title: 7_POST [mRNA]

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645.

label_protocol: 100 ng of total RNA from each sample, isolated from human adipose tissue, was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay.


title: 36_PRE [mRNA]

status: Public on Dec 31 2014

type: RNA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Gene expression data from human adipose tissue.

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm (R version 3.0.2) and then LIMMA was applied to calculate significant differential expression between samples.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human adipose tissue, pre surgery-induced weight loss

extract_protocol: RNA was extracted following Qiagen protocol.

tag: tissue

value: subcutaneous adipose

tag: gender

value: female

tag: condition

value: PRE surgery-induced weight loss

tag: individual


title: 12_POST [miRNA]

hyb_protocol: Sample was hybridized to Affymetrix miRNA 3.0 array using an Affymetrix GeneChip Hybridization Oven 645.

source_name: human adipose tissue, post surgery-induced weight loss

label_protocol: 350 ng of total RNA from each sample, isolated from human adipose tissue, was processed, labelled according to the Affymetrix GeneChip® WT Terminal Labeling Kit.

value: POST surgery-induced weight loss


title: 10_POST [miRNA]


title: 36_POST [mRNA]


title: 34_POST [mRNA]


title: 33_PRE [mRNA]


title: 31_PRE [mRNA]


title: 25_POST [mRNA]


title: 33_POST [mRNA]


title: 7_PRE [mRNA]


title: 29_POST [mRNA]


title: 34_PRE [mRNA]


title: 26_POST [mRNA]


title: 26_PRE [mRNA]


title: 24_POST [mRNA]


title: 20_PRE [mRNA]


title: 22_POST [mRNA]


title: 21_PRE [mRNA]


title: 31_POST [mRNA]


title: 29_PRE [mRNA]


title: 22_PRE [mRNA]


title: 24_PRE [mRNA]


title: 25_PRE [mRNA]


title: 2_PRE [mRNA]


title: 21_POST [mRNA]


title: R29953

description: Gene expression data from non-malignant nevus

hyb_protocol: Sample was hybridized to Affymetrix HumanGene 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.0.2) with aroma.affymetrix and bioconductor packages

source_name: Total RNA from nevus tissue

label_protocol: 100ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

extract_protocol: RNA was extracted following the RNA-easy Qiagen protocol.

value: skin

tag: biopsy type

value: nevus


title: 10_PRE [mRNA]


title: R29245

description: Gene expression data from NCoR positive MM sample

source_name: Total RNA from malignant melanoma (MM) sample

value: malignant melanoma

tag: ncor status

value: positive


title: R31106

description: Gene expression data from NCoR negative MM sample

value: negative


title: 20_POST [mRNA]


title: R29955


title: 12_POST [mRNA]


title: 2_WT_1

hyb_protocol: Sample was hybridized to Affymetrix Mouse Gene 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

data_processing: Data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.0.2) with aroma.affymetrix and bioconductor packages.

organism: Mus musculus

source_name: WT_bone marrow cells

extract_protocol: RNA was extracted following Quiagen protocol

tag: strain background

tag: genotype/variation

value: WT

tag: cell type

value: sorted Ter119+CD71+ bone marrow cells


title: 4_KO_1

source_name: Parp-2 KO_bone marrow cells


title: R29238


title: R31107


title: 1_WT_2


title: R29234


title: R29239


title: 15_PRE [mRNA]


title: 10_POST [mRNA]


title: 3_KO_2


title: R29237


title: 12_PRE [mRNA]


title: 2_POST [mRNA]


title: R29236


title: Control rep2

status: Public on Dec 30 2014

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

description: Gene Expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 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 theGenePix Scanner using settings suggested by Agilent

data_processing: The scanned images were analyzed with Feature Extraction Software v 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SCC9 cell line

label_protocol: DNA microarrays were used to evaluate gene expression differences between three stably PROX1-overexpressing clone and a control-transfected SCC9 cell clone. Microarray analysis was performed using Agilent Whole Human Genome Microarray 4_44K arrays and the One Color Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, USA). Two biological replicates were included for each experimental condition. Target cDNA was generated from 1 _g polyadenylated mRNA, which was reverse-transcribed and labeled with Cy3.

extract_protocol: Total RNA was extracted from homogenized cells with TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

treatment_protocol: SCC9 cells were transfected with pCMV6 empty vector or pCMV6-PROX1 expression vector (Origene, Rockville, USA Origene), containing the full length human PROX1 cDNA, using Lipofectamine 2000 (Invitrogen) following the manufacturer«s instructions. Transfected cells were selected in medium with 300ug/ml G418 (Invitrogen). Cell clones were individually expanded and analyzed for PROX1 mRNA and protein expression. Global gene expression was analysed by DNA microarrays in two biological replicates of cells over-expressing PROX1 and controls.

tag: cell line

tag: treatment

value: pCMV6 empty vector


title: Control rep1

description: Gene Expression


title: PROX1 rep 2

description: Gene Expression

value: pCMV6-PROX1 expression vecto


title: PROX1 rep1

description: Gene Expression


title: 21_POST [miRNA]


title: 10_PRE [miRNA]


title: 15_POST [mRNA]


title: Control 1

status: Public on Jun 20 2014

description: Sample 21

source_name: healthy control

label_protocol: Microarray analysis was performed using Agilent Whole Human Genome Microarray 4x44K arrays and the One Color Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, USA). Target cDNA was generated from 800ng of total RNA, which was reverse-transcribed and labeled with Cy3.

extract_protocol: Total RNA was isolated from peripheral mononuclear cells using illustra RNAspin Mini Kit (GE Healthcare Lifesciences). The quality and concentration of the RNA was determined with the RNA Nano Chip Kit and the 2100 Bioanalyzer (Agilent Technologies). A total o 23 samples were used in this study.

treatment_protocol: In this study we investigate whole-genome gene expression profiles of mononuclear cells from survivor (n=5)  and non-survivor (n=5) septic patients, as well as from 3 healthy controls. Blood samples were collected at the time of sepsis diagnosis and seven days later (D0 and D7, respectively)

tag: diagnosis

value: Healthy volunteer

tag: outcome

value: mononuclear cells


title: RajiVp 1

description: Gene Expression

source_name: cell line

extract_protocol: Total RNA was isolated using Trizol (Invitrogen), following the manufacturer's protocol.

treatment_protocol: Burkitt's lymphoma cell line Raji was treated with NaB isolated or combined with VP-16 for 24 hours. Cells were collected by centrifugation and total RNA was extracted using Trizol. DNA microarrays were used to access global gene expression modulation upon treatment of Raji cell line with VP-16 and a combination of NaB and VP-16. Gene expression of treated cells was compared with controls consisting of untreated cells. Microarray analysis was performed using Agilent Whole Human Genome Microarray 4_44K arrays and labeled using the One Color Quick Amp Labeling Kit (Agilent Technologies). Two biological replicates were included for each experimental condition.

value: Raji

value: Treated for 24 hours with VP-16


title: P260_D0

description: Sample 19

source_name: septic patient_survivor

tag: time point

value: D0 (at the time of sepsis diagnosis)

value: Severe sepsis

value: Alive


title: RajiC 2

description: Gene Expression

value: Control (untreated)


title: Control 3

description: Sample 23


title: RajiVpNB 2

description: Gene Expression

value: Treated for 24 hours with a combination of NaB and VP-16


title: P260_D7

description: Sample 20

value: D7 (7 days after diagnosis)


title: RajiNB 1

description: Gene Expression

value: Treated for 24 hours with NaB


title: P254_D7

description: Sample 18

source_name: septic patient_non-survivor

value: Septic shock

value: Dead


title: RajiVpNB 1

description: Gene Expression


title: Control 2

description: Sample 22


title: RajiC 1

description: Gene Expression


title: P239_D7

description: Sample 16


title: P254_D0

description: Sample 17


title: RajiNB 2

description: Gene Expression


title: RajiVp 2

description: Gene Expression


title: P229_D7

description: Sample 14


title: P239_D0

description: Sample 15


title: P227_D0

description: Sample 11


title: P227_D7

description: Sample 12


title: P217_D7

description: Sample 10


title: P140_D0

description: Sample 3


title: P107_D0

description: Sample 1


title: P229_D0

description: Sample 13


title: P217_D0

description: Sample 9


title: P140_D7

description: Sample 4


title: Patient 15_OSCC

status: Public on Jun 08 2014

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Hybridization signals were detected and quantified using Illumina scanner and BeadStudio version 3.2.7.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: OSCC

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

extract_protocol: Total RNA was prepared from tissue using mirVana miRNA Isolation Kit (Ambion Inc.) in compliance with the manufacturer's protocol.

value: Male

tag: age


title: Patient 15_Surgical margin

source_name: Surgical margin


title: Patient 13_Surgical margin


title: Patient 14_OSCC


title: P143_D0

description: Sample 5


title: Patient 13_OSCC


title: Patient 16_OSCC


title: Patient 12_Surgical margin


title: Patient 14_Surgical margin


title: P146_D7

description: Sample 8


title: Patient 16_Surgical margin


title: P146_D0

description: Sample 7


title: Patient 12_OSCC


title: Patient 11_Surgical margin


title: P107_D7

description: Sample 2


title: Patient 11_OSCC


title: Patient 9_Surgical margin


title: Patient 9_OSCC


title: Patient 8_Surgical margin


title: Patient 10_Surgical margin

value: Female


title: Patient 10_OSCC


title: Patient 8_OSCC


title: Patient 7_Surgical margin


title: Patient 6_Surgical margin


title: 1_09B1194-5

status: Public on Nov 19 2014

type: genomic

hyb_protocol: Sample was hybridized to Affymetrix® Genome-Wide Human SNP Array 6.0 using a GeneChip Hybridization Oven 640 and posteriorly washed and stained using the Fluidics Station 450

data_processing: The data were analyzed using the AGC and ChAS softwares

label: Biotin

molecule: genomic DNA

label_protocol: 500ng starting genomic DNA were processed using the Affymetrix® Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev. 2)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: QIAMP Tissue Kit. (QIAGEN)

value: breast cancer tumor

tag: ctc status

value: CTC-


title: Patient 6_OSCC


title: Patient 5_Surgical margin


title: Patient 4_OSCC


title: Patient 4_Surgical margin


title: Patient 5_OSCC


title: Patient 2_Surgical margin


title: 10_09B13923


title: Patient 3_OSCC


title: Patient 2_OSCC


title: 4_09B11204


title: 5_09B8799-1T

value: CTC+


title: Patient 3_Surgical margin


title: Patient 1_OSCC


title: 41_09B6942


title: 8_09B11916-1T


title: 14_09B13230_1


title: 12_09B13568_1


title: 9_09B16403-1


title: 20_09B7608


title: FaDu_control_rep1

description: Gene Expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (and Cy5-labelled cRNA, if applicable)  was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 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.

data_processing: The scanned images were analyzed with Feature Extraction Software v.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 0.2 ug RNA using the One-Color or Two-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoVue (GE Healthcare) Spectrophotometer. For two-color labeling samples were labeled with Cy5 and a reference RNA with Cy3(Universal Human Reference RNA, Agilent)

extract_protocol: Total RNA was prepared from cell culture using mirVana miRNA Isolation Kit (Ambion Inc.) in compliance with the manufacturer’s protocol. RNA integrity and concentration were assessed using the RNA 6000 Nano Assay kit with Agilent 2100 Bioanalyzer according to the manufacturer's instructions (Agilent Technologies).

treatment_protocol: SCC25 and FaDu cell lines were grown in a Dulbecco´s Modified Eagle´s medium/Nutrient Mixture F-12 Ham (DMEM/F12) supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 and 95% air at 37°C. Keratinocytes were plated on a support layer, called feeder-layer, composed of murine fibroblasts of the type 3T3-Swiss albino (ATCC, catalog number CCL-92), which were irradiated (60 Gy), and maintained in an incubator at 37°C, in a humidified atmosphere containing 5% CO2 and grown as previously described. For transfection, we used the siPORT NeoFx reagent (Ambion) following the manufacturer protocol. For up-regulation, Ambion Pre-miR™ miRNA Precursor Molecule (miR-10b and miR-196a) was used, with Ambion's Pre-miR negative control #1. Successful up-regulation was achieved with 50nM final Pre-miR miRNA Precursor concentration.

value: FaDu

value: squamous cell carcinoma

value: control

source_name: Universal Human Reference RNA, Agilent

tag: sample type

value: reference RNA


title: SCC25_control_rep2

description: Gene Expression


title: SCC25_control_rep1

description: Gene Expression


title: control_rep2

description: Gene Expression

source_name: control

value: normal keratinocyte


title: SCC25_mir10b_rep1

description: Gene Expression


title: FaDu_mir10b_rep2

description: Gene Expression


title: 13_09B13566_1

tag: tissue


title: SCC25_mir10b_rep2

description: Gene Expression


title: mir196_rep2

description: Gene Expression


title: FaDu_control_rep2

description: Gene Expression


title: FaDu_mir10b_rep1

description: Gene Expression


title: 7_09B14293


title: control_rep1

description: Gene Expression


title: 6_09B10720-1T


title: G10

status: Public on Dec 31 2013

description: Gene expression data from FiPS generated with OCT4, ZNF521, KLF4 and cMYC

hyb_protocol: Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: G10:FiPS ZNF521+OKM

label_protocol: In general 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix). Samples were hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640.  ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

growth_protocol: We have generated iPS cells from human foreskin derived fibroblasts at passage 5 in culture using different transcription factors able to replace OCT4 and SOX2 in the reprogramming process. Our dataset also includes human embryonic stem cell lines (ES[4] and ES[10] cell lines) and the parental fibroblast from where iPS have been derived.

extract_protocol: RNA from iPS cells, parental fibroblasts and human embryonic stem cells have been isolated using Trizol method followed by DNAse treatment.


title: G13

description: Gene expression data from FiPS generated with GATA3VP16, SOX2vP16, KLF4 and cMYC

source_name: G13:FiPS GSKM


title: G17

description: Gene expression data from FiPS generated with OCT4, SOX3, KLF4 and cMYC

source_name: G17: FIPS SOX3+OKM


title: G15

description: Gene expression data from FiPS generated with OCT4, ZIC2, ZNF521, ASCL1, HESX1,FOXD5,KLF4 and cMYC

source_name: G15: FIPS OKM+5F ECTO


title: mir196_rep1

description: Gene Expression


title: S17

description: Gene expression data from FiPS derivated with Yamanaka factors

source_name: S17: FiPS OSKM

value: Control 4F iPS


title: P143_D7

description: Sample 6

value: Severe sepsis

value: Alive

value: mononuclear cells


title: 2_09B99104-2T


title: G8

description: Gene expression data from FiPS generated with OCT4, SOX1, KLF4 and cMYC

source_name: G8: FiPS SOX1+OKM


title: G9

source_name: G9: FiPS SOX1+OKM

value: FiPS generated with OCT4, SOX1, KLF4 and cMYC


title: G14

source_name: G14:FiPS GSKM

value: FiPS generated with GATA3VP16, SOX2vP16, KLF4 and cMYC


title: G16

description: Gene expression data from FiPS generated with OCT4, ZIC2, ZNF521, ASCL1, HESX1,FOXD5,KLF4 and cMY

source_name: G16:FIPS OKM+5F ECTO

value: FiPS generated with OCT4, ZIC2, ZNF521, ASCL1, HESX1,FOXD5,KLF4 and cMYC


title: ES4 p15

description: Gene expression data from human embryonic stem cells

source_name: ES4 p15:Human Embryonic Stem cell line ES[4]

value: Control Human Embryonic stem cells


title: ES10p13

source_name: ES10p13: Human Embryonic Stem cell line ES[10]


title: Vp13

source_name: Vp13: FiPS OSKM


title: G5d

description: Gene expression data from WT fibroblast

source_name: G5: Human fibroblast

value: Control fibroblasts


title: G6

description: Gene expression data from WT fibroblast

source_name: G6: Human fibroblast


title: HCTRL-4

status: Public on Dec 23 2013

description: Gene expression data from peripheral blood B lymphocytes

hyb_protocol: Sample was hybridized to Affymetrix Human Exon 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

source_name: Total RNA from purified B lymphocytes from peripheral blood

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

value: Peripheral blood

value: Healthy Control


title: HCTRL-7


title: HCTRL-3


title: HCTRL-2


title: SCC25 2

status: Public on Dec 30 2013

description: Gene expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 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.

data_processing: The scanned images were analyzed with Feature Extraction Software v.9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SCC25 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoVue (GE Healthcare) Spectrophotometer.

treatment_protocol: Cell lines were grown in a Dulbecco´s Modified Eagle´s medium/Nutrient Mixture F-12 Ham (DMEM/F12) supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 and 95% air at 37°C. Human oral epithelial tissue was obtained from healthy volunteers undergoing dental surgeries, following previously published procedures, after approval by the Research Ethics Committee of IPEN under License Number 087/CEP-IPEN/SP and with  informed consent signature. Keratinocytes were grown on a fibroblast feeder-layer in a Dulbecco’s Modified Eagle Medium (DMEM; Gibco, New York, NY, USA) F-12 Nutrient Mixture (HAM, Gibco, New York, NY, USA) (2:1), with 10% Bovine Serum Product Fetal Clone III (Hyclone, Logan, Utah, USA), penicillin (100 U/ml), streptomycin (100 lg/ml), gentamicin (50 lg/ml), and amphotericin B (2.5 lg/ml) glutamine (4 mM), adenine (0.18 mM) (Sigma–Aldrich, St. Louis, MO, USA), insulin (5 lg/ml) (Sigma–Aldrich, St Louis, MO, USA), hydrocortisone (0.4 lg/ml) (Sigma–Aldrich, St Louis, MO, USA), cholera toxin (0.1 nM) (Sigma–Aldrich, St Louis, MO, USA), triiodotyronine (20 pM) (Sigma–Aldrich, St Louis, MO, USA) and  epidermal growth factor (10 ng/ml) (R&D Systems, Minneapolis, MN, USA)


title: HCTRL-6


title: Keratinocyte 1

description: Gene expression

source_name: Keratinocyte

value: Keratinocyte


title: MALD1-5

source_name: Total RNA from purified B lymphocytes from peripheral blood with t(11;14)(q13;q32)


title: HCTRL-8


title: Keratinocyte 2

description: Gene expression


title: HCTRL-5


title: MALD1-2


title: HCTRL-1


title: S1

description: Gene expression data from WT fibroblast

source_name: S1: Human fibroblast


title: MCL-5

value: MCL


title: SCC25 1

description: Gene expression


title: MALD1-4


title: MCL-2


title: MCL-3


title: MCL-4


title: MALD1-3


title: MCL-1


title: MALD1-1


title: Mostra 7_45d

status: Public on Mar 01 2013

description: Gene expression data from porcine tissue cells.

hyb_protocol: Sample was hybridized to a GeneChip Porcine Genome Array (Affymetrix) using a GeneChip Hybridization Oven 645.

data_processing: The data were analyzed using the RMA algorithm, and then LIMMA was applied to calculate significant differential expression between conditions.

organism: Sus scrofa

source_name: Myocardial sample, Infarct Core, 45 days, ID2

label_protocol: 200 ng of total RNA were amplified and labeled using the 3' IVT Express Kit and control reagents (Affymetrix).

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen).

tag: crossbreed

value: Landrace x Large White

tag: gender

value: female

tag: weight

value: myocardium

value: surgically induced myocardial infarction (MI)

tag: myocardial sample

value: infarct core

tag: time

value: 6 weeks

tag: pig id


title: Mostra 1_45d

source_name: Myocardial sample, Remote, 45 days, ID2

value: remote


title: Mostra 53

source_name: Myocardial sample, Infarct Core, 6 days, ID7

value: 1 week


title: Mostra 54

source_name: Myocardial sample, Remote, 6 days, ID8


title: Mostra 3_45d

source_name: Myocardial sample, Remote, 45 days, ID3


title: Mostra 5_45d

source_name: Myocardial sample, Remote, 45 days, ID5


title: Mostra 4_45d

source_name: Myocardial sample, Infarct Core, 45 days, ID3


title: Mostra 21

source_name: Myocardial sample, Infarct Core, 30 days, ID22

value: 4 weeks


title: Mostra 34

source_name: Myocardial sample, Remote, 6 days, ID7


title: Mostra 30

source_name: Myocardial sample, Sham Operated, 0 days, ID30

value: sham operation


title: Mostra 37

source_name: Myocardial sample, Infarct Core, 6 days, ID8


title: Mostra 31

source_name: Myocardial sample, Sham Operated, 0 days, ID31


title: Mostra 19

source_name: Myocardial sample, Remote, 30 days, ID18


title: Mostra 26

source_name: Myocardial sample, Infarct Core, 30 days, ID20


title: Mostra 8

source_name: Myocardial sample, Infarct Core, 30 days, ID18


title: Mostra 38

source_name: Myocardial sample, Remote, 6 days, ID9


title: Mostra 39

source_name: Myocardial sample, Infarct Core, 6 days, ID9


title: Mostra 6_45d

source_name: Myocardial sample, Infarct Core, 45 days, ID5


title: Mostra 33

source_name: Myocardial sample, Sham Operated, 0 days, ID33


title: Mostra 1

source_name: Myocardial sample, Remote, 30 days, ID22


title: 35D7V Patient 5

status: Public on Dec 30 2011

description: Patient 5

hyb_protocol: Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). Hybridization procedures strictly followed protocols provided by the manufacturer (GE Healthcare).

scan_protocol: Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.1 software (Axon Instruments).

data_processing: The fluorescent images were captured using GenePix Pro v.4.1™ (Axon Instruments Inc) and the light intensities were quantified and corrected for background noise with the CodeLink™ Expression Analysis v4.1. Spots with background contamination, shape irregularity, or pixel saturation were filtered out. Only spots flagged as “good” (G) or “low” (L) were considered in the subsequent analysis. For differential gene expression evaluation, the results were analyzed in the mean space (MS), where M = log2 (expression ratio) and S = log2 (mean intensity) (Koide et al., 2006). Due to the small number of replicates, differentially expressed genes were identified according to the HTself method (Vencio and Koide, 2005), which takes advantage of self-self experiments to define an intensity-dependent fold-change cutoff. Since our microarray system is a one-color platform, we built virtual experiments combining two replicates of actual hybridizations (pseudo-ratios). We performed two independent self-self experiments and defined a fold-change cutoff with a 95% confidence level using a window size and pace of 1.2 and 0.5, respectively, in the S axis. We considered a gene as differentially expressed if its intensity signals were above (up-regulated) or below (down-regulated) the dynamic cutoff level defined by the self-self experiments.

source_name: CD14+ cells isolated from peripheral blood

label_protocol: Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). Labeling procedures strictly followed protocols provided by the manufacturer (GE Healthcare).

extract_protocol: Total RNA was extracted with RNeasy™ spin columns and treated with RNAse free-DNAse (Qiagen).

tag: sex

value: FEMALE

tag: status

value: Healthy donor


title: 34D7 Patient 4

description: Patient 4


title: 34D7V Patient 4

description: Patient 4


title: Mostra 2

source_name: Myocardial sample, Remote, 30 days, ID20


title: 33D7 Patient 3

description: Patient 3


title: 25D7V Patient 2

description: Patient 2


title: 25D7 Patient 2

description: Patient 2


title: 25D6 Patient 2

description: Patient 2


title: 35D7 Patient 5

description: Patient 5


title: Patient 3

status: Public on May 31 2009

description: Patient 3

scan_protocol: Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.0 software (Axon Instruments).

data_processing: Generated data were batch normalized using CodeLink Software v.2.3. Statistical analysis for the identification of differentially expressed genes was carried out using the BayBoots tool (Vencio et al., 2006).

source_name: primary osteosarcoma

label_protocol: Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). Labeling procedures strictly followed protocols provided by the manufacturer (GE Healthcare). A

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent following the protocol described by the manufacturer (Invitrogen).

tag: SEX

value: Male

tag: status after 5 years

value: Dead

tag: PRAME

value: Positive

tag: HIST

value: osteoblastic


title: 24D6 Patient 1

description: Patient 1


title: 25D0 Patient 2

description: Patient 2


title: Patient 3_b

description: Patient 3


title: 24D0 Patient 1

description: Patient 1


title: Patient 2_b

description: Patient 2

value: Alive

value: giant cell


title: Patient 6

description: Patient 6

value: Negative

value: chondroblastic


title: Patient 5

description: Patient 5


title: Patient 5_b

description: Patient 5


title: Patient 2

description: Patient 2


title: Patient 6_b

description: Patient 6


title: Patient 4

description: Patient 4

value: anaplastic


title: Patient 4_b

description: Patient 4


title: 24D7V Patient 1

description: Patient 1


title: Patient 1

description: Patient 1

value: telangiectatic


title: 33D7V Patient 3

description: Patient 3


title: Pool 2

status: Public on Nov 24 2008

description: Margins: cases 5,6,7,8,9

data_processing: Generated data (Discovery spots, Flags G=GOOD and L=LIMIT) were median-normalized using CodeLink

source_name: Oral Squamous Cell Carcinoma

tag: Pool 2


title: Patient 1_b

description: Patient 1


title: Pool 1

description: Margins: cases 1,2,3,4

tag: Pool 1


title: Patient 9

description: Patient 9

tag: Subsite

value: Floor of mouth

tag: Status after 3 years

value: dead by disease

tag: Pathological State

tag: Perineural Invasion

value: No


title: 24D7 Patient 1

description: Patient 1

tag: age


title: Patient 7

description: Patient 7


title: Patient 4

description: Patient 4

value: dead by commorbidity

value: Yes


title: G12

source_name: G12:FiPS GSKM

tag: cell type

value: FiPS generated with GATA3VP16, SOX2vP16, KLF4 and cMYC


title: Patient 3

description: Patient 3

value: Tongue


title: Patient 6

description: Patient 6

value: Male

value: alive


title: Patient 8

description: Patient 8


title: Patient 5

description: Patient 5


title: Patient 2

description: Patient 2


title: siWT-1

status: Public on Oct 03 2008

city: Pamplona

first: Carmen

last: Berasain

state: Navarra

address: Avda. Pio XII 55

institute: CIMA

description: PLC/PRF/5 were transfected in triplicate with WT1 specific siRNAs (siWT) and siRNAs control (siGL)

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2 chip according to the protocols provided by the manufacturer.

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

data_processing: RMA

source_name: PLC/PRF/5 cells transfected with 2 duplexes of specific siRNA targeting exons 7 and 10 of WT1

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: Cells were grown in DMEM

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells were transfected with siRNA duplexes using the Dharmafect reagent

tag: Human hepatoma cell line


title: GalC+ biological replicate 3

status: Public on Jun 01 2008

city: Bethesda

first: Joe

middle: A

last: Nielsen

state: MD

address: 49 Convent Drive BD49,5A75

country: USA

institute: NIH/NINDS

description: Oligodendrocytes were FAC sorted using cell surface expression of A2B5 and GALC to purifiy oligodendrocyte progenitors (A2B5+) and oligodendrocytes (GALC+) from postnatal day rat whole brains.

hyb_protocol: Affymetrix standard protocols were followed using the hybridization oven 640, and washing with the fluidics station 450

scan_protocol: The microarrays were scanned with a genechip scanner 3000 7G

data_processing: Cel files were imported into Genespring for preprocessing using RMA, and normalization using a global per-chip and per-gene normalization strategy

organism: Rattus norvegicus

source_name: GalC+ oligodendrocytes

label_protocol: Affymetrix small sample labeling protocol

extract_protocol: RNAeasy-Qiagen

tag: Fluorescent activated cell sorted GalC+ oligodendrocytes isolated from post-natal day 7 rat whole brain


title: siGL-3

source_name: PLC/PRF/5 cells transfected with the siRNA control siGL


title: siGL-1

source_name: PLC/PRF/5 cells transfected with the siRNA control duplex siGL


title: siGL-2


title: siWT-3


title: siWT-2


title: A2B5+ biological replicate 4

source_name: A2B5+ oligodendrocytes

extract_protocol: RNeasy-Qiagen

tag: Fluorescent activated cell sorted A2B5+ oligodendrocytes isolated from post-natal day 7 rat whole brain


title: A2B5+ biological replicate 3


title: GalC+ biological replicate 4


title: A2B5-2

status: Public on Sep 30 2006

description: Single A2B5+ and single O4+ cells were sorted directly from whole brain dissociates using flow cytometry

data_processing: Affymetrix CEL files were imported into Genespring and GCRMA was used for preprocessing of the data.  The data was normalized in Genespring using global per chip and per gene normalization

source_name: single A2B5+ cells sorted directly from whole brain dissociates using flow cytometry

tag: Postnatal day7 male Sprague Dawley pups


title: A2B5-3


title: A2B5+ biological replicate 1


title: A2B5-1

tag: Postnatal day7 male sprague Dawley pups


title: O4-1

source_name: single O4+ cells sorted directly from whole brain dissociates using flow cytometry


title: A2B5-4


title: A2B5+ biological replicate-2


title: GalC+ biological replicate 1


title: A2B5-5


title: O4-2


title: O4-3


title: O4-4


title: GalC+ biological replicate 2


title: Patient 1

description: Patient 1

tag: Subiste

tag: SEX