title: 442111A01 - WT_1 vs. mtr4_1

hyb_protocol: mtr4_1 Cy5 / WT_1 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: Control, biological rep2

status: Public on Jun 30 2013

type: RNA

city: Cincinnati

first: Susumu

last: Goyama

state: Ohio

address: 3333 Burnet Avenue

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from Runx1-intact MLL-ENL cells

hyb_protocol: Labeled probes were hybridized to the Mouse Genome 430 2.0 Array (Affymetrix).

scan_protocol: GeneChips were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Expression data were extracted from image files produced on GeneChip Operating software 1.0 (Affymetrix). Normalization and expression value calculation were performed using DNA-Chip Analyzer (www.dchip.org).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Runx1-intact MLL-ENL cells

label_protocol: labeling of fragmented cDNA was carried out using the NuGen Ovation Biotin labeling system (NuGEN Technologies).

extract_protocol: Total RNA was prepared using Rneasy mini kit (QIAGEN).

tag: genotype

tag: strain


title: P7-2

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

description: lncRNAs and mRNAs expression

hyb_protocol: Each labeled cRNA was fragmented and heated at 60°C for 30min,50ul hybridization solution was assembled to the lncRNA expression microarray slide and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Median normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies)

source_name: whole testis from postnatal day 7

label_protocol: Each sample was amplified and transcribed into Cy3 fluorescent cRNA without 3' bias utilizing a random priming method

extract_protocol: RNA were extracted using Trizol reagent and DNAase I treatment were performed to eliminate genomic DNA contamination, then mRNA was purified from total RNA after removal of rRNA

treatment_protocol: testes were freshly dissected out from embryonic or postnatal mice, snap freezed in liquid nitrogen and stored at -80 freezer.

tag: tissue

value: whole testis

tag: developmental stage

value: postnatal day 7


title: E15.5-3

description: lncRNAs and mRNAs expression

source_name: whole testis from embryonic Day 15.5

value: embryonic Day 15.5


title: E15.5-1

description: lncRNAs and mRNAs expression


title: P7-1

description: lncRNAs and mRNAs expression


title: E15.5-2

description: lncRNAs and mRNAs expression


title: Control, biological rep3


title: Runx1-KO, biological rep1

description: Gene expression data from Runx1-deficient MLL-ENL cells

source_name: Runx1-deficient MLL-ENL cells


title: Control, biological rep1


title: Preeclampsia2

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

hyb_protocol: Standard Agilent

scan_protocol: With scanner Agilent Technologies Scanner G2505C US92003687

data_processing: Standard Agilent

organism: Homo sapiens

source_name: HUVEC cells exposed to preeclamptic plasma

label_protocol: GE1_107_Sep09 (Read Only)

growth_protocol: Culture of HUVEC cells in DMEM + 10% SVF and Penicillin Streptomycin

extract_protocol: TriZol RNA extraction

treatment_protocol: 24 hour culture with 10% of plasma from pregnant women after overnight starving without SVF

tag: cell type

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: Runx1-KO, biological rep2


title: E12.5-3

description: lncRNAs and mRNAs expression

source_name: whole testis from embryonic Day 12.5

value: embryonic Day 12.5


title: Runx1-KO, biological rep3


title: AEC_19

status: Public on Jun 29 2013

city: Barcelona

first: M. Carmen

last: López-Sabater

state: Barcelona

address: Av. Joan XXIII S/N

department: Food Science and Nutrition

country: Spain

institute: University of Barcelona

description: SAMPLE 123

data_processing:
We tested 5 candidate housekeeping genes (PPIB, FPGS, GAPDH; B2M, TRAP1), however for the normalization we used the housekeeping gene PPIB.
Data were processed using SDS 2.4  and Data Assist 3.0 softwares (Applied Biosystems, Foster City, CA)
Target gene signals normalized to housekeeping gene; 2^-ΔΔCt, where  ΔΔCt=[(Ct target (unknown sample)−Ct endogenous control (unknown sample))]−[(Ct target (reference sample)−Ct endogenous control (reference sample))]
Matrix normalized worksheet reports normalized signal (against housekeeping gene).
Fold Change worksheet reports test/control (i.e., AE children/Healthy children) .

label: RT-PCR

source_name: mRNA of whole blood

label_protocol: 700 ng of total RNA were reverse-transcribed in the thermal cycler PTC-100 into cDNA using the SuperScript cDNA Synthesis Kit, according to the manufacturer’s protocol (Invitrogen, USA). The reaction mixture was incubated at 25°C for 10 min and then at 42°C for 60 min. Finally, the mixture was heated at 85°C for 5 min. To identify altered gene expression in peripheral blood, we used PCR with TaqMan Low-Density Array (TLDA) microfluidic cards (Applied Biosystems, USA).A total of 100 μL of reaction mixture, with 16 μL of cDNA (560 ng), 34 µL of H2O and 50 μL of TaqMan Universal PCR Master Mix (Applied Biosystems, USA), were added to each TLDA port after vortexing. The card was centrifuged for 1 min x 2 at 1900 rpm to distribute the samples from the loading port to each well. The TLDA was sealed with a TaqMan low-density array sealer (Applied Biosystems, USA) and the PCR amplification was performed using an ABI Prism 7900HT sequence detection system (Applied Biosystems, USA). The thermal cycler conditions were as follows: 2 min at 50°C, then 10 min at 94.5°C, followed by 40 cycles for 30 s at 97°C and 1 min at 59.7°C. Each sample was measured in duplicate in the same TLDA card.

extract_protocol: Total RNA was isolated from peripheral blood of children at 4 years of age using PAXgen kit, acording to the manufacture's protocol (Quiagen, Germany).

tag: group

value: test


title: AEC_17

description: SAMPLE 121


title: AEC_18

description: SAMPLE 122


title: AEC_20

description: SAMPLE 124


title: Control2

source_name: HUVEC cells exposed to control plasma


title: CD19+CD5+CD1dhigh Splenocytes

city: Ann Arbor

first: Matthew

last: Klinker

state: MI

address: 109 Zina Pitcher Place, 4368

institute: University of Michigan

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

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

data_processing: Data was analyzed using the affy Bioconductor package implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: CD5+CD1dhigh B cells

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

extract_protocol: RNA was isolated from lysed cell by Qiagen Qiacube according to manufacturer's instructions.

value: splenocyte

tag: cell type subpopulation

value: CD19+CD5+CD1dhigh B cells


title: CD19+CD5-CD1dhigh Splenocytes

source_name: CD5-CD1dhigh B cells

value: CD19+CD5-CD1dhigh B cells


title: Preeclampsia1


title: AEC_16

description: SAMPLE 120


title: AEC_7

description: SAMPLE 111


title: AEC_8

description: SAMPLE 112


title: AEC_6

description: SAMPLE 110


title: E12.5-1

description: lncRNAs and mRNAs expression


title: E12.5-2

description: lncRNAs and mRNAs expression


title: AEC_13

description: SAMPLE 117


title: AEC_14

description: SAMPLE 118


title: AEC_9

description: SAMPLE 113


title: AEC_11

description: SAMPLE 115


title: AEC_12

description: SAMPLE 116


title: AEC_15

description: SAMPLE 119


title: AEC_10

description: SAMPLE 114


title: AEC_2

description: SAMPLE 106


title: AEC_3

description: SAMPLE 107


title: AEC_5

description: SAMPLE 109


title: 319_MIRA

type: genomic

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: DNA methylation profile in 319

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Loess normalization was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio

molecule: genomic DNA

source_name: MIRA enriched DNA_from treated, no tumor

label_protocol: According to standard NimbleGen Protocol

extract_protocol: Genomic DNA was isolated using standard phenol/chloroform extraction and ethanol precipitation method.

value: Big Blue® mouse

value: Seminal vesicles (SV)

tag: enrichment procedure

value: MIRA

tag: antibodies/kit  information

value: In Lab purified His-MBD3L1 & GST-MBD2b

tag: treatment

value: B(a)P

source_name: Genomic Input DNAs_from treated, no tumor

value: Seminal vesicles  (SV) from mice injected with chronic doses of B(a)P


title: AEC_1

description: SAMPLE 105


title: MDACC 20167

city: San Francisco

first: David

middle: A.

last: Solomon

address: 513 Parnassus Ave, HSW 450

department: Pathology

institute: University of California, San Francisco

description:
Urothelial carcinoma with STAG2 mutation
TW07

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
.CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.2 Software.  Copy number data files (.CYCHP files) were generated using the ChAS Analysis Files for the CytoScan HD Array version NA32.1 as a reference
The copy number data files (.CYCHP files) contain the whole genome copy number data for the 12 STAG2-mutant urothelial carcinomas of the bladder accessible using Affymetrix Chromosome Analysis Suite v1.2.2 Software.

source_name: STAG2-mutant urothelial carcinoma

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Genomic DNA was prepared directly from snap-frozen urothelial carcinoma primary tumor samples using Qiagen QIAamp DNA Extraction Kits.

tag: patient gender

value: female

tag: patient age at specimen collection

tag: procedure at collection

value: transurethral resection

tag: pathologic stage at collection

value: pTa

tag: stag2 mutation present in tumor

value: 2809G>T, 2810T>C, 2811..2812delAT; 767V>frameshift (complex indel)


title: AEC_4

description: SAMPLE 108


title: MDACC 20711

description:
Urothelial carcinoma with STAG2 mutation
TW10

value: male

value: 2607(-1)G>A; 699N>frameshift (splice site)


title: MDACC 20837

description:
Urothelial carcinoma with STAG2 mutation
TW12

value: 1522G>C; 338D>H (missense)


title: HC_100

description: SAMPLE 100

value: control


title: HC_101

description: SAMPLE 101


title: HC_103

description: SAMPLE 103


title: HC_104

description: SAMPLE 104


title: HC_102

description: SAMPLE 102


title: MDACC 21460

description:
Urothelial carcinoma with STAG2 mutation
TW11


title: HC_97

description: SAMPLE 97


title: HC_99

description: SAMPLE 99


title: HC_96

description: SAMPLE 96


title: HC_98

description: SAMPLE 98


title: HC_91

description: SAMPLE 91


title: HC_92

description: SAMPLE 92


title: HC_93

description: SAMPLE 93


title: HC_94

description: SAMPLE 94


title: Control1

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: HC_90

description: SAMPLE 90


title: 318_MIRA

description: DNA methylation profile in 318

treatment_protocol: mice injected with chronic doses of B(a)P


title: 320_MIRA

description: DNA methylation profile in 320


title: HC_88

description: SAMPLE 88


title: HC_89

description: SAMPLE 89


title: HC_82

description: SAMPLE 82


title: HC_85

description: SAMPLE 85


title: HC_76

description: SAMPLE 76


title: HC_83

description: SAMPLE 83


title: HC_80

description: SAMPLE 80


title: HC_84

description: SAMPLE 84


title: HC_78

description: SAMPLE 78


title: HC_79

description: SAMPLE 79


title: HC_81

description: SAMPLE 81


title: HC_77

description: SAMPLE 77


title: HC_86

description: SAMPLE 86


title: HC_87

description: SAMPLE 87


title: HC_74

description: SAMPLE 74


title: HC_73

description: SAMPLE 73


title: HC_75

description: SAMPLE 75


title: HC_72

description: SAMPLE 72


title: HC_71

description: SAMPLE 71


title: HC_70

description: SAMPLE 70


title: HC_53

description: SAMPLE 53


title: HC_56

description: SAMPLE 56


title: HC_54

description: SAMPLE 54


title: HC_59

description: SAMPLE 59


title: HC_58

description: SAMPLE 58


title: HC_51

description: SAMPLE 51


title: HC_63

description: SAMPLE 63


title: HC_60

description: SAMPLE 60


title: HC_66

description: SAMPLE 66


title: HC_68

description: SAMPLE 68


title: HC_62

description: SAMPLE 62


title: HC_67

description: SAMPLE 67


title: HC_57

description: SAMPLE 57


title: HC_65

description: SAMPLE 65


title: HC_52

description: SAMPLE 52


title: HC_61

description: SAMPLE 61


title: HC_69

description: SAMPLE 69


title: HC_55

description: SAMPLE 55


title: HC_64

description: SAMPLE 64


title: HC_95

description: SAMPLE 95


title: HC_50

description: SAMPLE 50


title: HC_36

description: SAMPLE 36


title: HC_37

description: SAMPLE 37


title: HC_34

description: SAMPLE 34


title: HC_35

description: SAMPLE 35


title: HC_33

description: SAMPLE 33


title: HC_30

description: SAMPLE 30


title: HC_32

description: SAMPLE 32


title: HC_31

description: SAMPLE 31


title: HC_23

description: SAMPLE 23


title: HC_26

description: SAMPLE 26


title: HC_29

description: SAMPLE 29


title: HC_27

description: SAMPLE 27


title: HC_28

description: SAMPLE 28


title: HC_25

description: SAMPLE 25


title: HC_24

description: SAMPLE 24


title: 209_MIRA

description: DNA methylation profile in 209

source_name: MIRA enriched DNA_from untreated

value: DMSO

source_name: Genomic Input DNA_from untreated

value: Seminal vesicles  (SV) from mice injected with chronic doses of DMSO


title: HC_22

description: SAMPLE 22


title: HC_21

description: SAMPLE 21


title: MDACC 20107

description:
Urothelial carcinoma with STAG2 mutation
TW06

value: 3642delC; 1045R>frameshift (deletion)


title: MDACC 20363

description:
Urothelial carcinoma with STAG2 mutation
TW08

value: 896(-8)A>G; 129G>frameshift (splice site)


title: HC_43

description: SAMPLE 43


title: HC_48

description: SAMPLE 48


title: HC_45

description: SAMPLE 45


title: HC_40

description: SAMPLE 40


title: HC_42

description: SAMPLE 42


title: HC_39

description: SAMPLE 39


title: HC_41

description: SAMPLE 41


title: HC_47

description: SAMPLE 47


title: HC_38

description: SAMPLE 38


title: HC_44

description: SAMPLE 44


title: HC_46

description: SAMPLE 46


title: HC_49

description: SAMPLE 49


title: HC_20

description: SAMPLE 20


title: MDACC 20586

description:
Urothelial carcinoma with STAG2 mutation
TW09


title: HC_19

description: SAMPLE 19


title: HC_17

description: SAMPLE 17


title: HC_16

description: SAMPLE 16


title: HC_18

description: SAMPLE 18


title: HC_15

description: SAMPLE 15


title: MDACC 20031

description:
Urothelial carcinoma with STAG2 mutation
TW04

value: 1527(+1)G>A; 339K>frameshift (splice site)


title: HC_14

description: SAMPLE 14


title: MDACC 10076

description:
Urothelial carcinoma with STAG2 mutation
TW03

value: 800C>A; 97S>Stop (nonsense)


title: MDACC 20099

description:
Urothelial carcinoma with STAG2 mutation
TW05


title: Ercc1 KO P7 MEF 3% rep2

city: Pittsburgh

first: Saleem

middle: A

last: Khan

state: PA

address: 450 Technology Drive

department: Microbiology and Molecular Genetics

institute: University of Pittsburgh

description: MicroRNA expression of Ercc1-/- MEFs grown to passage 7 in 3% Oxygen

hyb_protocol: Labeled miRNA was mixed with GE Blocking Agent and Hi-RPM Hybridization Buffer for a total volume of 45 µl. The labeled samples were hybridized to Agilent microarray slides at 55˚C for 20 hours in a rotator rack. Following hybridization, the slides were washed with Agilent-supplied Gene Expression Wash Buffers 1 and 2. Slides were immediately scanned with an Agilent Microarray Scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting for 8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 5%).

data_processing: Data extraction of scanned images used Agilent Feature Extraction Software protocol miRNA_107_Sep09 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data was analyzed using Genespring GX version 10. WT and Ercc1-/- MEFs at passage 3 and passage 7 grown in 20% and 3% O2 were compared using Welch's t-test (p<0.05) and differentially expressed miRNAs with at least a 2-fold change in expression were considered to be potential senescence-associated miRNAs

source_name: Ercc1 KO MEF P7 3% O2, Replicate 2

label_protocol: We used the Agilent mouse miRNA microarrays (V2) (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. Each microarray contains sixteen to twenty oligonucleotide probes for each of the 627 mouse miRNAs and 39 mouse viral miRNAs based on the Sanger database version 12. The array contains 281 positive controls consisting of high-signal endogenous mouse-specific probes, and 434 negative controls consisting of random sequences that have low signal and poor hybridization to mouse RNA. RNA (120 ng) was isolated from MEFs using the Ultraspec RNA Isolation System, dephosphorylated with calf intestinal alkaline phosphatase, and then denatured with dimethyl sulfoxide. The 3’ ends were then ligated to a Cyanine3-pCp molecule using T4 RNA ligase. Labeled RNA was purified using a MicroBio-spin 6 column containing Bio-Gel P-6 in Tris buffer (Bio-Rad Laboratories, Inc. Hercules, CA, USA).

growth_protocol: WT and Ercc1-/- MEFs were grown in  20% O2 and 3% O2 until passage 3 and passage 7. Cells were harvested when they reached approximately 80% confluence and collected for RNA isolation.

extract_protocol: RNA was extracted using the Ultraspec RNA Isolation System (Biotecx, Houston, TX, USA). Following isolation, RNA quantity was measured using a Nanodrop (Thermo Fisher Scientific Inc., Waltham, MA, USA). RNA quality was assessed by formaldehyde-agarose gel electrophoresis.

tag: oxygen

tag: passage

value: Mouse Embryonic Fibroblast

value: FVB/n C57Bl/6


title: WT P3 MEF 3% rep2

description: MicroRNA expression of WTMEFs grown to passage 3 in 3% Oxygen

source_name: WT MEF P3 3% O2, Replicate 2

tag: genotype

value: Wild type


title: Ercc1 KO P3 MEF 3% rep2

description: MicroRNA expression of Ercc1-/- MEFs grown to passage 3 in 3% Oxygen

source_name: Ercc1 KO MEF P3 3% O2, Replicate 2

tag: strain


title: Ercc1 KO P7 MEF 20% rep2

description: MicroRNA expression of Ercc1-/- MEFs grown to passage 7 in 20% Oxygen

source_name: Ercc1 KO MEF P7 20% O2, Replicate 2


title: Ercc1 KO P3 MEF 20% rep2

description: MicroRNA expression of Ercc1-/- MEFs grown to passage 3 in 20% Oxygen

source_name: Ercc1 KO MEF P3 20% O2, Replicate 2


title: HC_13

description: SAMPLE 13


title: WT P7 MEF 20% rep2

description: MicroRNA expression of WT MEFs grown to passage 7 in 20% Oxygen

source_name: WT MEF P7 20% O2, Replicate 2


title: WT P7 MEF 3% rep2

description: MicroRNA expression of WTMEFs grown to passage 7 in 3% Oxygen

source_name: WT MEF P7 3% O2, Replicate 2


title: HC_12

description: SAMPLE 12


title: HC_11

description: SAMPLE 11


title: Ercc1 KO P7 MEF 20% rep1

source_name: Ercc1 KO MEF P7 20% O2, Replicate 1


title: Ercc1 KO P3 MEF 3% rep1

source_name: Ercc1 KO MEF P3 3% O2, Replicate 1


title: WT P7 MEF 20% rep1

source_name: WT MEF P7 20% O2, Replicate 1


title: WT P7 MEF 3% rep1

source_name: WT MEF P7 3% O2, Replicate 1


title: Ercc1 KO P3 MEF 20% rep1

source_name: Ercc1 KO MEF P3 20% O2, Replicate 1


title: Ercc1 KO P7 MEF 3% rep1

source_name: Ercc1 KO MEF P7 3% O2, Replicate 1


title: WT P3 MEF 3% rep1

source_name: WT MEF P3 3% O2, Replicate 1


title: WT P3 MEF 20% rep1

description: MicroRNA expression of WT MEFs grown to passage 3 in 20% Oxygen

source_name: WT MEF P3 20% O2, Replicate 1


title: Vehicle_5days_Yes Wood Stick_spleen_male_rat_3005

city: North Chicago

first: Amy

last: Ditewig

state: IL

address: 1 North Waukegan Road

department: Exploratory Toxicology

institute: AbbVie Inc

hyb_protocol: Approximately 20 ug of cRNA was fragmented and hybridized for 16 hr at 45C on RG 230 2.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Workstation 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: log2 mean scaled and 10% trimmed

organism: Rattus norvegicus

source_name: Vehicle, yes wood stick, spleen, animal 3005

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

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

treatment_protocol: Rats were dosed orally with either vehicle or 40 mg/kg/day cyclophosphamide for 5 days

tag: tissue

value: Spleen

value: Wild Type

tag: age

value: Sprague-Dawley Rats

value: Vehicle, yes wood stick

tag: subject

value: animal 3005


title: MDACC 10057

description:
Urothelial carcinoma with STAG2 mutation
TW01

source_name: STAG2-mutant urothelial carcinoma

value: male

value: transurethral resection

value: pTa

value: 1156C>T; 216R>Stop (nonsense)


title: 317_MIRA

description: DNA methylation profile in 317

source_name: MIRA enriched DNA_from treated, no tumor

value: Big Blue® mouse

value: Seminal vesicles (SV)

value: MIRA

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: B(a)P

source_name: Genomic Input DNAs_from treated, no tumor

value: Seminal vesicles  (SV) from mice injected with chronic doses of B(a)P


title: HC_10

description: SAMPLE 10

source_name: mRNA of whole blood

tag: group

value: control


title: HC_9

description: SAMPLE 9


title: MDACC 10059

description:
Urothelial carcinoma with STAG2 mutation
TW02

value: 2287C>T; 593Q>Stop (nonsense)


title: HC_8

description: SAMPLE 8


title: Cyclophosphamide_5days_40mpk_Yes Wood Stick_spleen_male_rat_4001

source_name: Cyclophosphamide, 40 mg/kg/day, yes wood stick, spleen, animal 4001

value: Spleen

value: animal 4001


title: HC_7

description: SAMPLE 7


title: Cyclophosphamide_5days_40mpk_Yes Wood Stick_spleen_male_rat_4005

source_name: Cyclophosphamide, 40 mg/kg/day, yes wood stick, spleen, animal 4005

value: Wild Type

value: Sprague-Dawley Rats

value: animal 4005


title: Cyclophosphamide_5days_40mpk_No Wood Stick_spleen_male_rat_2005

source_name: Cyclophosphamide, 40 mg/kg/day, no wood stick, spleen, animal 2005

value: animal 2005


title: PM2i-iPSC (Agilent)

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

description: Gene expression of iPS

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: gProcessed signal value calculated by Agilent Scanner Feature Extract Software

source_name: combinations of purmorphamine-treated MEFs treated with 2i/LIF

label_protocol: standard Agilent protocol

extract_protocol: RNA was prepared using Trizol reagents (Invitrogen) following the manufacturer's recommendations.

tag: developmental stage

value: embryo

tag: cell type


title: MEF (Agilent)

description: Gene expression of MEF

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: HC_6

description: SAMPLE 6


title: Vehicle_5days_Yes Wood Stick_spleen_male_rat_3003

source_name: Vehicle, yes wood stick, spleen, animal 3003

value: Vehicle, yes wood stick

value: animal 3003


title: WT P3 MEF 20% rep2

source_name: WT MEF P3 20% O2, Replicate 2

value: Wild type

value: Mouse Embryonic Fibroblast

value: FVB/n C57Bl/6


title: HC_5

description: SAMPLE 5


title: Vehicle_5days_No Wood Stick_spleen_male_rat_1005

source_name: Vehicle, no wood stick, spleen, animal 1005

value: Vehicle, no wood stick

value: animal 1005


title: Cyclophosphamide_5days_40mpk_No Wood Stick_spleen_male_rat_2003

source_name: Cyclophosphamide, 40 mg/kg/day, no wood stick, spleen, animal 2003

value: animal 2003


title: subject C 60 mins after exercise

city: Tokyo

first: Takayuki

last: Akimoto

address: Hongo 7-3-1

country: Japan

institute: The University of Tokyo

hyb_protocol: Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees C and washed with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

scan_protocol: Hybridization signals were detected by DNA microarray scanner G2505B (Agilent Technologies) with resolution of 10 micrometres . The scanned images were analyzed using Agilent Feature Extraction ver. 9.1.3.1.

data_processing: At first Hy3 (samples) signal was normalized with division used Hy5 (Universal reference) signal. Then each signal value of unique probe ID was calculated from average of Hy3/Hy5 normalized signal intensities of replicated probes.

source_name: serum_60m after exercise

label_protocol: miRCURY LNA microRNA Hi Power Labeling kit

extract_protocol: Total RNA extracted using QIAzol following manufacturer's instructions

value: healthy male

tag: timepoint

value: 60 mins after an acute resistance exercise

value: serum

source_name: Total RNA from the pooled serum

value: Pooled human serum


title: subject B 3 days after exercise

source_name: serum_3d after exercise

value: 1day after an acute resistance exercise


title: subject C 1 day after exercise

source_name: serum_1d after exercise

value: 3 days after an acute resistance exercise


title: subject C 3 days after exercise


title: subject C before exercise

description: C-pre

source_name: serum_before exercise

value: before an acute resistance exercise


title: ES (Agilent)

description: Gene expression of ES

source_name: mouse embryonic stem cells from 129/Ola mice

value: blastocysts

tag: genetic background


title: subject B 1 day after exercise


title: subject B 60 mins after exercise


title: HC_3

description: SAMPLE 3

value: control


title: HC_4

description: SAMPLE 4


title: Vehicle_5days_No Wood Stick_spleen_male_rat_1003

source_name: Vehicle, no wood stick, spleen, animal 1003

value: Spleen

value: Wild Type

value: Sprague-Dawley Rats

tag: treatment

value: animal 1003


title: Vehicle_5days_No Wood Stick_spleen_male_rat_1001

source_name: Vehicle, no wood stick,spleen, animal 1001

value: animal 1001


title: PCC6803_WT_combined_iron+manganese_depletion_rep_1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocol GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw expression data were subjected to a background correction by subtraction using the R package limma. The raw arrays were normalized using cyclic loess normalization using the normalizeBetweenArrays function of limma. Due to strong deviations in one of the three repeats for the 0Mn and 0Fe0Mn conditions, the corresponding replicates were excluded from further analysis.

organism: Synechocystis sp. PCC 6803

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis 6803 was grown in modified BG11 medium (YBG11; Shcolnick et al.,2007) in glass Erlenmeyer flasks. Cultures were maintained under constant shaking,illuminated with 60 μmol photons m-2 s-1 at 30C. Prior to an experiment, cultures were spun down and washed in a 20 mM of 2-(N-morpholino) ethanesulfonic acid (MES) and 10 mM ethylenediaminetetraacetic acid (EDTA; Kd, 1024) pH 5.0 buffer, in order to  remove excess metal ions. Cultures where resuspended in one of four media types: 1) Control media; 10 μM Fe and 1 μM Mn. 2) 0Mn; Mn was omitted from the media. 3) 0Fe; Fe was omitted form the media and 50 μM of the siderophore deferoxamine B (DFB; Kd, 1030) were added (Kranzler et al., 2011). 4) 0Fe0Mn; contained DFB and no added Mn or Fe.

extract_protocol: Cultures used for microarray analysis were centrifuged at 9,000 g at 4 0C, resuspended in phenol-chloroform extraction and frozen.

treatment_protocol: Prior to an experiment, cultures were spun down and washed in a 20 mM of 2-(N-morpholino) ethanesulfonic acid (MES) and 10 mM ethylenediaminetetraacetic acid (EDTA; Kd, 10^24) pH 5.0 buffer, in order to  remove excess metal ions. Cultures where resuspended in one of four media types: 1) Control media; 10 μM Fe and 1 μM Mn. 2) 0Mn; Mn was omitted from the media. 3) 0Fe; Fe was omitted form the media and 50 μM of the siderophore deferoxamine B (DFB; Kd, 1030) were added (Kranzler et al., 2011). 4) 0Fe0Mn; contained DFB and no added Mn or Fe.

tag: media type


title: subject B before exercise

description: B-pre


title: HC_2

description: SAMPLE 2

source_name: mRNA of whole blood


title: subject A 3 days after exercise


title: HC_1

description: SAMPLE 1


title: subject A 1 day after exercise


title: Cyclophosphamide_5days_40mpk_Yes Wood Stick_spleen_male_rat_4003

source_name: Cyclophosphamide, 40 mg/kg/day, yes wood stick, spleen, animal 4003

value: animal 4003


title: PCC6803_WT_iron_depletion_rep_3

value: 0Fe; Fe was omitted form the media + 50 μM DFB


title: PCC6803_WT_combined_iron+manganese_depletion_rep_2

value: 0Fe0Mn; contained DFB and no added Mn or Fe


title: Vehicle_5days_Yes Wood Stick_liver_male_rat_3001

source_name: Vehicle, yes wood stick, liver, animal 3001

value: Liver

value: Vehicle, yes wood stick

value: animal 3001


title: subject A 60 mins after exercise

value: healthy male

value: 60 mins after an acute resistance exercise

value: serum

value: Pooled human serum


title: Cyclophosphamide_5days_40mpk_No Wood Stick_liver_male_rat_2003

source_name: Cyclophosphamide, 40 mg/kg/day, no wood stick, liver, animal 2003

value: animal 2003


title: PCC6803_WT_standard_conditions_rep_3

value: Control media; 10 μM Fe and 1 μM Mn


title: OM2i-iPSCs  (Agilent)

description: Gene expression of iPS

source_name: combinations of oxysterol -treated MEFs treated with 2i/LIF

value: embryo


title: Artery_uninjured_rep1

city: Xuzhou

first: Dong

middle: ye

last: Li

state: Jiangsu

address: No. 84 West Huaihai Road

department: Institute of Cardiovascular Disease Research

country: China

institute: Xuzhou Medical College

description: Gene expression in uninjured wistar rat common carotid artery

hyb_protocol: 1.65ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was incubated at 60°C for exactly 30 minutes to fragment RNA in a reaction volume of 55ul containing 25x Agilent Fragmentation Buffer and 10x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GExHybridization Buffer was added to the fragmentation mixture and hybridized onto the Whole Rat Genome Oligo Microarray (4x44K, Agilent Technologies) for 17 hours at 65Â°C in an Agilent hybridization oven rotator. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then slowly remove the slide rack minimizing droplets on the slides.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
Quantile normalization and subsequent data processing was performed using Agilent Feature Extraction software (version 10.7.3.1) and the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, then genes that at least 5 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
Please note: Two raw data files, Sample 1 and Sample 3, contain raw data hybridized to the Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Probe Name version) array. The raw data file of Sample 2 is from a later batch and contains raw data from the Agilent-028282 Whole Rat Genome Microarray 4x44K v3 (Probe Name version). The ProbeNames in the Sample data table are from a median merger of each probe in both arrays according to the GenBank Accession numbers. Then the arrays are quantile standardized. So the ProbeNames in the matrix are the names that were merged for the same GenBank Accession corresponding to the later edition of the Agilent microarray probes names.

label_protocol: One microgram of RNA was amplified and transcribed into fluorescent cRNA using the One-Color Quick Amp Labeling protocol (version 5.7, Agilent Technologies), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from the frozen common carotid artery of each animal using TRIzol® reagent (Invitrogen) according to the manufacturer's instructions.Total RNA from each sample was quantified using the NanoDrop ND-1000 Spectrophotometer and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Harvested arteries were flushed rapidly with ice-cold phosphate buffer saline (PBS). These specimens were frozen in a -86°C freezer (Thermo Scientific Forma ULT; USA).

value: wistar rat

value: whole artery

tag: gender

value: male

value: uninjured


title: PCC6803_WT_manganese_depletion_rep_3

value: 0Mn; Mn was omitted from the media


title: Artery_injured_7d_rep1

description: Gene expression in injured wistar rat common carotid artery at day 7

source_name: CommonCarotidArtery, injured, 7d,  replicate1

value: balloon injured at 7 days


title: Artery_injured_21d_rep1

description: Gene expression in injured wistar rat common carotid artery at day 21

source_name: CommonCarotidArtery, injured, 21d, replicate1

value: balloon injured at 21 days


title: subject A before exercise

description: A-pre

value: before an acute resistance exercise


title: PCC6803_WT_manganese_depletion_rep_2


title: PCC6803_WT_iron_depletion_rep_2

value: 0Fe; Fe was omitted form the media + 50 μM DFB


title: PCC6803_WT_standard_conditions_rep_2


title: PCC6803_WT_standard_conditions_rep_1


title: Vehicle_5days_Yes Wood Stick_liver_male_rat_3005

source_name: Vehicle, yes wood stick, liver, animal 3005

value: Liver

value: Wild Type

value: Sprague-Dawley Rats

value: Vehicle, yes wood stick

value: animal 3005


title: PCC6803_WT_high_carbon_2

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

growth_protocol: The glucose-tolerant strain Synechocystis sp. PCC 6803 was obtained from N. Murata (National Institute for Basic Biology, Okazaki, Japan) and served as the wild type (WT).Cells were grown photoautotrophically in batch cultures using glass vessels of 3-cm diameter with 5-mm glass tubes for aeration (blubbing flow rate was 5 ml min-1) under continuous illumination of 130 µmol photons m-2s-1  (Osram L58 W 32/3) at 29°C in BG11 medium (Rippka et al., 1979). Cultivation of the mutant Δsml0013::Km was performed in the presence of 50 µgml-1 kanamycin (Km).

extract_protocol: Cells from 5 ml of culture were harvested by centrifugation at 4,000 rpm for 5 min at 4°C and were immediately frozen at -80°C. Total RNA was extracted after pre-treatment with hot phenol and chloroform by the High PureRNA isolation kit (Roche Diagnostics).

treatment_protocol: For CO2-shift experiments, cells were pre-cultivated with air enriched with 5% CO2 (defined as high CO2, HC) in BG11medium of pH 8.0. Then, cells were harvested by centrifugation (5 min at 3000 g, 20°C). The pellet was washed and re-suspended in fresh BG11medium of pH 7.0 at an optical density at 750 nm (OD750) of 0.8. After 1 h cultivation under HC conditions, CO2 limitation was set by shifting the exponentially growing cultures to bubbling with ambient air containing 0.035% CO2 (defined as low CO2, LC).

tag: genotype/varitaion

value: wild type

tag: co2 condition

value: high (5% CO2)


title: PCC6803_WT_iron_depletion_rep_1


title: Vehicle_5days_Yes Wood Stick_liver_male_rat_3003

source_name: Vehicle, yes wood stick, liver, animal 3003

value: animal 3003


title: Cyclophosphamide_5days_40mpk_Yes Wood Stick_liver_male_rat_4003

source_name: Cyclophosphamide, 40 mg/kg/day, yes wood stick, liver, animal 4003

value: animal 4003


title: Vehicle_5days_No Wood Stick_liver_male_rat_1005

source_name: Vehicle, no wood stick, liver, animal 1005

value: Vehicle, no wood stick

value: animal 1005


title: Cyclophosphamide_5days_40mpk_Yes Wood Stick_liver_male_rat_4005

source_name: Cyclophosphamide, 40 mg/kg/day, yes wood stick, liver, animal 4005

value: animal 4005


title: Vehicle_5days_Yes Wood Stick_spleen_male_rat_3001

source_name: Vehicle, yes wood stick, spleen, animal 3001

value: Spleen

value: animal 3001


title: Cyclophosphamide_5days_40mpk_No Wood Stick_liver_male_rat_2001

source_name: Cyclophosphamide, 40 mg/kg/day, no wood stick, liver, animal 2001

value: animal 2001


title: Cyclophosphamide_5days_40mpk_No Wood Stick_liver_male_rat_2005

source_name: Cyclophosphamide, 40 mg/kg/day, no wood stick, liver, animal 2005

value: animal 2005


title: Cyclophosphamide_5days_40mpk_No Wood Stick_spleen_male_rat_2001

source_name: Cyclophosphamide, 40 mg/kg/day, no wood stick, spleen, animal 2001


title: Cyclophosphamide_5days_40mpk_Yes Wood Stick_liver_male_rat_4001

source_name: Cyclophosphamide, 40 mg/kg/day, yes wood stick, liver, animal 4001

value: animal 4001


title: PCC6803_WT_high_carbon_1


title: sigL mutant T7-3

city: Beijing

first: Fuping

last: Song

address: No 2 West Yuan-Ming-Yang Road

institute: Instititue of plant protection, CAAS

description: gene expression after T7 in SSM medium

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

organism: Bacillus thuringiensis

source_name: sigL mutant

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The B. thuringiensis strains were grown at 30°C with vigorous shaking (220 rpm) in Schaeffer’s sporulation medium (SSM)

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: 2 ml samples were separately harvested from B. thuringiensis HD73 and HD(ΔsigL::kan) strains grown in Schaeffer’s sporulation medium (SSM) at stages T7 of stationary phase (7 hours after the end of the exponential phase).


title: HD73  T7-3

description: gene expression after T7 in SSM medium


title: Uninduced (Affymetrix)

description: Gene expression data from Uninduced

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: Bmi1-transduced mouse embryonic astrocytes

label_protocol: standard Affymetrix protocol

value: embryo


title: PCC6803_WT_24h_low_carbon_1

value: low (ambient air containing 0.035% CO2)


title: sigL mutant T7-1

description: gene expression after T7 in SSM medium


title: sigL mutant T7-2

description: gene expression after T7 in SSM medium


title: Vehicle_5days_No Wood Stick_liver_male_rat_1001

source_name: Vehicle, no wood stick, liver, animal 1001

value: Liver

value: Wild Type

value: Sprague-Dawley Rats

value: animal 1001


title: Ast (Affymetrix)

description: Gene expression data from Ast

source_name: mouse embryonic astrocytes

value: mouse embryonic astrocytes


title: ES (Affymetrix)

description: Gene expression data from ES

source_name: mouse embryonic stem cells

value: blastocyst

value: mouse embryonic stem cells


title: Vehicle_5days_No Wood Stick_liver_male_rat_1003

source_name: Vehicle, no wood stick, liver, animal 1003

value: Vehicle, no wood stick

value: animal 1003


title: HD73  T7-2

description: gene expression after T7 in SSM medium


title: HD73  T7-1

description: gene expression after T7 in SSM medium


title: PCC6803_Δsml0013::Km_24h_low_carbon_2

value: Δsml0013::Km mutant


title: Bmi1-spheres (Affymetrix)

description: Gene expression data from Bmi1-spheres

source_name: De-differentiated cells from Bmi1-transduced mouse embryonic astrocytes under NSC culture condition


title: PCC6803_Δsml0013::Km_high_carbon_2

value: high (5% CO2)


title: PCC6803_Δsml0013::Km_high_carbon_1


title: PCC6803_WT_24h_low_carbon_2

value: wild type


title: PCC6803_Δsml0013::Km_24h_low_carbon_1


title: 14249122 - 30C-1 vs 30P-1

status: Public on Jun 28 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: effect of phenanthrene and sucrose

hyb_protocol: 30P-1 Cy5 / 30C-1 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: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

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: whole plant - Media   MS/2  hygrometry   60%  Temperature   22°C  Light   16h

extract_protocol: 30P-1:12.5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-30min; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 30min. solvant=DMSO

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: 30C-1:25ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment


title: 14227200 - 4S-2 vs 4P-2

description: effect of phenanthrene and sucrose

hyb_protocol: 4P-2 Cy5 / 4S-2 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: 4P-2:5.6ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-4h; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 4hr. solvent=DMSO

tag: harvest date

extract_protocol: 4S-2:6.7ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:sucrose+phenanthrene-4h; compound based treatment (compound addition); sucrose+phenanthrene: quantity 3%, time 4hr. 3% sucrose+0.2mM phenanthrene


title: 14248936 - 30P-2 vs 30C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 30C-2 Cy5 / 30P-2 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: 30C-2:12.2ug. (Qiagen_RNeasy.pdf)

extract_protocol: 30P-2-A:4.1ug. (Qiagen_RNeasy.pdf)


title: 14249139 - 4P-1 vs 4S-1

description: effect of phenanthrene and sucrose

hyb_protocol: 4S-1 Cy5 / 4P-1 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: 4S-1:32.7ug. (Qiagen_RNeasy.pdf)

extract_protocol: 4P-1:17.8ug. (Qiagen_RNeasy.pdf)


title: 14249142 - 2P-1 vs 4P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 4P-1 Cy5 / 2P-1 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: 2P-1:20.3ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-2h; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 2hr. solvent=DMSO


title: 14249137 - 30P-2 vs 30S-2

description: effect of phenanthrene and sucrose

hyb_protocol: 30S-2 Cy5 / 30P-2 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: 30S-2:4.7ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:sucrose+phenanthrene-30min; compound based treatment (compound addition); sucrose+phenanthrene: quantity 3%, time 30min. 3% sucrose+0.2mM phenanthrene


title: 14249145 - 4P-2 vs 4C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 4C-2 Cy5 / 4P-2 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: 4C-2:14ug. (Qiagen_RNeasy.pdf)


title: 14227208 - 2P-1 vs 30P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 30P-1 Cy5 / 2P-1 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: 14248928 - 30P-2 vs t0-2

description: effect of phenanthrene and sucrose

hyb_protocol: t0-2 Cy5 / 30P-2 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: t0-2:31.4ug. (Qiagen_RNeasy.pdf)


title: 14248929 - t0-1 vs 30S-1

description: effect of phenanthrene and sucrose

hyb_protocol: 30S-1 Cy5 / t0-1 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: 30S-1:18.8ug. (Qiagen_RNeasy.pdf)

extract_protocol: t0-1:16.6ug. (Qiagen_RNeasy.pdf)


title: 14249135 - 30S-1 vs 30P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 30P-1 Cy5 / 30S-1 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: 14227211 - 2S-2 vs 4S-2

description: effect of phenanthrene and sucrose

hyb_protocol: 4S-2 Cy5 / 2S-2 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: 2S-2:10.5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:sucrose+phenanthrene-2h; compound based treatment (compound addition); sucrose+phenanthrene: quantity 3%, time 2hr. 3% sucrose+0.2mM phenanthrene


title: 14249138 - 4C-1 vs 4P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 4P-1 Cy5 / 4C-1 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: 4C-1:14.7ug. (Qiagen_RNeasy.pdf)


title: 14248930 - 30S-2 vs t0-2

description: effect of phenanthrene and sucrose

hyb_protocol: t0-2 Cy5 / 30S-2 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: 14248927 - t0-1 vs 30P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 30P-1 Cy5 / t0-1 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: 14249143 - 4P-2 vs 2P-2

description: effect of phenanthrene and sucrose

hyb_protocol: 2P-2 Cy5 / 4P-2 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: 2P-2:20.3ug. (Qiagen_RNeasy.pdf)


title: 14227209 - 30P-3 vs 2P-2

description: effect of phenanthrene and sucrose

hyb_protocol: 2P-2 Cy5 / 30P-3 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: 30P-2-B:14.7ug. (Qiagen_RNeasy.pdf)


title: 14227210 - 4S-1 vs 2S-1

description: effect of phenanthrene and sucrose

hyb_protocol: 2S-1 Cy5 / 4S-1 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: 2S-1:12.8ug. (Qiagen_RNeasy.pdf)


title: 14249134 - 2C-2 vs 30C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 30C-2 Cy5 / 2C-2 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: 2C-2:7.3ug. (Qiagen_RNeasy.pdf)


title: 14249133 - 30C-1 vs 2C-1

description: effect of phenanthrene and sucrose

hyb_protocol: 2C-1 Cy5 / 30C-1 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: 2C-1:18.8ug. (Qiagen_RNeasy.pdf)

extract_protocol: 30C-1:25ug. (Qiagen_RNeasy.pdf)


title: 14249132 - 2C-2 vs 4C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 4C-2 Cy5 / 2C-2 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: 14248937 - t0-1 vs 30C-1

description: effect of phenanthrene and sucrose

hyb_protocol: 30C-1 Cy5 / t0-1 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: 14249131 - 4C-1 vs 2C-1

description: effect of phenanthrene and sucrose

hyb_protocol: 2C-1 Cy5 / 4C-1 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: 14248940 - 2C-1 vs 2P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 2P-1 Cy5 / 2C-1 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: 14227204 - 8S-1 vs 4S-1

description: effect of phenanthrene and sucrose

hyb_protocol: 4S-1 Cy5 / 8S-1 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: 8S-1:10.5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:sucrose+phenanthrene-8h; compound based treatment (compound addition); sucrose+phenanthrene: quantity 3% time 8hr. 3% sucrose+0.2mM phenanthrene


title: 14249141 - 2P-2 vs 2C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 2C-2 Cy5 / 2P-2 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: 14248926 - 30C-2 vs t0-2

description: effect of phenanthrene and sucrose

hyb_protocol: t0-2 Cy5 / 30C-2 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: 30C-2:12.2ug. (Qiagen_RNeasy.pdf)


title: 14227213 - 8P-2 vs 4P-2

description: effect of phenanthrene and sucrose

hyb_protocol: 4P-2 Cy5 / 8P-2 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: 4P-2:5.6ug. (Qiagen_RNeasy.pdf)

extract_protocol: 8P-2:20.5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-8h; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 8hr. solvent=DMSO


title: 14227202 - 4C-1 vs 8C-1

description: effect of phenanthrene and sucrose

hyb_protocol: 8C-1 Cy5 / 4C-1 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: 8C-1:14.3ug. (Qiagen_RNeasy.pdf)


title: 14227203 - 8C-2 vs 4C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 4C-2 Cy5 / 8C-2 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: 4C-2:14ug. (Qiagen_RNeasy.pdf)

extract_protocol: 8C-2:5ug. (Qiagen_RNeasy.pdf)


title: 14227197 - 24P-2 vs 8P-2

description: effect of phenanthrene and sucrose

hyb_protocol: 8P-2 Cy5 / 24P-2 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: 24P-2:3.6ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-24h; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 24hr. solvent=DMSO


title: 14227195 - 8S-2 vs 8P-2

description: effect of phenanthrene and sucrose

hyb_protocol: 8P-2 Cy5 / 8S-2 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: 8S-2:32.7ug. (Qiagen_RNeasy.pdf)


title: 14227198 - 24C-1 vs 24P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 24P-1 Cy5 / 24C-1 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: 24P-1:18.5ug. (Qiagen_RNeasy.pdf)

extract_protocol: 24C-1:14ug. (Qiagen_RNeasy.pdf)


title: 14248931 - 30S-1 vs 2S-1

description: effect of phenanthrene and sucrose

hyb_protocol: 2S-1 Cy5 / 30S-1 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: 30S-1:18.8ug. (Qiagen_RNeasy.pdf)


title: 14248934 - 2S-2 vs 2P-2

description: effect of phenanthrene and sucrose

hyb_protocol: 2P-2 Cy5 / 2S-2 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: 2P-2:20.3ug. (Qiagen_RNeasy.pdf)

extract_protocol: 2S-2:10.5ug. (Qiagen_RNeasy.pdf)


title: 14227212 - 4P-1 vs 8P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 8P-1 Cy5 / 4P-1 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: 8P-1:34.3ug. (Qiagen_RNeasy.pdf)

extract_protocol: 4P-1:17.8ug. (Qiagen_RNeasy.pdf)


title: 14227205 - 4S-2 vs 8S-2

description: effect of phenanthrene and sucrose

hyb_protocol: 8S-2 Cy5 / 4S-2 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: 4S-2:6.7ug. (Qiagen_RNeasy.pdf)


title: 14227196 - 8P-1 vs 24P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 24P-1 Cy5 / 8P-1 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.