled using lmFit and eBayes functions in limma.

source_name: Cerebellum, A-T case

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

growth_protocol: Human frozen tissue was obtained from the NICHD Brain and Tissue Bank of Developmental Disorders at the University of Maryland, Baltimore, MD.

extract_protocol: Total cellular RNA was extracted with an RNeasy kit from Qiagen, Inc.

treatment_protocol: Frozen samples were not treated.

value: cerebellum

tag: diagnosis

value: ataxia-telangiectasia

tag: age

value: average age 21 yrs


title: A-T case, rep 3

description:
Total cellular RNA
Replicate 3


title: Lepromatous leprosy form - LL 123R


title: Normal control, rep 1

description:
Total cellular RNA
Replicate 1

source_name: Cerebellum, normal control

value: free of known CNS neurological disease

value: age-matched (average age 25 yrs)


title: Normal control, rep 3

description:
Total cellular RNA
Replicate 3


title: A-T case, rep 1

description:
Total cellular RNA
Replicate 1


title: Normal control, rep 2

description:
Total cellular RNA
Replicate 2


title: Normal control, rep 4

description:
Total cellular RNA
Replicate 4


title: Tuberculoid leprosy form - TT 16B


title: MEF-Senescent 3

status: Public on Oct 29 2015

city: Dongguan

first: Yu-ning

last: Chen

address: Xin Cheng Avenue 1#, Songshan Lake

country: China

institute: Guangdong Medical University

description: Biological replicate 3 of 3. Senescent MEFs, harvested after serial passages.

hyb_protocol: Microarrys with labeled samples were hybridized at 40°C for 16 hours in the hybridization chamber and washed using buffers recommended in the manufacturer's protocol

scan_protocol: Slides were scanned using a Genepix 4000B laser scanner (Molecular Devices, Sunnyvale, CA, USA) and images were analyzed using Genepix Pro 7.0 software (Molecular Devices, Sunnyvale, CA, USA)

data_processing: The raw data were account for the differences in individual hybridization intensities, which were then normalized with subtract background correction and quantile normalization method

organism: Mus musculus

source_name: primary MEFs from whole mouse embryos e13.5

label_protocol: Two μg of total RNA was reverse transctibed into aRNA and labeled using Amino Allyl MessageAmp II aRNA kits (Life Technologies, Carlsbad, CA, USA) according to manufacturer's protocol

growth_protocol: Primary MEFs were isolated from 13.5-day-old embryos of C57/BL6 mice and maintained in DMEM supplemented with 10%FBS in a humidified incubator with 5% CO2 at 37°C. Serial passage was performed when the cells reached 80% conﬂuence

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain

value: Whole embryo

tag: passage


title: K10


title: MEF-Senescent 1

description: Biological replicate 1 of 3. Senescent MEFs, harvested after serial passages.


title: MEF-Senescent 2

description: Biological replicate 2 of 3. Senescent MEFs, harvested after serial passages.


title: MEF-Young 2

description: Biological replicate 2 of 3. Young MEFs, harvested after serial passages.


title: MEF-Young 3

description: Biological replicate 3 of 3. Young MEFs, harvested after serial passages.


title: Ma-Mel-15_siJUN_untreated_rep2

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital Bonn

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Variance stabilization and normalization using vsn package from bioconductor in R without background correction

label_protocol: 100ng RNA was converted to biotinylated cRNA using one round of amplification with Illumina Labelling Kit and one round of T7 polymerase

growth_protocol: The human melanoma cell line Ma-Mel-15 was cultured in RPMI/10% FCS.

extract_protocol: Total RNA was isolated 48hours after siRNA transfection using RLT buffer (Quiagen) and purified using spin columns. RNA quality was assayed using Agilent Bioanalyzer.

treatment_protocol: Ma-Mel-15 human melanoma cell cultures were transiently transfected (RNAiMax, Lipofectamin) with control siRNA, siRNA against MITF (pool of 4 siRNAs), siRNA against c-JUN (pool of 4 siRNAs) or combinations of siMITF and siJUN. Cells were then either treated with TNF-alpha (1000U/ml) for 24 hours or left untreated.

tag: cell line

value: melanoma cell line Ma-Mel-15

tag: sirna

value: siJUN

tag: genotype

value: JUN depletion

tag: biological replicate

tag: agent

value: untreated


title: Ma-Mel-15_siMITF_siJUN_untreated_rep2

value: MITF and JUN depletion


title: Ma-Mel-15_siMITF_TNF_rep2

value: siMITF

value: MITF depletion

value: TNF


title: Ma-Mel-15_siJUN_TNF_rep1


title: Ma-Mel-15_siMITF_siJUN_TNF_rep2


title: MEF-Young 1

description: Biological replicate 1 of 3. Young MEFs, harvested after serial passages.

tag: tissue


title: Ma-Mel-15_siMITF_untreated_rep2


title: Ma-Mel-15_siJUN_TNF_rep2


title: Ma-Mel-15_siMITF_rep2

extract_protocol: Total RNA was isolated 48hours after siRNA transfection using RLT buffer (Quiagen) and purified using spin columns. RNA quality was assayed using Agilent Bioanalyzer

treatment_protocol: Ma-Mel-15 human melanoma cell cultures were transiently transfected (RNAiMax, Lipofectamin) with control siRNA or siRNA against MITF (pool of 4 active siRNAs).

tag: time

value: 48 hours


title: Ma-Mel-15_siNT_TNF_rep2

value: siNT

value: control


title: Ma-Mel-15_siJUN_untreated_rep1


title: Ma-Mel-15_siMITF_untreated_rep1


title: Ma-Mel-15_siNT_TNF_rep1


title: Ma-Mel-15_siMITF_TNF_rep1


title: Ma-Mel-15_siNT_rep1


title: Ma-Mel-15_siNT_untreated_rep1


title: Ma-Mel-15_siNT_rep2


title: Ma-Mel-15_siNT_untreated_rep2


title: Ma-Mel-15_siMITF_siJUN_untreated_rep1


title: MZ7_siMITF_TNF10_rep2

data_processing: Variance stabilization and normalisation using vsn package from bioconductor in R without background correction

growth_protocol: The human melanoma cell line MZ7 was cultured in RPMI/10% FCS.

extract_protocol: Total RNA was isolated using RLT buffer (Quiagen) and purified using spin columns. RNA quality was assayed using Agilent Bioanalyzer

treatment_protocol: MZ7 melanoma cell cultures were transiently transfected (RNAiMax, Lipofectamin) with control siRNA or siRNA against MITF (pool of 4 active siRNAs) and then stimulated for 24hours with 10, 100 or 1000U/ml TNF-alpha or left untreated.

tag: cell type

value: melanoma

tag: tnf [units/ml]

tag: stimulation duration

value: 24 hours


title: MZ7_siMITF_untreated_rep2


title: Ma-Mel-15_siMITF_siJUN_TNF_rep1


title: MZ7_siNT_TNF100_rep2


title: Ma-Mel-15_siMITF_rep1


title: MZ7_siNT_TNF10_rep2


title: MZ7_siMITF_untreated_rep1


title: MZ7_siNT_TNF100_rep1


title: MZ7_siNT_TNF1000_rep2


title: MZ7_siNT_TNF10_rep1


title: MZ7_siNT_untreated_rep2


title: MZ7_siMITF_TNF1000_rep2


title: MZ7_siMITF_TNF100_rep2


title: MZ7_siMITF_TNF10_rep1


title: MZ7_siNT_TNF1000_rep1


title: MZ7_siMITF_TNF1000_rep1


title: MZ7_siMITF_TNF100_rep1


title: tonsil_total_epi_3_crypt

city: Vancouver

first: Catherine

last: Kang

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: British Columbia Cancer Research Centre

description: SAMPLE 10

data_processing: The data were normalised using quantile normalisation with Gene-E

source_name: Palatine tonsils, epithelium, crypt

label_protocol: 70 ng of RNA was labeled with TotalTM-96 RNA Amplification Kit (Ambion)

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser 2100 using the Agilent RNA 6000 Nanokit or Picokit (Agilent Technologies).

tag: Sex

value: male

value: 24 yo

value: epithelium

value: total-epithelial-enriched

tag: original id

tag: location

value: crypt


title: tonsil_total_epi_3_surface

description: SAMPLE 9

source_name: Palatine tonsils, epithelium, surface

value: surface


title: tonsil_total_epi_1_crypt

description: SAMPLE 8

value: 7 yo


title: tonsil_total_epi_1_surface

description: SAMPLE 7


title: tonsil_prog_2_surface

description: SAMPLE 3

value: 20 yo

value: progenitor-enriched


title: tonsil_prog_3_crypt

description: SAMPLE 6


title: tonsil_prog_2_crypt

description: SAMPLE 4


title: tonsil_prog_1_crypt

description: SAMPLE 2


title: peach-mescarp_treated-with-GA3_cold-storage_rep3

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: 0.8 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Hi-RPM Agilent hybridization buffer wa\s added to the fragmentation mixture and hybridized to Agilent Whole peach Genome Oligo Microarrays (GPL20329) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (C) using one color scan setting for 8x60k G3 Microarray Formats (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Microarray data produced by the Agilent microarray scanner were pre-processed deleting from the analysis every spot that was not considered ‘well above background’ by the Agilent pre-processing software (Agilent Feature Extraction Software).

organism: Prunus persica

source_name: peach mesocarp, of fruit treated with GA3 at pit hardening, after 15 days of cold storage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Peach [P. persica (L.) Batsch cv. Chimarrita] fruits were used in the current study. Peach trees (20 plants) were grown following standard agronomic practices in a commercial orchard in Farroupilha, Southern Brazil

extract_protocol: Total RNA extraction was carried out from 2 g of pulp, using a cetyltrimethylammonium bromide (CTAB) method described by Zeng and Yang, 2002 (Plant Mol. Biol. Report. 20: 417–417. doi:10.1007/BF02772130.)

treatment_protocol: Three biological replicates of 20 trees were selected based on uniformity and conducted as follows: GA treatment, plants were sprayed at 400L ha−1 of a GA solution consisting of 50 mgL−1 of GA (Pro-Gibb, Abbot Laboratories, North Chicago, USA, 10% m/m) supplemented with 0.05% (v/v) surfactant (Silwet, Momentive Performance Materials Inc., Waterford, NY) pH 4.5, at the initial stage of the pit hardening (45 days after anthesis, DAA). Untreated control plants were sprayed with hormone free solution. Fruits from treated and control plants were harvested at light green ground coloration, corresponding to the pre-climacteric stage.

tag: cultivar

value: Chimarrita

value: mesocarp

tag: postharvest treatment

value: 15 days of cold storage

tag: hormone treatment

value: GA3 at pit hardening


title: peach-mescarp_treated-with-GA3_cold-storage_rep1


title: peach-mescarp_treated-with-GA3_cold-storage_rep2


title: JSUB-4

city: New York

first: Jianbo

last: Sun

department: Microbiology and Immunology

institute: Columbia University

hyb_protocol: standard LC Sciences protocol

scan_protocol: Scan with Axon GenePix 4000B Microarray Scanner, Pixel size is10 µm, sample A gain is 340

data_processing: standard LC Sciences protocol

source_name: mouse primary splenic B cells

label_protocol: standard LC Sciences protocol

growth_protocol:
all cells were cultured in RPMI1640 medium plus anti-Cd40 antibody for 48h and LPS+PMA+Ionomycin for the last 5h
stain cells with Cd19, Cd1d, Cd5 antibody and Il10 detection kit for cell sorting by FACSAria

extract_protocol: total RNA was extracted with Trizol, rRNA was depleted with the Ribo-Zero rRNA removal kit (Epicentre)

tag: cell types

value: B cells

tag: cell subtypes


title: JSUB-3

description: prepared at same time as JSUB-4 but not JSUB-2


title: JSUB-2


title: peach-mescarp_not-treated-with-GA3_cold-storage_rep3

source_name: peach mesocarp after 15 days of cold storage

value: not treated, control


title: peach-mescarp_treated-with-GA3_harvest_rep1

source_name: peach mesocarp, of fruit treated with GA3 at pit hardening, at harvest

value: not treated, sampled at harvest


title: peach-mescarp_not-treated-with-GA3_harvest_rep1

source_name: peach mesocarp at harvest


title: peach-mescarp_not-treated-with-GA3_harvest_rep3


title: peach-mescarp_treated-with-GA3_harvest_rep2


title: MM cell line RPMI 8226_si_eIF4G_2

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

description: gene expression data of anti (Si)) eIF4G transfected cells

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

data_processing: Gene-level analyses was performed. RMA normalization, summarization by mean and batch effect removal, all were done by Partek Genomics suite (version 6.4) Copyright ©

source_name: multiple myeloma cell line

growth_protocol: The MM cell line RPMI 8226 were cultured in RPMI 1640 as described previously (Biological Industries, Kibbutz Beit-Haemek, Israel)(Zismanov V, Lishner M, Tartakover-Matalon S, Radnay J, Shapiro H, Drucker L. Tetraspanin-induced death of myeloma cell lines is autophagic and involves increased UPR signalling. Br J Cancer. 2009;101:1402-1409).

extract_protocol: RNeasy kit (Qiagen, Valencia, CA, USA), according to manufacture's protocol

treatment_protocol: Si RNA were designed by Qiagen. SI RNA were delivered into RPMI 8226 MM cell line using lipofectaime2000 (Invitorgene, Carlsbad, CA, USA). Fluorescence (≥10,000 events/analysis) was analyzed by flow cytometery (Navios, Beckman Coulter, USA) and determined in 96% of the cells (transfection efficiency).

tag: date

tag: cell line

value: RPMI 8226

value: multiple myeloma

tag: treatment

value: Si (anti) eIF4G transfection


title: MM cell line RPMI 8226_negative_control_2

description: gene expression data of negative control Si transfected cells

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: Negative control Si transfection


title: peach-mescarp_not-treated-with-GA3_cold-storage_rep2


title: peach-mescarp_not-treated-with-GA3_cold-storage_rep1


title: MM cell line RPMI 8226_si_eIF4E_2

description: gene expression data of anti (Si)) eIF4E transfected cells

label_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: Si (anti) eIF4E transfection


title: MM cell line RPMI 8226_negative_control_1


title: JSUB-1

description: prepared at same time as JSUB-2 but not as JSUB-4


title: MM cell line RPMI 8226_si_eIF4E_1


title: peach-mescarp_not-treated-with-GA3_harvest_rep2


title: Blood_PD_patient_38

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Samples were hybridized to HG−U133A 2.0 arrays (Affymetrix, Santa Clara, CA), washed, and stained (GeneChip Fluidics Station 450).

scan_protocol: Samples were scanned on an HP Gene Array Scanner 3000 7G according to standard manufacturer’s instructions (Affymetrix).

data_processing: Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) version 2.8.0 with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied (Irizarry RA et al. 2003). Data were then filtered based on Affymetrix detection call and probeset intensity, so that only probesets that had a present call and intensity value >100 in at least half the arrays of the smaller group (i.e. the healthy controls) were retained. Microarray data were then imported in the Multiexperiment Viewer (MeV) software (Saeed A et al. 2003) version 4.5.1 for Windows XP, and statistical analysis was performed with the SAM (Significance Analysis of Microarrays) (Tusher VG et al. 2001) and Rank Product (RP) modules (Breitling R et al. 2004) to detect significantly differentially expressed genes. SAM test was run using 1000 permutations and a False Discovery Rate (FDR) of 10%. RP was run using 100 permutations and an FDR of 0.005%.

source_name: Blood from PD patient

label_protocol: Biotinylated cDNA targets were prepared according to manufacturer's instructions (OvationTM RNA Amplification System V2, OvationTM WB Reagent and FL−OvationTM cDNA Biotin Module V2). RNA quantity was determined by the Nanodrop and RNA quality was determined by A260/A280 ratio and the presence of 2 distinct ribosomal bands on gel electrophoresis.

extract_protocol: RNA was extracted per Paxgene Blood RNA Extraction Kit (PreAnalytiX, Qiagen). Globin reduction was not conducted on any sample in this study since it has been shown to have little impact on probe detection when using OvationTM Whole Blood Solution NuGEN Technologies, Inc (San Carlos, CA, USA).

treatment_protocol: Paxgene RNA tubes were inverted 8–10 times and placed in a -80°C freezer until RNA extraction. Tubes were thawed at room temperature for 24 hours prior to RNA isolation.

tag: diagnosis

value: Parkinson's disease

value: blood


title: MM cell line RPMI 8226_si_eIF4G_1


title: Blood_PD_patient_41

tag: tissue


title: tonsil_prog_1_surface

description: SAMPLE 1

value: male

tag: age

value: 7 yo

value: epithelium

value: surface


title: Blood_PD_patient_40


title: tonsil_prog_3_surface

description: SAMPLE 5

value: 24 yo

tag: cell type

value: progenitor-enriched


title: peach-mescarp_treated-with-GA3_harvest_rep3

value: Chimarrita

value: mesocarp

value: GA3 at pit hardening


title: Blood_PD_patient_36


title: Blood_PD_patient_35


title: Blood_PD_patient_39


title: Blood_PD_patient_24


title: Blood_PD_patient_30


title: Blood_PD_patient_28


title: Blood_PD_patient_32


title: Blood_PD_patient_25


title: Blood_PD_patient_26


title: Blood_PD_patient_19


title: Blood_PD_patient_22


title: Blood_PD_patient_34


title: Blood_PD_patient_31


title: Blood_PD_patient_33


title: Blood_healthy_control_16

source_name: Blood from healthy control

value: Healthy


title: Blood_healthy_control_19


title: Blood_PD_patient_29


title: Blood_PD_patient_37


title: Blood_PD_patient_16


title: Blood_healthy_control_18


title: Blood_healthy_control_17


title: Blood_PD_patient_27


title: Blood_PD_patient_20


title: Blood_PD_patient_23


title: Blood_PD_patient_18


title: Blood_healthy_control_20


title: Blood_PD_patient_17


title: Blood_healthy_control_14


title: Blood_PD_patient_21


title: Blood_healthy_control_15


title: MZ7_siNT_untreated_rep1

value: melanoma

tag: sirna

value: siNT

tag: tnf [units/ml]

tag: biological replicate

value: 24 hours


title: Blood_healthy_control_13


title: Blood_PD_patient_12


title: Blood_PD_patient_9


title: Blood_PD_patient_15


title: Blood_PD_patient_10


title: Blood_healthy_control_11


title: Blood_PD_patient_13


title: Blood_healthy_control_8


title: Blood_PD_patient_7


title: Blood_healthy_control_12


title: Blood_PD_patient_6


title: Blood_healthy_control_9


title: Blood_PD_patient_11


title: Blood_healthy_control_7


title: Blood_healthy_control_5


title: Blood_healthy_control_3


title: Blood_healthy_control_2


title: pH 6.1 vs pH7_summarization of 3 technical replicates

city: La Plata

first: Antonio

last: Lagares

state: Bs As

department: Ciencias Biológicas

country: Argentina

institute: IBBM

description: Summarization of 3 Technical Replicates with 3 internal replicates each

hyb_protocol: Microarrays were prehybridized for 45 min at 42 °C in Easyhyb hybridization solution supplemented with 5 μg/ml sonicated salmon sperm DNA. Following prehybridization microarrays were washed in Milli-Q water (21 °C, 1 min), dunked in ethanol (21 °C, 10 s) and centrifuged (185×g, 3 min, 20 °C). Hybridization was performed at 42 °C for 16 h in Easyhyb hybridization solution supplemented with 50 μg/ml sonicated salmon sperm DNA in a final volume of 65 μl under a cover slip. Before applying the hybridization sample to the microarray, it was denatured for 5 min at 65 °C. Microarrays were washed once in 2× SSC, 0.2% SDS (5 min, 42 °C), twice in 0.2× SSC, 0.1% SDS (2 min, 21 °C) and twice in 0.2× SSC (2 min, 21 °C)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.  Data have been summarized across 3 technical replicates and 3 internal replicates on each array. Processed data file includes M-value (log2 fold-change Cy5/Cy3 representing pH6.1/pH7), P-value and A-value.
Data analysis was carried out according to Ruberg et al, 2003 (PMID 14651866). Briefly,genes were regarded as differentially expressed if P ≤ 0.05, M-values ≥ 1 or ≤ −1 and A-values ≥ 9.0. Normalization and t-statistics were carried out using the EMMA 1.0 microarray data analysis software developed at the Center for Genome Research at Bielefeld University (http://emma.cebitec.uni-bielefeld.de).

organism: Sinorhizobium meliloti

source_name: Chemostat cultures cells

label_protocol: Fluorescent-labeled cDNA was prepared according to an amino-allyl dye coupling protocol. Starting from 10 to 20 μg total RNA amino-allyl modified first strand cDNA was synthesized by reverse transcription using random hexamer primers, SuperScriptII reverse transcriptase and a dNTP + aa-dUTP mixture. After hydrolysis and cleanup using Microcon-30 filters the N-hydroxysuccinimidyl ester dyes were coupled to the amino-allyl-labeled first-strand cDNA. Uncoupled dye was removed using QiaQuick PCR Purification columns.

growth_protocol: Cells growth at constant Dilution rate and controlled pH 7.0

extract_protocol: Total RNA was prepared using the RNeasy mini kit (QIAGEN, Hildesheim, Germany). By ribolysation (30 s; speed, 6.5; Hybaid, Heidelberg, Germany) cells were disrupted in the RLT buffer provided with the kit in Fast Protein Tubes (Qbiogene, Carlsbad, CA).

tag: strain

growth_protocol: Cells growth at constant Dilution rate and controlled pH 6.1


title: Blood_PD_patient_4


title: Blood_PD_patient_5


title: Blood_healthy_control_4


title: Blood_PD_patient_2


title: HaCaT_MSU_2

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20101102). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Features were filtered out based on Flag assignment by the Feature Extraction software and based on signal intensity. Features which were not positive, significant or above the background were considered as [NOT DETECTED]. Other features were considerate as [DETECTED]. Then, we retained features where at least 100 percent of samples in any 1 out of 2 conditions (i.e. MSU treated vs control) have flags in [DETECTED]. The second filtration criterion was based on the signal intensity of probes. Entities where at least 100 percent of samples in any 1 out of 2 conditions (i.e. MSU treated vs control) have values within cut-off (i.e. 10-100th Percentile) were retained.

source_name: MSU-treated  HaCaT cell line - Replicate 2

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 150 ng total RNA, amplification yield was 9.7±0.6 μg cRNA and specific activity was 20.3±1.3 pmol Cy3 per μg cRNA.

growth_protocol: HaCaT were obtained from Cell Lines Service (Eppelheim, Germany) and grown in DMEM medium (PAN biotech, Aidenbach, Germany) supplemented with 10% FBS (Life Technology, Grand Island, NY, USA), L-glutamine and non-essential amino acid.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Before the treatment HaCaT cells were cultured in serum-free medium for 12hrs. HaCaT were treated with MSU (1mg/ml) vs DMEM control for 12hrs then submitted to RNA extration and gene expression profiling. Triplicate experiments were performed: HaCaT control (n=3), MSU-treated (n=3).

value: monosodium urate

value: HaCaT


title: Blood_PD_patient_3

value: Parkinson's disease


title: Blood_healthy_control_6

value: blood


title: HaCaT_MSU_1

source_name: MSU-treated  HaCaT cell line - Replicate 1


title: HaCaT_MSU_3

source_name: MSU-treated  HaCaT cell line - Replicate 3


title: Blood_PD_patient_1


title: HaCaT_Control_3

source_name: Untreated control HaCaT cell line - Replicate 3

value: Control


title: HaCaT_Control_2

source_name: Untreated control HaCaT cell line - Replicate 2


title: HaCaT_Control_1

source_name: Untreated control HaCaT cell line - Replicate 1


title: Blood_healthy_control_1


title: Mus - Day 7 r4

status: Public on Oct 28 2015

city: Gainesville

first: Jason

middle: Orr

last: Brant

state: FL

address: 2197 Mowry Rd

department: Biostatistics

institute: University of Florida

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized using RMA. Analyzed using BRB array tools

source_name: mm-Day 7 r4

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

extract_protocol: Extraction of total RNA was performed with QIAGEN Rneasy mini kit according to the manufacturer's instructions.

treatment_protocol: 8mm full-thickness excisional wounds on dorsal region

value: Dorsal skin wound day 7

value: 6-12 months


title: Mus - Day 7 r1

source_name: mm-Day 7 r1


title: Mus - Day 7 r3

source_name: mm-Day 7 r3


title: Mus - Day 7 r5

source_name: mm-Day 7 r5


title: Mus - Day 14 r6

source_name: mm-Day 14 r6

value: Dorsal skin wound day 14


title: Mus - Day 0 r5

source_name: mm-Day 0 r5

value: Dorsal Skin (normal)


title: Aco - Day 14 r5

organism: Acomys cahirinus

source_name: a-Day 14 r5


title: Mus - Day 14 r5

source_name: mm-Day 14 r5


title: Mus - Day 0 r2

source_name: mm-Day 0 r2


title: Mus - Day 0 r1

source_name: mm-Day 0 r1


title: Aco - Day 0 r5

source_name: a-Day 0 r5


title: Mus - Day 7 r2

source_name: mm-Day 7 r2


title: Mus - Day 7 r6

source_name: mm-Day 7 r6


title: Aco - Day 7 r5

source_name: a-Day 7 r5


title: Mus - Day 14 r1

source_name: mm-Day 14 r1


title: Mus - Day 0 r6

source_name: mm-Day 0 r6


title: Mus - Day 0 r4

source_name: mm-Day 0 r4


title: Mus - Day 14 r3

source_name: mm-Day 14 r3


title: Mus - Day 14 r2

source_name: mm-Day 14 r2


title: Mus - Day 0 r3

source_name: mm-Day 0 r3


title: Aco - Day 7 r4

source_name: a-Day 7 r4


title: Mus - Day 14 r4

source_name: mm-Day 14 r4


title: Blood_PD_patient_14

source_name: Blood from PD patient


title: Aco - Day 0 r4

source_name: a-Day 0 r4


title: Sham saline saline sample 53

city: Clermont-Ferrand

first: Simon

last: Loiodice

address: 28 Place Henir Dunant

department: Faculté de médecine

institute: Université d'Auvergne

description: Gene expression data from DS of rats during conditioning

hyb_protocol: RNA were hybridized on Affymetrix Rat230_2 GeneChip® arrays. The array were washed, stained and scanned using a GeneArray scanner (Agilent) and scanned with Affymetrix GeneChip® Command Console.

data_processing: The data were processed with Affymetrix GeneChip® Command console. Array studio software (Omicsoft Corporation, USA) was used to analyse the microarray CEL files, applying the MAS5 algorithm for normalisaion.

organism: Rattus norvegicus

source_name: Dorsal striatum dissected from male rats

label_protocol: 100 ng of Total RNA was labelled using the 3’IVT express kit protocol (Affymetrix, UK), and hybridized on Affymetrix Rat230_2 GeneChip® arrays. The array were washed, stained and scanned using a GeneArray scanner (Agilent) and scanned with Affymetrix GeneChip® Command Console.

growth_protocol: Immediately following the post-conditioning test on day eleven, thus 24h or 48h after the last administration of pramipexole or saline (depending on their distribution in compartment), animals were sacrificed under pentobarbital anaesthesia and the brain was quickly sampled at 4°C on fresh ice.

extract_protocol: Total RNA from each sample was extracted individually using a combined Trizol/RNeasy® method (Life Technologies, and Qiagen, France, respectively). The RNA quantity was checked by UV spectrophotometry. The RNA quality was assessed by calculating RNA integrity number (RIN) using a Bioanalyzer 2100 (Agilent Technologies, France) or using a Nanodrop analyzer (Thermo Fischer Scientific, USA).

treatment_protocol: The dorsal striatum (DS) was dissected out according to stereotaxic coordinate from Franklin and Paxinos.

value: dorsal striatum

tag: model

value: sham

value: saline treated

tag: conditioning

value: saline conditionned

tag: Sex

value: male

tag: background strain

value: Crl:OFA (Sprague Dawley)


title: Sham saline saline sample 54

scan_protocol: The array were washed, stained and scanned using a GeneArray scanner (Agilent) and scanned with Affymetrix GeneChip® Command Console.


title: Sham saline saline sample 56


title: Aco - Day 14 r4

source_name: a-Day 14 r4


title: Sham saline saline sample 52


title: Sham saline saline sample 55


title: Aco - Day 7 r3

source_name: a-Day 7 r3


title: Aco - Day 14 r3

source_name: a-Day 14 r3


title: Sham saline saline sample 50


title: Sham saline saline sample 51


title: Sham saline ppx sample 48

value: ppx conditionned


title: Aco - Day 7 r1

source_name: a-Day 7 r1


title: Aco - Day 14 r2

source_name: a-Day 14 r2


title: Aco - Day 0 r2

source_name: a-Day 0 r2


title: Aco - Day 7 r2

source_name: a-Day 7 r2


title: Aco - Day 0 r3

source_name: a-Day 0 r3


title: Sham saline ppx sample 43


title: Sham saline ppx sample 49


title: Sham saline ppx sample 47


title: Sham L-dopa saline sample 42

value: L-dopa treated


title: Sham saline ppx sample 44


title: Sham saline ppx sample 45


title: Aco - Day 14 r1

source_name: a-Day 14 r1


title: Sham saline ppx sample 46


title: Sham L-dopa saline sample 41


title: SAMPLE 122_HUES-1_p37

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human embryonic stem cell

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to  Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters.

source_name: HUES-1_passage 37

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human iPSCs and ESCs were maintained in an undifferentiated state in the presence of bFGF. The cultures were incubated at 37 ºC in a humidified incubator with 3 or 5% CO2.

extract_protocol: Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: human embryonic stem cell

tag: passage number


title: SAMPLE 121_HUES-1_p37


title: Sham L-dopa saline sample 38


title: SAMPLE 120_TIG/MKOS #106_p40

description: Gene expression in human iPS cell

source_name: TIG/MKOS #106_passage 40

tag: provenance somatic cell

value: TIG/MKOS #106

value: human iPS cell


title: SAMPLE 116_TIG/MKOS #56_p30

description: Gene expression in human iPS cell

source_name: TIG/MKOS #56_passage 30

value: TIG/MKOS #56


title: Sham L-dopa saline sample 39


title: Sham L-dopa saline sample 40


title: SAMPLE 123_HUES-1_p37


title: SAMPLE 119_TIG/MKOS #106_p40

description: Gene expression in human iPS cell


title: Aco - Day 0 r1

source_name: a-Day 0 r1


title: SAMPLE 117_TIG/MKOS #56_p30

description: Gene expression in human iPS cell


title: SAMPLE 118_TIG/MKOS #106_p40

description: Gene expression in human iPS cell


title: SAMPLE 115_201B7_p40

description: Gene expression in human iPS cell

source_name: 201B7_passage 40

value: HDF


title: Sham L-dopa saline sample 36


title: Sham L-dopa saline sample 37


title: Sham L-dopa ppx sample 34


title: Sham L-dopa ppx sample 35


title: SAMPLE 114_KhES-3_p28

source_name: KhES-3_passage 28


title: Sham L-dopa ppx sample 33


title: Sham L-dopa ppx sample 32


title: SAMPLE 112_KhES-3_p28


title: SAMPLE 109_201B7_p45

description: Gene expression in human iPS cell

source_name: 201B7_passage 45


title: SAMPLE 113_KhES-3_p28


title: SAMPLE 111_201B7_p45

description: Gene expression in human iPS cell


title: Sham L-dopa ppx sample 30

source_name: Dorsal striatum dissected from male rats


title: SAMPLE 110_201B7_p45

description: Gene expression in human iPS cell


title: Sham L-dopa ppx sample 31


title: Lesion saline saline sample 28

value: lesionned


title: Lesion saline saline sample 27


title: Lesion saline saline sample 26


title: SAMPLE 108_253G1_p37

description: Gene expression in human iPS cell

source_name: 253G1_passage 37


title: Sham L-dopa ppx sample 29


title: SAMPLE 107_253G1_p37

description: Gene expression in human iPS cell


title: SAMPLE 104_TIG/MKOS #56_p30

description: Gene expression in human iPS cell


title: SAMPLE 106_253G1_p37

description: Gene expression in human iPS cell


title: Lesion saline ppx sample 21


title: Lesion saline ppx sample 16


title: Lesion saline saline sample 23


title: SAMPLE 103_TIG/MKOS #19_p37

description: Gene expression in human iPS cell

source_name: TIG/MKOS #19_passage 37

value: TIG/MKOS #19


title: Lesion saline ppx sample 18


title: SAMPLE 105_253G1_p32

description: Gene expression in human iPS cell

source_name: 253G1_passage 32


title: Lesion saline saline sample 24


title: SAMPLE 102_TIG/MKOS #19_p37

description: Gene expression in human iPS cell


title: Lesion saline saline sample 22


title: Lesion saline ppx sample 17


title: Lesion saline ppx sample 19


title: Lesion saline ppx sample 20


title: SAMPLE 96_TIG/MKOS #56_p25

description: Gene expression in human iPS cell

source_name: TIG/MKOS #56_passage 25


title: SAMPLE 100_TIG/MKOS #106_p35

description: Gene expression in human iPS cell

source_name: TIG/MKOS #106_passage 35


title: SAMPLE 97_TIG/MKOS #56_p25

description: Gene expression in human iPS cell


title: Lesion L-dopa saline sample 12


title: SAMPLE 101_TIG/MKOS #19_p37

description: Gene expression in human iPS cell


title: Lesion L-dopa saline sample 14


title: SAMPLE 95_TIG/MKOS #56_p25

description: Gene expression in human iPS cell


title: SAMPLE 98_TIG/MKOS #106_p35

description: Gene expression in human iPS cell


title: Lesion saline saline sample 25


title: SAMPLE 93_TIG/MKOS #19_p32

description: Gene expression in human iPS cell

source_name: TIG/MKOS #19_passage 32


title: Lesion L-dopa saline sample 13


title: Lesion saline ppx sample 15


title: SAMPLE 99_TIG/MKOS #106_p35

description: Gene expression in human iPS cell


title: SAMPLE 94_TIG/MKOS #19_p32

description: Gene expression in human iPS cell


title: SAMPLE 92_TIG/MKOS #19_p32

description: Gene expression in human iPS cell


title: Lesion L-dopa saline sample 11


title: SAMPLE 90_HUES-1_p29

source_name: HUES-1_passage 29


title: SAMPLE 91_HUES-1_p29


title: Lesion L-dopa saline sample 9


title: Lesion L-dopa saline sample 10


title: Lesion L-dopa saline sample 8


title: SAMPLE 87_253G1_p42

description: Gene expression in human iPS cell

source_name: 253G1_passage 42


title: SAMPLE 88_253G1_p42

description: Gene expression in human iPS cell


title: SAMPLE 85_201B7_p53

description: Gene expression in human iPS cell

source_name: 201B7_passage 53


title: Lesion L-dopa ppx sample 5


title: Lesion L-dopa ppx sample 7


title: Lesion L-dopa ppx sample 4


title: SAMPLE 83_201B7_p53

description: Gene expression in human iPS cell


title: Lesion L-dopa ppx sample 3


title: SAMPLE 84_201B7_p53

description: Gene expression in human iPS cell


title: SAMPLE 89_HUES-1_p29


title: Lesion L-dopa ppx sample 6


title: SAMPLE 86_253G1_p42

description: Gene expression in human iPS cell


title: SAMPLE 79_201B7_p40

description: Gene expression in human iPS cell


title: SAMPLE 78_201B7_p40

description: Gene expression in human iPS cell


title: Lesion L-dopa ppx sample 2


title: Lesion L-dopa ppx sample 1


title: UtE-iPS-11_p18

description: Gene expression in human iPS cell

source_name: UtE-iPS-11, passage 18

value: human uterine endometrium (hUtE) cell

tag: cell-line name


title: SAMPLE 81_MRC-iPS-25 (Tic)_p17

description: Gene expression in human iPS cell

source_name: MRC-iPS-25 (Tic)_passage 17

tag: cell line

value: MRC-iPS-25 (Tic)


title: SAMPLE 80_MRC-iPS-25 (Tic)_p17

description: Gene expression in human iPS cell


title: SAMPLE 77_KhES-3_p28


title: CBA/Ca 24h post pneumococcal strain D39 infection, replicate 5

city: Leicester

first: Peter

middle: W

last: Andrew

address: University Rd

department: Infection, Immunity and Inflammation

institute: University of Leicester

description:
raplicate 5
C39-24-7

data_processing: The data were normalised using quantile normalisation with IlluminaGenomeStudio, batch correction was done using dCHIP and differences in expression were analysed in ArrayTrack

source_name: mouse lung

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

extract_protocol: Lung were extracted, cut and immediatelly immersed in RNA-later. RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: CBA/CaOlaHsd

value: 9 weeks

tag: gender

value: female

value: lung

tag: pneumococcal strain

value: D39, serotype 2, ST595


title: CBA/Ca 24h post pneumococcal strain D39 infection, replicate 3

description:
raplicate 3
C39-24-10

tag: tissue


title: CBA/Ca 24h post pneumococcal strain D39 infection, replicate 4

description:
raplicate 4
C39-24-9

tag: age


title: SAMPLE 76_KhES-3_p28

tag: cell type


title: CBA/Ca 24h post pneumococcal strain D39 infection, replicate 1

description:
raplicate 1
C39-24-8


title: SAMPLE 75_253G1_p32

description: Gene expression in human iPS cell


title: CBA/Ca 24h post pneumococcal strain D39 infection, replicate 2

description:
raplicate 2
C39-24-12


title: CBA/Ca 12h post pneumococcal strain D39 infection, replicate 5

description:
raplicate 5
C39-12-3


title: SAMPLE 74_253G1_p32

description: Gene expression in human iPS cell


title: CBA/Ca 12h post pneumococcal strain D39 infection, replicate 4

description:
raplicate 4
C39-12-2


title: CBA/Ca 12h post pneumococcal strain D39 infection, replicate 1

description:
raplicate 1
C39-12-1


title: SAMPLE 73_201B7_p40

description: Gene expression in human iPS cell


title: CBA/Ca 12h post pneumococcal strain D39 infection, replicate 3

description:
raplicate 3
C39-12-5


title: SAMPLE 72_201B7_p40

description: Gene expression in human iPS cell


title: CBA/Ca 12h post pneumococcal strain D39 infection, replicate 2

description:
raplicate 2
C39-12-6


title: SAMPLE 71_MRC-iPS-16 (Fetch)_p13

description: Gene expression in human iPS cell

source_name: MRC-iPS-16 (Fetch)_passage 13

value: MRC-iPS-16 (Fetch)


title: BALB/c 24h post pneumococcal strain D39 infection, replicate 4

description:
raplicate 4
B39-24-12

value: BALB/cOlaHsd