title: Pt077A Leukoplakia_Buccal mucosa, cheek left-curette_1

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: aCGH analysis

hyb_protocol: Labeled DNAs were hybridized to Human Genome CGH 105K array platform (Agilent Technologies) following the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0. Briefly, fluorescent-labeled reference and tumor DNAs (4 µg each) were mixed with 25 µg of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1 (Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization and Drying Solution (Agilent) for 1 minute at room temperature.

scan_protocol: Slides were scanned immediately after washing by the Agilent G2565BA Scanner using two color scan setting for 2x105k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100%) . Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were processed by Feature Extraction version 9.5.3.1 (Agilent Technologies). Data files were analyzed byAgilent CGH Analytics Software (version 3.5.14) according to ADM-2 algorithm. The quality of each experiment was assessed by QC metric tool.

source_name: Leukoplakia

label_protocol: DNA was amplified using GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich). We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). For each array, amplified test and reference DNAs (2 µg each) were labeled by Bioprime Labeling Kit (Invitrogen, Paisley, UK). Briefly,  amplified DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) (reference and test samples, respectively) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: DNA was extracted using ArchivePure DNA (5-Prime) with some modifications: after protein precipitation the DNA was purified by phenol-chloroform extraction and collected by ethanol precipitation using 20 µg of glycogen (20 mg/ml). DNA quality was assessed by agarose gel and ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: Samples were processed to obtain DAPI stained nuclei suspensions following the method of Otto et al., (Methods Cell Biol., Academic Press San Diego, 1994; 211-217) with modifications. High resolution DNA flow cytometry of these samples was used to obtain DNA content histograms and to evaluate the DNA Index (DI), as previously described in details (Donadini et al., 2010, Cell. Oncol. 32, 373-383). DNA diploid controls were represented by gender-specific human lymphocytes. The mean CV of the corresponding DNA diploid G0-G1 peaks was 1.2±0.2%. The DNA diploid (DI=1) and aneuploid sublines were sorted using a Cyflow Space FCM equipped with a PPCS unit (Partec GmbH) at the purity of about 99%.

tag: main site-sampling

value: Buccal mucosa, cheek left-curette

tag: histology

value: Leukoplakia without dysplasia

tag: age (years)

tag: dna index

value: Male

source_name: Human Genomic DNA: male Cat G147A Promega, Madison, WI


title: Pt077A Leukoplakia_Buccal mucosa, cheek left- biopsy

status: Public on Oct 20 2011

type: genomic

description: aCGH analysis

molecule: genomic DNA

organism: Homo sapiens

value: Buccal mucosa, cheek left-biopsy

tag: gender


title: Surgical sample O-2-6

type: RNA

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

description:
O-2-6
Gene expression data from surgical sample of esophageal cancer.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 ﾟC on GeneChip Human Genome Array U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings by Expression Console ver 1.1.

label: biotin

molecule: total RNA

source_name: Esophagus, cancerous portion, surgical

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All esophageal cancer tissues and non-cancerous tissues were provided by the Central Hospital or East Hospital at the National Cancer Center after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.

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

treatment_protocol: All surgical samples were obtained from esophageal cancer patients without neoadjuvant therapy, and all biopsy samples were obtained before treatment. For the surgical samples, trained pathologists carefully excised bulk tissue samples from the main tumor, leaving a clear margin from the surrounding normal tissue. Surgical and biopsy samples were immediately frozen at -80 ﾟC until use. Frozen samples were placed in the ISOGEN solution (Nippon Gene, Toyama, Japan) and homogenised befor total RNA extraction.

tag: disease state

value: esophageal cancer

tag: tissue

value: cancerous portion of esophagus

tag: sample type

value: surgical


title: Surgical sample O-3-7

description:
O-3-7
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-15

description:
O-1-15
Gene expression data from surgical sample of esophageal cancer.


title: Pt076A Leukoplakia_Tongue, border  left- biopsy

description: aCGH analysis

value: Tongue, border  left-biopsy

value: Female

source_name: Human Genomic DNA: female Cat G152A,Promega, Madison, WI


title: Surgical sample O-3-2

description:
O-3-2
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-2-5

description:
O-2-5
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-14

description:
O-1-14
Gene expression data from surgical sample of esophageal cancer.


title: Pt076A Leukoplakia_Tongue, border left- curette

description: aCGH analysis

value: Tongue, border left-curette


title: Pt061A Leukoplakia_Buccal mucosa, retromolar trigone right- curette

description: aCGH analysis

value: Buccal mucosa, retromolar trigone right-curette


title: Surgical sample O-1-9

description:
O-1-9
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-8

description:
O-1-8
Gene expression data from surgical sample of esophageal cancer.


title: Pt062A Leukoplakia_Hard palate- curette

description: aCGH analysis

value: Hard palate-curette


title: Surgical sample O-1-7

description:
O-1-7
Gene expression data from surgical sample of esophageal cancer.


title: Pt074A Leukoplakia_Tongue- biopsy

description: aCGH analysis

value: Tongue-biopsy

value: Severe dysplastic leukoplakia


title: Surgical sample O-1-10

description:
O-1-10
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-6

description:
O-1-6
Gene expression data from surgical sample of esophageal cancer.


title: Pt077A Leukoplakia_Buccal mucosa, cheek left-curette_2

description: aCGH analysis


title: Surgical sample O-1-3

description:
O-1-3
Gene expression data from surgical sample of esophageal cancer.


title: Biopsy sample D-2-6

description:
D-2-6
Gene expression data from biopsy sample of esophageal cancer.

source_name: Esophagus, cancerous portion, biopsy

value: biopsy


title: Surgical sample O-1-2

description:
O-1-2
Gene expression data from surgical sample of esophageal cancer.


title: Biopsy sample D-2-5

description:
D-2-5
Gene expression data from biopsy sample of esophageal cancer.


title: Surgical sample O-1-4

description:
O-1-4
Gene expression data from surgical sample of esophageal cancer.


title: Pt059A  Leukoplakia_Buccal mucosa, cheek right- curette

description: aCGH analysis

value: Buccal mucosa, cheek right-curette


title: Pt035A Leukoplakia_Buccal mucosa-biopsy_1

description: aCGH analysis

value: Buccal mucosa-biopsy

value: Mild dysplastic leukoplakia


title: Biopsy sample D-2-1

description:
D-2-1
Gene expression data from biopsy sample of esophageal cancer.


title: Pt033B Leukoplakia_Gingiva-curette

description: aCGH analysis

value: Gingiva-curette

value: Leukoplakia without dysplasia


title: Pt049B Leukoplakia_Buccal mucosa- biopsy

description: aCGH analysis


title: Pt055A Leukoplakia_Buccal mucosa, cheek left-curette

description: aCGH analysis

value: Buccal mucosa, cheek left-curette

value: Male


title: Pt035A Leukoplakia_Buccal mucosa-biopsy_2

description: aCGH analysis


title: Biopsy sample D-2-2

description:
D-2-2
Gene expression data from biopsy sample of esophageal cancer.

value: esophageal cancer

value: cancerous portion of esophagus


title: Pt043A Leukoplakia_Buccal mucosa, cheek right-biopsy

description: aCGH analysis

value: Buccal mucosa, cheek right-biopsy


title: Surgical sample O-1-5

description:
O-1-5
Gene expression data from surgical sample of esophageal cancer.

value: surgical


title: Pt031B Leukoplakia_Hard palate- curette

description: aCGH analysis


title: Biopsy sample A-2-4

description:
A-2-4
Gene expression data from biopsy sample of esophageal cancer.


title: Pt053B Leukoplakia_Tongue- biopsy

description: aCGH analysis

value: Female


title: Surgical sample O-1-1

description:
O-1-1
Gene expression data from surgical sample of esophageal cancer.


title: Pt036B Leukoplakia_Tongue-curette

description: aCGH analysis

value: Tongue-curette


title: Biopsy sample D-1-1

description:
D-1-1
Gene expression data from biopsy sample of esophageal cancer.


title: Pt024B Leukoplakia_Tongue- curette

description: aCGH analysis

value: Moderate dysplastic leukoplakia


title: Biopsy sample D-1-2

description:
D-1-2
Gene expression data from biopsy sample of esophageal cancer.


title: Pt022B Near mucosa_Buccal mucosa-curette

description: aCGH analysis

source_name: Near mucosa

value: Buccal mucosa-curette

value: non dysplastic


title: Biopsy sample A-2-1

description:
A-2-1
Gene expression data from biopsy sample of esophageal cancer.

value: biopsy


title: Biopsy sample A-1-9

description:
A-1-9
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample D-1-3

description:
D-1-3
Gene expression data from biopsy sample of esophageal cancer.


title: Pt042A  Leukoplakia_Buccal mucosa, cheek right-biopsy

description: aCGH analysis


title: Pt029A Leukoplakia_Buccal mucosa, cheek right-biopsy

description: aCGH analysis


title: Pt022B Leukoplakia_Buccal mucosa- biopsy

description: aCGH analysis


title: Pt013C Leukoplakia_Tongue- biopsy

description: aCGH analysis

value: Tongue-biopsy


title: Pt014A Leukoplakia_Buccal mucosa, cheek right-biopsy

description: aCGH analysis


title: Biopsy sample A-1-14

description:
A-1-14
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample A-1-6

description:
A-1-6
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample A-1-12

description:
A-1-12
Gene expression data from biopsy sample of esophageal cancer.


title: Pt017B Near mucosa_Tongue-curette

description: aCGH analysis


title: Pt013A Leukoplakia_Buccal mucosa, cheek left-biopsy

description: aCGH analysis

value: Buccal mucosa, cheek left-biopsy


title: Biopsy sample A-1-1

description:
A-1-1
Gene expression data from biopsy sample of esophageal cancer.


title: Pt012B Leukoplakia_Tongue-curette

description: aCGH analysis

value: Mild dysplastic leukoplakia


title: Biopsy sample A-1-13

description:
A-1-13
Gene expression data from biopsy sample of esophageal cancer.


title: Pt022B Leukoplakia_Buccal mucosa- curette

description: aCGH analysis


title: Pt017B Leukoplakia_Tongue-curette

description: aCGH analysis


title: Pt020A Leukoplakia_Left gingiva-biopsy

description: aCGH analysis

value: Left gingiva-biopsy


title: Pt012A Leukoplakia_Buccal mucosa, cheek left-biopsy

description: aCGH analysis


title: snf1-tor1_N_03

city: Kgs. Lyngby

first: Jie

last: Zhang

address: Kemitorvet 220

department: CFB

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station 450.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.6. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Saccharomyces cerevisiae

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: strains were grown in 1.2 l bioreactor (with working olume 0.5 l) at 30°C, pH 5.0 and aerobically. The C-lim contains 10 g/L glucose and the N-lim medium contains 1g/L amonia sulfate, dilution rate 0.1h-1

extract_protocol: Total RNA was isolated from frozen cell pellets using Qiagen Rnaesy Kit (Qiagen)

treatment_protocol: biomass samples were taken at steadystate, cooled down imeediately and centrifuged with cooling, The cell prllets were frozen in liquid nitrogen

tag: genotype

tag: medium

value: N-lim


title: siRNA Ncl-2 +Tc, rep2

city: Shanghai

first: Ying

last: Jin

address: 225 South Chongqing Road

department: Shanghai Stem Cell Institute

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Replicate 2 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using the Illumina Bead Array Reader.

data_processing: The data were normalised using cubic spline with Illumina Genome Studio V2010.1.

organism: Mus musculus

source_name: CGR8 ES cells, siRNA Ncl-2, +Tc

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

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

tag: strain

tag: cell line

tag: cell type

value: embryonic stem cells (ESCs)

tag: sirna

tag: induction

value: tetracycline


title: Pt008A Leukoplakia_Gingiva-biopsy

description: aCGH analysis

value: Gingiva-biopsy


title: siRNA Ncl-2 +Tc, rep3

description: Replicate 3 of 3.


title: snf1-tor1_N_01


title: snf1-tor1_C_02

value: C-lim


title: snf1-tor1_C_03


title: siRNA Ncl-2 +Tc, rep1

description: Replicate 1 of 3.


title: tor1_N_11


title: snf1-tor1_C_01


title: tor1_N_10


title: tor1_N_09


title: ACKERMAN_WT_3 [gene-level]

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
ACKERMAN_WT_3.CEL
cerebellum from P30 female wild type

hyb_protocol: GeneChip® Mouse Exon 1.0 ST Arrays (Affymetrix) were hybridized with 2.3µg of biotin-labeled cDNA for 16 hours at 45°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChipTM Scanner 3000 (Affymetrix) laser confocal slide scanner.

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: cerebellar total RNA from P30 female wild type

label_protocol: Total RNA was isolated by TRIzolPlus (Invitrogen) and cDNA was synthesized, labeled and fragmented using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Age and gender-matched wild type and NMF291–/– mice.

extract_protocol: The cerebellar total RNAs were extracted by Trizol.

treatment_protocol: The NMF291 mutant mice carry a mutation (5-nucleotide-deletion) in mouse Rnu2-8 (U2 snRNA) gene.

tag: genotype/variation

value: WT


title: snf1-tor1_N_02


title: siRNA Ncl-1 +Tc, rep3

description: Replicate 3 of 3.

source_name: CGR8 ES cells, siRNA Ncl-1, +Tc


title: ACKERMAN_WT_2 [gene-level]

description:
ACKERMAN_WT_2.CEL
cerebellum from P30 female wild type


title: siRNA Ncl-1 +Tc, rep1

description: Replicate 1 of 3.


title: siRNA Ncl-2 -Tc, rep2

description: Replicate 2 of 3.

source_name: CGR8 ES cells, siRNA Ncl-2, -Tc


title: tor1_C_09


title: siRNA Ncl-2 -Tc, rep3

description: Replicate 3 of 3.


title: siRNA Ncl-1 +Tc, rep2

description: Replicate 2 of 3.


title: Pt002C Leukoplakia_Buccal mucosa-curette

description: aCGH analysis

value: Leukoplakia without dysplasia


title: tor1_C_08


title: ACKERMAN_MUT_3 [gene-level]

description:
ACKERMAN_MUT_3.CEL
cerebellum from P30 female NMF291–/–

source_name: cerebellar total RNA from P30 female NMF291–/–


title: ACKERMAN_MUT_2 [gene-level]

description:
ACKERMAN_MUT_2.CEL
cerebellum from P30 female NMF291–/–


title: tor1_C_07


title: siRNA Ncl-2 -Tc, rep1

description: Replicate 1 of 3.


title: snf1_N_11


title: snf1_N_10


title: snf1_N_09


title: ACKERMAN_WT_1 [gene-level]

description:
ACKERMAN_WT_1.CEL
cerebellum from P30 female wild type


title: WT_N_10

value: wild type


title: ACKERMAN_MUT_1 [gene-level]

description:
ACKERMAN_MUT_1.CEL
cerebellum from P30 female NMF291–/–


title: snf1_C_12


title: WT_C_11


title: Combination Rapamycin and Nimotuzumab 3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene data after tumor extracted on Day 18

hyb_protocol: The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Human 8x60k (AMADID No: 027114). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

data_processing: Data extraction from Images was done using Feature Extraction software Version 10.7 and Normalization of the data was done in GeneSpring GX V 11.5

source_name: Combination

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: A431 cells were grown in DMEM medium (10% FBS), 5*10^6 cells were injected in to the mice sub cutaneously.

extract_protocol: Tissue was homogenized using Tissue Homogenizer and RNA isolation was done using TRIzol method.

treatment_protocol: Six doses of each treatment were given to the mice intra peritonealy. Dosings were given on day 7,9,11,14,16 and 18. The mice were then sacrificed on Day 18, two hours after the last dosing.

tag: source cell line

value: tumor xenograft

tag: treatment

value: Rapamycin and Nimotuzumab


title: siRNA Ncl-1 -Tc, rep1

description: Replicate 1 of 3.

source_name: CGR8 ES cells, siRNA Ncl-1, -Tc


title: WT_N_09


title: snf1_C_11


title: WT_C_10


title: siRNA Ncl-1 -Tc, rep3

description: Replicate 3 of 3.


title: siRNA EGFP +Tc, rep2

description: Replicate 2 of 3.

source_name: CGR8 ES cells, siRNA EGFP, +Tc

value: EGFP

value: control


title: siRNA Ncl-1 -Tc, rep2

description: Replicate 2 of 3.


title: snf1_C_10


title: Pt012A Leukoplakia_Buccal mucosa, cheek right-biopsy

description: aCGH analysis

tag: main site-sampling

value: Buccal mucosa, cheek right-biopsy

tag: histology

value: Male


title: WT_N_11


title: Combination Rapamycin and Nimotuzumab 1

scan_protocol: The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Human 8x60k (AMADID No: 027114). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)


title: siRNA EGFP +Tc, rep1

description: Replicate 1 of 3.


title: siRNA EGFP -Tc, rep3

description: Replicate 3 of 3.

source_name: CGR8 ES cells, siRNA EGFP, -Tc


title: siRNA EGFP +Tc, rep3

description: Replicate 3 of 3.


title: Biopsy sample D-1-8

description:
D-1-8
Gene expression data from biopsy sample of esophageal cancer.

value: esophageal cancer

value: cancerous portion of esophagus

value: biopsy


title: Nimotuzumab 3

source_name: Nimotuzumab

value: Nimotuzumab


title: Nimotuzumab 4


title: Combination Rapamycin and Nimotuzumab 2


title: WT_C_09


title: Biopsy sample D-1-9

description:
D-1-9
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample D-1-7

description:
D-1-7
Gene expression data from biopsy sample of esophageal cancer.


title: siRNA EGFP -Tc, rep1

description: Replicate 1 of 3.

value: embryonic stem cells (ESCs)


title: siRNA EGFP -Tc, rep2

description: Replicate 2 of 3.


title: Nimotuzumab 2


title: Biopsy sample D-1-4

description:
D-1-4
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample D-1-6

description:
D-1-6
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample D-1-5

description:
D-1-5
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample D-1-11

description:
D-1-11
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample A-1-8

description:
A-1-8
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample D-1-10

description:
D-1-10
Gene expression data from biopsy sample of esophageal cancer.


title: Nimotuzumab 1


title: Biopsy sample A-1-7

description:
A-1-7
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample A-1-5

description:
A-1-5
Gene expression data from biopsy sample of esophageal cancer.


title: Rapamycin 3

source_name: Rapamycin

value: Rapamycin


title: Rapamycin 4


title: Biopsy sample A-1-4

description:
A-1-4
Gene expression data from biopsy sample of esophageal cancer.


title: Rapamycin 2


title: Control 2

source_name: Control

value: untreated


title: Biopsy sample A-1-3

description:
A-1-3
Gene expression data from biopsy sample of esophageal cancer.


title: Rapamycin 1


title: Biopsy sample A-1-11

description:
A-1-11
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample A-1-2

description:
A-1-2
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample A-1-10

description:
A-1-10
Gene expression data from biopsy sample of esophageal cancer.


title: Control 1

description: Gene data after tumor extracted on Day 18


title: Pichia stipitis Xylose Replicate 3

type: mixed

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

department: Biology

country: USA

institute: Dickinson College

description: Biological replicate 3 of 3. Experimental xylose-grown cells, harvested after 3 generations.

hyb_protocol: Arrays were hybridized in a NimbleGen hybridization system 12 (BioMicro) following the standard NimbleGen operating protocol. See www.nimblegen.com.

scan_protocol: Arrays were scanned using a GenePix 4000B scanning laser (Molecular Devices) following the standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al.  (2004) Genome Biol 5: R80).  The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3).  Gene-level expression changes were summarized with the median value of each probe set contained completely within each predicted ORF.  See the included file PstiProbeMapping.txt for a mapping of probes to genes.

organism: Scheffersomyces stipitis CBS 6054

source_name: Pichia stipitis CBS 6054 xylose

label_protocol: Sample labeling was performed as described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414, using cyanine dyes (Amersham), Superscript III (Invitrogen), and amino-allyl-dUTP (Ambion).  RNA collected from cells grown in each sugar condition was labeled with Cy5 dye and was directly compared to a genomic DNA reference sample labeled with Cy3 dye.

growth_protocol: Pichia stipitis CBS 6054 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase.  Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures.  Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture.  Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.

extract_protocol: Cell collection, lysis, and total RNA isolation were performed as previously described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414.  Following total RNA isolation, RNA was further purified with LiCl and RNeasy Mini kit (Qiagen).  RNA concentration was determined by NanoDrop spectrophotometer (Thermo Scientific).

treatment_protocol: One culture was treated with 2% glucose for 3 generations growth; the other culture was treated with 2% xylose for 3 generations growth.

value: 2% xylose for 3 generations growth

source_name: Pichia stipitis CBS 6054 genomic

value: Genomic DNA was extracted from cells growing in log phase


title: Pichia stipitis Xylose Replicate 2

description: Biological replicate 2 of 3. Experimental xylose-grown cells, harvested after 3 generations.


title: Pichia stipitis Glucose Replicate 2

description: Biological replicate 2 of 3. Control glucose-grown cells, harvested after 3 generations.

source_name: Pichia stipitis CBS 6054 glucose

value: 2% glucose for 3 generations growth


title: Pichia stipitis Glucose Replicate 1

description: Biological replicate 1 of 3. Control glucose-grown cells, harvested after 3 generations.


title: 047array1 2

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Auto-gain scanning with Tecan technology

data_processing: Background correciton, intra and between array normalisation, limma algorithm for statistical comparion. Data normalization was done with FlexArray 1.6.1. Reference: Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007), FlexArray: A statistical data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada, URL : http://genomequebec.mcgill.ca/FlexArray)

organism: Bos taurus

source_name: Glucose

label_protocol:
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries

extract_protocol: This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100% of RNA. RNA extraction from larger samples should be done using another kit or technique.

treatment_protocol: In vitro culture with 5 mM of Glucose (treatment) or 0.2 mM (control) during cleavage stage (days 0 to 3) and transfert in normal IVC medium until development to blastocyst stage.

tag: developmental stage

tag: breed (cattle)

tag: time of embryo collection

value: 180 hpf (hours post-in-vitro fertilization)

tag: bsa source

value: sigma

tag: picture available

value: Yes

tag: dose

value: 5 mM

tag: number per pool

tag: in vitro production

source_name: vitro


title: 056 Array1 1


title: 047array2 2


title: Pichia stipitis Xylose Replicate 1

description: Biological replicate 1 of 3. Experimental xylose-grown cells, harvested after 3 generations.


title: Pichia stipitis Glucose Replicate 3

description: Biological replicate 3 of 3. Control glucose-grown cells, harvested after 3 generations.


title: Rest of body_0.16/0gossypol_replicate 3

city: Stockholm

first: Maria de la Paz

last: Celorio-Mancera

address: Svante Arrheniusväg 18 B

department: Zoology

country: Sweden

institute: Stockholm University

description:
pooled from 10 animals
Har RC T7 vs Ct-rep 3

hyb_protocol: 825 ng of each cyanine 3 and cy5 labeled cRNA was used for each array and hybridization was carried out at 65oC for 17 hours. Slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

scan_protocol: As per manufacturers instruction, using an Agilent microarray scanner.

data_processing: Note that each sample was labelled with either Cy3 and Cy5. Data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data for both dye channels from output files were analyzed using the GeneSpring GX11  and GeneSifter microarray analysis software and the Rank Products method. The data points were normalized between arrays to the median intensity and were subjected log base 2-transformation. The matrix includes the log transformed ratios obtained by GeneSpring GX11 analysis. [The second value column contains the inversed ratio calculated from the same raw data file]

organism: Helicoverpa armigera

source_name: Rest of body Detrimental (0.16% gossypol)

label_protocol: Agilent Technologies spike-in RNA was added to 500 ng of total RNA and labeled using a combination of the QuickAmp Labeling kit (Agilent Technologies) for two-color arrays following the manufacturer´s instructions. Labeled amplified cRNA samples were purified using Qiagen RNeasy MinElute columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >825 ng and the specific activity >8.0 pmol Cy3 or Cy5 per ug cRNA

growth_protocol: Helicoverpa armigera larvae were collected from Toowoomba, Queensland, Australia, in 2003 and reared under laboratory conditions (26 °C, 55% RH, 16:8 hr = L:D) in Jena, Germany.  The colony was maintained for about 25 generations prior to the start of this study, exclusively by about 50 single-pair crosses per generation, avoiding brother-sister mating to minimize inbreeding.  The artificial diet for larval rearing was purchased from BioServ (F9772, Frenchtown, NJ, USA). Gossypol from cotton seeds (G8761, racemic mixture, Sigma-Aldrich, MO, USA) was incorporated into the artificial diet using a carrier material of non-nutritive cellulose, Alphacel in various concentrations (CT=0.0, T1=0.0004, T2=0.0016, T3=0.004, T4=0.008, T5=0.016, T6=0.04, or T7=0.16% (w/v)).

extract_protocol: Tissues were snap-frozen in liquid nitrogen. The frozen tissue was transferred to a liquid nitrogen cooled mortar and ground. The homogenate was covered with 1 ml Trizol reagent (Sigma-Aldrich, St. Louis, MIS). Further steps were performed according to the manufacturers instruction, replacing choloroform with 1-bromo-3-chloro-propane. Also, an additional DNAse (Turbo DNAse, Ambion, Austin, TX) treatment was included to eliminate any contaminating DNA. TotalRNA was dissolved in RNA Storage Solution (Ambion) and RNA content and quality was measured photometrically.

treatment_protocol: Larvae were ice-cold anesthesized prior to dissection which took place under phosphate-buffered saline.

tag: colony/larval stage

value: Toowoomba 5th instar

source_name: Rest of body Control (0%gossypol)


title: Rest of body_0.016/0gossypol_replicate 3

description:
pooled from 10 animals
Har RC T5 vs Ct-rep3

source_name: Rest of body Hormetic (0.016% gossypol)


title: 056 Array3 1


title: Rest of body_0.16/0gossypol_replicate 1

description:
pooled from 10 animals
Har RC T7 vs Ct-rep 1


title: 056 Array2 1


title: 047array3 2


title: Rest of body_0.16/0gossypol_replicate 2

description:
pooled from 10 animals
Har RC T7 vs Ct-rep 2


title: 056 Array4 1


title: 047array4 2


title: Rest of body_0.016/0gossypol_replicate 4

description:
pooled from 10 animals
Har RC T5 vs Ct-rep4


title: Rest of body_0.016/0gossypol_replicate 2

description:
pooled from 10 animals
Har RC T5 vs Ct-rep2


title: Spathaspora passalidarum Xylose Replicate 3

data_processing: Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al.  (2004) Genome Biol 5: R80).  The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3).  Gene-level expression changes were summarized with the median value of each probe set contained completely within each predicted ORF.  See the included file SpasProbeMapping.txt for a mapping of probes to genes.

organism: Spathaspora passalidarum NRRL Y-27907

source_name: Spathaspora passalidarum NRRL Y-27907 xylose

growth_protocol: Spathaspora passalidarum NRRL Y-27907 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase.  Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures.  Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture.  Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.

source_name: Spathaspora passalidarum NRRL Y-27907 genomic


title: Control 3

tag: tissue

value: tumor xenograft


title: Rest of body_0.16/0gossypol_replicate 4

description:
pooled from 10 animals
Har RC T7 vs Ct-rep 4


title: Spathaspora passalidarum Xylose Replicate 2


title: Spathaspora passalidarum Xylose Replicate 1


title: CLL40

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: aCLL patients

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. The WACA algorithm (F Lepretre et al., NAR 2010) was finally used for CGH waves correction for fine and reliable genomics comparisons.

source_name: atypical chronic lymphocytic leukemia

label_protocol: manufacturer's instructions

extract_protocol: manufacturer's instructions

treatment_protocol: Total DNA extracted using manufacturer's instructions

tag: disease

value: atypical chronic lymphocytic leukemia

source_name: Promega male control DNA

value: normal


title: CLL35

description: aCLL patients


title: CLL31

description: aCLL patients


title: Candida tenuis Xylose Replicate 3

data_processing: Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al.  (2004) Genome Biol 5: R80).  The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3).  Gene-level expression changes were summarized with the median value of each probe set contained completely within each predicted ORF.  See the included file CtenProbeMapping.txt for a mapping of probes to genes.

organism: Yamadazyma tenuis ATCC 10573

source_name: Candida tenuis NRRL Y-1498 xylose

growth_protocol: Candida tenuis NRRL Y-1498 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase.  Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures.  Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture.  Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.

source_name: Candida tenuis NRRL Y-1498 genomic


title: Rest of body_0.016/0gossypol_replicate 1

description:
pooled from 10 animals
Har RC T5 vs Ct-rep1


title: CLL30

description: aCLL patients


title: CLL39

description: aCLL patients


title: CLL36

description: aCLL patients


title: Rest of body_0/0.16gossypol_replicate 4

description:
pooled from 10 animals
Har RC Ct vs T7-rep4


title: Spathaspora passalidarum Glucose Replicate 3

source_name: Spathaspora passalidarum NRRL Y-27907 glucose


title: Spathaspora passalidarum Glucose Replicate 2


title: CLL29

description: aCLL patients


title: CLL28

description: aCLL patients


title: Spathaspora passalidarum Glucose Replicate 1


title: Candida tenuis Xylose Replicate 2


title: CLL34

description: aCLL patients


title: Rest of body_0/0.16gossypol_replicate 3

description:
pooled from 10 animals
Har RC Ct vs T7-rep3


title: Rest of body_0/0.16gossypol_replicate 2

description:
pooled from 10 animals
Har RC Ct vs T7-rep2


title: CLL27

description: aCLL patients


title: Candida tenuis Glucose Replicate 3

source_name: Candida tenuis NRRL Y-1498 glucose


title: Rest of body_0/0.16gossypol_replicate 1

description:
pooled from 10 animals
Har RC Ct vs T7-rep1


title: CLL26

description: aCLL patients


title: Candida tenuis Xylose Replicate 1


title: Candida tenuis Glucose Replicate 1


title: Candida tenuis Glucose Replicate 2


title: CLL25

description: aCLL patients


title: Patient 599 plasma

city: Seville

first: Sonia

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

country: Spain

institute: IBIS

data_processing: Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. .

label: FAM

source_name: Plasma

label_protocol: FAM

extract_protocol: Total RNA containing small RNA was extracted from plasma by Trizol LS Reagent and from bronchoalveolar cell fraction by Trizol Reagent (Invitrogen, Carlsbad, CA)

tag: sample type

value: Plasma

tag: subject

value: Patient 599

tag: disease state

value: Adenocarcinoma

tag: gender

value: Male

tag: age (y)


title: Patient 729 plasma

value: Patient 729


title: Patient 557 plasma

value: Patient 557

value: Interstitial lung disease


title: Patient 784 plasma

value: Patient 784


title: Rest of body_0/0.016gossypol_replicate 3

description:
pooled from 10 animals
Har RC Ct vs T5-rep3


title: Patient 539 plasma

value: Patient 539

value: Healthy

value: Female


title: Rest of body_0/0.016gossypol_replicate 1

description:
pooled from 10 animals
Har RC Ct vs T5-rep1


title: Patient 514 plasma

value: Patient 514


title: Rest of body_0/0.016gossypol_replicate 2

description:
pooled from 10 animals
Har RC Ct vs T5-rep2


title: Rest of body_0/0.016gossypol_replicate 4

description:
pooled from 10 animals
Har RC Ct vs T5-rep4


title: CLL24

description: aCLL patients


title: CLL22

description: aCLL patients


title: Gut_0.16/0gossypol_replicate 4

description:
pooled from 10 animals
Har T7 vs Ct-rep4

source_name: Gut Detrimental (0.16% gossypol)

source_name: Gut Control (0%gossypol)


title: CLL21

description: aCLL patients


title: CLL23

description: aCLL patients


title: ACKERMAN_WT_3 [exon-level]

description:
ACKERMAN_WT_3.CEL
cerebellum from P30 female wild type

source_name: cerebellar total RNA from P30 female wild type

tag: genotype/variation

value: WT


title: CLL20

description: aCLL patients


title: ACKERMAN_WT_1 [exon-level]

description:
ACKERMAN_WT_1.CEL
cerebellum from P30 female wild type


title: CLL19

description: aCLL patients


title: Gut_0.16/0gossypol_replicate 1

description:
pooled from 10 animals
Har T7 vs Ct-rep1

value: Toowoomba 5th instar


title: Gut_0.16/0gossypol_replicate 3

description:
pooled from 10 animals
Har T7 vs Ct-rep3


title: Gut_0.16/0gossypol_replicate 2

description:
pooled from 10 animals
Har T7 vs Ct-rep2


title: CLL18

description: aCLL patients


title: Patient 505 plasma

value: Patient 505


title: Patient 784 bronchoalveolar fluid cytology

source_name: Bronchoalveolar fluid citology

value: Bronchoalveolar cell fraction


title: wt vs IRF8 KO-3

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

description: Replicate 2.

hyb_protocol: Slides were hybridized with probes according to the standard hybridization.

scan_protocol: Scanned on a GenePix 4000B scanner. Images were quantified using GenePix Pro 4.1 software.

data_processing: Raw data (gpr file) and images were uploaded to the mAdb microarray Database (NCBI/NIH) for normalization. Median normalized log2 ratio Cy5/Cy3 data sets were extracted from mAdb. Signal calculation=Mean Intensity minus Median Background. Any Features designated Control were excluded.  Normalization method: Precalculated 50th Percentile (Median). Both Chan A and Chan B Signal/Background Ratios >= 1.000 and Both Chan A and Chan B Signal >= 100.  Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B)

source_name: wt primary CD11b-positive cells

label_protocol: Ten µg of total RNA were used for cDNA synthesis, probe preparation and labeling using the FairPlay DNA Microarray Labeling Kit (Strategene). Monoreactive Cy3 and Cy5 were obtained from GE HealthCare. All reactions were carried out following the manufacturer's instructions

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

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

treatment_protocol: Primary cells without any treatment

value: wt

source_name: IRF8 KO primary CD11b-positive cells

value: IRF8 KO


title: CLL17

description: aCLL patients

value: atypical chronic lymphocytic leukemia

value: normal


title: Gut_0.016/0gossypol_replicate 4

description:
pooled from 10 animals
Har G T5 vs Ct-rep4

source_name: Gut Hormetic (0.016% gossypol)


title: Patient 460 plasma

value: Plasma

value: Patient 460

value: Male


title: CLL16

description: aCLL patients


title: Patient 435 plasma

value: Patient 435

value: Interstitial lung disease


title: ACKERMAN_MUT_3 [exon-level]

description:
ACKERMAN_MUT_3.CEL
cerebellum from P30 female NMF291–/–

source_name: cerebellar total RNA from P30 female NMF291–/–


title: ACKERMAN_MUT_1 [exon-level]

description:
ACKERMAN_MUT_1.CEL
cerebellum from P30 female NMF291–/–


title: Patient 385 plasma

value: Patient 385

value: Adenocarcinoma


title: Gut_0.016/0gossypol_replicate 3

description:
pooled from 10 animals
Har G T5 vs Ct-rep3


title: CLL14

description: aCLL patients


title: wt vs IRF8 KO-2

description: Replicate 1.


title: ACKERMAN_MUT_2 [exon-level]

description:
ACKERMAN_MUT_2.CEL
cerebellum from P30 female NMF291–/–


title: Patient 557 bronchoalveolar fluid cytology

value: Patient 557


title: Gut_0.016/0gossypol_replicate 1

description:
pooled from 10 animals
Har G T5 vs Ct-rep1


title: CLL13

description: aCLL patients


title: Gut_0.016/0gossypol_replicate 2

description:
pooled from 10 animals
Har G T5 vs Ct-rep2


title: Patient 729 bronchoalveolar fluid cytology

value: Patient 729


title: ACKERMAN_WT_2 [exon-level]

description:
ACKERMAN_WT_2.CEL
cerebellum from P30 female wild type

value: WT


title: Gut_0/0.16gossypol_replicate 4

description:
pooled from 10 animals
Har G Ct vs T7-rep4

value: Toowoomba 5th instar


title: Patient 599 bronchoalveolar fluid cytology

value: Patient 599


title: Patient 514 bronchoalveolar fluid cytology

value: Bronchoalveolar cell fraction

value: Patient 514


title: CLL12

description: aCLL patients


title: CLL10

description: aCLL patients


title: Patient 539 bronchoalveolar fluid cytology

value: Patient 539

value: Healthy

value: Female


title: CLL8

description: aCLL patients

value: atypical chronic lymphocytic leukemia

value: normal


title: CLL7

description: aCLL patients


title: CLL38

description: CLL patients

source_name: typical chronic lymphocytic leukemia

value: typical chronic lymphocytic leukemia


title: Patient 460 bronchoalveolar fluid cytology

value: Patient 460

value: Male


title: Patient 435 bronchoalveolar fluid cytology

value: Patient 435

value: Interstitial lung disease


title: CLL37

description: CLL patients


title: Gut_0/0.16gossypol_replicate 3

description:
pooled from 10 animals
Har G Ct vs T7-rep3


title: Patient 505 bronchoalveolar fluid cytology

value: Patient 505

value: Adenocarcinoma


title: CLL9

description: aCLL patients


title: Gut_0/0.16gossypol_replicate 2

description:
pooled from 10 animals
Har G Ct vs T7-rep2


title: Gut_0/0.016gossypol_replicate 4

description:
pooled from 10 animals
Har G Ct vs T5-rep4


title: Gut_0/0.16gossypol_replicate 1

description:
pooled from 10 animals
Har G Ct vs T7-rep1


title: CLL15

description: CLL patients


title: CLL32

description: CLL patients


title: CLL6

description: aCLL patients


title: CLL4

description: aCLL patients


title: CLL11

description: CLL patients


title: CLL5

description: CLL patients


title: CLL33

description: CLL patients


title: Patient 385 bronchoalveolar fluid cytology

value: Patient 385


title: Normal lymphoid cell line WEIS3E5 (expression data)

status: Public on Oct 19 2011

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: RMA Bioconductor (default parameters) and log2 transformation.

source_name: Normal lymphoid cell line

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Tripure method (Roche) according to the manufacturer instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the BioAnalyzer (Agilent Inc).

tag: conditions

value: Normal

tag: treatment protocol

value: The WEIS3E5 cells were harvested after 3 days of growth

tag: growth protocol

value: The normal CD8+ lymphoid cell line WEIS3E5 was maintained in Isocove Dubelcco medium supplemented with 10% human serum HS54, L-Arginine, L-Asparagine, L-glutamine, 2-mercaptoéthanol and methyltryptophane as well as with 10 ng/mL of IL-7 and 50 U/mL of IL-2.

tag: cell line


title: Gut_0/0.016gossypol_replicate 2

description:
pooled from 10 animals
Har G Ct vs T5-rep2

value: Toowoomba 5th instar


title: CLL2

description: CLL patients


title: CLL3

description: CLL patients


title: ex vivo T lymphocytes (expression data)

source_name: ex vivo T lymphocytes

value: ex vivo

value: Ex vivo T lymphocytes were isolated from blood sample of a patient with hemochromatosis using CD3 antibody coupled to magnetic beads (Miltenyi Biotec).

tag: cell type

value: ex vivo T lymphocytes


title: ex vivo B lymphocytes (expression data)

source_name: ex vivo B lymphocytes

value: Ex vivo B lymphocytes were isolated from blood sample of a patient with hemochromatosis using CD20 antibody coupled to magnetic beads (Miltenyi Biotec).

value: ex vivo B lymphocytes


title: Breast cancer cell line MDA-MB-361 5 AZA (expression data)

source_name: Breast cancer cell line

value: Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days before being harvested. They were detached from the culture flask using a cell scraper.

value: MDA-MB-361 5-AZA cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.

tag: agent


title: Breast cancer cell line MDA-MB-231 WT (expression data)

value: WT

value: Cells were harvested after 5 or 6 passages. They were detached from the culture flask using a cell scraper.

value: MDA-MB-231 WT cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line ZR-75-1 WT (expression data)

value: ZR-75-1 WT cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line ZR-75-1 5 AZA (expression data)

value: ZR-75-1 5-AZA cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: CLL1

description: aCLL patients

source_name: atypical chronic lymphocytic leukemia

value: atypical chronic lymphocytic leukemia

source_name: Promega male control DNA

value: normal


title: Breast cancer cell line MDA-MB-231 5 AZA (expression data)

value: MDA-MB-231 5-AZA cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day


title: Gut_0/0.016gossypol_replicate 1

description:
pooled from 10 animals
Har G Ct vs T5-rep1


title: Breast cancer cell line MCF-7 5-AZA (expression data)

value: MCF-7 5-AZA cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: Breast cancer cell line T47D WT (expression data)

value: T47D WT cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Normal breast cell line MCF10A (expression data)

source_name: Normal breast cell line

value: Normal

value: MCF10A WT cells were maintained in DMEM/F12 (1:1) medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Gut_0/0.016gossypol_replicate 3

description:
pooled from 10 animals
Har G Ct vs T5-rep3

value: Toowoomba 5th instar


title: Breast cancer cell line MCF-7 WT (expression data)

value: MCF-7 WT cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line T47D 5 AZA (expression data)

value: T47D 5-AZA cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: Breast cancer cell line MDA-MB-361 WT (expression data)

value: MDA-MB-361 WT cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line SKBR3 5 AZA (expression data)

value: Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days before being harvested. They were detached from the culture flask using a cell scraper.

value: SKBR3 5-AZA cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: Normal lymphoid cell line WEIS3E5 (methylation data)

hyb_protocol: DNA samples were hybridized onto the HumanMethylation27 BeadChips during 16 hours at 48°C. Unhybridized and non-specifically hybridized DNA were washed from the BeadChips, according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA).

scan_protocol: The BeadChips were scanned with the Illumina BeadArrayTM Reader.

data_processing: Initial data analysis was performed with the Methylation module of the Genome Studio software provided by Illumina.

label: C-Bio and A-DNP

label_protocol: Labelled nucleotides were added to extend the primers hybridized to the DNA and primers were stained according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA).

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Mini Kit according to the supplier’s instructions (Qiagen, Hilden, Germany). This included the recommended proteinase K and RNase A digestions. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Genomic DNA from  cells was extracted using the QIAamp DNA Mini Kit according to the supplier’s instructions (Qiagen, Hilden, Germany). This included the recommended proteinase K and RNase A digestions. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Cells were harvested after 5 or 6 passages. They were detached from the culture flask using a cell scraper.

value: The WEIS3E5 cells were harvested after 3 days of growth

value: The normal CD8+ lymphoid cell line WEIS3E5 was maintained in Isocove Dubelcco medium supplemented with 10% human serum HS54, L-Arginine, L-Asparagine, L-glutamine, 2-mercaptoéthanol and methyltryptophane as well as with 10 ng/mL of IL-7 and 50 U/mL of IL-2.

tag: methylation barcode


title: Breast cancer cell line R12C9

value: The R12C9 cells were harvested after 3 days of growth.

value: The normal CD4+ lymphoid cell line R12C9 was maintained in Isocove Dubelcco medium supplemented with 10% human serum HS54, L-Arginine, L-Asparagine, L-glutamine, 2-mercaptoéthanol and methyltryptophane as well as with 10 ng/mL of IL-7 and 50 U/mL of IL-2.


title: Breast cancer cell line ZR-75-1 5 AZA (methylation data)

value: ZR-75-1 5-AZA cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: ex vivo T lymphocytes (methylation data)

value: ex vivo

value: Ex vivo T lymphocytes were isolated from blood sample of a patient with hemochromatosis using CD3 antibody coupled to magnetic beads (Miltenyi Biotec).

value: ex vivo T lymphocytes


title: Breast cancer cell line MDA-MB-361 5 AZA (methylation data)

value: MDA-MB-361 5-AZA cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: ex vivo B lymphocytes (methylation data)

value: Ex vivo B lymphocytes were isolated from blood sample of a patient with hemochromatosis using CD20 antibody coupled to magnetic beads (Miltenyi Biotec).

value: ex vivo B lymphocytes


title: Breast cancer cell line MDA-MB-361 WT (methylation data)

value: WT

value: Cells were harvested after 5 or 6 passages. They were detached from the culture flask using a cell scraper.


title: Breast cancer cell line SKBR3 5 AZA (methylation data)


title: Breast cancer cell line ZR-75-1 WT (methylation data)

value: ZR-75-1 WT cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line T47D WT (methylation data)

value: T47D WT cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line SKBR3 WT (expression data)

value: SKBR3 WT cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line MDA-MB-231 WT (methylation data)

value: MDA-MB-231 WT cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line T47D 5 AZA (methylation data)

value: Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days before being harvested. They were detached from the culture flask using a cell scraper.

value: T47D 5-AZA cells were maintained in RPMI medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: Normal breast tissue from patient P2_N122 (methylation data)

scan_protocol: Labelled nucleotides were added to extend the primers hybridized to the DNA and primers were stained according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA).

data_processing: Data analysis was performed with the Methylation module of the Genome Studio software provided by Illumina using default parameters. Average beta value is defined as the ratio of signal from a methylated probe (C not converted to T) relative to the sum of both methylated (C not converted to T) and unmethylated probes (C bisulfite-converted to T) (? value=C/[(T+C)+100]

source_name: Normal breast tissue

label_protocol: Please see hyb protocol (since labeling occurs AFTER hybridization).

extract_protocol: Genomic DNA from frozen samples was extracted from twenty 10-um sections using the Qiagen-DNeasy Blood &Tissue Kit according to the supplierâ??s instructions (Qiagen, Hilden, Germany). This included a proteinase K digestion at 55Â°C overnight. DNA was quantitated with the NanoDropÂ® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

value: Normal breast tissue

tag: quality control

tag: subtype ihc

value: Normal

tag: grade

tag: node

tag: size bin

tag: age bin

tag: er


title: Breast cancer cell line SKBR3 WT (methylation data)


title: Breast cancer cell line MDA-MB-231 5 AZA (methylation data)

value: MDA-MB-231 5-AZA cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day


title: Normal breast tissue from patient P2_N123 (methylation data)

tag: tissue


title: Normal breast cell line MCF10A (methylation data)

value: MCF10A WT cells were maintained in DMEM/F12 (1:1) medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast cancer cell line BT20 WT (methylation data)

value: BT20 WT cells were maintained in MEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Normal breast tissue from patient P2_N121 (methylation data)


title: Normal breast tissue from patient P2_N127 (methylation data)


title: Breast cancer cell line MCF-7 5-AZA (methylation data)

value: MCF-7 5-AZA cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: Normal breast tissue from patient P2_N125 (methylation data)


title: Normal breast tissue from patient P2_N124 (methylation data)


title: Normal breast tissue from patient P2_N128 (methylation data)


title: Breast tumor from patient P2_43 (methylation data)

source_name: Breast tumor

value: Breast tumor

value: LumB


title: Breast tumor from patient P2_31 (methylation data)


title: Normal breast tissue from patient P2_N126 (methylation data)


title: Breast tumor from patient P2_34 (methylation data)


title: Breast tumor from patient P2_37 (methylation data)


title: Breast cancer cell line MCF-7 WT (methylation data)

value: MCF-7 WT cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: Breast tumor from patient P2_51 (methylation data)


title: Breast tumor from patient P2_33 (methylation data)


title: Breast tumor from patient P2_39 (methylation data)


title: Breast tumor from patient P2_50 (methylation data)


title: Breast tumor from patient P2_35 (methylation data)


title: Breast tumor from patient P2_47 (methylation data)


title: Breast tumor from patient P2_30 (methylation data)


title: Breast tumor from patient P2_54 (methylation data)


title: Breast tumor from patient P2_36 (methylation data)


title: Breast tumor from patient P2_32 (methylation data)


title: Breast tumor from patient P2_29 (methylation data)


title: Breast tumor from patient P2_55 (methylation data)


title: Breast tumor from patient P2_53 (methylation data)


title: Breast tumor from patient P2_40 (methylation data)


title: Breast tumor from patient P2_49 (methylation data)


title: Breast tumor from patient P2_56 (methylation data)


title: Breast cancer cell line BT20 5 AZA (methylation data)

value: BT20 5-AZA cells were maintained in MEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.


title: Breast tumor from patient P2_41 (methylation data)


title: Breast tumor from patient P2_48 (methylation data)


title: Breast tumor from patient P2_42 (methylation data)


title: Breast tumor from patient P2_58 (methylation data)


title: Breast tumor from patient P2_45 (methylation data)


title: Breast tumor from patient P2_57 (methylation data)


title: Breast tumor from patient P2_7 (methylation data)

value: LumA


title: Breast tumor from patient P2_52 (methylation data)


title: Breast tumor from patient P2_38 (methylation data)


title: Breast tumor from patient P2_46 (methylation data)


title: Breast tumor from patient P2_8 (methylation data)


title: Breast tumor from patient P2_5 (methylation data)


title: Breast tumor from patient P2_9 (methylation data)


title: Breast tumor from patient P2_3 (methylation data)


title: Breast tumor from patient P2_44 (methylation data)


title: Breast tumor from patient P2_4 (methylation data)


title: Breast tumor from patient P2_25 (methylation data)


title: Breast tumor from patient P2_23 (methylation data)


title: Breast tumor from patient P2_28 (methylation data)


title: Breast tumor from patient P2_2 (methylation data)


title: Breast tumor from patient P2_6 (methylation data)


title: Breast tumor from patient P2_10 (methylation data)


title: Breast tumor from patient P2_21 (methylation data)


title: Breast tumor from patient P2_12 (methylation data)


title: Breast tumor from patient P2_15 (methylation data)


title: Breast tumor from patient P2_26 (methylation data)


title: Breast tumor from patient P2_13 (methylation data)


title: Breast tumor from patient P2_19 (methylation data)


title: Breast tumor from patient P2_11 (methylation data)


title: Breast tumor from patient P2_22 (methylation data)


title: Breast tumor from patient P2_14 (methylation data)


title: Breast tumor from patient P2_1 (methylation data)


title: Breast tumor from patient P2_18 (methylation data)


title: Breast tumor from patient P2_20 (methylation data)


title: Breast tumor from patient P2_16 (methylation data)


title: Breast tumor from patient P2_17 (methylation data)


title: Breast tumor from patient P2_62 (methylation data)


title: Breast tumor from patient P2_64 (methylation data)


title: Breast tumor from patient P2_61 (methylation data)


title: Breast tumor from patient P2_63 (methylation data)


title: Breast tumor from patient P2_60 (methylation data)


title: Breast tumor from patient P2_67 (methylation data)


title: Breast tumor from patient P2_27 (methylation data)


title: Breast tumor from patient P2_59 (methylation data)


title: Breast tumor from patient P2_84 (methylation data)


title: Breast tumor from patient P2_80 (methylation data)


title: Breast tumor from patient P2_82 (methylation data)


title: Breast tumor from patient P2_81 (methylation data)


title: Breast tumor from patient P2_65 (methylation data)


title: Breast tumor from patient P2_68 (methylation data)


title: Breast tumor from patient P2_79 (methylation data)


title: Breast tumor from patient P2_70 (methylation data)


title: Breast tumor from patient P2_76 (methylation data)


title: Breast tumor from patient P2_77 (methylation data)


title: Breast tumor from patient P2_66 (methylation data)


title: Breast tumor from patient P2_96 (methylation data)

value: Basal


title: Breast tumor from patient P2_83 (methylation data)


title: Breast tumor from patient P2_72 (methylation data)


title: Breast tumor from patient P2_73 (methylation data)


title: Breast tumor from patient P2_69 (methylation data)


title: Breast tumor from patient P2_86 (methylation data)


title: Breast tumor from patient P2_74 (methylation data)


title: Breast tumor from patient P2_93 (methylation data)


title: Breast tumor from patient P2_92 (methylation data)


title: Breast tumor from patient P2_71 (methylation data)


title: Breast tumor from patient P2_88 (methylation data)


title: Breast tumor from patient P2_89 (methylation data)


title: Breast tumor from patient P2_111 (methylation data)


title: Breast tumor from patient P2_75 (methylation data)


title: Breast tumor from patient P2_91 (methylation data)


title: Breast tumor from patient P2_116 (methylation data)


title: Breast tumor from patient P2_94 (methylation data)


title: Breast tumor from patient P2_95 (methylation data)


title: Breast tumor from patient P2_118 (methylation data)


title: Breast tumor from patient P2_98 (methylation data)


title: Breast tumor from patient P2_114 (methylation data)


title: Breast tumor from patient P2_120 (methylation data)


title: Breast tumor from patient P2_97 (methylation data)


title: Breast tumor from patient P2_117 (methylation data)


title: Breast tumor from patient P2_113 (methylation data)


title: Breast tumor from patient P2_85 (methylation data)


title: Breast tumor from patient P2_110 (methylation data)


title: Breast tumor from patient P2_108 (methylation data)


title: Breast tumor from patient P2_107 (methylation data)


title: Breast tumor from patient P2_115 (methylation data)


title: Breast tumor from patient P2_109 (methylation data)


title: Breast tumor from patient P2_112 (methylation data)


title: F5 wdr-5/wdr-5 #4

city: Palo Alto

first: Eric

middle: Lieberman

last: Greer

state: CA

address: Alway M314 300 Pasteur Drive

department: Genetics

institute: Stanford University

description: F5 wdr-5/wdr-5 #4

hyb_protocol: Affymetrix protocol was followed by Stanford Protein and Nucleic Acid facility

scan_protocol: Again scanning was performed according to affymetrix protocol by Stanford Protein and Nucleic Acid facility

data_processing: Background adjustment and normalization was performed with RMA (Robust Multiarray Analysis) in R

organism: Caenorhabditis elegans

source_name: whole worm L3 lysates

label_protocol: Labeling was performed at the Stanford Protein and Nucleic Acid facility using biotin

growth_protocol: Worms were grown at 20 degrees

extract_protocol: RNAqueous kit (Ambion) was used

treatment_protocol: Worms were washed several times with M9 buffer prior to extraction

tag: generation

tag: day of birth


title: Breast tumor from patient P2_102 (methylation data)


title: Breast tumor from patient P2_90 (methylation data)


title: F5 +/+ (from wdr-5) #1

description: F5 +/+ (from wdr-5) #1

tag: genotype/variation

value: +/+ (from wdr-5)


title: Breast tumor from patient P2_119 (methylation data)


title: Breast tumor from patient P2_106 (methylation data)


title: F5 wdr-5/wdr-5 #1

description: F5 wdr-5/wdr-5 #1


title: F5 +/+ (from wdr-5) #5

description: F5 +/+ (from wdr-5) #5


title: F5 +/+ (from wdr-5) #4

description: F5 +/+ (from wdr-5) #4


title: Breast tumor from patient P2_104 (methylation data)


title: F5 wdr-5/wdr-5 #2

description: F5 wdr-5/wdr-5 #2


title: F5 wdr-5/wdr-5 #5

description: F5 wdr-5/wdr-5 #5


title: Breast tumor from patient P2_99 (methylation data)


title: F5 +/+ (from wdr-5) #6

description: F5 +/+ (from wdr-5) #6


title: F5 wdr-5/wdr-5 #6

description: F5 wdr-5/wdr-5 #6


title: F5 wdr-5/wdr-5 #3

description: F5 wdr-5/wdr-5 #3


title: HCT116 DKO replicate 2

hyb_protocol: DNA samples were hybridized onto the HumanMethylation27 BeadChips during 16 hours at 48°C. Unhybridized and non-specifically hybridized DNA were washed from the BeadChips, according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA). Labelled nucleotides were added to extend the primers hybridized to the DNA and primers were stained according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA).

data_processing:
Data analysis was performed with the Methylation module of the Genome Studio software provided by Illumina using default parameters.

Average beta value is defined as the ratio of signal from a methylated probe (C not converted to T) relative to the sum of both methylated (C not converted to T) and unmethylated probes (C bisulfite-converted to T) (? value=C/[(T+C)+100]

label: biotin and DNP

source_name: HCT116 DKO cell line

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium (Gibco) supplemented with 10% fetal calf serum (Gibco).

extract_protocol: Genomic DNA from HCT116 cells was extracted using the QIAamp DNA Mini Kit according to the supplier’s instructions (Qiagen, Hilden, Germany). This included the recommended proteinase K and RNase A digestions. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

value: HCT116 cell line

tag: genome/variation

value: DNMT1 and DNMT3B double knock out


title: HCT116 DKO replicate 1


title: Breast tumor from patient P2_103 (methylation data)


title: Breast tumor from patient P2_87 (methylation data)


title: HCT116 WT replicate 2

source_name: HCT116 wild type cell line

value: wild type


title: F5 +/+ (from wdr-5) #2

description: F5 +/+ (from wdr-5) #2


title: HCT116 DKO replicate 3


title: Breast tumor from patient P_N13 (methylation data)

description: no additional information

tag: subtypeihc

tag: sizebin

tag: agebin

tag: subtypege


title: Breast tumor from patient P_N4 (methylation data)

description: no additional information

tag: methylation barcode


title: F5 +/+ (from +/+) #5

description: F5 +/+ (from +/+) #5


title: F5 +/+ (from +/+) #6

description: F5 +/+ (from +/+) #6


title: F5 +/+ (from +/+) #1

description: F5 +/+ (from +/+) #1


title: Breast tumor from patient P_N6 (methylation data)

description: no additional information

tag: quality control


title: F4 wdr-5/wdr-5 #3

description: F4 wdr-5/wdr-5 #3


title: F4 wdr-5/wdr-5 #4

description: F4 wdr-5/wdr-5 #4


title: Breast tumor from patient P2_101 (methylation data)

tag: subtype ihc


title: HCT116 WT replicate 1

tag: cell type


title: F5 +/+ (from +/+) #4

description: F5 +/+ (from +/+) #4


title: Breast tumor from patient P2_105 (methylation data)

tag: grade

tag: node


title: F5 +/+ (from +/+) #3

description: F5 +/+ (from +/+) #3


title: F5 +/+ (from +/+) #2

description: F5 +/+ (from +/+) #2


title: Breast tumor from patient P_97 (methylation data)

description: no additional information


title: Breast tumor from patient P_94 (methylation data)

description: no additional information


title: F4 +/+ (from wdr-5) #3

description: F4 +/+ (from wdr-5) #3


title: F4 wdr-5/wdr-5 #5

description: F4 wdr-5/wdr-5 #5


title: F4 wdr-5/wdr-5 #6

description: F4 wdr-5/wdr-5 #6


title: Group2_ctrl_9

city: Bethesda

first: Atsushi

last: Terunuma

state: MD

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

institute: National Cancer Institute

description: biopsied 24 hours after exposure

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: GC-RMA

source_name: skin with no exposure control

label_protocol: IVT Labeling Kit (Affymetrix)

extract_protocol: RNeasy (Qiagen)

treatment_protocol: no exposure control

tag: gender

value: female

value: skin


title: F4 wdr-5/wdr-5 #2

description: F4 wdr-5/wdr-5 #2


title: Breast tumor from patient P_93 (methylation data)

description: no additional information

tag: er


title: F4 wdr-5/wdr-5 #1

description: F4 wdr-5/wdr-5 #1


title: Breast tumor from patient P_N1 (methylation data)

description: no additional information

value: Normal


title: F4 +/+ (from wdr-5) #5

description: F4 +/+ (from wdr-5) #5


title: Breast tumor from patient P_99 (methylation data)

description: no additional information


title: F4 +/+ (from +/+) #6

description: F4 +/+ (from +/+) #6


title: HCT116 WT replicate 3


title: F4 +/+ (from wdr-5) #1

description: F4 +/+ (from wdr-5) #1


title: Group2_ctrl_3

description: biopsied 24 hours after exposure

tag: tissue


title: Group2_100R_9

description: biopsied 24 hours after exposure

source_name: skin treated with 100 J/m2 ssR

treatment_protocol: 100 J/m2 ssR


title: F4 +/+ (from wdr-5) #4

description: F4 +/+ (from wdr-5) #4

tag: generation


title: F4 +/+ (from wdr-5) #2

description: F4 +/+ (from wdr-5) #2

tag: day of birth


title: F4 +/+ (from +/+) #4

description: F4 +/+ (from +/+) #4

tag: genotype/variation


title: F4 +/+ (from +/+) #5

description: F4 +/+ (from +/+) #5


title: Breast tumor from patient P_92 (methylation data)

description: no additional information


title: Breast tumor from patient P_91 (methylation data)

description: no additional information


title: Breast tumor from patient P_96 (methylation data)

description: no additional information


title: Breast tumor from patient P_95 (methylation data)

description: no additional information


title: Group2_ctrl_5

description: biopsied 24 hours after exposure


title: Group2_ctrl_6

description: biopsied 24 hours after exposure


title: F4 +/+ (from wdr-5) #6

description: F4 +/+ (from wdr-5) #6


title: Group2_100R_6

description: biopsied 24 hours after exposure


title: Group2_100R_5

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_90 (methylation data)

description: no additional information


title: Group2_ctrl_2

description: biopsied 24 hours after exposure

value: male


title: Breast tumor from patient P_9 (methylation data)

description: no additional information


title: Group2_100R_4

description: biopsied 24 hours after exposure


title: F4 +/+ (from +/+) #2

description: F4 +/+ (from +/+) #2


title: Group2_100R_3

description: biopsied 24 hours after exposure


title: Group2_ctrl_4

description: biopsied 24 hours after exposure


title: F4 +/+ (from +/+) #3

description: F4 +/+ (from +/+) #3


title: Breast tumor from patient P_88 (methylation data)

description: no additional information


title: F4 +/+ (from +/+) #1

description: F4 +/+ (from +/+) #1


title: Group2_R_4

description: biopsied 24 hours after exposure

source_name: skin treated with 1 MED ssR

treatment_protocol: 1 MED ssR


title: Breast tumor from patient P_89 (methylation data)

description: no additional information


title: Group2_LowR_5

description: biopsied 24 hours after exposure

source_name: skin treated with 0.1 MED ssR

treatment_protocol: 0.1 MED ssR


title: Group2_LowR_6

description: biopsied 24 hours after exposure


title: Group2_100R_2

description: biopsied 24 hours after exposure


title: Group2_R_2

description: biopsied 24 hours after exposure


title: Group2_R_9

description: biopsied 24 hours after exposure


title: Group2_R_5

description: biopsied 24 hours after exposure


title: Group2_LowR_4

description: biopsied 24 hours after exposure


title: testis wt, 17dpp, Rep3

city: Ithaca

first: John

last: Schimenti

state: NY

department: Biomedical Sciences

institute: Cornell University

description: wt testis at 17dpp

hyb_protocol: According to Affymetrix standard procedure, 10 micrograms of fragmented cRNA were hybridized to an array for 16-18 hours at 45°C with constant rotation at 60 rpm. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using theAffymetrix GeneArray3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: wt testis at 17dpp

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Regular mouse growth conditions

extract_protocol: Total RNA extraction was performed from homogenized testes using Qiagen RNAeasy minikit according to the manufacturer's instructions.

value: testis

tag: genotype

value: wt

tag: age


title: testis wt, 17dpp, Rep5

description: wt testis at 17dpp


title: Group2_LowR_2

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_85 (methylation data)

description: no additional information

tag: subtypeihc

tag: sizebin


title: Group2_R_3

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_87 (methylation data)

description: no additional information

tag: agebin

tag: subtypege


title: testis wt, 17dpp, Rep4

description: wt testis at 17dpp


title: Group2_LowR_3

description: biopsied 24 hours after exposure


title: Group2_ss100_5

description: biopsied 24 hours after exposure

source_name: skin treated with sunscreen + 100 J/m2 ssR

treatment_protocol: sunscreen + 100 J/m2 ssR


title: Group2_ss100_6

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_83 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode


title: Breast tumor from patient P_86 (methylation data)

description: no additional information


title: Group2_ss100_9

description: biopsied 24 hours after exposure


title: Group2_ss100_4

description: biopsied 24 hours after exposure


title: Group2_ss_9

description: biopsied 24 hours after exposure

source_name: skin treated with sunscreen + 1 MED ssR

treatment_protocol: sunscreen + 1 MED ssR


title: testis, Repro9 mutant, 17dpp, Rep4

description: mutant testis at 17dpp

source_name: mutant testis at 17dpp


title: Breast tumor from patient P_80 (methylation data)

description: no additional information


title: testis wt, 17dpp, Rep2

description: wt testis at 17dpp


title: testis, Repro9 mutant, 17dpp, Rep3

description: mutant testis at 17dpp


title: Breast tumor from patient P_84 (methylation data)

description: no additional information


title: Breast tumor from patient P_79 (methylation data)

description: no additional information


title: Breast tumor from patient P_81 (methylation data)

description: no additional information


title: Group2_ss100_2

description: biopsied 24 hours after exposure


title: testis wt, 17dpp, Rep1

description: wt testis at 17dpp


title: Group2_LowR_9

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_8 (methylation data)

description: no additional information


title: Group2_ss_6

description: biopsied 24 hours after exposure


title: Group2_ss_5

description: biopsied 24 hours after exposure


title: testis wt, 14dpp, Rep3

description: wt testis at 14dpp

source_name: wt testis at 14dpp


title: Group2_ss_3

description: biopsied 24 hours after exposure


title: Group2_ss100_3

description: biopsied 24 hours after exposure


title: Group2_ssLow_9

description: biopsied 24 hours after exposure

source_name: skin treated with sunscreen + 0.1 MED ssR

treatment_protocol: sunscreen + 0.1 MED ssR


title: Group2_ss_2

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_75 (methylation data)

description: no additional information


title: Breast tumor from patient P_73 (methylation data)

description: no additional information


title: Group2_ssLow_6

description: biopsied 24 hours after exposure


title: testis, Repro9 mutant, 17dpp, Rep5

description: mutant testis at 17dpp


title: Group2_ssLow_4

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_72 (methylation data)

description: no additional information


title: Group2_ss_4

description: biopsied 24 hours after exposure


title: testis wt, 14dpp, Rep2

description: wt testis at 14dpp


title: testis wt, 14dpp, Rep1

description: wt testis at 14dpp


title: testis, Repro9 mutant, 14dpp, Rep2

description: mutant testis at 14dpp

source_name: mutant testis at 14dpp


title: Group1_ctrl_5

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_71 (methylation data)

description: no additional information


title: Group1_ctrl_4

description: biopsied 24 hours after exposure


title: testis, Repro9 mutant, 14dpp, Rep4

description: mutant testis at 14dpp


title: Breast tumor from patient P_78 (methylation data)

description: no additional information


title: testis, Repro9 mutant, 17dpp, Rep1

description: mutant testis at 17dpp


title: Breast tumor from patient P_77 (methylation data)

description: no additional information


title: testis, Repro9 mutant, 17dpp, Rep2

description: mutant testis at 17dpp


title: Group2_ssLow_5

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_69 (methylation data)

description: no additional information


title: Breast tumor from patient P_74 (methylation data)

description: no additional information


title: Group1_100A_9

description: biopsied 24 hours after exposure

source_name: skin treated with 100 J/m2 ssA

treatment_protocol: 100 J/m2 ssA


title: Group2_ssLow_3

description: biopsied 24 hours after exposure


title: Group2_R_6

description: biopsied 24 hours after exposure


title: Group1_ctrl_10

description: biopsied 24 hours after exposure


title: Group1_ctrl_2

description: biopsied 24 hours after exposure


title: Group1_ctrl_9

description: biopsied 24 hours after exposure


title: Chlamydomonas nitrogen stress 48h

city: Bielefeld

first: Jörg

last: Toepel

address: Universitätsstrasse 27

country: Germany

institute: University of Bielefeld

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

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (10.7.3.1; Agilent).

data_processing: Agilent Feature Extraction Software (10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii

label_protocol: 1 µg of total RNA were labeld according to the agilent quick amplification labeling kit

growth_protocol: TAP media with or without nitrogen

extract_protocol: Total RNA extracted using Phenol Chloroform extraction

tag: strain

value: wt cc3491

tag: time (h)


title: Chlamydomonas nitrogen stress 24h


title: testis, Repro9 mutant, 14dpp, Rep5

description: mutant testis at 14dpp


title: Group1_ctrl_8

description: biopsied 24 hours after exposure


title: Group1_ctrl_7

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_66 (methylation data)

description: no additional information

source_name: Breast tumor

tag: grade

tag: node


title: Group2_ssLow_2

description: biopsied 24 hours after exposure

tag: gender


title: Chlamydomonas nitrogen stress 72h


title: Group1_ctrl_6

description: biopsied 24 hours after exposure

tag: tissue


title: Breast tumor from patient P_70 (methylation data)

description: no additional information

tag: er


title: Breast tumor from patient P_65 (methylation data)

description: no additional information


title: WT-mock treatment replicate-3

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from__WT-mock treatment replicate-3

hyb_protocol: Samples were hybridized onto Affymetrix mouse 430 2.0 Arrays (Affymetrix) according to manufacturer's recommendations

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: WT-mock treatment replicate-3

label_protocol: RNA targets were prepared as previously described (1) and 15 mg of fragmented and labeled cRNA was subjected to GeneChip hybridization

growth_protocol: Mouse embryo fibroblast (MEF) were isolated from wt and CIKS deficient mice (ko) after 11-14 days and cultured in vitro

extract_protocol: Mouse embryo fibroblasts were lysed in RLT-buffer, assigned a random processing order by treatment, homogenized with Qiashredder, and extracted in a 96-well format as described previously (1). RNA quality was determined using 2100 Bioanalyzer (Agilent Technologies, Santa Clare, CA) using RNA pico kit.

treatment_protocol: The cells were treated in four different ways: 1. no stimulation (ref); 2. Stimulated with IL-17 (17); Stimulated with TNFa (a); stimulated with IL-17 and TNFa (17a). The cells were lysed after 2 hours in RLT buffer.

tag: cell type

value: embryo fibroblast

tag: treatment

tag: genotype variation

value: WT


title: Breast tumor from patient P_64 (methylation data)

description: no additional information


title: testis, Repro9 mutant, 14dpp, Rep3

description: mutant testis at 14dpp

tag: genotype

tag: age


title: WT-mock treatment replicate-1

description: Gene expression data from__WT-mock treatment replicate-1

source_name: WT-mock treatment replicate-1


title: Breast tumor from patient P_63 (methylation data)

description: no additional information

tag: subtypeihc

tag: sizebin


title: testis, Repro9 mutant, 14dpp, Rep1

description: mutant testis at 14dpp


title: Breast tumor from patient P_7 (methylation data)

description: no additional information

tag: agebin

tag: subtypege


title: Group1_100A_4

description: biopsied 24 hours after exposure


title: Chlamydomonas sulfur stress 4aplus_24

growth_protocol: TAP media with or without sulfur


title: Chlamydomonas sulfur stress npq4_96


title: WT-mock treatment replicate-6

description: Gene expression data from__WT-mock treatment replicate-6

source_name: WT-mock treatment replicate-6


title: Chlamydomonas nitrogen stress 96h


title: Breast tumor from patient P_68 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode


title: Breast tumor from patient P_67 (methylation data)

description: no additional information


title: Group1_100A_10

description: biopsied 24 hours after exposure


title: WT-mock treatment replicate-5

description: Gene expression data from__WT-mock treatment replicate-5

source_name: WT-mock treatment replicate-5


title: Group1_100A_8

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_60 (methylation data)

description: no additional information


title: WT-mock treatment replicate-4

description: Gene expression data from__WT-mock treatment replicate-4

source_name: WT-mock treatment replicate-4


title: WT-IL17 and TNFa treatment replicate-5

description: Gene expression data from__WT-IL17 and TNFa treatment replicate-5

source_name: WT-IL17 and TNFa treatment replicate-5

value: IL17 and TNFa


title: WT-IL17 and TNFa treatment replicate-3

description: Gene expression data from__WT-IL17 and TNFa treatment replicate-3

source_name: WT-IL17 and TNFa treatment replicate-3


title: Chlamydomonas sulfur stress npq4_24

tag: strain

tag: time (h)


title: Chlamydomonas sulfur stress npq4_72


title: Chlamydomonas sulfur stress 4aplus_96


title: Group1_100A_7

description: biopsied 24 hours after exposure


title: Chlamydomonas sulfur stress 4aplus_72


title: Group1_A_9

description: biopsied 24 hours after exposure

source_name: skin treated with 1 MED ssA

treatment_protocol: 1 MED ssA


title: WT-mock treatment replicate-2

description: Gene expression data from__WT-mock treatment replicate-2

source_name: WT-mock treatment replicate-2


title: Group1_100A_5

description: biopsied 24 hours after exposure


title: Group1_100A_6

description: biopsied 24 hours after exposure


title: Group1_A_8

description: biopsied 24 hours after exposure


title: Chlamydomonas sulfur stress 4aplus_48


title: Breast tumor from patient P_59 (methylation data)

description: no additional information

value: LumB

tag: grade

tag: node


title: Group1_A_6

description: biopsied 24 hours after exposure

tag: gender

tag: tissue


title: Breast tumor from patient P_58 (methylation data)

description: no additional information

tag: er

value: LumA


title: Breast tumor from patient P_55 (methylation data)

description: no additional information


title: Breast tumor from patient P_56 (methylation data)

description: no additional information

value: Basal


title: WT-TNFa treatment replicate-6

description: Gene expression data from__WT-TNFa treatment replicate-6

source_name: WT-TNFa treatment replicate-6

tag: cell type

tag: treatment

value: TNFa


title: Chlamydomonas sulfur stress cc125_48


title: WT-IL17 and TNFa treatment replicate-6

description: Gene expression data from__WT-IL17 and TNFa treatment replicate-6

source_name: WT-IL17 and TNFa treatment replicate-6

tag: genotype variation


title: Group1_A_4

description: biopsied 24 hours after exposure


title: Group1_A_2

description: biopsied 24 hours after exposure


title: WT-TNFa treatment replicate-4

description: Gene expression data from__WT-TNFa treatment replicate-4

source_name: WT-TNFa treatment replicate-4


title: Breast tumor from patient P_62 (methylation data)

description: no additional information


title: Breast tumor from patient P_52 (methylation data)

description: no additional information


title: Breast tumor from patient P_61 (methylation data)

description: no additional information


title: Group1_LowA_10

description: biopsied 24 hours after exposure

source_name: skin treated with 0.1 MED ssA

treatment_protocol: 0.1 MED ssA


title: WT-TNFa treatment replicate-2

description: Gene expression data from__WT-TNFa treatment replicate-2

source_name: WT-TNFa treatment replicate-2


title: Group1_100A_2

description: biopsied 24 hours after exposure

source_name: skin treated with 100 J/m2 ssA


title: Breast tumor from patient P_51 (methylation data)

description: no additional information


title: Breast tumor from patient P_50 (methylation data)

description: no additional information


title: Chlamydomonas sulfur stress wt cc3491_48

source_name: Chlamydomonas reinhardtii


title: Group1_A_10

description: biopsied 24 hours after exposure


title: WT-TNFa treatment replicate-1

description: Gene expression data from__WT-TNFa treatment replicate-1

source_name: WT-TNFa treatment replicate-1


title: Chlamydomonas sulfur stress wt cc3491_24


title: Breast tumor from patient P_6 (methylation data)

description: no additional information

source_name: Breast tumor


title: WT-IL17 and TNFa treatment replicate-4

description: Gene expression data from__WT-IL17 and TNFa treatment replicate-4

source_name: WT-IL17 and TNFa treatment replicate-4


title: Chlamydomonas sulfur stress npq4_48


title: Chlamydomonas sulfur stress cc125_96


title: WT-IL17 treatment replicate-5

description: Gene expression data from__WT-IL17 treatment replicate-5

source_name: WT-IL17 treatment replicate-5


title: WT-IL17 treatment replicate-4

description: Gene expression data from__WT-IL17 treatment replicate-4

source_name: WT-IL17 treatment replicate-4


title: WT-IL17 and TNFa treatment replicate-2

description: Gene expression data from__WT-IL17 and TNFa treatment replicate-2

source_name: WT-IL17 and TNFa treatment replicate-2


title: Group1_LowA_7

description: biopsied 24 hours after exposure


title: Group1_A_7

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_57 (methylation data)

description: no additional information


title: Chlamydomonas sulfur stress cc125_72


title: WT-TNFa treatment replicate-5

description: Gene expression data from__WT-TNFa treatment replicate-5

source_name: WT-TNFa treatment replicate-5


title: Group1_LowA_4

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_46 (methylation data)

description: no additional information


title: Chlamydomonas sulfur stress cc125_24


title: WT-IL17 and TNFa treatment replicate-1

description: Gene expression data from__WT-IL17 and TNFa treatment replicate-1

source_name: WT-IL17 and TNFa treatment replicate-1


title: Breast tumor from patient P_47 (methylation data)

description: no additional information


title: Chlamydomonas sulfur stress wt cc3491_96


title: Chlamydomonas sulfur stress wt cc3491_72


title: WT-TNFa treatment replicate-3

description: Gene expression data from__WT-TNFa treatment replicate-3

source_name: WT-TNFa treatment replicate-3


title: Group1_A_5

description: biopsied 24 hours after exposure

source_name: skin treated with 1 MED ssA


title: Group1_LowA_9

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_44 (methylation data)

description: no additional information


title: Group1_LowA_8

description: biopsied 24 hours after exposure


title: WT-IL17 treatment replicate-6

description: Gene expression data from__WT-IL17 treatment replicate-6

source_name: WT-IL17 treatment replicate-6


title: Chlamydomonas sulfur stress label2


title: Group1_100R_10

description: biopsied 24 hours after exposure

source_name: skin treated with 100 J/m2 ssR


title: Group1_100R_9

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_5 (methylation data)

description: no additional information


title: Chlamydomonas sulfur stress 24h rep1


title: Group1_LowA_6

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_49 (methylation data)

description: no additional information


title: Chlamydomonas sulfur stress 24h rep2


title: Breast tumor from patient P_42 (methylation data)

description: no additional information


title: KO-mock treatment replicate-4

description: Gene expression data from__KO-mock treatment replicate-4

source_name: KO-mock treatment replicate-4

value: KO


title: Chlamydomonas sulfur stress 24h rep5


title: Group1_LowA_5

description: biopsied 24 hours after exposure

source_name: skin treated with 0.1 MED ssA


title: Group1_100R_6

description: biopsied 24 hours after exposure


title: WT-IL17 treatment replicate-2

description: Gene expression data from__WT-IL17 treatment replicate-2

source_name: WT-IL17 treatment replicate-2


title: Group1_100R_7

description: biopsied 24 hours after exposure


title: Group1_LowA_2

description: biopsied 24 hours after exposure


title: Group1_100R_5

description: biopsied 24 hours after exposure


title: WT-IL17 treatment replicate-3

description: Gene expression data from__WT-IL17 treatment replicate-3

source_name: WT-IL17 treatment replicate-3


title: Breast tumor from patient P_45 (methylation data)

description: no additional information


title: Chlamydomonas sulfur stress 24h rep4

source_name: Chlamydomonas reinhardtii


title: WT-IL17 treatment replicate-1

description: Gene expression data from__WT-IL17 treatment replicate-1

source_name: WT-IL17 treatment replicate-1


title: Chlamydomonas sulfur stress 24h rep3


title: KO-mock treatment replicate-5

description: Gene expression data from__KO-mock treatment replicate-5

source_name: KO-mock treatment replicate-5


title: KO-IL17 and TNFa treatment replicate-5

description: Gene expression data from__KO-IL17 and TNFa treatment replicate-5

source_name: KO-IL17 and TNFa treatment replicate-5


title: KO-mock treatment replicate-6

description: Gene expression data from__KO-mock treatment replicate-6

source_name: KO-mock treatment replicate-6