title: H3K9me2 ChIP in ∆sir2 cells

tag: genotype/variation

value: ∆sir2 cells

value: Abcam

value: Whole-cell extract DNA


title: 100uM cyclo, 4hrs rep3

status: Public on Dec 01 2011

type: RNA

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

hyb_protocol: See http://www.flyarrays.com/ under protocols. Modifications by Scott:-use 5uL 50mM EDTA-precipitate probe for at least 1 hour-use 20uL DIG EasyHyb per humidifying well-final hyb volume is 80uL

scan_protocol: Images of the hybridized microarrays were obtained using a ScanArray 4000 scanner (Perkin-Elmer) and were quantified using QuantArray 3.0 software (Perkin-Elmer)

data_processing: Data were normalized using lowest sub-grid normalization (Yang, 2002) and Genetraffic Duo (Stratagene /Agilent) analysis software.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster, Kc 167 cells, 100uM cycloheximide, 4hrs

label_protocol: CDMC Direct Labeling Protocol. See http://www.flyarrays.com/ under protocols.

extract_protocol: Cultures are grown to a minimum density of 5x10^6 cells per mL prior to extraction.  Trizol is used at a ratio of 1 mL per 10^7 cells.  Extraction procedure is as described by the manufacturer with centrifugation in a Sorvall SS-34 rotor.  Final pellets are air dried and then resuspended in Sigma 18 meg-ohm water to obtain a final RNA concentation of no less than 4ug per uL.

tag: cell line

tag: tissue

value: embryo-derived

tag: developmental stage

value: late embryonic

tag: agent

value: 100uM cycloheximide

tag: time point

tag: cell extraction

value: The sample had an [RNA] of 4.19 ug per uL and an OD ratio of 1.97. Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water

source_name: Drosophila melanogaster, Kc 167 cells, Ethanol Control

value: Ethanol Control

value: The sample had an [RNA] of 4.88 ug per uL and an OD ratio of 1.97.Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water


title: H3K9me2 ChIP in ∆dcr1 cells

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: log. growing cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220). Immunoprecipitated DNA was recovered by incubation with protein G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C.

value: ∆dcr1 cells

tag: antibody

tag: antibody vendor

tag: antibody catalog#

tag: input


title: 2496-TF

city: Stanford

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine

description: squamous cell lung carcinoma _Tumor Front_2496

hyb_protocol: Purified and dye-labeled sample and reference cDNA was combined for two-color hybridizations with 520 µl hybridization buffer (4x SSC, 50% formamide, 2% SDS), agitated for 30 min at 60 °C, heated for 10 min at 70 °C on a thermo mixer and subsequently applied to preheated (60 °C) gasket slides (Agilent Technologies, Santa Clara, USA). Microarrays were place onto loaded gasket slides, assembled in SureHyb hybridization chambers (Agilent) and incubated for 23 hours at 42 °C and a rotation speed of 4 rpm in an Agilent DNA Microarray Hybridization Oven. Hybridized arrays were washed at 35 °C with (i) 0.5x SSC, 0.1% SDS for 4 minutes; (ii) 0.05x SSC, 0.1% SDS for 4 minutes; (iii) 0.05x SSC for 2 minutes; (iv) 0.05x SSC, 0.05% Tween-20 for 30 seconds. Immediately thereafter, slides were dried by centrifugation in 50 ml Falcon tubes at 2500 rpm for 5 minutes. All hybridization experiments were repeated with inversely labeled sample and reference.

scan_protocol: Microarray read out was accomplished in a two-color Agilent Scanner G25505B with 5 µm resolution and automatically adjusting PMT voltages according to manufacturer’s specification. Recorded images were analyzed using GenePix Pro 6.0 software (Axon).

data_processing: Following image extraction, low quality spots were filtered and the background intensities were corrected by normexp with offset 50  (Ritchie, ME, Silver, J, et al., 2007) and within array robustspline normalization was applied. Quantile normalization was applied between arrays for further normalization. Annotation of oligonucleotide probes present on the gene expression array was retrieved by alignment to EnsEMBL database version 55_37.

organism: Homo sapiens

source_name: tumor invasion front

label_protocol: For amplification and labeling 25 ng of total RNA from each area or reference mRNA (Universal Human Reference RNA, Agilent) were subjected to two rounds of linear amplification using the in-vitro transcription-based TAcKLE protocol (Schlingemann J, Thuerigen O, et al., 2005). Subsequent generation of cDNA yielded separately labeled Cy3 and Cy5 tumor- and reference samples, respectively. (21).

growth_protocol: Primary squamous cell lung carcinoma samples were obtained from the Thorax Clinic, University of Heidelberg, Germany.

extract_protocol: For RNA isolation, microdissected tissues from consecutive cryosections were pooled into a final volume of 350 μL QIAzol Lysis Reagent (Qiagen, Hilden, Germany). Total RNA extraction was carried out using a miRNEasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions and subsequently examined for integrity using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: RNA samples from each patient were distinguished according to  i) inner tumor, ii) tumor invasion front, iii) adjacent lung front, and iv) normal lung

tag: diagnosis

value: squamous cell lung carcinoma

tag: location

value: Tumor Front

source_name: Universal Human Reference RNA (Stratagene)

value: pooled cell line derivations


title: 2496-NL

description: squamous cell lung carcinoma _Normal Lung_2496

source_name: distant normal lung

value: Normal Lung


title: H3K9me2 ChIP in wild-type

value: wild type

value: wild type cells


title: 10uM ecdy 4hrs rep2

source_name: Drosophila melanogaster, Kc 167 cells, 10uM 20-hydroxy-ecdysone, 4hrs

value: 10uM 20-hydroxy-ecdysone

value: The sample had an [RNA] of 4.35 ug per uL and an OD ratio of 2.02. Details:3mL Trizol600uL chloroform2.5mL isopropanol1.5mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water

value: Six tubes of control cells (3.0x10^7 cells per tube) were extracted separately.  Following verification of the quality of each sample by spec ratio they were pooled.  The final sample had an [RNA] of 3.17 ug per uL and an OD ratio of 2.02.Details (per tube):3mL Trizol600uL chloroform2.5mL isopropanol1.5mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water


title: 2496-TC

description: squamous cell lung carcinoma _Tumor Center_2496

source_name: inner-tumor

value: Tumor Center


title: 100uM cyclo, 4hrs rep1

value: embryo-derived

value: The sample had an [RNA] of 5.11 ug per uL and an OD ratio of 1.94. Details:5.0 mL Trizol1 mL chloroform3.5 mL isopropanol2.5 mL 75% EtOH-brought up in 50 uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 5.79 ug per uL and an OD ratio of 1.92.Details:5.0 mL Trizol1 mL chloroform3.5 mL isopropanol2.5 mL 75% EtOH-brought up in 50 uL Sigma 18 meg-ohm water


title: 2490-TC

description: squamous cell lung carcinoma _Tumor Center_2490


title: 2502-TC

description: squamous cell lung carcinoma _Tumor Center_2502


title: 100uM cyclo, 4hrs rep2

value: late embryonic

value: 100uM cycloheximide

value: The sample had an [RNA] of 3.84 ug per uL and an OD ratio of 2.00. Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 4.85 ug per uL and an OD ratio of 2.02.Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water


title: 0.5uM ecdy 4hrs rep 1

description: 0.5uM ecdy 4hrs (12700039) May 20, 04

hyb_protocol: See http://www.flyarrays.com/ under protocols.Modifications by Scott:-use 5uL 50mM EDTA-precipitate probe for at least 1 hour-use 20uL DIG EasyHyb per humidifying well-final hyb volume is 80uL

source_name: 0.5uM 20-hydroxy-ecdysone, 4hrs

growth_protocol: Cultures are grown to a minimum density of 5x10^6 cells per mL prior to extraction.  Trizol is used at a ratio of 1 mL per 10^7 cells.  Extraction procedure is as described by the manufacturer with centrifugation in a Sorvall SS-34 rotor.  Final pellets are air dried and then resuspended in Sigma 18 meg-ohm water to obtain a final RNA concentation of no less than 4ug per uL.

extract_protocol: Trizol Method

tag: rna sample

value: The sample had an [RNA] of 5.14 ug per uL and an OD ratio of 1.99. Details:4mL Trizol800uL chloroform3mL isopropanol1.8mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water

source_name: Ethanol Control

value: The sample had an [RNA] of 4.39 ug per uL and an OD ratio of 2.01. Details:4.0mL Trizol800uL chloroform3.0mL isopropanol1.8mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water


title: After step-up, Time 5, replicate 4

city: Durham

first: Ji

last: Zhang

state: NC

address: Room 136 Hudson Hall

department: Department of Biomedical Engineering

institute: Duke University

hyb_protocol: • Make hybridization buffer fresh each time.  • Add 38 ul hybridization buffer to 12 ul fragmented Cy Dye labeled aa-aRNA.  • Add 1ul each poly dA and appropriate Cot-1 DNA.  • Heat at 95ºC for 2 minutes and put on ice to cool down.  • Mix well and load sample to the array slide with lifter cover slip.  • Hybridize overnight in 42ºC water bath.

scan_protocol: Scanned by GenePix 4000B and quantified using GenePix software

data_processing: LOWESS normalized. Agilent GeneSpring GX was used.

organism: Sus scrofa

source_name: Cultured endothelial cells

label_protocol: Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion), and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes, and reference RNA sample was labeled with Cy3 dyes.

growth_protocol: Porcine aortic endothelial cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum. Passage 3 - 5 cells were used.

extract_protocol: Qiagen RNeasy  kit following manufacturer's protocol

tag: cell type

value: Cultured endothelial cells

value: 180 minutes

source_name: reference RNA

value: cultured porcine aortic endothelial cells (passage 3)


title: 2490-LF

description: squamous cell lung carcinoma _Lung Front_2490

source_name: adjacent lung

value: squamous cell lung carcinoma

value: Lung Front

value: pooled cell line derivations


title: 10uM ecdy 4hrs rep3

value: 10uM 20-hydroxy-ecdysone

value: The sample had an [RNA] of 5.46 ug per uL and an OD ratio of 2.00. Details:3mL Trizol600uL chloroform2.5mL isopropanol1.5mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water

value: Ethanol Control

value: Six tubes of control cells (3.0x10^7 cells per tube) were extracted separately.  Following verification of the quality of each sample by spec ratio they were pooled.  The final sample had an [RNA] of 3.87 ug per uL and an OD ratio of 1.98.Details (per tube):3mL Trizol600uL chloroform2.5mL isopropanol1.5mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water


title: After step-up, Time 4, replicate 4

value: 90 minutes


title: 2490-TF

description: squamous cell lung carcinoma _Tumor Front_2490

value: Tumor Front


title: 0.5uM E 100uM Cyclo rep3

source_name: Drosophila melanogaster, Kc 167 cells, 0.5uM ecdy 100uM cyclo, 4hrs

value: embryo-derived

value: late embryonic

value: 0.5uM ecdy 100uM cyclo

value: The sample had an [RNA] of 3.91 ug per uL and an OD ratio of 1.95. Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 4.88 ug per uL and an OD ratio of 1.97.Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water


title: After step-up, Time 2, replicate 4

value: Cultured endothelial cells

value: 15 minutes


title: 2275-TF

description: squamous cell lung carcinoma _Tumor Front_2275


title: 2490-NL

description: squamous cell lung carcinoma _Normal Lung_2490

value: Normal Lung


title: 2275-NL

description: squamous cell lung carcinoma _Normal Lung_2275

value: squamous cell lung carcinoma


title: After step-up, Time 1, replicate 4

value: 5 minutes

value: cultured porcine aortic endothelial cells (passage 3)


title: 0.5uM ecdy 4hr Glands rep1

source_name: Drosophila melanogaster, Oregon R, salivary glands, 0.5uM 20-hydroxy-ecdysone, 4hrs, Glands

value: Oregon R

tag: genotype

value: db cn bw

value: salivary gland

value: late 3rd instar

value: 0.5uM 20-hydroxy-ecdysone

value: The sample had an [RNA] of 1.24 ug per uL and an OD ratio of 1.48. Details:0.5 mL Trizol100 uL chloroform300 mL isopropanol250 mL 75 percent EtOH-brought up in 10 uL Sigma 18 meg-ohm water

source_name: Drosophila melanogaster, Oregon R, salivary glands, Ethanol control, 4hrs, Glands

value: Ethanol control

value: The sample had an [RNA] of 0.45 ug per uL and an OD ratio of 1.76.Details:mL Trizol uL chloroform mL isopropanol mL 75 percent EtOH-brought up in 35uL Sigma 18 meg-ohm water


title: 0.5uM ecdy 4hr Glands rep2

value: The sample had an [RNA] of 0.39 ug per uL and an OD ratio of 2.11. Details:0.5 mL Trizol100 uL chloroform300 mL isopropanol200 mL 75 percent EtOH-brought up in 10 uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 0.35 ug per uL and an OD ratio of 2.13.Details:mL Trizol uL chloroform mL isopropanol mL 75 percent EtOH-brought up in 35uL Sigma 18 meg-ohm water


title: Preconditioned by basal shear stress, Time 0, replicate 4


title: After step-up, Time 3, replicate 4

value: 45 minutes


title: 0.5uM ecdy 4hr Glands rep3

value: The sample had an [RNA] of 0.52 ug per uL and an OD ratio of 2.05. Details:0.5 mL Trizol100 uL chloroform300 mL isopropanol200 mL 75 percent EtOH-brought up in 10 uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 0.52 ug per uL and an OD ratio of 2.05.Details:mL Trizol uL chloroform mL isopropanol mL 75 percent EtOH-brought up in 35uL Sigma 18 meg-ohm water


title: 2275-TC

description: squamous cell lung carcinoma _Tumor Center_2275

value: Tumor Center

value: pooled cell line derivations


title: 0.0625uM P 4hr rep3

source_name: Drosophila melanogaster, Kc 167 cells, 0.0625 uM ponasterone A, 4hrs

value: embryo-derived

value: late embryonic

value: 0.0625 uM ponasterone A

value: The sample had an [RNA] of 3.83 ug per uL and an OD ratio of 2.01Details:2.5 mL Trizol500 uL chloroform1.9 mL isopropanol1.2 mL 75% EtOH-brought up in 20 uL Sigma 18 meg-ohm water

source_name: Drosophila melanogaster, Kc 167 cells, 22.0C EtOH control

value: 22.0C EtOH control

value: The sample had an [RNA] of 2.95 ug per uL and an OD ratio of 2.Details:5 mL Trizol1000 uL chloroform3.8 mL isopropanol2.4 mL 75% EtOH-brought up in 40 uL Sigma 18 meg-ohm water


title: 0.0625uM P 4hr rep1

value: The sample had an [RNA] of 3.16 ug per uL and an OD ratio of 1.98. Details:2.5 mL Trizol500 uL chloroform1.9 mL isopropanol1.2 mL 75% EtOH-brought up in 20 uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 3.99 ug per uL and an OD ratio of 1.99.Details:2.5 mL Trizol500 uL chloroform1.9 mL isopropanol1.2 mL 75% EtOH-brought up in 20 uL Sigma 18 meg-ohm water


title: 0.0625uM P 4hr rep2

value: The sample had an [RNA] of 4.19 ug per uL and an OD ratio of 1.98. Details:2.5 mL Trizol500 uL chloroform1.9 mL isopropanol1.2 mL 75% EtOH-brought up in 20 uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 2.45 ug per uL and an OD ratio of 2.Details:5 mL Trizol1000 uL chloroform3.8 mL isopropanol2.4 mL 75% EtOH-brought up in 40 uL Sigma 18 meg-ohm water


title: 2275-LF

description: squamous cell lung carcinoma _Lung Front_2275

value: squamous cell lung carcinoma

value: Lung Front


title: 0.5uM E 100uM Cyclo rep2

value: 0.5uM ecdy 100uM cyclo

value: The sample had an [RNA] of 4.32 ug per uL and an OD ratio of 2.01. Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water

source_name: Drosophila melanogaster, Kc 167 cells, Ethanol Control

value: Ethanol Control

value: The sample had an [RNA] of 4.85 ug per uL and an OD ratio of 2.02.Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water


title: After step-up, Time 5, replicate 3

value: Cultured endothelial cells

value: 180 minutes

value: cultured porcine aortic endothelial cells (passage 3)


title: After step-up, Time 4, replicate 3

value: 90 minutes


title: 0.5uM E 100uM Cyclo rep1

value: embryo-derived

value: late embryonic

value: The sample had an [RNA] of 6.53 ug per uL and an OD ratio of 2.02. Details:5.0 mL Trizol1 mL chloroform3.5 mL isopropanol2.5 mL 75% EtOH-brought up in 50 uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 5.79 ug per uL and an OD ratio of 1.92.Details:5.0 mL Trizol1 mL chloroform3.5 mL isopropanol2.5 mL 75% EtOH-brought up in 50 uL Sigma 18 meg-ohm water


title: 2269-TF

description: squamous cell lung carcinoma _Tumor Front_2269

value: Tumor Front

value: pooled cell line derivations


title: 2269-TC

description: squamous cell lung carcinoma _Tumor Center_2269

value: Tumor Center


title: After step-up, Time 6, replicate 3

value: 360 minutes


title: After step-up, Time 3, replicate 3

value: 45 minutes


title: 2269-NL

description: squamous cell lung carcinoma _Normal Lung_2269

value: squamous cell lung carcinoma

value: Normal Lung


title: After step-up, Time 2, replicate 3

value: 15 minutes


title: After step-up, Time 1, replicate 3

value: 5 minutes


title: Tg-PPARa/Tg-Sirt1 rep2

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

description: Gene expression data from Tg-Sirt1/Tg-PPARα

hyb_protocol: The Affymetrix GeneChip arrays were hybridized and washed using the manufacturer's protocol.

scan_protocol: Affymetrix GeneChip arrays were scanned using the Affymetrix GeneArray scanner.

data_processing: The microarray data were normalized using the Robust Multichip Average (RMA) method. We discarded probe sets that did not have signals above background in more than 75% of the arrays for all samples using the Affymetrix MAS5 present/absent calls.

label: biotin

organism: Mus musculus

source_name: Cardiac-specific overexpression of Sirt1 and PPARα

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

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

value: heart

tag: gender

value: male

tag: genetic background

value: FVB

tag: age

value: 10-11 weeks old


title: B6C3Fe a/a-bpck mutant

city: Tianjin

first: E

last: Du

address: ping jiang road 23#, Hexi district

country: China

institute: Tianjin institude of Urology

description: Mouse in fast phase of renal corpuscle proliferation

hyb_protocol: Following fragmentation,30μl of cRNA were hybridized for 16 hr at 45℃ on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 7G 4C.

data_processing: The data were analyzed with dChip (Dec.2010 version)

source_name: B6C3Fe a/a-bpck mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: mice were maintained at the Research and Resource Center at University of Louisville.

treatment_protocol: Animal care and experimental procedures conformed to National Institutes of Health guidelines and were approved by the Institutional Animal Care and Use Committee at the University of Louisville  (protocol # 09014), Louisville, KY.

tag: tissue

value: kidney

tag: genotype/variation

value: B6C3Fe a/a-bpck mutant

value: postnatal 3 days


title: wild type

source_name: wild type

value: wild type


title: Tg-PPARa/Tg-Sirt1 rep1


title: Tg-PPARa rep2

description: Gene expression data from Tg-PPARα

source_name: Cardiac-specific overexpression of PPARα

value: Tg-PPARa


title: Preconditioned by basal shear stress, Time 0, replicate 3

value: Cultured endothelial cells

value: cultured porcine aortic endothelial cells (passage 3)


title: 1418-NL

description: squamous cell lung carcinoma _Normal Lung_1418

source_name: distant normal lung

source_name: Universal Human Reference RNA (Stratagene)

value: pooled cell line derivations


title: 2269-LF

description: squamous cell lung carcinoma _Lung Front_2269

value: Lung Front


title: Tg-PPARa rep1

description: Gene expression data from Tg-PPARα


title: 1418-TF

description: squamous cell lung carcinoma _Tumor Front_1418

source_name: tumor invasion front

value: squamous cell lung carcinoma

value: Tumor Front


title: After step-up, Time 5, replicate 2

value: 180 minutes


title: Tg-Sirt2 rep2

description: Gene expression data from Tg-Sirt1

source_name: Cardiac-specific overexpression of Sirt1


title: After step-up, Time 6, replicate 2

source_name: Cultured endothelial cells

value: 360 minutes


title: After step-up, Time 4, replicate 2

value: 90 minutes

source_name: reference RNA


title: 1418-LF

description: squamous cell lung carcinoma _Lung Front_1418

source_name: adjacent lung


title: Tg-Sirt1 rep1

description: Gene expression data from Tg-Sirt1

value: heart

value: male


title: 1417-TC

description: squamous cell lung carcinoma _Tumor Center_1417

source_name: inner-tumor

value: Tumor Center


title: After step-up, Time 3, replicate 2

value: 45 minutes


title: 1417-NL

description: squamous cell lung carcinoma _Normal Lung_1417

value: Normal Lung


title: WT rep2

description: Gene expression data from Control (wildtype)

source_name: wildtype heart

value: FVB

value: 10-11 weeks old

value: WT


title: After step-up, Time 2, replicate 2

value: Cultured endothelial cells

value: 15 minutes


title: 1417-TF

description: squamous cell lung carcinoma _Tumor Front_1417

value: pooled cell line derivations


title: 1417-LF

description: squamous cell lung carcinoma _Lung Front_1417

value: Lung Front


title: WT rep1


title: After step-up, Time 6, replicate 1

value: cultured porcine aortic endothelial cells (passage 3)


title: 1404-TC

description: squamous cell lung carcinoma _Tumor Center_1404

value: squamous cell lung carcinoma


title: WT rep1

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using RMA in the bioconducter and normalized using cross correlation.  The trimmed mean target intensity of each array was set to 10.

source_name: sorted HSCs (lin-sca1+ckit+CD150+CD48-) of wild type mice

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

growth_protocol: All mice were kept in a sterile barrier facility approved by the Beth Israel Deaconess Medical Center Institutional Animal Care and Use Committee.

treatment_protocol: Adult HSCs were collected after sorting  using the markers (lin-sca1+ckit+CD150+CD48-)  and placed on ice in the Trizol solution (GibcoBRL).

value: sorted HSCs (lin-sca1+ckit+CD150+CD48-)

value: wild type mice

value: adult


title: Preconditioned by basal shear stress, Time 0, replicate 2


title: After step-up, Time 4, replicate 1

value: 90 minutes


title: WT rep2


title: 1404-TF

description: squamous cell lung carcinoma _Tumor Front_1404

value: Tumor Front


title: WT rep3


title: After step-up, Time 5, replicate 1

value: 180 minutes


title: 1404-NL

description: squamous cell lung carcinoma _Normal Lung_1404


title: 1404-LF

description: squamous cell lung carcinoma _Lung Front_1404


title: After step-up, Time 1, replicate 1

value: 5 minutes


title: After step-up, Time 1, replicate 2


title: PU.1 ki/ki rep2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: sorted HSCs (lin-sca1+ckit+CD150+CD48-) of PU.1ki/ki mice

value: knock-in mice


title: After step-up, Time 3, replicate 1

value: 45 minutes


title: PU.1 ki/ki rep1


title: 1331-NL

description: squamous cell lung carcinoma _Normal Lung_1331

value: Normal Lung


title: 1317-TF

description: squamous cell lung carcinoma _Tumor Front_1317


title: 1331-TC

description: squamous cell lung carcinoma _Tumor Center_1331

value: Tumor Center


title: 1331-TF

description: squamous cell lung carcinoma _Tumor Front_1331


title: After step-up, Time 2, replicate 1

value: Cultured endothelial cells


title: PU.1 ki/ki rep3


title: Static cell, rep 4

source_name: Static cell

value: cultured porcine aortic endothelial cells


title: Preconditioned by basal shear stress, Time 0, replicate 1


title: 1317-TC

description: squamous cell lung carcinoma _Tumor Center_1317

value: pooled cell line derivations


title: Long term preconditioned for 30 hours, rep 4

source_name: Long term preconditioned for 30 hours


title: 1317-NL

description: squamous cell lung carcinoma _Normal Lung_1317


title: 1316-TF

description: squamous cell lung carcinoma _Tumor Front_1316


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30B2)

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

hyb_protocol: The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample and re-suspended in 120 microlitres salt-based hybridisation buffer (supplied with the microarray slides).  This was heated at 95 oC for 3 min then cooled on ice for 3 min.  The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated for 18 h at 42 °C.  Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 °C) SSC buffers for 5 min each at 37oC: 1× SSC/0.1 % SDS, 1× SSC, 0.2× SSC and 0.01× SSC.  Microarray slides were dried by centrifugation at 500 × g for 2 min before scanning.

scan_protocol: Slides were scanned on an Affymetrix 428 scanner.

data_processing:
The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5).
Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

organism: Escherichia coli

source_name: E. coli 30 mins

label_protocol: RNA (15-20 micrograms) was annealed to 9 micrograms pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC.  This was supplemented with 4 microlitres of 5× First-strand buffer (Invitrogen), 2 microlitres dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 2 microlitres l 0.1 M DTT, 2 microlitres 1 mM Cy3 (Perkin Elmer) and 1 microlitre Superscript II reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 2 hours.  The reaction was terminated by the addition of NaOH (5 microlitres of 1 M) and HCl (5 microlitres of 1 M) before the addition of TE buffer (200 microlitres).  Labelled cDNA was purified using a Qiaquick purification kit (Qiagen).

extract_protocol: Zn-depleted custom-built chemostats were grown for 50 h.  At this point, ZnSO4.7H2O in water was added to a final concentration of 0.2 M in the chemostat.  A 10 ml sample of culture was taken using a polypropylene pipette tip immediately prior to Zn addition and 2.5, 7, 10 and 30 min after addition.  The culture was pipetted directly into RNAprotect (Qiagen) to stabilize RNA.  Total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.  RNA was quantified using a BioPhotometer (Eppendorf).  A control experiment was carried out in which water was added.

tag: strain

tag: agent

tag: time

value: 30 mins

label_protocol: RNA (15-20 micrograms) was annealed to 9 micrograms pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC.  This was supplemented with 4 microlitres of 5× First-strand buffer (Invitrogen), 2 microlitres dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 2 microlitres l 0.1 M DTT, 2 microlitres 1 mM Cy5 (Perkin Elmer) and 1 microlitre Superscript II reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 2 hours.  The reaction was terminated by the addition of NaOH (5 microlitres of 1 M) and HCl (5 microlitres of 1 M) before the addition of TE buffer (200 microlitres).  Labelled cDNA was purified using a Qiaquick purification kit (Qiagen).


title: Long term preconditioned for 30 hours, rep 3


title: Preconditioned for 24 hours, rep 4

source_name: Preconditioned for 24 hours


title: 1316-TC

description: squamous cell lung carcinoma _Tumor Center_1316


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10B1)

source_name: E. coli 10 mins

value: 10 mins


title: 1316-NL

description: squamous cell lung carcinoma _Normal Lung_1316

value: squamous cell lung carcinoma


title: 1317-LF

description: squamous cell lung carcinoma _Lung Front_1317

value: Lung Front


title: 1299-TF

description: squamous cell lung carcinoma _Tumor Front_1299


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10B2)


title: Preconditioned for 24 hours, rep 3


title: Static cell, rep 3


title: 1299-TC

description: squamous cell lung carcinoma _Tumor Center_1299


title: 1316-LF

description: squamous cell lung carcinoma _Lung Front_1316


title: 3.1het

city: NEW YORK

first: Jianlong

last: Wang

state: NEW YORK

address: 1428 MADISON AVE

department: Developmental and Regenerative Biology

institute: Mount Sinai School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Array 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Differential gene expressions upon knockout of Zfp281 was analyzed by comparing  Null versus Wildtype samples on Affymetrix gene expression microarrays. All arrays were RMA normalized using R.2.9.0. Differentially expressed genes: Log2 fold change > 1 for up-regulated, < -1 for down-regulated were identified, using Limma.

source_name: Zfp281 heterozygous ESC line #3.1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All ESCs were maintained on primary mouse embryonic fibroblasts with DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 1000 U ml-1 of LIF (Chemicon)

treatment_protocol: No additional treatment is involved.

value: embryonic stem cells (ESC)

value: Zfp281 heterozygous


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30B1)


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7B2)

source_name: E. coli 7 mins

value: 7 mins


title: 5het

source_name: Zfp281 heterozygous ESC line #5


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5B2)

source_name: E. coli 2.5 mins

value: 2.5 mins


title: Preconditioned for 24 hours, rep 2


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7B1)


title: Long term preconditioned for 30 hours, rep 2


title: 3.3wt

source_name: Zfp281 wild-type ESC line #3.3

value: Zfp281 wild-type


title: 3.2wt

source_name: Zfp281 wild-type ESC line #3.2


title: 1299-NL

description: squamous cell lung carcinoma _Normal Lung_1299

source_name: distant normal lung

source_name: Universal Human Reference RNA (Stratagene)


title: 1299-LF

description: squamous cell lung carcinoma _Lung Front_1299

source_name: adjacent lung


title: Static cell, rep 2

source_name: reference RNA


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5B1)


title: 1297-TF

description: squamous cell lung carcinoma _Tumor Front_1297

source_name: tumor invasion front

value: Tumor Front


title: Long term preconditioned for 30 hours, rep 1


title: 3wt

source_name: Zfp281 wild-type ESC line #3


title: Preconditioned for 24 hours, rep 1


title: 3.38null

source_name: Zfp281 deficient ESC line #3.38

value: Zfp281 deficient


title: 3.34null

source_name: Zfp281 deficient ESC line #3.34


title: 1297-TC

description: squamous cell lung carcinoma _Tumor Center_1297

source_name: inner-tumor


title: Acute shear stress, Time 5, rep 4

source_name: Preconditioned + 180 minutes acute shear stress


title: Acute shear stress, Time 6, rep 4

source_name: Preconditioned + 360 minutes acute shear stress


title: 7null

source_name: Zfp281 deficient ESC line #7


title: Acute shear stress, Time 2, rep 4

source_name: Preconditioned + 15 minutes acute shear stress


title: Acute shear stress, Time 3, rep 4

source_name: Preconditioned + 45 minutes acute shear stress


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 0B2)

source_name: E. coli 0 mins

value: 0 mins


title: Static cell, rep 1

source_name: Static cell


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 0B1)


title: 1219a-T4-TF

description: squamous cell lung carcinoma _Tumor Front_1219a


title: 1219a-T4-TC

description: squamous cell lung carcinoma _Tumor Center_1219a


title: Acute shear stress, Time 4, rep 4

source_name: Preconditioned + 90 minutes acute shear stress


title: 1219a-T3-TC


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10A3)

source_name: E. coli 10 mins


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30A1)

source_name: E. coli 30 mins


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7A2)

source_name: E. coli 7 mins


title: 1209a-TC

description: squamous cell lung carcinoma _Tumor Center_1209a

source_name: Universal Human Reference RNA (Stratagene)


title: 1219a-T3-TF

source_name: tumor invasion front


title: Preconditioned by basal shear stress, Time 0, rep 4

source_name: Preconditioned + 0 minutes acute shear stress

source_name: reference RNA


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10A2)


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10A1)


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30A2)


title: 1219a-T3-LF

description: squamous cell lung carcinoma _Lung Front_1219a

source_name: adjacent lung


title: Acute shear stress, Time 1, rep 4

source_name: Preconditioned + 5 minutes acute shear stress


title: Acute shear stress, Time 6, rep 3


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5A1)

source_name: E. coli 2.5 mins


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 0A2)


title: 1219a-T4-LF


title: 1209a-NL

description: squamous cell lung carcinoma _Normal Lung_1209a

source_name: distant normal lung

value: Normal Lung


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (0A1)


title: Acute shear stress, Time 3, rep 3


title: 1209a-LF

description: squamous cell lung carcinoma _Lung Front_1209a


title: Acute shear stress, Time 4, rep 3


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7A1)


title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5A2)


title: 1219a-NL

description: squamous cell lung carcinoma _Normal Lung_1219a


title: 1209a-TF

description: squamous cell lung carcinoma _Tumor Front_1209a


title: Acute shear stress, Time 2, rep 3


title: Acute shear stress, Time 1, rep 3


title: Acute shear stress, Time 6, rep 2

source_name: Preconditioned + 360 minutes acute shear stress


title: Zebrafish NMLF at 11d after surgery, spinal cord transected 2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

hyb_protocol: Standard Affymetrix protocols were used for hybridization.

scan_protocol: Standard Affymetrix protocols were used for scanning.

data_processing:
CHP and CEL files were produced using Affymetrix software.
Programmatic identifier: GeneChip.CallGEBaseCall.1
Algorithm: ExpressionStat 5.0

organism: Danio rerio

source_name: Zebrafish brain, laser capture microdissected NMLF region

label_protocol: Standard Affymetrix protocols were used for preparation of bio-cDNA.

growth_protocol: Zebrafish were kept in aquaria with a 14-hour light and 10-hour dark cycle at 28C.

extract_protocol: Microdissected tissues were collected in Qiagen buffer RLT and processed with the RNeasy Micro kit.  RNA samples were amplified using the RampUP kit (Genisphere).

treatment_protocol: Laser capture microdissection, using the PALM system (Carl Zeiss).

tag: treatment

value: Injured


title: Zebrafish NMLF at 11d after surgery, spinal cord transected 3


title: Acute shear stress, Time 5, rep 2

source_name: Preconditioned + 180 minutes acute shear stress


title: Zebrafish NMLF at 11d after surgery, sham control 1

value: Control


title: Preconditioned by basal shear stress, Time 0, rep 3

value: cultured porcine aortic endothelial cells


title: Zebrafish NMLF at 11d after surgery, sham control 2


title: Zebrafish NMLF at 11d after surgery, spinal cord transected 1


title: Acute shear stress, Time 5, rep 3


title: Mock treated HF

city: Jerusalem

first: Jacob

last: Rachmilewitz

address: Ein Kerem

country: Israel

institute: Hadassah hospitals

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000

data_processing: The data were RMA normalized

source_name: HF treated with PBS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Human fibroblats (HF) were grown in DMEM, 37C, 5% C02

extract_protocol: Cells were harvested and RNA was extracted  using 5PRIME PerfectPure RNA Cultured Cell Kit (#2900319) according to manufacturer's instructions

treatment_protocol: 150,000 HF were treated with either PBS or with H2O2 500uM for 1h, after which they were washed and new medium was added and incubated with/without 600,000 monocytes for 24h

value: Skin fibroblasts

value: PBS

tag: monocytes

value: no


title: Zebrafish NMLF at 11d after surgery, sham control 3


title: Acute shear stress, Time 2, rep 2

source_name: Preconditioned + 15 minutes acute shear stress


title: Acute shear stress, Time 1, rep 2


title: Zebrafish NMLF at 12h after surgery, spinal cord transected 2


title: Zebrafish NMLF at 12h after surgery, spinal cord transected 3


title: H2O2 treated HF

source_name: HF treated with H2O2


title: Mock treated HF incubated  with monocytes

source_name: HF treated with PBS and incubated with monocytes for 24h

value: yes


title: H2O2 treated HF mixed with monocytes

source_name: RNA of HF treated with H2O2 and mixed with monocytes' RNA


title: H2O2 treated HF incubated with monocytes

source_name: HF treated with H2O2 and incubated with monocytes for 24h


title: Preconditioned by basal shear stress, Time 0, rep 2


title: Mock treated HF mixed with monocytes

source_name: RNA of HF treated with PBS and mixed with monocytes' RNA


title: Zebrafish NMLF at 12h after surgery, sham control 3


title: Zebrafish NMLF at 12h after surgery, spinal cord transected 1


title: Acute shear stress, Time 3, rep 2

source_name: Preconditioned + 45 minutes acute shear stress


title: Acute shear stress, Time 4, rep 2

source_name: Preconditioned + 90 minutes acute shear stress


title: 14269063 - Col-0 H2O R3 vs Col-0 Cyclocitral R3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description:
arabidopsis thaliana (columbia)  - age: 4week dev.stage (Boyes et al. Plant Cell 2001):boyes: 1.08
Is beta-cyclocitral a bioactive molecule involved in stress response ?

hyb_protocol: Col-0_Cyclocitral R3 Cy5 / Col-0_H2O R3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: Col-0 Cyclocitral R3

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: aerial - Media=compost hygrometry=55% Temperature=22°C/18°C Light=250 µmol m-2s-1

treatment_protocol: Name:beta-cyclocitral - compound based treatment - compound addition,beta-cyclocitral:quantity 50ul time 4hour . Cyclo: Plants of Arabidopsis thaliana (Col-0 ecotype) were grown for 4 weeks under controlled conditions : 250 µmol m-2 s-1, photoperiod of 8h/16h, temperature of 22°C/18°C and 55% of humidity. Plants were then transferred (after 1 hour of light) in a transparent airtight box (about 22 litres) under controlled conditions (60 µmol.m-2s-1, 22°C) in presence of 50 µl of pure beta-cyclocitral. Plants were then harvested after 4 hours of treatment.

value: beta-cyclocitral

tag: ecotype

value: whole plant

value: 4 wk

source_name: Col-0 H2O R3

value: control


title: 14269062 - Col-0 Cyclocitral R2 vs Col-0 H2O R2

hyb_protocol: Col-0_H2O R2 Cy5 / Col-0_Cyclocitral R2 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: Col-0 H2O R2

source_name: Col-0 Cyclocitral R2


title: Zebrafish NMLF at 12h after surgery, sham control 2


title: Zebrafish NMLF at 12h after surgery, sham control 1


title: Acute shear stress, Time 6, rep 1

source_name: reference RNA


title: 14269061 - Col-0 H2O R2 vs Col-0 Cyclocitral R2

hyb_protocol: Col-0_Cyclocitral R2 Cy5 / Col-0_H2O R2 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: Acute shear stress, Time 4, rep 1


title: Acute shear stress, Time 5, rep 1


title: 14269103 - Col-0 H2O R1 vs Col-0 Cyclocitral R1

hyb_protocol: Col-0_Cyclocitral R1 Cy5 / Col-0_H2O R1 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: Col-0 Cyclocitral R1

source_name: Col-0 H2O R1


title: 14269064 - Col-0 Cyclocitral R3 vs Col-0 H2O R3

hyb_protocol: Col-0_H2O R3 Cy5 / Col-0_Cyclocitral R3 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: Zebrafish NMLF at 4h after surgery, spinal cord transected 3

source_name: Zebrafish brain, laser capture microdissected NMLF region


title: Zebrafish NMLF at 4h after surgery, spinal cord transected 2


title: Acute shear stress, Time 2, rep 1


title: Zebrafish NMLF at 4h after surgery, sham control 3


title: Acute shear stress, Time 3, rep 1


title: Zebrafish NMLF at 4h after surgery, spinal cord transected 1


title: 14269104 - Col-0 Cyclocitral R1 vs Col-0 H2O R1

hyb_protocol: Col-0_H2O R1 Cy5 / Col-0_Cyclocitral R1 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: Zebrafish NMLF at 4h after surgery, sham control 1


title: NSW_220_Yes_638_rep4

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

description:
Gene expression after HGP treatment in NSW with 220 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

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: Bos indicus

source_name: skeletal muscle, NSW, 220, HGP, replicate 4

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: Total RNA was extracted from muscle biopsy samples using TRIZOL (Invitrogen); with the aqueous phase being processed through Rneasy Mini Kit columns (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: HGP treatment group received Revalor-H (200mg Trenbolone acetate and 20mg estradiol) implants 2 months prior to collection of samples. Needle biopsy samples from Longissimus dorsi muscle were collected with animals under local anaesthetic.

value: Biopsied Longissimus dorsi

tag: site

value: New South Wales NSW

value: Revalor-H


title: NSW_000_No_715_rep5

description:
Gene expression after no HGP treatment in NSW with 000 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, NSW, 000, No HGP replicate 5


title: Zebrafish NMLF at 4h after surgery, sham control 2


title: NSW_221_Yes_712_rep2

description:
Gene expression after HGP treatment in NSW with 221 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, NSW, 221, HGP, replicate 2


title: Acute shear stress, Time 1, rep 1

source_name: Preconditioned + 5 minutes acute shear stress


title: WA_221_No_999_rep3

description:
Gene expression after no HGP treatment in WA with 221 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, WA, 221, No HGP, replicate 3

value: Western Australia WA


title: NSW_000_No_636_rep4

source_name: skeletal muscle, NSW, 000, No HGP replicate 4


title: NSW_220_Yes_612_rep3

source_name: skeletal muscle, NSW, 220, HGP, replicate 3


title: NSW_000_Yes_546_rep4

description:
Gene expression after HGP treatment in NSW with 000 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, NSW, 000, HGP, replicate 4


title: Preconditioned by basal shear stress, Time 0, rep 1

source_name: Preconditioned + 0 minutes acute shear stress


title: Medulloblastoma Ptch1+/- Nos2-/- 751

hyb_protocol: Cy5-labeled tumor DNA was combined with corresponding Cy3-labeled reference to receive either sex-matched sample pairs or pairs of different gender for means of internal negative or positive control. Hybridization mix was prepared with 37.8 ml nuclease-free water, 50 µl Cot-1 DNA (1 mg/ml), 5.2 µl Agilent 100 x CGH Blocking Agent, and 260 µl Agilent 2 x CGH Hybridization Buffer, for each sample/reference pair. Subsequently, 353 µl of hybridization mix was added to the labeled DNA, thoroughly mixed and heated for 3 minutes at 95 °C. Following a further incubation for 30 minutes at 37 °C, the sample hybridization mix was centrifuged for 1 minute at 10 000 x g and 27 µl of Agilent-CGHblock was added. The sample mix was then applied to G4415A Mouse Genome CGH 244A microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Microarray hybridization was conducted at 20 rpm rotation speed for 40 hours at 65°C. Washing procedures were carried out as described in the manufacturer’s protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol).

scan_protocol: Microarray read out was accomplished in a two-color Agilent Scanner G25505B with 5 µm resolution and automatically adjusting PMT voltages according to manufacturer’s specification. Recorded images were analyzed using Feature Extraction 9.1 software (Agilent).

data_processing: Raw intensity data tables were filtered according to i) mean-to-median ratio (< 3), ii) minimal signal intensity (> 90), and iii) signal-to-background ratio (> 1.5) in both color channels, respectively. For arrays showing high levels of noise, meaning an average noise bandwidth of more than 2-fold the overall calculated balanced state, the filter criteria were slightly adjusted with i) mean-to-median ratio lying within 1 x interquartile range, ii) minimal signal intensity (> 200), and iii) signal-to-background ratio (> 2), again being applied on both color channels, respectively. Finally, array-wise data normalization was performed using the LOESS algorithm. Annotation of oligonucleotide probes on CGH arrays were retrieved from the PIMS© database and referred to EnsEMBL database version 56.

source_name: Medulloblastoma sample, Ptch1+/- Nos2-/-

label_protocol: Labeling of genomic DNA was conducted using the Agilent Genomic DNA ULS labeling kit. Samples were initially precipitated in 200 mM NaCl and 70 % ethanol for 60 minutes at  80 °C. Following centrifugation for 30 minutes at 10000xg, DNA pellets were washed with 70 % ethanol and dissolved in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH7.5) and brought to a concentration of 125 ng/µl. Per sample, a total of 2 µg DNA in 16 µl was used for heat fragmentation at 95 °C for 10 minutes. Subsequently, each sample was incubated for 3 minutes on ice and centrifuged for 1 minute at 6000xg before being mixed with 2 µl ULS-Cy3 or ULS-Cy5 and 2 ml 10 x labeling solution (Agilent). According to the designed experimental setup, tumor samples were labeled with Cy5 and corresponding reference DNA from wildtype mice of the same genetic background was labeled with Cy3. Labeling reactions were incubated for 30 minutes at 85 °C and then cooled down on ice for 3 minutes. Removal of non-reacted Cy-ULS was performed on KREApure columns (Kreatech). Therefore, columns were briefly resuspended and spun dry for 1 minute at 16 000xg with loosened cap and removed bottom closure. The flow-through was discarded and 300 ml nuclease-free water was added to each column followed be centrifugation for 1 minute at 16000xg. The prepared columns were then transferred to new collection tubes and ULS-labeling reaction was added. Purified labelled DNA was eluted by centrifugation for 1 minute at 16000xg.

growth_protocol: Conservation breeding of the Nos2 knock-out mouse strains B6;129P2-Nos2tm1Lau/J and Ptch1 knockt-out mouse B6;129P2-Ptch1tm1Mps/Ptch1+ (Jackson Laboratory) was conducted on wooden litter at 22±2 °C and 55±5 % relative humidity. Illumination was set to 320 Lux with a 12 hour day-night rhythm. Grain pellets (15 mm) and ozonized pH-adjusted (pH2.6-3.0) drinking water were available ad libitum. Accordingly, crossbreeding was performed under theses standard conditions.

extract_protocol: Genomic DNA of tumor specimen was isolated from interphases of CsCl density gradient centrifugation by ethanol precipitation, proteinase K digest, and phenol/chloroform extraction.

value: B6;129P2-Ptch1tm1Mps Nos2tmLau/J

value: C57BL/6 129P2 mixed

value: tumor

tag: disease state

value: medulloblastoma

source_name: Reference pooled tissue

value: various pooled tissues

value: healthy


title: NSW_000_Yes_609_rep5

source_name: skeletal muscle, NSW, 000, HGP, replicate 5


title: NSW_220_Yes_583_rep2

source_name: skeletal muscle, NSW, 220, HGP, replicate 2


title: NSW_221_No_391_rep2

description:
Gene expression after no HGP treatment in NSW with 221 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, NSW, 221, No HGP, replicate 2


title: coi1-13, biological replicate 2

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

institute: Institute of plant physiology & ecology, SIBS, CAS

description: Gene expression data of mutant coi1-13 Young uppermost internodes

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with Affymetrix GeneChip® Operating Software (GCOS, Version 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Oryza sativa

source_name: Oryza sativa_coi1-13 Young uppermost internodes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit and Genechip Sample Cleanup Module (Affymetrix)

extract_protocol: Total RNA was extracted from Young uppermost internodes using the Trizol method (Invitrogen) and purified with RNeasy MiniKit (Qiagen). cDNA was synthesized and purified with one-cycle cDNA Synthesis Kit (Affymetrix) and GeneChip Sample Cleanup Module (Affymetrix), respectively.

value: coi1-13, mutant

value: Young uppermost internodes


title: Medulloblastoma Ptch1+/- Nos2-/- 626


title: NSW_220_Yes_378_rep1

source_name: skeletal muscle, NSW, 220, HGP, replicate 1


title: Medulloblastoma Ptch1+/- Nos2-/- 164


title: coi1-13, biological replicate 3


title: Medulloblastoma Ptch1+/- Nos2-/- 673


title: NSW_000_No_504_rep3

source_name: skeletal muscle, NSW, 000, No HGP replicate 3


title: NSW_221_Yes_505_rep1

source_name: skeletal muscle, NSW, 221, HGP, replicate 1


title: coi1-13, biological replicate 1


title: Medulloblastoma Ptch1+/- Nos2-/- 321


title: Nipponbare, biological replicate 3

description: Gene expression data of wild type Nipponbare Young uppermost internodes

source_name: Oryza sativa_Nipponbare Young uppermost internodes

value: Nipponbare, wild-type


title: Medulloblastoma Ptch1+/- Nos2-/- 180

source_name: Medulloblastoma sample, Ptch1+/-


title: Nipponbare, biological replicate 1


title: Medulloblastoma Ptch1+/- Nos2-/- 620


title: NSW_000_Yes_373_rep3

source_name: skeletal muscle, NSW, 000, HGP, replicate 3


title: NIH3T3 quiescent IgG.2

city: Barcelona

first: oriol

last: bachs

email: obachs@ub.edu, raffaellapippa@ub.edu

address: Casanova 143

department: Cell Biology, Immunology and Neurosciences

country: Spain

institute: University of Barcelona

hyb_protocol: 4 ug of each labeled DNA was hybridized onto each of the two slides of the Agilent Mouse Promotor 244K microarray set according to the manufacturer's protocol for mammalian CHIP on chip (v9.1, November 2006) with mouse Cot DNA and Agilent blocking reagent in 1X Agilent hybridizations buffer 40 hours at 65ºC in a rotating chamber at 10 rpm. Slides chambers were disamembled in Oligo aCGH/ChIP-on-chip Wash Buffer 1 and washed with agitation 5 minutes in the same buffer at room temperature followed by 5 minutes in Oligo aCGH/ChIP-on-chip Wash Buffer 2 at 31 ºC, and two steps without agitation to recue background and remove water componen t 1 minute in acetonitrile and 30 seconds at room temperature, and 30 seconds Agilent Stabilization and Washing solution at room temperature after which slides came out dry and protected from photobleaching. Two separate comparisons were performed (IP versus input and IgG versus input) on two slide sets, for a total of four slides.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT and 5 um resolution.

data_processing: Raw data was extracted using Feature Extraction (Agilent). The data analysis was performed using LIMMA package from R of Bioconductor while the intrachip normalization was obtained with LOESS method.

source_name: IgG IP

label_protocol: DNA was amplified and labelled according to the manufacturer's protocol for mammalian CHIP on chip (v9.1, November 2006) modified by adding microcentrifugation column purification steps instead of ethanol precipitations between different enzymatic reactions. Estimated nanogram amounts of p27  (IP) or control (IgG) immunoprecipitated DNA (below the detection limit of the nanodrop spectrophotometer) or 200 ng of input DNA were polished by blunt ending with T4 DNA polymerase (NEB) followed by purification with Qiaquick (Qiagen) columns. Double stranded DNA linkers (generated by annealing primers JW102 5’-GCGGTGACCCGGGAGATCTGAATTC-3‘ and JW103 5’-GAATTCAGATC-3‘) were ligated to the ends of blunt ended DNA fragments with T4 DNA ligase (NEB), followed by purification with Qiaquick (Qiagen) columns. Amplification was performed by two or three rounds of ligation mediated PCR using Taq polymerase (Applied Biosystems) with Thermopol buffer (NEB) with primer JW102, with at least 4 technical repetitions in the second round to obtain at least 10 ug of DNA. Amplified template was labelled by random priming with the Bioprime CGH labelling kit (Invitrogen) with Cy5-dUTP (2 reactions each for IP and IgG samples), and Cy3-dUTP (4 reactions for input)  using 2 ug of template per reaction. Unincorporated deoxynucleotides were removed by microcentrifugation columns afrom the Invitrogen kit and quantified by Nanodrop spectrophotometry to verify yield specific activity according to specifications.

growth_protocol: NIH3T3 cells were cultured in Dulbecco's modified Eagle Medium (DMEM) supplemented with 10% donor bovine serum (DBS) and maintained at 37ºC and 5% CO2

extract_protocol: NIH3T3 cells were maintained without serum during 24 h at 37ºC and 5% CO2. Cells were fixed with formaldehyde at room temperature for 10 min. Fixation was blocked with glycine, and cells were washed twice in cold 1x PBS before lysation. Chromatin was sheared to an average of 800 bp as verified on a 1% agarose gel. Clarified lysates were agitated overnight at 4ºC with anti-IgG polyclonal  antibody (SIGMA). Following this incubation Protein G/A agarose was added and allowed to bind for 2hours at 4ºC. Immunoprecipitates were washed three times in 1x RIPA, three times with RIPA-NaCl, two times with LiCl buffer and two times with 1x TE before eluition. Crosslinks were reversed overnight at 65ºC. DNA was purified by incubation with Proteinase K (Roche) for 2 h at 55ºC, and using the Illustra GFX PCR DNA Purification kit (GE healthcare). DNA was sonicated prior to processing and fragments of 500-800bp were analyzed.

treatment_protocol: For serum starvation, cells were maintained without serum during 24 h.

value: quiescent NIH3T3

tag: antibody

value: IgG control immunopreciptation

source_name: input

value: N/A (input DNA reference)


title: Medulloblastoma Ptch1+/- 683


title: WA_221_Yes_369_rep1

description:
Gene expression after HGP treatment in WA with 221 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, WA, 221, HGP, replicate 1


title: WA_220_Yes_361_rep3

description:
Gene expression after HGP treatment in WA with 220 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, WA, 220, HGP, replicate 3


title: WA_221_No_354_rep4

source_name: skeletal muscle, WA, 221, No HGP, replicate 4


title: Nipponbare, biological replicate 2


title: ZR13_MAS5

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

country: Japan

institute: The University of Tokyo

hyb_protocol: Labeled aRNA samples were hybridized to GeneChip Rat Genome 230 2.0 Arrays (Affymetrix). The arrays were washed, stained with the Fluidics Station (Affymetrix).

scan_protocol: Scanned with the GeneChip Scanner (Affymetrix).

data_processing: Data acquisition was performed using the GeneChip Operating Software (Affymetrix) and analyzed using the MAS5 program (Affymetrix).

organism: Rattus norvegicus

source_name: diencephalone, zinc-deficiency for 10 days followed by zinc-recovery for 6 days

label_protocol: One hundred nanograms of total RNA from each sample was reverse-transcribed, amplified and labeled using the GeneChip 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol.

extract_protocol: Total RNA samples were isolated from individual diencephalons using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and cleaned up using the RNeasy Mini Kit with a DNase treatment (Qiagen, Valencia, CA, USA). The RNA quality and quantity were examined by agarose gel electrophoresis and a spectrophotometer.

value: SD rat

tag: Sex

value: male

value: zinc-deficiency for 10 days from 5-wk-old followed by zinc-recovery for 6 days


title: Medulloblastoma Ptch1+/- 679

source_name: Reference pooled tissue


title: ZR10_MAS5


title: ZRPF6_MAS5

source_name: diencephalone, pair-feeding to ZR for 16 days

value: pair-feeding to ZR for 16 days from 5-wk-old


title: LM5312_opaR+_biological replicate 3

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

department: Microbiology

institute: University of Iowa

hyb_protocol: Samples (~4.5 ug) were hybridized to the chips in the DNA Core Facility at the University of Iowa according to the standard Affymetrix protocols for E. coli

scan_protocol: Analysis was done using the following software available at the University of Iowa DNA facility: Affymetrix Gene Chip Operating Software (1.2.1), Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.0.

data_processing: Using the raw signal output generated by GTYPE, processing and comparisons were made by using R version 2.8.1 GUI 1.27 Tiger build 32-bit (5301) (http://www.r-project.org) within Bioconductor software for bioinformatics (http://www.bioconductor.org). The complete data set was preprocessed by using the GCRMA method to perform optical adjustment, background adjustment, normalization, and summarization functions

organism: Vibrio parahaemolyticus

source_name: opaR+: opaque strain grown on plate

label_protocol: cDNA was synthesized according to the Affymetrix Prokaryotic Target Preparation Protocol using the Superscript II Reverse Transcriptase kit (Invitrogen) and pD(N)6 random hexamers (GE Healthcare). Approximately 36 ug of RNA was converted to ~7 ug cDNA, which was purified with the MinElute PCR purification kit (Qiagen) and fragmented with RQ1 DNase to yield fragments between 50 and 200 bp. cDNA was labeled with Biotin-ddUTP using the BioArray Terminal Labeling Kit (Enzo).

growth_protocol: To examine V. parahaemolyticus grown on plates a single colony of the strain to be examined was streaked as a lawn over the entire surface of a fresh HI plate. The following day, 5 ml of HI broth was used to suspend the cells on the plate, which were then diluted to an OD600nm = 0.05. Fifty µl of the diluted cells were spread onto an HI plate. After 6 h of growth, cells were harvested from the plate and diluted to OD600nm of 1.0 by using RNAprotect (Qiagen) that had been diluted 2-fold in 1x DPBS pH 7.1 (Gibco).

extract_protocol: Cells in RNAprotect were centrifuged and lysed by using lysozyme, proteinase K, and QIAzol (Qiagen) according to manufacturer’s protocol (Qiagen RNAprotect Bacteria Reagent Handbook). For each RNA preparation, 2 ml of plate-grown cells were extracted and the RNA purified using 4 RNeasy minicolumns (Qiagen), which yielded ~50 ug RNA. This RNA was treated twice with RQ1 DNase (12 U, Promega) at 37ºC for one hour and purified after treatment using the RNeasy minikit

tag: colony morphology

value: opaque


title: ZR15_MAS5


title: ZR7_MAS5


title: Medulloblastoma Ptch1+/- 758

tag: genotype


title: NSW_220_No_357_rep4

description:
Gene expression after no HGP treatment in NSW with 220 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, NSW, 220, No HGP, replicate 4

value: Biopsied Longissimus dorsi

value: New South Wales NSW


title: ZRPF5_MAS5


title: LM6633_opaR+_biological replicate 2


title: NSW_220_No_336_rep3

source_name: skeletal muscle, NSW, 220, No HGP, replicate 3


title: NIH3T3 quiescent p27.2

source_name: p27 IP

tag: cell type

value: p27 test immunoprecipitation


title: Medulloblastoma Ptch1+/- 227

tag: genetic background

value: C57BL/6 129P2 mixed

value: tumor

value: medulloblastoma


title: Medulloblastoma Ptch1+/- 223

value: various pooled tissues

value: healthy


title: LM6633_opaR+_biological replicate 1


title: NSW_000_Yes_329 _rep1

source_name: skeletal muscle, NSW, 000, HGP, replicate 1

value: Revalor-H


title: LM5674_DopaR_biological replicate 4

source_name: DopaR: translucent strain grown on plate

value: translucent


title: NSW_000_Yes_331_rep2

source_name: skeletal muscle, NSW, 000, HGP, replicate 2


title: NSW_220_No_311_rep2

source_name: skeletal muscle, NSW, 220, No HGP, replicate 2


title: ZRPF4_MAS5


title: NSW_000_No_322_rep2

source_name: skeletal muscle, NSW, 000, No HGP replicate 2


title: LM5674_DopaR_biological replicate 3


title: NSW_220_No_281_rep1

source_name: skeletal muscle, NSW, 220, No HGP, replicate 1


title: WA_220_Yes_308_rep4

source_name: skeletal muscle, WA, 220, HGP, replicate 4

value: Western Australia WA


title: NSW_000_No_251_rep1

source_name: skeletal muscle, NSW, 000, No HGP replicate 1


title: ZRPF2_MAS5


title: ZD9_MAS5

source_name: diencephalone, zinc-deficiency for 10 days

value: zinc-deficiency for 10 days from 5-wk-old


title: LM5674_DopaR_biological replicate 1


title: ZD8_MAS5

value: SD rat


title: LM5674_DopaR_biological replicate 2


title: WA_220_No_245_rep4

description:
Gene expression after no HGP treatment in WA with 000 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, WA, 220, No HGP, replicate 4


title: GBM20

city: Charlestown

first: Mikkel

last: Noerholm

state: MA

address: 149 13th Street

department: Neurology

institute: MGH

hyb_protocol: Hybridization to Agilent microarrays was carried out by Miltenyi according to manufacturer’s recommendations. Briefly, 1.4 µg amplified RNA was hybridized to Agilent 4x44K Human Microarrays and the arrays were washed.

scan_protocol: The arrays were scanned on an Agilent Scanner G2505C. Raw data was generated by image analysis using Feature Extraction version 10.5.1.1 (Agilent).

data_processing: The data were normalized.

source_name: microvesicle RNA, GBM

label_protocol: Linear amplification was carried out by Miltenyi according to manufacturer’s recommendations. Briefly, exoRNA was linearly amplified and fluorescently labeled with Cy3 using [XXX Kit Name] (Agilent).

extract_protocol: One mL of serum was transferred to an ultracentrifuge tube, diluted 1:1 with cold PBS and centrifuged at 110,000g for 70 min at 4°C. The supernatant was carefully aspirated off without disturbing the microvesicle pellet. The pellet was treated for 15 min with 50 μL DNase (Ambion), 700 μL miRNeasy lysis buffer was added to the tube and the RNA was isolated following the manufacturer’s recommendations. After elution of the RNA from the column in water, the RNA was precipitated by adding 100% EtOH and incubation at -20°C, centrifugation and removal of the supernatant. The pellet was left to dry and dissolved in 14 μL of nuclease-free water and stored at -80°C until needed.

treatment_protocol: Blood samples were collected into a BD Vacutainer SST (#367985). The blood was left to clot for 30 min and serum was isolated according to manufacturer’s recommendations within two hours of collection. Serum was filtered by slowly passing it through a 0.8 µm syringe filter, aliquoted into 1.8 mL cryotubes and kept at -80°C until used.

value: blood

value: serum microvesicles

value: glioblastoma multiforme


title: PF6_MAS5

source_name: diencephalone, pair-feeding to ZD for 10 days

value: male

value: pair-feeding to ZD for 10 days from 5-wk-old


title: WA_221_Yes_242_rep4

source_name: skeletal muscle, WA, 221, HGP, replicate 4

value: Biopsied Longissimus dorsi


title: WA_000_Yes_240_rep4

description:
Gene expression after HGP treatment in WA with 000 genotype
The tenderness genotypes are based on alleles for the genes Calpastatin, Calpain 3 and Calpain 1; where the numbers indicate tender/favoured = 2, intermediate = 1 and tough/unfavoured = 0.
For example 221 means that an animal has favoured genotype for Calpastatin, Calpain 3 and the intermediate genotype for Calpain 1.

source_name: skeletal muscle, WA, 220, HGP treated, replicate 4


title: PF1_MAS5


title: ZD3_MAS5


title: NSW_000_No_236_rep7

source_name: skeletal muscle, NSW, 000, No HGP replicate 7

value: New South Wales NSW


title: PF4_MAS5


title: GBM18


title: ZD2_MAS5


title: PF2_MAS5


title: WA_000_Yes_232_rep3

source_name: skeletal muscle, WA, 220, HGP treated, replicate 3


title: GBM17


title: NSW_221_No_246_rep1

source_name: skeletal muscle, NSW, 221, No HGP, replicate 1


title: GBM19


title: GBM16


title: WA_220_No_239_rep3

source_name: skeletal muscle, WA, 220, No HGP, replicate 3


title: WA_221_Yes_227_rep3

source_name: skeletal muscle, WA, 221, HGP, replicate 3


title: WA_000_No_214_rep2

source_name: skeletal muscle, WA, 000, No HGP, replicate 2


title: NSW_221_No_216_rep3

source_name: skeletal muscle, NSW, 221, No HGP, replicate 3


title: GBM13


title: Ctrl5

source_name: microvesicle RNA, healthy control


title: WA_000_Yes_197_rep2

source_name: skeletal muscle, WA, 220, HGP treated, replicate 2


title: WA_221_No_117_rep2

source_name: skeletal muscle, WA, 221, No HGP, replicate 2


title: NSW_000_No_160_rep6

source_name: skeletal muscle, NSW, 000, No HGP replicate 6


title: Ctrl3


title: Ctrl2


title: GBM11


title: Ctrl7


title: GBM12


title: pre-miR-1 6

city: Bethesda

middle: Scott

last: Hudson

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

description: Gene expression data from LNCaP cells transfected with pre-miR oligos

hyb_protocol: GeneChip® Human Genome U133A 2.0 (Affymetrix Inc., Santa Clara, CA) arrays were used following standard Affymetrix procedures as outlined in the Affymetrix technical manual. GeneChips® were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: Microarray data (CEL files) were normalized using RMA and MAS.5 filtered for  genes with their detection calls as “P” or “M” within at least 3 samples.

source_name: Prostate cancer LNCaP cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were plated in six-well plates at 2.5x105 cells per well, allowed to grow for 48-72 hours and then switched to antibiotic free media before being transfected.

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen, Carlsbad, CA) as directed by the manufacturer. The quantity and quality of RNA was assessed with a Nanodrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Pre-miRNA and control oligonucleotides (Ambion, Austin, TX) at 30-nM final concentration were transfected using Lipofectamine 2000 (Invitrogen, Carlsbad, CA), as directed by the manufacturer. Briefly, cells were plated in six-well plates at 2.5X10^5 cells per well, grown for 48-72 hr, and then switched to antibiotic free media prior to transfection. Next, 1.5 µl oligos at 50µM and 4 µl Lipofectamine 2000 were added individually to 250 µl of Opti-MEM (Invitrogen) and then combined and incubated for at least 20 minutes, before being added to cells (2.5 ml media in total). Cells were collected at 24 hr for microarray studies.

tag: transfection

tag: experiment

tag: batch

tag: cell line

value: LNCaP


title: WA_221_Yes_111_rep2

source_name: skeletal muscle, WA, 221, HGP, replicate 2

tag: tissue


title: pre-miR-1 5


title: pre-miR-control 6

value: pre-miR-control


title: pre-miR-1 4


title: WA_220_No_98_rep2

source_name: skeletal muscle, WA, 220, No HGP, replicate 2


title: pre-miR-control 5


title: WA_221_No_105_rep1

source_name: skeletal muscle, WA, 221, No HGP, replicate 1


title: Ctrl8


title: GBM15

source_name: microvesicle RNA, GBM


title: Ctrl4


title: NSW_221_Yes_112_rep3

source_name: skeletal muscle, NSW, 221, HGP, replicate 3


title: Ctrl1


title: LM4476_LuxO*_biological replicate 1

source_name: LuxO*: translucent strain grown on plate


title: WA_000_No_54_rep1

source_name: skeletal muscle, WA, 000, No HGP, replicate 1


title: WA_220_No_92_rep1

source_name: skeletal muscle, WA, 220, No HGP, replicate 1


title: pre-miR-27b 3


title: LM4476_LuxO*_biological replicate 2


title: WA_000_Yes_22_rep1

source_name: skeletal muscle, WA, 220, HGP treated, replicate 1


title: pre-miR-control 4


title: pre-miR-control 3


title: Dorsomorphin-treated stimulated CD4+ T cells-replicate2

city: London

first: Masahiro

last: Ono

address: 30 Guilford Street

department: Immunobiology Unit

institute: Institute of Child Health

description: Primary culture from CD4+ T cells

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

data_processing: summarization by the mas5 algorithm and RMA normalization using the the R/Bioconductor package affy.

source_name: Primary CD4+ T cells

label_protocol: Affymetrix GeneChip IVT Labeling Kit according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

extract_protocol: RNeasy

tag: strain

value: BALB/c

value: primary CD4+ T cells

value: stimulated and dorsomorphin


title: pre-miR-206 3


title: Control stimulated CD4+ T cells-replicate2

description: Primary culture from CD4+ T cells

tag: treatment

value: stimulated


title: Control stimulated CD4+ T cells-replicate1

description: Primary culture from CD4+ T cells


title: pre-miR-206 2


title: WA_220_Yes_11_rep2

source_name: skeletal muscle, WA, 220, HGP, replicate 2

value: Revalor-H


title: pre-miR-27b 2


title: WA_220_Yes_7_rep1

source_name: skeletal muscle, WA, 220, HGP, replicate 1

value: Western Australia WA


title: Dorsomorphin-treated stimulated CD4+ T cells-replicate1

description: Primary culture from CD4+ T cells


title: pre-miR-control 2


title: WT Columbia, biological rep3 at Mich

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description: m-WT_x104, Analysis conducted at the University of Michigan

hyb_protocol: The cRNA was fragmented in the presence of heat and Mg2+, followed by hybridization to the Affymetrix ATH1 Arabidopsis genechip for 16 hr at 45C.  The arrays were then washed and stained using the Affymetrix Fluidics Station 400.

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

data_processing: The data were preprocessed in R using RMA with custom CDF files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp)

source_name: WT Columbia

label_protocol: Biotin-labeled cRNA was synthesized according to the standard Affymetrix protocol from poly(A) RNA present in the total RNA prep.

growth_protocol: Seedlings were grown for 5 days in continuous light at 23C on vertically-oriented dishes containing MS media + 1% sucrose.

extract_protocol: WER::GFP-expressing cells were collected by FACS.  Total RNA was extracted from GFP-positive cells using the Rneasy kit (Qiagen, Inc).

treatment_protocol: Root were cut approximately 2 mm from the tip, including the entire developmental region.

value: Wild type (Columbia ecotype) WER::GFP

value: root epidermal cells


title: Dorsomorphin-treated CD4+ T cells-replicate1

description: Primary culture from CD4+ T cells

value: dorsomorphin


title: WT Columbia, biological rep2 at Mich

description: m-WT_S10, Analysis conducted at the University of Michigan


title: pre-miR-27b 1


title: Dorsomorphin-treated CD4+ T cells-replicate2

description: Primary culture from CD4+ T cells


title: wer myb23 mutant, biological rep3 at Mich

description: m-WERMYB23_S5, Analysis conducted at the University of Michigan

source_name: wer myb23 mutant

value: wer-1 myb23-1 WER::GFP


title: pre-miR-206 1


title: Control CD4+ T cells-replicate1

description: Primary culture from CD4+ T cells

value: control


title: WT Columbia, biological rep1 at Mich

description: m-WT_108, Analysis conducted at the University of Michigan


title: pre-miR-control 1


title: quiescent WT MEFs

description: Gene expression data from WT MEFs cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix 430 2.0 murine array. Chips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Scanner Axon 4000B

data_processing: The normalization of the arrays was done using the rma method as implemented in the Affy package of R Bioconductor. Quality control measurements were done using ArrayQualityMetrics package of R Bioconductor.

source_name: WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Wt and p27delta51 MEFs were cultured in DMEM supplemented with 10% fetal bovin serum (FBS). All cultures were maintained at 37ºC and 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Kit (QIagen). RNAs from quiescent MEFs from wt or delta51 mice were analyzed using a Bioanalyzer (Agilent). Only samples with RIN number greater than 9 and a ratio A260/280 over than 2 were further used in microarray analysis. Retrotranscription was made followed by labeling with biotin.

treatment_protocol: For serum starvation, cells were maintained without serum during 72 h.

value: MEFs

tag: genotype/variation

value: wild type


title: wer myb23 mutant, biological rep1 at Mich

description: m-WERMYB23_101, Analysis conducted at the University of Michigan


title: quiescent p27delta51 MEFs

description: Gene expression data from p27delta51 MEFs cells


title: ttg mutant, biological rep3 at Mich

description: m-TTG_99, Analysis conducted at the University of Michigan

source_name: ttg mutant

value: ttg1-13 WER::GFP


title: Control CD4+ T cells-replicate2

description: Primary culture from CD4+ T cells


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep8

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

hyb_protocol: Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays. Following the hybridisation for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

scan_protocol: All Affymetrix Bovine Genome Array microarrays were scanned using an Affymetrix GeneChip® Scanner 3000.

data_processing: Affymetrix® GeneChip® Bovine Genome Array data were analysed using Bioconductor [http://www.bioconductor.org] contained within the R statistical package (http://www.r-project.org). Normalisation of raw data was performed using the Factor Analysis for Robust Microarray Summarization (FARMS) algorithm. The FARMS algorithm uses only perfect match probes and a quantile normalization procedure, which provides the signal intensities.

organism: Bos taurus

label_protocol: Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The single stranded cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2. The enzymatically and chemically fragmented product (50-100 nt) was labelled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

extract_protocol: All RNA extractions were performed within two hours of blood collection. Briefly, 7.5 ml of whole heparinised blood was mixed with 42.5 ml of erythrocyte blood lysis buffer (10 mM KHCO3, 150 mM NH4Cl, 1 mM EDTA pH 8.0), and incubated for 5 min at room temperature with gentle agitation. Following centrifugation (750g for 10 min) the pelleted cells were washed once with 1× phosphate buffered saline (Invitrogen Ltd., Paisley, UK). The cell pellet was then fully resuspended in 2 ml Trizol® reagent (Invitrogen Ltd., Paisley, UK) and RNA was extracted as per the manufacturer’s instructions. The RNA was further purified using an RNeasy® kit with on-column DNase treatment (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions. RNA quantity and quality was assessed using both the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Cork, Ireland). All samples displayed a 260/280 ratio greater than 1.8 and RNA integrity numbers (RIN) greater than 8.0.

treatment_protocol: Sixteen animals were used for this study. Eight infected animals were selected from a panel of naturally M. bovis infected animals maintained for on-going disease surveillance at the Department of Agriculture, Fisheries and Food, Backweston Laboratory Campus (Celbridge, Co. Kildare, Ireland). These animals had a positive single intradermal comparative tuberculin test (SICTT) result and were also positive in the whole blood IFN-γ-based BoviGAM® assay [Prionics AG, Switzerland] (data not shown). Cattle were confirmed for BTB following detailed post-mortem pathological examination. Non-infected controls animals were sex matched and age-matched to the infected animals and were selected from a herd with no recent history of M. bovis infection. The control animals were shown to be negative for both the SICTT and IFN-γ tests (data not shown).

value: Peripheral blood leukocyte

tag: cattle breed

value: Holstein-Friesian

value: Female

tag: infection status

value: Control

tag: agent


title: wer myb23 mutant, biological rep2 at Mich

description: m-WERMYB23_4, Analysis conducted at the University of Michigan


title: Cell Line U138OTR, biological rep 1

city: Durham

first: Jason

middle: W

last: Reeves

state: North Carolina

address: 101 Science Dr

institute: Duke University

hyb_protocol: Following fragmentation, 10ug of biotinylated cRNA was hybridized for 16hr at 45C onto the Affymetrix Human Genome U133A Plus 2.0 Array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 according to standard protocols.

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

data_processing: data normalized using Bioconductor in R using either RMA or MAS5.0 normalization protocols (RMA provided, see website for MAS5).  Batch corrected expression values calculated by factor regression across Affymetrix doping and housekeeping controls

source_name: GBM Serum Cell Line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2ug of Total RNA (ExpressionAnalysis Techinical Manual, 2005, Affymetrix).

growth_protocol: Xenograft lines grown SC or IC until 200 mm^3, cell lines cultured to 70% confluence in either serum free or serum containing media

extract_protocol: Total RNA extracted using Qiagen midi (xenograft), or mini (cell lines) kits.  Xenograft tissue pulverized in liquid nitrogen and homogenized using a rotor-stator homogenizer

tag: date of array

tag: line number

tag: line type

value: Serum Cell Line


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep7

tag: Sex