title: GFPlow vs GFPhi sort_2

source_name: FACS sorted epithelial intestinal cells from Lgr5-EGFP-ires-CreERT2 mice

growth_protocol: Cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice were used, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlow).

extract_protocol: Rna was isolated using Trizol (Invitrogen)

tag: genome/variation

value: epithelial intestinal cells

tag: lgr5 expression level


title: Lgr5-GFP_high adenoma vs Lgr5-GFP_low adenoma array_1 dyeswap

status: Public on Aug 13 2012

type: RNA

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using featuere extraction (V.9.5.3, Agilent Technologies).

molecule: total RNA

organism: Mus musculus

source_name: FACS sorted intestinal adenoma cells from induced Apc_fl/fl-Lgr5-EGFP-ires-CreERT2 mice

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: RNA was isolated from two FACS sorted cell populations of intestinal adenomas from induced Apc_fl/fl-Lgr5_EGFP_ires_CreERT2 mice : adenoma GFP-high cells and adenoma GFP-low cells.

extract_protocol: RNA was isolated using Trizol (Invitrogen).

tag: gfp level

value: low

tag: strain

value: high


title: Lgr5-GFP_high adenoma vs Lgr5-GFP_low adenoma array_1


title: WAT_Nonobese [469]

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probe set scaling to target signal 100. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median

label: biotin

organism: Homo sapiens

source_name: Abdominal subcutaneous adipose tissue

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: RNA was extracted using the Nucleospin RNA11 kit (Macherey-Nagel, Duren, Germany). RNA samples were treated with RNase-free DNase (Macherey-Nagel).

tag: tissue

value: White adipose tissue

tag: genotype

value: female

tag: age


title: WAT_Nonobese [404]


title: Lgr5-GFP_high adenoma vs Lgr5-GFP_low adenoma array_2


title: Knockin.2.1.2 [methylation]

type: genomic

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

country: USA

institute: Emory University

description: HCT116 IDH1 R132H heterzygous knockin

scan_protocol: Followed the manufacturer's (Illumina) specifications on an iScan

data_processing: Data were interpreted in GenomeStudio v2010.3 Methylation Module 1.8.5 and exported for analysis

label: biotin nucleotide or dinitrophenyl labeled

molecule: genomic DNA

source_name: cell culture

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

growth_protocol: Cell lines were cultured in McCoy’s 5A Medium supplemented with 10% FBS. All cells were maintained in 5% CO2 at 37°C

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen)

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: cell line

tag: genotype/variation

value: IDH1 R132H


title: Day 3 post-carbon depletion, biological replicate 2/2

city: Leiden

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: The RMA Bioconductor package was used for data processing

label: Biotin

organism: Aspergillus niger

source_name: Mycelial biomass

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol:
Conidial suspensions for inoculation of bioreactor cultures were prepared by growing the A. niger laboratory strain N402 (cspA1 derivative of ATCC9029) (Bos et al., 1988) on solidified (1.5% agar) complete medium (CM) for three days at 30◦C in the dark. Spores were harvested with sterile physiological salt solution (0.9% NaCl) and filtered through Myracloth (Calbiochem, San Diego, CA, USA) to retain mycelial debris and solidified medium. CM contained per liter: 10 g glucose, 6 g NaNO3 , 1.5 g KH2PO4 , 0.5 g KCl, 0.5 g MgSO4 · 7H2O, 1 g casamino acids, 5 g yeast extract and 1 ml trace metal solution. e pH was adjusted to 5.8 with NaOH. e trace metal solution, modi ed from Vishniac et al. (1957), contained per liter: 10 g EDTA, 4.4 g ZnSO4 · 7H2O, 1.01 g MnCl2 · 4H2O, 0.32 g CoCl2 · 6H2O, 0.315 g CuSO4 · 5H2O, 0.22 g (NH4) · 6Mo7O24 · 4H2O, 1.47 g CaCl2 · 2H2O and 1 g FeSO4 · 7H2O. Minimal medium (MM) for bioreactor cultivations contained per liter: 4.5 g NH4Cl, 1.5 g KH2PO4 , 0.5 g KCl, 0.5 g MgSO4 · 7H2O and 1 ml trace metal solution. e pH was set to 3 with HCl. Aer autoclavation, 16 ml of heat-sterilized 50% (w/v) maltose monohydrate solution were added per kg of MM.
Batch cultures were performed in 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific) as previously described by Jørgensen et al. (2010). Briefly, autoclaved bioreactor vessels were filled with 5 L (kg) sterile MM. During cultivation at 30◦C, the controller was set to maintain pH 3 by addition of titrants (2 M NaOH and 1 M HCl). Sterile air was supplied at a rate of 1 L per min. Prior to inoculation, 1.5 ml of 10% (w/v) filter-sterilized yeast extract was added to enhance conidial germination. Cultures were inoculated with freshly harvested spore suspensions to give 10 to the power of 9 conidia per liter. To reduce the loss of hydrophobic conidia during germination, the stirrer speed was set to 250 rpm and the culture was aerated via the headspace during the first six hours aer inoculation. Subsequently, the stirrer speed was increased to 750 rpm, 0.5 ml of polypropyleneglycol P2000 was added as antifoam agent and air was supplied via the sparger.

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen).

treatment_protocol: Day 1 post-carbon starvation during maltose-limited submerged batch cultivation

value: N402 wild-type (ATCC 64974)

tag: culture age

value: day 3 post-carbon depletion


title: GFPlow vs GFPhi sort_1

tag: cell type


title: Day 6 post-carbon depletion, biological replicate 1/2

value: day 6 post-carbon depletion


title: Day 3 post-carbon depletion, biological replicate 1/2


title: Knockin.2.1.1 [methylation]

description: HCT116 IDH1 R132H heterzygous knockin

hyb_protocol: Followed the manufacturer's (Illumina) specifications


title: GFPhi vs GFPlow sort_2


title: GFPhi vs GFPlow sort_1


title: Day 1 post-carbon depletion, biological replicate 2/2

value: day 1 post-carbon depletion


title: Knockin.1.2.2 [methylation]

description: HCT116 IDH1 R132H heterzygous knockin


title: WAT_Nonobese [134]


title: WAT_Nonobese [136]


title: Day 1 post-carbon depletion, biological replicate 1/2


title: Knockin.1.1.1 [methylation]

description: HCT116 IDH1 R132H heterzygous knockin


title: WAT_Nonobese [199]


title: HOG.IDH1.Wtplus [methylation]

description: HOG overexpressing IDH1 Wt

value: HOG

value: IDH1 wild-type plus


title: Knockin.1.2.1 [methylation]

description: HCT116 IDH1 R132H heterzygous knockin


title: WAT_Obese [126]


title: HCT116.Parent1.4 [methylation]

description: HCT116 wild-type parent

value: IDH1 wild-type


title: WAT_Nonobese [101]


title: Hpl1 Hpl2 KO 1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Hpl1 Hpl2 KnockOut Mutant Replicate 1

hyb_protocol: After a two-hour reaction, 1.5 μg of purified, Cy3-labeled cRNA were hybridized to an oligonucleotide C. elegans Microarray (015061, 4x44K, Agilent Technologies) for 17 hours at 65˚C, then washed according to manufacturer's protocol.

scan_protocol: Slides were scanned using an Agilent G2505B scanner, and data were extracted using the Feature Extraction software version 9.5 (Agilent Technologies).

data_processing: Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

organism: Caenorhabditis elegans

source_name: Hpl1 Hpl2 KnockOut Mutant Replicate 1

label_protocol: 600 ng of total RNA were reverse-transcribed and amplified, thereby incorporating Cyanine 3-CTP nucleotides, using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent One-Color Microarray-Based Gene Expression Analysis, protocol version 5.5, February 2007; Agilent Technologies).

growth_protocol: For the microarray studies 80 to 100 L4 and young adult worms raised at 21°C were used.

extract_protocol: Total RNA was extracted using the standard Trizol method following the manufacturer’s protocol.

value: whole organism


title: HOG.IDH1.R132Hplus [methylation]

description: HOG overexpressing IDH1 R132H

value: IDH1 R132H plus


title: Knockin.1.1.2 [methylation]

description: HCT116 IDH1 R132H heterzygous knockin


title: Lgr5ki_GFPbrigth_sort_c

hyb_protocol: cRNA was hybridized to Affymetrix Mouse HT MG-430 PM plate arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: The expression data extracted from the raw celfiles  were  normalized with the RMA-sketch algorithm from Affymetrix Power Tools. (All) Data were analyzed using the R2 web application, which is freely available at (http://r2.amc.nl).

source_name: FACS sorted epithelial intestinal cells cells from Lgr5-EGFP-ires-CreERT2 mice

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 100-300ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol.

growth_protocol: Sorted cells of intestines from Lgr5-EGFP-ires-CreERT2 mice expressing GFP under the control of the Lgr5 promoter were used. RNA was isolated from three independent FACS runs from two different cell populations: one expressing GFP at high levels (GFPbright) and the other expressing GFP at low levels (GFPdim).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,


title: Hpl1 Hpl2 His24 KO 2

description: Hpl1 Hpl2 His24 KnockOut Mutant Replicate 2


title: Lgr5ki_GFPdim_sort_c


title: Hpl1 Hpl2 His24 KO 1

description: Hpl1 Hpl2 His24 KnockOut Mutant Replicate 1


title: WAT_Nonobese [43]


title: Hpl1 Hpl2 KO 2

description: Hpl1 Hpl2 KnockOut Mutant Replicate 2

source_name: Hpl1 Hpl2 KnockOut Mutant Replicate 2


title: WAT_Obese [48]


title: WAT_Nonobese [24]


title: WAT_Nonobese [83]


title: Lgr5ki_GFPbrigth_sort_b


title: Lgr5ki_GFPdim_sort_b


title: HCT116.Parent1.2 [methylation]

description: HCT116 wild-type parent


title: Hpl2 His24 KO 1

description: Hpl2 His24 KnockOut Mutant Replicate 1

source_name: Hpl2 His24 KnockOut Mutant Replicate 1


title: Lgr5ki_GFPbrigth_sort_a


title: Hpl1 His24 KO 1

description: Hpl1 His24 KnockOut Mutant Replicate 1

source_name: Hpl1 His24 KnockOut Mutant Replicate 1


title: HCT116.Parent1.3 [methylation]

description: HCT116 wild-type parent


title: HCT116.Parent1.1 [methylation]

description: HCT116 wild-type parent


title: Hpl1 His24  KO 2

description: Hpl1 His24 KnockOut Mutant Replicate 2

source_name: Hpl1 His24 KnockOut Mutant Replicate 2


title: ARD 534_b

status: Public on Aug 12 2012

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: PAIS (AIS3, Sinnecker classification); age: 28 months; Holterhus et al., BMC Genomics 2007

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2, Average Beta

label: Cy5 and Cy3

source_name: ARD 534_b, genomic DNA, second hybridization

label_protocol: Standard Illumina Protocol

growth_protocol: as described before (Holterhus et al. BMC Genomics 8,376; 2007)

extract_protocol: genomic DNA was extracted from genital fibroblast cell lines using Qiagen DNeasy Blood & Tissue Kit according to Qiagen's instruction

value: genital fibroblast cell line

tag: phenotype

value: AIS

tag: classification

value: PAIS (AIS3, Sinnecker classification)

value: 28 months

tag: reference

value: Holterhus et al., BMC Genomics 2007


title: ARD 465_b

description: CAIS (AIS5, Sinnecker classification); age: 65 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 465_b, genomic DNA, second hybridization

value: CAIS (AIS5, Sinnecker classification)

value: 65 months


title: ARD 407_b

description: PAIS (AIS2, Sinnecker classification); age: 12 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 407_b, genomic DNA, second hybridization

value: PAIS (AIS2, Sinnecker classification)

value: 12 months


title: ARD 465_a

source_name: ARD 465_a, genomic DNA, first hybridization


title: ARD 534_a

source_name: ARD 534_a, genomic DNA, first hybridization


title: Hpl2 His24 KO 2

description: Hpl2 His24 KnockOut Mutant Replicate 2

source_name: Hpl2 His24 KnockOut Mutant Replicate 2


title: WAT_Nonobese [13]

value: White adipose tissue

value: female


title: Lgr5ki_GFPdim_sort_a

value: low


title: Scrotum 1_a

description: male control; age: 360 months; Holterhus et al., BMC Genomics 2007

source_name: Scrotum 1_a, genomic DNA, first hybridization

value: control

value: male control

value: 360 months


title: Scrotum 13_b

description: male control; age: 697 months

source_name: Scrotum 13_b, genomic DNA, second hybridization

value: 697 months


title: ARD 407_a

source_name: ARD 407_a, genomic DNA, first hybridization


title: Scrotum 8_b

description: MAIS (AIS1, Sinnecker classification); age: 372 months; Holterhus et al., BMC Genomics 2007

source_name: Scrotum 8_b, genomic DNA, second hybridization

value: MAIS (AIS1, Sinnecker classification)

value: 372 months


title: Scrotum 13_a

description: male control; age: 697 months

source_name: Scrotum 13_a, genomic DNA, first hybridization

value: genital fibroblast cell line


title: Scrotum 12_b

description: male control; age: 110 months; Holterhus et al., BMC Genomics 2007

source_name: Scrotum 12_b, genomic DNA, second hybridization

value: 110 months


title: Scrotum 15_b

description: male control; age 62 months

source_name: Scrotum 15_b, genomic DNA, second hybridization

value: 62 months


title: Scrotum 9_a

description: male control; age: 408 months; Holterhus et al., BMC Genomics 2007

source_name: Scrotum 9_a, genomic DNA, first hybridization

value: 408 months

value: Holterhus et al., BMC Genomics 2007


title: Scrotum 15_a

description: male control; age 62 months

source_name: Scrotum 15_a, genomic DNA, first hybridization


title: Scrotum 11_a

description: male control; age: 386 months; Holterhus et al., BMC Genomics 2007

source_name: Scrotum 11_a, genomic DNA, first hybridization

value: 386 months


title: Scrotum 11_b

source_name: Scrotum 11_b, genomic DNA, second hybridization


title: Scrotum 5_a

description: male control; age: 19 months; Holterhus et al., BMC Genomics 2007

source_name: Scrotum 5_a, genomic DNA, first hybridization

value: 19 months


title: Scrotum 12_a

source_name: Scrotum 12_a, genomic DNA, first hybridization


title: Scrotum 8_a

source_name: Scrotum 8_a, genomic DNA, first hybridization

value: AIS


title: WAT_Nonobese [202]

source_name: Abdominal subcutaneous adipose tissue

value: White adipose tissue


title: Scrotum 5_b

source_name: Scrotum 5_b, genomic DNA, second hybridization


title: WAT_Nonobese [398]

value: female


title: Scrotum 4_b

description: male control; age: 15 months; Holterhus et al., BMC Genomics 2007

source_name: Scrotum 4_b, genomic DNA, second hybridization

value: 15 months


title: Scrotum 3_b

description: male control; age: 151 months

source_name: Scrotum 3_b, genomic DNA, second hybridization

value: control

value: 151 months


title: Scrotum 9_b

source_name: Scrotum 9_b, genomic DNA, second hybridization

value: male control


title: Scrotum 1_b

source_name: Scrotum 1_b, genomic DNA, second hybridization

value: 360 months


title: Scrotum 3_a

description: male control; age: 151 months

source_name: Scrotum 3_a, genomic DNA, first hybridization


title: Scrotum 4_a

source_name: Scrotum 4_a, genomic DNA, first hybridization


title: 95E1022

description: PAIS (AIS2, Sinnecker classification); age: 76 months; mutation in AR locus: Y571H, 2073T>C

source_name: 95E1022, genomic DNA

value: PAIS (AIS2, Sinnecker classification)

value: 76 months

tag: genetic variation

value: mutation in AR locus:Y571H, 2073T>C


title: brain_treatment_rep2

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with the rank invariant normalization in the Illumina BeadStudio 1.5.1.3 software

source_name: brain, treatment

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Mice were given a normal diet for six weeks

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer

treatment_protocol: Control group was given distilled water while treatment group was given OPP (1500 ppm GAE) as drinks ad libitum

value: BALB/c

value: 12 weeks

tag: gender

value: male

value: brain


title: 94E366

description: CAIS (AIS5, Sinnecker classification); age: 29 months; mutation in AR locus: 2128-11A>T

source_name: 94E366, genomic DNA

value: genital fibroblast cell line

value: CAIS (AIS5, Sinnecker classification)

value: 29 months

value: mutation in AR locus:2128-11A>T


title: 07E1268

description: PAIS (AIS3, Sinnecker classification); age: 18 months; mutation in AR locus: M742V

source_name: 07E1268, genomic DNA

value: AIS

value: PAIS (AIS3, Sinnecker classification)

value: 18 months

value: mutation in AR locus:M742V


title: brain_control_rep3

description: replicate 3

source_name: brain, control


title: brain_treatment_rep3

description: replicate 3


title: brain_control_rep2

description: replicate 2


title: 94RD0031

source_name: 94RD0031, genomic DNA


title: brain_control_rep1

description: replicate 1


title: 84RD0200

description: CAIS (AIS5, Sinnecker classification); age: 470 months; mutation in AR locus: 264GdeltaAT -> GGT

source_name: 84RD0200, genomic DNA

value: 470 months

value: mutation in AR locus:264GdeltaAT -> GGT


title: 01RD0259

description: PAIS; age: 206 months; mutation in AR locus: R855C

source_name: 01RD0259, genomic DNA

value: PAIS

value: 206 months

value: mutation in AR locus:R855C


title: 95RD0370

description: CAIS (AIS5, Sinnecker classification); age: 58 months; mutation in AR locus: L744F

source_name: 95RD0370, genomic DNA

value: 58 months

value: mutation in AR locus:L744F


title: C112

description: CAIS (AIS5, Sinnecker classification); age: 22 months; negative androgen binding

source_name: C112, genomic DNA

value: 22 months

value: negative androgen binding


title: 86E993

description: CAIS (AIS5, Sinnecker classification); age: 1 month; mutation in AR locus: R831X, AR-rec, exon 7

source_name: 86E993, genomic DNA

value: genital fibroblast cell line

value: 1 month

value: mutation in AR locus:R831X, AR-rec, exon 7


title: brain_treatment_rep1

description: replicate 1

value: BALB/c

value: 12 weeks

value: male

value: brain


title: C872_C812

description: CAIS (AIS5, Sinnecker classification); age: 2 months; mutation in AR locus: D695N, negative androgen binding

source_name: C872_C812, genomic DNA

value: AIS

value: CAIS (AIS5, Sinnecker classification)

value: 2 months

value: mutation in AR locus:D695N, negative androgen binding


title: ARD 1097_b

description: CAIS (AIS5, Sinnecker classification), age: 15 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 1097_b, genomic DNA, second hybridization

value: 15 months

value: Holterhus et al., BMC Genomics 2007


title: ARD 1144_b

description: CAIS (AIS5, Sinnecker classification); age: 51 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 1144_b, genomic DNA, second hybridization

value: 51 months


title: EB_E20_Hypoxia_Rep2

city: College Station

first: Mariappan

last: Muthuchamy

state: TX

address: 346A Reynolds Medical Building

department: Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

description: no additional information

hyb_protocol: Spotted arrays were incubated 45 min @48ºC with 35 rpm orbital agitation in prehybridization buffer (5X SSC , 0.1% SDS, 0.2% BSA) and then gently agitated 2 x 5 min in nuclease-free water followed by 2 x 5 min in isopropanol before being spun dry and maintained at 48ºC until hybridization. Equal mass, dye-coupled amplified RNA samples were mixed, column purified, and fragmented by hydrolysis (Fragmentation Reagents, Ambion, Austin, TX) prior to hybridization. The sample was then diluted to approximately 0.25X with Slidehyb Glass Hybridization buffer (Ambion) and applied directly to the array surface. The sample was then covered with a Hybrislip (Grace Biolabs, Bend, OR) and incubated for 18hrs @48ºC. Following hybridization, the arrays were gently agitated in 48ºC 1X SSC, 0.1% SDS for 6 min followed by room temperature 1X SSC, 0.1% SDS for 6 min followed room temperature 0.1X SSC for 2 x 6 min. The slides were then scanned immediately.

scan_protocol: The array is scanned at 635 nm and 532 nm wavelengths with a 10 µm resolution using GenePix 4000A scanner (Molecular Devices, Sunnyvale, CA). Image analysis and data extraction was performed using GenePix Pro 6.0 software (Molecular Devices).

data_processing: Unprocessed fluorescence intensity data was exported to Microsoft Excel 11.2 software for quality control evaluation. Data points were flagged as absent if the mean Cy3 (reference) feature intensity was significantly greater than the mean Cy3 background intensity (p<0.01, two-sample Welch t-test). The flagged raw feature and GenePix-specified local background intensity values for both dye channels were then imported into GeneSpring GX 7.3 software (Agilent Technologies) and normalized by 1) subtracting the local background intensity from the feature intensity for each channel, 2) setting all Cy5 measurements less than 1 to 1, 3) applying a per-gene and per-array, intensity-dependent (LOWESS) normalization utilizing 20% of data for smoothing and a Cy3 channel cutoff of 1, and 4) dividing each normalized Cy5:Cy3 ratio by the median normalized Cy5:Cy3 ratio for that gene across all arrays. Values obtained from replicate oligos on the same array were averaged. Because every sample is compared to the same arbitrary reference sample, the normalized Cy5:Cy3 ratios for each gene were directly comparable across all arrays. Those measurements flagged as absent in the reference channel were excluded from further analysis

source_name: Embryonic stem (ES) cells

label_protocol: Total cellular RNA was subjected to one round of linear amplification using the Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, TX). Briefly, mRNA is reverse transcribed to form cDNA containing a T7 promoter. After conversion of the cDNA to double-stranded DNA, T7 RNA Polymerase is used to generate numerous antisense copies of each mRNA. During the second round of in vitro transcription, 5-(3-aminoallyl)-UTP is incorporated into the amplified RNA, which is then chemically coupled to NHS esters of Cy3 or Cy5 dye (GE Healthcare, Piscataway, NJ).

extract_protocol: Total RNA was isolated from EBs (E10, E14, E17, E20) using RNA STAT-60 (Tel-Test Inc., Friendswood, TX). Briefly, cells were lysed in RNA STAT-60 by repetitive pipetting. Then chloroform was added to separate the lysate into an aqueous phase containing exclusively the total RNA and an organic phase containing DNA and other proteins. The total RNA was precipitated out by the addition of isopropanol, further washed with ethanol and solubilized in water. The RNA was subsequently DNase treated with DNA-freeTM (Ambion, Austin, TX) and analyzed for both quality and quantity using the Agilent 2100 Bioanalyzer and RNA6000 Nano LabChip Kit (Agilent Technologies).

treatment_protocol: Embryonic stem (ES) cells derived from 129/SvJ mice were cultured on a feeder layer of mitotically inactivated primary mouse embryonic fibroblasts, as we have described previously (Ezekiel UR et al. Electronic J. Biotech. 10: 328-335, 2007). The ES cells were maintained in an undifferentiated state by supplementing the ES media with leukemia inhibitory factor (LIF; Chemicon International, Temecula, CA). After three passages, ES cell differentiation was achieved by the removal of fibroblasts and LIF. At E3.5, EBs were maintained in normoxia (21% O2) in 100 mm bacterial culture plates (Corning Incorporated, Corning, NY) and cultured with Dulbecco modified Eagle medium (DMEM; Gibco, Eggenstein, Germany) containing 4,500 mg/L D-glucose, L-glutamine, Pyrodoxine Hydrochloride and 25 mM HEPES buffer. DMEM was additionally supplemented with 15% Fetal Bovine Serum (FBS; Gibco), 1.2 mM Sodium Pyruvate (Gibco), 0.12% Monothioglycerol (Sigma, St. Louis, Missouri) and 1% Antibiotic/Antimycotic (Gibco). For the microarray experiments, EBs were transferred on days E8, E12, E15 and E18 to hypoxia (2.6% O2) or maintained in normoxia. After 2 days of differential oxygen treatments, these EBs were analyzed at E10, E14, E17 and E20 respectively. Hypoxia was achieved in a humidified chamber flushed with 95% N2/5% CO2 until the oxygen level was stably maintained at 2.6%.

tag: timepoint

tag: stress

value: Hypoxia

source_name: Universal Mouse Reference RNA

value: Stratagene Universal Mouse Reference RNA


title: ARD 1144_a

source_name: ARD 1144_a, genomic DNA, first hybridization


title: EB_E20_Hypoxia_Rep3

description: no additional information


title: EB_E20_Normoxia_Rep4

description: no additional information

value: Normoxia


title: EB_E20_Normoxia_Rep3

description: no additional information


title: EB_E20_Hypoxia_Rep4

description: no additional information


title: EB_E20_Normoxia_Rep2

description: no additional information


title: EB_E20_Hypoxia_Rep1

description: no additional information


title: ARD 682_b

description: CAIS (AIS5, Sinnecker classification); age: 14 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 682_b, genomic DNA, second hybridization

value: genital fibroblast cell line

value: 14 months


title: ARD 774_a

description: PAIS (AIS2, Sinnecker classification); age: 11 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 774_a, genomic DNA, first hybridization

value: PAIS (AIS2, Sinnecker classification)

value: 11 months


title: ARD 774_b

source_name: ARD 774_b, genomic DNA, second hybridization


title: EB_E17_Hypoxia_Rep1

description: no additional information


title: EB_E17_Normoxia_Rep3

description: no additional information


title: EB_E17_Hypoxia_Rep2

description: no additional information


title: EB_E20_Normoxia_Rep1

description: no additional information


title: EB_E17_Hypoxia_Rep3

description: no additional information


title: ARD 659_a

description: PAIS (AIS4, Sinnecker classification); age: 46 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 659_a, genomic DNA, first hybridization

value: PAIS (AIS4, Sinnecker classification)

value: 46 months


title: ARD 446_b

description: PAIS (AIS2, Sinnecker classification); age: 92 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 446_b, genomic DNA, second hybridization

value: 92 months


title: ARD 659_b

source_name: ARD 659_b, genomic DNA, second hybridization

value: AIS


title: ARD 1097_a

source_name: ARD 1097_a, genomic DNA, first hybridization

value: CAIS (AIS5, Sinnecker classification)


title: ARD 682_a

source_name: ARD 682_a, genomic DNA, first hybridization


title: EB_E17_Normoxia_Rep4

description: no additional information


title: EB_E17_Hypoxia_Rep4

description: no additional information


title: ARD 411_a

description: CAIS (AIS5, Sinnecker classification); age: 4 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 411_a, genomic DNA, first hybridization

value: 4 months


title: EB_E14_Hypoxia_Rep4

description: no additional information


title: ARD 411_b

source_name: ARD 411_b, genomic DNA, second hybridization


title: ARD 527_a

description: PAIS (AIS2, Sinnecker classification); age: 18 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 527_a, genomic DNA, first hybridization

value: 18 months


title: ARD 446_a

source_name: ARD 446_a, genomic DNA, first hybridization


title: ARD 527_b

source_name: ARD 527_b, genomic DNA, second hybridization


title: EB_E17_Normoxia_Rep1

description: no additional information


title: EB_E14_Hypoxia_Rep3

description: no additional information


title: ARD 402_b

description: CAIS (AIS5, Sinnecker classification); age: 12 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 402_b, genomic DNA, second hybridization

value: 12 months


title: ARD 402_a

source_name: ARD 402_a, genomic DNA, first hybridization

value: Holterhus et al., BMC Genomics 2007


title: EB_E14_Hypoxia_Rep2

description: no additional information

source_name: Embryonic stem (ES) cells

source_name: Universal Mouse Reference RNA


title: EB_E14_Hypoxia_Rep1

description: no additional information


title: EB_E17_Normoxia_Rep2

description: no additional information


title: EB_E14_Normoxia_Rep4

description: no additional information


title: EB_E14_Normoxia_Rep2

description: no additional information


title: ARD 377_b

description: PAIS (AIS4, Sinnecker classification); age: 14 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 377_b, genomic DNA, second hybridization


title: ARD 306_b

source_name: ARD 306_b, genomic DNA, second hybridization


title: EB_E10_Hypoxia_Rep2

description: no additional information


title: EB_E14_Normoxia_Rep3

description: no additional information


title: EB_E10_Hypoxia_Rep1

description: no additional information


title: ARD 306_a

source_name: ARD 306_a, genomic DNA, first hybridization


title: ARD 84_a

description: PAIS (AIS3, Sinnecker classification); age: 8 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 84_a, genomic DNA, first hybridization

value: PAIS (AIS3, Sinnecker classification)

value: 8 months


title: ARD 377_a

source_name: ARD 377_a, genomic DNA, first hybridization


title: EB_E10_Hypoxia_Rep3

description: no additional information

value: Hypoxia

value: Stratagene Universal Mouse Reference RNA


title: ARD 84_b

source_name: ARD 84_b, genomic DNA, second hybridization

value: genital fibroblast cell line


title: EB_E10_Normoxia_Rep4

description: no additional information

value: Normoxia


title: EB_E10_Hypoxia_Rep4

description: no additional information


title: EB_E14_Normoxia_Rep1

description: no additional information


title: ARD 1_b

description: PAIS (AIS3, Sinnecker classification); age: 9 months; Holterhus et al., BMC Genomics 2007

source_name: ARD 1_b, genomic DNA, second hybridization

value: 9 months


title: Bone marrow mesenchymal stem cells from psoriasis patient,replicate 3

status: Public on Aug 11 2012

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description:
psoriasis patient
US10283824_252800411485_S01_GE1_107_Sep09_2_1

hyb_protocol: According to the instructions of Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization.

source_name: Bone marrow mesenchymal stem cells from psoriasis patient 3

label_protocol: RNA was amplified and labeled with Cy5 using Agilent’s Low Input Quick Amp WT Labeling Kit according to the manufacturer’s instruction

growth_protocol: Bone marrow mononuclear cells (BMMNC) of 7 psoriatic patients, 4 healthy volunteers and 3 aborted fetuses were isolated and the BMMSCs were cultured using the adherent method.

extract_protocol: Total RNA from BMMNC was extracted using Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacturer’s instructions.

value: bone marrow

value: mesenchymal stem cells

tag: subject status

value: psoriasis patient


title: Bone marrow mesenchymal stem cells from psoriasis patient,replicate 4

description:
psoriasis patient
US10283824_252800411426_S01_GE1_107_Sep09_2_1

source_name: Bone marrow mesenchymal stem cells from psoriasis patient 4


title: ARD 1_a

source_name: ARD 1_a, genomic DNA, first hybridization


title: Bone marrow mesenchymal stem cells from aborted fetus,replicate 3

description:
aborted fetus
US10283824_252800411426_S01_GE1_107_Sep09_1_4

source_name: Bone marrow mesenchymal stem cells from aborted fetus 3

value: aborted fetus


title: Bone marrow mesenchymal stem cells from psoriasis patient,replicate 6

description:
psoriasis patient
US10283824_252800411426_S01_GE1_107_Sep09_2_3

source_name: Bone marrow mesenchymal stem cells from psoriasis patient 6


title: Bone marrow mesenchymal stem cells from psoriasis patient,replicate 7

description:
psoriasis patient
US10283824_252800411426_S01_GE1_107_Sep09_2_4

source_name: Bone marrow mesenchymal stem cells from psoriasis patient 7


title: Bone marrow mesenchymal stem cells from psoriasis patient,replicate 1

description:
psoriasis patient
US10283824_252800411485_S01_GE1_107_Sep09_1_3

source_name: Bone marrow mesenchymal stem cells from psoriasis patient 1


title: FOXM1 siRNA

city: guangzhou

first: nu

last: zhang

address: no.58 Zhongshan 2 road

department: neurosurgery

institute: 1st affiliated hospital of Sun Yat-sen university

hyb_protocol: Array hybridization and wash were performed using the GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by the MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: U87 glioma cell transfected with FOXM1 siRNA

label_protocol: Total RNA were amplified, labeled and purified by using the GeneChip 3'IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer's instructions to obtain biotin-labeled cRNA.

growth_protocol: 37 degrees with 5% CO2 humid cuture, 10% FBS in DMEM medium.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: According to the Lipofectamin 2000 (Invitogen).

value: glioblastoma cells

tag: sirna


title: Bone marrow mesenchymal stem cells from psoriasis patient,replicate 2

description:
psoriasis patient
US10283824_252800411485_S01_GE1_107_Sep09_1_4

source_name: Bone marrow mesenchymal stem cells from psoriasis patient 2


title: EB_E10_Normoxia_Rep2

description: no additional information

source_name: Embryonic stem (ES) cells

tag: strain

source_name: Universal Mouse Reference RNA


title: Bone marrow mesenchymal stem cells from aborted fetus,replicate 2

description:
aborted fetus
US10283824_252800411426_S01_GE1_107_Sep09_1_3

source_name: Bone marrow mesenchymal stem cells from aborted fetus 2

tag: tissue


title: Bone marrow mesenchymal stem cells from aborted fetus,replicate 1

description:
aborted fetus
US10283824_252800411426_S01_GE1_107_Sep09_1_2

source_name: Bone marrow mesenchymal stem cells from aborted fetus 1


title: Bone marrow mesenchymal stem cells from psoriasis patient,replicate 5

description:
psoriasis patient
US10283824_252800411426_S01_GE1_107_Sep09_2_2

source_name: Bone marrow mesenchymal stem cells from psoriasis patient 5


title: Jeko-1 DZNep 1uM 72hr

city: Tampa

first: jianguo

last: tao

state: FL

address: 12902 Magnolia Dr

institute: H Lee Moffitt Cancer Center

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using DataAssist™ Software https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=606580
For the normalization it uses the average of endogenous contrls:RNU44, RNU48 and RNU6B;the Maximum allowable CT value: 32.0;
Target gene signals normalized to Endogenous Control; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_EC)]
The DataAssist™ Software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. Fold Change worksheet reports test/control (i.e., Jeko-1 DZNep 1uM 72hr/Jeko-1 Con) ratios.

label: Taqman

source_name: human mantle cell lyphoma cell line

label_protocol: Reverse transcription was performed from 1 ug total RNA using the TaqMan® MicroRNA Reverse Transcription Kit(Applied Biosystem). Quantitative real-time PCR were performed by 7900HT Fast Real-Time PCR System.

extract_protocol: Total RNA was extracted with Trizol.

value: B cell lymphoma

tag: agent

value: DZNep

tag: time


title: Jeko-1 con-1

description: Control

tag: cell line

value: no treat


title: None target siRNA

source_name: U87 glioma cell transfected with none target siRNA

value: control


title: EB_E10_Normoxia_Rep3

description: no additional information


title: Bone marrow mesenchymal stem cells from healthy subject,replicate 3

description:
healthy subject
US10283824_252800411425_S01_GE1_107_Sep09_1_4

source_name: Bone marrow mesenchymal stem cells from healthy subject 3

value: healthy subject


title: Bone marrow mesenchymal stem cells from healthy subject,replicate 4

description:
healthy subject
US10283824_252800411485_S01_GE1_107_Sep09_1_2

source_name: Bone marrow mesenchymal stem cells from healthy subject 4


title: Jeko-1 con

description: Control


title: EB_E10_Normoxia_Rep1

description: no additional information


title: Jeko-1 DZNep 1uM 72hr-1

description: Test


title: Bone marrow mesenchymal stem cells from healthy subject,replicate 1

description:
healthy subject
US10283824_252800411426_S01_GE1_107_Sep09_1_1

source_name: Bone marrow mesenchymal stem cells from healthy subject 1


title: Bone marrow mesenchymal stem cells from healthy subject,replicate 2

description:
healthy subject
US10283824_252800411425_S01_GE1_107_Sep09_1_3

source_name: Bone marrow mesenchymal stem cells from healthy subject 2


title: TB_week26_patient:5754

status: Public on Aug 10 2012

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

hyb_protocol: Fragmented and biotinylated cDNA was hybridised to Human U133 Plus 2.0 Affymetrix GeneChips at 45C, 60 rpm for 18 hours. GeneChips were washed and stained with an Affymetrix GeneChip Fluidics station 450, protocol EukGE-WS2v4_450.

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: GC-RMA summarised and baseline normalised to median of all arrays using GeneSpring GX11.5

label: NuGEN Ovation® Whole Blood Solution

source_name: Blood

label_protocol: 3 ng mRNA processed using NuGEN Ovation® Whole Blood Solution

growth_protocol: Ex vivo human blood, 5ml mixed in 50ml RNA/DNA Stabilization reagent (Roche Applied Science)

extract_protocol: mRNA Isolation Kit for Blood/Bone Marrow (Roche Applied Science) and Turbo DNA-free™ treatment (Ambion: Applied Biosystems)

treatment_protocol: Tuberculosis patients, samples taken at beginning and end of conventional combination therapy (2HRZE/4HR)

tag: time point

value: Week 26

value: blood

tag: sample time

value: at end of treatment


title: TB_diagnosis_patient:5754

value: Week 0

value: at diagnosis


title: TB_diagnosis_patient:5760


title: TB_week26_patient:5709


title: TB_diagnosis_patient:5709


title: TB_diagnosis_patient:5655


title: TB_week26_patient:5760


title: TB_week26_patient:5600


title: TB_week26_patient:5122


title: TB_diagnosis_patient:5600


title: TB_week26_patient:5418


title: TB_week26_patient:5655


title: TB_diagnosis_patient:5037


title: TB_diagnosis_patient:5418


title: TB_week26_patient:5118


title: TB_diagnosis_patient:5122


title: TB_week26_patient:5037


title: TB_week2_patient:5761

description: NuGEN Ovation® Whole Blood Solution

molecule: polyA RNA

treatment_protocol: Tuberculosis patients, samples taken at different time points during conventional combination therapy (2HRZE/4HR)

tag: diagnosis

value: Tuberculosis

value: Week 2


title: TB_week1_patient:5730

description: NuGEN Ovation® Whole Blood Solution

value: Week 1


title: TB_week1_patient:5761

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5118


title: TB_week4_patient:5761

description: NuGEN Ovation® Whole Blood Solution

value: Week 4


title: TB_diagnosis_patient:5761

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5730

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5730

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5566

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5563

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5566

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5566

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5563

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5730

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5566

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5761

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5730

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5566

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5547

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5547

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5521

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5521

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5563

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5563

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5547

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5563

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5485

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5547

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5547

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5476

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5521

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5521

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5476

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5463

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5485

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5476

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5485

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5476

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5476

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5485

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5521

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5485

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5463

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5463

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5463

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5425

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5425

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5463

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5425

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5421

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5425

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5421

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5420

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5421

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5420

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5419

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5390

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5420

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5425

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5419

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5421

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5421

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5419

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5420

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5403

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5420

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5419

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5419

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5403

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5403

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5390

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5403

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5390

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5384

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5390

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5403

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5390

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5384

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 20

city: New York

first: Athanasios

last: Zavras

state: NY

address: 630 West 168th St.

institute: Columbia University

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2

source_name: blood from cancer-free controls

extract_protocol: Genomic DNA was extracted and purified from blood samples using Qiagen DNeasy Kit according to standard instructions.

value: Blood

value: Female

tag: age

tag: disease state

value: Cancer-free controls


title: TB_week2_patient:5374

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5384

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5384

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5374

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5366

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5366

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5366

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5374

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5384

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 15

value: Male


title: genomic DNA from blood 23


title: TB_week1_patient:5366

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 19


title: genomic DNA from blood 17


title: TB_week4_patient:5374

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 22


title: genomic DNA from blood 18


title: genomic DNA from blood 10

source_name: blood from cancer cases

value: HNSCC


title: genomic DNA from blood 14


title: genomic DNA from blood 21


title: genomic DNA from blood 24


title: TB_week1_patient:5374

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 13


title: genomic DNA from blood 12


title: genomic DNA from blood 11


title: Sinorhizobium meliloti Rm1021, biological replicate1

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

organism: Sinorhizobium meliloti

source_name: Rm1021 (wildtype)

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: For each biological replicate, a single bacterial colony was inoculated into 20 milliliters of LB medium, supplemented with streptomycin at 500 micrograms per microliter, and grown with shaking at 200 rpm at 30 degrees celsius in a 250 milliliter baffled flask to an OD-600 of 0.6 to 0.8

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: genotype/variation

value: wild type


title: TB_diagnosis_patient:5366

description: NuGEN Ovation® Whole Blood Solution


title: Sinorhizobium meliloti Rm1021, biological replicate3


title: genomic DNA from blood 16


title: Sinorhizobium meliloti podJ1 deletion mutant, biological replicate3

source_name: podJ1 deletion mutant

value: podJ1 deletion mutant


title: genomic DNA from blood 7


title: TB_week26_patient:5351

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5351

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5351

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5351

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5351

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 8


title: genomic DNA from blood 9


title: TB_week4_patient:5273

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5273

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 4


title: Sinorhizobium meliloti podJ1 deletion mutant, biological replicate2


title: genomic DNA from blood 6


title: TB_week26_patient:5273

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5336

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5116

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5336

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5336

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:5116

description: NuGEN Ovation® Whole Blood Solution


title: Sinorhizobium meliloti Rm1021, biological replicate2


title: TB_week2_patient:5273

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5336

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5336

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5116

description: NuGEN Ovation® Whole Blood Solution


title: genomic DNA from blood 5


title: genomic DNA from blood 1


title: TB_week1_patient:5116

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5116

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5273

description: NuGEN Ovation® Whole Blood Solution


title: Sinorhizobium meliloti podJ1 deletion mutant, biological replicate1


title: 3day_IRI60

city: Kyoto

first: Takaomi

last: Adachi

address: Kajiicho 465

department: Nephrology

country: Japan

institute: kyoto prefectural university of medicine

description: Gene expression data from kidney exposed to 60min IRI 3day after IRI.

hyb_protocol: 10 ug of cRNA were hybridized according to the GeneChip 3’IVT Express Kit User Manual. GeneChips were washed and stained according to the GeneChip 3’IVT Express Kit User Manual.

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

data_processing: The data were analyzed using Affymetrix GeneChip Command Console Software and Affymetrix Expression Console Software.

source_name: Kidney exposed to 60 min IRI, collected at 3 day after IRI.

label_protocol: Biotinylated cRNA were prepared according to the GeneChip 3’IVT Express Kit User Manual from 250 ug total RNA.

growth_protocol: Mice were maintained in the animal facility of Kyoto Prefectural University of Medicine, Japan.

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

treatment_protocol: MIce were anesthetized with intraperitoneal injection of 50 mg / kg pentobarbital sodium and placed on a homeothermic table to maintain body temperature at 40 ˚C. Flank incisions were made to expose renal pedicles. Renal pedicles were clamped by unilateral with arterial microclamps, and released after each time of clamping (0 min, 45 min, 60 min) and the wounds were sutured, kidneys were collected at indicated times after reperfusion.

value: FVB/N

value: male

value: 6-8 week

tag: weight

value: within 22-26 g


title: 3day_IRI0

description: Gene expression data from kidney exposed to 0min IRI 3day after IRI.

source_name: Kidney exposed to 0 min IRI, collected at 3 day after IRI.

tag: gender


title: genomic DNA from blood 2


title: 1day_IRI0

description: Gene expression data from kidney exposed to 0min IRI 1day after IRI.

source_name: Kidney exposed to 0 min IRI, collected at 1 day after IRI.


title: genomic DNA from blood 3


title: 3day_IRI45

description: Gene expression data from kidney exposed to 45min IRI 3day after IRI.

source_name: Kidney exposed to 45 min IRI, collected at 3 day after IRI.


title: TB_week2_patient:5108

description: NuGEN Ovation® Whole Blood Solution

value: blood


title: TB_week4_patient:5108

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:5108

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:5094

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:5108

description: NuGEN Ovation® Whole Blood Solution

value: Week 0


title: TB_diagnosis_patient:5094

description: NuGEN Ovation® Whole Blood Solution

value: Tuberculosis


title: Rag2-deficient Ets1-deficient mature NK cell replicate 1

city: Chicago

first: Barbara

last: Kee

state: IL

address: 924 East 57th Street

department: Pathology

institute: University of Chicago

description: Ets1-- mNK replicate 1

hyb_protocol: RNA was hybridized to MOE430_2 chips according to the manufacturer's manual

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: Murine BM from 129 mice

label_protocol: Biotinylated cRNA was prepared according to the standard AffymetrixTM; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using AffymetrixTM GeneChipTM Expression 3‚Äôamplification kit.

extract_protocol: Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

value: Bone Marrow

tag: genotype

value: Rag2-- Ets1--

tag: background strain

value: 8-14 weeks


title: Granulocyt-monocyte progenitor replicate 3

description: GMP replicate 3

source_name: Murine BM from C57bl/6 mice

value: Wild type


title: TB_week4_patient:5094

description: NuGEN Ovation® Whole Blood Solution

value: Week 4


title: TB_week26_patient:4955

description: NuGEN Ovation® Whole Blood Solution

value: Week 26


title: Rag2-deficient mature NK cell replicate 1

description: Ets1 ++ mNK replicate 1

value: Rag2-- Ets1++


title: TB_week26_patient:5094

description: NuGEN Ovation® Whole Blood Solution


title: TB_week26_patient:5108

description: NuGEN Ovation® Whole Blood Solution


title: CD4 T cell replicate 2

description: CD4 T replicate 2


title: Granulocyt-monocyte progenitor replicate 1

description: GMP replicate 1


title: 1day_IRI45

description: Gene expression data from kidney exposed to 45min IRI 1day after IRI.

source_name: Kidney exposed to 45 min IRI, collected at 1 day after IRI.


title: Rag2-deficient mature NK cell replicate 2

description: Ets1 ++ mNK replicate 2


title: TB_week2_patient:4955

description: NuGEN Ovation® Whole Blood Solution

value: Week 2


title: Rag2-deficient Ets1-deficient mature NK cell replicate 2

description: Ets1-- mNK replicate 2


title: Granulocyt-monocyte progenitor replicate 2

description: GMP replicate 2


title: Pro B cell replicate 2

description: ProB replicate 2


title: CD4 T cell replicate 1

description: CD4 T replicate 1


title: 1day_IRI60

description: Gene expression data from kidney exposed to 60min IRI 1day after IRI.

source_name: Kidney exposed to 60 min IRI, collected at 1 day after IRI.


title: Muller glia_uninjured_0 days post injury_rep2

city: Ann Arbor

first: Rajesh

last: Ramachandran

state: Michigan

address: 109 Zina Pitcher Place

department: Molecular and Behavioral Neuroscience Institute

institute: University of Michigan

description:
Gene expression of Uninjured Muller glia
SAMPLE 2

hyb_protocol: 1.5 ug of Alexa 555-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent zebrafish (Danio rerio) oligo microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 015064_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: Alexa 555

organism: Danio rerio

source_name: Uninjured Muller glia, 0 dpi

label_protocol: Alexa 555 labeled cRNA was prepared from 0.7 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions,

growth_protocol: Fishes were grown at 14-10 light-dark cycles, fed thrice daily and maintained as per the animal care protocols of University of Michigan.

extract_protocol: Total RNA was isolated Muller glia and Muller glia derived retinal progenitors obtained from zebrafish retina using standard Trizol method.

treatment_protocol: Fishes were anesthetized using tricaine methane sulfonate prior to retinal injury using a 30G needle from the back of the eye. Each fish received one poke per quadrant of the eye circle. Uninjured fishes were not given any injury. Experiments were done ss per the University of Michigan animal care protocol.

value: gfap:gfp transgenic (GFP under gfap promoter)

value: 7 months old zebrafish retina

value: uninjured retinas

tag: cell type

value: Muller glia


title: Muller glia derived progenitors_4 day post injury_rep2

description:
Gene expression of Injured Muller glia derived retinal progenitors
SAMPLE 4

source_name: Injured Muller glia derived retinal progenitors, 4 dpi

value: 1016 tuba1a:gfp transgenic

value: 8 months old zebrafish retina

value: retinas at 4 days post injury


title: Pro B cell replicate 1

description: ProB replicate 1


title: Muller glia_uninjured_0 days post injury_rep1

description:
Gene expression of Uninjured Muller glia
SAMPLE 1


title: Common Lymphoid Progenitor replicate 3

description: CLP replicate 3


title: TB_week4_patient:4896

description: NuGEN Ovation® Whole Blood Solution

value: blood


title: TB_week26_patient:4896

description: NuGEN Ovation® Whole Blood Solution

value: Tuberculosis


title: TB_week1_patient:4955

description: NuGEN Ovation® Whole Blood Solution

value: Week 1


title: Muller glia derived progenitors_4 day post injury_rep1

description:
Gene expression of Injured Muller glia derived retinal progenitors
SAMPLE 3

value: 1016 tuba1a:gfp transgenic (GFP under tuba1a promoter )


title: Common Lymphoid Progenitor replicate 2

description: CLP replicate 2

value: Bone Marrow

value: 8-14 weeks


title: TB_diagnosis_patient:4955

description: NuGEN Ovation® Whole Blood Solution

value: Week 0


title: Multipotent progenitor replicate 2

description: MPP replicate 2

value: Wild type


title: Common Lymphoid Progenitor replicate 1

description: CLP replicate 1


title: TB_week4_patient:4869

description: NuGEN Ovation® Whole Blood Solution

value: Week 4


title: TB_week1_patient:4896

description: NuGEN Ovation® Whole Blood Solution


title: TB_week1_patient:4869

description: NuGEN Ovation® Whole Blood Solution


title: TB_diagnosis_patient:4896

description: NuGEN Ovation® Whole Blood Solution


title: TB_week2_patient:4869

description: NuGEN Ovation® Whole Blood Solution

value: Week 2


title: TB_week2_patient:4896

description: NuGEN Ovation® Whole Blood Solution


title: TB_week4_patient:4955

description: NuGEN Ovation® Whole Blood Solution


title: Lymphoid primed multipotent progenitor replicate 2

description: LMPP replicate 2


title: TB_week26_patient:4869

description: NuGEN Ovation® Whole Blood Solution

value: Week 26


title: WT Hematopoietic stem cell replicate 1

description: HSC replicate 1


title: Multipotent progenitor replicate 1

description: MPP replicate 1


title: Lymphoid primed multipotent progenitor replicate 1

description: LMPP replicate 1


title: MUTZ-5_JQ1_3_core

city: Boston

first: Christopher

last: Ott

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
M5_JQ1_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis

hyb_protocol: 5.5ug of fragmented, biotinylated cDNA was hybridized according to the standard Affymetrix protocol for the Exon1.0ST array.

data_processing: RMA probe analysis using Affymetrix Expression Console software using 'core' and 'extended' gene-level analysis

label_protocol: 5.5ug of amplified single-stranded cDNA was fragmented and biotinylated using the Affymetrix Terminal Label and Control Kit.

growth_protocol: Cell grown in RPMI media supplemented with 20% FBS, 1% pen/strep, 1% L-glutamine

extract_protocol: RNA extracted with Trizol reagent and purified per Trizol protocol; RNA further purified using RNeasy kit columns (Qiagen)

treatment_protocol: Cells treated with either DMSO or 500nM JQ1 for 8 hours

value: human acute lymphoblastic leukemia cells

tag: exposed to

value: 500nM JQ1 for 8hrs


title: AhR reconstituted hepatocytes suspension culture replicate 1

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: AhR reconst Susp rep1

hyb_protocol: 1.5μg of cRNA from each sample was hybridized to MouseWG-6 v2.0 Expression BeadChip (Illumina) microarrays according to the manufacturer’s specification.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing: Microarray raw intensity values were background subtracted using the BeadStudio Data Analysis Software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006).

source_name: AhR null hepatocytes stably expressing TetR and HisMyc tagged mouse AhR_suspension culture_8h

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labeled cRNA using the Illumina TotalPrep RNA amplification kit (Ambion).

growth_protocol: Mouse AhR null hepatocytes (AhR-/- Hepa) (Murray et al., 2005) were routinely grown in Minimum Essential Medium Alpha (Gibco), supplemented with 10% fetal calf serum, 100U/ml penicillin, 100μg/ml streptomycin, and cultured at 34°C with 5% CO2. Dexamethasone was added to the hepatocyte culture medium at 100nM final concentration to promote cell survival.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer instructions and all samples were profiled on the Bioanalyzer (Agilent) for RNA degradation.

treatment_protocol: Confluent mouse AhR null hepatocytes stably expressing either TetR alone or in combination with HisMyc epitope tagged mAhR were treated with vehicle alone (0.1% DMSO), 10μM YH439 or grown as suspension cultures for 8 h in biological triplicates. Suspension cultures were prepared by dislodging cells from tissue culture flasks with 0.05% Trypsin/530μM EDTA, resuspending in semi-solid media containing 1.68% methylcellulose, and incubation in the same manner as adherent cultures (Monk et al., 2001).

tag: strain

tag: background cell line

value: AhR null hepatocytes (AhR-/- Hepa)

tag: stably expressing

value: TetR (pLenti6/TR) and HisMyc tagged AhR (pLV501_HisMyc_mAhR)

value: SV40 tsA209 mutant virus transformed, TetR and HisMyc tagged AhR stable reconstituted hepatocytes

tag: treated with

value: Suspension culture

tag: treatment duration

value: 8 hours


title: WT Hematopoietic stem cell replicate 2

description: HSC replicate 2

tag: tissue


title: MUTZ-5_DMSO_2_core

description:
M5_DMSO_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis

tag: cell line

value: DMSO for 8hrs


title: AhR reconstituted hepatocytes 10μM YH439 replicate 2

description: AhR reconst YH439 rep2

source_name: AhR null hepatocytes stably expressing TetR and HisMyc tagged mouse AhR_10μM YH439_8h


title: MUTZ-5_JQ1_2_core

description:
M5_JQ1_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: AhR reconstituted hepatocytes suspension culture replicate 2

description: AhR reconst Susp rep2


title: TB_week1_patient:5094

description: NuGEN Ovation® Whole Blood Solution

source_name: Blood

tag: diagnosis

value: Tuberculosis

tag: time point

value: Week 1

value: blood


title: MUTZ-5_JQ1_3_extended

description:
M5_JQ1_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis


title: AhR reconstituted hepatocytes suspension culture replicate 3

description: AhR reconst Susp rep3


title: MUTZ-5_DMSO_1_extended

description:
M5_DMSO_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis


title: AhR reconstituted hepatocytes 10μM YH439 replicate 1

description: AhR reconst YH439 rep1


title: MUTZ-5_DMSO_2_extended

description:
M5_DMSO_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis


title: TB_diagnosis_patient:4869

description: NuGEN Ovation® Whole Blood Solution


title: MUTZ-5_JQ1_1_core

description:
M5_JQ1_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: MUTZ-5_JQ1_2_extended

description:
M5_JQ1_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis


title: MUTZ-5_DMSO_3_core

description:
M5_DMSO_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: WM-266-4 CT16 3

city: Turku

first: Jyrki

last: Heino

address: Vatselankatu 2

department: Biochemistry

country: Finland

institute: University of Turku

description: WM-266-4 transfected with CT16 containing plasmid Rep 3

data_processing: The microarray data were normalized using the quantile normalization method in Bioconductor  (http://www.bioconductor.org)

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit

growth_protocol: The cells were maintained at 5% CO2 and 37°C in Dulbecco's Modified Eagle Medium (DMEM) (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum.

extract_protocol: RNA was extracted with Trizol reagent followed by purification with Qiagen’s RNeasy MiniKit, (cat no74106) according to the manufacturer’s protocol. The DNase treatment was included and done with Qiagen’s RNase free DNase Set (cat no 79254) according to Qiagen’s protocol. cRNA quality was controlled by BioRad’s Experion electrophoresis station.

tag: plasmid

value: CT16 in pEXPR-IBA103


title: MUTZ-5_JQ1_1_extended

description:
M5_JQ1_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis


title: AhR reconstituted hepatocytes 10μM YH439 replicate 3

description: AhR reconst YH439 rep3


title: MUTZ-5_DMSO_1_core

description:
M5_DMSO_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: AhR reconstituted hepatocytes 0.1% DMSO control replicate 3

description: AhR reconst DMSO rep3

source_name: AhR null hepatocytes stably expressing TetR and HisMyc tagged mouse AhR_0.1% DMSO_8h

value: 0.1% DMSO


title: AhR reconstituted hepatocytes 0.1% DMSO control replicate 2

description: AhR reconst DMSO rep2


title: MUTZ-5_DMSO_3_extended

description:
M5_DMSO_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis


title: WM-266-4 CT16 2

description: WM-266-4 transfected with CT16 containing plasmid Rep 2


title: WM-266-4 IBA 3

description: WM-266-4 transfected with control plasmid Rep 3


title: MHH-CALL4_JQ1_3_extended

description:
M4_JQ1_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis


title: AhR null hepatocytes suspension culture replicate 3

description: AhR null Susp rep3

source_name: AhR null hepatocytes stably expressing TetR_suspension culture_8h

value: TetR (pLenti6/TR) alone

value: SV40 tsA209 mutant virus transformed, TetR stable AhR null hepatocytes


title: AhR null hepatocytes suspension culture replicate 1

description: AhR null Susp rep1


title: WM-266-4 IBA 1

description: WM-266-4 transfected with control plasmid Rep 1


title: A2058 CT16 siRNA Rep3

description: A2058 CT16 siRNA Rep3

source_name: A2058 CT16 siRNA

treatment_protocol: The cells were treated with CT16 siRNA or control siRNA for 48 h

tag: treatment

value: CT16 siRNA


title: AhR null hepatocytes 10μM YH439 replicate 1

description: AhR null YH439 rep1

source_name: AhR null hepatocytes stably expressing TetR_10μM YH439_8h


title: AhR reconstituted hepatocytes 0.1% DMSO control replicate 1

description: AhR reconst DMSO rep1


title: MHH-CALL4_JQ1_2_core

description:
M4_JQ1_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: A2058 Ctrl siRNA Rep3

description: A2058 Ctrl siRNA Rep3

source_name: A2058 Ctrl siRNA

value: Control siRNA


title: A2058 Ctrl siRNA Rep2

description: A2058 Ctrl siRNA Rep2


title: WM-266-4 IBA 2

description: WM-266-4 transfected with control plasmid Rep 2


title: MHH-CALL4_DMSO_3_core

description:
M4_DMSO_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis

value: human acute lymphoblastic leukemia cells


title: MHH-CALL4_JQ1_1_extended

description:
M4_JQ1_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis

value: 500nM JQ1 for 8hrs


title: MHH-CALL4_JQ1_3_core

description:
M4_JQ1_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: A2058 CT16 siRNA Rep2

description: A2058 CT16 siRNA Rep2


title: AhR null hepatocytes 0.1% DMSO control replicate 3

description: AhR null DMSO rep3

source_name: AhR null hepatocytes stably expressing TetR_0.1% DMSO_8h

value: AhR null hepatocytes (AhR-/- Hepa)


title: AhR null hepatocytes suspension culture replicate 2

description: AhR null Susp rep2


title: seedling_venom-treated_48hr_replicate2_rescan [48V2_B2]

city: Athens

first: Adam

middle: W.

last: Barb

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

description:
growth chamber raised
10 Pinus taeda seedlings cut at soil line, placed into 20 mg/ml S. noctilio venom solution until absorbed, transferred to water, flash frozen at 48hr and ten seedlings pooled.

hyb_protocol: Hybridization was carried out as described previously: Lorenz WW, Yu Y-S, Simões M, Dean JFD: Processing the Loblolly Pine PtGen2 cDNA Microarray. Journal of Visualized Experiments 2009, 25.  50 pmol each of Cy-5 and Cy-3 labeled target was combined in a single tube and dried in a vacuum desiccator at 45oC to a volume of 1-2 µL.  cDNAs were resuspended in 60uL hybridization buffer (30% formamide, 5X SSC, 5X Denhardt’s, 1% PolyA RNA, 0.1% SDS), vortexed briefly and heated in a 95oC water bath for 5 min.. Targets were loaded at the bottom edge of the LifterSlip™ by way of capillary action.  Slides were placed in a HybChamber™ (Genomic Solutions, Ann Arbor, MI ) and 20µL of 100mM DTT was added to humidity wells located at each end of the chamber.  The chamber was assembled, wrapped in aluminum foil, and incubated in a 48oC shaking water bath set at 50 rpm for 14-16 hr.

scan_protocol: The microarrays were scanned using a ProScanArray™ confocal scanner (Perkin Elmer, Waltham, MA).  Scans were conducted with the 532 nm and 635 nm lasers and data were collected at a 10 µm resolution.  Laser power remained constant at 90% and gain settings typically ranged between 55-65%.

data_processing: Raw fluorescence data were processed with an image analysis algorithm in ImaGene software, ver. 7.5 (Bio-Discovery Inc., El Segundo, CA, USA) was used to quantify signal and background intensity.  Probes that had been duplicated on the array as internal controls were flagged to leave a single representative for each duplicated set and signal means were determined without background correction.  An in house Perl script was used to import the raw Imagene signal intensity data, to calculate Wang et al. flags (Wang et al. Bioinformatics 2003,19:1341-1347) and to convert the data into a readily exportable file for downstream BRB array tools statistical analysis.  Normalization and Statistical Analysis:  Data was filtered and normalized using BRB-Array Tools, an R-based integrated package for the visualization and statistical analysis of DNA microarray gene expression data (Simon et al.  Cancer Informatics 2007, 3:11-17).  Using the reference design experimental module, raw signal intensity data from all samples (a total of 12 slides were hybridized and scanned and each slide was subsequently re-scanned at a higher gain to yield a set of scan duplicates, 24 total data files, that were required to meet the statistical number of slides required by BRB Array Tools analysis  were used in this preliminary analysis) was log2 transformed and normalized by the Lowess plus print tip method.  Spot signals were filtered by employing Wang flagging and gene filters were employed to remove any gene with 50% or more missing or filtered data.   Normalized signal intensity ratios were calculated for identification of differentially expressed genes (DEGs) that were determined via paired comparisons among the two venom treatment groups versus control using the class comparison tool and utilizing a random variance t-test for computation of P-values.  Control of the proportion of false discoveries was accomplished the multivariate permutation test with the number of permutations at the default setting of 1000.  All paired treatment comparison analyses were performed with a false discovery rate (FDR) of 0.1 and a confidence level of 90%.

organism: Pinus taeda

label_protocol: First-Strand cDNA Synthesis and Purification  Synthesis of amino-allyl and amino-hexyl modified cDNA and was done with an Invitrogen SuperScriptTM Indirect cDNA Labeling System (Invitrogen Corp., Carlsbad, CA) according to the manufacturer’s protocol with a few modifications.  Briefly, each cDNA synthesis reaction contained 20µg of DNase treated total RNA annealed to 2µL anchored oligo(dT)20 primer plus 1µL random hexamer primer.  Reactions were carried out in a 45oC water bath for 12-14 hr.  Samples were purified on S.N.A.P™ columns supplied with the kit and washed three times with 500µL wash buffer.  cDNA was eluted twice with 50µL DEPC-water, EtOH precipitated ( 10µL of 3M Sodium Acetate, pH5.2, 2µL 20mg/mL glycogen, and 300uL -20oC 100% EtOH) at -80oC for 30 min.  Pellets were washed three times with -20oC 70% EtOH followed by resuspending in 5µL 2X coupling buffer that had been warmed to 43 oC.     Cy Dye Coupling and Assessment of Labeling Efficiency  Cy-5 and Cy-3 dyes (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), were prepared on the same day as labeling by dissolving each in 80µL DMSO.  Five microliters of dye was added to the resuspended cDNA sample and incubated in the dark for 1 hour.   Next, 20uL of 3M sodium acetate, pH5.2 and 500uL loading buffer was added to the dye-coupled cDNA.  The sample was passed over a S.N.A.P. column and washed three times as described above.  Labeled cDNA was eluted in 65µL DEPC-water.   Nucleic acid and Cy dye concentrations of labeled target cDNAs were determined using a NanoDrop ND-1000 and concentrations were converted to pmol to calculate a ratio for efficiency of labeling.  Typical ratios were in the range of 20-40 pmol n.t./pmol dye and total dye incorporated typically ranged from 200-400 pmol.

growth_protocol: commercial potting soil, 16hr/8hr diurnal cycle, transferred to Conetainers at 6 weeks, water every 3-4 days, fertilizer monthly (14.5g MiracleGro, 1.2g chelated iron/4L water)

extract_protocol: RNA Extraction was carried out as described previously:Lorenz WW, Sun F, Liang C, Kolychev D, Wang HM, Zhao X, Cordonnier-Pratt MM, Pratt LH, Dean JFD: Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiology 2006, 26(1):1-16 and Lorenz WW, Yu Y-S, Dean JFD: An Improved Method of RNA Isolation from Loblolly Pine (P. taeda L.) and Other Conifer Species Journal of Visualized Experiments 2010, 36

treatment_protocol: P. taeda seedlings cut at soil line, cut ends placed in 50 µl each of 20 mg/ml S. noctilio venom or water. After uptake, seedlings transferred to water until sample collection. At two time points after treatment (24, 48 h), two sets of 10 venom-treated seedlings pooled, 1 set of 10 water control seedlings pooled. Total of six samples for microarray analysis:  Bordeaux JM, Lorenz WW, Dean JFD:  Biomarker genes highlight intraspecific and interspecific variations in the responses of Pinus taeda L. and Pinus radiata D. Don to Sirex noctilio F. acid gland secretions

tag: developmental stage

value: seedlings, 5mo old

value: 7-56 half-sib

tag: agent

value: 20 mg/ml S. noctilio venom solution

source_name: Reference sample

tag: reference sample components

value: CCLONES 40430, 43680, 41586 first flush candle and needle tissue, 500 mg ea.; CCLONES 41201, 41396, 44686, 45226, drought-stressed, drought recovered, and well-watered roots from each genotype, 250 mg ea.; Genotype 7-56, callus tissue (needle origin), 250 mg.


title: seedling_venom-treated_48hr_replicate1_rescan [48V2_B1]

tag: genotype


title: MHH-CALL4_DMSO_3_extended

description:
M4_DMSO_3.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis

tag: cell type

value: DMSO for 8hrs


title: AhR null hepatocytes 0.1% DMSO control replicate 2

description: AhR null DMSO rep2

value: 8 hours


title: WM-266-4 CT16 1

description: WM-266-4 transfected with CT16 containing plasmid Rep 1


title: A2058 CT16 siRNA Rep1

description: A2058 CT16 siRNA Rep1


title: AhR null hepatocytes 0.1% DMSO control replicate 1

description: AhR null DMSO rep1


title: AhR null hepatocytes 10μM YH439 replicate 2

description: AhR null YH439 rep2


title: MHH-CALL4_JQ1_2_extended

description:
M4_JQ1_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis

tag: exposed to


title: AhR null hepatocytes 10μM YH439 replicate 3

description: AhR null YH439 rep3

tag: strain


title: A2058 Ctrl siRNA Rep1

description: A2058 Ctrl siRNA Rep1


title: MHH-CALL4_DMSO_2_core

description:
M4_DMSO_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: seedling_venom-treated_48hr_replicate2 [48V2_A2]


title: MHH-CALL4_DMSO_1_core

description:
M4_DMSO_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis


title: C47_3h_2

city: Heidelberg

first: Doreen

last: Heckmann

institute: DKFZ

description:
replicate 2
C47_3h_2

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing:
The data were normalised using quantile normalization with JMP Genomics (v.4.0).
quantile normalized (columns 'value' and 'exp'). Data for each sample are shown in five colomns. The first two columns (Value and detection_pval) were originated from Illumina software; the mean and n columns indicate the mean signal and the number of beads; exp shows the log2 transformed product by multiplying mean and n.

label_protocol: Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-8 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine J. et al., 1992). In brief, 250 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion, Inc., Austin, TX). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: The colon cancer cell line SW480 was grown in RPMI supplemented with 10 % fetal calf serum, penicillin (100 IU/ml) and streptomycin (100 µg/ml) at 37 °C in a humified atmosphere containing 5 % CO2. Lentiviral overexpression of CXCR4 and CXCR7 was established by transduction of SW480 cells and flow cytometric sort as described in Heckmann D. et al., 2011.

extract_protocol: Total RNA was extracted RNeasy Mini Kit, according to the manufacturer’s instructions.

treatment_protocol: SW480Wildtype, SW480CXCR4, SW480CXCR7, and SW480CXCR4/CXCR7 cells were exposed to 100 ng/ml SDF-1α for 3 and 12 h.

tag: gender

value: male

value: colon cancer cells

value: tumor

tag: tumor stage

value: Dukes' type B

tag: genotype/variation

value: SW480CXCR4/CXCR7=C47 (lentiviral overexpression of CXCR4/CXCR7)

value: 100 ng/ml SDF-1α for 3hr


title: leukemia BM23_miR196b+MA9_P2

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

hyb_protocol: The RNA quality control, cRNA amplification, hybridization, and image scan were conducted in the Functional Genomics Facility of University of Chicago

scan_protocol: Affymetrix GeneChip Mouse Gene 1.0 ST

data_processing: The quantified signals were normalized using Robust Multi-array Average (RMA), which is a robust algorithm of background-adjustment, quantile normalization, and log-transformation. Partek Genomics Suite (Partek Inc., St. Louis, MI) was used for the analysis of the normalized data. Then mediancentering genes for each array and median-centering each gene across all arrays were also conducted for heatmap illustration

treatment_protocol: A total of 24 mouse bone marrow samples including 9 primary (including 3 each of negative control, MLL-AF9, and miR-196b+MLL-AF9) and 15 secondary (including 3 negative control, 6 MLL-AF9, and 6 miR-196b+MLL-AF9) obtained from the in vivo mouse bone marrow

tag: strain background

value: leukemic bone marrow

tag: tissue type


title: leukemia BM22_miR196b+MA9_P1

label_protocol: The RNA quality control, cRNA amplification, hybridization, and image scan were conducted in the Functional Genomics Facility of University of Chicago

tag: tissue


title: t(9;11)_THP-1

scan_protocol: Affymetrix Genechip human Exon 1.0 ST

data_processing:
Partek was used to do Robust Multi-array Average (RMA) nomalization, which is a robust algorithm of background-adjustment, quantile normalization, and log-transformation. Probes which cannot annotated with refseq genes are filtered out.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: leukemia cell line

growth_protocol: All of the AML patient samples were obtained at the time of diagnosis or relapse and with informed consent at the University of Chicago Hospital (UCH) or other collaborative hospitals, and were approved by the institutional review board of the institutes/hospitals.

extract_protocol: The RNA quality control, cRNA amplification, hybridization, and image scan were conducted in the Functional Genomics Facility of University of Chicago

tag: sample type

value: MLL-associated samples

tag: karyotype

tag: abnormality


title: MHH-CALL4_DMSO_2_extended

description:
M4_DMSO_2.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis

scan_protocol: Standard Affymetrix protocol

tag: cell line

value: human acute lymphoblastic leukemia cells


title: leukemia BM18_Control_P3

value: primary_negative control


title: C7_3h_2

description:
replicate 2
C7_3h_2

value: SW480CXCR7=C7 (lentiviral overexpression of CXCR7)


title: seedling_venom-treated_48hr_replicate1 [48V1_A1]

tag: developmental stage

value: seedlings, 5mo old

tag: time point


title: leukemia BM24_miR196b+MA9_P3


title: leukemia BM19_MA9_P1


title: seedling_venom-treated_48hr_replicate1 [48V2_A1]

value: 7-56 half-sib

tag: agent

tag: reference sample components


title: seedling_venom-treated_48hr_replicate2 [48V1_A2]

tag: genotype

value: 20 mg/ml S. noctilio venom solution


title: leukemia BM21_MA9_P3


title: seedling_venom-treated_48hr_replicate1_rescan [48V1_B1]

value: CCLONES 40430, 43680, 41586 first flush candle and needle tissue, 500 mg ea.; CCLONES 41201, 41396, 44686, 45226, drought-stressed, drought recovered, and well-watered roots from each genotype, 250 mg ea.; Genotype 7-56, callus tissue (needle origin), 250 mg.


title: t(11;19)_KOPN1

value: MLL-ENL


title: C4_3h_2

description:
replicate 2
C4_3h_2

tag: cell type

value: SW480CXCR4=C4 (lentiviral overexpression of CXCR4)

tag: exposed to


title: t(6;11)_ML-2


title: seedling_venom-treated_24hr_replicate1_rescan [24V2_B1]

description:
growth chamber raised
10 Pinus taeda seedlings cut at soil line, placed into 20 mg/ml S. noctilio venom solution until absorbed, transferred to water, flash frozen at 24hr and ten seedlings pooled.


title: MHH-CALL4_DMSO_1_extended

description:
M4_DMSO_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/extended' analysis

value: DMSO for 8hrs


title: C47_3h_1

description:
replicate 1
C47_3h_1

tag: gender

value: male

value: colon cancer cells


title: t(9;11)_MONOMAC6


title: seedling_venom-treated_48hr_replicate2_rescan [48V1_B2]


title: seedling_venom-treated_24hr_replicate2_rescan [24V2_B2]


title: leukemia BM20_MA9_P2


title: C7_3h_1

description:
replicate 1
C7_3h_1

value: tumor

tag: tumor stage

value: Dukes' type B


title: UN_3h_2

description:
replicate 2
UN_3h_2

tag: genotype/variation

value: SW480Wildtype=UN (untransduced)

value: 100 ng/ml SDF-1α for 3hr


title: N_CD34-2

description:
BM-CD34-1516
CN43

source_name: CD34+hematopoietic stem/progenitor

value: normal bone marrow samples


title: t(4;11)_KOCL48

value: MLL-associated samples


title: leukemia BM17_MA9_S6

tag: strain background

value: leukemic bone marrow


title: C4_3h_1

description:
replicate 1
C4_3h_1


title: leukemia BM14_miR196b+MA9_S4

tag: tissue type


title: seedling_venom-treated_24hr_replicate2_rescan [24V1_B2]


title: C47_12h_2

description:
replicate 2
C47_12h_2

tag: tissue

value: SW480CXCR4/CXCR7=C47 (lentiviral overexpression of CXCR4/CXCR7)

value: 100 ng/ml SDF-1α for 12hr


title: UN_3h_1

description:
replicate 1
UN_3h_1


title: seedling_venom-treated_24hr_replicate1 [24V2_A1]

value: seedlings, 5mo old

value: 7-56 half-sib


title: C47_12h_1

description:
replicate 1
C47_12h_1


title: leukemia BM15_miR196b+MA9_S5


title: N_CD34-3

description:
BM-CD34-1028
CN42

tag: sample type


title: seedling_venom-treated_24hr_replicate2 [24V2_A2]

value: 20 mg/ml S. noctilio venom solution

value: CCLONES 40430, 43680, 41586 first flush candle and needle tissue, 500 mg ea.; CCLONES 41201, 41396, 44686, 45226, drought-stressed, drought recovered, and well-watered roots from each genotype, 250 mg ea.; Genotype 7-56, callus tissue (needle origin), 250 mg.


title: N_MNC-3

description:
BM-MNC-2000
CN40

source_name: mononuclear cell (MNC)

tag: karyotype

value: NC-MNC


title: C7_12h_2

description:
replicate 2
C7_12h_2

value: SW480CXCR7=C7 (lentiviral overexpression of CXCR7)


title: leukemia BM12_Control_P2

value: primary_negative control


title: C7_12h_1

description:
replicate 1
C7_12h_1

value: male

value: colon cancer cells


title: leukemia BM16_miR196b+MA9_S6


title: seedling_venom-treated_24hr_replicate2 [24V1_A2]


title: seedling_venom-treated_24hr_replicate1_rescan [24V1_B1]


title: MHH-CALL4_JQ1_1_core

description:
M4_JQ1_1.CEL
CEL file (available on Series records) analyzed using 'Gene-level/core' analysis

value: human acute lymphoblastic leukemia cells

value: 500nM JQ1 for 8hrs


title: C4_12h_2

description:
replicate 2
C4_12h_2

value: tumor

value: Dukes' type B

value: SW480CXCR4=C4 (lentiviral overexpression of CXCR4)


title: leukemia BM11_miR196b+MA9_S2

value: leukemic bone marrow


title: N_MNC-1

description:
BM-hMNC-1656
CN4

value: normal bone marrow samples


title: leukemia BM13_miR196b+MA9_S3


title: C4_12h_1

description:
replicate 1
C4_12h_1

value: 100 ng/ml SDF-1α for 12hr


title: leukemia BM10_miR196b+MA9_S1


title: leukemia BM9_MA9_S5


title: N_CD33-5

description:
BM-CD33-1295
CN36


title: seedling_venom-treated_24hr_replicate1 [24V1_A1]

value: seedlings, 5mo old


title: leukemia BM7_MA9_S3


title: seedling_water control_48hr_replicate1 [48C_A1]

description:
growth chamber raised
10 Pinus taeda seedlings cut at soil line, placed into water, flash frozen at 48hr and ten seedlings pooled.

source_name: water control_48hr

value: 7-56 half-sib

value: water control


title: C47_0h_2

description:
replicate 2
C47_0h_2

value: SW480CXCR4/CXCR7=C47 (lentiviral overexpression of CXCR4/CXCR7)

value: PBS


title: leukemia BM8_MA9_S4


title: seedling_water control_48hr_replicate2_rescan [48C_B2]

value: CCLONES 40430, 43680, 41586 first flush candle and needle tissue, 500 mg ea.; CCLONES 41201, 41396, 44686, 45226, drought-stressed, drought recovered, and well-watered roots from each genotype, 250 mg ea.; Genotype 7-56, callus tissue (needle origin), 250 mg.


title: N_CD34-1

description:
BM-CD34-0403
CN30


title: N_CD33-2

description:
BM-CD33-1521
CN27


title: seedling_water control_48hr_replicate2 [48C_A2]


title: UN_12h_1

description:
replicate 1
UN_12h_1

value: SW480Wildtype=UN (untransduced)


title: seedling_water control_48hr_replicate1_rescan [48C_B1]


title: seedling_water control_24hr_replicate2_rescan [24C_B2]

description:
growth chamber raised
10 Pinus taeda seedlings cut at soil line, placed into water, flash frozen at 24hr and ten seedlings pooled.

source_name: water control_24hr


title: C47_0h_1

description:
replicate 1
C47_0h_1

value: male


title: N_MNC-2

description:
BM-MNC-1860
CN37

value: NC-MNC


title: N_CD33-4

description:
BM-CD33-1298
CN35


title: leukemia BM5_MA9_S1


title: leukemia BM3_Control_S2

value: secondary_negative control


title: MLL_DX-9

source_name: primary untreated leukemia

value: MLL-associated samples

value: MLL-ENL

tag: abnormality


title: seedling_water control_24hr_replicate1 [24C_A1]


title: MLL_DX-4


title: leukemia BM4_Control_S3


title: MLL_DX-7


title: seedling_water control_24hr_replicate1_rescan [24C_B1]


title: MLL_DX-2


title: C7_0h_2

description:
replicate 2
C7_0h_2

tag: cell line

value: colon cancer cells

value: tumor

value: Dukes' type B

value: SW480CXCR7=C7 (lentiviral overexpression of CXCR7)


title: leukemia BM6_MA9_S2

value: leukemic bone marrow


title: C4_0h_2

description:
replicate 2
C4_0h_2

value: SW480CXCR4=C4 (lentiviral overexpression of CXCR4)


title: C7_0h_1

description:
replicate 1
C7_0h_1


title: seedling_water control_24hr_replicate2 [24C_A2]

tag: developmental stage

value: seedlings, 5mo old

value: 7-56 half-sib


title: C4_0h_1

description:
replicate 1
C4_0h_1


title: leukemia BM2_Control_S1


title: UN_12h_2

description:
replicate 2
UN_12h_2

value: 100 ng/ml SDF-1α for 12hr


title: MLL_DX-11