title: aCML #150 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #151 SNP6.0

status: Public on Jun 30 2010

type: genomic

city: Salisbury

first: Andy

last: Chase

address: Salisbury District Hospital

country: United Kingdom

institute: Wessex Regional Genetics Laboratory

description: hybridised to Affymetrix SNP 6.0 array

hyb_protocol: Processed by Almac Diagnostic (Craigavon, UK).  Hybridisation according to Affymetrix protocols. Array washed and stained on the GeneChip® fluidics station 450 .

scan_protocol: Processed by Almac Diagnostic (Craigavon, UK).  Array scanned using a GeneChip® Scanner 3000 7G.

data_processing:
Chp files were produced using Affymetrix Genotyping Console version 3.0.2 (birdseed-v2 algorithm); data was analysed using Partek Genomic Suite 6.5 and CNAG version 3.2 using Hapmap normal references
Affymetrix SNP 6.0 CEL and CHP files

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: hematopoietic

label_protocol: Processed by Almac Diagnostic (Craigavon, UK). Biotin labeled according to Affymetrix protocols.

extract_protocol: Qiagen QIAamp DNA extraction kit

tag: tissue

value: blood

tag: disease state

value: CMML

tag: patient gender

value: male


title: aCML #068 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: aCML


title: CMML #149 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #139 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #143 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: female


title: aCML #062 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #069 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML/CEL #137 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: aCML/CEL


title: aCML #138 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #145 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #144 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #136 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML/CEL #129 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #142 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #063 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML/CEL #134 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #131 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #132 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML/CEL #130 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #140 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #135 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #128 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #141 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #124 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #133 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #122 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #120 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #038 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #040 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #126 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #123 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #125 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #008 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #119 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #009 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML/CNL #010 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: CMML/CNL


title: aCML #003 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #053 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #056 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #121 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #028 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #034 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #118 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #066 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #117 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #127 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #046 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #050 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #051 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #116 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #047 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #115 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #114 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #109 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #072 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #110 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #112 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #107 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #025 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #105 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #052 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #108 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #113 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #111 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #102 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #104 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #019 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #101 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #017 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #100 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #103 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #106 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #018 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #071 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #054 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #034 custom CGH

description: No additional information

hyb_protocol: Cy3 and Cy5 labeled DNA was combined together with Cot-1 DNA, Agilent blocking reagent and Agilent hybridisation buffer, denatured for 3 min. at 95ºC and incubated at 37ºC for 30 min. The hybridisation mix was applied to the array slide and mounted into an Agilent SureHyb chamber and rotated at 65ºC for 24 hours. Slides were then washed and dried manually using Agilent buffers.

scan_protocol: Arrays were scanned using an Agilent G250B microarray scanner and Agilent Scan Control software (version A.7.0.1)

data_processing: Microarray images were analysed by Agilent Feature Extraction software

source_name: Hematopoietic

label_protocol: According to Agilent guidelines. 1.5 µg DNA was digested with AluI and RsaI (final size 200-500bp), then labelled with Cy3 or Cy5 using Exo-Klenow fragment and random primers.

tag: gender

source_name: Pooled Human Genomic DNA (Promega)

value: Normal peripheral blood


title: CMML #097 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #089 custom CGH

description: No additional information


title: aCML #099 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #048 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #098 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #096 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #005 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #015 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #058 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #017 custom CGH

description: No additional information


title: CMML #120 custom CGH

description: No additional information


title: MDS/MPD #074 custom CGH

description: No additional information

value: MDS/MPD


title: aCML #107 custom CGH

description: No additional information


title: CMML #090 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #089 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #091 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #122 custom CGH

description: No additional information


title: CMML #095 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #086 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #093 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MF #170 custom CGH

description: No additional information

value: MF


title: CMML #085 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CD34+CD90+C

status: Public on Jun 29 2010

type: RNA

city: Toronto

first: Michael

last: Milyavsky

state: Ontario

address: 101 College street

department: Department of Stem Cell and Developmental Biology

country: Canada

institute: Ontario Cancer Institute, Toronto General Research Institute, University Health Network

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring GX 10

molecule: total RNA

source_name: human cord blood cells

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: CD34+CD90+ cord blood cell


title: CMML #073 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CD34+CD90-A

description: replicate 1

value: CD34+CD90- cord blood cell


title: CMML #088 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CD34+CD90-B

description: replicate 2


title: CD34+CD90-C


title: CMML #084 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #033 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CD34+CD90+A

description: replicate 1


title: aCML/CMML #081 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: aCML/CMML


title: CMML #087 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #078 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: 4009754_WT

status: Public on Jun 20 2010

city: Nanjing

first: Feng

last: Zheng

address: 293 East Zhongshan Road

country: China

institute: Research Institute for Medicine of Nanjing Command

hyb_protocol: After pre-hybridization, microarray slides were hybridized with the relevant samples at 65℃ for 15 h. This was repeated 4 times for both samples (WT and RGG).

scan_protocol: All hybridization slides were scanned by GenePix 4100A scanner after appropriate washing, and the average pixel intensity values were quantified using GenePix Pro 4.1.

data_processing: The microarray data were normalized by quantile normalization and logarithmically transformed before further analysis.

organism: Streptococcus suis 05ZYH33

source_name: Streptococcus suis 2, 05ZYH33 wild-type strain, postexponential phase of growth

label_protocol: cDNA was labeled with Cy3-dCTP during the reverse transcription and purified using QIAquick Nucleotide Removal Kit (Qiagen).

growth_protocol: The strain was grown in Todd-Hewitt broth (THB) to OD600=0.9 in the absence of antibiotics.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen), and purified using RNeasy Mini Kit (Qiagen).

tag: strain


title: CMML #079 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #094 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: Belinka biological rep B rep 2

status: Public on Jun 15 2010

city: Villeneuve d'Ascq

first: Stephane

last: Fenart

address: Cité Scientifique

department: Biology

country: France

institute: University Lille 1

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

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 NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). Processed data then consist of log2(intensities) files  (.calls files).

organism: Linum usitatissimum

source_name: cultivar : Belinka

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed byDNase digestion with the DNA-Free set (Ambion). RNA quality and concentration was determined by analysis with an Experion bioanalyzer (Biorad) using RNA Std chips.

tag: cultivar

value: Belinka

value: outter stem tissue

tag: developmental stage

value: green capsule stage


title: CD34+CD90+B

description: replicate 2


title: Drakkar biological rep C rep 1

scan_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

source_name: cultivar : Drakkar

value: Drakkar


title: Belinka biological rep C rep 1

label_protocol: According to standard NimbleGen protocols (www.nimblegen.com)


title: Drakkar biological rep C rep 2


title: Belinka biological rep B rep 1


title: Belinka biological rep C rep 2


title: CMML #061 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: blood


title: Belinka biological rep A rep 2


title: Drakkar biological rep B rep 1


title: 4009754_RGG

source_name: Streptococcus suis 2, 05ZYH33 rgg isogenic mutant strain, postexponential phase of growth

value: 05ZYH33 rgg isogenic mutant


title: Drakkar biological rep A rep 2


title: Drakkar biological rep A rep 1


title: CMML #092 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: CMML


title: E3 rep2

source_name: cultivar : Barbara

value: Barbara

value: Embryo tissue

value: 40 days after flowering


title: E2 rep1

value: 20 days after flowering


title: E2 rep2


title: Belinka biological rep A rep 1


title: E3 rep1


title: aCML #011 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: aCML

value: female


title: E1 rep1

value: 10 days after flowering


title: SIGC rep2

source_name: cultivar : Hermes

value: Hermes

value: inner stem tissue


title: SOGC rep2


title: E1 rep2


title: SOGC rep1


title: SIGC rep1


title: aCML/CMML #001 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: aCML/CMML

value: male


title: HES #080 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: HES


title: CMML #002 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: L rep2

value: leaf tissue

value: green capsule stage


title: SIV rep1

value: vegetative stage


title: aCML #023 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: blood


title: R rep2

value: root tissue


title: L rep1


title: R rep1


title: SOV rep2

value: outter stem tissue


title: HES #082 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: HES #083 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #076 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: Drakkar biological rep B rep 2

value: Drakkar


title: SOV rep1


title: CMML #075 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: CMML


title: CELEGANS_RN6390_8H_REP2

status: Public on Jun 12 2010

city: Boston

first: Javier

middle: E

last: Irazoqui

state: MA

address: 55 Fruit St GRJ1416

department: Pediatrics

country: USA

institute: Massachusetts General Hospital

hyb_protocol: RNA samples were hybridized to Affymetrix full-genome GeneChips for C. elegans at the Harvard Medical School Biopolymer Facility, according to instructions from Affymetrix (http://www.affymetrix.com).

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix .cel files were uploaded into the Resolver Gene Expression Data Analysis System, version 5.1 (Rosetta Inpharmatics, http://www.rii.com) at the Harvard Center for Genomic Research (http://www.cgr.harvard.edu) for analysis. For each condition, three replicate microarrays were normalized and analyzed using the Resolver intensity error model for single color chips. The two conditions were then compared in Resolver to determine fold change for each probe set and a p-value, using a modified t test. Genes with a 2-fold or greater fold change and a p-value <0.01 were considered differentially expressed.  Differentially expressed probe sets were compared for S. aureus infection.

organism: Caenorhabditis elegans

source_name: Staphylococcus aureus infection, 8h

label_protocol: RNA samples were prepared and hybridized to Affymetrix full-genome GeneChips for C. elegans at the Harvard Medical School Biopolymer Facility, according to instructions from Affymetrix (http://www.affymetrix.com). Briefly, 5 μg of total RNA was reverse transcribed using an oligo dT-T7 primer and Superscript II reverse transcriptase, followed by second-strand cDNA synthesis. The double-stranded cDNA was then purified using a DNA purification kit (Qiagen), and used as the template for in vitro transcription using T7 RNA polymerase and biotinylated nucleotides.

growth_protocol: synchronized fer-15;fem-1 C. elegans were grown on OP50 lawns on NGM plates under standard conditions

extract_protocol: Animals were washed in M9 buffer, and resuspended in Trireagent (MRC). Total RNA was extracted using TRI Reagent (Molecular Research Center, http://www.mrcgene.com) according to the manufacturer's instructions, followed by purification on RNeasy columns (Qiagen, http://www1.qiagen.com).

treatment_protocol: L4 synchronized populations were collected in M9 buffer, washed, and infected on RN6390 lawns on TSA plates at 25 C, or fed OP50 on NGM plates at the same temperature, for 8 h

value: infected


title: no albendazole exposure, biological rep 3

status: Public on Jun 14 2010

city: Glasgow

first: Steven

middle: Thomas

last: Laing

address: 464 Bearsden Road

department: Veterinary Medicine

institute: University of Glasgow

description: Gene expression data from adult C. elegans exposed to 1.5% v/v DMSO for 4 hrs

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained according to manufacturer supplied protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 scanner

data_processing: The data were analyzed with R and Bioconductor packages (e.g. limma) using RMA as the normalization method.

source_name: Adult C. elegans exposed to 1.5% v/v DMSO for 4 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: Synchronised CB3474 L1 (approx. 10000 per experimental condition) were grown in liquid culture at 20oC, 240 rpm for 70 hrs

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

treatment_protocol: 70 hr CB3474 cultures were exposed to 300 µg/ml ABZ (diluted from 20mg/ml ABZ in DMSO stock) or DMSO only for four hours, then were harvested by sucrose flotation

value: whole nematode

tag: genotype

tag: culture method

value: liquid culture

tag: age

value: 70hrs from L1 (20oC)

tag: treatment

value: 1.5% v/v DMSO for 4 hrs


title: no albendazole exposure, biological rep 1


title: Monosomic ch5 derivative rep2

status: Public on Jun 09 2010

city: Atlanta

first: Hong

last: Qin

state: GA

address: 350 Spelman Ln SW, Box 1183

institute: Spelman College

hyb_protocol: Anti-sense RNA was hybridized as recommended by CombiMatrix. Hybridization was carried in the Functional Genomics Center at the University of Rochester Medical Center.

scan_protocol: ScanArray Lite microarray laser scanner (Perkin Elmer, Boston, MA) at a 5 µm resolution.  The resulting 16-bit TIFF files were quantified with Microarray Imager software (CombiMatrix Corporation, Mukilteo, WA).

data_processing: The scanned 16-bit TIFF files were quantified with Microarray Imager software (CombiMatrix Corporation, Mukilteo, WA). Datafile were ported to R. Background signals were taken as the median values of control-probes. Background correct signals were normalized by non-chr5 genes.

organism: Candida albicans

label_protocol: 2ug of total RNA from each batch was used to synthesize Cy5-dUTP labeled anti-sense RNA, using the Ambio Amino Allyl Message Amp II aRNA Aimplication Kit.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, Ambion Amino Allyl Message Amp II aRNA Amplification Kit (Ambion, Austin, TX).  Anti-sense RNA was hybridized to an individual chip as recommended by CombiMatrix Corporation.

value: Sor55, derivative of 3153A

tag: genome/variation

value: monosomic chr5


title: SIV rep2

value: Hermes

value: inner stem tissue


title: parental strain rep3

value: 3153A parental


title: CELEGANS_RN6390_8H_REP1


title: no albendazole exposure, biological rep 2


title: CELEGANS_RN6390_8H_REP3


title: aCML #004 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: aCML

value: male


title: Monosomic ch5 derivative rep3


title: CELEGANS_OP50_8H_REP2

source_name: Escherichia coli control, 8h

value: uninfected


title: parental strain rep2


title: albendazole exposure, biological rep 1

description: Gene expression data from adult C. elegans exposed to 300 µg/ml ABZ and 1.5% v/v DMSO for 4 hrs

source_name: Adult C. elegans exposed to 300 µg/ml ABZ and 1.5% v/v DMSO for 4 hrs

value: 300 µg/ml ABZ and 1.5% v/v DMSO (excipient) for 4 hrs


title: Monosomic ch5 derivative rep1


title: CELEGANS_OP50_8H_REP1


title: parental strain rep1


title: CELEGANS_OP50_8H_REP3


title: CMML #077 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: blood


title: hiPS 11

status: Public on Jun 07 2010

first: Niels

last: Geijsen

address: 185 Cambridge St. CPZN 4-4256

department: Center for Regenerative Medicine

description: US45102879_251485044613_S01_GE1-v5_95_Feb07_1_3.txt

hyb_protocol: Cy-3 labelled cRNA was hybridized using Agilent Hybridization Kit following the manufacturer's protocols.

scan_protocol: The washed microarray slides were scanned in Agilent Technologies Scanner following the manufacturer's protocols.

data_processing: The background subtracted signal and the signal to background ratio of each feature were uploaded into GeneSifter gene expression analysis program. The projects were median-normalized before analysis. The data uploaded here are original files prior to median normalization. The GeneSifter processed data is linked as a supplementary file to GSE21792.

source_name: human induced pluripotent stem cells

label_protocol: 1 microgram of the total RNA from each sample was labelled by the Agilent QuickAmp 1-Color Labeling Kit following the manufacturer's protocols.

growth_protocol: Human ES and iPS were grown in standard conditions with FGF on feeder MEFs. Human LR5-iPS were grown in the presence of human LIF and Doxycycline inducible expression of 5 reprogramming factors: OCT4, SOX2, KLF4, MYC and NANOG.

extract_protocol: Cells were size-sorted by forward scatter and side scatter on FACS-ARIA II. Total RNA of the sorted cells were extracted by TRIzol following the manufacturer's protocol.

treatment_protocol: no special treatment

value: human induced pluripotent stem cells


title: LD-hiPS 1

description: US45102879_251485044613_S01_GE1-v5_95_Feb07_1_1.txt

source_name: converted human LR5-iPS cells

value: converted human LR5-iPS cells


title: hiPS 12

description: US45102879_251485044613_S01_GE1-v5_95_Feb07_1_4.txt


title: hLR5-2

description: US45102879_251485044612_S01_GE1-v5_95_Feb07_1_1.txt

source_name: human LR5-iPS cells

value: human LR5-iPS cells


title: LD-hiPS 2

description: US45102879_251485044613_S01_GE1-v5_95_Feb07_1_2.txt


title: hLR5-3

description: US45102879_251485044612_S01_GE1-v5_95_Feb07_1_2.txt


title: hLR5-1

description: US45102879_251485044614_S01_GE1-v5_95_Feb07_1_3.txt


title: HuES 14

description: US45102879_251485044614_S01_GE1-v5_95_Feb07_1_2.txt

source_name: human ES

value: human embryonic stem cells


title: HuES 3

description: US45102879_251485044614_S01_GE1-v5_95_Feb07_1_1.txt


title: H9

description: US45102879_251485044614_S01_GE1-v5_95_Feb07_1_4.txt


title: human PBMC derived iPS cells GM#1

status: Public on Jun 01 2010

city: Machida-shi

first: Kenji

last: Nagao

state: Tokyo

address: 3-6-6, Asahi-machi,

department: Innovative Drug Research Laboratories

country: Japan

institute: Kyowa Hakko Kirin Co., Ltd.

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Humna Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Agilent Gene Expression Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent). Data were processed using Per Chip Normalization: Normalize to 75 percentile with GeneSpring GX software.

source_name: human PBMC derived iPS cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

extract_protocol: RNAs of iPS cell lines were isolated using the RNeasy Mini Kit (Qiagen). RNAs of BMMNCs or PBMNCs were isolated using the TRIZOL (Invitrogen).

value: iPS cells derived from peripheral blood mononuclear cells (PBMCs)

tag: cell line

tag: race

value: Latino


title: albendazole exposure, biological rep 2

value: whole nematode

value: liquid culture

value: 70hrs from L1 (20oC)


title: human PBMC derived iPS cells FP#1

value: Caucasian

value: female


title: human PBMC derived iPS cells Nega#8


title: YJB9233_aCGH

first: Anna

last: Selmecki

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: no additional information

hyb_protocol: Slides were hybridized overnight in a 37C waterbath

scan_protocol: Slides were scanned using a ScanArray (Perkin Elmer) and accompanying ScanArray Express software.

data_processing: Data were extracted using GenePix Pro and GeneTraffic software. Global Lowess normalization.

label_protocol: DNA was digested with HaeIII, purified, and labeled using an Invitrogen Bioprime aCGH labeling kit.

growth_protocol: DNA was isolated after minimal growth in YPAD at 30C

extract_protocol: Phenol Chloroform DNA extraction

value: YJB9233 is SN87

source_name: SC5314 (reference)

value: SC5314 (first sequenced strain)


title: YJB10546_aCGH

description: no additional information

growth_protocol: DNA was isolated after overnight growth in YPAD at 30C


title: YJB10552_aCGH

description: no additional information

value: YJB10552 (aka Sou+5)


title: human PBMC derived iPS cells GM#6

value: male


title: smDicer KO_jejunum_rep1

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 N. Virginia St.

department: Physiology and Cell biology

institute: University of Nevada School of Medicine

description: Gene expression data from a smDicer knockout mouse.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using Omicsoft Array Studio software and normalized using the RMA algorithm.

organism: Mus musculus

source_name: Smooth muscle-specific Dicer knockout

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The transgenic smDicer KO mice were generated.

extract_protocol: Total RNAs were isolated using the mirVana miRNA isolation kit according to the manufacturer's instructions.

value: jejunum

tag: genotype/variation

value: Knockout

value: 3 weeks


title: YJB10549_aCGH

description: no additional information


title: Control WT_jejunum_rep1

description: Gene expression data from a wild type control mouse.

source_name: Wild type control

value: Wild type


title: YJB9235_aCGH

description: no additional information

value: YJB9235 is SN152


title: human peripheral blood mononuclear cells

source_name: human peripheral blood derived mononuclear cells

value: peripheral blood derived mononuclear cells (PBMCs)

value: Hispanic


title: human BMMC derived iPS cells FP#17

source_name: human BMMC derived iPS cells

value: iPS cells derived from bone marrow mononuclear cells (BMMCs)

value: African American


title: Liver_double_gel_day8_rep3

city: Blacksburg

first: Chris

last: Lasher

state: VA

address: 103 Lucas Dr Apt B

department: Genetics, Bioinformatics, and Computational Biology

institute: Virginia Polytechnic and State University

description: Rat hepatocytes grown between two layers of collagen gel, collected on day 8 after deposition of second layer of collagen gel

hyb_protocol: Randomly fragmented cRNA was hybridized to GeneChip Rat Genome 230 2.0 array (Affymetrix, Santa Clara, CA), and the arrays were washed and stained according to Affymetrix’s ptotocols.

scan_protocol: The arrays were scanned using an Affymetrix 7G scanner according to Affymetrix’s ptotocols.

data_processing: The BioConductor package for R was used to perform initial statistical analysis of the DNA microarray data.  The data from 24 chips (2 culture conditions × 4 time points × 3 replicates) were normalized using the Robust Multichip Average method and used for further analysis.  The affylmGUI interface to Linear Models for Microarray Data (LIMMA) was used to perform differential gene expression analysis. For each contrast, LIMMA was used to compute a p-value for each probe set that indicated the statistical significance of the difference of the expression levels of that probe set between the two conditions in the contrast.

organism: Rattus norvegicus

source_name: liver, double gel, day 8

label_protocol: Isolated RNA samples in triplicate at each time point were labeled according to the Affymetrix Standard Target labeling process. Briefly, total RNA was converted into double-stranded complementary DNA using a T7- oligo (dT) primer (5’ – GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG–(dT)24 –3’) and reverse transcription. Synthesized cDNA was converted into biotinylated cRNA by transcription using T7 RNA polymerase.

growth_protocol: Hepatocytes were cultured on collagen-coated 6-well sterile tissue culture plates (Becton Dickinson Labware, Franklin Lakes, NJ) and were maintained in culture medium that consisted of DMEM supplemented with 10% heat-inactivated fetal bovine serum (Hyclone, UT) 200 U/mL penicillin, 200 μg/mL streptomycin, 20 ng/mL epidermal growth factor (BD Biosciences, San Jose, CA) 0.5 U/mL insulin (USP, Rockville MD) , 14 ng/mL glucagon and 7.5 μg/mL hydrocortisone. A collagen gelling solution was prepared by mixing 9 parts of  type I collagen (BD Biosciences) solution and 1 part of 10X DMEM.  Sterile 6-well tissue culture plates were coated with 0.5 ml of the gelling solution and incubated at 37 oC for 1h to promote gel formation.  Isolated hepatocytes were suspended in hepatocyte culture medium at a concentration of 1x106 cells/ml and seeded on the collagen-coated wells at a density of 1 million cells/well.  Collagen sandwich cultures were formed by the deposition of a second layer of collagen 24h later.  Hepatocytes maintained in stable collagen sandwich and in unstable confluent monolayer cultures served as positive and negative controls, respectively.  Hepatocyte cultures were maintained at 37°C in a humidified gas mixture of 90% air/10% CO2. The culture medium was replaced every 24 hours.

extract_protocol: Primary rat hepatocytes cultured in CS and HM cultures were maintained for an eight-day culture period. On days 1, 2, 3 and 8 after deposition of second layer of collagen gel on hepatocytes, total RNA was extracted and purified from cells for each culture system using RNeasy mini kit (QIAGEN, Valencia, CA) according to manufacturer’s protocol.

tag: culture type

value: collagen sandwich

tag: day

value: hepatocyte


title: WO-2_aCGH

description: no additional information

hyb_protocol: Slides were hybridized overnight in a 37C waterbath.


title: Liver_double_gel_day8_rep1


title: MDS/MPN #074 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

source_name: hematopoietic

tag: tissue

value: blood

tag: disease state

value: MDS/MPN


title: smDicer KO_jejunum_rep2


title: Liver_double_gel_day3_rep1

description: Rat hepatocytes grown between two layers of collagen gel, collected on day 3 after deposition of second layer of collagen gel

source_name: liver, double gel, day 3


title: YJB9234_aCGH

description: no additional information

value: YJB9234 is SN95


title: Control WT_jejunum_rep2


title: Liver_double_gel_day2_rep3

description: Rat hepatocytes grown between two layers of collagen gel, collected on day 2 after deposition of second layer of collagen gel

source_name: liver, double gel, day 2


title: Liver_double_gel_day3_rep2


title: human bone marrow mononuclear cells

source_name: human bone marrow derived mononuclear cells

value: bone marrow derived mononuclear cells (BMMCs)

value: Caucasian

tag: gender

value: female


title: Liver_double_gel_day3_rep3

tag: cell type


title: Liver_double_gel_day2_rep2


title: albendazole exposure, biological rep 3

value: whole nematode

value: liquid culture

value: 70hrs from L1 (20oC)

value: 300 µg/ml ABZ and 1.5% v/v DMSO (excipient) for 4 hrs


title: Liver_double_gel_day8_rep2


title: Liver_double_gel_day1_rep2

description: Rat hepatocytes grown between two layers of collagen gel, collected on day 1 after deposition of second layer of collagen gel

source_name: liver, double gel, day 1


title: Liver_double_gel_day1_rep3


title: Liver_double_gel_day2_rep1


title: Liver_single_gel_day8_rep1

description: Rat hepatocytes grown on a monolayer of collagen gel, collected on day 8 after deposition of second layer of collagen gel

source_name: liver, single gel, day 8

value: monolayer culture


title: Liver_single_gel_day2_rep3

description: Rat hepatocytes grown on a monolayer of collagen gel, collected on day 2 after deposition of second layer of collagen gel

source_name: liver, single gel, day 2


title: Liver_single_gel_day3_rep2

description: Rat hepatocytes grown on a monolayer of collagen gel, collected on day 3 after deposition of second layer of collagen gel

source_name: liver, single gel, day 3


title: Liver_single_gel_day3_rep1


title: Liver_single_gel_day8_rep3


title: Liver_double_gel_day1_rep1


title: Liver_single_gel_day3_rep3


title: Liver_single_gel_day1_rep3

description: Rat hepatocytes grown on a monolayer of collagen gel, collected on day 1 after deposition of second layer of collagen gel

source_name: liver, single gel, day 1


title: Liver_single_gel_day2_rep2


title: ESFT26

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

description:
Fusion 7-6
O461

hyb_protocol: Hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions.

scan_protocol: HuEx1.0 microarrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G following the manufacturer’s instructions.

data_processing: Signal intensities from core probesets were quantile normalized by robust multichip averaging and transcript expression levels median summarized using Partek Genomics Suite software version 6.5 (Partek, St. Louis, MO). Statistical correlations between BMI-1 and differentiation genes were assessed with the Spearman’s rank correlation tests, with the expected false discovery rate (FDR) controlled using the Benjamini and Hochberg procedure.

source_name: primary tumor biopsy, low BMI1

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara).

extract_protocol: Qiagen miRNA easy kit.

value: Ewing sarcoma family tumor

tag: bmi1 status

value: low


title: Liver_single_gel_day8_rep2


title: Liver_single_gel_day1_rep1


title: Liver_single_gel_day1_rep2


title: ESFT24

description:
Fusion 7-6
O457


title: ESFT23

description:
Fusion 7-6
M944


title: ESFT21

description:
Fusion 7-6
N228

source_name: primary tumor biopsy, high BMI1

value: high


title: ESFT25

description:
Fusion negative
O458


title: Liver_single_gel_day2_rep1


title: ESFT22

description:
Fusion 7-5
L678


title: ESFT 2

description:
Fusion 7-7
L308


title: ESFT 6

description:
Fusion 7-6
L389


title: ESFT 5

description:
Fusion 7-6
L315


title: ESFT 4

description:
Fusion 7-5
L312


title: Day4_1

status: Public on May 31 2010

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
4026751014_A

hyb_protocol: Labeled, amplified cRNA (1.5 ug per array) was hybridized to a ver. 2 of the Illumina HumanRef-8 BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the protocol outlined in the BeadChip manual. Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc.).

data_processing: Array data processing and analysis was performed using Illumina BeadStudio software 3.1.3.0. Non-normalized data was obtained directly from the BeadStudio software and arranged in probe level (n=22184). Normalized data was obtained by the quantile normalization method using the same software.

label: Biotin

label_protocol: Biotin-labelled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure. Briefly, 500 ng of total RNA was used for cDNA synthesis, followed by an amplication/labeling step (in vitro transcription) to synthesize biotin-labelled cRNA according to the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). The cRNA concentrations were measured by the RiboGreen method (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) using the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

growth_protocol: Human breast cancer MCF7 cells were purchased from the American Type Culture Collection and cultured in DMEM (MyClone, Logan, UT) supplemented with 10% FBS (WelGENE, Daegu, Korea), and 1% penicillin/streptomycin solution at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA from MCF7 cells was isolated using the Trizol reagent (Invitrogen, CA) according to the manufacturer’s instruction.

treatment_protocol: For irradiation, cells were exposed to gamma-ray with a 137Cs gamma ray source (Atomic Energy of Canada, Mississauga, Canada) at a dose rate of 3.0 Gy/min.

value: human breast cancer cells

value: IR 6 Gy

tag: time

value: 4 days


title: Day4_3

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
4026751014_C


title: Day3_4

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_H

value: 3 days


title: WT, biological replicate 3

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

country: Germany

institute: Uniklinikum Giessen

description: Biological replicate 3

hyb_protocol: Hybridization was performed at 65°C over-night on Agilent G4122F mouse whole genome microarrays (Agilent Technologies, Böblingen, Germany) as indicated by the supplier.

scan_protocol: Slides were scanned using the GenePix 4100A scanner (MDS Analytical Technologies, Ismaning, Germany) and analyzed with GenePix software V5.1 (MDS). PMT gains were manually adjusted to get some saturated pixels while matching the intensity histograms of Cy5 and Cy3 fluorescence.

data_processing:
The experiment contains two data sets of 4 hybridizations each. One set of data was in obtained from 1x44k arrays (GSM476104-GSM476107) and a second set of hybridizations was done on the newer 4x44k arrays (GSM476108-GSM476111).
For the analysis, the data of all eight arrays were assembled into a data structure corresponding to GPL4134. The missing dark corner features and spike-in-features were taken from the GPL4134 arrays only. All other spots were matched by their probe IDs. This data set was then analysed to produce the matrix file. The correlation of spot intensities between the two sets was checked carfully and is within the acceptable margins of error, demonstrating that the two sets of data are in fact comparable and the spot matching worked. Further, the analysis of the individual sets gives very similar results to the combined analysis (limma uses a variance estimate from all arrays, the results are not expected to be identical). The data in the matrix file is the result of the combined analysis, what is to be preferred over the individual analyses since the variance estimates are slightly more robust when more arrays are involved.
MA data was calculated from the Genepix data and lowess-nomalized using R (http://www.R-project.org).

source_name: alveolar macrophages

label_protocol: Purified total RNA was amplified and Cy-labeled using the dual-color QuickAmp kit (Agilent Technologies, Palo Alto, CA) following the kit instructions.

growth_protocol: RPMI medium with dialysed 1%FSC, 37ºC, 5%CO2 incubator

extract_protocol: RNA was extracted using the RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: 10 micromolar serotonin (Sigma Aldrich), for 4h

tag: strain

value: alveolar macrophages

tag: stimulation

value: yes

value: no


title: WT, biological replicate 4

description: Biological replicate 4


title: Day4_2

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
4026751014_B


title: Day2_4

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_G

value: 2 days


title: WT, biological replicate 1

description: Biological replicate 1


title: Day4_4

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
4026751014_D


title: KO, biological replicate 1

description: Biological replicate 1


title: WT, biological replicate 2

description: Biological replicate 2


title: Day2_3

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_C


title: Day3_3

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_D


title: Day0_3

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_A

value: 0 days


title: Day3_1

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_D


title: Day0_4

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_E


title: KO, biological replicate 3

description: Biological replicate 3


title: Day1_3

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_B

value: 1 days


title: Day3_2

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_H


title: KO, biological replicate 2

description: Biological replicate 2


title: Day1_4

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1714478014_F


title: Day0_2

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_E


title: Day1_1

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_B


title: Day1_2

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_F


title: Day2_2

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_G


title: Day0_1

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_A


title: 100Hz_LR_24h_DH2 rat

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

institute: Shanghai Biochip Co., Ltd.

description: Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42°C for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50°C), 0.1 SSC/0.2%SDS(50°C) and 0.1 SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: the tissue of spinal dorsal horn of 100Hz electroacupuncture low responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and non-sensitivity on electroacupuncture analgesia was labeled with Cy3.

extract_protocol: Total RNA was prepared from DH using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit.

tag: time point

value: Sprague-Dawley

tag: electroacupuncture frequency

tag: group

value: low responder (LR) rats

tag: tissue type

value: dorsal horn (DH)

source_name: the tissue of DH of control rats

extract_protocol: Total RNA was prepared from DH of control rats using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit.

tag: reference

value: rats sacrificed after stayed in their home cages without receiving electroacupuncture stimulation


title: 100Hz_HR_24h_DH3 rat

source_name: the tissue of spinal dorsal horn of 100Hz electroacupuncture high responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and sensitivity on electroacupuncture analgesia was labeled with Cy3.

value: high responder (HR) rats


title: 100Hz_LR_24h_DH5 rat


title: Day2_1

description:
Gene expression profile using Illumina HumanRef-8 V2 array.
1690411282_C

tag: cell line

tag: treatment


title: KO, biological replicate 4

description: Biological replicate 4

tag: genome/variation


title: 100Hz_LR_24h_DH3 rat


title: 100Hz_LR_24h_DH4 rat


title: 2Hz_LR_24h_DH4 rat

source_name: the tissue of spinal dorsal horn of 2Hz electroacupuncture low responder(LR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and non-sensitivity on electroacupuncture analgesia was labeled with Cy3.


title: 2Hz_LR_24h_DH3 rat


title: 100Hz_HR_24h_DH1 rat


title: 100Hz_HR_24h_DH2 rat


title: 2Hz_LR_24h_DH2 rat


title: 100Hz_HR_24h_DH4 rat


title: 2Hz_HR_24h_DH2 rat

source_name: the tissue of spinal dorsal horn of 2Hz electroacupuncture high responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and sensitivity on electroacupuncture analgesia was labeled with Cy3.


title: 100Hz_HR_24h_DH5 rat


title: 2Hz_HR_24h_DH1 rat


title: 2Hz_HR_24h_DH3 rat


title: 2Hz_LR_24h_DH1 rat


title: 100Hz_LR_24h_DH1 rat


title: 2Hz_LR_24h_DH5 rat


title: 2Hz_HR_24h_DH4 rat


title: 2Hz_HR_24h_DH5 rat


title: LAPC cell PBS treated mouse

first: carl

last: virtanen

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

description: no further description

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Default settings for Affymetrix 7G scanner.

data_processing: Processing by MAS5 with default parameters

source_name: Isolated virus activated plasmacytoid cells from mouse

label_protocol: Standard Affymetrix 2 round 3' expression labeling protocol.

extract_protocol: Qiagen RNeasy

treatment_protocol: PBS treated and sacrificed 8d post infection

tag: age

value: 8-12 weeks

value: FACS sorted cells from mediastinal lymph nodes


title: LAPC cell flu mouse

description: no further description

treatment_protocol: 500 pfu infection with influenza virus and sacrificed 8d post infection

tag: tissue


title: WT T cells, cultured 3 days with IL-6, replicate 1

status: Public on May 30 2010

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description: Gene expression data from CD4+ T cells activated for three days

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: According to Affymetrix protocol

data_processing: RMA signals were summarized using GeneSpring GX 10.0.1 (Agilent) and normalized by quantile normalization.

source_name: WT T cells activated in with a STAT3-activating cytokine IL-6

label_protocol: RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

growth_protocol: Naïve sorted CD4+ CD44- CD62L+ T cells were grown for three days in the presence of anti-CD3 and anti-CD28, in the presence of 10ug/ml IL-6 and/or 2.5 ug/ml TGFb or medium alone.

extract_protocol: Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

treatment_protocol: No further treatment.

tag: cell

value: CD4+ T cell

tag: genotype


title: STAT3-deficient T cells, cultured 3 days with medium, replicate 1

source_name: STAT3-deficient T cells activated in neutral conditions

value: CD4 Cre; STAT3floxed


title: WT T cells, cultured 3 days with medium, replicate 2

source_name: WT T cells activated in neutral conditions


title: WT T cells, cultured 3 days with TGFb, replicate 2

source_name: WT T cells activated with a non-STAT3-activating cytokine TGFb


title: STAT3-deficient T cells, cultured 3 days with TGFb, replicate 1

source_name: STAT3-deficient T cells activated with a non-STAT3-activating cytokine TGFb


title: STAT3-deficient T cells, cultured 3 days with TGFb, replicate 2


title: STAT3-deficient T cells, cultured 3 days with medium, replicate 2


title: WT T cells, cultured 3 days with medium, replicate 1


title: STAT3-deficient T cells, cultured 3 days with IL-6 and TGFb, replicate 2

source_name: STAT3-deficient T cells activated with Th17-polarizing cytokines IL-6 and TGFb.


title: WT T cells, cultured 3 days with TGFb, replicate 1


title: WT T cells, cultured 3 days with IL-6 and TGFb, replicate 1

source_name: WT T cells activated with Th17-polarizing cytokines IL-6 and TGFb.


title: WT T cells, cultured 3 days with IL-6 and TGFb, replicate 2


title: WT T cells, cultured 3 days with IL-6, replicate 2


title: STAT3-deficient T cells, cultured 3 days with IL-6 and TGFb, replicate 1


title: STAT3-deficient T cells, cultured 3 days with IL-6, replicate 2

source_name: STAT3-deficient T cells activated in with a STAT3-activating cytokine IL-6


title: trained myog-deleted mouse gastrocnemius, biological rep1

status: Public on May 29 2010

city: HOUSTON

first: JAMES

middle: ERIC

last: MEADOWS

state: TX

address: 1515 HOLCOMBE BLVD

department: BIOCHEMISTRY

institute: MD ANDERSON CANCER CENTER

description: Myogenin gene deletion performed at 3 months of age

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChiP Scanner 3000, 7G Upgrade

data_processing: The data were analyzed with Genespring version 11.0.1 (RMA algorithm). The baseline transformation was set to the median of all samples. Unpaired two-tailed t-tests were performed and significance cutoff was set to p<0.05. Fold-change cutoff was set to FC>=1.4

source_name: Gastrocnemius (Medial & Lateral), trained, 6 months

label_protocol: Biotinylated cRNA were prepared according to the small-sample Affymetrix protocol from 100 ng total RNA (Eukaryotic Small Sample Target Labeling Technique Manual, 2001, Affymetrix).

growth_protocol: Mice were allowed unrestricted access to voluntary exercise running wheels for 6 months and then subjected to an involuntary treadmill for 2 weeks to determine overall exercise endurance.

treatment_protocol: Tamoxifen-induced myogenin gene deletion performed at 2-3 months of age.  Unrestricted access to exercise running wheels between 2-3  months of age to 8-9 months of age.  Involuntary treadmill running for 2 weeks following training.

value: Mixed SV/129 & C57BL/6

tag: sex

value: Female

value: Gastrocnemius (Medial & Lateral)

value: Myog-deleted

value: 8 months

tag: training

value: 6 months of training


title: STAT3-deficient T cells, cultured 3 days with IL-6, replicate 1


title: trained myog-deleted mouse gastrocnemius, biological rep3


title: trained myog-deleted mouse gastrocnemius, biological rep2


title: trained wild type mouse gastrocnemius, biological rep3

value: Wild type


title: trained wild type mouse gastrocnemius, biological rep1


title: trained wild type mouse gastrocnemius, biological rep2


title: Schistosomulum 1

city: Sao Carlos

first: Ricardo

last: DeMarco

state: Sao Paulo

address: Av trabalhador Sao Carlense 400

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Raw data were subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.31 (Roche NimbleGen, Inc.). Processed data is represented in log2 scale. Probe level data were summarised to yield gene level data and differential expression analysis was carried out using Limma (Smyth Stat Appl Genet Mol Biol 3 article 3)

organism: Schistosoma mansoni

source_name: Day 3 schistosomula were obtained by mechanically transforming cercariae, and culturing the bodies for 3 days at 37°C in M169 media

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) with the inclusion of high salt solution at the isopropanol precipitation step. Glycoblue was also included at this point to aid visualisation and recovery of the RNA pellet. Double-stranded cDNA was synthesised

tag: life cycle stage

value: Day 3 in vitro cultured schistosomula


title: Cercaria 2

source_name: Cercariae were obtained by exposing infected snails to bright lights for 2 hours, concentrated by cooling on ice, and washed twice with water

value: Cercariae


title: Egg 1

source_name: Eggs were obtained from livers of infected mice 7 weeks post infection. They were washed carefully in saline.

value: Eggs


title: Snail 3

organism: Biomphalaria glabrata

source_name: Snail

value: not applicable


title: Sample48_Mock_cy5_Treated_cy3_MDS

city: Rockville

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42°C for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95ºC prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42°C.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air, and scanned with an Axon GenePix 4000 scanner (http://intranet.jtc.jcvsf.org/sops/M008.pdf).  All wash buffers were supplemented with 1-ml of 0.1M DTT per liter of wash buffer.

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42°C for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95ºC prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42°C.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner.

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html)). The mev file generated from MIDAS were used to generate the data table, where VALUE is the log2 (QUERY/REF), i.e., the base 2 logarithm of the ratio of QUERY_INTEGRATED_INTENSITY over REF_INTEGRATED_INTENSITY, QUERY_INTEGRATED_INTENSITY is the geometric mean of the integrated intensities (IA or IB) of in-slide replicates for the query channel, and REF_INTEGRATED_INTENSITY is the geometric mean of the integrated intensities (IA or IB) of in-slide replicates for the reference channel.

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans UA159 without CSP

growth_protocol: Cells were grown in Todd-Hewitt–Yeast Extract (THYE) broth at 37°C without CSP to mid-log phase.

extract_protocol: Cells were pelleted and stored at -20ºC until RNA extraction, using the Ambion MirVANA RNA kit (Austin, TX). RNA quantity and quality was assessed by measuring total RNA using a nanodrop 1000 spectrophotometer (Thermo Scientific) and visualizing RNA on an agarose gel.  Purified RNA was stored at -80 degree Celsius.

treatment_protocol: Cell culture growing in the absence of Competence stimulating peptide (CSP).

tag: strain

tag: sample no

tag: csp

value: no

source_name: Streptococcus mutans UA159 with CSP

label_protocol: DNA probes for microarray experiments were generated by adding 2 µg of total RNA in a mixture containing 6 µg of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42°C overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70°C for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Cells were grown in Todd-Hewitt–Yeast Extract (THYE) broth at 37°C with 2 μM CSP to mid-log phase.

treatment_protocol: Cell culture growing in the presence of Competence stimulating peptide (CSP).

value: yes


title: Germ ball 1

source_name: Germ balls recovered by careful dissection of Biomphalaria glabrata snails 21-26 days after infection with 40 miracidia each

value: Germ balls


title: Egg 2

growth_protocol: Eggs were obtained from livers of infected mice 7 weeks post infection. They were washed carefully in saline.


title: Germ ball 2

growth_protocol: Germ balls recovered by careful dissection of Biomphalaria glabrata snails 21-26 days after infection with 40 miracidia each


title: Schistosomulum 3

growth_protocol: Day 3 schistosomula were obtained by mechanically transforming cercariae, and culturing the bodies for 3 days at 37°C in M169 media


title: Sample32_Mock_cy5_Treated_cy3_MDS

label_protocol: DNA probes for microarray experiments were generated by adding 2 µg of total RNA in a mixture containing 6 µg of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42°C overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70°C for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA)


title: Sample31_Mock_cy5_Treated_cy3_MDS


title: Snail 1


title: Cercaria 1

growth_protocol: Cercariae were obtained by exposing infected snails to bright lights for 2 hours, concentrated by cooling on ice, and washed twice with water


title: Schistosomulum 2


title: Cercaria 3


title: Snail 2


title: Egg 3


title: Sample969_Mock_cy3_Treated_cy5_MDS


title: Sample47_Mock_cy3_Treated_cy5_MDS


title: Germ ball 3


title: 4T1 biological replicate 4 (gene)

city: Montréal

first: Amandine

last: Bemmo

state: Québec

address: 740, Dr Penfield Avenue

department: Human Genetics

institute: McGill University

description: gene expression array

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Human Exon 1.0 ST array (Affymetrix) at 45˚C for 16-20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip® Hybridization, Wash and Stain kit, and the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: The Affymetrix Power Tools software package (Affymetrix) was used to quantile normalize the probe fluorescence intensities and to summarize the probe set (representing exon expression) and meta-probe set (representing gene expression) intensities. Transcript assignments were based on mm8 build. The library files for gene expression and exon expression are MoEx-1_0-st-v1.r2.dt1.mm8.core.mps.mask and MoEx-1_0-st-v1.r2.dt1.mm8.full.ps, respectively. Probeset intensities (exon data) : Probe logarithmic intensity error model (PLIER) for probe set intensities. The probeset_dabg.txt file on the Series record: Detection Above BackGround (DABG) statistics for probe set presence/absence. The meta probeset intensities (gene data): Iterative Probe logarithmic intensity error (ITER-PLIER) for meta-probe set intensities.

label_protocol: Biotin-labelled target for the microarray experiment were prepared using 1µg of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix)

growth_protocol: All cell lines were grown in DMEM supplemented with 10% fetal bovine serum, 10 mmol/L HEPES, 1 mmol/L sodium pyruvate, 1.5 g/L sodium bicarbonate, penicillin/streptomycin, and fungizone.

extract_protocol: Total RNA was purified using RNeasy Mini Kit Columns following the manufacturers instructions. We assessed The RNA quality using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Tumors were hybridized independently at the functional genomics facility of McGill University and Genome Quebec Innovation Centre (Montreal, Quebec, Canada).

treatment_protocol: Four mice were injected (1×10^-5 cells) with 168FARN, five mice with 4T07 and four mice with 4T01. Tumor volumes were calculated using the following formula: (?LW^2)/6, where L is the length and W is the width of the tumor. Tumors were surgically removed, using a cautery unit, once they reached a volume between 100 and 125 mm^3.


title: 4T07 biological replicate 1 (gene)

description: gene expression array


title: 4T1 biological replicate 1 (gene)

description: gene expression array


title: 4T1 biological replicate 2 (gene)

description: gene expression array


title: 4T1 biological replicate 3 (gene)

description: gene expression array


title: 4T07 biological replicate 2 (gene)

description: gene expression array


title: 4T07 biological replicate 3 (gene)

description: gene expression array


title: 4T07 biological replicate 4 (gene)

description: gene expression array


title: 168FARN biological replicate 4 (gene)

description: gene expression array


title: 168FARN biological replicate 2 (gene)

description: gene expression array


title: siRNA-IRF4-1 (HuT-102 cells + IRF4 siRNA)

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: HuT-102 cells, a human cutaneous T cell lymphoma, were transiently transfected with siRNAs against human IRF4. Cells were incubated for 60 h at 37°C. Total RNA samples were prepared from the cells.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: Affymetrix Expression Stat 5.0

source_name: Human cutaneous T cell lymphoma HuT-102 cells

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: cell type

value: cutaneous T cell lymphoma HuT-102 cells


title: Control-2 (HuT-102 cells + luciferase siRNA)

description: HuT-102 cells, a human cutaneous T cell lymphoma, were transiently transfected with siRNAs against firefly luciferase. Cells were incubated for 60 h at 37°C. Total RNA samples were prepared from the cells.


title: Sample967_Mock_cy3_Treated_cy5_MDS


title: gingival_fibroblast_59y_Female_Japanese

status: Public on May 28 2010

city: Nagoya

first: Ryuji

last: Kato

state: Aichi

address: Furocho, Chikusa-ku

department: Graduate School of Engineering

institute: Nagoya University

description: Gene expression data from primary cultured human fibroblasts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on Human Genome Focus Array (Affymetrix). Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using GeneChip Scanner 3000 7G

data_processing: The data were analyzed with ArrayAssist® (Stratagene) using software's default analysis settings and global scaling as normalization method(MAS5 selected). riefly, from 8,500 probes on the array, normalization and scaling (MAS5), flag-positive gene selection, unpaired t-test, and CV selection (<20) resulted in obtaining 5,284 genes to analyze. GO (Gene ontology) analysis was performed by the software’s default settings to find the gene group related to same category of biological function by searching the common key terms that had been reported with the genes.

source_name: Explant cultured human gingivel tissue

label_protocol: Biotinylated cRNA were synthesized according to GeneChip Eukaryotic Target Preparetion & Hybridization Manual.

growth_protocol: Dermal and gingival tissues were obtained from healthy volunteers whose informed consent was obtained according to the protocol approved by the ethics committee of Nagoya University Hospital.  After enzymatic digestion, tissues were cultured by explant primary culture and passaged in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine albumin at 37°C under the presence of 5% CO2 for about 4 weeks. Total mRNAs were extracted from cells between 4-5 passages.

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

tag: tissue origin

value: gingival

value: fibroblast


title: 168FARN biological replicate 3 (gene)

description: gene expression array


title: gingival_fibroblast_36y_Female_Japanese 2


title: dermal_fibroblast_69y_Female_Japanese

source_name: Explant cultured human dermal tissue

value: dermal


title: Control-1 (HuT-102 cells + luciferase siRNA)


title: gingival_fibroblast_38y_Female_Japanese

value: Female


title: 168FARN biological replicate 1 (gene)

description: gene expression array


title: gingival_fibroblast_40y_Female_Japanese


title: dermal_fibroblast_46y_Female_Japanese 2


title: dermal_fibroblast_68y_Female_Japanese


title: gingival_fibroblast_51y_Female_Japanese


title: gingival_fibroblast_56y_Male_Japanese

value: Male


title: siRNA-IRF4-2 (HuT-102 cells + IRF4 siRNA)


title: dermal_fibroblast_50y_Female_Japanese


title: gingival_fibroblast_36y_Female_Japanese


title: dermal_fibroblast_29y_Male_Japanese


title: dermal_fibroblast_41y_Male_Japanese


title: gingival_fibroblast_29y_Male_Japanese


title: dermal_fibroblast_36y_Female_Japanese


title: PPARgamma KO MEFs with wtPPARgamma treated with MRL24 rep3

city: Boston

first: Jang Hyun

last: Choi

address: 44 Binney st

description: Gene expression data from MEFs

hyb_protocol: The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45°C. The chip was then transferred to a fluidics instrument for washes to remove unbound cRNA. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were added using biotinylated anti-streptavidin antibody and SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values

label_protocol: cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).

growth_protocol: All cells were propagated in DMEM containing 10% fetal bovine serum.

extract_protocol: Trizol (Invitrogen) extraction, followed by purification using Quagen RNeasy column.

treatment_protocol: Adipocytes were treated with 1 uM rosiglitazone or MRL24 for 24h.

value: differentiated MEFs, adipocytes


title: PPARgamma KO MEFs with wtPPARgamma treated with MRL24 rep1

description: Gene expression data from MEFs


title: PPARgamma KO MEFs with wtPPARgamma treated with rosiglitazone rep3

description: Gene expression data from MEFs


title: PPARgamma KO MEFs with wtPPARgamma treated with rosiglitazone rep2

description: Gene expression data from MEFs


title: 4T07 biological replicate 4 (exon)

description: exon expression array


title: 4T07 biological replicate 1 (exon)

description: exon expression array


title: PPARgamma KO MEFs with wtPPARgamma treated with rosiglitazone rep1

description: Gene expression data from MEFs


title: PPARgamma KO MEFs with wtPPARgamma treated with MRL24 rep2

description: Gene expression data from MEFs


title: 168FARN biological replicate 4 (exon)

description: exon expression array


title: PPARgamma KO MEFs with mutPPARgamma rep3

description: Gene expression data from MEFs

source_name: PPARgamma KO MEFs with mutPPARgamma


title: PPARgamma KO MEFs with mutPPARgamma rep2

description: Gene expression data from MEFs


title: PPARgamma KO MEFs with wtPPARgamma rep2

description: Gene expression data from MEFs

source_name: PPARgamma KO MEFs with wtPPARgamma


title: 4T1 biological replicate 3 (exon)

description: exon expression array


title: PPARgamma KO MEFs with mutPPARgamma rep1

description: Gene expression data from MEFs


title: PPARgamma KO MEFs with wtPPARgamma rep3

description: Gene expression data from MEFs


title: 168FARN biological replicate 3 (exon)

description: exon expression array


title: 4T07 biological replicate 3 (exon)

description: exon expression array


title: 4T1 biological replicate 4 (exon)

description: exon expression array


title: KO liver-8 months

first: Chuxia

last: Deng

address: 9000 Rockville Pike

institute: NIDDK, National Institutes of Health

description: Gene expression from 3 pairs SIRT6Co/Co ;Alb-Cre mouse liver tissue at 8 months of age

hyb_protocol: Hybridization was done as defined in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay

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

data_processing: Array data were analyzed by Expression console 1.0v RMA quantification analysis.

source_name: Liver tissue

label_protocol: The amplified cDNA was labeled biotin for hybridization. Then the array was stained with streptavidine–phycoerythrine (SAPE)--> biotinylated anti-streptavidin (goat) antibody--> streptavidine–phycoerythrine (SAPE)

extract_protocol: RNA STAT-60 extraction of total RNA was performed according to the manufacturer's instructions.

value: Liver

value: 8 months

value: SIRT6Co/Co ;Alb-Cre


title: dermal_fibroblast_46y_Female_Japanese


title: 4T1 biological replicate 1 (exon)

description: exon expression array


title: 168FARN biological replicate 2 (exon)

description: exon expression array


title: WT liver-2 months

description: Gene expression from 3 pairs of WT SIRT6 mouse liver tissue at 2 months of age

value: 2 months

value: WT SIRT6


title: 4T07 biological replicate 2 (exon)

description: exon expression array


title: male biological replicate M3a

status: Public on May 27 2010

city: Arlington

first: Jeff

last: Demuth

email: jpdemuth@uta.edu, eprince@uta.edu

address: Box 19498 501 S. Nedderman Dr

institute: The University of Texas at Arlington

hyb_protocol: Performed by Roche NimbleGen http://www.nimblegen.com/products/exp/index.html

data_processing:
RMA normalization performed by Roche NimbleGen. Log2 values exported from ArrayStar 3.0.
http://www.dnastar.com/products/arraystar.php
http://www.nimblegen.com/products/exp/index.html

organism: Tribolium castaneum

source_name: 20 whole, virgin, adult males between 48 and 168 hours old

growth_protocol: Beetles grown on standard media (organic whole wheat flour with 5% Brewers yeast) at 29°C.

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: Grown with only male beetles.


title: CLL B-cell tel+ 29975902

city: Cardiff

first: Duncan

last: Baird

address: Heath Park

department: School of Medicine

institute: Cardiff University

hyb_protocol: Each labeled DNA was resuspended in 5.6ul Sample Tracking Control as provided in the manufacture's kit. Master mix hybridization buffer (provided in the kit) was prepared in an according to manufacture's protocol and 20ul hybridization solution was added to each sample pair. Sample tubes were placed at 42C for 5 minutes before loading onto HX3 mixer provided in the kit. Arrays were hybridized for 40-72 h at 42C in the hybridization system. The arrays slides were washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC as in manufacture's protocol.

scan_protocol: Arrays were scanned on at 532nm (for Cy3) and 635nm (for Cy5) using a MS 200 Microarray Scanner

data_processing: Arrays were processed using NimbleScan 2.5 software according to standard protocols. Normalization compensates for inherent differences in signal between Cy3 and Cy5 dyes. After combining the signal intensity information with the genomic coordinate information, and applying spatial correction (for 2.1M, 3x720K, and 12x135K arrays arrays), the Cy3 and Cy5 signal intensities are normalized to one another using qspline normalization (Workman C, et al., 2002).

source_name: CLL B-cell DNA dysfunctional telomeres

label_protocol: 500ng of test DNA and reference DNA were labeled with diluted Cy3-Random Nonamers and diluted Cy5-Random Nonamers in a 100ul reactions, respectively as in manufacture's protocol (http://www.nimblegen.com/products/lit/cgh_userguide_v6p0.pdf)

extract_protocol: 5x10E6 cells were lysed in 300ul of lysis buffer(100mM NaCl, 10mM Tris-HCl pH 8.0, 5mM EDTA pH8.0, 0.5% SDS and H2O) with 3ul RNase (10mg/ml) and 3ul Proteinase K (20mg/ml) at 45C for overnight. The Lysate was then incubated on rotator for 20 minutes with 300ul of ultra high purity phenol/chloroform and centrifuged at 13000g for 5 minutes. The aqueous and interphase layer was then transferred into a fresh tube containing 300ul of phenol/chloroform and incubated on rotator for another 20 minutes. The aqueous phase was then tranferred carefully to a fresh tube and mixed gently with 30ul 3M NaOAc pH 5.2.  The 100% ice cold Ethanol was added in the volume of 900ul and DNA pellet was left at -20C for at least 20 minutes. The pellet was then incubated on ice with 70% ice cold Ethanol and air dried. The DNA pellet was resuspended in 50ul of 10mM Tris-HCl pH 8.0.

value: B-cell

tag: disease status

value: CLL

tag: telomere dysfunction

tag: cll binet stage

value: C

source_name: Reference DNA

extract_protocol: Genomic DNA from six pooled male or female individuals was provided by NimbleGen and used as a common reference.

tag: sample type

value: pooled reference


title: female biological replicate F3b

department: Biology

scan_protocol: Performed by Roche NimbleGen http://www.nimblegen.com/products/exp/index.html

source_name: 20 whole, virgin, adult females between 48 and 168 hours old

treatment_protocol: Grown with only female beetles.


title: CLL B-cell tel+ 34641402

value: yes


title: male biological replicate M2

label_protocol:
Performed by Roche NimbleGen
http://www.nimblegen.com/products/exp/index.html


title: CLL B-cell tel+ 29976002


title: PHN_R3

city: Ottawa

first: Brandon

last: Smith

address: 1200 Montreal Road

department: Institute for Biological Sciences

institute: National Research Council Canada

description: no additional information

hyb_protocol: Labelled RNA samples were hybridized to microarrays in a 35 µl final volume composed of 400 mM Na2HPO4 (pH 7.0), 5% SDS, 0.8% BSA, and 12% formamide. Hybridisation mixtures were denatured at 95°C for 4 minutes and immediately pipetted onto glass slides covered with 22×25 mm LifterSlips (Erie Scientific Company, Portsmouth, NH). Hybridizations were performed in custom-made sealed chambers submerged in a 37°C water bath overnight (18 hours).  Slide washes were 3 min long: once in 2X SSC/0.025% SDS, three times in 0.8X SSC, and twice in cold 0.4X SSC. Immediately following the last wash, slides were dried by centrifugation.

scan_protocol: Slides were scanned with a ScanArray 5000XL (Packard BioScience, Meriden, CT) confocal scanner at 10 µm resolution.

data_processing: Microarray scans were analysed with QuantArray software version 3.0 (Packard BioScience, Meriden, CT) using an adaptive quantitation method. Spots of poor quality on the arrays were flagged for removal from the data processing. Cy3 mean pixel intensities were background subtracted, log transformed, and replicate spots on the arrays were averaged. Microarray data were normalised between arrays using a standard median centering procedure. miRNAs were considered expressed if their normalised log2 hybridisation signal was ≥ 2. Differentially-expressed miRNAs were identified using a SAM (significance analysis of microarrays) threshold of 5% and a fold-change of 2.

source_name: Primary Human Neurons

label_protocol: RNA labelling and hybridization to the microarrays was carried out using a method adapted from Thomson et al. 2004 (Thomson JM, Parker J, Perou CM, Hammond SM. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1: 47-53). Briefly, 10 or 25 µg total RNA was PEG-precipitated (as above), resuspended in 6 µl water, and mixed into a labelling reaction (final volume 10 µl) consisting of 500 ng 5’-phophate-cytidyl-uridyl-Cy3-3’ (Dharmacon, Chicago, IL), 10% DMSO, 0.1 mM ATP, 50 mM HEPES (pH 7.8), 3.5 mM DTT, 20 mM MgCl2, 0.1 µg BSA, and 20 U T4 RNA ligase (NEB, Ipswitch, MA). Reactions were incubated on ice in the dark for 2 hours before precipitation with 0.27 M sodium acetate, 20 µg glycogen, and 2.7 volumes ethanol in a 200 µl final volume. Following 10 min incubation on ice and 10 min centrifugation, the pellet was washed in 70% ethanol, centrifuged 5 min, briefly dried, and resuspended in 6 µl water.

growth_protocol: Fresh primary human neurons (PH-N) from 21-week fetuses were obtained from ScienCell Research Laboratories (Carlsbad, CA) and were directly pelleted for RNA extraction

extract_protocol: Total RNA was isolated from the cells using TRI-Reagent (Molecular Research Center, Cincinnati, OH) according to the manufacturer’s instructions. High molecular-weight RNAs were removed by precipitation with 12.5% PEG-8000 and 1.25 M NaCl.

value: Primary Human Neurons from 21-week fetuses


title: male biological replicate M3b


title: WT liver-8 months

description: Gene expression from 3 pairs WT SIRT6 mouse liver tissue at 8 months of age


title: female biological replicate F3a


title: CLL B-cell tel+ 29975602

value: A


title: CLL B-cell tel+ 34641502


title: female biological replicate F4


title: CLL B-cell tel- 34637002

source_name: CLL B-cell DNA stable telomeres

value: no


title: CLL B-cell tel- 34637202


title: male biological replicate M1


title: PPARgamma KO MEFs with wtPPARgamma rep1

institute: Dana-Farber Cancer Institute

description: Gene expression data from MEFs


title: CLL B-cell tel+ 29975802


title: CLL B-cell tel- 29975702


title: PHN_R1

description: no additional information


title: PHAe_R1

description: no additional information

source_name: Primary Human Embryonic Astrocytes

growth_protocol: Frozen primary human embryonal astrocytes (PH-Ae) from 9-10 week embryos were received from StemCell Technologies (Vancouver, BC, Canada) and were cultured as recommended by the supplier until harvest for RNA extraction.

value: Primary Human Astrocytes from 9-10 week embryos


title: PHN_R2

description: no additional information


title: PHAe_R3

description: no additional information


title: PHAf_R12

description: no additional information

source_name: Primary Human Fetal Astrocytes

growth_protocol: Frozen primary human fetal astrocytes (PH-Af) from 20-21 week fetuses were received from ALLCELLS (Emeryville, CA) and cultured in Astrocyte Medium provided by the company. Cells were then harvested for RNA extraction.

value: Primary Human Astrocytes from 20-21-week fetuses


title: PHAe_R2

description: no additional information


title: PHAf_R10

description: no additional information


title: PHAf_R9

description: no additional information


title: PHAf_R8

description: no additional information


title: HF-23896-(1), Agilent

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: Tumor vs. Normal

hyb_protocol: Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol

scan_protocol: Agilent's user manual (Agilent scanner)

data_processing: Tumor samples were assayed on Agilent Human Genome CGH 244A Microarrays. Human male genomic DNA (Promega P/N G1471) was used as reference.  Individual log2 ratios of background subtracted signal intensities were obtained from the Agilent Feature Extraction software version 9.5. The log2 ratios were centered to a median of zero and the resulting log2 ratio values for each probe were segmented using GLAD [3]. All probes within the genomic bounds of a given GLAD-derived segment were given the mean copy number value of probes within that segment.

label_protocol: Agilent's Genomic DNA Labeling Kit Plus

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

tag: organ

value: Lung Cancer

source_name: male genomic DNA (Promega P/N G1471)

tag: reference

value: male genomic DNA (Promega P/N G1471)


title: PHAf_R7

description: no additional information


title: female biological replicate F2


title: PHAf_R5

description: no additional information


title: PHAf_R6

description: no additional information


title: PHAf_R4

description: no additional information


title: PHAf_R11

description: no additional information


title: PHAf_R3

description: no additional information


title: PHAf_R1

description: no additional information


title: PHAf_R2

description: no additional information


title: NT2_N_R2

description: no additional information

source_name: Ntera2/D1 derived Neurons

growth_protocol: 28-day RA-treated NT2 cells were trypsinized, transferred to new T-75 flasks, and grown for 9 days in RA-free HG/DMEM supplemented with 5% FBS and mitotic inhibitors (1µM cytosine β-D-arabinofuranoside, 10µM uridine, and 10µM 5-Fluoro-2’deoxyuridine). After 9 days, neurons (NT2-N) were separated from underlying astrocytes (NT2-A) by gentle trypsinization (0.015% v/v) and mechanical shake-off and were replated in poly-D-lysine and Matrigel-coated 10 cm plates. They were grown for one week in conditioned medium before being harvested for RNA extraction

value: Ntera2/D1-derived Neurons


title: 4T1 biological replicate 2 (exon)

description: exon expression array

tag: cell line


title: CLL B-cell tel- 29975502

value: Male

value: B


title: NT2_N_R1

description: no additional information


title: 168FARN biological replicate 1 (exon)

description: exon expression array


title: NT2_28D_R2

description: no additional information

source_name: Ntera2/D1 cells, 28 Day Retinoic Acid treated

growth_protocol: Human embryonal teratocarcinoma Ntera2/D1 (NT2) cells (Stratagene, La Jolla, CA) were cultured in high glucose Dulbecco’s modified Eagle’s medium (HG/DMEM, Invitrogen, Burlington, Ontario, Canada) supplemented with 10% fetal bovine serum (FBS, Wisent, Saint-Jean, Quebec, Canada).

treatment_protocol: The cells were seeded at a density of 2 × 106 cells per T75 flask and treated with 10µM all-trans retinoic acid (RA, Sigma, Oakville, Ontario, Canada) in fresh medium every two days during a 28-day differentiation timecourse. Cells were harvested by tripsinization and centrifugation 0, 2, 4, 6, 8, 12, 14, 21, and 28 days following addition of RA. Time-course experiments were repeated several times to ensure multiple biological replicates for microarray analysis.

tag: agent

value: Retinoic Acid

tag: time

value: 28 Days


title: whole blood, Carrier replicate 6, test set, batch 3

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HuGene 1.0 ST v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with fluidics protocol FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner using GCOS version 1.4 software with default settings.

data_processing: Raw CEL-files were imported into Expression Console 1.0 (Affymetrix). PLIER was used for array normalization and signal calculation independently for each hybridization batch. Normalized signal values were imported into Genespring GX 7.3 (Agilent Technologies) and gene wise Z-score normalization across all samples of each hybridization batch was applied.

source_name: whole blood

label_protocol: Samples were enzymatically amplified, fragmented and biotinylated using GeneChip® Whole Transcript (WT) Sense Target Labeling Kit (Affymetrix).

extract_protocol: Whole blood was collected in BD PAXgene Blood RNA Tubes (BD Diagnostics) according the recommendations of the manufacturer. RNA was extracted with PAXGene Blood RNA Kit (Qiagen) according to the manfacturer.

tag: dyt1 mutation status

value: delta GAG

tag: dystonia

value: Carrier

tag: hybridization batch

tag: dataset

value: test set


title: whole blood, Carrier replicate 5, test set, batch 3


title: whole blood, symptomatic replicate 8, test set, batch 3

value: symptomatic


title: whole blood, Carrier replicate 4, test set, batch 3


title: whole blood, control replicate 5, test set, batch 3

value: WT

value: control


title: whole blood, Carrier replicate 3, test set, batch 3


title: KO liver-2 months

description: Gene expression from 3 pairs SIRT6Co/Co ;Alb-Cre mouse liver tissue at 2 months of age

tag: tissue

value: Liver

tag: age

value: 2 months

tag: genotype

value: SIRT6Co/Co ;Alb-Cre


title: whole blood, symptomatic replicate 6, test set, batch 3


title: whole blood, symptomatic replicate 7, test set, batch 3


title: NT2_A_R2

description: no additional information

source_name: Ntera2/D1 derived Astrocytes

growth_protocol: 28-day RA-treated NT2 cells were trypsinized and grown overnight in RA-free HG/DMEM supplemented with 5% FBS. Neurons were removed by mechanical shake-off and the astrocytic cells remaining in the flask following NT2-N shake-off were incubated overnight before replating following a second NT2-N shake-off to remove the last of the neurons. NT2-A cells were harvested for RNA extraction 2, 4, and 8 weeks after the 28th day of RA treatment.

tag: cell type

value: Ntera2/D1-derived Astrocytes


title: NT2_A_R1

description: no additional information


title: NT2_28D_R3

description: no additional information


title: NT2_21D_R3

description: no additional information

source_name: Ntera2/D1 cells, 21 Day Retinoic Acid treated

value: 21 Days


title: male biological replicate M4

tag: strain


title: whole blood, control replicate 4, test set, batch 3


title: whole blood, control replicate 3, test set, batch 3


title: NT2_21D_R1

description: no additional information


title: NT2_28D_R1

description: no additional information


title: NT2_14D_R1

description: no additional information

source_name: Ntera2/D1 cells, 14 Day Retinoic Acid treated

value: 14 Days


title: NT2_12D_R2

description: no additional information

source_name: Ntera2/D1 cells, 12 Day Retinoic Acid treated

value: 12 Days


title: NT2_12D_R3

description: no additional information


title: NT2_21D_R2

description: no additional information


title: NT2_12D_R1

description: no additional information


title: NT2_14D_R3

description: no additional information


title: NT2_8D_R5

description: no additional information

source_name: Ntera2/D1 cells, 8 Day Retinoic Acid treated

value: 8 Days


title: NT2_8D_R6

description: no additional information


title: whole blood, control replicate 6, test set, batch 3


title: whole blood, symptomatic replicate 5, test set, batch 3


title: whole blood, symptomatic replicate 4, test set, batch 3


title: whole blood, control replicate 2, test set, batch 3


title: whole blood, symptomatic replicate 3, test set, batch 3


title: NT2_8D_R4

description: no additional information


title: whole blood, control replicate 1, test set, batch 3


title: NT2_8D_R2

description: no additional information


title: whole blood, symptomatic replicate 2, test set, batch 3


title: NT2_8D_R3

description: no additional information


title: whole blood, Control replicate 9, training set, batch 2

value: Control

value: training set


title: whole blood, Control replicate 8, training set, batch 2


title: NT2_8D_R1

description: no additional information

value: Retinoic Acid


title: female biological replicate F1


title: whole blood, Carrier replicate 2, test set, batch 3

value: delta GAG


title: whole blood, symptomatic replicate 1, test set, batch 3


title: whole blood, Control replicate 6, training set, batch 2


title: whole blood, Carrier replicate 1, test set, batch 3

value: Carrier


title: whole blood, Control replicate 7, training set, batch 2


title: NT2_6D_R2

description: no additional information

source_name: Ntera2/D1 cells, 6 Day Retinoic Acid treated

value: 6 Days


title: whole blood, Control replicate 4, training set, batch 2


title: NT2_6D_R1

description: no additional information


title: NT2_4D_R1

description: no additional information

source_name: Ntera2/D1 cells, 4 Day Retinoic Acid treated

value: 4 Days


title: NT2_4D_R2

description: no additional information


title: NT2_2D_R2

description: no additional information

source_name: Ntera2/D1 cells, 2 Day Retinoic Acid treated

value: 2 Days


title: NT2_2D_R1

description: no additional information


title: whole blood, Control replicate 5, training set, batch 2

value: WT


title: NT2_undiff_R3

description: no additional information

source_name: Ntera2/D1 cells, untreated

value: untreated

value: control


title: NT2_undiff_R4

description: no additional information