title: E34VZ replicate 2

source_name: Repl.2_Ventricular Zone Embryonic day 34


title: wholeblood_812581_1

status: Public on Jun 01 2016

type: RNA

city: Toronto

first: Jan

last: Heng

state: ON

address: 25 Orde Street

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HumanGene 2.1 ST (GeneTitan)

scan_protocol: Affymetrix Gene Titan

data_processing: Data were normalized using RMA and differential expression was determined using Limma with multiple hypothesis testing (Benjamini and Hochberg); Bioconductor, R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood, maternal peripheral

label_protocol: Labeling was performed according to standard Affymetrix protocols (Ambion WT kit)

extract_protocol:
Sample collection protocol: Peripheral maternal blood collected using PAXgene tubes.
PAXgene Blood RNA system kit was used to isolate total RNA.

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue

value: peripheral maternal blood


title: DD8P6a

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation after background subtraction using the Gene Expression Module 1.8.0 of GenomeStudio V2010.3 (Illumina).

source_name: Cells with high bone forming capacity in vivo

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand   reverse transcription step, followed by a single in vitro transcription   (IVT) amplification that incorporates biotin-labeled nucleotides.   Subsequent steps include array hybridization, washing, blocking, and   streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively   detected for downstream analysis.

extract_protocol: The RNA was isolated using the RNeasy Mini Kit (Qiagen), including RNase-free Dnase (Qiagen) digestion   (RNase-free DNase Set, Quiagen) has been applied on the columns during   isolation.

tag: cell type

value: Bone marrow derived stromal cells immortalized with telomerase gene

tag: treatment

value: No treatment basal culture condition

tag: passage


title: CB8a

description: replicate 1

source_name: Cells with low bone forming capacity in vivo


title: Relapsing_DLBCL_primary (case10)

type: genomic

city: Basel

first: Darius

last: Juskevicius

address: Schoenbeinstr. 40

department: Molecuar Pathology

country: Switzerland

institute: Institute of Pathology

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 25 rpm for at least 24 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visulaized and analyzed using Agilent Genomic Workbench v7.0 and the ADM2 algorithm.

molecule: genomic DNA

source_name: FFPE tissue biopsy

label_protocol: A 100-500 nanogram aliquot of each sample and reference DNA was heat digested then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.

extract_protocol: H&E- and CD20-stained sections of FFPE blocks or fresh-frozen tissue were reviewed to evaluate tumor content. Only tissues with >70% tumor content were used. Depending on the distribution of tumor cells, 25µm-thick sections were cut or punches were taken from the tumor-rich tissue areas. Prior to overnight Proteinase K digestion, paraffin sections were deparaffinized and rehydrated by serial xylene and ethanol washes, respectively. Genomic DNA (gDNA) was extracted by automation using Maxwell® 16 FFPE plus LEV DNA Purification Kit. gDNA from samples with extremely scarce tumor material was isolated by the phenol-chloroform extraction as described previously22. Yields were quantified by the Qubit assay.

tag: disease state

value: Diffuse large B cell lymphoma (DLBCL)

tag: specimen

value: Relapsing DLBCL primary

tag: case

source_name: Reference pooled 46XX

value: pooled normal (46,XX) reference (Promega)


title: wholeblood_812573_2


title: CB4a

description: replicate 1


title: P15VZ replicate 3

city: San Juan de Alicante

first: Victor

last: Borrell

state: Alicante

address: Av Ramon y Cajal s/n

department: Institute of Neuroscience

country: Spain

institute: CSIC

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Mustela putorius furo

source_name: Repl.3_Ventricular Zone Postnatal day 1.5

label_protocol: 85ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the LowInputQuick Amp Labeling kit  (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

tag: developmental stage

value: Postnatal day 1.5


title: W144_REJECTION

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: peripheral vein blood from patient sample W144 at rejection time point

hyb_protocol: The hybridization procedure was performed after control of RNA quality and integrity and according to the “One-Colour Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to RISET 1.0 microarrays using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37°C) Agilent Gene Expression Wash Buffer 2 containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Inc.). The Agilent Feature Extraction Software (FES v. 10.2.1.3/10.5.1.1) was used to read out and process the microarray image files.

data_processing: Chips were processed using LIMMA package using normexp method for background substraction and quantile normalisation.

extract_protocol: Peripheral vein blood was drawn directly into PAXgene Blood RNA tubes (QIAgen, Crawley UK). Whole-blood RNA was extracted using the PAXgene Blood RNA Kit including DNAse I treatment (QIAgen). Quality and integrity of PAXgene purified RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

tag: patient

value: peripheral vein blood


title: Relapsing_DLBCL_primary (case9)


title: Relapsing_DLBCL_primary (case8)

source_name: Frozen tissue biopsy


title: wholeblood_812566_2


title: wholeblood_812566_1


title: E34SVZ replicate 3

source_name: Repl.3_Subventricular Zone Embryonic day 34

value: Embryonic day 34


title: E34SVZ replicate 1

source_name: Repl.1_Subventricular Zone Embryonic day 34


title: E30VZ replicate 3

source_name: Repl.3_Ventricular Zone Embryonic day 30

value: Embryonic day 30


title: AD10a

description: replicate 1


title: Relapsing_DLBCL_primary (case6)


title: Relapsing_DLBCL_primary (case7)


title: CF1a

description: replicate 1


title: wholeblood_812573_1


title: wholeblood_812562_2


title: Relapsing_DLBCL_primary (case5.1)


title: Relapsing_DLBCL_primary (case5.2)


title: wholeblood_812562_1


title: W138_REJECTION

description: peripheral vein blood from patient sample W138 at rejection time point


title: W132_REJECTION

description: peripheral vein blood from patient sample W132 at rejection time point


title: E30VZ replicate 1

source_name: Repl.1_Ventricular Zone Embryonic day 30


title: W131_REJECTION

description: peripheral vein blood from patient sample W131 at rejection time point


title: W134_REJECTION

description: peripheral vein blood from patient sample W134 at rejection time point


title: wholeblood_812559_1


title: Relapsing_DLBCL_primary (case4)


title: wholeblood_812559_2


title: W123_REJECTION

description: peripheral vein blood from patient sample W123 at rejection time point


title: P15VZ replicate 2

source_name: Repl.2_Ventricular Zone Postnatal day 1.5


title: E30VZ replicate 2

source_name: Repl.2_Ventricular Zone Embryonic day 30


title: W122_REJECTION

description: peripheral vein blood from patient sample W122 at rejection time point


title: W139_REJECTION

description: peripheral vein blood from patient sample W139 at rejection time point


title: genomic RNA from adjacent normal tissue of OT44

city: new delhi

first: binay

last: panda

address: 1649A vasant kunj

country: India

institute: ganit labs foundation

scan_protocol: HiScan, Illumina

data_processing: Analyzed with GenomeStudio V2011.1 Gene Expression module 1.9.0 (Illumina). Transformed and normalized using VST and LOESS methods, provided within R Bioconductor package, lumi. Batch correction was performed using ComBat

label_protocol: Standard Illumina hybridization protocol

extract_protocol: Total RNA was extracted using PureLink RNA mini kit (Invitrogen) and RNA quality was checked on the bioanalyzer using RNA Nano6000 chip (Agilent). RNA samples with poor RIN numbers (≤7) on the bioanalyzer chip, indicating partial degradation of RNA were processed using Illumina WGDASL assay and the ones with good RIN numbers (>7) were biotin-labelled using Illumina TotalPrep RNA Amplification kit (Ambion) as per the manufacturer’s recommendations.

tag: subject id

tag: disease

value: Oral tongue squamous cell carcinomas (OTSCC)

tag: tissue type

value: adjacent normal tissue

tag: patient age (yrs)

tag: patient gender

value: M

tag: tumor stage

tag: tumor grade

tag: tumor nodal status

tag: patient survival status

value: Alive

tag: patient overall survival (months)

tag: patient disease-free survival (months)


title: genomic RNA from adjacent normal tissue of OT39

value: Dead (unrelated)


title: W126_REJECTION

description: peripheral vein blood from patient sample W126 at rejection time point

tag: tissue


title: wholeblood_812551_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: genomic RNA from tumor tissue of OT39

tag: subject id

tag: disease

value: tumor tissue

value: MDSCC


title: wholeblood_812551_2

value: peripheral maternal blood


title: wholeblood_812546_2


title: genomic RNA from tumor tissue of OT44

tag: tissue type

tag: patient age (yrs)

value: WDSCC


title: Relapsing_DLBCL_primary (case2)

tag: disease state

tag: specimen

tag: case


title: W115_REJECTION

description: peripheral vein blood from patient sample W115 at rejection time point

tag: patient


title: wholeblood_812546_1


title: wholeblood_812555_1


title: genomic RNA from tumor tissue of OT35

tag: patient gender

tag: tumor stage

tag: tumor grade

tag: tumor nodal status

tag: patient survival status

tag: patient overall survival (months)


title: W112_REJECTION

description: peripheral vein blood from patient sample W112 at rejection time point

tag: tissue


title: W109_REJECTION

description: peripheral vein blood from patient sample W109 at rejection time point


title: genomic RNA from adjacent normal tissue of OT35

tag: patient disease-free survival (months)


title: W108_REJECTION

description: peripheral vein blood from patient sample W108 at rejection time point


title: wholeblood_812518_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: W125_REJECTION

description: peripheral vein blood from patient sample W125 at rejection time point


title: wholeblood_812518_2C


title: genomic RNA from adjacent normal tissue of OT3

tag: subject id

tag: disease

tag: tissue type

tag: patient age (yrs)


title: W104_REJECTION

description: peripheral vein blood from patient sample W104 at rejection time point

tag: patient


title: genomic RNA from tumor tissue of OT24

tag: patient gender

tag: tumor stage

tag: tumor grade


title: genomic RNA from tumor tissue of OT3

tag: tumor nodal status

tag: patient survival status

tag: patient overall survival (months)


title: Sp_W_D28_8002x8010_23

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description: Gene expression data from a Mice Gene expression data from a Mice West Nile Virus infected

hyb_protocol: Individual sense-strand DNA targets were hybridized to Mouse Gene 2.1 ST 24-Array Plates (Affymetrix, Inc.) using the GeneTitan Multi-Channel (MC) Instrument for hybridization, array staining and washing and scanning.  Quality Control Metrics for Hybridization, Labeling and Sample quality were generated using the Affymetrix Expression Console software.  All samples passed the QC criteria.

scan_protocol: Affy arrays were scanned with an Affymetrix GeneTitan

data_processing: Data was analyzed using R(3.01) and oligo and limma packages. Matrix was generated use RMA. Samples were background corrected and quantile normalized both through standard RMA and oligomask. Both filtered and unfiltered outputs are included in this submission.

organism: Mus musculus

source_name: Spleen Tissue from West Nile Virus infected Line 8002x8010 at Day 28

label_protocol: RNA samples were prepared for whole transcriptome expression analysis using the WT PLUS Reagent Kit following the manufacturer’s recommended protocol (Affymetrix, Inc. Santa Clara, CA).  100 ng of total RNA was used to prepare the hybridization ready targets.

growth_protocol: Age- and sex-matched eight to ten week old mice were subcutaneously inoculated in the rear footpad with 100 PFU WN-TX.  3 animals from each line and condition were humanely euthanized for necropsy and RNA from the spleen was isolated.

extract_protocol: Spleen tissues were thawed, transferred to lysis buffer either TRIzol (Life Technologies) or RLT Reagent (Qiagen Inc.) and homogenized. RNA was isolated using Qiagen miRNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip.

treatment_protocol: Per the manufacturer's protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation  overnight, tissue was removed from RNAlater and stored at -80°C until RNA isolation in TRIzol or RLT buffer.

tag: Sex

value: male

tag: tissue

value: Spleen

tag: collaborative cross line (genetic background)

tag: animal number (rxid)

tag: treatmock infectedent

value: West Nile Virus infected

tag: timepoint

value: Day 28

tag: batch


title: genomic RNA from adjacent normal tissue of OT24

tag: subject id

tag: disease

tag: patient disease-free survival (months)


title: W99_REJECTION

description: peripheral vein blood from patient sample W99 at rejection time point

tag: patient


title: Sp_W_D28_8002x8010_17


title: wholeblood_812509_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_812477_1


title: wholeblood_812509_2


title: wholeblood_812459_2


title: genomic RNA from tumor tissue of OT2

tag: tissue type

tag: patient age (yrs)

tag: patient gender

tag: tumor stage

tag: tumor grade

tag: tumor nodal status

tag: patient survival status

tag: patient overall survival (months)


title: genomic RNA from adjacent normal tissue of OT2

tag: subject id

tag: disease


title: Sp_W_D21_8002x8010_117

source_name: Spleen Tissue from West Nile Virus infected Line 8002x8010 at Day 21

tag: Sex

tag: tissue

tag: collaborative cross line (genetic background)

tag: animal number (rxid)

tag: treatmock infectedent

tag: timepoint

value: Day 21

tag: batch


title: wholeblood_812477_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: W96_REJECTION

description: peripheral vein blood from patient sample W96 at rejection time point

tag: patient

value: peripheral vein blood


title: W103_REJECTION

description: peripheral vein blood from patient sample W103 at rejection time point


title: Sp_W_D21_8002x8010_119


title: W92_REJECTION

description: peripheral vein blood from patient sample W92 at rejection time point


title: W88_REJECTION

description: peripheral vein blood from patient sample W88 at rejection time point


title: genomic RNA from tumor tissue of OT14

tag: tissue type

tag: patient age (yrs)

tag: patient gender

tag: tumor stage

tag: tumor grade

tag: tumor nodal status

tag: patient survival status

tag: patient overall survival (months)

tag: patient disease-free survival (months)


title: genomic RNA from adjacent normal tissue of OT15

tag: subject id

tag: disease


title: Sp_W_D28_8002x8010_16

tag: Sex

tag: tissue

tag: collaborative cross line (genetic background)

tag: animal number (rxid)

tag: treatmock infectedent

tag: timepoint

tag: batch


title: Sp_W_D12_8002x8010_82

source_name: Spleen Tissue from West Nile Virus infected Line 8002x8010 at Day 12

value: Day 12


title: wholeblood_812448_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_812459_1


title: wholeblood_812407_1


title: wholeblood_812407_2


title: Sp_W_D12_8002x8010_85


title: W89_REJECTION

description: peripheral vein blood from patient sample W89 at rejection time point

tag: patient


title: W66_REJECTION

description: peripheral vein blood from patient sample W66 at rejection time point


title: Sp_W_D7_8002x8010_96

source_name: Spleen Tissue from West Nile Virus infected Line 8002x8010 at Day 7

value: Day 7


title: W75_REJECTION

description: peripheral vein blood from patient sample W75 at rejection time point


title: W78_REJECTION

description: peripheral vein blood from patient sample W78 at rejection time point


title: Sp_W_D12_8002x8010_83


title: wholeblood_812396_2

source_name: whole blood, maternal peripheral


title: Sp_M_D28_8002x8010_26

description: Gene expression data from a Mice Gene expression data from a Mice Mock infected

source_name: Spleen Tissue from Mock infected Line 8002x8010 at Day 28

value: Mock infected


title: wholeblood_812387_2


title: Sp_M_D28_8002x8010_24


title: Sp_M_D28_8002x8010_25


title: wholeblood_812448_1


title: Sp_W_D7_8002x8010_95


title: W83_REJECTION

description: peripheral vein blood from patient sample W83 at rejection time point


title: W65_REJECTION

description: peripheral vein blood from patient sample W65 at rejection time point


title: wholeblood_812396_1


title: Sp_W_D28_8024x8049_16

source_name: Spleen Tissue from West Nile Virus infected Line 8024x8049 at Day 28


title: W52_REJECTION

description: peripheral vein blood from patient sample W52 at rejection time point


title: W55_REJECTION

description: peripheral vein blood from patient sample W55 at rejection time point


title: W60_REJECTION

description: peripheral vein blood from patient sample W60 at rejection time point


title: wholeblood_812387_1


title: W56_REJECTION

description: peripheral vein blood from patient sample W56 at rejection time point


title: W51_REJECTION

description: peripheral vein blood from patient sample W51 at rejection time point


title: Sp_W_D12_8024x8049_76

description: Gene expression data from a Mice Gene expression data from a Mice West Nile Virus infected

source_name: Spleen Tissue from West Nile Virus infected Line 8024x8049 at Day 12


title: wholeblood_812359_2


title: wholeblood_812359_1


title: wholeblood_812366_1


title: Sp_W_D28_8024x8049_17


title: Sp_W_D21_8024x8049_71

source_name: Spleen Tissue from West Nile Virus infected Line 8024x8049 at Day 21


title: wholeblood_812342_2


title: W42_REJECTION

description: peripheral vein blood from patient sample W42 at rejection time point


title: wholeblood_812366_2


title: wholeblood_812342_1


title: Sp_W_D7_8024x8049_130

source_name: Spleen Tissue from West Nile Virus infected Line 8024x8049 at Day 7


title: Sp_W_D7_8024x8049_136


title: genomic RNA from adjacent normal tissue of OT14

value: Oral tongue squamous cell carcinomas (OTSCC)

tag: tissue type

value: adjacent normal tissue

tag: patient age (yrs)

tag: patient gender

tag: tumor stage

tag: tumor grade

tag: tumor nodal status

tag: patient survival status

tag: patient overall survival (months)

tag: patient disease-free survival (months)


title: W49_REJECTION

description: peripheral vein blood from patient sample W49 at rejection time point

tag: tissue


title: wholeblood_812344_2

tag: individual id


title: wholeblood_812344_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: W41_REJECTION

description: peripheral vein blood from patient sample W41 at rejection time point


title: Sp_W_D21_8024x8049_85

tag: Sex

tag: collaborative cross line (genetic background)

tag: animal number (rxid)

tag: treatmock infectedent

tag: timepoint

tag: batch


title: Sp_W_D12_8024x8049_74


title: Sp_M_D28_8024x8049_8

source_name: Spleen Tissue from Mock infected Line 8024x8049 at Day 28


title: Relapsing_DLBCL_primary (case3)

source_name: Frozen tissue biopsy

tag: disease state

value: Diffuse large B cell lymphoma (DLBCL)

tag: specimen

value: Relapsing DLBCL primary

tag: case

source_name: Reference pooled 46XX

value: pooled normal (46,XX) reference (Promega)


title: W40_REJECTION

description: peripheral vein blood from patient sample W40 at rejection time point

tag: patient


title: Relapsing_DLBCL_primary (case1)

source_name: FFPE tissue biopsy


title: W138_NON-TOL

description: peripheral vein blood from patient sample W138 before weaning

source_name: patient sample W138 before weaning


title: Sp_W_D12_8048x8026_55

source_name: Spleen Tissue from West Nile Virus infected Line 8048x8026 at Day 12


title: wholeblood_812329_2

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: W134_NON-TOL

description: peripheral vein blood from patient sample W134 before weaning

source_name: patient sample W134 before weaning

tag: tissue


title: Sp_W_D28_8048x8026_68

source_name: Spleen Tissue from West Nile Virus infected Line 8048x8026 at Day 28


title: Sp_W_D28_8048x8026_67


title: wholeblood_812324_2

tag: individual id


title: wholeblood_812329_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: wholeblood_812324_1


title: wholeblood_812309_1


title: W139_NON-TOL

description: peripheral vein blood from patient sample W139 before weaning

source_name: patient sample W139 before weaning


title: W21_REJECTION

description: peripheral vein blood from patient sample W21 at rejection time point


title: W38_REJECTION

description: peripheral vein blood from patient sample W38 at rejection time point


title: Sp_W_D12_8048x8026_54

tag: Sex


title: W144_NON-TOL

description: peripheral vein blood from patient sample W144 before weaning

source_name: patient sample W144 before weaning


title: Sp_M_D28_8024x8049_7

description: Gene expression data from a Mice Gene expression data from a Mice Mock infected

tag: collaborative cross line (genetic background)


title: W131_NON-TOL

description: peripheral vein blood from patient sample W131 before weaning

source_name: patient sample W131 before weaning


title: wholeblood_812302_1

source_name: whole blood, maternal peripheral


title: W132_NON-TOL

description: peripheral vein blood from patient sample W132 before weaning

source_name: patient sample W132 before weaning


title: Sp_W_D7_8048x8026_155

source_name: Spleen Tissue from West Nile Virus infected Line 8048x8026 at Day 7

tag: animal number (rxid)


title: wholeblood_812296_2


title: wholeblood_812309_2


title: Sp_W_D7_8048x8026_156

tag: treatmock infectedent


title: Sp_M_D28_8048x8026_85

source_name: Spleen Tissue from Mock infected Line 8048x8026 at Day 28

tag: timepoint


title: W126_NON-TOL

description: peripheral vein blood from patient sample W126 before weaning

source_name: patient sample W126 before weaning


title: W125_NON-TOL

description: peripheral vein blood from patient sample W125 before weaning

source_name: patient sample W125 before weaning


title: wholeblood_812302_2


title: Sp_W_D7_8048x8026_154

tag: batch


title: W108_NON-TOL

description: peripheral vein blood from patient sample W108 before weaning

source_name: patient sample W108 before weaning


title: Sp_M_D28_8048x8026_77


title: wholeblood_812285_2


title: Sp_M_D28_8048x8026_84


title: wholeblood_812292_2


title: W109_NON-TOL

description: peripheral vein blood from patient sample W109 before weaning

source_name: patient sample W109 before weaning


title: Sp_W_D21_16211x13140_123

description: Gene expression data from a Mice Gene expression data from a Mice West Nile Virus infected

source_name: Spleen Tissue from West Nile Virus infected Line 16211x13140 at Day 21


title: wholeblood_812285_1


title: W112_NON-TOL

description: peripheral vein blood from patient sample W112 before weaning

source_name: patient sample W112 before weaning


title: wholeblood_812292_1


title: Sp_W_D12_16211x13140_152

source_name: Spleen Tissue from West Nile Virus infected Line 16211x13140 at Day 12


title: wholeblood_812296_1


title: W122_NON-TOL

description: peripheral vein blood from patient sample W122 before weaning

source_name: patient sample W122 before weaning


title: wholeblood_812282_1


title: wholeblood_812268_2


title: W123_NON-TOL

description: peripheral vein blood from patient sample W123 before weaning

source_name: patient sample W123 before weaning


title: Sp_W_D7_16211x13140_170

source_name: Spleen Tissue from West Nile Virus infected Line 16211x13140 at Day 7


title: W104_NON-TOL

description: peripheral vein blood from patient sample W104 before weaning

source_name: patient sample W104 before weaning


title: wholeblood_812261_2


title: W103_NON-TOL

description: peripheral vein blood from patient sample W103 before weaning

source_name: patient sample W103 before weaning


title: wholeblood_812261_1


title: Sp_W_D21_16211x13140_124


title: Sp_M_D28_16211x13140_46

source_name: Spleen Tissue from Mock infected Line 16211x13140 at Day 28


title: Sp_W_D7_16211x13140_166


title: wholeblood_812249_2

source_name: whole blood, maternal peripheral


title: Sp_M_D28_16211x13140_45


title: W96_NON-TOL

description: peripheral vein blood from patient sample W96 before weaning

source_name: patient sample W96 before weaning


title: W88_NON-TOL

description: peripheral vein blood from patient sample W88 before weaning

source_name: patient sample W88 before weaning


title: W89_NON-TOL

description: peripheral vein blood from patient sample W89 before weaning

source_name: patient sample W89 before weaning


title: W92_NON-TOL

description: peripheral vein blood from patient sample W92 before weaning

source_name: patient sample W92 before weaning


title: W99_NON-TOL

description: peripheral vein blood from patient sample W99 before weaning

source_name: patient sample W99 before weaning


title: Sp_W_D28_8002x3032_80

source_name: Spleen Tissue from West Nile Virus infected Line 8002x3032 at Day 28


title: W83_NON-TOL

description: peripheral vein blood from patient sample W83 before weaning

source_name: patient sample W83 before weaning


title: wholeblood_812236_2


title: wholeblood_812236_1


title: Sp_W_D28_8002x3032_79


title: wholeblood_812249_1


title: Sp_W_D21_8002x3032_85

source_name: Spleen Tissue from West Nile Virus infected Line 8002x3032 at Day 21


title: W66_NON-TOL

description: peripheral vein blood from patient sample W66 before weaning

source_name: patient sample W66 before weaning


title: W78_NON-TOL

description: peripheral vein blood from patient sample W78 before weaning

source_name: patient sample W78 before weaning


title: Sp_W_D21_8002x3032_86


title: Sp_W_D28_8002x3032_81


title: wholeblood_812235_2


title: Sp_W_D21_8002x3032_93


title: wholeblood_812234_2


title: wholeblood_812235_1


title: wholeblood_812232_2


title: Sp_W_D12_8002x3032_147

source_name: Spleen Tissue from West Nile Virus infected Line 8002x3032 at Day 12


title: Sp_W_D12_8002x3032_130


title: Sp_W_D7_8002x3032_190

source_name: Spleen Tissue from West Nile Virus infected Line 8002x3032 at Day 7


title: wholeblood_812234_1


title: Sp_W_D12_16211x13140_172

source_name: Spleen Tissue from West Nile Virus infected Line 16211x13140 at Day 12


title: W75_NON-TOL

description: peripheral vein blood from patient sample W75 before weaning

source_name: patient sample W75 before weaning


title: W65_NON-TOL

description: peripheral vein blood from patient sample W65 before weaning

source_name: patient sample W65 before weaning


title: W56_NON-TOL

description: peripheral vein blood from patient sample W56 before weaning

source_name: patient sample W56 before weaning


title: wholeblood_812230_2

source_name: whole blood, maternal peripheral


title: W51_NON-TOL

description: peripheral vein blood from patient sample W51 before weaning

source_name: patient sample W51 before weaning


title: W60_NON-TOL

description: peripheral vein blood from patient sample W60 before weaning

source_name: patient sample W60 before weaning


title: Sp_W_D7_8002x3032_189

description: Gene expression data from a Mice Gene expression data from a Mice West Nile Virus infected


title: Sp_M_D28_8002x3032_87

description: Gene expression data from a Mice Gene expression data from a Mice Mock infected

source_name: Spleen Tissue from Mock infected Line 8002x3032 at Day 28


title: W49_NON-TOL

description: peripheral vein blood from patient sample W49 before weaning

source_name: patient sample W49 before weaning


title: W55_NON-TOL

description: peripheral vein blood from patient sample W55 before weaning

source_name: patient sample W55 before weaning


title: wholeblood_812228_2


title: Sp_M_D28_8002x3032_88


title: wholeblood_812230_1


title: W42_NON-TOL

description: peripheral vein blood from patient sample W42 before weaning

source_name: patient sample W42 before weaning


title: Sp_W_D28_3252x8042_151

source_name: Spleen Tissue from West Nile Virus infected Line 3252x8042 at Day 28


title: wholeblood_812228_1


title: wholeblood_812232_1


title: Sp_W_D28_3252x8042_150


title: W52_NON-TOL

description: peripheral vein blood from patient sample W52 before weaning

source_name: patient sample W52 before weaning


title: W40_NON-TOL

description: peripheral vein blood from patient sample W40 before weaning

source_name: patient sample W40 before weaning


title: Sp_W_D21_3252x8042_206

source_name: Spleen Tissue from West Nile Virus infected Line 3252x8042 at Day 21


title: wholeblood_810657_2


title: Sp_M_D28_8002x3032_109


title: wholeblood_812226_1


title: Sp_W_D28_3252x8042_149


title: W41_NON-TOL

description: peripheral vein blood from patient sample W41 before weaning

source_name: patient sample W41 before weaning


title: wholeblood_810657_1


title: wholeblood_812226_2


title: Sp_W_D21_3252x8042_205


title: W38_NON-TOL

description: peripheral vein blood from patient sample W38 before weaning

source_name: patient sample W38 before weaning


title: wholeblood_810619_2


title: Sp_W_D21_3252x8042_204


title: wholeblood_810568_2


title: Sp_W_D12_3252x8042_161

source_name: Spleen Tissue from West Nile Virus infected Line 3252x8042 at Day 12


title: wholeblood_810568_1


title: wholeblood_810563_2


title: Control_3

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

description: AoECs+control scrambled oligo

hyb_protocol: Standard Illumina hybridization protocol: Two library samples were analyzed on two separate bead arrays each (2 technical replicates). These were Ctrl_1 and moR21_3, and the technical replicates are indicated by a & b (e.g. Ctrl_1a).

data_processing: The data were normalised using quantile normalisation using the lumiN command in the lumi package in R

source_name: AoSMCs (primary mouse aortic SMCs)

label_protocol: Total RNA samples hybridized to Illumina BeadChips were prepared using the Illumina TotalPrep RNA Amplification kit from Applied Biosystems/Ambion, catalog # AMIL1791 (library preparation & array hybridization was performed by the Yale Center for Genome Analysis).

growth_protocol: Mouse aortic smooth muscle cells (MAoSMC) were harvested and grown as follows. Briefly, several mouse aortas were obtained sterilely and placed into 100mm dish containing media. The adventia was cleaned off and the aorta was cut horizontally into 10-15 pieces. Each piece was placed into a 6 or 12 well collagen Biocoat plate (Fisher). Explants were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing antibiotics and 10% bovine growth serum (BGS) for 3-7 days. When the well was 50-75% confluent, the explants were removed, and the MAoSMCs were cultured in low glucose phenol red-free DMEM containing antibiotics and 10% fetal bovine serum (FBS). Before experimental use, MAoSMCs were grown in low glucose DMEM supplemented with 5% dextran-coated charcoal-treated fetal bovine serum.

extract_protocol: Total RNA was purified with the RNeasy mini kit (Qiagen)

treatment_protocol: MAoSMC were transfected with scrambled control or moR-21 mimetics at 5nM final concentration, using RNAiMAX (Life Technologies) according to the supplier’s instructions. Triplicate samples were prepared for each treatment.

tag: cell type

value: AoSMCs (primary mouse aortic SMCs)

tag: treatment

value: scambled oligo


title: Sp_W_D7_3252x8042_194

source_name: Spleen Tissue from West Nile Virus infected Line 3252x8042 at Day 7


title: moR21_3_replicate_B

description: AoECs+moR-21 mimetic oligo

value: moR-21 mimetic oligo


title: W21_NON-TOL

description: peripheral vein blood from patient sample W21 before weaning

source_name: patient sample W21 before weaning


title: wholeblood_810619_1

source_name: whole blood, maternal peripheral

value: peripheral maternal blood


title: Sp_W_D12_3252x8042_160

value: male

value: Spleen


title: moR21_3_replicate_A

description: AoECs+moR-21 mimetic oligo


title: Sp_W_D7_3252x8042_193

value: West Nile Virus infected


title: Sp_W_D12_3252x8042_159


title: wholeblood_810563_1


title: wholeblood_810533_2


title: wholeblood_812268_1


title: Sp_M_D28_3252x8042_174

source_name: Spleen Tissue from Mock infected Line 3252x8042 at Day 28

value: Day 28


title: Control_2

description: AoECs+control scrambled oligo


title: moR21_2

description: AoECs+moR-21 mimetic oligo


title: Control_1_replicate_B

description: AoECs+control scrambled oligo


title: wholeblood_810545_1


title: Sp_M_D28_3252x8042_175


title: moR21_1

description: AoECs+moR-21 mimetic oligo


title: wholeblood_810529_2


title: W115_NON-TOL

description: peripheral vein blood from patient sample W115 before weaning

source_name: patient sample W115 before weaning

value: peripheral vein blood


title: wholeblood_810545_2


title: Sp_W_D7_3252x8042_152


title: Control_1_replicate_A

description: AoECs+control scrambled oligo


title: Sp_M_D28_3252x8042_158


title: wholeblood_810533_1


title: Sp_W_D28_3032x16188_99

source_name: Spleen Tissue from West Nile Virus infected Line 3032x16188 at Day 28


title: wholeblood_810529_1


title: Sp_W_D28_3032x16188_98


title: wholeblood_810521_2


title: wholeblood_810516_2


title: wholeblood_810518_2


title: wholeblood_810521_1


title: Sp_W_D12_3032x16188_89

source_name: Spleen Tissue from West Nile Virus infected Line 3032x16188 at Day 12

value: Day 12


title: wholeblood_810518_1


title: Sp_W_D28_3032x16188_100


title: Sp_W_D12_3032x16188_87


title: wholeblood_810516_1


title: Sp_W_D7_3032x16188_66

source_name: Spleen Tissue from West Nile Virus infected Line 3032x16188 at Day 7

value: Day 7


title: Sp_W_D7_3032x16188_40


title: Sp_M_D28_3032x16188_91

source_name: Spleen Tissue from Mock infected Line 3032x16188 at Day 28

value: Mock infected


title: Sp_M_D28_3032x16188_93


title: Sp_W_D7_3032x16188_41


title: Sp_M_D28_3032x16188_92


title: wholeblood_810507_1


title: wholeblood_810507_2


title: wholeblood_810501_1


title: wholeblood_810494_1


title: wholeblood_810477_1


title: wholeblood_810469_2


title: wholeblood_810469_1


title: wholeblood_810462_2


title: wholeblood_810462_1


title: Myeloma sample [EMC_7513398_v1]

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

description: chips run by Aros

hyb_protocol: Hybridization according to protocol in hybridization ovens for 16 to 18 hours at 50 °C and 60 rpm (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G, controlled by AGCC software, was used, according to a standard protocol (Affymetrix).

data_processing:
Bioconductor CRLMM
Out of 906,600 tagging SNPs, only the 370, 605 autosomal SNPs with a homozygosity in at least  5% of patients, a genotype call in at least 95% of patients and fulfilling a Hardy-Weinberg equilibrium P > 10^-5 were used.

source_name: Myeloma sample (germ line DNA; amplified)

label_protocol: Biotin labeling according to standard protocol (Affymetrix)

extract_protocol: DNA was extracted using salting out precipitation

treatment_protocol: All patients were treated within the HOVON65/GMMG-HD4 study. Samples were untreated.

tag: sample group

value: no BIPN or less than grade 2

value: Peripheral blood


title: wholeblood_810460_1


title: Myeloma sample [EMC_4701469_v1]

description: chips run by Aros


title: wholeblood_810494_2


title: wholeblood_810439_2A


title: Myeloma sample [EMC_4883263_v1]

description: chips run by Aros


title: Myeloma sample [EMC_6388848_v1]

description: chips run by Aros


title: wholeblood_810460_2


title: Myeloma sample [EMC_6701439_v1]

description: chips run by Aros


title: wholeblood_810447_2


title: wholeblood_810439_1B


title: wholeblood_810432_2


title: Myeloma sample [EMC_8554962_v1]

description: chips run by Aros

value: BiPN (grade 2 or higher)


title: Myeloma sample [EMC_7016200_v1]

description: chips run by Aros


title: Myeloma sample [EMC_8175779_v1]

description: chips run by Aros


title: Myeloma sample [EMC_8010231_v1]

description: chips run by Aros


title: Myeloma sample [EMC_7586132_v1]

description: chips run by Aros


title: Myeloma sample [EMC_7400090_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4509906_v1]

description: chips run by Aros


title: wholeblood_810447_1


title: wholeblood_810501_2


title: wholeblood_810432_1


title: wholeblood_810430_2C


title: Myeloma sample [EMC_4599949_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4051656_v1]

description: chips run by Aros


title: Myeloma sample [EMC_5097470_v1]

description: chips run by Aros


title: Myeloma sample [EMC_9316669_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4210542_v1]

description: chips run by Aros


title: wholeblood_810421_2


title: Myeloma sample [EMC_5287161_v1]

description: chips run by Aros


title: Myeloma sample [EMC_8779054_v1]

description: chips run by Aros


title: wholeblood_810421_1


title: wholeblood_810416_2


title: Myeloma sample [EMC_6857834_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4003974_v1]

description: chips run by Aros


title: Myeloma sample [EMC_3322151_v1]

description: chips run by Aros


title: wholeblood_810413_1


title: wholeblood_810401_2


title: wholeblood_810416_1


title: wholeblood_810413_2


title: Myeloma sample [EMC_8104205_v1]

description: chips run by Aros


title: wholeblood_810430_1


title: Myeloma sample [EMC_1895195_v1]

description: chips run by Aros


title: Myeloma sample [EMC_6958045_v1]

description: chips run by Aros


title: wholeblood_810392_2A


title: wholeblood_810392_1


title: Myeloma sample [EMC_1636111_v1]

description: chips run by Aros


title: wholeblood_810401_1


title: PDAC-60039

type: protein

city: Tempe

first: Benjamin

middle: A

last: Katchman

state: AZ

address: 727 E. Tyler St.

institute: Arizona State University

description: The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.

hyb_protocol: Plasma hybridization was performed on TECAN HS 4800 Pro. 1. Protein arrays were blocked with 5% milk PBST (0.2% Tween) for 1 hour at RT; 2. 150ul 1:50 diluted serum was applied to each slide with medium agitation 16 hours at 4oC; 3. Slides were incubated with 150ul 1:500 dilution of Dylight 649-linked anti-human secondary antibodies (Jackson Immunoresearch) in milk PBST.

scan_protocol: Slides were scanned by TECAN PowerScanner at 50% gain, 50% laser and 10µm resolution.

data_processing: 1. The background signal estimated by the 25th percentile of the negative control; 2. Normalize the array by the median.

label: Serum samples are not labeled

molecule: protein

source_name: Peripheral Blood

label_protocol: No labeling was performed on the serum sample

extract_protocol: Peripheral blood samples were drawn from the antecubital vein and serum was prepared according to a standardized protocol before freezing serum aliquots at -80oC

value: Serum

tag: disease state

value: Benign Pancreatic Disease Control

tag: array batch


title: PDAC-60161


title: wholeblood_810384_1

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: wholeblood_810424_1

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: Myeloma sample [EMC_5767476_v1]

description: chips run by Aros

tag: tissue


title: wholeblood_810424_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: wholeblood_515122_2


title: PDAC-60035


title: Myeloma sample [EMC_3404986_v1]

description: chips run by Aros


title: Myeloma sample [EMC_1209981_v1]

description: chips run by Aros


title: PDAC-60184


title: PDAC-60133


title: Myeloma sample [EMC_6823541_v1]

description: chips run by Aros


title: Myeloma sample [EMC_8827217_v1]

description: chips run by Aros


title: Myeloma sample [EMC_9412346_v1]

description: chips run by Aros


title: PDAC-60045


title: SET morfolino rep_3

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

hyb_protocol: Affymetrix protocols and procedures were followed

data_processing: Data were processed using GeneSpring software (Agilent). RMA normalization was performed and only probes above the background threshold were considered for further evaluation.

organism: Danio rerio

source_name: 48 hpf setb MO1 embryos

growth_protocol: Embryos were bred under standard conditions

extract_protocol: Phenotypes were scored and identified as normal-like, mild and  moderate. Total RNA was extracted using RNeasy protect mini kit (Qiagen).

treatment_protocol: One-cell stage embryos were injected with control morpholino and MO1. RNA was extracted from 48hpf embryos.

value: setb MO1-injected


title: wholeblood_515122_1


title: Myeloma sample [EMC_4441491_v1]

description: chips run by Aros


title: Myeloma sample [EMC_1120513_v1]

description: chips run by Aros


title: PDAC-60177


title: wholeblood_810384_2


title: PDAC-60020


title: PDAC-60038


title: Myeloma sample [EMC_6662026_v1]

description: chips run by Aros


title: Control morfolino rep_3

scan_protocol: Affymetrix protocols and procedures were followed

source_name: 48 hpf control MO embryos

value: injected with control morpholino


title: Myeloma sample [EMC_9927154_v1]

description: chips run by Aros


title: Myeloma sample [EMC_9502076_v1]

description: chips run by Aros


title: SET morfolino rep_1

label_protocol: Affymetrix protocols and procedures were followed


title: SET morfolino rep_2

source_name: 48 hpf setb MO1embryos


title: Myeloma sample [EMC_7928572_v1]

description: chips run by Aros


title: PDAC-60019


title: Control morfolino rep_2


title: Control morfolino rep_1


title: PDAC-60167


title: PDAC-60178


title: Myeloma sample [EMC_9085506_v1]

description: chips run by Aros


title: Myeloma sample [EMC_1971493_v1]

description: chips run by Aros


title: heart ventricles at T90d post-injury, biological rep2

city: Luxembourg

first: Francisco

last: Azuaje

address: 84, Val Fleuri

department: Oncology

country: Luxembourg

institute: Luxembourg Institute of Health

description: Gene expression data from Zebrafish heart ventricles 90 days after injury

hyb_protocol: Arrays were hybridized, washed and stained using the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit.

scan_protocol: GeneChip Scanner 3000 according to the manufacturer’s standard procedure (P/N 702731 Rev 3)

data_processing: Microarray data were pre-processed by Partek® Genomics Suite version 6.5 using the robust multi-chip analysis (RMA) [Irizarry et.al. 2003] with GC-content correction.

label_protocol: 250 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT Reagent kit (Affymetrix) according to the manufacturer’s standard protocols (P/N 4425209 Rev.B and P/N 702808 Rev.6)

growth_protocol: Experiments were conducted with adult zebrafish between 10 and 11 months old.

extract_protocol: Extraction was performed as previously described in [Rodius at al. 2014]

treatment_protocol: Cryoinjury was performed as described previously [Gonzalez-Rosa et.al. 2012]. Animals were sacrificed at different time-points after surgery, from 4h to 90 days, by immersion in 0.16% tricaine (Sigma Aldrich, Bornem, BE). Hearts were dissected in PBS containing 2U/mL heparin and 0.1M KCl, then 5 heart ventricles were pooled in TRIzol® (Invitrogen, Carlsbad, CA) for RNA extraction. Hearts of uninjured fish served as control.

value: heart ventricle


title: PDAC-60032


title: Myeloma sample [EMC_1117698_v1]

description: chips run by Aros


title: Myeloma sample [EMC_8388516_v1]

description: chips run by Aros


title: PDAC-60172


title: PDAC-60097


title: PDAC-60046


title: Myeloma sample [EMC_8446359_v1]

description: chips run by Aros


title: heart ventricles at T90d post-injury, biological rep1

source_name: Zebrafish heart ventricles 90 days after injury


title: Myeloma sample [EMC_8148158_v1]

description: chips run by Aros


title: Myeloma sample [EMC_5303062_v1]

description: chips run by Aros


title: heart ventricles at T14d post-injury, biological rep1

description: Gene expression data from Zebrafish heart ventricles 14 days after injury


title: heart ventricles at T7d post-injury, biological rep3

description: Gene expression data from Zebrafish heart ventricles 7 days after injury


title: Myeloma sample [EMC_9785535_v1]

description: chips run by Aros


title: PDAC-60160


title: heart ventricles at T14d post-injury, biological rep2

source_name: Zebrafish heart ventricles 14 days after injury


title: PDAC-60043


title: heart ventricles at T14d post-injury, biological rep3


title: Myeloma sample [EMC_4178775_v1]

description: chips run by Aros


title: heart ventricles at T3d post-injury, biological rep3

description: Gene expression data from Zebrafish heart ventricles 3 days after injury


title: PDAC-60195


title: Myeloma sample [EMC_2918873_v1]

description: chips run by Aros


title: heart ventricles at T7d post-injury, biological rep2

source_name: Zebrafish heart ventricles 7 days after injury


title: PDAC-60193


title: heart ventricles at T3d post-injury, biological rep2

source_name: Zebrafish heart ventricles 3 days after injury


title: Myeloma sample [EMC_3432341_v1]

description: chips run by Aros


title: PDAC-60109


title: PDAC-60063


title: Myeloma sample [EMC_9934156_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4690756_v1]

description: chips run by Aros


title: heart ventricles at T3d post-injury, biological rep1


title: heart ventricles at T7d post-injury, biological rep1


title: PDAC-60148


title: PDAC-60023


title: heart ventricles at T1d post-injury, biological rep3

description: Gene expression data from Zebrafish heart ventricles 1 day after injury


title: PDAC-60150


title: heart ventricles at T1d post-injury, biological rep2

source_name: Zebrafish heart ventricles 1 day after injury


title: heart ventricles at T1d post-injury, biological rep1


title: Myeloma sample [EMC_6780594_v1]

description: chips run by Aros


title: Myeloma sample [EMC_8886422_v1]

description: chips run by Aros


title: heart ventricles at T90d post-injury, biological rep3


title: PDAC-60042


title: PDAC-60033


title: Myeloma sample [EMC_1530409_v1]

description: chips run by Aros


title: Myeloma sample [EMC_3209396_v1]

description: chips run by Aros


title: Myeloma sample [EMC_7412631_v1]

description: chips run by Aros


title: PDAC-60175


title: heart ventricles at T4h post-injury, biological rep2

description: Gene expression data from Zebrafish heart ventricles 4 hours after injury


title: heart ventricles at T4h post-injury, biological rep3

source_name: Zebrafish heart ventricles 4 hours after injury


title: Myeloma sample [EMC_4911935_v1]

description: chips run by Aros


title: PDAC-60153


title: Myeloma sample [EMC_9645561_v1]

description: chips run by Aros


title: heart ventricles at T0, biological rep3

description: Gene expression data from Zebrafish heart ventricles uninjured

source_name: Zebrafish heart ventricles uninjured


title: heart ventricles at T4h post-injury, biological rep1


title: PDAC-60182


title: PDAC-60071


title: PDAC-60176


title: heart ventricles at T0, biological rep2


title: Myeloma sample [EMC_7995886_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4120151_v1]

description: chips run by Aros


title: A2780s_Control-treated

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

country: China

institute: West China Second Hospital, Sichuan University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). LncRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Ovarian cancer

label_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

tag: cell line

value: Ovarian cancer cells

tag: treated with

value: none (control)


title: Myeloma sample [EMC_3928169_v1]

description: chips run by Aros


title: PDAC-60271


title: heart ventricles at T0, biological rep1


title: Myeloma sample [EMC_8877891_v1]

description: chips run by Aros


title: PDAC-60112


title: A2780s_CXCL14-treated


title: PDAC-60119


title: PDAC-60284


title: PDAC-60168


title: Myeloma sample [EMC_3156664_v1]

description: chips run by Aros


title: Myeloma sample [EMC_5306907_v1]

description: chips run by Aros


title: Myeloma sample [EMC_5131591_v1]

description: chips run by Aros


title: Myeloma sample [EMC_7896795_v1]

description: chips run by Aros


title: PDAC-60202


title: Myeloma sample [EMC_3642430_v1]

description: chips run by Aros


title: PDAC-60099


title: Myeloma sample [EMC_3991552_v1]

description: chips run by Aros


title: genomic DNA from tumor tissue of OT55

description: tumor tissue from the oral tongue sub-site

hyb_protocol: bisulphite converted DNA was used as template for target preparation to hybridize on the beadchip and was processed as per the manufacturer’s instructions following Infinium HD and Infinium protocol for HumanMethylation450K BeadChip (Illumina, San Diego, CA) respectively

scan_protocol: data were collected using the HiScan (Illumina) reader

data_processing: GenomeStudio V2011.1 methylation module1.1.1 (Illumina)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tissue samples DNeasy Blood and Tissue kit (Qiagen, Valencia,  CA) as per the manufacturer’s specifications

tag: subject id

tag: patient age (yrs)

tag: patient grade

value: M

tag: disease

value: Oral tongue squamous cell carcinomas (OTSCC)

tag: tissue type

tag: tumor grade

value: MDSCC

tag: tumor stage

tag: tumor nodal status

tag: survival status

value: Dead

tag: overall survival (months)

tag: disease-free survival (months)


title: Myeloma sample [EMC_3846445_v1]

description: chips run by Aros

tag: sample group


title: genomic DNA from peripheral blood of OT55

description: peripheral blood from the oral tongue sub-site


title: Myeloma sample [EMC_4942874_v1]

description: chips run by Aros

tag: tissue


title: PDAC-60203

tag: disease state

tag: array batch


title: PDAC-60034


title: Larvae_Primed_1

city: Princeton

first: Ann

middle: Thomas

last: Tate

state: NJ

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

hyb_protocol: Gene Expression Hybridization Kit (Agilent) with naïve versus saline or naïve versus primed cy3/cy5 labeled cRNA on each array. We washed the slide using the Gene Expression Wash Buffer Kit (Agilent) with Triton X-102 and an acetonitrile wash step as per the Protocol for Two Color Microarray Based Gene Expression Analysis (Agilent)

scan_protocol: Agilent C Scanner

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

organism: Tribolium castaneum

source_name: whole pooled primed larvae

label_protocol: Agilent Quick Amp Labeling kit as per manufacturer's protocol

growth_protocol: Beetles kept in yeast-fortified flour at 30 deg C in the dark in ~70% humidity.

extract_protocol: Total RNA extracted using Qiagen Microarray RNeasy mini kit and Qiashredders as per manufacturer's instructions

treatment_protocol: Adult female beetles left naïve or jabbed with sterile saline or heat killed Bt solution. Mated to adult males and 2.5 weeks later, offspring colleceted and jabbed with live Bt (~20 vegetative cells per infection). 15 larvae/treatment pooled and flash frozen 24 hours later

tag: maternal treatment

value: heat killed Bacillus thuringiensis

source_name: whole pooled naïve larvae

value: naïve


title: Myeloma sample [EMC_3203175_v1]

description: chips run by Aros


title: PDAC-60154


title: Larvae_Saline_1

source_name: whole pooled saline larvae

value: saline


title: Myeloma sample [EMC_7234583_v1]

description: chips run by Aros


title: PDAC-60169


title: PDAC-60276


title: PDAC-60127


title: Myeloma sample [EMC_9029784_v1]

description: chips run by Aros


title: PDAC-60051


title: Myeloma sample [EMC_7590823_v1]

description: chips run by Aros

value: no BIPN or less than grade 2


title: PDAC-60294


title: genomic DNA from adjacent normal tissue of OT54

description: adjacent normal tissue from the oral tongue sub-site

value: F

value: Alive


title: Myeloma sample [EMC_5295070_v1]

description: chips run by Aros

value: Peripheral blood


title: PDAC-60204

value: Serum

value: Benign Pancreatic Disease Control


title: Myeloma sample [EMC_5441871_v1]

description: chips run by Aros


title: PDAC-60073


title: Myeloma sample [EMC_4661471_v1]

description: chips run by Aros


title: genomic DNA from tumor tissue of OT53

value: tumor tissue from the oral tongue sub-site


title: Myeloma sample [EMC_1758222_v1]

description: chips run by Aros

value: BiPN (grade 2 or higher)


title: genomic DNA from tumor tissue of OT54


title: PDAC-60084


title: genomic DNA from tumor tissue of OT52


title: genomic DNA from adjacent normal tissue of OT53

value: adjacent normal tissue from the oral tongue sub-site


title: PDAC-60117


title: Myeloma sample [EMC_2675958_v1]

description: chips run by Aros


title: Myeloma sample [EMC_7997006_v1]

description: chips run by Aros


title: genomic DNA from tumor tissue of OT51

value: WDSCC


title: PDAC-60031


title: genomic DNA from adjacent normal tissue of OT51


title: genomic DNA from adjacent normal tissue of OT50

value: M


title: Myeloma sample [EMC_2909282_v1]

description: chips run by Aros


title: Myeloma sample [EMC_6865063_v1]

description: chips run by Aros


title: genomic DNA from adjacent normal tissue of OT52

value: Oral tongue squamous cell carcinomas (OTSCC)


title: PDAC-60098


title: genomic DNA from adjacent normal tissue of OT49


title: Myeloma sample [EMC_5338721_v1]

description: chips run by Aros


title: Myeloma sample [EMC_5479293_v1]

description: chips run by Aros


title: PDAC-60025


title: PDAC-60149


title: genomic DNA from tumor tissue of OT49

value: PDSCC


title: PDAC-60300


title: genomic DNA from tumor tissue of OT50

value: MDSCC

value: Dead


title: PDAC-60179


title: Myeloma sample [EMC_7458566_v1]

description: chips run by Aros


title: Myeloma sample [EMC_7183205_v1]

description: chips run by Aros


title: genomic DNA from peripheral blood of OT48

value: peripheral blood from the oral tongue sub-site


title: Myeloma sample [EMC_6396092_v1]

description: chips run by Aros


title: genomic DNA from tumor tissue of OT48


title: Myeloma sample [EMC_2589011_v1]

description: chips run by Aros


title: Myeloma sample [EMC_2853771_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4420316_v1]

description: chips run by Aros


title: genomic DNA from peripheral blood of OT47


title: PDAC-60041


title: PDAC-60191


title: genomic DNA from tumor tissue of OT47


title: Myeloma sample [EMC_1556076_v1]

description: chips run by Aros


title: PDAC-60074


title: PDAC-60083


title: PDAC-60022


title: PDAC-60181


title: PDAC-45

value: PDAC


title: genomic DNA from peripheral blood of OT46


title: genomic DNA from tumor tissue of OT45


title: genomic DNA from peripheral blood of OT45


title: PDAC-10


title: genomic DNA from tumor tissue of OT44


title: Myeloma sample [EMC_6155680_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4349115_v1]

description: chips run by Aros

value: no BIPN or less than grade 2


title: genomic DNA from peripheral blood of OT44


title: genomic DNA from tumor tissue of OT46


title: Myeloma sample [EMC_4456933_v1]

description: chips run by Aros


title: PDAC-13


title: Myeloma sample [EMC_6947179_v1]

description: chips run by Aros


title: Myeloma sample [EMC_9173869_v1]

description: chips run by Aros


title: PDAC-35


title: PDAC-29


title: genomic DNA from tumor tissue of OT42


title: genomic DNA from peripheral blood of OT42


title: PDAC-34


title: Myeloma sample [EMC_3389578_v1]

description: chips run by Aros


title: Myeloma sample [EMC_2333904_v1]

description: chips run by Aros


title: PDAC-59


title: Myeloma sample [EMC_2164351_v1]

description: chips run by Aros


title: genomic DNA from peripheral blood of OT43


title: genomic DNA from tumor tissue of OT43


title: PDAC-14


title: Myeloma sample [EMC_8297831_v1]

description: chips run by Aros


title: genomic DNA from adjacent normal tissue of OT41

value: F


title: genomic DNA from tumor tissue of OT41

value: Alive


title: PDAC-60


title: Myeloma sample [EMC_2289739_v1]

description: chips run by Aros

value: Peripheral blood


title: PDAC-32

value: Serum


title: Myeloma sample [EMC_6444399_v1]

description: chips run by Aros


title: genomic DNA from peripheral blood of OT40


title: genomic DNA from adjacent normal tissue of OT38


title: PDAC-52


title: Myeloma sample [EMC_2824230_v1]

description: chips run by Aros


title: genomic DNA from tumor tissue of OT40


title: PDAC-31


title: PDAC-20


title: Myeloma sample [EMC_6892515_v1]

description: chips run by Aros


title: PDAC-37


title: PDAC-55


title: Myeloma sample [EMC_7813784_v1]

description: chips run by Aros


title: genomic DNA from adjacent normal tissue of OT35


title: genomic DNA from tumor tissue of OT38


title: Myeloma sample [EMC_5667708_v1]

description: chips run by Aros


title: genomic DNA from adjacent normal tissue of OT37


title: Myeloma sample [EMC_9215882_v1]

description: chips run by Aros


title: PDAC-30


title: PDAC-15


title: PDAC-6


title: genomic DNA from tumor tissue of OT37


title: Myeloma sample [EMC_5298576_v1]

description: chips run by Aros


title: PDAC-7


title: Myeloma sample [EMC_2095227_v1]

description: chips run by Aros


title: genomic DNA from adjacent normal tissue of OT33


title: PDAC-18


title: genomic DNA from tumor tissue of OT33


title: PDAC-24


title: genomic DNA from tumor tissue of OT34


title: Myeloma sample [EMC_8046394_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4063141_v1]

description: chips run by Aros


title: Myeloma sample [EMC_4475026_v1]

description: chips run by Aros


title: PDAC-16


title: PDAC-68


title: Myeloma sample [EMC_8750884_v1]

description: chips run by Aros


title: genomic DNA from peripheral blood of OT34


title: Myeloma sample [EMC_5977326_v1]

description: chips run by Aros


title: genomic DNA from adjacent normal tissue of OT36


title: Myeloma sample [EMC_2129996_v1]

description: chips run by Aros


title: genomic DNA from tumor tissue of OT31


title: PDAC-11


title: PDAC-22


title: PDAC-4


title: PDAC-23


title: Myeloma sample [EMC_2815137_v1]

description: chips run by Aros


title: genomic DNA from peripheral blood of OT32


title: PDAC-44


title: genomic DNA from peripheral blood of OT30


title: PDAC-67


title: genomic DNA from peripheral blood of OT31


title: PDAC-50


title: genomic DNA from tumor tissue of OT32


title: genomic DNA from peripheral blood of OT29


title: genomic DNA from tumor tissue of OT36


title: genomic DNA from tumor tissue of OT30


title: PDAC-33


title: PDAC-36


title: PDAC-9


title: genomic DNA from tumor tissue of OT28


title: genomic DNA from adjacent normal tissue of OT28


title: PDAC-41


title: PDAC-12


title: genomic DNA from tumor tissue of OT35


title: genomic DNA from adjacent normal tissue of OT27


title: genomic DNA from adjacent normal tissue of OT26


title: PDAC-42


title: genomic DNA from tumor tissue of OT29


title: PDAC-21


title: PDAC-5


title: PDAC-48


title: PDAC-38


title: genomic DNA from peripheral blood of OT25


title: PDAC-8


title: PDAC-26


title: genomic DNA from tumor tissue of OT24


title: genomic DNA from tumor tissue of OT25


title: genomic DNA from tumor tissue of OT23


title: genomic DNA from tumor tissue of OT26


title: PDAC-17


title: PDAC-39


title: PDAC-66


title: PDAC-63


title: PDAC-40


title: PDAC-57


title: genomic DNA from tumor tissue of OT22


title: genomic DNA from adjacent normal tissue of OT22


title: PDAC-56


title: PDAC-28


title: PDAC-25


title: genomic DNA from peripheral blood of OT21


title: genomic DNA from tumor tissue of OT19


title: PDAC-27


title: genomic DNA from adjacent normal tissue of OT20


title: genomic DNA from adjacent normal tissue of OT19


title: PDAC-64


title: PDAC-49


title: genomic DNA from tumor tissue of OT21


title: PDAC-58


title: PDAC-43


title: genomic DNA from tumor tissue of OT18


title: genomic DNA from adjacent normal tissue of OT18


title: genomic DNA from peripheral blood of OT23


title: PDAC-19


title: PDAC-54


title: PDAC-46


title: PDAC-65


title: genomic DNA from tumor tissue of OT17


title: genomic DNA from tumor tissue of OT27


title: genomic DNA from adjacent normal tissue of OT15


title: genomic DNA from adjacent normal tissue of OT17


title: genomic DNA from peripheral blood of OT16


title: IRF-8si with CpG ODN - repeat 4 - mAdbID:120452

city: Hilden

first: Folkert

last: Steinhagen

address: Breddert 37

institute: National Cancer Institute

description: mAdb experiment ID: 120452

hyb_protocol: Hybridization Protocol Other: The pre-hyb solution was: 5X SSC buffer, 0.1% SDS solution, and 0.1% RNase/DNase free BSA in water. The solution was heated to 55C, then slides were added (fully emerged in the solution) and rocked at room temperature for 30 min. Slides were rinsed thoroughly with room temp water (5x 1 min). The air can was used to blow dry the slides and spun at 500 rpm for 4 min. Mixer was attached to the slide right away and stored at 42 C. Probes were then purified and added.

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46721;; 3.64544 Temperature: 24.984 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

data_processing:
BRB Array Tools Data Processing Protocol
Calculation Method: Gene expression analysis was performed using BRB ArrayTools Version 3.8.1 developed by the NCI BRB (Bethesda, MD, USA). Data were background-corrected, flagged values were removed, spots in which both signals were <110 were filtered, ratios were log base 2-transformed, and lowest intensity-dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes.

source_name: Universal Human Reference RNA

label_protocol:
Cy3 Labeling Protocol
Other: cDNAs were purified using a MinElute PCR purification kit (Qiagen). Ten microliters of cDNA was labeled with Cy3 reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M NaHCO3 for 90 min in the dark.

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), as specified by the manufacturer.

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: IRF-8si with CpG ODN

label_protocol:
Cy5 Labeling Protocol
Other: cDNAs were purified using a MinElute PCR purification kit (Qiagen). Ten microliters of cDNA was labeled with Cy5 reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M NaHCO3 for 90 min in the dark.

treatment_protocol:
Agent: TLR9 ligand 'K' (CpG-B) ODN
Treatment dose: 1 uM
Treatment time: 9 hours
In-vitro treatment: Cells from the pDC cell line, CAL-1, were transfected with 0.5 nM of siRNA targeting IRF-8 (IRF-8si). They were then stimulated with 1 uM of (K-type) CpG ODN (phosphorothioate oligonucleotide expressing immunostimulatory CpG motif) for 9 hours.

tag: cell line

tag: cell type

value: plasmacytoid dendritic cells (pDC)

value: Leukemia


title: IRF-8si Unstimulated - repeat 4 - mAdbID:116733

description: mAdb experiment ID: 116733

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48064;; 3.80535 Temperature: 28.4631 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

source_name: IRF-8si Unstimulated

treatment_protocol: In-vitro treatment: Cells from the pDC cell line, CAL-1, were transfected with 0.5 nM of siRNA targeting IRF-8 (IRF-8si).


title: IRF-5si with CpG ODN - repeat 4 - mAdbID:120451

description: mAdb experiment ID: 120451

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.45195;; 3.6436 Temperature: 24.2515 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

source_name: IRF-5si with CpG ODN

treatment_protocol:
Agent: TLR9 ligand 'K' (CpG-B) ODN
Treatment dose: 1 uM
Treatment time: 9 hours
In-vitro treatment: Cells from the pDC cell line, CAL-1, were transfected with 0.5 nM of siRNA targeting IRF-5 (IRF-5si). They were then stimulated with 1 uM of K-type CpG ODN (phosphorothioate oligonucleotide expressing immunostimulatory CpG motif) for 9 hours.


title: genomic DNA from peripheral blood of OT14

tag: subject id

tag: patient age (yrs)


title: Control-si Unstimulated - repeat 4 - mAdbID:116731

description: mAdb experiment ID: 116731

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46721;; 3.7019 Temperature: 26.1437 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

source_name: Control-si Unstimulated

treatment_protocol: In-vitro treatment: Cells from the pDC cell line, CAL-1, were transfected with 0.5 nM of control siRNA (Contsi).


title: IRF-5si Unstimulated - repeat 4 - mAdbID:116735

description: mAdb experiment ID: 116735

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.44249;; 3.81878 Temperature: 29.3786 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

source_name: IRF-5si Unstimulated

treatment_protocol: In-vitro treatment: Cells from the pDC cell line, CAL-1, were transfected with 0.5 nM of siRNA targeting IRF-5 (IRF-5si).


title: Control-si with CpG ODN - repeat 3 - mAdbID:120453

description: mAdb experiment ID: 120453

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4608;; 3.65093 Temperature: 25.6554 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

source_name: Control-si with CpG ODN

treatment_protocol:
Agent: TLR9 ligand 'K' (CpG-B) ODN
Treatment dose: 1 uM
Treatment time: 9 hours
In-vitro treatment: Cells from the pDC cell line, CAL-1, were transfected with 0.5 nM of control siRNA (Contsi). They were then stimulated with 1 uM of (K-type) CpG ODN (phosphorothioate oligonucleotide expressing immunostimulatory CpG motif) for 9 hours.


title: genomic DNA from tumor tissue of OT16

tag: patient grade

tag: disease

value: tumor tissue from the oral tongue sub-site


title: IRF-8si Unstimulated - repeat 3 - mAdbID:116509

description: mAdb experiment ID: 116509

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46904;; 3.72509 Temperature: 26.632 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: genomic DNA from adjacent normal tissue of OT12

tag: tissue type

value: adjacent normal tissue from the oral tongue sub-site

tag: tumor grade


title: genomic DNA from tumor tissue of OT13

value: M

value: High Grade Dysplasia

tag: tumor stage

tag: tumor nodal status


title: IRF-8si with CpG ODN - repeat 3 - mAdbID:116505

description: mAdb experiment ID: 116505

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.51795;; 4.04509 Temperature: 27.517 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: genomic DNA from adjacent normal tissue of OT11

value: Oral tongue squamous cell carcinomas (OTSCC)

tag: survival status

tag: overall survival (months)


title: genomic DNA from peripheral blood of OT9

tag: disease-free survival (months)


title: genomic DNA from tumor tissue of OT14

value: MDSCC


title: Control-si Unstimulated - repeat 3 - mAdbID:116500

description: mAdb experiment ID: 116500

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48033;; 3.83007 Temperature: 28.9514 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

tag: tissue


title: genomic DNA from tumor tissue of OT15

value: PDSCC


title: genomic DNA from adjacent normal tissue of OT13


title: genomic DNA from tumor tissue of OT12


title: genomic DNA from tumor tissue of OT10


title: genomic DNA from tumor tissue of OT20


title: IRF-5si with CpG ODN - repeat 3 - mAdbID:116496

description: mAdb experiment ID: 116496

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4727;; 3.70678 Temperature: 25.8995 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

tag: disease state


title: IRF-8si with CpG ODN - repeat 2 - mAdbID:116258

description: mAdb experiment ID: 116258

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47484;; 3.67718 Temperature: 25.2586 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: Control-si with CpG ODN - repeat 4 - mAdbID:116499

description: mAdb experiment ID: 116499

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4727;; 3.78491 Temperature: 28.0969 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: genomic DNA from peripheral blood of OT24

value: peripheral blood from the oral tongue sub-site


title: genomic DNA from tumor tissue of OT8

value: Dead


title: IRF-8si Unstimulated - repeat 2 - mAdbID:116260

description: mAdb experiment ID: 116260

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4785;; 3.6903 Temperature: 25.9301 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: genomic DNA from tumor tissue of OT11


title: IRF-5si Unstimulated - repeat 3 - mAdbID:116256

description: mAdb experiment ID: 116256

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47575;; 3.81817 Temperature: 29.0124 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: genomic DNA from adjacent normal tissue of OT8


title: genomic DNA from peripheral blood of OT7


title: Control-si with CpG ODN - repeat 2 - mAdbID:116254

description: mAdb experiment ID: 116254

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46965;; 3.68236 Temperature: 24.8619 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: genomic DNA from tumor tissue of OT9

scan_protocol: data were collected using the HiScan (Illumina) reader


title: genomic DNA from tumor tissue of OT7

value: MDSCC; Invasive SCC


title: genomic DNA from adjacent normal tissue of OT6


title: genomic DNA from peripheral blood of OT10


title: IRF-5si with CpG ODN - repeat 2 - mAdbID:116252

description: mAdb experiment ID: 116252

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46873;; 3.78704 Temperature: 27.8222 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: IRF-8si with CpG ODN - repeat 1 - mAdbID:115674

description: mAdb experiment ID: 115674

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46294;; 3.7199 Temperature: 26.8761 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: IRF-5si Unstimulated - repeat 2 - mAdbID:115805

description: mAdb experiment ID: 115805

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48552;; 3.76568 Temperature: 27.8222 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: IRF-5si with CpG ODN - repeat 1 - mAdbID:115802

description: mAdb experiment ID: 115802

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47026;; 3.72204 Temperature: 26.7846 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: Control-si Unstimulated - repeat 1 - mAdbID:115800

description: mAdb experiment ID: 115800

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.45134;; 3.82672 Temperature: 29.4397 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: IRF-5si Unstimulated - repeat 1 - mAdbID:114969

description: mAdb experiment ID: 114969

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47179;; 3.68938 Temperature: 25.5028 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: Control-si Unstimulated - repeat 2 - mAdbID:116245

description: mAdb experiment ID: 116245

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48552;; 3.8197 Temperature: 28.7988 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).


title: genomic DNA from tumor tissue of OT6


title: ALDH-CD44-_Cisplatin_Exp4

city: Ann Arbor

first: Sean

middle: Patrick

last: McDermott

state: MI

address: 2800 Plymouth Rd

department: Internal Medicine - Hem/Onc

institute: University of Michigan

hyb_protocol: Following Labeling procedure, 3.75 ug of cDNA were hybridized at [48C – 3’; 48C – WT] on Human Gene ST 2.1 strips, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing:
CEL files processed using R and Bioconductor after loading the following, and associated, packages: oligo, genefilter, affycoretools, limma, ReportingTools, sva, gplots, hwriter, pd.hugene.2.1.st, hugene21sttranscriptcluster.db. Files were preprocessed by Robust Multiarray Average (RMA) with background substraction, quantile normalization, and median polish using the oligo package. Data was fitted with robust probe level linear models to all the probesets. Since microarrays were performed on two different days and flow cytometry performed on four separate days, batch effects (experiments) were accounted for using ComBat in the sva package. Differentially expressed genes were identified using univariate comparisons. First, the relative reliability of each array is estimated by measuring how well the expression values for that array follow the linear model. Second, data is fitted to a linear model (limma package). Third, the estimated coefficients and standard errors are computed. Finally, initial statistics are determined using an empirical Bayesian model. Multiple testing comparisons were adjusted using Benjamini and Hochberg (aka FDR). Probes with an adjusted p-value <0.05 were considered statistically significant.
log2 values following background substraction, quantile normalization, median polish (RMA) are included in the sample data table. The normalized data were further fitted with robust probe level linear models to all the probesets (fitProbeLevelModel), and after account for flow cytometry batch effects (ComBat) [provided in the 'Matrix_Combat.txt' file].

source_name: ALDH-CD44- cells from cisplatin treated UM-SCC-22b

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 30 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

growth_protocol: UM-SCC-22b cells were grown in DMEM/10% FBS/1% PenStrep/3X Glutamax/1mM Sodium Pyruvate. 50,000 cells were plated in 12 wells in two 6-well plates.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit following the manufacturer instructions. Briefly, c ollected cells from flow cytometry were centrifuged at 337g for 5min at 4C. Excess volume was removed with a p1000 pipettor and the remaining sample transferred to 1.5mL microcentrifuge tube. Tubes were centrifuged at 300g for 5min at 4C. Supernatant was removed with a p200 pipettor until <30uL sample remained. 350uL RLT was added to cell pellets (in <30uL) and vortexed for 30sec. 350uL 70% EtOH was added to each sample and mixed until no viscosity remained. The sample was transferred to spin column, centrifuged 8000g x 15sec. Then 700uL RW1 added to spin column, centrifuged 8000g x 15sec. Then 500uL RPE buffer to spin column, centrifuged 8000g x 15sec. Then 500uL RPE buffer to spin column, centrifuged 8000g x 2min. Spin columns were placed on new collection tube and centrifuged 8000g x 1min. Spin columns were placed on 1.5mL RNAse-free centrifuge tubes. 15 or 30uL of RNAse-free water added to membrane and then centrifuged 8000g x 1min.

treatment_protocol: Media was replaced with fresh media with or without 2μM (micromolar) cisplatin. Media was replaced on days 1, 3 and 5. On day 6, cells were harvested with 0.25% trypsin, counted, filtered through 35um membranes into 5mL FACS tubes, and centrifuged at 337g for 5min at 4C. Cell pellets were suspended in 985uL Aldefluor Assay Buffer. 10uL of 0.1mg/mL DAPI was added. 5uL of DEAB, as an inhibitor of the Aldefluor reaction, was added to a separate 5mL FACS tube. 5uL of activated Aldefluor reagent was added to 995uL of cells/DAPI. 500uL of this solution was immediately transferred to the tube containing DEAB. Cells were incubated for 30min at 37C. Tubes were centrifuged at 337g for 5min at 4C and placed on ice. Cell pellets were suspended in 300uL Aldefluor Assay Buffer. 0.5uL CD44-APC was added to tubes, except the DEAB control tube. Samples were incubated for exactly 15min on ice and then centrifuged. Cell pellets were suspended on ice in Aldefluor assay buffer for a final concentration of 1-3x106 cells/mL. Flow cytometry sorting was performed on a Beckman Coulter MoFlo XDP with 355nm, 488nm, and 633nm lasers with appropriate filters. Gating for CD44+ and Aldefluor+ events were determined using the DEAB sample as a fluorescence minus one control. Gates for CD44+ and ALDH+ cells was set at 0.1%. ALDH+CD44+ and ALDH-CD44- cells from control and cisplatin groups were collected into separate 5mL FACS tubes containing 1mL of PBS/3% FBS.

value: head and neck squamous cell carcinoma (HNSCC) cell line

tag: cell fraction

tag: treated with

value: with 2uM cisplatin for 5 days

tag: experiment batch


title: ALDH+CD44+_Control_Exp4

source_name: ALDH+CD44+ cells from control treated UM-SCC-22b

tag: cell line

tag: cell type

value: none (control) for 5 days


title: ALDH+CD44+_Cisplatin_Exp4

source_name: ALDH+CD44+ cells from cisplatin treated UM-SCC-22b


title: genomic DNA from adjacent normal tissue of OT5

tag: subject id

tag: patient age (yrs)

value: Alive


title: ALDH-CD44-_Control_Exp4

source_name: ALDH-CD44- cells from control treated UM-SCC-22b


title: IRF-8si Unstimulated - repeat 1 - mAdbID:115671

description: mAdb experiment ID: 115671

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47514;; 3.69182 Temperature: 25.9301 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: Control-si with CpG ODN - repeat 1 - mAdbID:115807

description: mAdb experiment ID: 115807

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47789;; 3.82519 Temperature: 28.7378 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) and analyzed using the GenePix Pro 6.0 software tool (Axon Instruments).

value: plasmacytoid dendritic cells (pDC)


title: genomic DNA from tumor tissue of OT5

tag: patient grade

tag: disease


title: genomic DNA from peripheral blood of OT3

tag: tissue type

tag: tumor grade


title: genomic DNA from peripheral blood of OT4

tag: tumor stage

tag: tumor nodal status


title: ALDH-CD44-_Cisplatin_Exp3

hyb_protocol: Following Labeling procedure, 2.5 ug of cDNA were hybridized at [48C – 3’; 48C – WT] on Human Gene ST 2.1 plates, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515)

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 10 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 2.5 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)


title: genomic DNA from tumor tissue of OT3

tag: survival status

tag: overall survival (months)


title: 11

city: Amsterdam

first: Guangquan

last: Chen

address: boelelaan 1085

department: Animal ecology

institute: Vrije Universiteit

description:
TCA
total RNA from 30 animals
spiked soil

hyb_protocol: 1.65 ug of Cy3-labeled (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 4 - 180 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm) 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), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan settings for 4x35k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039425_D_F_20120307) to obtain mean Green intensities and median Green background intesities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizion was done.

organism: Folsomia candida

source_name: TCA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, one-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil: 20 adult animals were incubated per container; containing a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: tissue

value: whole animal


title: ALDH-CD44-_Control_Exp3


title: genomic DNA from tumor tissue of OT2

value: tumor tissue from the oral tongue sub-site

tag: disease-free survival (months)


title: ALDH+CD44+_Control_Exp3

tag: cell fraction


title: 10

description:
HMF
total RNA from 30 animals
spiked soil

source_name: HMF


title: genomic DNA from adjacent normal tissue of OT1

value: F

value: adjacent normal tissue from the oral tongue sub-site


title: genomic DNA from tumor tissue of OT4

value: M


title: ALDH+CD44+_Cisplatin_Exp3

tag: treated with


title: 9

description:
LUFA
total RNA from 30 animals
spiked soil

source_name: LUFA


title: ALDH-CD44-_Cisplatin_Exp2

tag: experiment batch


title: 6

description:
FDCA
total RNA from 30 animals
spiked soil

source_name: FDCA


title: ALDH-CD44-_Control_Exp2

tag: cell line


title: ALDH-CD44-_Cisplatin_Exp1

tag: cell type


title: genomic DNA from tumor tissue of OT1

tag: subject id

value: Oral tongue squamous cell carcinomas (OTSCC)

value: WDSCC


title: 7


title: ALDH+CD44+_Control_Exp2


title: 2


title: 1


title: 5


title: 8


title: 12


title: ALDH+CD44+_Cisplatin_Exp2


title: ALDH+CD44+_Cisplatin_Exp1


title: ALDH-CD44-_Control_Exp1


title: 3


title: 4


title: ALDH+CD44+_Control_Exp1


title: G0S2 knockout MEF passage 10 rep 2

city: Urbana

last: Spinella

state: IL

address: 2001 South Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois

description: biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: immortalized MEF

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

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

tag: strain

tag: age

value: 12 day embryos

tag: genotype/variation

value: G0S2 knockout


title: Wild-type MEF passage 10 rep 2

description: biological replicate 2

value: wild type


title: Wild-type MEF passage 10 rep 1

description: biological replicate 1


title: G0S2 knockout MEF passage 10 rep 1

description: biological replicate 1


title: DeltaBcLTF2_Light_r4

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF2, subjected to a light stimulation. It is the fourth of three deltaBcLTF2_light (DeltaLTF2_L) biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization on microarrays were done using the procedures established by NimbleGen (Roche)  and the reagents from Invitrogen (Life technologies, France).

scan_protocol: Scanning was performed  using NimbleScan.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS website (http://anais.versailles.inra.fr/).

organism: Botrytis cinerea B05.10

source_name: Botrytis cinerea B0510_deltaBcLTF2

label_protocol: Synthesis of double-stranded cDNA and Cy3-labeling were done using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)

growth_protocol: Wild type B05.10 and the deltaBcLTF2 mutant were grown for 3-4 days on solid CM before non-sporulating mycelia were transferred to solid CM covered with cellophane overlays. Cultures were incubated for 54 h in darkness, and then half of the cultures were transferred to white light. After 60 min all four cultures (WT-D; WT-L; deltaBcLTF2-D; deltaBcLTF2-L) were harvested.

extract_protocol: Total RNA was extracted using the Trizol procedure. Total RNA was treated with the DNA-free kit to remove any trace of DNA (Ambion - Applied Biosystems, France).

tag: genotype

value: Mutant deltaBcLTF2

tag: light treatment

value: Light


title: DeltaBcLTF2_Dark_r4

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF2, cultured in darkness. It is the fourth of three deltaBcLTF2_dark (DeltaLTF2_D) biological replicates used in this experiment, each from separate cultures.

value: Dark


title: G0S2 knockout MEF passage 10 rep 3

description: biological replicate 3


title: Wild-type MEF passage 10 rep 3

description: biological replicate 3


title: DeltaBcLTF2_Light_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF2, subjected to a light stimulation. It is the first of three deltaBcLTF2_light (DeltaLTF2_L) biological replicates used in this experiment, each from separate cultures.


title: DeltaBcLTF2_Dark_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF2, cultured in darkness. It is the first of three deltaBcLTF2_dark (DeltaLTF2_D) biological replicates used in this experiment, each from separate cultures.


title: DeltaBcLTF2_Light_r3

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF2, subjected to a light stimulation. It is the third of three deltaBcLTF2_light (DeltaLTF2_L) biological replicates used in this experiment, each from separate cultures.