title: PXB 0282-0001 HBV 6w

description:
PXB 0282-0001
HBV-infected mice were euthanized 6 weeks after infection

source_name: HBV 6w

value: Week 6


title: PXB 0282-0015 HBV 6w

status: Public on Dec 01 2014

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description:
PXB 0282-0015
HBV-infected mice were euthanized 6 weeks after infection

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

molecule: total RNA

organism: Homo sapiens

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Mice were inoculated with serum samples from HCV or HBV carriers via the tail vein. Mice were sacrificed by diethyl ether anesthesia. Human hepatocytes from mouse livers were finely dissected and stored in liquid nitrogen after submergence in RNA later solution.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: Interferon-alpha (7,000IU/g body weight) was administered at week 8 six hours prior to sacrifice in 5 HBV-infected and 5 HCV-infected mice.

tag: experiment model

value: human hepatocyte chimeric mice

tag: inoculated with

value: serum samples from HBV carriers

tag: time

tag: tissue

value: human hepatocytes from mouse liver


title: PXB 282-26 HBV day10

description:
PXB 282-26
HBV-infected mice were euthanized 10 days after infection

source_name: HBV day10

value: Day 10


title: HT1080_QUE_100_r1-nf

city: Research Triangle Park

first: Rebecca

middle: A

last: Clewell

state: NC

address: 6 Davis Drive

department: Institute for Chemical Safety Sciences

country: USA

institute: The Hamner Institutes for Health Sciences

description: Sample 133

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Analysis of gene expression data was performed using Partek software (Partek Inc., St. Louis, MO) utlising GC-RMA normalisation. A 1-way ANOVA with interactions was performed to compare gene expression between the treated and control cells. Probability values were adjusted for multiple comparisons using a false discovery rate of 5%

label: biotin

label_protocol: RNA samples were prepared for microarray hybridization using the GeneAtlas™ 3’ IVT Express Kit according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).  Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA. The cDNA was then converted into a double-stranded DNA template for transcription. Amplified cRNA (aRNA) was transcribed in vitro, with incorporation of a biotin-congugated nucleotide.  The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate, and samples were fragmented to prepare the biotin-labeled aRNA samples for hybridization onto Affymetrix® GeneChip™

growth_protocol: HT1080 cells were grown under the conditions recommended by ATCC:  Eagle’s Minimum Essential media (EMEM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 100 mg/L streptomycin and 100 U/mL of penicillin G at 37 °C in a humidified atmosphere of 95% air and 5% CO2

extract_protocol: total RNA was collected from the treated cells using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA).  A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA (Qiagen)

treatment_protocol: Cells were plated in complete media containing 10% heat-inactivated FBS and allowed to attach overnight. Stock solutions of chemicals were prepared in DMSO at 1,000-fold higher concentrations than the final target doses.  Stock solutions were aliquoted and stored at -20C for up to 1 week. Dosing solutions were prepared immediately prior to treatment of the cells by diluting stock solutions 1:200 in complete media.  24 hrs after seeding the cells, the media in each well was supplemented with the dosing solutions (1:5 v/v), for a final chemical dilution of 1:1000 (0.1% vehicle). Cells were maintained in original complete media throughout the course of the experiment.  Immediately following treatment, media was removed and the cells were washed with PBS and prepared for subsequent analyses

tag: cell line

tag: cell type

value: human fibrosarcoma cells

tag: treated with

value: quercetin (QUE) for 24hrs


title: HT1080_QUE_80_r3

description: Sample 129


title: HT1080_QUE_80_r2

description: Sample 128


title: MW1-css2-4 vs. MW1-Bl6

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using Agilent G256BA scanner Imagene feature extraction

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

organism: Mus musculus

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA isolation using Trizol v1.0 (tissue sections)

tag: strain

value: P14 hypocampus


title: first visit [GG1_000191]

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression module)

data_processing: The raw log2 transformed probes were normalized by ANOVA fitting technical effects of date of hybridization and RIN score. The reason why there are so many missing probes in the normalized dataset is because they are below the expression threshold and so not included in the normalization process.

source_name: whole peripheral blood

label_protocol: Illumina BeadArray protocol

extract_protocol: Total RNA was extracted from whole peripheral blood using Tempus Spin RNA Isolation kit. Quality control was performed using Agilent's Bioanalyzer.

tag: age

tag: Sex

value: M

tag: body mass index

tag: ethnicity

value: CAU

tag: gad7 score

tag: hybridization batch

value: Z

tag: rin


title: first visit [GG1_000187]


title: MW1-css1-12 vs. MW1-Bl6


title: HT1080_QUE_80_r4

description: Sample 130


title: MW1-bl6-11 vs. MW1-Bl6


title: MW1-css1-6 vs. MW1-Bl6


title: HT1080_QUE_60_r6

description: Sample 126


title: HT1080_QUE_80_r1-nf

description: Sample 127


title: PXB 282-25 HBV day10

description:
PXB 282-25
HBV-infected mice were euthanized 10 days after infection


title: MW1-bl6-5 vs. MW1-Bl6


title: first visit [GG1_000186]

value: F


title: HT1080_QUE_60_r5

description: Sample 125


title: first visit [GG1_000188]

value: AFR

tag: anxiety case/control

value: control


title: first visit [GG1_000185]


title: first visit [GG1_000200]


title: PXB 282-34 HCV day10

description:
PXB 282-34
HCV-infected mice were euthanized 10 days after infection

source_name: HCV day10

value: serum samples from HCV carriers


title: first visit [GG1_000183]

value: case


title: first visit [GG1_000184]


title: PXB 282-30 HBV day10

description:
PXB 282-30
HBV-infected mice were euthanized 10 days after infection


title: PXB 264-5 control

description:
PXB 264-5
Uninfected, untreated control mice

source_name: control

value: none (control)

value: Day 0


title: first visit [GG1_000182]


title: PXB 201-014 control

description:
PXB 201-014
Uninfected, untreated control mice

value: human hepatocyte chimeric mice


title: HT1080_QUE_60_r3

description: Sample 123


title: Cancer cell culture supernatant exosome US45103013_19710060_S01

city: Heidelberg

first: Shijing

last: Yue

address: Im Neuenheimer Feld 365

department: Tumor cell biology

country: Germany

institute: University hospital Heidelberg

description: To assist in orientation of the array and positioning of the image analysis grid, Hy3™ fluorescent labeled “landing lights” are present in all 4 corners plus one extra in lower right corner of the 36 sub-arrays, 180 total.

hyb_protocol: The Hy3™-labeled samples were hybridized to the miRCURY LNA™ microRNA Array, 7th gen. – human, mouse and rat (Exiqon, Denmark). This array covers all annotated human microRNAs present in miRBase v. 14.0 as well as more than 350 miRPlus™ candidate microRNAs. The hybridization was carried out according to the manufacturer’s instructions on a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: The microarray slides were scanned using an Agilent G2505C Microarray Scanner System (Agilent Technologies, Inc., USA) and stored in an ozone-free (< 2.0ppb) environment to prevent bleaching of the fluorescent dye.

data_processing: Image analysis was carried out using the ImaGene® 9.0 software of the miRCURY LNA™ microRNA Array Analysis Software package. Quantified signals were background corrected, using local background and normalized using Quantile normalization algorithm. Expression profiles of microRNAs across different samples were clustered using the average Hierarchical clustering algorithm in the Nexus Expression™ 2 software of the miRCURY LNA™ microRNA Array Analysis Software package

label: Hy3™ fluorescent

source_name: Cancer cell culture supernatant

label_protocol: The microRNA was labeled using the miRCURY LNA™ microRNA Power Labeling Kit (Exiqon, Denmark) according to the manufacturer’s instructions.

extract_protocol: MicroRNA was extracted from exosomes and exosomes depleted serum using the miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions

value: cancer cell lines

tag: rna subtype

value: microRNA


title: MW1-Bl6 vs. MW1-css1-9


title: HT1080_QUE_60_r4

description: Sample 124


title: HT1080_QUE_60_r2-nf

description: Sample 122


title: HT1080_QUE_30_r6

description: Sample 120


title: PXB 264-4 control

description:
PXB 264-4
Uninfected, untreated control mice

tag: experiment model

value: human hepatocytes from mouse liver


title: MW1-Bl6 vs. MW1-css2-7


title: PXB 201-012 control

description:
PXB 201-012
Uninfected, untreated control mice

tag: inoculated with


title: first visit [GG1_000180]


title: first visit [GG1_000181]


title: HT1080_QUE_60_r1

description: Sample 121

value: human fibrosarcoma cells


title: PXB 201-006 control

description:
PXB 201-006
Uninfected, untreated control mice

tag: time


title: HT1080_QUE_30_r5

description: Sample 119

value: quercetin (QUE) for 24hrs


title: MW1-Bl6 vs. MW1-bl6-2

value: P14 hypocampus


title: MW1-Bl6 vs. MW1-css2-1


title: MW1-Bl6 vs. MW1-bl6-8


title: Patient exosome US45103013_19710061_S01

source_name: Patient serum

tag: tissue

value: serum


title: Patient serum US45103013_19714547_S01


title: MW1-Bl6 vs. MW1-css1-3


title: Healthy serum US45103013_19714546_S01

source_name: Healthy serum


title: Healthy exosome US45103013_19714545_S01


title: first visit [GG1_000179]


title: first visit [GG1_000178]

value: CAU


title: PXB 282-53 control

description:
PXB 282-53
Uninfected, untreated control mice


title: HT1080_QUE_30_r4

description: Sample 118

tag: cell line


title: first visit [GG1_000175]

value: Z


title: HT1080_QUE_30_r3

description: Sample 117

tag: cell type


title: HT1080_QUE_30_r1

description: Sample 115

tag: treated with


title: first visit [GG1_000177]

value: M


title: first visit [GG1_000174]

value: AFR


title: HT1080_QUE_30_r2

description: Sample 116


title: HT1080_QUE_10_r5

description: Sample 113


title: first visit [GG1_000173]

value: F


title: HT1080_QUE_10_r4

description: Sample 112


title: TLH9(cl14)S32i, biological rep2

city: Bron

first: Pierre-Yves

last: Bourillot

address: 18 Avenue du Doyen Lépine

country: France

institute: INSERM U1208

description: Gene expression data from TLH9S3(cl14)2i hESc

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U219 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

label: Biotin

label_protocol: Complementary RNA (cRNA) was prepared using the IVT Express (200-100 ng) kit (Affymetrix) according to the manufacturer’s instructions, starting from 100 ng total RNA.

growth_protocol:
All hESCs were routinely cultured at 37°C in 5% O2 in the ES basal medium containing Knockout DMEM, 20% KO-SR, 1 mM glutamine, 0.1 mM b-mercaptoethanol (Sigma), and 1% nonessential amino acid (Gibco), on growth-inactivated MEF or 0.2% gelatin coated dishes alternatively (for TL-OS3-10 cells only). For OSCAR, H9, F-OS3, F-H9S3, and R-OS3 cells, the complete ES medium was supplemented with 4-8 ng/ml FGF2. The culture medium of TL-OS3 and TL-H9S3 cells was supplemented with 10,000 U/ml recombinant human LIF (hLIF, house made) and 250 nM 4'OHT (4-Hydroxytamoxifen, Calbiochem 579002) unless otherwise indicated. For TL2i-OS3 and TL2i-H9S3 cells, the culture medium was supplemented with 10,000 U/ml hLIF, 250 nM 4'OHT, 3 ¼M CHIR99021 (Stemgent, 04-0004) and 1 ¼M PD325901 (Stemgent, 04-0006). Oscar, H9, F-, and R- hES cells were manually split and passaged every 6 days. TL- and TL2i- cells can be regularly passaged by single-cell dissociation with 0.05% trypsin-EDTA (Gibico) or Accutase (Gibico, A11105-01) every 4 days.
Prior to infection, undifferentiated OSCAR (P16) and H9 (P28) hES cells were manually collected and treated with 0.05% trypsin-EDTA (Gibco) for 8 minutes at 37°C till the clumps were dissociated into single cells. After centrifugation, the cells were re-suspended in a 1.5 ml - eppendorf tube at the density of 6 x 104 cells/ml in conventional ES medium containing GAE-STAT3-ERT2 lentivirus in the presence of 10 g/ml polybrene (Sigma) and 10 M Rock inhibitor Y-27632 (Calbiochem). The cells were incubated for 5 hours at 37°C in 5% O2 before being re-plated at clonal density into 96-well plates containing MEF in the medium supplemented with 20% KO-SR and 4 ng/ml FGF2. 8-12 days later, individual undifferentiated colonies by morphology were transferred to the wells of 4-well plates for further culture.

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were washed with PBS and colonies were harvested by manual picking for RNA extraction

value: Human embryonic stem cell

tag: genetic modification

value: STAT3-ERT2 overexpression

tag: culture condition

value: MEFs + hLIF + 4-hydroxytamoxifen + CHIR99021 + PD325901


title: first visit [GG1_000169]

tag: age

tag: Sex

value: case


title: first visit [GG1_000170]

tag: body mass index

tag: ethnicity


title: HT1080_QUE_10_r3

description: Sample 111


title: TLH9(cl14)S3, biological rep2

description: Gene expression data from TLH9S3(cl14) hESc

value: MEFs + hLIF + 4-hydroxytamoxifen


title: TLH9(cl14)S3, biological rep1


title: TLH9(cl14)S3, biological rep3


title: HT1080_QUE_3_r6

description: Sample 108


title: first visit [GG1_000171]

tag: gad7 score

tag: hybridization batch


title: HT1080_QUE_10_r2

description: Sample 110


title: first visit [GG1_000167]

tag: anxiety case/control

value: control

tag: rin


title: HT1080_QUE_10_r1

description: Sample 109


title: TLH9(cl14)S32i, biological rep1


title: first visit [GG1_000168]


title: first visit [GG1_000176]


title: first visit [GG1_000166]


title: first visit [GG1_000164]


title: first visit [GG1_000165]


title: FH9(cl14)S3, biological rep1

description: Gene expression data from FH9S3(cl14) hESc

value: MEFs + bFGF


title: HT1080_QUE_3_r2

description: Sample 104


title: FH9(cl14)S3, biological rep2


title: TLH9(cl2)S32i, biological rep3

description: Gene expression data from TLH9S3(cl2)2i hESc


title: TLH9(cl14)S32i, biological rep3


title: FH9(cl14)S3, biological rep3


title: HT1080_QUE_3_r3

description: Sample 105


title: first visit [GG1_000163]


title: HT1080_QUE_3_r4

description: Sample 106


title: first visit [GG1_000162]


title: HT1080_QUE_3_r5

description: Sample 107


title: HT1080_QUE_3_r1

description: Sample 103


title: TLH9(cl2)S32i, biological rep2


title: first visit [GG1_000161]


title: HT1080_QUE_1_r6

description: Sample 102


title: TLH9(cl2)S32i, biological rep1


title: TLH9(cl2)S3, biological rep2

description: Gene expression data from TLH9S3(cl2) hESc


title: TLH9(cl2)S3, biological rep3


title: first visit [GG1_000160]


title: TLH9(cl2)S3, biological rep1


title: first visit [GG1_000158]


title: HT1080_QUE_1_r4

description: Sample 100


title: first visit [GG1_000157]


title: FH9(cl2)S3, biological rep3

description: Gene expression data from FH9S3(cl2) hESc


title: HT1080_QUE_1_r3

description: Sample 99


title: FH9(cl2)S3, biological rep2


title: HT1080_QUE_1_r2

description: Sample 98


title: first visit [GG1_000156]


title: FH9(cl2)S3, biological rep1


title: first visit [GG1_000159]


title: first visit [GG1_000155]


title: HT1080_QUE_1_r5

description: Sample 101


title: first visit [GG1_000154]


title: ROscarS3, biological rep2

description: Gene expression data from ROscarS3 hESc

value: Oscar

value: Reverted to MEFs + bFGF


title: first visit [GG1_000153]


title: first visit [GG1_000152]


title: HT-1080_MMS_DMSO_r6

description: Sample 96

value: human fibrosarcoma cells

value: DMSO (vehicle) for 24hrs


title: HT-1080_MMS_DMSO_r5

description: Sample 95


title: HT-1080_MMS_DMSO_r4

description: Sample 94


title: TLOscarS32i, biological rep3

description: Gene expression data from TLOscarS32i hESc


title: TLOscarS32i, biological rep2


title: ROscarS3, biological rep1

description: Gene expression data from ROscarS3 hESc


title: HT1080_QUE_1_r1

description: Sample 97

value: quercetin (QUE) for 24hrs


title: HT-1080_MMS_DMSO_r3

description: Sample 93


title: HT-1080_MMS_DMSO_r2

description: Sample 92


title: ROscarS3, biological rep3

description: Gene expression data from ROscarS3 hESc


title: TLOscarS32i, biological rep1


title: HT-1080_MMS_DMSO_r1

description: Sample 91


title: first visit [GG1_000150]

value: CAU


title: first visit [GG1_000149]

value: AMI

value: Z


title: first visit [GG1_000148]

value: AFR


title: first visit [GG1_000151]

value: F


title: HT-1080_MMS_500_r6

description: Sample 90

value: methyl methanesulfonate (MMS) for 24hrs


title: TLOscarS3, biological rep2

description: Gene expression data from TLOscarS3 hESc

value: Human embryonic stem cell

value: STAT3-ERT2 overexpression


title: TLOscarS3, biological rep1


title: HT-1080_MMS_500_r5

description: Sample 89


title: HT-1080_MMS_500_r4

description: Sample 88


title: first visit [GG1_000145]

value: M


title: first visit [GG1_000143]


title: TLOscarS3, biological rep3

value: MEFs + hLIF + 4-hydroxytamoxifen


title: HT-1080_MMS_500_r3

description: Sample 87


title: HT1080_QUE_10_r6

description: Sample 114


title: FOscarS3, biological rep2

description: Gene expression data from FOscarS3 hESc


title: first visit [GG1_000147]


title: HT-1080_MMS_500_r2

description: Sample 86


title: FOscarS3, biological rep3

description: Gene expression data from FOscarS3 hESc


title: first visit [GG1_000144]

value: control


title: HT-1080_MMS_300_r5

description: Sample 84


title: Oscar, biological rep2

description: Gene expression data from Oscar hESc

source_name: Oscar

value: MEFs + bFGF


title: FOscarS3, biological rep1

description: Gene expression data from FOscarS3 hESc

value: Oscar


title: first visit [GG1_000141]


title: Oscar, biological rep3

description: Gene expression data from Oscar hESc


title: first visit [GG1_000142]

value: ASN


title: HT-1080_MMS_300_r6

description: Sample 85

value: human fibrosarcoma cells


title: Oscar, biological rep1

description: Gene expression data from Oscar hESc


title: HT-1080_MMS_300_r3

description: Sample 82


title: HT-1080_MMS_300_r2

description: Sample 81


title: HT-1080_MMS_300_r4

description: Sample 83


title: first visit [GG1_000140]

value: case


title: first visit [GG1_000138]


title: first visit [GG1_000136]


title: HT-1080_MMS_300_r1

description: Sample 80


title: first visit [GG1_000137]


title: first visit [GG1_000139]


title: Negative Control exp2

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: NegCTR CD34+ cells

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: Cord Blood CD34+ cells

label_protocol: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments.  Briefly, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in 24-well plates at 5 x 10^5/mL in Iscove modified Dulbecco medium (IMDM; Euroclone) containing 20% Human Serum (Bio-Whittaker), stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last nucleofection. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: Electroporation program on CD34+ cells was based on a previously published protocol (Salati, Stem Cells, 2008), optimized to be performed on the 4D-Nucleofector™ System (Lonza, Basel, Switzerland; http://www.lonza.com). A mix of 3 Silencer Select siRNAs targeting human JARID2 was used (Life Technologies, http://www.lifetechnologies.com). Briefly, each sample was electroporated 3 times, once every 24 hours, starting from the day after CD34+ cell purification. For each electroporation, 4x105 CD34+ cells were resuspended in 100 uL of P3 Primary Cell Solution (Lonza), containing 3 ug of siRNA mix and pulsed with program DS112. To exclude non-specific effects given by iRNA nucleofection, a sample transfected with a non-targeting siRNA (NegCTR; Silencer Select Negative #2 Control siRNA, Life Technologies) was included. After each transfection, CD34+ cells were transferred into pre-warmed fresh medium in 24-well plates and maintained in the same culture conditions as before.   For liquid culture differentiation assays, 24 hours after the last nucleofection CD34+ cells were plated (5 x 10^5/mL) in IMDM added with 20% BIT 9500 serum substitute (bovine serum albumin, insulin, and transferrin; StemCell Technologies), in order to set up a multilineage cell culture (SCF, 50 ng/mL; Flt3L, 50 ng/mL; TPO, 20 ng/mL; IL-3, 10 ng/mL; IL-6, 10 ng/mL; all cytokines from Miltenyi) (Bianchi E et al Blood 2010).

tag: treatment

value: siNT

tag: experiment

value: Cord Blood

value: CD34+ cells


title: siRNA-JARID2 exp2

description: siRNA-JARID2 CD34+ cells


title: first visit [GG1_000135]

value: CAU

value: Z


title: mRNA (3) t58 F5

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
mRNA (3)  alkaline stress t58
Third replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F5.

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

data_processing:
Raw image quantization and background subtraction. Final value was the result of the local background sustraction to the raw data.
Background_subtracted Raw signals are available on the series record.  For Processed data, we normalized by using ArrayStat software (Median Absolute Deviation) and show only final value. Normalized data are available on the series record.

organism: Saccharomyces cerevisiae

source_name: 58 min after change to YPD pH 8

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were permeabilized with 20 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Exponential growth in YPD  buffered with TAPS 50mM pH 5.5. Then cells were pelleted (time t0) and resuspended in the same medium but pH 8. Aliquots were taken afterwards at 6, 13, 20, 30, 40 and 58 min.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: strain


title: HT-1080_MMS_100_r5

description: Sample 78


title: Negative Control exp3

description: NegCTR CD34+ cells

tag: tissue


title: mRNA (3) t20 F2

description:
mRNA (3)  alkaline stress t20
Third replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F2.

source_name: 20 min after change to YPD pH 8


title: mRNA (3) t30 F3

description:
mRNA (3)  alkaline stress t30
Third replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F3.

source_name: 30 min after change to YPD pH 8


title: mRNA (3) t13 F1

description:
mRNA (3)  alkaline stress t13
Third replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F1.

source_name: 13 min after change to YPD pH 8


title: HT-1080_MMS_100_r6

description: Sample 79

tag: cell line


title: first visit [GG1_000132]

value: F


title: first visit [GG1_000134]

value: AFR


title: HT-1080_MMS_100_r2

description: Sample 75

tag: cell type

value: methyl methanesulfonate (MMS) for 24hrs


title: mRNA (3) t6 F8

description:
mRNA (3)  alkaline stress t6
Third replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F8.

source_name: 6 min after change to YPD pH 8


title: first visit [GG1_000131]


title: mRNA (3) t40 F4

description:
mRNA (3)  alkaline stress t40
Third replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F4.

source_name: 40 min after change to YPD pH 8


title: HT-1080_MMS_100_r4

description: Sample 77

tag: treated with


title: HT-1080_MMS_100_r3

description: Sample 76


title: Negative Control exp6

description: NegCTR CD34+ cells


title: siRNA-JARID2 exp6

description: siRNA-JARID2 CD34+ cells


title: first visit [GG1_000130]


title: mRNA (2) t58 F6

description:
mRNA (2)  alkaline stress t58
Second replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F6.


title: mRNA (3) t0 F6

description:
mRNA (3)  alkaline stress t0
Third replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F6.

source_name: Yeast cells grown in YPD pH 5.5 to exponential phase.


title: HT-1080_MMS_30_r5

description: Sample 72


title: HT-1080_MMS_30_r6

description: Sample 73


title: HT-1080_MMS_100_r1

description: Sample 74


title: mRNA (2) t40 F5

description:
mRNA (2)  alkaline stress t40
Second replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F5.


title: first visit [GG1_000128]


title: mRNA (2) t30 F4

description:
mRNA (2)  alkaline stress t30
Second replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F4.


title: first visit [GG1_000126]


title: first visit [GG1_000129]


title: first visit [GG1_000125]


title: HT-1080_MMS_30_r4

description: Sample 71


title: first visit [GG1_000124]


title: HT-1080_MMS_30_r1

description: Sample 68


title: mRNA (2) t13 F2

description:
mRNA (2)  alkaline stress t13
Second replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F2.


title: mRNA (2) t20 F3

description:
mRNA (2)  alkaline stress t20
Second replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F3.


title: siRNA-JARID2 exp3

description: siRNA-JARID2 CD34+ cells


title: mRNA (2) t6 F1

description:
mRNA (2)  alkaline stress t6
Second replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F1.


title: mRNA (2) t0 F8

description:
mRNA (2)  alkaline stress t0
Second replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F8.


title: mRNA (1) t58 F8

description:
mRNA (1)  alkaline stress t58
First replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F8.


title: first visit [GG1_000121]


title: first visit [GG1_000123]


title: HT-1080_MMS_10_r5

description: Sample 66


title: first visit [GG1_000120]


title: HT-1080_MMS_30_r2

description: Sample 69


title: HT-1080_MMS_10_r2

description: Sample 63


title: first visit [GG1_000122]


title: HT-1080_MMS_10_r3

description: Sample 64


title: mRNA (1) t20 F4

description:
mRNA (1)  alkaline stress t20
First replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F4.


title: HT-1080_MMS_30_r3

description: Sample 70


title: HT-1080_MMS_10_r4

description: Sample 65


title: first visit [GG1_000118]


title: mRNA (1) t13 F3

description:
mRNA (1)  alkaline stress t13
First replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F3.


title: first visit [GG1_000119]


title: HT-1080_MMS_10_r1

description: Sample 62


title: mRNA (1) t40 F6

description:
mRNA (1)  alkaline stress t40
First replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F6.


title: mRNA (1) t30 F5

description:
mRNA (1)  alkaline stress t30
First replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F5.


title: HT-1080_MMS_10_r6

description: Sample 67


title: HT-1080_MMS_3_r6

description: Sample 61


title: mRNA (1) t6 F2

description:
mRNA (1)  alkaline stress t6
First replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F2.


title: first visit [GG1_000117]


title: first visit [GG1_000116]


title: HT-1080_MMS_3_r5

description: Sample 60


title: first visit [GG1_000115]


title: mRNA (1) t0 F1

description:
mRNA (1)  alkaline stress t0
First replica: cDNA labelling from wt strain BY4741. Hybridization on macrochip F1.


title: HT-1080_MMS_3_r3

description: Sample 58


title: first visit [GG1_000114]


title: HT-1080_MMS_3_r4

description: Sample 59


title: GRO (3) t58 F5

description:
GRO (3)  alkaline stress t58
Third replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F5.


title: GRO (3) t40 F4

description:
GRO (3)  alkaline stress t40
Third replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F4.


title: 546780A12 - pti1-4_flg_bio3 vs. pti1-4_mock_bio3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Analysis of flg22-induced transcriptional changes in oxi1, OXI1oe, pti1-4, CA-MPK4 and ice1 mutant lines

hyb_protocol: pti1-4_mock_bio3 Cy5 / pti1-4_flg_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias. Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - 0,5x MS (sigma6899), 0.5g/L MES, pH media:5.7, 0.5g/l Agar Type E  hygrometry: 45%  temperature: 22°C  light: 6h - 22h

treatment_protocol: Name:30 min H2O - compound based treatment - control,h2o:time 30min .

tag: genotype

tag: ecotype

value: Columbia

value: seedling

value: 2 weeks

tag: developmental stage

value: boyes:1.14 (Boyes et al. Plant Cell 2001)

value: mock

treatment_protocol: Name:30 min 1µM flg22 - compound based treatment - biotic stress,flg22:quantity 1uM time 30min .


title: GRO (3) t30 F3

description:
GRO (3)  alkaline stress t30
Third replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F3.


title: HT-1080_MMS_3_r1

description: Sample 56


title: 546780A10 - pti1-4_flg_bio2 vs. pti1-4_mock_bio2

hyb_protocol: pti1-4_mock_bio2 Cy5 / pti1-4_flg_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age


title: first visit [GG1_000112]

tag: Sex

tag: body mass index

value: control


title: first visit [GG1_000111]

tag: ethnicity

tag: gad7 score


title: 546780A09 - pti1-4_mock_bio2 vs. pti1-4_flg_bio2

hyb_protocol: pti1-4_flg_bio2 Cy5 / pti1-4_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT-1080_MMS_3_r2

description: Sample 57


title: GRO (3) t20 F2

description:
GRO (3)  alkaline stress t20
Third replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F2.


title: first visit [GG1_000113]

value: M

tag: hybridization batch


title: HT-1080_MMS_1_r5

description: Sample 54

value: human fibrosarcoma cells


title: first visit [GG1_000110]

tag: rin


title: 546780A11 - pti1-4_mock_bio3 vs. pti1-4_flg_bio3

hyb_protocol: pti1-4_flg_bio3 Cy5 / pti1-4_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: treatment


title: GRO (3) t13 F1

description:
GRO (3)  alkaline stress t13
Third replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F1.


title: 546780A08 - pti1-4_flg_bio1 vs. pti1-4_mock_bio1

hyb_protocol: pti1-4_mock_bio1 Cy5 / pti1-4_flg_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: first visit [GG1_000109]

tag: anxiety case/control


title: 546780A07 - pti1-4_mock_bio1 vs. pti1-4_flg_bio1

hyb_protocol: pti1-4_flg_bio1 Cy5 / pti1-4_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT-1080_MMS_1_r3

description: Sample 52


title: 546780A06 - pti1-4_mock_bio3 vs. col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / pti1-4_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: col


title: 546780A05 - col_mock_bio3 vs. pti1-4_mock_bio3

hyb_protocol: pti1-4_mock_bio3 Cy5 / col_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT-1080_MMS_1_r6

description: Sample 55


title: GRO (3) t6 F8

description:
GRO (3)  alkaline stress t6
Third replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F8.

tag: strain


title: GRO (3) t0 F6

description:
GRO (3)  alkaline stress t0
Third replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F6.


title: 546780A04 - pti1-4_mock_bio2 vs. col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / pti1-4_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: tissue


title: GRO (2) t58 F6

description:
GRO (2)  alkaline stress t58
Second replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F6.


title: first visit [GG1_000108]

value: case


title: GRO (2) t40 F5

description:
GRO (2)  alkaline stress t40
Second replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F5.


title: HT-1080_MMS_1_r2

description: Sample 51

tag: cell line


title: first visit [GG1_000104]


title: first visit [GG1_000107]


title: first visit [GG1_000106]


title: first visit [GG1_000103]


title: GRO (2) t30 F4

description:
GRO (2)  alkaline stress t30
Second replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F4.


title: 546780A03 - col_mock_bio2 vs. pti1-4_mock_bio2

hyb_protocol: pti1-4_mock_bio2 Cy5 / col_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 546780A02 - pti1-4_mock_bio1 vs. col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / pti1-4_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT-1080_MMS_1_r4

description: Sample 53

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).

tag: cell type


title: 532980A08 - oxi_flg_bio1 vs. oxi_mock_bio1

hyb_protocol: oxi_mock_bio1 Cy5 / oxi_flg_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: oxi

extract_protocol: oxi_flg_bio1:100mg. (Qiagen_RNeasy.pdf)


title: 532980A07 - oxi_mock_bio1 vs. oxi_flg_bio1

hyb_protocol: oxi_flg_bio1 Cy5 / oxi_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT1080_ETP_DMSO_r6

description: Sample 49

tag: treated with

value: DMSO (vehicle) for 24hrs


title: GRO (2) t20 F3

description:
GRO (2)  alkaline stress t20
Second replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F3.


title: HT-1080_MMS_1_r1

description: Sample 50


title: first visit [GG1_000102]

hyb_protocol: Illumina's BeadArray protocol


title: GRO (2) t13 F2

description:
GRO (2)  alkaline stress t13
Second replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F2.


title: first visit [GG1_000101]

value: CAU


title: 532980A06 - 1093_flg_bio3 vs. 1093_mock_bio3

hyb_protocol: 1093_mock_bio3 Cy5 / 1093_flg_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype


title: HT1080_ETP_DMSO_r4

description: Sample 47


title: GRO (2) t0 F8

description:
GRO (2)  alkaline stress t0
Second replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F8.

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.


title: HT1080_ETP_DMSO_r5

description: Sample 48


title: first visit [GG1_000100]

value: Z


title: 546780A01 - col_mock_bio1 vs. pti1-4_mock_bio1

hyb_protocol: pti1-4_mock_bio1 Cy5 / col_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype


title: HT1080_ETP_DMSO_r2-nf

description: Sample 44


title: HT1080_ETP_3_r6

description: Sample 42

value: etoposide (ETP) for 24hrs


title: HT1080_ETP_DMSO_r3

description: Sample 46


title: HT1080_ETP_DMSO_r2-o

description: Sample 45


title: first visit [GG1_000099]

value: F


title: GRO (1) t58 F8

description:
GRO (1)  alkaline stress t58
First replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F8.


title: first visit [GG1_000098]

value: ASN


title: first visit [GG1_000097]

value: AFR


title: GRO (2) t6 F1

description:
GRO (2)  alkaline stress t6
Second replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F1.


title: HT1080_ETP_DMSO_r1

description: Sample 43


title: GRO (1) t40 F6

description:
GRO (1)  alkaline stress t40
First replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F6.


title: 532980A05 - 1093_mock_bio3 vs. 1093_flg_bio3

hyb_protocol: 1093_flg_bio3 Cy5 / 1093_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

value: seedling

tag: developmental stage


title: HT1080_ETP_3_r5

description: Sample 41


title: 532980A04 - 1093_mock_bio3 vs. col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / 1093_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age

value: 2 weeks

value: boyes:1.14 (Boyes et al. Plant Cell 2001)


title: 532980A02 - col_flg_bio3 vs. col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / col_flg_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: mock

extract_protocol: col_flg_bio3:100mg. (Qiagen_RNeasy.pdf)


title: GRO (1) t30 F5

description:
GRO (1)  alkaline stress t30
First replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F5.


title: GRO (1) t13 F3

description:
GRO (1)  alkaline stress t13
First replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F3.


title: GRO (1) t20 F4

description:
GRO (1)  alkaline stress t20
First replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F4.


title: first visit [GG1_000093]

tag: Sex

value: control


title: HT1080_ETP_3_r4

description: Sample 40

value: human fibrosarcoma cells


title: 532980A01 - col_mock_bio3 vs. col_flg_bio3

description: Analysis of flg22-induced transcriptional changes in oxi1, OXI1oe, pti1-4, CA-MPK4 and ice1 mutant lines

hyb_protocol: col_flg_bio3 Cy5 / col_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: col


title: first visit [GG1_000094]

value: M

tag: body mass index


title: 532980A03 - col_mock_bio3 vs. 1093_mock_bio3

hyb_protocol: 1093_mock_bio3 Cy5 / col_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT1080_ETP_3_r2

description: Sample 38


title: 532979A12 - 1093_flg_bio2 vs. 1093_mock_bio2

hyb_protocol: 1093_mock_bio2 Cy5 / 1093_flg_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GRO (1) t0 F1

description:
GRO (1)  alkaline stress t0
First replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F1.


title: first visit [GG1_000092]

tag: ethnicity


title: first visit [GG1_000095]

tag: gad7 score


title: 532979A10 - 1093_mock_bio2 vs. col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / 1093_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT1080_ETP_3_r3

description: Sample 39


title: 532979A11 - 1093_mock_bio2 vs. 1093_flg_bio2

hyb_protocol: 1093_flg_bio2 Cy5 / 1093_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: first visit [GG1_000091]

tag: hybridization batch


title: GRO (1) t6 F2

description:
GRO (1)  alkaline stress t6
First replica: Run-on labelling from wt strain BY4741. Hybridization on macrochip F2.


title: first visit [GG1_000089]

value: case

tag: rin


title: first visit [GG1_000090]


title: first visit [GG1_000088]


title: HT1080_ETP_1_r6

description: Sample 36


title: HT1080_ETP_1_r5

description: Sample 35


title: 532979A09 - col_mock_bio2 vs. 1093_mock_bio2

hyb_protocol: 1093_mock_bio2 Cy5 / col_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: treatment


title: 532979A07 - col_mock_bio2 vs. col_flg_bio2

hyb_protocol: col_flg_bio2 Cy5 / col_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: col_flg_bio2:100mg. (Qiagen_RNeasy.pdf)


title: HT1080_ETP_3_r1

description: Sample 37

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).


title: first visit [GG1_000087]


title: first visit [GG1_000085]


title: HT1080_ETP_1_r3

description: Sample 33


title: 532979A05 - 1093_mock_bio1 vs. 1093_flg_bio1

hyb_protocol: 1093_flg_bio1 Cy5 / 1093_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT1080_ETP_1_r4-nf

description: Sample 34


title: 532979A08 - col_flg_bio2 vs. col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / col_flg_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT1080_ETP_1_r2

description: Sample 32


title: first visit [GG1_000083]

hyb_protocol: Illumina's BeadArray protocol


title: 532979A06 - 1093_flg_bio1 vs. 1093_mock_bio1

hyb_protocol: 1093_mock_bio1 Cy5 / 1093_flg_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT1080_ETP_0.03_r6

description: Sample 29


title: 532979A04 - 1093_mock_bio1 vs. col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / 1093_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: first visit [GG1_000082]

tag: anxiety case/control


title: 532979A01 - col_mock_bio1 vs. col_flg_bio1

hyb_protocol: col_flg_bio1 Cy5 / col_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: col_flg_bio1:100mg. (Qiagen_RNeasy.pdf)


title: HT1080_ETP_1_r1

description: Sample 31


title: 532979A03 - col_mock_bio1 vs. 1093_mock_bio1

hyb_protocol: 1093_mock_bio1 Cy5 / col_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: first visit [GG1_000084]


title: HT1080_ETP_0.003_r6

description: Sample 28


title: 532979A02 - col_flg_bio1 vs. col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / col_flg_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: first visit [GG1_000081]


title: HT1080_ETP_0.3_r5

description: Sample 27


title: 532935A04 - oxi_flg_bio3 vs. oxi_mock_bio3

hyb_protocol: oxi_mock_bio3 Cy5 / oxi_flg_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: oxi

extract_protocol: oxi_flg_bio3:100mg. (Qiagen_RNeasy.pdf)


title: first visit [GG1_000080]

value: CAU


title: first visit [GG1_000078]

value: Z


title: HT1080_ETP_0.03_r5

description: Sample 26

value: etoposide (ETP) for 24hrs


title: first visit [GG1_000077]

value: F


title: first visit [GG1_000076]


title: 532935A02 - oxi_flg_bio2 vs. oxi_mock_bio2

hyb_protocol: oxi_mock_bio2 Cy5 / oxi_flg_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: oxi_flg_bio2:100mg. (Qiagen_RNeasy.pdf)


title: HT1080_ETP_0.3_r4

description: Sample 24


title: HT1080_ETP_0.003_r5

description: Sample 25


title: 101_DNA_methylation

type: genomic

city: New York

first: Marsha

last: Reyngold

state: NY

address: 1275 York Ave

department: Radiation Oncology

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: strandard Illumina protocol

scan_protocol: arrays were imagined using BeadArray Reader using strandard recommended Illumina scanner settings

data_processing:
data were analyzed using Partek software (version 6.5)
Processed data are presented as Average Beta. Raw data (unmethylated_and_methylated_signals.txt) are available on the series level where the Unmethylated (Signal_A) and methylated (Signal_B) signal intensities are provided.

molecule: genomic DNA

source_name: breast tumor tissue_AZ_primary tumor

label_protocol: biotin

extract_protocol: Genomic DNA was extracted from snap-frozen tissue sections using DNeasy Tissue kit (Qiagen)

value: breast tumor

tag: unique patient id

value: AZ

tag: sample type

value: primary tumor


title: 532934A06 - oxi_mock_bio3 vs. col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / oxi_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

tag: tissue

value: seedling


title: 97_DNA_methylation

source_name: breast tumor tissue_AY_primary tumor

value: AY


title: HT1080_ETP_0.03_r4

description: Sample 23

tag: cell line

tag: cell type


title: 532935A01 - oxi_mock_bio2 vs. oxi_flg_bio2

hyb_protocol: oxi_flg_bio2 Cy5 / oxi_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype

value: 2 weeks

value: boyes:1.14 (Boyes et al. Plant Cell 2001)

value: mock


title: 98_DNA_methylation

source_name: breast tumor tissue_AY_lymph node metastasis

value: lymph node metastasis


title: 96_DNA_methylation

source_name: breast tumor tissue_AX_lymph node metastasis

value: AX


title: 99_DNA_methylation

source_name: breast tumor tissue_AO_primary tumor

value: AO


title: 102_DNA_methylation

source_name: breast tumor tissue_AZ_lymph node metastasis


title: first visit [GG1_000075]

source_name: whole peripheral blood


title: 532934A05 - col_mock_bio3 vs. oxi_mock_bio3

hyb_protocol: oxi_mock_bio3 Cy5 / col_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: oxi

tag: ecotype

value: col


title: HT1080_ETP_0.3_r6

description: Sample 30

value: human fibrosarcoma cells

tag: treated with


title: HT1080_ETP_0.003_r4

description: Sample 22

value: etoposide (ETP) for 24hrs


title: HT1080_ETP_0.003_r3

description: Sample 21


title: 100_DNA_methylation

source_name: breast tumor tissue_AO_lymph node metastasis


title: 95_DNA_methylation

source_name: breast tumor tissue_AX_primary tumor


title: 532934A03 - col_mock_bio2 vs. oxi_mock_bio2

hyb_protocol: oxi_mock_bio2 Cy5 / col_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age

tag: developmental stage


title: first visit [GG1_000073]

tag: Sex

value: F

tag: body mass index

value: CAU

value: case

value: Z


title: HT1080_ETP_0.03_r3-nf

description: Sample 19


title: 532934A04 - oxi_mock_bio2 vs. col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / oxi_mock_bio2 Cy3 : 30pmol. (chip_hybridization.doc)

value: Columbia


title: first visit [GG1_000074]

tag: ethnicity

value: AFR

tag: gad7 score


title: first visit [GG1_000072]

value: ASN

tag: hybridization batch

tag: rin


title: HT1080_ETP_0.3_r3-nf

description: Sample 20

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).


title: 94_DNA_methylation

source_name: breast tumor tissue_AW_lymph node metastasis

value: breast tumor

value: AW


title: first visit [GG1_000071]

tag: anxiety case/control


title: first visit [GG1_000070]

value: M


title: 92_DNA_methylation

source_name: breast tumor tissue_AV_lymph node metastasis

tag: unique patient id

value: AV

value: lymph node metastasis


title: HT1080_ETP_0.03_r2

description: Sample 17