title: rpoS_nutrient_broth_rep1

description: Technical replicate 1 of biological replicate 1


title: wild type-3

status: Public on Dec 31 2012

type: RNA

city: Ithaca

first: Ji-Young

last: Lee

state: NY

address: Tower Rd.

country: USA

institute: Boyce Thompson Institute

hyb_protocol: GeneChip_ Arabidopsis Tiling 1.0R arrays (catalog no. 900594; Affymetrix) were hybridized with 6.5-7.0 micrograms of double-stranded cDNA that had been fragmented (with uracil DNA glycosylase) and terminally labeled (with biotin using a terminal deoxynucleotidyl transferase  (DLR; Affymetrix WT Double-stranded DNA Terminal Labeling Kits, catalog no. 900812)). This cDNA was then resuspended with a control Oligonucleotide B2 (catalog no. 900301; Affymetrix) in 200 microliters of hybridization cocktail. The arrays were subsequently hybridized in a rotating (60 rpm) oven at 45 C for 16 h. These were then washed and stained in the GeneChip Fluidics Station 450 (Wash and Stain kit, catalog no. 900720; Affymetrix), using the EukGE-WS2v4 washing protocol.

scan_protocol: Scanning was done using the GeneChip Scanner 7G plus and image analysis was carriedout in GCOS (catalog no. 690036; Affymetrix)

data_processing: Microarray data were normalized using RMA algorithm (Irizarry et al., 2003) in BIOCONDUCTOR, with Tiling 1.0R array CDF that contains gene-specific single-copy exonic probe sets (Naouar et al., 2009).

label: Biotin

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: wild type-3

label_protocol: Approximatley 300 micrograms of poly-adenylated RNA was then further amplified and purified according to manufacturer’s instructions (GeneChip Whole Transcript Double-Stranded Target Assay Manual from Affymetrix Inc.) for labeling. Labeled DNA was generated after fragmentation using the GeneChip-WT Double Stranded DNA Terminal Labeling Kit (Affymetrix) following manufacture's recommendations (GeneChip Whole Transcript Double-Stranded Target Assay Manual from Affymetrix Inc.).

growth_protocol: Wild-type Col-0, shr-2 and shr-2 phb-6 plants harboring WOL::erGFP were germinated and grown for 6 days on solid Murashige and Skoog (MS) medium (4.3g MS salts, 10g sucrose, 8g agar and pH to 5.7-5.8 with 1M NaOH. Bring up volume to 1L with dH2O) at 22-23 ºC with the cycle of 16 hour light and 8 hour dark periods in a plant growth chamber.

extract_protocol: Following protoplasting and cell sorting RNA was extracted from sorted cells (2-2.5 million) using RNeasy micro kit (Invitrogen) following manufacture's recommendations. RNA integrity was determined on a Bioanalyzer (Agilent BioAnalyzer 2100). Poly-adenylated RNA was isolated from this using RiboMinus Plant Kit (Invitrogen). Probe preparation was carried out according to the manufacturer’s instructions (GeneChip Whole Transcript Double-Stranded Target Assay Manual from Affymetrix Inc.).

treatment_protocol: On 6 DAG root samples were collected by cutting them (1cm long from the root tip) with a #10 surgical blade for protoplast isolation. Protoplasts were prepared from root tissues as described by Birnbaum et al. (2003) and GFP expressing protoplasts were collected from BD-Biosciences FACS Aria high speed flow cell sorter.

tag: ecotype

tag: tissue

value: Root

tag: genotype/variation

value: wild type


title: rpoS_nutrient_broth_rep3

city: Corvallis

first: Joyce

last: Loper

state: OR

address: 3420 NW Orchard Ave

department: Horticultural Crops Research Laboratory

institute: USDA-ARS

description: Technical replicate 1 of biological replicate 2

hyb_protocol: Combine Cy3 and Cy5 samples and 1 microliter cy-labeled arabidopsis 70-mer positional controls (This is a pool of 4 70-mers labeled with Cy3 and Cy5 for a total of 8 70-mers at 2 ng/microliter each. The sequences are: At2g14610a_219_rev - AAAAAAATATATCAACAATGGCAAAGCTACCGATACGAAACAATATTAGGAAAAATGTGTGTAAGrpoSA; At2g14610b_265_rev - AATTTAAACTGCGTATTAGTGTTTGGAAAAAAAAAACAAAGTGTATACAATGTCAATCGGTGATCTTTTT; At2g14610c_305_rev - TTAATAACATATAATATTGAATAGGATATCATAGGATATTATTACGTAATAATATCCTATGGTGTCATTT; At2g14610d_298_rev - CGACTTTTCTTGCTTAGAAGTCTTTGCATTGTTAATAGATTGTTGAAAAGGTTTATTCATTACTTTCATG).  Dry using a speed vac.  Make pre-hybridization buffer by combining:  0.5 g BSA;  37 mL DEPC water;  12.5 mL 20X SSC;  0.5 mL 10% SDS.  Incubate pre-hybridization buffer for 20 minutes at 42 degrees C.  Filter using a 0.45 micrometer cellulose acetate filter into a coplin jar.  Incubate for 20 minutes at 42 degrees C.  Make hybridization buffer by combining:  500 microliters fomamide;  250 microliters 20X SSC;  10 microliters 10% SDS;  240 microliters DEPC water.  Filter hybridization buffer through a 0.45 micrometer cellulose acetate filter.  Add 50 uL sheared salmon sperm DNA (Ambion) to hybridization buffer.  Add 60 microliters hybridization buffer to speed vac-dried probes.  Put slide into pre-hybridization buffer in coplin jar.  Incubate for 45 minutes at 42 degrees C.  Wash slide 4 times in water and 3 times in isopropanol for 2 minutes per wash with gentle shaking by hand.  Dry slide by spinning.  Clean 25 mm x 60 mm lifterslip (Erie Scientific Company) by dipping in MilliQ water for 5 minutes at room temperature.  Dip in 100% EtOH and dry with a Chem Wipe.  Heat probes for 15 minutes at 95 degrees C with occassional flicking to resuspend probes.  Remove probes from heat block and centrifuge for 2 minutes at 15,000g.  Place lifterslip onto slide and add probes by allowing capillary action to pull the probes under the lifterslip.  Hybridize overnight at 42 degrees C.  Wash slide 2 times in glass staining dish with 1X SSC, 0.2% SDS for 5 minutes at 42 degrees C.  Wash slide in 0.1X SSC, 0.1% SDS for 5 minutes at room temperature.  Wash slide 3 times in 0.1X SSC for 5 minutes at room temperature.  Dry slide by spinning.

scan_protocol: Slides were scanned at 10 micrometer resolution using an Axon 4000B scanner with GenePix 4.0 software.

data_processing: Tiff images were processed using TIGR-Spotfinder (www.tigr.org/software) with Otsu thresholding, a minimum spot size of 10 and a maximum spot size of 15, and applying the default quality control filter options. The data were normalized ignoring controls with the LOWESS algorithm in block mode with a smooth parameter of 0.33 by using TIGR-MIDAS (www.tigr.org/software). Channel 'A' = Cy3. Channel 'B' = Cy5.

molecule: total RNA

organism: Pseudomonas protegens

source_name: rpoS mutant of P. protegens Pf-5

label_protocol: Make spike-in control pools from RNA amplified from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) using the MegaScript Kit (Ambion) by combining for Cy5 pool:  5.2 microliters 20.3 ng/microliter cab RNA;  12.5 microliters 16.839 ng/microliter ltp4 RNA;  18.6 microliters 22.634 ng/microliter rca RNA;  41.8 microliters 15.068 ng/microliter rbcL RNA;  4.7 microliters 13.279 ng/microliter ltp6 RNA;  11.8 microliters 21.313 ng/microliter rcp1 RNA;  40.7 microliters 23.23 ng/microliter nac RNA;  4.6 microliters 18.177 ng/microliter xcp2 RNA;  14.7 microliters 11.436 ng/microliter prk RNA;  18.9 microliters 11.084 ng/microliter tim RNA;  826.5 microliters water.  And for Cy3 pool:  5.2 microliters 20.3 ng/microliter cab RNA;  12.5 microliters 16.839 ng/microliter ltp4 RNA;  18.6 microliters 22.634 ng/microliter rca RNA;  41.8 microliters 15.068 ng/microliter rbcL RNA;  1.6 microliters 13.279 ng/microliter ltp6 RNA;  3.9 microliters 21.313 ng/microliter rcp1 RNA;  13.6 microliters 23.23 ng/microliter nac RNA;  13.9 microliters 18.177 ng/microliter xcp2 RNA;  44.1 microliters 11.436 ng/microliter prk RNA;  56.8 microliters 11.084 ng/microliter tim RNA;  788.1 microliters water.  To label RNA sample combine:  4 micrograms RNA;  2 microliters 3 mg/mL random hexamers (Invitrogen);  2 microliters arabidopsis spike-in control RNA;  DEPC water to a final volume to 17.5 microliters.  Mix and incubated at 70 degrees C for 10 minutes.  Snap-freeze in dry ice/ethanol for 30 seconds and centrifuged for 1 minute at approximately 16,000g.  Add:  6 microliters 5X Superscript II buffer (Invitrogen);  3 microliters 0.1 M dithiothreitol;  1.2 microliters aminoallyl-dNTP mix containing 12.5 mM dATP, 12.5 mM dCTP, 12.5 mM dGTP, 4.16 mM dTTP, and 8.33 mM aadUTP;  2 microliters SuperScript II (Invitrogen).  Mix and incubated overnight at 42 degrees C.  Add:  10 microliters 1 M NaOH;  10 microliters 0.5 M EDTA.  Incubate for 15 minutes at 65 degrees C.  Add:  25 microliters 1 M Tris pH 7.4;  400 microliters PB buffer (Qiagen).  Apply sample to QIAquick column (Qiagen).  Centrifuge for 1 minute at 15,000g.  Wash with 750 microliters phosphate wash buffer (84.25 mL 95% EtOH + 15.25 mL water + 0.5 mL 1 M KPO4 pH 8.5 solution made by combining 0.5 mL 1M KH2PO4 with 9.5 mL 1M K2HPO4).  Centrifuge for 1 minute at 15,000g.  Repeat wash.  Empty collection tube and centrifuge for 1 minute at 15,000g.  Transfer column to fresh tube.  Add 30 microliters phosphate elution buffer (4 mM KPO4 solution made by diluting 1 M KPO4 pH 8.5 solution).  Incubate for 1 minute.  Centrifuge for 1 minute at 15,000g.  Repeat elution for a final volume of 60 microliters.  Dry sample using a speed vac.  Resuspend cDNA in 4.5 microliters 0.1 M carbonate buffer (1 M Na2CO3 buffer pH 9.0 diluted 1:10 with water).  Allow the sample to resuspend for 15 minutes at room temperature.  Add 4.5 microliters NHS-Cy (Amersham) resuspended in 73 microliters DMSO.  Incubate for 1 hour at room temperature in the dark.  Add 4.5 microliters 4 M hydroxylamine.  Incubate for 15 minutes at room temperature in the dark.  Add:  35 microliters 100 mM NaOAc pH 5.2;  500 microliters PB buffer.  Apply to Qiaquick column.  Centrifuge for 1 minute at 15,000g.  Wash with 750 microliters PE buffer (Qiagen).  Centrifuge for 1 minute at 15,000g.  Repeat wash.  Empty collection tube and centrifuge for 1 minute at 15,000g.  Transfer column to fresh tube.  Add 30 microliters EB buffer (Qiagen).  Incubate for 1 minute.  Centrifuge for 1 minute at 15,000g.  Repeat elution for a final volume of 60 microliters.  Check quality of probes spectrophotometrically from 200nm to 700nm.  Store at -80 degrees C.  Use this protocol to label 12 ug RNA and combine products for one hyb.

growth_protocol: Bacterial cultures were first inoculated from frozen stocks onto King’s Medium B agar (King, et al., 1954) for overnight incubation at 27ºC. This plate was used to  inoculate a 5 ml broth culture of nutrient broth amended with 1% glycerol (NBgly) grown shaking at 200 rpm for 16-18 hours at 27ºC. Inoculum was washed in  sterile NBgly broth prior to inoculation and resuspended in 20 ml of NBgly broth in a 125 ml erlenmeyer flask to an OD600 of ~0.05. Three replicate cultures were  grown with shaking (200 rpm) at 20ºC until harvest at the specified optical density of 2.0-2.4. For each replicate culture, RNA was pretreated with RNAProtect  (Qiagen, Valencia, CA) for 10 minutes, centrifuged and pellets were stored at -80°C until extracted.

extract_protocol: Extractions were done using the RNA/DNA Midi Kit (Qiagen, Valencia, CA) followed by an on-column DNAse treatment (RNeasy Mini Kit with DNAse I; Qiagen, Valencia, CA). PCR was performed on the RNA to determine that detectable DNA had been removed and RNA samples were analyzed for quality using the BioAnalyzer 2100 (Agilent, Palo Alto, CA).

tag: strain

value: rpoS mutant

source_name: P. protegens Pf-5 wild-type

value: wild-type


title: wild type-2

source_name: wild type-2


title: shr-2 phb-6-DM2

source_name: shr-2 phb-6-DM2

value: shr-2 phb-6


title: shr-2-1


title: wild type-1

source_name: wild type-1


title: shr-2 phb-6-DM1

source_name: shr-2 phb-6-DM1


title: rpoS_nutrient_broth_rep6

description: Technical replicate 2 of biological replicate 3


title: Melanoma (methylome) Mel.7

type: genomic

city: Duarte

first: Arthur

last: Li

address: 1500 E Duarte Rd

institute: City of Hope

description: DNA Methylation Profile in Mel.7

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

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

molecule: genomic DNA

organism: Homo sapiens

source_name: MIRA enriched samples

label_protocol: According to standard NimbleGen Protocol

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

tag: braf mutational status

value: Wild-type

value: Melanoma

tag: enrichment procedure

value: MIRA

tag: affinity purification

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

tag: sample type

value: MIRA enriched samples

source_name: Genomic Input DNA

value: input DNA


title: Melanocyte (methylome) Mel.23

description: DNA Methylation Profile in Mel.23

tag: cell type

value: melanocytes


title: Melanoma (methylome) Mel.14

description: DNA Methylation Profile in Mel.14


title: Melanoma (methylome) Mel.10

description: DNA Methylation Profile in Mel.10


title: Melanoma (methylome) Mel.4

description: DNA Methylation Profile in Mel.4


title: shr-2-2


title: Melanocyte (methylome) Mel.25

description: DNA Methylation Profile in Mel.25


title: Melanoma (methylome) Mel.2

description: DNA Methylation Profile in Mel.2


title: Melanoma (methylome) Mel.1

description: DNA Methylation Profile in Mel.1

value: Mutant

tag: braf mutation


title: Melanoma (methylome) Mel.3

description: DNA Methylation Profile in Mel.3


title: Melanoma (methylome) Mel.8

description: DNA Methylation Profile in Mel.8


title: Melanocyte (methylome) Mel.22

description: DNA Methylation Profile in Mel.22


title: Melanoma (methylome) Mel.6

description: DNA Methylation Profile in Mel.6


title: Melanocyte (methylome) Mel.26

description: DNA Methylation Profile in Mel.26


title: Melanocyte (methylome) Mel.21

description: DNA Methylation Profile in Mel.21


title: Melanoma (methylome) Mel.12

description: DNA Methylation Profile in Mel.12


title: Melanoma (methylome) Mel.5

description: DNA Methylation Profile in Mel.5


title: HK1-EBER_rep3

city: Kuala Lumpur

first: Lu Ping

last: Tan

address: Jalan Pahang

department: Molecular Pathology Unit

country: Malaysia

institute: Institute for Medical Research

description: EBERs plasmid containing 10 tandem repeats of the EBER-1 and EBER-2 subfragment inserted into a pcDNA 3 plasmid was introduced into HK1 cells by the lipofection method.

hyb_protocol: Samples were hybridized and analysed on GeneChip ® Human Gene 1.0 ST Array, with three repeats.

scan_protocol: Microarray scanning and data acquisition were carried out at ORIGEN LABS (Singapore), using an Affymetrix 3000 7G Scanner.

data_processing: CEL files were generated from GCOS and analyzed in GeneSpring GX10. RMA16 normalization was performed and signal intensities that showed <20th percentile were excluded. This resulted in 24067 transcripts (see matrix table).

label: biotin

source_name: HK1 cell line

label_protocol: 300ug total RNA was reverse transcribed into cDNA, processed using GeneChip® Whole Transcript (WT) Sense Target Labelling Assay.

growth_protocol: Mycoplasma-free, stably transfected HK1 cells were maintained in the exponential growth phase in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 10 U of penicillin per ml and 10 μg streptomycin per ml at 37°C in a 5% CO2 humidified atmosphere.  Stable transfectants were selected by culturing in fully supplemented medium containing G418.  Colonies that emerged were pooled and used for this microarray experiment.

extract_protocol: Total RNA was extracted from each cell line with TRIZOL® (Invitrogen) reagent

tag: cell line

tag: plasmid

value: EBERs-positive


title: HK1-EBER_rep1


title: HK1-EBER_rep2


title: HK1-vector_rep3

description: The pcDNA3.1 plasmid WITHOUT the insert of interest was introduced into HK1 cells by the lipofection method.  This served as the vector control.

value: EBERs-negative


title: HK1-vector_rep1


title: HK1-vector_rep2


title: MT.CRTS-19

city: daejeon

first: Tae-Wook

last: Kang

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: KRIBB

description: Blood genomic DNA in patient with rectal cancer

hyb_protocol: The labeled DNA was hybridized to a Genomic-Wide Human SNP Array 6.0 for 16-18 hours in a rotating oven at 50℃ and 60 rpm.

scan_protocol: The SNP Array 6.0 was scanned with the Affymetirx GeneChip Scanner 3000 using Affymetrix GeneChip Operating Software (GCOS; version 1.4

data_processing: Signal intensity data was analyzed by the Dynamic Model (DM algorithm. A contrast QC of greater than or equal to 0.4 should be used to determine whether a sample should be repeated or used for downstream ananlysis.

label_protocol: The fragmented DNA was labeled using DNA Labeling Reagent and TdT enzyme for 4.25 hours at 37℃.

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

tag: gender

value: male

value: rectal

tag: trg disease state

tag: cr

tag: er

tag: ryn

tag: analysis

value: analysed


title: MT.CRTS-16

source_name: Blood genomic DNA in patient with rectal cancer


title: MT.CRTS-22


title: MT.CRTS-17


title: MT.CRTS-14

value: female


title: BN_M520

city: Utrecht

first: Victor

last: Guryev

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: Hybridization was done at 37C according to Nimblegen standard aCGH protocol

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 SegMNT data extraction.

organism: Rattus norvegicus

source_name: BN rat

label_protocol: Labelling was done using standard Nimblegen protocol for aCGH

extract_protocol: DNA was extracted from 100 milligrams of liver tissue using Qiagen DNAEasy blood and tissue DNA isolation kit

value: BN

tag: tissue

value: liver

source_name: M520 rat


title: MT.CRTS-21


title: MT.CRTS-18


title: M520_BN


title: MT.CRTS-12


title: MT.CRTS-15


title: MTCRT2-3


title: MT.CRTS-20


title: MTCRT2-10


title: MT.CRTS-13


title: 9


title: rpoS_pea_seed_rep6

scan_protocol: Slides were scanned at 10 micrometer resolution using an Axon 4200A scanner with GenePix 4.0 software.

growth_protocol: Overnight cultures of Pf-5 and the rpoS mutant were grown in 50 ml of NBGly in a 250 ml Erlenmeyer flask with shaking (200 rpm) at 27ºC.  Cultures were centrifuged 5 min at 5,000 x g and the pellet washed with sterile distilled water.  Washed cells were diluted to OD600=0.5 in sterile distilled water.  Pea seeds (Pisum sativum cv. Sugar Snap) were surface sterilized in 95% ethanol for 2 min, followed by treatment with 20% bleach for 15 min.  Seeds were washed 3-4 times in sterile distilled water (10 min each).  Seeds that swelled during sterilization (indicating broken seed coats) were discarded.  Intact seed (180 per sample) were placed in the OD600=0.5 bacterial solutions for 5 min and then transferred onto sterile moistened filter paper (Whatmann #3) in petri dishes (20 seed/dish).  Petri dishes were placed in a sealed box with wet paper towels to maintain humidity and placed at 20ºC for 24 h.  After 24 h, seed was placed in a solution of two parts RNAprotect bacteria (Qiagen) and one part sterile distilled water.  Seed were vortexed at maximum speed for 30 sec to remove bacteria from the seed surfaces.  The liquid was decanted into a centrifuge tube, incubated 5 min, and centrifuged 10 min at 5,000 x g.  Pellets were stored at -80ºC.

extract_protocol: RNA extractions were done using the RNA/DNA Midi Kit (Qiagen) according to the provided protocol.  300 µl TE buffer with lysozyme (1 mg/mL) and ~250 µl volume of acid washed glass beads (212-300 µm; Sigma-Aldrich, St. Louis, MO) were added to the thawed bacterial pellet and the pellet vortexed for 5 min at the maximum setting.  A volume of 1.2 ml Buffer QRL1 with 10 µl 2-mercaptoethanol (Sigma-Aldrich) per ml was added, and the mixture vortexed another 2-3 min.  After settling, the liquid was transferred to a microfuge tube and spun 1 min at maximum speed to remove residual beads.  A volume of 1.25 ml supernatant was used to complete the RNA isolation according to the provided protocol.  All RNA was subjected to an on-column DNAse treatment (RNeasy Mini Kit with DNAse I; Qiagen) and used to perform PCR to confirm removal of detectable DNA.  RNA quality was analyzed on a BioAnalyzer 2100 (Agilent, Palo Alto, CA).

tag: genotype/variation

value: rpoS mutant

value: wild-type


title: rpoS_pea_seed_rep5

description: Technical replicate 1 of biological replicate 3

tag: strain


title: MTCRT2-11


title: MTCRT2-8


title: 5


title: MT.CRTS-11


title: MT.CRT 63


title: rpoS_pea_seed_rep3


title: rpoS_pea_seed_rep2

description: Technical replicate 2 of biological replicate 1


title: MTCRT2-7


title: rpoS_pea_seed_rep1


title: rpoS_pea_seed_rep4

description: Technical replicate 2 of biological replicate 2


title: gacA_pea_seed_rep5

hyb_protocol: Combine Cy3 and Cy5 samples and 1 microliter cy-labeled arabidopsis 70-mer positional controls (This is a pool of 4 70-mers labeled with Cy3 and Cy5 for a total of 8 70-mers at 2 ng/microliter each. The sequences are: At2g14610a_219_rev - AAAAAAATATATCAACAATGGCAAAGCTACCGATACGAAACAATATTAGGAAAAATGTGTGTAAGGACAA; At2g14610b_265_rev - AATTTAAACTGCGTATTAGTGTTTGGAAAAAAAAAACAAAGTGTATACAATGTCAATCGGTGATCTTTTT; At2g14610c_305_rev - TTAATAACATATAATATTGAATAGGATATCATAGGATATTATTACGTAATAATATCCTATGGTGTCATTT; At2g14610d_298_rev - CGACTTTTCTTGCTTAGAAGTCTTTGCATTGTTAATAGATTGTTGAAAAGGTTTATTCATTACTTTCATG).  Dry using a speed vac.  Make pre-hybridization buffer by combining:  0.5 g BSA;  37 mL DEPC water;  12.5 mL 20X SSC;  0.5 mL 10% SDS.  Incubate pre-hybridization buffer for 20 minutes at 42 degrees C.  Filter using a 0.45 micrometer cellulose acetate filter into a coplin jar.  Incubate for 20 minutes at 42 degrees C.  Make hybridization buffer by combining:  500 microliters fomamide;  250 microliters 20X SSC;  10 microliters 10% SDS;  240 microliters DEPC water.  Filter hybridization buffer through a 0.45 micrometer cellulose acetate filter.  Add 50 uL sheared salmon sperm DNA (Ambion) to hybridization buffer.  Add 60 microliters hybridization buffer to speed vac-dried probes.  Put slide into pre-hybridization buffer in coplin jar.  Incubate for 45 minutes at 42 degrees C.  Wash slide 4 times in water and 3 times in isopropanol for 2 minutes per wash with gentle shaking by hand.  Dry slide by spinning.  Clean 25 mm x 60 mm lifterslip (Erie Scientific Company) by dipping in MilliQ water for 5 minutes at room temperature.  Dip in 100% EtOH and dry with a Chem Wipe.  Heat probes for 15 minutes at 95 degrees C with occassional flicking to resuspend probes.  Remove probes from heat block and centrifuge for 2 minutes at 15,000g.  Place lifterslip onto slide and add probes by allowing capillary action to pull the probes under the lifterslip.  Hybridize overnight at 42 degrees C.  Wash slide 2 times in glass staining dish with 1X SSC, 0.2% SDS for 5 minutes at 42 degrees C.  Wash slide in 0.1X SSC, 0.1% SDS for 5 minutes at room temperature.  Wash slide 3 times in 0.1X SSC for 5 minutes at room temperature.  Dry slide by spinning.

source_name: gacA mutant of P. protegens Pf-5

growth_protocol: Overnight cultures of Pf-5 and the gacA mutant were grown in 50 ml of NBGly in a 250 ml Erlenmeyer flask with shaking (200 rpm) at 27ºC.  Cultures were centrifuged 5 min at 5,000 x g and the pellet washed with sterile distilled water.  Washed cells were diluted to OD600=0.5 in sterile distilled water.  Pea seeds (Pisum sativum cv. Sugar Snap) were surface sterilized in 95% ethanol for 2 min, followed by treatment with 20% bleach for 15 min.  Seeds were washed 3-4 times in sterile distilled water (10 min each).  Seeds that swelled during sterilization (indicating broken seed coats) were discarded.  Intact seed (180 per sample) were placed in the OD600=0.5 bacterial solutions for 5 min and then transferred onto sterile moistened filter paper (Whatmann #3) in petri dishes (20 seed/dish).  Petri dishes were placed in a sealed box with wet paper towels to maintain humidity and placed at 20ºC for 24 h.  After 24 h, seed was placed in a solution of two parts RNAprotect bacteria (Qiagen) and one part sterile distilled water.  Seed were vortexed at maximum speed for 30 sec to remove bacteria from the seed surfaces.  The liquid was decanted into a centrifuge tube, incubated 5 min, and centrifuged 10 min at 5,000 x g.  Pellets were stored at -80ºC.

value: gacA mutant


title: MTCRT2-4


title: gacA_pea_seed_rep4


title: gacA_pea_seed_rep3


title: MTCRT2-5


title: 8


title: gacA_pea_seed_rep1


title: MTCRT2-2


title: MT.CRTS-10


title: gacA_pea_seed_rep6


title: gacA_pea_seed_rep2


title: CMO-Male-Liver-Replicate3

city: Thunder Bay

first: Shannon

middle: L

last: Costigan

state: ON

address: 955 Oliver Rd

department: Biology

country: Canada

institute: Lakehead University

hyb_protocol: Agilent manufactured Fathead minnow microarrays based on the EcoArray platform (22K unique probes, GLP7282) were hybridized in Agilent hybridization chambers and incubated overnight at 65°C. The slides were washed for 1 min in 6X SSPE, 0.005% N-Laurosylsarcosine; 1 min in 0.06X SSPE, 0.005% N-Laurosylsarcosine; and then dried by dipping the slides in two trays containing a stabilization and drying solution for 60 s and 30 s.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and raw images were processed using Agilent’s Feature Extraction Software, Version 9.5.3.

data_processing: log2 transformed signal ratio between the experimental channel and the reference channel was calculated for each spot following background correction of the spot intensities. Data for male and female fish were analyzed independently.  The raw data were LOWESS normalized within arrays and scaled between arrays using the limma package implemented in the R environment for statistical computing (http://www.R-project.org)

organism: Pimephales promelas

source_name: Total liver RNA from CMO exposed male FHM labeled with Cyanine-5 (red)

label_protocol: The RNA samples were labeled using Agilent’s Quick-AMP 2-Color Labeling kit (#5190-0444).  Each experimental array sample was prepared by combining 825 ng of Cy5 labelled liver RNA sample with 825 ng of the Cy3 labelled reference sample.

extract_protocol: RNA isolation was performed using the manufacturer’s recommended ratio of 1 ml TRIzol reagent (Invitrogen) per 100 mg of liver.

tag: developmental stage

value: sexually mature adult

tag: treatment

value: 100% final effluent

source_name: Pooled reference sample from all river water exposed (control) FHM (3 female and 3 male)

value: reference pool


title: CMO-Male-Liver-Replicate1


title: CMO-Male-Liver-Replicate2


title: MT.CRT 69


title: TK-Male-Liver-Replicate3

source_name: Total liver RNA from TK exposed male FHM labeled with Cyanine-5 (red)

value: 25% treated kraft effluent


title: lung165T_cancer tissue_Affymetrix SNP6

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

description: Hybridized to SNP6.0

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol GeneChip Scanner 3000.

data_processing: CEL files and TXT files generated by Affymetrix GTYPE using the DM algorithm. The raw CEL files were imported into Partek software using its default settings.  Control probes in Affymetrix SNP6.0 were excluded, and two pre-background adjustments were performed, adjust for fragment length and adjust for probe sequence.  'Signal' = Summarized signal [Lung_adeno_61_pairs_intensity.txt].

source_name: lung165T_cancer tissue

label_protocol: Affymetrix standard protocol

extract_protocol: Genomic DNA was isolated by proteinase K- phenol - chloroform extraction following standard protocols with 0.5% SDS and 200μg/ml proteinase K.

treatment_protocol: lung tissue specimens

value: cancer lung tissue


title: MT.CRT 43


title: MT.CRT 29


title: lung167T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung167T_cancer tissue


title: MTCRT2-6


title: lung165N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung165N_normal tissue

value: normal lung tissue


title: MT.CRT 27


title: lung167N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung167N_normal tissue


title: MT.CRT 50


title: TK-Male-Liver-Replicate2


title: MT.CRT 48


title: MT.CRT 28


title: UTK-Male-Liver-Replicate2

source_name: Total liver RNA from UTK exposed male FHM labeled with Cyanine-5 (red)

value: 10% untreated kraft effluent


title: MT.CRT 26


title: MT.CRT 41


title: TK-Male-Liver-Replicate1


title: UTK-Male-Liver-Replicate1


title: MT.CRT 25


title: UTK-Male-Liver-Replicate3


title: MT.CRT 22


title: MT.CRT 20


title: lung158T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung158T_cancer tissue


title: Control-Male-Liver-Replicate2

source_name: Total liver RNA from river water exposed male FHM labeled with Cyanine-5 (red)

value: Control


title: MT.CRT 23

value: male


title: lung159N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung159N_normal tissue


title: MT.CRT19

value: rectal


title: MT.CRT 47

value: analysed


title: MT.CRT 21


title: lung159T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung159T_cancer tissue

value: female


title: CMO-Female-Liver-Replicate3

source_name: Total liver RNA from CMO exposed female FHM labeled with Cyanine-5 (red)


title: Control-Male-Liver-Replicate3


title: CMO-Female-Liver-Replicate2


title: lung157T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung157T_cancer tissue


title: Control-Male-Liver-Replicate1


title: CMO-Female-Liver-Replicate1


title: TK-Female-Liver-Replicate2

source_name: Total liver RNA from TK exposed female FHM labeled with Cyanine-5 (red)


title: lung158N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung158N_normal tissue


title: UTK-Female-Liver-Replicate2

source_name: Total liver RNA from UTK exposed female FHM labeled with Cyanine-5 (red)


title: UTK-Female-Liver-Replicate3


title: UTK-Female-Liver-Replicate1


title: TK-Female-Liver-Replicate1


title: lung156N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung156N_normal tissue


title: Control-Female-Liver-Replicate2

source_name: Total liver RNA from river water exposed female FHM labeled with Cyanine-5 (red)

source_name: Pooled reference sample from all river water exposed (control) FHM (3 female and 3 male)


title: lung156T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung156T_cancer tissue


title: Control-Female-Liver-Replicate3


title: lung153T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung153T_cancer tissue


title: 1

source_name: Blood genomic DNA in patient with rectal cancer


title: TK-Female-Liver-Replicate3


title: lung157N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung157N_normal tissue


title: lung155T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung155T_cancer tissue


title: Control-Female-Liver-Replicate1


title: Guana Island_1

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description:
Sample name: GA_1
Gene expression of gonad in field-collected queen conch

hyb_protocol: Samples were hybridized for 17 hours per the Agilent protocol.

scan_protocol: Samples were scanned at the University of Florida ICBR using the Agilent 2505B DNA microarray scanner

data_processing: Intensity values were determined by the Agilent Feature Extraction software.  Raw data were imported into JMP-Genomics, log2-transformed, and quantile normalized.

organism: Aliger gigas

source_name: gonad

label_protocol: RNA samples were labeled with Cy3-CTP following the Agilent protocol for one-color gene expression microarrays.

growth_protocol: Samples were collected in the field.

extract_protocol: Ovary total RNA was extracted via phenol-chloroform extraction with RNA STAT-60, followed by CsCl gradient centrifugation and ethanol precipitation.

value: gonad

tag: Sex

tag: collection site

value: Guana Island

tag: tbt contamination

value: control


title: Rhode Harbour_4

description:
Sample name: RH_4
Gene expression of gonad in field-collected queen conch

value: Rhode Harbour

value: Y


title: lung152T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung152T_cancer tissue


title: lung155N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung155N_normal tissue


title: Rhode Harbour_2

description:
Sample name: RH_2
Gene expression of gonad in field-collected queen conch


title: Guana Island_3

description:
Sample name: GA_3
Gene expression of gonad in field-collected queen conch


title: Guana Island_5

description:
Sample name: GA_5
Gene expression of gonad in field-collected queen conch


title: lung151T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung151T_cancer tissue


title: Guana Island_6

description:
Sample name: GA_6
Gene expression of gonad in field-collected queen conch


title: lung149T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung149T_cancer tissue


title: Trellis Bay_3

description:
Sample name: TB_3
Gene expression of gonad in field-collected queen conch

value: Trellis Bay


title: Rhode Harbour_3

description:
Sample name: RH_3
Gene expression of gonad in field-collected queen conch


title: lung151N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung151N_normal tissue


title: Trellis Bay_4

description:
Sample name: TB_4
Gene expression of gonad in field-collected queen conch


title: lung148T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung148T_cancer tissue


title: Guana Island_4

description:
Sample name: GA_4
Gene expression of gonad in field-collected queen conch


title: lung153N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung153N_normal tissue


title: 13689201 - 5_Col 0 G1 inf A vs 6_Col 0 G11 inf A

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in diferent mutants?

hyb_protocol: 6_Col 0 G11 inf A Cy5 / 5_Col 0 G1 inf A 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,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,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.

source_name: 6_Col0 G11 infected A

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

growth_protocol: rosette - Col-0, dcl2/4, dcl3/4 and dcl2/3/4 were grown until rosette state and inoculated with TCV. Ten days post-inoculation the leaves were harvested. temperature : 22°C light : long day

extract_protocol: 6_Col 0 G11 inf A:4.9ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol:
Name:viral siRNA _ suite (TCV) - time course study - pathogen infection,
tcv virus infection:time 10day .
Col-0, dcl2/4, dcl3/4 and dcl2/3/4 were grown until rosette state and inoculated with TCV virus. Ten days post-inoculation the leaves were harvested. The leaves were frozen with liquid nitrogen and kept at -80 until the totRNA was extracted. The same was made for the two generations: G1 and G11. Two independent total RNA extractions were made for each of the two generation (A and B).

tag: ecotype

value: columbia

value: wild type

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

source_name: 5_Col0 G1 infected A

extract_protocol: 5_Col 0 G1 inf A:5ug. (Extraction_ARN_au_Trizol.doc)


title: 13689202 - 6_Col 0 G11 inf A vs 5_Col 0 G1 inf A

hyb_protocol: 5_Col 0 G1 inf A Cy5 / 6_Col 0 G11 inf A 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: Trellis Bay_2

description:
Sample name: TB_2
Gene expression of gonad in field-collected queen conch


title: lung150T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung150T_cancer tissue


title: lung149N_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung149N_normal tissue


title: lung152N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung152N_normal tissue


title: lung146T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung146T_cancer tissue


title: lung150N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung150N_normal tissue


title: 13689199 - 10_dcl2/4 G11 inf A vs 9_dcl2/4 G1 inf A

hyb_protocol: 9_dcl2/4 G1 inf A Cy5 / 10_dcl2/4 G11 inf A 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.

source_name: 9_dcl2/4 G1 infected A

extract_protocol: 9_dcl2/4 G1 inf A:4.3ug. (Extraction_ARN_au_Trizol.doc)

value: dcl2/4 mutant

source_name: 10_dcl2/4 G11 infected A

extract_protocol: 10_dcl2/4 G11 inf A:5.2ug. (Extraction_ARN_au_Trizol.doc)


title: 13689200 - 9_dcl2/4 G1 inf A vs 10_dcl2/4 G11 inf A

hyb_protocol: 10_dcl2/4 G11 inf A Cy5 / 9_dcl2/4 G1 inf A 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: 13689196 - 11_dcl2/3/4 G1 inf A vs 12_dcl2/3/4 G11 inf A

hyb_protocol: 12_dcl2/3/4 G11 inf A Cy5 / 11_dcl2/3/4 G1 inf A 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.

source_name: 12_dcl2/3/4 G11 infected A

extract_protocol: 12_dcl2/3/4 G11 inf A:4.9ug. (Extraction_ARN_au_Trizol.doc)

value: dcl2/3/4 mutant

source_name: 11_dcl2/3/4 G1 infected A

extract_protocol: 11_dcl2/3/4 G1 inf A:3.5ug. (Extraction_ARN_au_Trizol.doc)


title: lung143T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung143T_cancer tissue

value: cancer lung tissue


title: 13689197 - 8_dcl3/4 G11 inf A vs 7_dcl3/4 G1 inf A

hyb_protocol: 7_dcl3/4 G1 inf A Cy5 / 8_dcl3/4 G11 inf A 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.

source_name: 7_dcl3/4 G1 infected A

extract_protocol: 7_dcl3/4 G1 inf A:4ug. (Extraction_ARN_au_Trizol.doc)

value: dcl3/4 mutant

source_name: 8_dcl3/4 G11 infected A

extract_protocol: 8_dcl3/4 G11 inf A:3.6ug. (Extraction_ARN_au_Trizol.doc)


title: lung144T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung144T_cancer tissue


title: lung145N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung145N_normal tissue

value: normal lung tissue


title: lung145T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung145T_cancer tissue


title: lung143N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung143N_normal tissue


title: 13689195 - 12_dcl2/3/4 G11 inf A vs 11_dcl2/3/4 G1 inf A

hyb_protocol: 11_dcl2/3/4 G1 inf A Cy5 / 12_dcl2/3/4 G11 inf A 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: lung146N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung146N_normal tissue


title: lung148N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung148N_normal tissue


title: lung144N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung144N_normal tissue


title: 13688971 - 15_dcl3/4 G1 ni A vs 16_dcl3/4 G11 ni A

hyb_protocol: 16_dcl3/4 G11 ni A Cy5 / 15_dcl3/4 G1 ni A 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.

source_name: 16_dcl3/4 G11 not_infected A

extract_protocol: 16_dcl3/4 G11 ni A:7.7ug. (Extraction_ARN_au_Trizol.doc)

source_name: 15_dcl3/4 G1 not_infected A

extract_protocol: 15_dcl3/4 G1 ni A:7ug. (Extraction_ARN_au_Trizol.doc)


title: 13688973 - 13_Col0 G1 ni A vs 14_Col 0 G11 ni A

hyb_protocol: 14_Col 0 G11 ni A Cy5 / 13_Col0 G1 ni A 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.

source_name: 14_Col0 G11 not_infected A

extract_protocol: 14_Col0 G11 ni A:6.1ug. (Extraction_ARN_au_Trizol.doc)

source_name: 13_Col0 G1 not_infected A

extract_protocol: 13_Col0 G1 ni A:5ug. (Extraction_ARN_au_Trizol.doc)


title: lung139T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung139T_cancer tissue


title: 13688963 - 17_dcl2/4 G1 ni A vs 18_dcl2/4 G11 ni A

hyb_protocol: 18_dcl2/4 G11 ni A Cy5 / 17_dcl2/4 G1 ni A 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.

source_name: 18_dcl2/4 G11 not_infected A

extract_protocol: 18_dcl2/4 G11 ni A:11ug. (Extraction_ARN_au_Trizol.doc)

source_name: 17_dcl2/4 G1 not_infected A

extract_protocol: 17_dcl2/4 G1 ni A:8.1ug. (Extraction_ARN_au_Trizol.doc)


title: 13688962 - 20_dcl2/3/4 G11 ni A vs 19_dcl2/3/4 G1 ni A

hyb_protocol: 19_dcl2/3/4 G1 ni A Cy5 / 20_dcl2/3/4 G11 ni A 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.

source_name: 19_dcl2/3/4 G1 not_infected A

extract_protocol: 19_dcl2/3/4 G1 ni A:5.8ug. (Extraction_ARN_au_Trizol.doc)

source_name: 20_dcl2/3/4 G11 not_infected A

extract_protocol: 20_dcl2/3/4 G11 ni A:5.4ug. (Extraction_ARN_au_Trizol.doc)


title: 13688965 - 18_dcl2/4 G11 ni A vs 17_dcl2/4 G1 ni A

hyb_protocol: 17_dcl2/4 G1 ni A Cy5 / 18_dcl2/4 G11 ni A 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: 13689198 - 7_dcl3/4 G1 inf A vs 8_dcl3/4 G11 inf A

hyb_protocol: 8_dcl3/4 G11 inf A Cy5 / 7_dcl3/4 G1 inf A 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.

source_name: 8_dcl3/4 G11 infected A

source_name: 7_dcl3/4 G1 infected A


title: 13688961 - 19_dcl2/3/4 G1 ni A vs 20_dcl2/3/4 G11 ni A

hyb_protocol: 20_dcl2/3/4 G11 ni A Cy5 / 19_dcl2/3/4 G1 ni A 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: 13688967 - 14_Col 0 G11 ni A vs 13_Col0 G1 ni A

hyb_protocol: 13_Col0 G1 ni A Cy5 / 14_Col 0 G11 ni A 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: lung137N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

hyb_protocol: Affymetrix standard protocol

source_name: lung137N_normal tissue

extract_protocol: Genomic DNA was isolated by proteinase K- phenol - chloroform extraction following standard protocols with 0.5% SDS and 200μg/ml proteinase K.


title: lung142N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung142N_normal tissue


title: lung139N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung139N_normal tissue


title: lung134T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung134T_cancer tissue


title: lung137T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung137T_cancer tissue


title: 13689203 - 1_Col 0 G11 ni A vs 2_Col 0 G11 inf A

hyb_protocol: 2_Col 0 G11 inf A Cy5 / 1_Col 0 G11 ni A 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.

source_name: 2_Col0 G11 infected A

extract_protocol: 2_Col 0 G11 inf A:4.9ug. (Extraction_ARN_au_Trizol.doc)

source_name: 1_Col0 G11 not_infected A

extract_protocol: 1_Col 0 G11 ni A:5.4ug. (Extraction_ARN_au_Trizol.doc)


title: 13689204 - 2_Col 0 G11 inf A vs 1_Col 0 G11 ni A

hyb_protocol: 1_Col 0 G11 ni A Cy5 / 2_Col 0 G11 inf A 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: 13688972 - 16_dcl3/4 G11 ni A vs 15_dcl3/4 G1 ni A

hyb_protocol: 15_dcl3/4 G1 ni A Cy5 / 16_dcl3/4 G11 ni A 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.

source_name: 15_dcl3/4 G1 not_infected A

source_name: 16_dcl3/4 G11 not_infected A


title: 13689193 - 4_dcl2/3/4 G11 inf A vs 3_dcl2/3/4 G11 ni A

hyb_protocol: 3_dcl2/3/4 G11 ni A Cy5 / 4_dcl2/3/4 G11 inf A 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.

source_name: 3_dcl2/3/4 G11 not_infected A

extract_protocol: 3_dcl2/3/4 G11 ni A:5.4ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol:
Name:viral siRNA_suite (TCV) - time course study - pathogen infection,
tcv virus infection:time 10day .
Col-0, dcl2/4, dcl3/4 and dcl2/3/4 were grown until rosette state and inoculated with TCV virus. Ten days post-inoculation the leaves were harvested. The leaves were frozen with liquid nitrogen and kept at -80 until the totRNA was extracted. The same was made for the two generations: G1 and G11. Two independent total RNA extractions were made for each of the two generation (A and B).

source_name: 4_dcl2/3/4 G11 infected A

extract_protocol: 4_dcl2/3/4 G11 inf A:6.1ug. (Extraction_ARN_au_Trizol.doc)


title: lung142T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung142T_cancer tissue


title: THP-1_on Gold_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: THP-1_on Gold_2

hyb_protocol: 1.6 µg labeled cRNA was hybridized to microarrays for 16h at 68°C and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Microarrays were scanned using the Agilent Scanner System. Data extractions were performed using Feature Extraction Software 10.7.1 (Agilent) with default patrameters of the GE1_107_Sep09 extraction protocol

data_processing: log2 transformed, median normalized to all samples, signal intensity expressed as relative to median signal intensity of all samples

source_name: monocytes

label_protocol: 500ng of total RNA were applied for Cy3-labelling reaction using the one color Quick Amp Labeling protocol (Agilent Technologies; Waldbronn, Germany).

growth_protocol: HEPES-buffered RPMI 1640 (GIBCO, Invitrogen, Paisley, UK) supplemented with 10 % fetal calf serum (PAA, Pasching, Austria), 2 mM L-glutamine (Invitrogen), 100 U/ml penicillin, 1 % non-essential amino acids and 0.1 mg/ml streptomycin (Sigma-Aldrich, Deisenhofen, Germany). Cell cultures were maintained at 37 °C in a humidified incubator with 5 % carbon dioxide. Only low-passage cultures were used in this study. Adherent cells were loosened using a small plastic scraper.

extract_protocol: RNAeasy

tag: cell line

tag: protocol

value: on Gold


title: lung134N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung134N_normal tissue

tag: gender


title: lung135N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung135N_normal tissue


title: lung133T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung133T_cancer tissue


title: lung132N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung132N_normal tissue


title: lung133N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung133N_normal tissue


title: THP-1_ctr_2


title: lung132T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung132T_cancer tissue


title: lung135T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung135T_cancer tissue


title: lung131T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung131T_cancer tissue


title: lung127N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung127N_normal tissue


title: 13689194 - 3_dcl2/3/4 G11 ni A vs 4_dcl2/3/4 G11 inf A

hyb_protocol: 4_dcl2/3/4 G11 inf A Cy5 / 3_dcl2/3/4 G11 ni A 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: lung130N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung130N_normal tissue


title: SmartDC 1

source_name: CD14+ monocytes

tag: genetic modification

value: lentiviral vector transduction of CD14+ monocytes for co-expression of GM-CSF, IL-4 and antigens result into “Self-differentiated Myeloid-derived Antigen-presenting-cells Reactive-against-Tumors’ (SmartDCs)

tag: cell type

value: SmartDC dendritic cells

tag: cell origin

value: CD14+ monocytes


title: lung130T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung130T_cancer tissue

value: female


title: SmartDC 2


title: THP-1_on Gold_1

description: THP-1_on Gold_1


title: lung136T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung136T_cancer tissue


title: Conv. DC 3

description: Conv. DC_3

value: WT

value: conventional dendritic cells


title: SmartDC/tWT1 2

value: A tricistronic lentiviral vector co-expressing a truncated form of WT1 (lacking the DNA-binding domain), GM-CSF and IL-4 was used to transduce human monocytes.


title: SmartDC/tWT1 3


title: lung127T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung127T_cancer tissue


title: lung131N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung131N_normal tissue


title: lung124T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung124T_cancer tissue


title: SmartDC/tWT1 1


title: Conv. DC 2

description: Conv. DC_2


title: lung126T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung126T_cancer tissue


title: lung125N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung125N_normal tissue


title: OV-90/CD157_DS

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

description: Technical replicate of OV-90_norm

hyb_protocol: Hybridization with dye-swap duplication was performed to compare sample versus reference. The same quantity of differentially labelled sample and reference was put together, fragmented and hybridized to oligonucleotide glass arrays with sequences representing >41K human unique genes and transcripts. All steps were performed using the Gene Expression Hybridization kit (Agilent Technologies) following the 60-mer oligo microarray processing protocol (Agilent Technologies).

scan_protocol: Slides were washed with the Agilent wash procedure and scanned with the dual-laser microarray scanner Agilent G2505B (Agilent Technologies).

data_processing: Images were then analysed using Feature Extraction software (Agilent Technologies) version 10.7. Raw data elaboration was carried out with Bioconductor (Gentleman et al., 2004), using R statistical language. The limma package was used to identify differentially expressed genes, applying a cut-off on the p-value, adjusted for multiple testing by the Benjamini-Hochberg approach (<0.01), followed by filtering on expression level (logFC >1 or < -1 in at least one cell line, excluding transcripts with opposite sign). This criterion allowed the identification of transcripts with concordant modulation and took into account intrinsic biological differences of distinct cell lines that might be reflected in the amplitude of fold changes.

source_name: OV-90/mock cell line

label_protocol: Labelling was performed using NHS ester Cy3 or Cy5 dyes (GE HealthCare, Buckinghamshire, UK) able to react with the modified RNA.

growth_protocol: The human EOC cell lines OVCAR-3 and OV-90 were purchased from American Type Culture Collection (ATCC, Manassas, VA). OVCAR-3 and OV-90 cells were transfected with the eukaryotic expression vector pcDNA3.1 containing the full-length cDNA for CD157 or no insert (mock).

extract_protocol: Total RNAs extracted from 70-80% confluent cultures using TRIZOL® reagent (Invitrogen). For each sample and reference pair, equal amounts of mRNA were amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion Inc., Austin, TX) to obtain amino allyl antisense RNA following the method developed by Eberwine and co-workers (Van Gelder et al, 1990). One round of amplification was performed and both dsDNA and aaRNA underwent a purification step using columns provided with the kit.

tag: transfection

value: eukaryotic expression vector pcDNA3.1 containing no insert

source_name: OV-90/CD157 cell line


title: THP-1_ctr_1

source_name: monocytes

value: control


title: OV-90/CD157_norm

description: Technical replicate of OV-90_DS

value: eukaryotic expression vector pcDNA3.1 containing the full-length cDNA for CD157


title: Conv. DC 1

description: Conv. DC_1


title: OVCAR3_rep1//CD157_DS

description: Technical replicate of OVCAR3_rep1_norm

source_name: OVCAR-3/mock cell line

source_name: OVCAR-3/CD157 cell line


title: OVCAR3_rep2/CD157_norm

description: Technical replicate of OVCAR3_rep2_DS


title: OVCAR3_rep2/CD157_DS

description: Technical replicate of OVCAR3_rep2_norm


title: OVCAR3_rep1/CD157_norm

description: Technical replicate of OVCAR3_rep1_DS


title: lung126N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung126N_normal tissue

tag: tissue


title: C77G_2

scan_protocol: Microarrays were scanned using the Agilent Scanner System. Data extractions were performed using Feature Extraction Software 10.7.1 (Agilent) with default patrameters of the GE1_105_Dec08 extraction protocol

source_name: CD4+CD25+ T cell

growth_protocol: expanded and stimulated (2h with 1:5 CD3/CD28 beads)

extract_protocol: RNeasy

tag: genotype/variation

value: C77G CD45 isoform

value: Blood


title: lung124N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung124N_normal tissue


title: lung123T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung123T_cancer tissue


title: lung121T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung121T_cancer tissue


title: hgCIN2.0

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
US22502676_251901512133_S01_CGH_105_Dec08_1_1.txt
US22502676_251901512077_S01_CGH_105_Dec08_1_1.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

source_name: Cervical tissue, microdissected

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37'C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).

tag: Stage

value: high-grade cervical intraepithelial neoplasia, >5years preceding hrHPV infection

source_name: Amplified FFPE cervical DNA from 5 individuals

value: normal cervix

tag: reference

value: Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11):994-1004


title: lung120N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung120N_normal tissue

value: normal lung tissue


title: lung123N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung123N_normal tissue


title: hgCIN.2.42

description:
251901512363_251901512363_S01_CGH_105_Dec08_1_2.txt
251901512362_251901512362_S01_CGH_105_Dec08_1_1.txt


title: lung120T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung120T_cancer tissue

value: cancer lung tissue


title: lung121N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung121N_normal tissue


title: wt_1

value: wild type


title: lung119N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung119N_normal tissue


title: lung125T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung125T_cancer tissue


title: hgCIN.2.41

description:
US22502676_251901512266_S01_CGH_105_Dec08_1_2.txt
US22502676_251901512267_S01_CGH_105_Dec08_1_2.txt


title: lung118T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung118T_cancer tissue


title: wt_2


title: lung115N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung115N_normal tissue


title: C77G_1


title: hgCIN.2.40

description:
US22502676_251901512267_S01_CGH_105_Dec08_1_1.txt
US22502676_251901512267_S01_CGH_105_Dec08_1_2.txt


title: lung119T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung119T_cancer tissue


title: lung116N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung116N_normal tissue


title: hgCIN.2.37

description:
US22502676_251901512361_S01_CGH_105_Dec08_1_2.txt
US22502676_251901512360_S01_CGH_105_Dec08_1_1.txt


title: lung116T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung116T_cancer tissue


title: lung115T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung115T_cancer tissue


title: hgCIN.2.36

description:
US22502676_251901512361_S01_CGH_105_Dec08_1_1.txt
US22502676_251901512360_S01_CGH_105_Dec08_1_1.txt


title: lung117N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung117N_normal tissue


title: hgCIN.2.34

description:
US22502676_251901512267_S01_CGH_105_Dec08_1_2.txt
US22502676_251901512267_S01_CGH_105_Dec08_1_2.txt


title: lung136N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung136N_normal tissue


title: hgCIN.2.38

description:
251901512362_251901512362_S01_CGH_105_Dec08_1_1.txt
251901512362_251901512362_S01_CGH_105_Dec08_1_1.txt


title: lung112N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung112N_normal tissue


title: lung113T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung113T_cancer tissue


title: lung114N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung114N_normal tissue


title: hgCIN.2.33

description:
US22502676_251901512360_S01_CGH_105_Dec08_1_1.txt
US22502676_251901512360_S01_CGH_105_Dec08_1_1.txt

source_name: Cervical tissue, microdissected

source_name: Amplified FFPE cervical DNA from 5 individuals


title: lung114T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung114T_cancer tissue


title: lung113N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung113N_normal tissue


title: hgCIN.2.31


title: hgCIN.2.29

description:
251901512362_251901512362_S01_CGH_105_Dec08_1_2.txt
251901512362_251901512362_S01_CGH_105_Dec08_1_1.txt


title: lung112T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung112T_cancer tissue


title: hgCIN.2.28


title: hgCIN.2.39

description:
US22502676_251901512266_S01_CGH_105_Dec08_1_2.txt
US22502676_251901512266_S01_CGH_105_Dec08_1_1.txt


title: hgCIN.2.35

description:
US22502676_251901512360_S01_CGH_105_Dec08_1_2.txt
US22502676_251901512360_S01_CGH_105_Dec08_1_1.txt


title: lung110N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung110N_normal tissue


title: lung107T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung107T_cancer tissue


title: hgCIN.2.25


title: lung109T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung109T_cancer tissue


title: hgCIN.2.26

description:
US22502676_251901512266_S01_CGH_105_Dec08_1_1.txt
US22502676_251901512266_S01_CGH_105_Dec08_1_1.txt


title: lung117T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung117T_cancer tissue


title: lung107N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung107N_normal tissue


title: hgCIN.2.110

description:
US22502676_251901510434_S01_CGH_105_Dec08_1_1.txt
US22502676_251901510434_S01_CGH_105_Dec08_1_1.txt


title: lung118N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung118N_normal tissue


title: lung110T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung110T_cancer tissue


title: lung106N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung106N_normal tissue


title: hgCIN.2.23

description:
US22502676_251901512077_S01_CGH_105_Dec08_1_2.txt
US22502676_251901512077_S01_CGH_105_Dec08_1_1.txt


title: hgCIN.2.24

description:
US22502676_251901512133_S01_CGH_105_Dec08_1_1.txt
US22502676_251901512133_S01_CGH_105_Dec08_1_2.txt


title: lung106T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung106T_cancer tissue


title: lung105T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung105T_cancer tissue


title: hgCIN.2.32


title: hgCIN.2.22


title: lung105N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung105N_normal tissue


title: hgCIN.2.30

description:
251901512363_251901512363_S01_CGH_105_Dec08_1_1.txt
251901512362_251901512362_S01_CGH_105_Dec08_1_1.txt


title: hgCIN.2.21

description:
MAF_251901510361_S01_CGH_105_Dec08_1_2.txt
MAF_251901510361_S01_CGH_105_Dec08_1_1.txt


title: lung104T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung104T_cancer tissue


title: hgCIN.2.27

source_name: Cervical tissue, microdissected


title: hgCIN.2.18

description:
US22502676_251901510360_S01_CGH_105_Dec08_1_1.txt
US22502676_251901510359_S01_CGH_105_Dec08_1_1.txt

source_name: Amplified FFPE cervical DNA from 5 individuals


title: hgCIN.2.20


title: hgCIN.2.17

description:
US22502676_251901510381_S01_CGH_105_Dec08_1_2.txt
US22502676_251901510381_S01_CGH_105_Dec08_1_1.txt


title: hgCIN.2.16

description:
US22502676_251901510359_S01_CGH_105_Dec08_1_2.txt
US22502676_251901510359_S01_CGH_105_Dec08_1_1.txt


title: lung104N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung104N_normal tissue


title: hgCIN.2.15

description:
US22502676_251901510435_S01_CGH_105_Dec08_1_1.txt
US22502676_251901510434_S01_CGH_105_Dec08_1_1.txt


title: lung102T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung102T_cancer tissue


title: lung103N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung103N_normal tissue


title: hgCIN.2.19

description:
US22502676_251901510383_S01_CGH_105_Dec08_1_2.txt
US22502676_251901510383_S01_CGH_105_Dec08_1_2.txt


title: hgCIN.2.14

description:
MAF_251901510362_S01_CGH_105_Dec08_1_2.txt
MAF_251901510361_S01_CGH_105_Dec08_1_1.txt


title: hgCIN.2.12

description:
MAF_251901510362_S01_CGH_105_Dec08_1_1.txt
MAF_251901510362_S01_CGH_105_Dec08_1_2.txt


title: lung103T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung103T_cancer tissue


title: lung109N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung109N_normal tissue


title: hgCIN.2.9

description:
MAL_251901510428_S01_CGH_105_Dec08_1_1.txt
MAL_251901510428_S01_CGH_105_Dec08_1_2.txt


title: lung101T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung101T_cancer tissue


title: hgCIN.2.10

description:
US22502676_251901510434_S01_CGH_105_Dec08_1_2.txt
US22502676_251901510434_S01_CGH_105_Dec08_1_1.txt


title: hgCIN.2.13

description:
MAF_251901510362_S01_CGH_105_Dec08_1_1.txt
MAF_251901510361_S01_CGH_105_Dec08_1_1.txt


title: lung102N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung102N_normal tissue


title: lung101N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung101N_normal tissue


title: hgCIN.2.7

description:
MAL_251901510427_S01_CGH_105_Dec08_1_2.txt
MAL_251901510427_S01_CGH_105_Dec08_1_1.txt


title: hgCIN.2.8


title: lung100T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung100T_cancer tissue


title: hgCIN.2.5

description:
US22502676_251901510435_S01_CGH_105_Dec08_1_2.txt
US22502676_251901510434_S01_CGH_105_Dec08_1_1.txt


title: lung83T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung83T_cancer tissue


title: hgCIN.2.4

description:
MAL_251901510428_S01_CGH_105_Dec08_1_2.txt
MAL_251901510428_S01_CGH_105_Dec08_1_2.txt


title: lung98N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung98N_normal tissue


title: lung98T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung98T_cancer tissue


title: lung99N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung99N_normal tissue


title: hgCIN.2.3

description:
MAL_251901510134_S01_CGH_105_Dec08_1_1.txt
MAL_251901510134_S01_CGH_105_Dec08_1_2.txt


title: lung92N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung92N_normal tissue


title: fat_Akt1+/-_35wk_rep4

city: Chiba

first: Aika

last: Nojima

country: Japan

institute: Chiba univeersity

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Rneasy lipid tissue mini kit(Quiagen).

tag: strain

tag: age


title: lung100N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung100N_normal tissue


title: fat_Akt1+/-_35wk_rep3


title: hgCIN.2.2

description:
MAF_251901510361_S01_CGH_105_Dec08_1_1.txt
MAF_251901510361_S01_CGH_105_Dec08_1_1.txt

source_name: Cervical tissue, microdissected


title: fat_Akt1+/-_35wk_rep2


title: hgCIN.2.1

description:
US22502676_251901510360_S01_CGH_105_Dec08_1_2.txt
US22502676_251901510359_S01_CGH_105_Dec08_1_1.txt

source_name: Amplified FFPE cervical DNA from 5 individuals


title: Pleural and ascites fluids without chylothorax, ITGA9 G404S mutation and OK-432 treatmuent NFC-r

city: Changhua

first: Gwo-Chin

last: Ma

address: 3F, 176, Zhanghua Rd.

department: Department of Genomic Medicine

institute: Changhua Christian Hospital

description: Transcriptional profile comparison of the pleural and ascites fluids in a reference fetal without chylothorax

hyb_protocol: 0.3 mg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a SurePrint G3 Human GE 8×60K oligo microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: Scanned on an Agilent G2565CA scanner, and images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Pleural fluid

label_protocol: 0.2 mg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer, USA) during the in vitro transcription process.

extract_protocol: Cell lines were lyzed by Trizol® Reagent (Invitrogen, USA) first, and purified by RNeasy Mini Kit (Qiagen, Germany). RNA isolated was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

tag: mutation

value: No ITGA9 mutation

tag: treatment

value: No OK-432 treatment

source_name: Ascites fluid


title: lung99T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung99T_cancer tissue

value: female


title: lung92T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung92T_cancer tissue


title: lung83N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung83N_normal tissue


title: fat_Akt1+/-_35wk_rep1


title: lung27T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung27T_cancer tissue


title: fat_Wt_35wk_rep3


title: fat_Wt_35wk_rep2


title: fat_Wt_35wk_rep4


title: fat_Wt_35wk_rep1


title: hgCIN.2.6

description:
US22502676_251901510383_S01_CGH_105_Dec08_1_1.txt
US22502676_251901510381_S01_CGH_105_Dec08_1_1.txt


title: fat_Akt1+/-_8wk_rep2


title: fat_Akt1+/-_8wk_rep1


title: fat_Akt1+/-_8wk_rep3


title: fat_Wt_8wk_rep2


title: fat_Wt_8wk_rep1


title: muscle_Akt1+/-_35wk_rep3

description: quadriceps_muscle_Akt1+/-_female_35wk_rep3


title: Pleural and ascites fluids with chylothorax and an ITGA9 G404S mutation before OK-432 Ind-B

description: Transcriptional profile comparison of the pleural and ascites fluids in a fetal with chylothorax and an ITGA9 G404S mutation before OK-432 treatment

value: ITGA9 G404S


title: lung32N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung32N_normal tissue


title: lung27N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung27N_normal tissue


title: fat_Wt_8wk_rep3


title: lung76N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung76N_normal tissue


title: muscle_Akt1+/-_35wk_rep4

description: quadriceps_muscle_Akt1+/-_female_35wk_rep4


title: muscle_Akt1+/-_35wk_rep2

description: quadriceps_muscle_Akt1+/-_female_35wk_rep2


title: muscle_Akt1+/-_35wk_rep1

description: quadriceps_muscle_Akt1+/-_female_35wk_rep1


title: lung76T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung76T_cancer tissue


title: lung20T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung20T_cancer tissue


title: muscle_Wt_35wk_rep2


title: Pleural and ascites fluids with chylothorax and an ITGA9 G404S mutation after OK-432 treatment Ind-A

description: Transcriptional profile comparison of the pleural and ascites fluids in a fetal with chylothorax and an ITGA9 G404S mutation after OK-432 treatment

value: OK-432 treatment


title: lung15T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung15T_cancer tissue


title: lung32T_cancer tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung32T_cancer tissue


title: muscle_Wt_35wk_rep1


title: muscle_Wt_35wk_rep3


title: muscle_Akt1+/-_8wk_rep3

description: quadriceps_muscle_Akt1+/-_female_8wk_rep3


title: muscle_Akt1+/-_8wk_rep2

description: quadriceps_muscle_Akt1+/-_female_8wk_rep2


title: lung15N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung15N_normal tissue


title: muscle_Akt1+/-_8wk_rep1

description: quadriceps_muscle_Akt1+/-_female_8wk_rep1


title: muscle_Wt_8wk_rep1


title: lung20N_normal tissue_Affymetrix SNP6

description: Hybridized to SNP6.0

source_name: lung20N_normal tissue


title: liver_Wt_35wk_rep4

value: liver


title: muscle_Wt_8wk_rep3


title: liver_Akt1+/-_35wk_rep3


title: muscle_Wt_8wk_rep2


title: liver_Akt1+/-_35wk_rep2


title: liver_Wt_35wk_rep1


title: liver_Wt_35wk_rep2


title: liver_Akt1+/-_35wk_rep4


title: 5hmC after Hydroxymethyl Collector in neurons, Chr7

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Cells were isolated by FACs sorting from nmouse cortex using GFP/RFP reported system at 15.5E embryonic development. GFP+ (under Nestin promoter), RFP - (Under Dbx promoter)

hyb_protocol: According to NimbleGen Kit

data_processing: Cy5/Cy3 log2 ratio scaled by NimbleScan software v2.5 with Tukey Biweight mean

source_name: 5hmC enriched DNA fraction after pull-down with Hydroxymethyl Collector. DNA was isolated from NPC

extract_protocol: For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For ChIp-ChIp experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by adding of 0.125M Glycine.  Sonicated chromatin was incubated with appropriate antibodies overnight and captured by A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR procedure. For hMeDIP, linker ligated DNA was denatured and incubated with 5hmC antibodies overnight at +4C with further purification with A/G plus beads and genome amplification by LM-PCR. For 5hmC enrichment with Hydroxymethyl Collector (Active Motif), sonicated DNA was glycosylated, labeled with biotin and purified according manufacturer instructions with further genome amplification by LM-PCR.

treatment_protocol: no treatment

value: neurons, cortex

tag: enrichment method

value: biotin capturing of glycosylated 5hmC DNA

tag: antibody

source_name: Input DNA from neurons

value: none, Input


title: 5mC neurons Chr7

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from neurons

value: MIRA


title: liver_Akt1+/-_8wk_rep2


title: liver_Wt_8wk_rep1


title: liver_Wt_35wk_rep3


title: liver_Akt1+/-_8wk_rep1


title: liver_Wt_8wk_rep3


title: liver_Wt_8wk_rep2


title: liver_Akt1+/-_8wk_rep3


title: 5hmC hMeDIP neurons Chr7

source_name: 5hmC enriched DNA fraction after pull-down with 5hmC antibodies.  DNA was isolated from neurons

value: hMeDIP


title: muscle_Wt_35wk_rep4


title: liver_Akt1+/-_35wk_rep1