title: Retinal endothelial cell_Human 6_Stimulated.LPS_Replicate 1

city: Portland

first: Justine

last: Smith

state: OR

address: 3181 SW Sam Jackson Park Road, Biomedical Research Building, Level 2

department: Casey Eye Institute

institute: Oregon Health & Science University

description: RNA input amount: 2ug; Hybridization date: 12/02/2005; Array lot: 4009762

hyb_protocol: Following fragmentation, 6.5 ug of cRNA were hybridized for 16 hrs at 45 °C on Human Genome Focus GeneChip Arrays. GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 400 for 193JS Set#1. 193JS Set#2-3 and 245JS Sets#1-3 were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip arrays were scanned using the Affymetrix GeneChip Scanner 3000 and GCOS version 1.2 software (Affymetrix), yielding cell fluorescence intensity (.CEL) files.

data_processing: Array data were preprocessed and normalized as two separate sets.  Sample assay names with the suffix, 193JS were grouped as set1 and all sample names with the suffix, 245JS were grouped as set2.  Data preprocessing and normalization were performed with the “affy“ and “gcrma” packages of the Bioconductor project (http://www.bioconductor.org) that run above the R statistical language environment. .CEL files were imported into the R environment. Perfect match (PM) probe data were corrected for background noise using the GeneChip robust multi-array analysis (GCRMA).  Corrected PM probe data were normalized with the algorithm based on rank invariant probes.  Gene expression values were determined using a linear model estimated by the median polish algorithm.

source_name: Retinal endothelial cell, lipopolysaccharide, 4 hours

label_protocol: Microarray assays were performed in the Affymetrix Microarray Core of the OHSU Gene Microarray Shared Resource.  Biotinylated cRNA target was prepared according to the standard Affymetrix one-cycle cDNA protocol from 1-2 ug total RNA (Expression Analysis Technical Manual, Ver. 701021 Rev.5).  Standard pre-mixed Affymetrix hybridization controls (bioB, bioC, bioD, and cre at 1.5, 5, 25, and 100 pM concentrations, respectively) and Control Oligo B2 were added directly to the hybridization cocktail according to manufacturer's protocol.

growth_protocol: Human eyes were obtained from 6 human cadaveric donors. No donor had a history of ocular disease. Death to isolation time varied from 8 to 19 hours. Cornea, if present, was excised, and iris was separated from the eye wall. Vitreous was removed from the posterior eyecup, and retina was separated from underlying choroid. Subsequently, choroid was separated from the eye wall and the retinal pigment epithelium was gently removed with a cotton bud. Choroid and retina were separately treated with graded solutions (0.25 to 3 mg/mL) of type II collagenase (Sigma-Aldrich, St Louis, MI) in HEPES-buffered MCDB-131 medium (Sigma-Aldrich; catalogue number 8537), supplemented with 2% fetal bovine serum (FBS) (Hyclone, Logan, UT) and 1 mg/mL amphotericin B (GIBCO, Invitrogen, Grand Island, NY), at 37 °C and 5 % CO2, until the tissue was visibly digested. In the case of retina, digestion with type II collagenase was preceded by treatment with dispase (GIBCO, Invitrogen); an overnight incubation with 0.3 mg/mL dispase achieved optimal digestion. Subsequently, endothelial cells were purified from stromal cells using magnetic beads (Dynabeads) (Dynal, Invitrogen, Brown Deer, WI) coated with mouse monoclonal anti-human CD31 antibody (BD Pharmingen, San Diego, CA). Cells were cultured in MCDB-131 medium supplemented with 10 – 20 % FBS, endothelial growth factors and 1 mg/mL amphotericin B (Clonetics, Cambrex Bioscience, Walkerville, MD; EGM-2 SingleQuot catalogue number cc-4176), but without addition of gentamicin, hydrocortisone and FBS), at 37 °C and 5 % CO2, and passed with the use of 0.05 % trypsin (GIBCO, Invitrogen). Cultured cells were used at passage 5 or less. Immediately prior to treatment, retinal and choroidal vascular endothelial cells were grown to confluence simultaneously in separate 10 cm polystyrene tissue culture dishes.

extract_protocol: Following the treatment, cell supernatants were removed. A 0.6 mL aliquot of RLT lysis buffer (Qiagen, Valencia, CA) was evenly spread across the cells of each plate, and plates were immediately stored at –80 °C. Upon thawing, cell lysates were collected using a cell scraper and immediately homogenized using Qiashredder spin columns (Qiagen). Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions, including the optional on-column DNase treatment. RNA was eluted from the column using nuclease-free water (Ambion, Austin, TX), with 2 rounds of 50 ml yielding a total elute of 100 ml. To concentrate the RNA, it was mixed in a solution containing 10 ml of 2 M sodium acetate at pH 4.0 (Stratagene, Cedar Creek, TX) and 110 ml of 100 % isopropanol, and precipitated overnight at –20 °C. RNA pellets were washed using graded solutions of ethanol, dried in air, and subsequently raised in 10 µl of nuclease-free water. Quantity and purity of the RNA were determined by spectrophotometry.

treatment_protocol: Once retinal and choroidal vascular endothelial cells had achieved confluence in the tissue culture dishes, the medium was changed to MCDB-131 supplemented with 5 % heat-inactivated FBS and endothelial growth factors. After overnight incubation, the medium was again changed as follows. For Humans 1, 2 and 3, separate dishes of choroidal and retinal endothelial cells were treated with 10 mL of either 3.0 x 106/mL tachyzoites in modified MCDB-131 medium or medium alone. For Humans 4, 5 and 6, separate dishes of choroidal and retinal endothelial cells were treated with 10 mL of either 100 ng/mL Escherichia coli 055:B55 LPS (Sigma-Aldrich) in modified MCDB-131 or medium alone. Plates were then incubated at 37 °C and 5 % CO2 for 4 hours.

tag: Gender

value: female

tag: Age

value: 49 years

tag: Cell

value: retinal endothelial

tag: Stimulus

value: lipopolysaccharide


title: Choroidal endothelial cell_Human 6_Unstimulated_Replicate 1

status: Public on May 25 2007

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Choroidal endothelial cell, medium alone, 4 hours

value: choroidal endothelial

value: medium alone


title: SVGR2 subclone 4-E12 GeneChip U133A

city: Providence

first: Kate

last: Manley

state: RI

address: 70 Ship St.

institute: Brown University

description: Gene expression data from SVGR2 glial cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human 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 with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: SVGR2 glial cells

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: Cells were cultured in supplemented with 10% fetal calf serum (Mediatech, Inc.) and maintained in a humidified 37°C CO2 incubator.

extract_protocol: Extraction of total RNA was performed using the Qiagen Rneasy midi kit according to the manufacturer's instructions.

treatment_protocol: Cells were left at 100% confluency before RNA was harvested.

tag: VGR2 cells are glial cells which are derived from SVG-A cells. They were created by subjecting SVG-A cells to multiple rounds of lytic infection by the human polyomavirus JCV. SVGR2 cells are the cells that survived this process and are resistant to JCV infection


title: Retinal endothelial cell_Human 6_Stimulated.LPS_Replicate 2


title: SVG-A subclone 1-D4 GeneChip U133A

description: Gene expression data from SVG-A glial cells.

source_name: SVG-A glial cells

tag: SVG-A glial cells


title: SVGR2 subclone 1-C4 GeneChip U133A


title: Choroidal endothelial cell_Human 6_Stimulated. LPS_Replicate 2

source_name: Choroidal endothelial cell, lipopolysaccharide, 4 hours


title: Choroidal endothelial cell_Human 6_Unstimulated_Replicate 2


title: SVG-A subclone 3-D6 GeneChip U133A


title: Retinal endothelial cell_Human 6_Unstimulated_Replicate 1

source_name: Retinal endothelial cell, medium alone, 4 hours


title: Retinal endothelial cell_Human 6_Unstimulated_Replicate 2


title: Choroidal endothelial cell_Human 6_Stimulated. LPS_Replicate 1


title: Choroidal endothelial cell_Human 4_Unstimulated_Replicate 2

description: RNA input amount: 2ug; Hybridization date: 10/19/2005; Array lot: 4009762

value: male

value: 36 years


title: Choroidal endothelial cell_Human 5_Stimulated. LPS_Replicate 1

description: RNA input amount: 2ug; Hybridization date: 11/22/2005; Array lot: 4009762

value: 46 years


title: Retinal endothelial cell_Human 5_Stimulated.LPS_Replicate 2


title: Choroidal endothelial cell_Human 5_Stimulated. LPS_Replicate 2


title: Choroidal endothelial cell_Human 4_Stimulated. LPS_Replicate 1


title: Choroidal endothelial cell_Human 4_Stimulated. LPS_Replicate 2


title: SVG-A subclone 4-G5 GeneChip U133A


title: Choroidal endothelial cell_Human 5_Unstimulated_Replicate 2


title: Retinal endothelial cell_Human 5_Stimulated.LPS_Replicate 1


title: Retinal endothelial cell_Human 5_Unstimulated_Replicate 1


title: Retinal endothelial cell_Human 5_Unstimulated_Replicate 2


title: Retinal endothelial cell_Human 4_Unstimulated_Replicate 1


title: Retinal endothelial cell_Human 4_Unstimulated_Replicate 2


title: Choroidal endothelial cell_Human 4_Unstimulated_Replicate 1


title: Retinal endothelial cell_Human 4_Stimulated.LPS_Replicate 1


title: Retinal endothelial cell_Human 4_Stimulated.LPS_Replicate 2


title: Retinal endothelial cell_Human 3_Stimulated.Toxoplasma_Replicate 2

description: RNA input amount: 2ug; Hybridization date: 06/17/2005; Array lot: 4005095

source_name: Retinal endothelial cell, Toxoplasma gondii, 4 hours

value: 44 years

value: Toxoplasma gondii


title: Choroidal endothelial cell_Human 3_Stimulated.Toxoplasma_Replicate 1

source_name: Choroidal endothelial cell, Toxoplasma gondii, 4 hours


title: Choroidal endothelial cell_Human 3_Unstimulated_Replicate 1


title: Choroidal endothelial cell_Human 3_Stimulated.Toxoplasma_Replicate 2


title: Choroidal endothelial cell_Human 2_Unstimulated_Replicate 1

description: RNA input amount: 1.5ug; Hybridization date: 03/01/2005; Array lot: 4005095

value: 37 years


title: Retinal endothelial cell_Human 3_Stimulated.Toxoplasma_Replicate 1


title: Retinal endothelial cell_Human 2_Stimulated.Toxoplasma_Replicate 1


title: Retinal endothelial cell_Human 3_Unstimulated_Replicate 1


title: Choroidal endothelial cell_Human 2_Unstimulated_Replicate 2


title: Choroidal endothelial cell_Human 2_Stimulated.Toxoplasma_Replicate 1


title: Choroidal endothelial cell_Human 3_Unstimulated_Replicate 2


title: Retinal endothelial cell_Human 2_Unstimulated_Replicate 2


title: Retinal endothelial cell_Human 2_Stimulated.Toxoplasma_Replicate 2


title: Choroidal endothelial cell_Human 1_Unstimulated_Replicate 2

description: RNA input amount: 1ug; Hybridization date: 10/08/2004; Array lot: 4003908

value: 4 years


title: Retinal endothelial cell_Human 1_Stimulated.Toxoplasma_Replicate 2


title: Choroidal endothelial cell_Human 1_Unstimulated_Replicate 1


title: Retinal endothelial cell_Human 2_Unstimulated_Replicate 1


title: Retinal endothelial cell_Human 1_Stimulated.Toxoplasma_Replicate 1


title: Choroidal endothelial cell_Human 1_Stimulated.Toxoplasma_Replicate 1


title: Choroidal endothelial cell_Human 1_Stimulated.Toxoplasma_Replicate 2


title: Choroidal endothelial cell_Human 2_Stimulated.Toxoplasma_Replicate 2


title: Retinal endothelial cell_Human 1_Unstimulated_Replicate 1


title: Soybean_Cotyledon_OI2

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Outer integument regions from cotyledon-stage seeds were microdissected using the LEICA LMD6000 system.

hyb_protocol: Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45°C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.

organism: Glycine max

source_name: Soybean cotyledon-stage outer integument captured by LCM

label_protocol: Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22°C.

extract_protocol: Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Seeds with length between 2.5 and 3.0 mm containing cotyledon-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from eight-micron sections using a Leica LMD6000 system.

tag: Laser capture microdissected (LCM) outer integument at the cotyledon stage, biological replicate 2

tag: Soybean cv. Asgrow A3237


title: Soybean_Cotyledon_SEED2

description: Whole seeds containing cotyledon-stage embryos were ground in liquid nitrogen using a mortar and pestle.

source_name: Soybean cotyledon-stage seed

extract_protocol: Total RNA was extracted using Plant RNA Isolation Reagent (Invitrogen, Carlsbad, CA).

tag: Whole Seed at the cotyledon stage, biological replicate 2


title: Soybean_Cotyledon_SEED1

tag: Whole Seed at the cotyledon stage, biological replicate 1


title: Soybean_Cotyledon_II2

description: Inner integument regions from cotyledon-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean cotyledon-stage inner integument captured by LCM

tag: Laser capture microdissected (LCM) inner integument at the cotyledon stage, biological replicate 2


title: Soybean_Cotyledon_OI1

tag: Laser capture microdissected (LCM) outer integument at the cotyledon stage, biological replicate 1


title: Soybean_Cotyledon_EPD2

description: Epidermis regions from cotyledon-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean cotyledon-stage epidermis captured by LCM

tag: Laser capture microdissected (LCM) epidermis at the cotyledon stage, biological replicate 2


title: Soybean_Cotyledon_HI2

description: Hilum regions from cotyledon-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean cotyledon-stage hilum captured by LCM

tag: Laser capture microdissected (LCM) hilum at the cotyledon stage, biological replicate 2


title: Soybean_Cotyledon_II1

tag: Laser capture microdissected (LCM) inner integument at the cotyledon stage, biological replicate 1


title: Soybean_Cotyledon_HI1

tag: Laser capture microdissected (LCM) hilum at the cotyledon stage, biological replicate 1


title: SVGR2 subclone 4-E12 GeneChip U133B


title: SVGR2 subclone 1-C4 GeneChip U133B


title: Soybean_Cotyledon_EPD1

tag: Laser capture microdissected (LCM) epidermis at the cotyledon stage, biological replicate 1


title: SVG-A subclone 4-G5 GeneChip U133B


title: SVG-A subclone 3-D6 GeneChip U133B


title: SVGR2 subclone 4-F6 GeneChip U133B


title: Soybean_Cotyledon_EN2

description: Endothelium regions from cotyledon-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean cotyledon-stage endothelium captured by LCM

tag: Laser capture microdissected (LCM) endothelium at the cotyledon stage, biological replicate 2


title: Soybean_Cotyledon_SUS2

description: Suspensor regions from cotyledon embryos were microdissected using the LEICA LMD6000 system.

source_name: Soybean cotyledon-stage suspensor captured by LCM

tag: Laser capture microdissected (LCM) suspensor at the cotyledon stage, biological replicate 2


title: Soybean_Cotyledon_ES2

description: Endosperm regions from cotyledon-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean cotyledon-stage endosperm captured by LCM

tag: Laser capture microdissected (LCM) endosperm at the cotyledon stage, biological replicate 2


title: Soybean_Cotyledon_EP1

description: Embryo proper regions from cotyledon embryos were microdissected using the LEICA LMD6000 system.

source_name: Soybean cotyledon-stage embryo proper captured by LCM

tag: Laser capture microdissected (LCM) embryo proper at the cotyledon stage, biological replicate 1


title: Soybean_Cotyledon_SUS1

tag: Laser capture microdissected (LCM) suspensor at the cotyledon stage, biological replicate 1


title: Soybean_Cotyledon_EN1

tag: Laser capture microdissected (LCM) endothelium at the cotyledon stage, biological replicate 1


title: SVG-A subclone 1-D4 GeneChip U133B

tag: SVG-A glial cells


title: Soybean_Cotyledon_ES1

tag: Laser capture microdissected (LCM) endosperm at the cotyledon stage, biological replicate 1

tag: Soybean cv. Asgrow A3237


title: Soybean_Cotyledon_EP2

tag: Laser capture microdissected (LCM) embryo proper at the cotyledon stage, biological replicate 2


title: ED14-MMH_Prox1_rep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = Met murine hepatocytes - Hex - HNF4a - MMP-2 - Type-IV collagen

hyb_protocol: - hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 micro gram labeled DNA per channel were mixed no fractionation probes were denatured for 3 min at 98 degree celcius hybridization at 63 degree celcius SSPE washes as recommended slides were dipped in acetonitril (10 s) then dried

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: 'Automic Imageprocessing for Microarrays' (for details: http://www.techfak.uni-bielefeld.de/ags/ai/projects/microarray/)

data_processing:
- dye swap design
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- afterwards we did a scaling procedure by division of each value with the standard deviation of the normalized log2-ratios (variance normalization)
- as statistical software we use 'R'

organism: Mus musculus

label_protocol:
- totalRNA was transcribed, amplified and labeled according to BD Atlas SMART fluorescent probe amplification kit with following modifications:
- RNA template was hydrolized after transcription (high pH, 30 min/70 degree celcius)
- PCR amplification progress was monitored and stopped before reaching saturation

extract_protocol:
- RNA was isolated with RNeasy kit (Qiagen) according to the manufactures standard protocol
- Subsequent DNase I treatment

tag: Geneticin regulated met-murine-hepatocyte cell line treated with an empty vector.

tag: Geneticin regulated met-murine-hepatocyte cell line transfected with Prox1.


title: ED14-MMH_Prox1_rep3


title: ED14-MMH_Prox1_rep6

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: 'Automatic Imageprocessing for Microarrays' (for details: http://www.techfak.uni-bielefeld.de/ags/ai/projects/microarray/)


title: T8 u112 B

status: Public on May 23 2007

city: San Francisco

first: Sajeev

last: Batra

institute: UCSF

description: T8 u112 B

hyb_protocol: Cy5 labeled sample was hybridized to the MEEBO array in 3 SSC at 63C 36 hours."

scan_protocol: MEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using the bundled GenePix 3.0 software."

data_processing: Spot analysis was performed with GenePix v3.0 and stored in a relational database (NOMAD).

source_name: Amplified RNA from bone marrow derived macrophages from female mice 2 months old C57/bl6

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then labeled with Cy5 using cyTM dye Post-labelling Reactive Dye pack (Amersham)."

extract_protocol: 1000000 macrophages were lysed in 1mL Trizol and flashed frozen in liquid nitrogen. Total RNA was extracted with chloroform, followed by Ethanol precipitation and purification using RNeasy kit (Qiagen USA, Valencia, CA)"

source_name: mouse universal reference RNA (Stratagene)

label_protocol: RNA from the Mouse Universal reference (Stratagene) was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then labeled with Cy3 using cyTM dye Post-labelling Reactive Dye pack (Amersham)?

tag: Universal RNA reference pool


title: ED14-MMH_Prox1_rep4

extract_protocol:
- Trizol (Invitrogen) isolation according to the manufactures standard protocol
- Subsequent DNase I treatment


title: ED14-MMH_Prox1_rep1

extract_protocol:
- RNA of the cells was isolated with RNeasy kit (Qiagen) according to the manufactures standard protocol
- Subsequent DNase I treatment


title: T8 mglA A

description: T8 mglA A

tag: Amplified RNA from bone marrow derived macrophages

extract_protocol: RNA from the Mouse Universal reference (Stratagene)


title: T8 mglA B

description: T8 mglA B


title: T8 u112 A

description: T8 u112 A


title: U112 A

description: U112 A


title: ED14-MMH_Prox1_rep5


title: T8 uninfected B

description: T8 uninfected B


title: T8 uninfected A

description: T8 uninfected A


title: Choroidal endothelial cell_Human 5_Unstimulated_Replicate 1

source_name: Choroidal endothelial cell, medium alone, 4 hours

tag: Gender

tag: Age

tag: Cell

tag: Stimulus


title: mgl A

description: mgl A


title: T4 u112 B

description: T4 u112 B


title: T1 uninfected A

description: T1 uninfected A


title: Feeder dependent ES cell line V6.5 (duplicate)

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

hyb_protocol: 1.65microgram of cRNA was fragmented and hybridized to Agilent  whole mouse genome oligo microarray kit G4122F using manufacturers instructions.

scan_protocol: Scanned by Agilent Software

data_processing: Signals were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.

source_name: ES Cells

label_protocol: Labeled  cRNA was prepared from 0.5 microgram of RNA using the Agilent one color labeling protocol

extract_protocol: RNA was extracted using the RNA easy Mini kit from Qiagen

tag: Feeder Dependent ES Cell Line V6.5


title: T1 u112 A

description: T1 u112 A


title: T1 mglA B

description: T1 mglA B


title: T1 u112 B

description: T1 u112 B


title: T4 mglA B

description: T4 mglA B


title: Feeder dependent ES cell line V6.5

tag: Feeder dependent ES cell line V6.5


title: Female Mouse Embryonic Fibroblast (duplicate)

source_name: Mouse Embryonic Fibroblast

tag: Female Mouse Embryonic Fibroblast


title: E.coli_BCadapted2_replicate2_50ppmBC

city: Aas

first: Solveig

last: Langsrud

address: Osloveien 1

country: Norway

institute: Matforsk, Norwegian Food Research Institute

description: The arrays were stripped between hybridisations according to the PanoramaTM E. coli gene arrays technical protocol (Sigma Genosys).

hyb_protocol: Purified labeled cDNA were hybridised to the PanoramaTM E. coli gene array, according to supplied protocol. [33P] dCTP from Amersham Bioscience was used for all hybridisations.

scan_protocol: The membranes were wrapped in clear plastic film and exposed to a Storage Phosphore Screen (Amersham Biosciences) for 6-7 days. After exposure the screens were scanned with Thyphoon 8600 variable mode imager (Amersham Biosciences).

data_processing: The software Imagene (BioDiscovery) was used for quantification of data and the software Genespring (Silicon Genetics) for normalisation. Pixel density for each spot was determined by laying down a grid of individual circles corresponding to each spot and the grid template for E. coli K-12 (Sigma genosys) was loaded for gene identification of each spot. No genes were flagged or no cut-off were made before normalisation in GeneSpring. The data was normalised by subtracting background based on all empty spots (negative controls) on the array. In addition each array was normalised to 50th percentile to adjust signal intensity of each array to all arrays. Each array was defined as independent samples in further data analysis.

organism: Escherichia coli

source_name: E. coli adapted in benzalkonium chloride

label_protocol: Labeled cDNA was prepared according to the PanoramaTM E. coli gene array protocol (Sigma Genosys), with some modifications. SuperscriptTM II Rnase H- Reverse Transcriptase (Invitrogen) and Sheared Salmon Sperm DNA (Ambidon) replaced equivalent components given in the Panorama protocol. The unincorporated nucleotides were removed with MicroSpinTM G-25 columns (Amersham Pharmacia Biotech), according to given protocol.

growth_protocol: Frozen cultures were inoculated in 5 ml TSB and incubated over-night. One ml culture was inoculated in 99 ml TSB with 50 µg ml-1 benzalkonium chloride in 500 ml baffled shake flask and incubated at 37 oC with shaking. Bacterial cells were harvested at mid log phase (~108 CFU ml-1).

extract_protocol: Bacterial cells were harvested directly from shake flask into RNAprotect (Qiagen) to secure stable RNA before cell lysis. One volume of culture (1x108 CFU ml-1) was added to two volumes of RNA protect, vortexed and incubated at room temperature for 5 min. The sample was then centrifuged at 5000 g for 10 min and the supernatant removed.Total RNA was isolated using RNeasy mini kit (Qiagen) according to the manufacturer’s recommendations. The concentration of RNA was determined by measuring the absorbance at 260 nm and 280 nm in an Ultrospec 3000 spectrophotometer (Pharmacia Biotech). The ratio between the measured absorbance at the two wavelengths shows an estimate of RNA purity with respect to contamination. (Qiagen Bench guide). RNA degradation was checked with an Agilent 2100 Bioanalyzer according to userguide from Agilent Technologies. Before cDNA labelling, variations in RNA concentrations were adjusted to 1 µg µl-1 for all array hybridizations.

treatment_protocol: Frozen cultures were inoculated in 5 ml TSB and incubated over-night. Two drops culture was inoculated in 5 ml TSB with benzalkonium chloride (BC) in a range of concentrations in 2 µg ml-1 steps. The cultures were incubated over night (20-24 h) and inspected visually for growth. The tube with highest BC concentration with visible growth was reinoculated (two drops) in tubes with fresh TSB, with a range of BC-concentrations in steps of 2 µg ml-1. The cultures were incubated over-night and inspected visually for growth. This procedure was continued in a total of 30-40 days until five reinoculations did not result in growth at higher concentrations of BC.

tag: E. coli K-12 ATCC47076 adapted to grow in benzalkonium chloride and pregrown in 50 ppm benzalkonium chloride


title: Induced Pluripotent Stem Cells

source_name: Induced Pluripotent Stem Cells

tag: Induced Pluripotent Stem Cells


title: Induced Pluripotent Stem Cells (duplicate)


title: Female Mouse Embryonic Fibroblast


title: T1 mglA A

description: T1 mglA A


title: uninfected A

description: uninfected A


title: E.coli_BCadapted3_replicate2_50ppmBC


title: E.coli_BCadapted1_replicate1_50ppmBC


title: E.coli_BCadapted1_replicate2_50ppmBC


title: E.coli_BCadapted3_replicate1_50ppmBC


title: E.coli_BCadapted3_replicate3_50ppmBC


title: E.coli_BCadapted2_replicate3_50ppmBC


title: E.coli_BCadapted2_replicate1_50ppmBC


title: E.coli_BCadapted1_replicate3_50ppmBC


title: E.coli_BCadapted3_replicate1

growth_protocol: Frozen cultures were inoculated in 5 ml TSB and incubated over-night. One ml culture was inoculated in 99 ml TSB in 500 ml baffled shake flask and incubated at 37 oC with shaking. Bacterial cells were harvested at mid log phase (~108 CFU ml-1).

tag: E. coli K-12 ATCC47076 adapted to grow in benzalkonium chloride


title: E.coli_BCadapted3_replicate3


title: E.coli_BCadapted3_replicate2


title: E.coli_BCadapted2_replicate1


title: E.coli_BCadapted1_replicate2


title: E.coli_BCadapted2_replicate3


title: E.coli_control_replicate2A

source_name: E. coli control

treatment_protocol: Frozen cultures were inoculated in 5 ml TSB and incubated over-night. One ml culture was inoculated in 99 ml TSB in 500 ml baffled shake flask and incubated at 37 oC with shaking. Bacterial cells were harvested at mid log phase (~108 CFU ml-1).

tag: E. coli K-12 ATCC47076


title: E.coli_control_replicate1B


title: E.coli_control_replicate3


title: E.coli_BCadapted2_replicate2


title: E.coli_control_replicate1A


title: sim_(105X6)_rep3

city: Ithaca

first: Jason

last: Mezey

state: NY

address: 101 Biotechnology Building, Cornell University

department: BSCB

institute: Cornell University

description: Gene expression data for adults 3 days postpupation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Drosophila Genome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix chips and scanner 3000

data_processing: The data were analyzed with Bioconductor Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Drosophila simulans

source_name: Drosophila adults three days postpupation

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

growth_protocol: vials of standard cornmeal medium with yeast at 25 C on a continuous light cycle.

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

treatment_protocol: 20 males knocked down by CO2

tag: 3 day old adult males


title: E.coli_control_replicate2B


title: sim_(99X105)_rep2


title: sim_(105X6)_rep1


title: sim_(105X6)_rep2


title: sim_(99X105)_rep1


title: sim_(99X105)_rep3


title: sim_(85X99)_rep2


title: T1 uninfected B

description: T1 uninfected B


title: sim_(77X85)_rep3


title: sim_(61X77)_rep3


title: sim_(85X99)_rep1


title: sim_(77X85)_rep2


title: sim_(77X85)_rep1


title: sim_(85X99)_rep3


title: sim_(43 X 61)_rep3


title: sim_(37X43)_rep2


title: sim_(43 X 61)_rep2


title: Young Men_Creatine Monohydrate Supplementation_subject11

city: Hamilton

first: Adeel

last: Safdar

state: ON

address: 1200 Main Street West

department: Kinesiology

country: Canada

institute: McMaster University

description: S3 - CrM vs. PL

hyb_protocol: Using a Lucidea Slide Pro machine, a human cDNA array (custom print) is loaded into the slide chamber. The cDNA probe (Cy3 and Cy5 and/or Control and Experimental) is mixed with a formamide hybe buffer, dextran sulfate and LNA and Cot-1 DNA blocker and then loaded into the slide chamber and with a slow mixing program, the cDNA probe is circulated over the array for 18 hours at a temperature of 50degreesC. The array is then washed with  2XSSC+0.2%SDS, 2XSSC and then 0.2XSSC, afterwards, the dendromer (Cy3/Cy5) is mixed with hybe buffer, Cot DNA, dextran sulfate and anti-fade and loaded into the slide chamber. The fluorescent dendromer is captured by the bound cDNA sequences on the array. The probe is circulated for 3 hours at 50degreesC, and then washed and scanned.

scan_protocol: The array was scanned using a Scan Array Express scanner. Control spots from each channel were first normalized with a test scan, by adjusting the PMT and POW settings. Then the array was scanned at 10um. The fist channel was Cy5 and the second channel was Cy3.

data_processing: The Cy5 and Cy3 images are analyzed using GenePix software and a gal file.

source_name: Amplified RNA (aRNA) from muscle biopsy.

label_protocol: 200 nanograms of amplified RNA was labeled using Genisphere's 350RP kit, which uses a two-step labeling process. First the aRNA is reverse transcribed and then ligated with a Cy3/Cy5 probe that has a capture sequence that will bind Cy3/Cy5.

extract_protocol: The total RNA was extracted from the skeletal muscle biopsy as described previously in detail by our group (Mahoney et al., 2004).  Briefly, ~25 mg of skeletal muscle was homogenized on ice in 1 mL of Trizol Reagent (Life Technologies, Cat. No.15596, Gaithersburg, MD).  The homogenate was incubated for 10 min at room temperature, followed by phase separation using 200 μL of chloroform and precipitation of the total RNA from the aqueous phase using 500 μL of isopropyl alcohol.  The RNA pellet was then washed three times in 75% ethanol and was re-suspended in 15 μL DEPC-treated water, aliquotted, and stored at -86°C.  We assessed total RNA quality by measuring the size distribution on an Agilent Bioanalyzer (1.0-1.5 kb, Agilent Technologies, Inc., Santa Clara, CA) and by measuring the spectrophotometric 260/280 ratio (>1.8). Prior to cDNA microarray analysis, the isolated RNA samples were treated with DNA-free DNase I (Ambion Inc, Austin, TX) according to the manufacturer’s instructions to remove any potential genomic DNA contamination. mRNA was amplified in a linear fashion using MessageAmp aRNA kit (Ambion Inc, Austin, TX) according to the manufacturer’s instructions.

treatment_protocol: In a randomized, placebo-controlled, crossover, double-blind design, 12 young, healthy, non-obese men were supplemented with either a placebo or creatine monohydrate (loading phase, 20 g/d x 3 d; maintenance phase, 5 g/d x 7 d) for 10 d.  Following a 28 day washout period, subjects were put on the alternate supplementation for 10 days.  Muscle biopsies of the vastus lateralis were obtained and immediately placed in RNase-free cryoviles, flash-frozen in liquid nitrogen, and stored at -86°C until further analysis.

tag: Young Men on Placebo

tag: Young Men wit Creatine Monohydrate Supplementation.


title: Young Men_Creatine Monohydrate Supplementation_subject12

description: S6 - CrM vs. PL


title: E.coli_BCadapted1_replicate1


title: sim_(43 X 61)_rep1


title: sim_(61X77)_rep1


title: Young Men_Creatine Monohydrate Supplementation_subject8

description: S12 - CrM vs. PL


title: sim_(37X43)_rep1


title: sim_(36X37)_rep3


title: Young Men_Creatine Monohydrate Supplementation_subject9

description: S16 - CrM vs. PL


title: sim_(36X37)_rep2


title: sim_(37X43)_rep3


title: sim_(61X77)_rep2


title: Young Men_Creatine Monohydrate Supplementation_subject10

description: S2 - CrM vs. PL


title: Young Men_Creatine Monohydrate Supplementation_subject7

description: S14 - CrM vs. PL


title: Young Men_Creatine Monohydrate Supplementation_subject4

description: S10 - CrM vs. PL


title: sim_(36X37)_rep1


title: Young Men_Creatine Monohydrate Supplementation_subject3

description: S9 - CrM vs. PL


title: sim_(11X36)_rep3


title: sim_(11X36)_rep2


title: Young Men_Creatine Monohydrate Supplementation_subject5

description: S13 - CrM vs. PL


title: san_rep3

organism: Drosophila santomea


title: sim_(6X11)_rep1


title: Pediococcus inopinatus and Pectinatus cerevisiiphilus detected by microarray

city: Bochum

first: Daniel

middle: Gilbert

last: Weber

address: Bürkle-de-la-Camp Platz 1

department: Molekulare Medizin

institute: IPA

description: RT-PCR amplification. All plastic wares were treated with 0.1% DEPC at 37°C over night and autoclaved. The RT-PCR amplification was carried out using T3 Thermocycler (Whatman Biometra, Göttingen, Germany). The RT reaction mixture contained 2.5 μl  pd(N)6 random hexamer 5´-phosphate [500 ng/μl]  (Roche, Darmstadt, Germany), 20 mM deoxynucleoside triphosphates, 0.5 μl T4 gene 32 protein [5 mg/ml] (Roche Diagnostics, Mannheim, Germany), 2 μl H2O and a maximum of 1.5 μg RNA. Samples were incubated at 65°C for 5 min, immediately chilled on ice and centrifuged. 4 μl First-strand buffer (Invitrogen, Carlsberg, USA), 2 μl 0.1 M DTT, 1 μl 2.5 mM MgCl2 and 40 U RNase-Inhibitor (Roche Diagnostics, Mannheim, Germany) were added to the mixture and incubated at 42°C for 2 min. Then, 200 U SuperScript II (Invitrogen, Carlsberg, USA) were added to the mixture and incubated at 42°C for 50 min followed by an incubation at 70°C for 15 min. An aliquot of 5 μl of the RT reaction mixture was used for PCR amplification. The PCR reaction mixture contained 5 μl 10x PCR buffer (Invitrogen, Carlsberg, USA), 2 mM deoxynucleoside triphosphates, 10 pmol of each primer (MWG AG Biotech, Ebersberg, Germany), 1.5 mM MgCl2, 5 U Taq-Polymerase (Invitrogen, Carlsberg, USA) in a total reaction volume of 50 μl. Samples were initially denatured at 94°C for 3 min, followed by 40 sequential cycles, denaturation at 95°C (1 min), annealing at 40°C (1 min), extension at 72°C (1 min) and a final extension at 72°C for 5 min followed by a cooling step down to 4°C. PCR products were analysed for correct size by agarose gel electrophoresis and ethidium bromide staining.

hyb_protocol: 1 μg Cy3-labeled cDNA was mixed with 3 μl 20x SSC, 0.5 μl 1 M HEPES (pH 7) and 0.5 μl 10% SDS, heated to 99°C for 2 min, chilled on ice, incubated at room temperature for 5 min, applied to the microarrays which were covered with a lifterslip (Erie Scientific Company, Portsmouth, USA) and incubated for 12 to 16 hours at 30°C in a moist chamber (1x SSC). After hybridization the microarrays were washed in a solution containing 2x SSC and 0.1% SDS, then in 1x SSC and then in 0.5x SSC. After washing microarrays were dried by centrifugation (15 min at 50 x g).

scan_protocol: After drying the microarrays the fluorescence at 532 nm (Cy3) was determined using an Axon Inc. GenePix 4000 laser scanner (Axon, Union City, USA). Acquired raw fluorescence data were stored as image files in TIFF format and were analysed quantitatively by using GenePix Pro 3.0 software (Axon, Union City, USA).

data_processing: Signal was defined of median spot fluorescence signal at 532 nm wavelength (F532) minus median background fluorescence signal (B532), defined by surrounding pixel intensity and the mean value of 70 replicate spots was calculated.

organism:
Pectinatus cerevisiiphilus
Pediococcus inopinatus

source_name: Beer spoilage bacteria

label_protocol: The cDNA was labeled with Cy3-fluorescent dyes using the Mirus Label IT-Kit (MoBiTec, Göttingen, Germany) according to the manufacturer’s instructions.

growth_protocol: Pediococcus inopinatus was cultured at 20°C in De Man-Rogosa-Sharpe MRS medium. Pectinatus cerevisiiphilus was cultured under anaerobic conditions at 30°C in peptone-yeast extract plus Fildes solution medium.

extract_protocol: Portions (40 ml) of exponentially growing cultures (OD600 of ~0.8) were chilled on ice and cells were harvested immediately by centrifugation (10 min, 300 x g, 4°C). All plastic wares were treated with 0.1% DEPC at 37°C over night and autoclaved. Total RNA was isolated according to Hurt et al. (2001) with several modifications. All steps were performed at 4°C. The samples were saturated with 170 μl denaturation solution containing 0.85 μl 2-mercaptoethanol and 1.5 ml extraction buffer and incubated for 30 min at 65°C, gently mixing and centrifuged at 1800 x g for 10 min. The supernatants were poured into tubes and chilled on ice. The pellet was resuspended in 830 μl extraction buffer, incubated for 10 min at 65°C gently mixing and centrifugated at 1800 x g for 10 min. The supernatants were combined, the same volume of phenol-chloroform was added and the sample was centrifugated at 1800 x g for 20 min. The aqueous phase was transferred to a new tube and precipated with 0.6 volumes ice cold ethanol (100%) at -20°C over night. The sample was centrifugated at 16000 x g for 20 min, washed with ice cold ethanol (70%) and centrifugated at 16000 x g for 10 min. The pellet was dried at 4°C and resuspended in 200 μl H2O. RNA concentration was determined by measurement the optical density at 260 nm (OD260).

tag: Pediococcus inopinatu DSMZ 20285 (T), Pectinatus cerevisiiphilus DSMZ 20467 (T)


title: yak_rep2

organism: Drosophila yakuba


title: Lactobacillus brevis and Pectinatus frisingensis detected by microarray

organism:
Pectinatus frisingensis
Levilactobacillus brevis

growth_protocol: Lactobacillus brevis was cultured at 30°C in De Man-Rogosa-Sharpe MRS medium. Pectinatus frisingensis was cultured under anaerobic conditions at 30°C in peptone-yeast extract plus Fildes solution medium.

tag: Lactobacillus brevis Isolate from Beck & Co., Bremen, Germany, Pectinatus frisingensis DSM 6306 (T)


title: sim_(6X11)_rep2


title: san_rep2


title: Young Men_Creatine Monohydrate Supplementation_subject1

description: S11 - CrM vs. PL


title: Young Men_Creatine Monohydrate Supplementation_subject2

description: S4 - CrM vs. PL


title: san_rep1


title: Pectinatus frisingensis detected by microarray

organism: Pectinatus frisingensis

growth_protocol: Pectinatus frisingensis was cultured under anaerobic conditions at 30°C in peptone-yeast extract plus Fildes solution medium.


title: sim_(6X11)_rep3


title: Lactobacillus brevis detected by microarray

organism: Levilactobacillus brevis

growth_protocol: Lactobacillus brevis was cultured at 30°C in De Man-Rogosa-Sharpe MRS medium.

tag: Isolate from Beck & Co., Bremen, Germany


title: Young Men_Creatine Monohydrate Supplementation_subject6

description: S15 - CrM vs. PL


title: yak_rep3


title: yak_rep1


title: sim_(11X36)_rep1


title: tei_rep1

organism: Drosophila teissieri


title: tei_rep2


title: T4 uninfected B

description: T4 uninfected B

tag: Amplified RNA from bone marrow derived macrophages

tag: Universal RNA reference pool


title: Megasphaera cerevisiae/Pectinatus cerevisiiphilus mix detected by microarray

organism:
Megasphaera cerevisiae
Pectinatus cerevisiiphilus

growth_protocol: Pectinatus cerevisiiphilus was cultured at 30°C under anaerobic conditions in peptone-yeast extract plus Fildes solution medium.

tag: Megasphaera cerevisiae DSMZ 20462(T), Pectinatus cerevisiiphilus DSMZ 20467 (T)


title: Pectinatus cerevisiiphilus detected by microarray

organism: Pectinatus cerevisiiphilus


title: Megasphaera cerevisiae detected by microarray

organism: Megasphaera cerevisiae

growth_protocol: Megasphaera cerevisiae was cultured at 30°C under anaerobic conditions in peptone-yeast extract plus Fildes solution medium.


title: Pediococcus inopinatus detected by microarray

organism: Pediococcus inopinatus

growth_protocol: Pediococcus inopinatus was cultured at 30°C in De Man-Rogosa-Sharpe MRS medium.


title: mau_rep1

organism: Drosophila mauritiana


title: mau_rep2


title: mau_rep3


title: tei_rep3


title: Pediococcud damnosus detected by microarray

organism: Pediococcus damnosus

growth_protocol: Pediococcus damnosus was cultured at 30°C in De Man-Rogosa-Sharpe MRS medium.


title: sec_rep2

organism: Drosophila sechellia


title: Sox2-KO, Tet(+), 96hr - #1(251411710013)

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Sox2-KO, Tet(-), 96hr

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.   The manual can be found at  https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961,  or through a WEB search on the manual title.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Mus musculus

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: TROZOL standard extraction method. The full protocol can be found in the Life Technologies CAT 15596. The following are the steps we used. 1.Homogenize tissue samples in 1 mL of TRIZOL Reagent per 50-100 mg of tissue using a glass-Teflon® or power homogenizer (Polytron, or Tekmar's TISSUMIZER® or equivalent). The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.  3.PHASE SEPARATION Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 4. RNA PRECIPITATION Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 5. RNA WASH Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8°C. 6. REDISSOLVING THE RNA At the end of the procedure, briefly dry the RNA pellet (ai

tag: embryonic stem cell 129/Ola   Transgenic and Knock down

source_name: Universal Mouse Reference Cell Line Pool

growth_protocol: The UMRR is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the UMRR for use as follows: 1.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  2.Carefully remove the supernatant. 3.Wash the pellet in 70% ethanol. 4.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: sec_rep3


title: Embryonic Fibroblast Line (MEF2) H3me3K4 Promoter Methylation ChIP-Chip (1/2)

type: genomic

hyb_protocol: Hybridization onto the mouse promoter array, which includes 244K features distributed onto two slides (Agilent –G4490), washing and scanning were carried out according to the manufacturers instructions.

scan_protocol: According to Agilent Scanning Software

data_processing: Log ratios were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.

molecule: genomic DNA

source_name: Embryonic Fibroblast (MEF2)

label_protocol: 10ng of each immuoprecipitated sample and corresponding inputs were amplified using the Whole Genome Amplification Kit (Sigma), and 2ug of amplified material was labeled with Cy5 (Perkin Elmer) using the Bioprime Kit (Invitrogen).

growth_protocol: Standard ESC media conditions

extract_protocol: Genome wide chromatin analysis ChIP was performed with about 1 million cells following the protocol on www.upstate.com. The cells were crosslinked with formaldehyde for 10 min at room temperature, subsequently lysed in 10mM Tris-EDTA pH 8.0 with 1%SDS, and sonicated on ice 6 times at 15 second pulses interrupted by 45 second pauses.  Clarified sheared chromatin was immunoprecipitated with antibodies to H3me3K4 (Abcam 8580) overnight at 4 C, collected with protein A beads for 2 hours, washed twice for 5 min and eluted with buffers (recipes on the Upstate website). Eluates were reverse crosslinked, RNAse and proteinase K treated, and DNA was purified using the Qiagen PCR purification kit.

tag: Elute from a histone H3 trimehtylated K4 chromatin immunoprecipitation

label_protocol: 10ng of each immuoprecipitated sample and corresponding inputs were amplified using the Whole Genome Amplification Kit (Sigma), and 2ug of amplified material was labeled with Cy3 (Perkin Elmer) using the Bioprime Kit (Invitrogen).

tag: Input for histone H3 trimehtylated K4 chromatin immunoprecipitation


title: Sox2-KO, Tet(+), 72hr - #1(251411710011)

description: Sox2-KO, Tet(-), 72hr


title: Lactobacillus perolens detected by microarray

organism: Schleiferilactobacillus perolens

growth_protocol: Lactobacillus perolens was cultured at 30°C in De Man-Rogosa-Sharpe MRS medium.

tag: DSMZ 12745 (T) - Deposited by I. Bohak, TU München, Technologie der Brauerei I, 85350 Freising-Weihenstephan, Germany.


title: Sox2-KO, Tet(+), 24hr - #1(251411710008)

description: Sox2-KO, Tet(-), 24hr


title: Lactobacillus coryniiformis detected by microarray

organism: Loigolactobacillus coryniformis

growth_protocol: Lactobacillus coryniiformis was cultured at 30°C in De Man-Rogosa-Sharpe MRS medium.


title: Sox2-KO, Tet(+), 6hr - #2(251411710006)

description: Sox2-KO, Tet(-), 6hr


title: Sox2-KO, Tet(+), 12hr - #1(251411710007)

description: Sox2-KO, Tet(-), 12hr


title: Sox2-KO, Tet(+), 24hr - #2(251411710009)

description: Sox2-KO, Tet(-), 24hr


title: sec_rep1


title: Sox2-KO, Tet(-), 0hr - #2(251411710002)

description: Sox2-KO, Tet(-), 0hr


title: Embryonic Stem Cell Line (V6.5) H3me3K27 Promoter Methylation ChIP-Chip (1/2)

source_name: ES Cell Line V6.5

extract_protocol: Genome wide chromatin analysis ChIP was performed with about 1 million cells following the protocol on www.upstate.com. The cells were crosslinked with formaldehyde for 10 min at room temperature, subsequently lysed in 10mM Tris-EDTA pH 8.0 with 1%SDS, and sonicated on ice 6 times at 15 second pulses interrupted by 45 second pauses.  Clarified sheared chromatin was immunoprecipitated with antibodies to H3me3K27 (Upstate 07-449) overnight at 4 C, collected with protein A beads for 2 hours, washed twice for 5 min and eluted with buffers (recipes on the Upstate website). Eluates were reverse crosslinked, RNAse and proteinase K treated, and DNA was purified using the Qiagen PCR purification kit.

tag: Elute from a histone H3 trimehtylated K27 chromatin immunoprecipitation

tag: Input for histone H3 trimehtylated K27 chromatin immunoprecipitation


title: Sox2-KO, Tet(+), 48hr - #1(251411710010)

description: Sox2-KO, Tet(-), 48hr


title: Sox2-KO, Tet(+), 3hr - #1(251411710003)

description: Sox2-KO, Tet(-), 3hr


title: Embryonic Stem Cell Line (E14) H3me3K27 Promoter Methylation ChIP-Chip (1/2)

source_name: ES Cell Line E14

extract_protocol: Genome wide chromatin analysis ChIP was performed with about 1 million cells following the protocol on www.upstate.com. The cells were crosslinked with formaldehyde for 10 min at room temperature, subsequently lysed in 10mM Tris-EDTA pH 8.0 with 1%SDS, and sonicated on ice 6 times at 15 second pulses interrupted by 45 second pauses.


title: Lactobacillus casei detected by microarray

organism: Lacticaseibacillus casei

growth_protocol: Lactobacillus casei was cultured at 30°C in De Man-Rogosa-Sharpe MRS medium.


title: Embryonic Fibroblast Line (MEF2) H3me3K27 Promoter Methylation ChIP-Chip (1/2)

description: Female MEFs

extract_protocol: Genome wide chromatin analysis ChIP was performed with about 1 million cells following the protocol on www.upstate.com. The cells were crosslinked with formaldehyde for 10 min at room temperature, subsequently lysed in 10mM Tris-EDTA pH 8.0 with 1%SDS, and sonicated on ice 6 times at 15 second pulses interrupted by 45 second pauses. Clarified sheared chromatin was immunoprecipitated with antibodies to H3me3K27 (Upstate 07-449) overnight at 4 C, collected with protein A beads for 2 hours, washed twice for 5 min and eluted with buffers (recipes on the Upstate website). Eluates were reverse crosslinked, RNAse and proteinase K treated, and DNA was purified using the Qiagen PCR purification kit.


title: mel_rep2

organism: Drosophila melanogaster


title: Sox2-KO, Tet(+), 72hr - #2(251411710012)

description: Sox2-KO, Tet(-), 72hr


title: Embryonic Stem Cell Line (V6.5) H3me3K4 Promoter Methylation ChIP-Chip (1/2)


title: Sox2-KO, Tet(+), 6hr - #1(251411710005)

description: Sox2-KO, Tet(-), 6hr


title: mel_rep3


title: Embryonic Stem Cell Line (V6.5) H3me3K4 Promoter Methylation ChIP-Chip (2/2)


title: Induced Pluripotent (iPS) Cells H3me3K27 Promoter Methylation ChIP-Chip (1/2)

source_name: Induced Pluripotent (iPS) Cells


title: Embryonic Fibroblast Line (MEF1) H3me3K27 Promoter Methylation ChIP-Chip (1/2)

description: Male MEFs

source_name: Embryonic Fibroblast (MEF1)


title: Embryonic Stem Cell Line (E14) H3me3K4 Promoter Methylation ChIP-Chip (1/1)


title: mel_rep1


title: Sox2-KO, Tet(-), 0hr - #1(251411710001)

description: Sox2-KO, Tet(-), 0hr


title: Embryonic Fibroblast Line (MEF1) H3me3K27 Promoter Methylation ChIP-Chip (2/2)

description: Male MEFs


title: Embryonic Fibroblast Line (MEF2) H3me3K27 Promoter Methylation ChIP-Chip (2/2)

description: Female MEFs


title: Embryonic Fibroblast Line (MEF2) H3me3K4 Promoter Methylation ChIP-Chip (2/2)


title: Embryonic Fibroblast Line (MEF1) H3me3K4 Promoter Methylation ChIP-Chip (1/2)


title: Induced Pluripotent (iPS) Cells H3me3K4 Promoter Methylation ChIP-Chip (1/2)

tag: Elute from a histone H3 trimehtylated K4 chromatin immunoprecipitation.

tag: Input for histone H3 trimehtylated K4 chromatin immunoprecipitation.


title: Exp 8 (-SB80)

status: Public on May 22 2007

first: Jai

middle: Moo

last: Shin

address: 11301 Wilshire Blvd

department: Physiology

description: Gene expressions affected by TNF alpha

hyb_protocol: For hybridization, Cy3- or Cy5-labeled cRNA from treated and vehicle treated cells were combined and hybridized to an Agilent 44K Whole Rat Genome Oligo Microarray (Agilent, Santa Clara, CA) according to manufacturer’s protocol.

scan_protocol: The oligonucleotide microarray slides were scanned with Agilent microarray scanner, and the signal intensity normalization was done with proprietary software from Agilent.

data_processing: GeneSpring

label: Cy3 and Cy5

organism: Rattus norvegicus

source_name: rat FLS

label_protocol: Total RNA was used for fluorescently labeled cRNA synthesis using Agilent Low RNA input Fluor Linear Amp Kit and protocol (Agilent, Santa Clara, CA).

extract_protocol: Cultured FLS were cultured to ~80% confluency, and then starved in DMEM containing 1% FCS for 24 hours. The cells were placed in culture medium containing 1% FCS in the presence or absence of TNF and SB 203580 for 24 hours. Total RNA was extracted with Ambion RNAqueous Kit (Ambion, Austin, TX) according to manufacturer’s protocol.

tag: FLS culture


title: Exp 6 (-SB80)

description: Gene expressions affected by TNF alpha


title: Exp 3 (-TNFa)

description: Gene expressions affected by TNF alpha

source_name: Rat FLS

extract_protocol: Cultured FLS were cultured to ~80% confluency, and then starved in DMEM containing 1% FCS for 24 hours. The cells were placed in culture medium containing 1% FCS in the presence or absence of TNF for 24 hours. Total RNA was extracted with Ambion RNAqueous Kit (Ambion, Austin, TX) according to manufacturer’s protocol.

tag: Rat FLS


title: Exp 4 (-TNFa)

description: Gene expressions affected by TNF alpha


title: Exp 3 (+TNFa)

description: Gene expressions affected by TNF alpha

tag: Cultured Fibroblast-Like Synoviocytes


title: Embryonic Stem Cell Line (V6.5) H3me3K27 Promoter Methylation ChIP-Chip (2/2)


title: Exp 2 (+TNFa)

description: Gene expressions affected by TNF alpha

tag: Cultured Rat Fibroblast-like Synoviocytes


title: Exp 4 (+TNFa)

description: Gene expressions affected by TNF alpha


title: Exp 1 (-TNFa)

description: Gene expressions affected by TNF alpha

extract_protocol: Cultured FLS were cultured to ~80% confluency, and then starved in DMEM containing 1% FCS for 24 hours. The cells were placed in culture medium containing 1% FCS in the presence or absence of TNF alpha (10ng/ml) for 24 hours. Total RNA was extracted with Ambion RNAqueous Kit (Ambion, Austin, TX) according to manufacturer’s protocol.


title: Exp 8 (+SB80)

description: Gene expressions affected by TNF alpha


title: Induced Pluripotent (iPS) Cells H3me3K27 Promoter Methylation ChIP-Chip (2/2)


title: Exp 7 (+SB80)

description: Gene expressions affected by TNF alpha


title: Exp 7 (-SB80)

description: Gene expressions affected by TNF alpha


title: Induced Pluripotent (iPS) Cells H3me3K4 Promoter Methylation ChIP-Chip (2/2)


title: Embryonic Fibroblast Line (MEF1) H3me3K4 Promoter Methylation ChIP-Chip (2/2)


title: Embryonic Stem Cell Line (E14) H3me3K27 Promoter Methylation ChIP-Chip (2/2)


title: Exp 6 (+SB80)

description: Gene expressions affected by TNF alpha


title: C73_1   ctrl  liver 7 days No. 64

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: vers chez les blanc

department: Bioanalytical Sciences

country: Switzerland

institute: Nestle Research Center

description: C73_1   ctrl  liver 7 days

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite version 5.0 followed by GEA

source_name: Liver

label_protocol: 5 ug of cRNA was used to make biotinylated RNA

extract_protocol: Clonetech

tag: ctrl  liver 7 days


title: T7_7   OTA  liver 7 days No. 66

description: T7_7   OTA  liver 7 days

treatment_protocol: Male Fischer 344 rats were administered Ochratoxin A (OTA) through the diet over two years. The initial daily dietary intake was 300 mg OTA/kg bw, but was held at 100 mg/rat after animal reached 333 g.

tag: OTA  liver 7 days


title: Exp 1 (+TNFa)

description: Gene expressions affected by TNF alpha


title: T19   OTA  kidney 7 months No. 63

description: T19   OTA  kidney 7 months

source_name: Kidney

tag: OTA  kidney 7 months


title: C03_21 CTRL liver 12 months No. 61

description: C03_21 CTRL liver 12 months

tag: CTRL liver 12 months


title: C73_3   ctrl  liver 7 days No. 65

description: C73_3   ctrl  liver 7 days


title: C03_20     CTRL liver 12 months No. 67

description: C03_20     CTRL liver 12 months


title: T18   OTA    liver  7 months No. 59

description: T18   OTA    liver  7 months

tag: OTA    liver  7 months


title: C10  ctrl kidney  7 months. No. 55

description: C10  ctrl kidney  7 months.

tag: ctrl kidney  7 months.


title: T16   OTA    liver  7 months No. 57

description: T16   OTA    liver  7 months


title: C9  ctrl    liver  7 months No. 56

description: C9  ctrl    liver  7 months

tag: ctrl    liver  7 months


title: T03_27  OTA kidney 12 months No. 60

description: T03_27  OTA kidney 12 months

tag: OTA kidney 12 months


title: T17   OTA    liver  7 months No. 58

description: T17   OTA    liver  7 months


title: C21 _3  CTRL  Kidney  21 days No. 50

description: C21 _3  CTRL  Kidney  21 days

tag: CTRL  Kidney  21 days


title: T21_7     OTA   kidney  21 days No. 54

description: T21_7     OTA   kidney  21 days

tag: OTA   kidney  21 days


title: Embryonic Stem Cell Line (E14) H3me3K4 Promoter Methylation ChIP-Chip (2/2)

tag: Elute from a histone H3 trimehtylated K4 chromatin immunoprecipitation

tag: Input for histone H3 trimehtylated K4 chromatin immunoprecipitation


title: T03_28      OTA kidney  12 months No. 53

description: T03_28      OTA kidney  12 months

tag: OTA kidney  12 months


title: T03 _ 26   OTA liver   12 months No. 49

description: T03 _ 26   OTA liver   12 months

tag: OTA liver   12 months


title: T21 _ 5   OTA kidney   21 days No. 51

description: T21 _ 5   OTA kidney   21 days

tag: OTA kidney   21 days


title: T21 _ 6   OTA kidney   21 days No. 52

description: T21 _ 6   OTA kidney   21 days


title: T7 _7    OTA kidney  7 days No. 48

description: T7 _7    OTA kidney  7 days

tag: OTA kidney  7 days


title: C7 _3  CTRL  Kidney  7 days No. 47

description: C7 _3  CTRL  Kidney  7 days

tag: CTRL  Kidney  7 days


title: T03 _ 29   OTA kidney   12 months No. 46

description: T03 _ 29   OTA kidney   12 months

tag: OTA kidney   12 months


title: C03 _ 20   CTRL kidney   12 months No. 44

description: C03 _ 20   CTRL kidney   12 months

tag: CTRL kidney   12 months


title: T8  OTA kidney  4 months No. 41

description: T8  OTA kidney  4 months

tag: OTA kidney  4 months


title: C7 _2  CTRL  Kidney  7 days No. 42

description: C7 _2  CTRL  Kidney  7 days


title: T03 _ 28   OTA kidney   12 months No. 45

description: T03 _ 28   OTA kidney   12 months


title: C3 ctrl kidney  4 months No. 38

description: C3 ctrl kidney  4 months

tag: ctrl kidney  4 months


title: T21_8  OTA   liver  21 days No. 32

description: T21_8  OTA   liver  21 days

tag: OTA   liver  21 days


title: C21_2 CTRL  Liver    21 days No. 34

description: C21_2 CTRL  Liver    21 days

tag: CTRL  Liver    21 days


title: T8 OTA  liver  4 months No. 37

description: T8 OTA  liver  4 months

tag: OTA  liver  4 months


title: T17     OTA kidney  7 months No. 43

description: T17     OTA kidney  7 months

tag: OTA kidney  7 months


title: C9    CTRL   kidney   7 months No. 33

description: C9    CTRL   kidney   7 months

tag: CTRL   kidney   7 months


title: T7      OTA  Kidney  4 mois No. 35

description: T7      OTA  Kidney  4 mois

tag: OTA  Kidney  4 mois


title: T21_5  OTA   liver  21 days No. 30

description: T21_5  OTA   liver  21 days


title: T6 OTA kidney  4 months No. 40

description:
T6 OTA kidney  4 months

(possibly a duplicate of GSM62768: generated using the CEL file for GSM62768)


title: T21_6  OTA   liver  21 days No. 31

description: T21_6  OTA   liver  21 days


title: C5   CTRL liver 4 months No. 36

description: C5   CTRL liver 4 months

tag: CTRL liver 4 months


title: C21_1  CTRL   liver  21 days No. 27

description: C21_1  CTRL   liver  21 days

tag: CTRL   liver  21 days


title: C21_3  CTRL   liver  21 days No. 28

description: C21_3  CTRL   liver  21 days


title: C21_2  CTRL   kidney   21 days No. 26

description: C21_2  CTRL   kidney   21 days

tag: CTRL   kidney   21 days


title: C21_4  CTRL   lkidney   21 days No. 25

description: C21_4  CTRL   lkidney   21 days

tag: CTRL   lkidney   21 days


title: C21_4  CTRL   liver  21 days No. 29

description: C21_4  CTRL   liver  21 days


title: T6 OTA kidney  4 months No. 39

description: T6 OTA kidney  4 months


title: T7_8   OTA liver   7 days No. 23

description: T7_8   OTA liver   7 days

tag: OTA liver   7 days


title: C7_4  CTRL   liver   7 days No. 24

description: C7_4  CTRL   liver   7 days

tag: CTRL   liver   7 days


title: T7_5   OTA liver   7 days No. 22

description: T7_5   OTA liver   7 days


title: C03_22 CTRL liver 12 months No. 19

description: C03_22 CTRL liver 12 months

tag: CTRL liver 12 months


title: T03_29   OTA liver 12 months No. 20

description: T03_29   OTA liver 12 months

tag: OTA liver 12 months


title: C03_22  CTRL kidney    12 months No. 21

description: C03_22  CTRL kidney    12 months

tag: CTRL kidney    12 months


title: T10    OTA   kidney  4 months No. 14

description: T10    OTA   kidney  4 months

tag: OTA   kidney  4 months


title: Blood_thalassemia_Hind (father)

city: Kaohsiung

first: Ta-Chih

last: Liu

address: 100, Shih-Chuan 1st Rd.

department: Department of Internal Medicine

country: Taiwan

institute: Kaohsiung Medical University Hospital

description: peripheral blood used for molecular diagnosis

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner 3000, GCOS 1.4

data_processing: DAT and CEL files were processed by Affymetrix GCOS 1.4 with default analysis settings. Calls generated by GTYPE 4.0 with confidence threshold 0.25. Copy numbers were generated by Affymetrix Chromosome Copy Number Tool, which uses reference set of 145 normal individuals.

organism: Homo sapiens

source_name: Blood from thalassemia patient's father of Kaohsiung Medical University

label_protocol: Standard Affymetrix procedures

extract_protocol: Extraction of genomic DNA with high molecular weight was performed using QIamp micro DNA extraction kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: Tissue

value: peripheral blood


title: C11      CTRL kidney    7 months No. 16

description: C11      CTRL kidney    7 months

tag: CTRL kidney    7 months


title: Hair_thalassemia_Xba (patient)

description: hair used for molecular diagnosis

source_name: Hair from thalassemia patient of Kaohsiung Medical University

value: hair


title: T7_6 OTA kidney  7 days  No. 18

description: T7_6 OTA kidney  7 days

tag: OTA kidney  7 days


title: C4     CTRL   kidney  4 months No. 13

description: C4     CTRL   kidney  4 months

tag: CTRL   kidney  4 months


title: T9     OTA    liver 4 months No. 12

description: T9     OTA    liver 4 months

tag: OTA    liver 4 months


title: Blood_thalassemia_Xba (mother)

source_name: Blood from thalassemia patient's mother of Kaohsiung Medical University


title: C11  ctrl  liver 7 months No. 10

description: C11  ctrl  liver 7 months

tag: ctrl  liver 7 months


title: Blood_thalassemia_Hind (mother)


title: T7    OTA   kidney    7 days No. 15

description: T7    OTA   kidney    7 days

tag: OTA   kidney    7 days


title: Mucosa_thalassemia_Xba (patient)

description: oral mucosa used for molecular diagnosis

source_name: Mucosa from thalassemia patient of Kaohsiung Medical University

value: oral mucosa


title: Blood_thalassemia_Xba (father)


title: C03 _21      CTRL kidney    12 months No. 17

description: C03 _21      CTRL kidney    12 months


title: C4     CTRL liver 4 months  No. 11

description: C4     CTRL liver 4 months

tag: CTRL liver 4 months


title: Hair_thalassemia_Hind (patient)

description: hair used for molecular diagnosis


title: Mucosa_thalassemia_Hind (patient)


title: Blood_thalassemia_Xba (patient)

source_name: Blood from thalassemia patient of Kaohsiung Medical University


title: T21_8  OTA  kidney  21 days No. 9

description: T21_8  OTA  kidney  21 days

tag: OTA  kidney  21 days


title: Blood_thalassemia_Hind (patient)


title: Exp 2 (-TNFa)

description: Gene expressions affected by TNF alpha

tag: Cultured Fibroblast-Like Synoviocytes


title: C3   ctrl  kidney  4 months No. 8

description: C3   ctrl  kidney  4 months

tag: ctrl  kidney  4 months


title: Family B/II_4 versus III_1

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Family B/II_4 versus III_1

hyb_protocol: Hybridization was done overnight at 42C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner (PMT settings: 100%/100%)

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

source_name: DNA isolated from blood

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from peripheral blood by means of Qiagen Genomic Tip columns

tag: uncle of an autistic patient (analysed in channel 2)

tag: male autistic patient


title: Family B/II_5 versus III_1

description: Family B/II_5 versus III_1

tag: aunt of an autistic patient (analysed in channel 2)


title: Family B/II_2 versus III_1

description: Family B/II_2 versus III_1

tag: mother of an autistic patient (analysed in channel 2)


title: Family A/III_1 versus I_2

description: Family A/III_1 versus I_2

tag: grandmother of autistic boy (analysed in channel 1)


title: Family B/II_3

description: Family B/II_3

tag: female reference DNA from a healthy donor


title: C7-4  CTRL     kidney    7 days No. 6

description: C7-4  CTRL     kidney    7 days

tag: CTRL     kidney    7 days


title: T03_28  OTA liver 12 months No. 62

description: T03_28  OTA liver 12 months

tag: OTA liver 12 months


title: T7  OTA    liver  4 months No. 3

description: T7  OTA    liver  4 months

tag: OTA    liver  4 months


title: C5  CTRL     kidney    4 months No. 5

description: C5  CTRL     kidney    4 months

tag: CTRL     kidney    4 months


title: C3 CTRL  liver  4 months No. 2

description: C3 CTRL  liver  4 months

tag: CTRL  liver  4 months


title: Family F/I_2 versus I_1

description: Family F/I_2 versus I_1

tag: mother of an autistic patient

tag: husband of female analysed in channel 1


title: T7  OTA    liver  4 months No. 4

description: T7  OTA    liver  4 months


title: Family A/II_2

description: Family A/II_2

scan_protocol: Slides were scanned using an Axon 4000B scanner (Axon Instruments, Union City, CA)

source_name: female reference DNA

tag: female reference

tag: unaffected female carrier of a duplication 16p13


title: Family A/III_3

description: Family A/III_3

scan_protocol: Slides were scanned using an Agilent Scanner (PMT settings 100/100%) with a resoltution of 10micrometre.

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

tag: mentally retarded girl

tag: female reference DNA


title: Family A/II_2 versus I_2

description: Family A/II_2 versus I_2

tag: mother of an autistic boy

tag: grandmother of an autistic boy


title: Family A/III_3 versus II_2

description: Family A/III_3 versus II_2

tag: mother of a mentally retarded girl (analysed in channel 1)


title: Family A/III_2 versus I_2

description: Family A/III_2 versus I_2

tag: male autistic patient

tag: grandmother of an autistic boy (analysed in channel 1)


title: Family B/II_2

description: Family B/II_2


title: Family A/III_1 versus II_2

description: Family A/III_1 versus II_2

source_name: mother of an autistic patient (analysed in channel 1)


title: Family A/III_2

description: Family A/III_2

tag: DNA isolated from blood of an autistic patient Gender

source_name: male reference DNA

tag: male reference DNA


title: T18      OTA kidney    7 months No. 7

description: T18      OTA kidney    7 months

tag: OTA kidney    7 months


title: FamilieB/II_1

tag: father of an autistic patient

tag: male reference DNA.


title: Family D/I_1

description: Family D/I_1

tag: DNA isolated from blood of the father of an autistic patient Gender


title: C10  ctrl  liver 7 months No. 1

description: C10  ctrl  liver 7 months

tag: ctrl  liver 7 months


title: Family B/III_1

description: Family B/III_1


title: Family B/II_1

description: Family B/II_1


title: Family B/I_2

description: Family B/I_2

tag: grandmother of autistic patient


title: S.mikatae_alpha_factor_60min_repeat4

status: Public on May 20 2007

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

description: S.mikatae a-type cells were compared before and after (60 minutes) addition of alpha factor (6uM).

hyb_protocol: Arrays were purchased from the Microarray Centre, University Health Network, Ontario, where PCR products are printed. For each hybridization, cDNA samples were labeled with Cy3 and Cy5 and combined with blockers: 5ug Herring sperm (Promega), 5ug tRNA (Gibco) and 17.5ug Poly A (Poly A oligos were synthesized with mixed length of 40, 50 and 60 Adenine residues). The labeled cDNAs were concentrated to 40ul using Microcon (Millipore) and 40ul of hybridization x2 solution (10x SSC, 50% formamide and 0.2% SDS) was added. Microarrays containing all yeast ORFs were pre-hybridized by incubating at 42ºC for 45 minutes in a solution containing 1% BSA, 25% formamide, 5x SSC and 0.1% SDS. The slides were washed in sterile water and dried by centrifugation (3 minutes, 2000 rpm).  The labeled samples were boiled for 5 minutes, centrifuged for 1 minute, hybridized on the slide and placed in a hybridization chamber (Corning) for overnight incubation at 42ºC. The slides were then washed for 5 minutes at 42ºC with a solution containing 2x SSC and 0.1% SDS. Additional wash was performed at room temperature with a solution containing 0.1x SSC and 0.1% SDS, followed by three additional washes at room temperature in 0.1x SSC solution.

scan_protocol: Images were obtained using Agilent's DNA microarray scanner. Image analysis was performed using SpotReader (Niles Scientific).

data_processing: The ratios of the two dyes were log2-transformed. Log2 ratios were then corrected for intensity-dependant and spatial-dependant biases by subtracting a Lowess curve followed by a median filter. Genes for which the two spots were significantly different were declared as 'missing values' (along with other genes which were flagged by the image analysis software or removed by manual inspection).

organism: Saccharomyces mikatae

source_name: S.mikatae a-type cells 60 minutes after addition of alpha factor (6uM)

label_protocol: The cDNA from alpha-factor treated and untreated cells was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

growth_protocol: Cells were grown on YPD to log phase at 30oC prior to addition of alpha-factor

extract_protocol: 5 O.D. units of cells were collected, pelleted and immediately frozen. Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

tag: Strain

value: a-type haploid derived from IFO 1815 wild type

source_name: S. mikatae grown in YPD at 30oC

label_protocol: cDNA was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

tag: For reference we used the same culture prior to addition of alpha-factor, in which cells were grown to log phase in YPD at 30oC.


title: S.cerevisiae_mating_90min_repeat1

description: S.cerevisiae a-type and alpha-type cells were mixed and incubated 90 minutes for mating. As reference we used the same cells without mixing them during incubation, but only mixing prior to mRNA extraction.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae a-type and alpha-type cells were mixed and applied on to 0.22um filter, the filter was placed on a YPD agar plate at 30oC for 90 minutes and then snap-freezed with liquid nitrogen

label_protocol: The cDNA was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

growth_protocol: Cells were grown on YPD to log phase at 30oC prior to mating

extract_protocol: 10 O.D. units of cells were collected from frozen filters. Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

value: BY4741 wild type, haploid and BY4742 wild type, haploid

source_name: non mixed S. cerevisiae a-type and alpha-type cells.

extract_protocol: 5 O.D. units of each of the a-type and alpha-type cells were collected from the filters and mixed. Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

tag: S. cerevisiae a-type and alpha-type cells were placed on separate filters and incubated on YPD agar plates at 30oC for 90 minutes


title: S.cerevisiae_mating_90min_repeat3


title: FamilieA/III_1 versus I_2

description: FamilieA/III_1 versus I_2


title: S.cerevisiae_mating_90min_repeat2


title: Family B/I_1

description: Family B/I_1

tag: male with borderline autistic features; grandfather of Family BIII_1


title: Family E/II_1

description: Family E/II_1

value: female


title: Family A/III_1

description: Family A/III_1


title: S.paradoxus_alpha_factor_60min_repeat3

description: S.paradoxus a-type cells were compared before and after (60 minutes) addition of alpha factor (6uM).

organism: Saccharomyces paradoxus

source_name: S.paradoxus a-type cells 60 minutes after addition of alpha factor (6uM)

value: a-type haploid derived from CBS432 wild type

source_name: S. paradoxus grown in YPD at 30oC


title: IGR Hrp1 binding (K080D) slide2

status: Public on May 19 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: Chip on CHIP

hyb_protocol: Robyr et al Methods 31 (2003)

scan_protocol: Chip reader

data_processing: genespring

organism: Schizosaccharomyces pombe

label_protocol: Robyr et al Methods 31 (2003)

extract_protocol: Robyr et al Methods 31 (2003)

source_name: Input

tag: Input


title: S.cerevisiae_alpha_factor_60min_repeat2

description: S.cerevisiae a-type cells were compared before and after (60 minutes) addition of alpha factor (6uM).

source_name: S.cerevisiae a-type cells 60 minutes after addition of alpha factor (6uM)

value: BY4741 wild type, haploid

source_name: S. cerevisiae grown in YPD at 30oC


title: IGR Hrp1 binding (K080D) slide1

description: Chip on CHIP


title: ORF Hrp1 binding (K080D) slide2

description: Chip on CHIP

source_name: input

tag: input


title: ORF Hrp3 binding (K080D) slide3

description: Chip on CHIP


title: Nap1D H3 desinty II

description: For the GeneChip® S. pombe Tiling Array from Affymetrix the DNA was amplified to obtain 5 micrograms of DNA then fragmented around 100 base pairs using DNAse I, labelled with biotin and hybridized according to Affymetrix recommendations (Lengronne et al., 2004). Antibodies specific for the anti-H3 epitope (9E10) were used for ChIP.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Signals were normalized with 50th percentile normalization using genespring software

source_name: Nap1 H3 desnity II

label_protocol: Affymetrix

extract_protocol: Affymetrix

tag: Affymetrix


title: S.cerevisiae_alpha_factor_60min_repeat1


title: ORF Hrp3 binding (K080D) slide2

description: Chip on CHIP


title: IGR Hrp3 binding (K080D) slide2

description: Chip on CHIP


title: ORF Hrp1 binding (K080D) slide3

description: Chip on CHIP


title: Nap1 myc

source_name: Hrp1 myc


title: Nap1D H3 desnity

source_name: Nap1D H3 density


title: Hrp3D H3 density Affymetrix tiling arrays

description: For the GeneChip® S. pombe Tiling Array from Affymetrix the DNA was amplified to obtain 5 micrograms of DNA then fragmented around 100 base pairs using DNAse I, labelled with biotin and hybridized according to Affymetrix recommendations (Lengronne et al., 2004). Antibodies specific for the anti-H3 epitope (1791 Abcam) were used for ChIP.

source_name: ChIP Hrp3 H3 density


title: Nap1 myc II

source_name: Nap1 myc II


title: ORF Hrp3 binding (K080D) slide1

description: Chip on CHIP


title: Hrp3 myc

source_name: Hrp3 myc


title: S.mikatae_alpha_factor_60min_repeat1


title: S.paradoxus_alpha_factor_60min_repeat2


title: Hrp3 binding affymetrix tiling arrays

description: For the GeneChip® S. pombe Tiling Array from Affymetrix the DNA was amplified to obtain 5 micrograms of DNA then fragmented around 100 base pairs using DNAse I, labelled with biotin and hybridized according to Affymetrix recommendations (Lengronne et al., 2004). Antibodies specific for the anti-myc epitope (9E10) were used for ChIP.


title: IGR Hrp3 binding (K080D) slide3

description: Chip on CHIP


title: IGR Hrp3 binding (K080D)

description: Chip on CHIP


title: S.cerevisiae_alpha_factor_60min_repeat3


title: S.paradoxus_alpha_factor_60min_repeat1


title: Hrp1 myc

source_name: ChIP Hrp1 myc


title: Hrp1D H3 desnity

source_name: Hrp1D chip H3


title: Hrp1D H3 density Affymetrix tiling arrays

source_name: Hrp1D H3 density

tag: ChIPed H3


title: Hrp1 binding affymetrix tiling arrays

hyb_protocol: affymetrix

scan_protocol: affymetrix

tag: CHIP IP hrp1-myc sample


title: Hrp3D H3 desnity

source_name: Hrp3D H3 density ChIP


title: Family B/III_2

description: Family B/III_2

source_name: DNA isolated from blood

tag: unaffected brother of an autistic patient


title: IGR Nap1D H3 density (AB130F)

description: Chip on CHIP

source_name: Chip nap1D H3 density

tag: nap1D H3


title: ORF Nap1D H3 density (AB130F)

description: Chip on CHIP


title: ORF Nap1D H3 density (AB130F) slide2

description: Chip on CHIP


title: IGR Nap1D H3 density (AB130F) slide2

description: Chip on CHIP


title: S.mikatae_alpha_factor_60min_repeat3

source_name: S.mikatae a-type cells 60 minutes after addition of alpha factor (6uM)

source_name: S. mikatae grown in YPD at 30oC


title: IGR C270F Nap1 binding

description: Chip on CHIP

source_name: CHIP nap1-myc

source_name: Input


title: S.mikatae_alpha_factor_60min_repeat2


title: ORF Hrp1 H3 density (I040F)

description: Chip on CHIP

source_name: Chip Hrp1D H3 density

source_name: wt H3 density

tag: wt


title: ORF C270F mst2 H3 density

description: Chip on CHIP

source_name: CHIP Histone H3 mst2D

tag: mst2 sample


title: IGR Hrp1 H3 density (I040F)

description: Chip on CHIP

tag: wt h3


title: IGR Hrp3D H3 density (A260E)

description: Chip on CHIP

source_name: Chip Hrp3D H3 density

tag: Hrp3D H3


title: ORF C270F gcn5 H3 density

description: Chip on CHIP

source_name: CHIP Histone H3 gcn5D

tag: gcn5 sample


title: ORF C270F Nap1 binding slide 2

description: Chip on CHIP


title: IGR Hrp3 H3 density (I040F)

description: Chip on CHIP

source_name: WT H3 density


title: ORF C270F mst2 H3 density slide2

description: Chip on CHIP


title: ORF C270F gcn5 H3 density slide2

description: Chip on CHIP


title: IGR C270F Nap1 binding slide2

description: Chip on CHIP


title: ORF Hrp3 H3 density (I040F)

description: Chip on CHIP

tag: wt H3


title: IGR C270F mst2 H3 density

description: Chip on CHIP


title: ORF Hrp3D H3 density (A260E)

description: Chip on CHIP

source_name: IGR Hrp3D H3 density (A260E)


title: IGR Hrp1 H3 density (B190D)

description: Chip on CHIP

tag: Hrp1D H3


title: ORF C270F Nap1 binding

description: Chip on CHIP


title: IGR Hrp1 binding (A260E)

description: Chip on CHIP


title: IGR C270F gcn5 H3 density

description: Chip on CHIP


title: IGR C270F mst2 H3 density slide2

description: Chip on CHIP


title: IGR C270F gcn5 H3 density slide2

description: Chip on CHIP


title: ORF Hrp1 H3 density (B190D)

description: Chip on CHIP


title: ORF Hrp1 binding (A260E)

description: Chip on CHIP


title: IGR A260E Hrp1 slide1

description: chip on chip

scan_protocol: chip reader

source_name: CHIP IP Hrp1-D H3 cter

extract_protocol: chip on chip

tag: CHIP IP Hrp1-D H3 cter

source_name: CHIP input Hrp1-D H3 cter

tag: CHIP input Hrp1-D H3 cter


title: HeLa p300-HAT inhibitor Vs HeLa DMSO - Experiment_1 - Dye Swap

status: Public on May 18 2007

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Grid and spot alignment is performed by using Scanarray microarray analysis software form PerkinElmer.

hyb_protocol: 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint. Small bubbles will not to lose hybridization. 3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using GeneSpring GX v7.3. Per spot per chip lowess normalization was done. To account for dye swap, the signal channel and control channel measurements for sample(s) 2 were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Biological analysis was done using Genotypic's Biointerpreter software.

source_name: HeLa cell line treated with p300-HAT inhibitor

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 40 µg total RNA was used in each of the labeling reactions

extract_protocol: Trizol Method

tag: HeLa cell line dervied from human cervical cancer tissues treated with p300-HAT inhibitor

source_name: HeLa cell line treated with DMSO

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 50 µg total RNA was used in each of the labeling reactions.

tag: HeLa cell line dervied from human cervical cancer tissues treated with DMSO


title: repeat 2 normoxia

city: Oxford

first: Jerome

middle: Tremblay

last: Brooks

state: Oxon

address: Parks Road

department: Department of Physiology Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

hyb_protocol: 1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 15 hours at 55 degrees celsius. The microarrays were washed and then stained with streptavidin conjugated to Cy3 fluorescent dye. The staining procedure relies on the affinity of streptavidin to biotin which is incorporated into the UTP residues of the hybridised cRNA sample. Arrays were then washed again and air dried.

scan_protocol: Microarrays were scanned under 532nm laser illumination using a confocal type image system (BeadArray Reader, Illumina California USA). Each sequence specific probe is represented on average by 30 beads on each microarray. Fluorescence intensities from each bead were determined and each specific probe signal was automatically calculated by BeadStudio software (Illumina California) using a trimmed average of the corresponding replicate bead signals. Background intensities were calculated and subtracted from each data point using ~ 700 negative control probes on each array.

data_processing:
Once the average signal intensity from each gene specific probe on the microarray had been determined, a small offset was added to each data point to reduce variability at low intensity levels and the data was normalized using the quantile normalisation method contained in the affy package (Gautier et al., 2004) on the R statistical analysis platform (www.r-project.org). The reduction in variability at low intensities is obtained at the expense of slighter lower differential expression values.
The data were then reviewed for gene expression and hypoxic regulation using the Genespring analysis platform (Agilent technologies USA). Statistical analysis was performed using the limma library from the bioconductor repository (www.bioconductor.org) running on the R-platform. A multiple testing correction was applied using the limma algorithm that controls for the false discovery rate. The three repeat cRNA samples hybridised to the six microarrays were considered as a paired set of hybridisations. The gene specific signal intensities in the normoxic cRNA samples were compared to that of the hypoxic cRNA samples. Ratios of the average signal intensities under hypoxia compared to normoxia were calculated for each transcript and the mean values of the signal intensities from the three repeated normoxic/hypoxic exposures were compared using the limma software package to perform a paired study design. The average signal intensities, the average hypoxia to normoxia expression ratios (for the three paired normoxic/hypoxic lymphocyte incubations) and the p values representing the significance of change of expression in hypoxic conditions for all of the transcripts assayed for on the Illumina Sentrix Human 6-Expression BeadChip platform are submitted as a Series table.

source_name: peripheral blood lymphocytes incubated at 20 % ambient oxygen for 20 hours.

label_protocol: Biotin-16 UTP of invitro transcribed RNA. Used Illumina RNA amplification kit ( Cat # 1755 Ambion US).

growth_protocol: Extracted peripheral blood lymphocytes were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (Sigma Aldrich lot # 110K8403) and 5mmol of L-glutamine and penicillin/streptomycin antibiotics (Sigma Aldrich).

extract_protocol: Total RNA was isolated from approximately 70,000 harvested lyphocytes from each incubation using a column based centrifugation method, designed by Ambion (USA RNAqueous-4PCR cat. # 1914) in accordance with the manufacturers instructions..

treatment_protocol: Peripheral blood lymphocytes were cultured for for 20 hours at 37 degrees celsius under either 20% oxygen or 1% ambient oxygen tensions.

tag: lymphocytes isolated from human male 33 years


title: repeat 3 normoxia


title: HeLa p300-HAT inhibitor Vs HeLa DMSO - Experiment_1


title: repeat 1 hypoxia

source_name: peripheral blood lymphocytes incubated at 1% ambient oxygen for 20 hours.


title: repeat 3 hypoxia

source_name: peripheral blood lymphocytes incubated at 1 % ambient oxygen for 20 hours.


title: HeLa p300-HAT inhibitor Vs HeLa DMSO Experiment_2


title: HeLa p300-HAT inhibitor Vs HeLa DMSO - Experiment_2 - Dye Swap


title: repeat 2 hypoxia


title: repeat 1 normoxia


title: Fig S2: Tris V (A18346) DNA

status: Public on May 17 2007

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: Channels originally misidentified

hyb_protocol: Description : 200 ng differentially labeled DNA from the reference strain and the strain of interest were mixed, combined with control targets and hybridization buffer, boiled for 5 minutes, and applied to a microarray consisting of 60mer probes for each yeast open reading frame (Agilent).  Microarrays were rotated at 60?C for 17 hours in a hybridization oven (Agilent).  Arrays were then washed according to the Agilent SSPE wash protocol.

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-12 Scan Time : 11:30:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file

source_name: WT

label_protocol: Description : 1 microg HhaI digested DNA was labeled with Klenow polymerase and Cy3- or Cy5-dCTP according to the BioPrime CGH labeling kit (Invitrogen), using half volume reactions.  Yield and dye incorporation were checked with a Nanodrop spectrophotometer.

extract_protocol: Description : To prepare genomic DNA, cells were grown to saturation in selective media. 15 mls of culture were spun down, rinsed and incubated for 60 minutes at 37oC in 1.5 mls of 1 M Sorbitol, 10 mM Na-phosphate, pH 7.0, 10 mM EDTA, 200 mg/ml zymolase and 150 mM b-mercaptoethanol.  Cells were pelleted and incubated in 1.5 mls of 50 mM EDTA, pH 8.0, 0.3% SDS, 200 mg/ml proteinase K and incubated for another 60 minutes at 65oC.  0.6 mls of 5 M KOAc was added and mixture was incubated on ice for 30 min.  The supernatant was subjected to a phenol/chloroform extraction and DNA was precipitated. The DNA was RNAse treated at 37oC for 2 hours (10 mM Tri-HCl, 1mM EDTA, pH 7.5, 1 mg/ml RNAse), followed by another phenol/chloroform extraction, and precipitated with ethanol.

tag: Strain Name

source_name: Trisome 5


title: Fig S2: Tris XIV (A18349) DNA (swap)

description: Fig S2: Tris XIV (A18349) DNA (swap)

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-12 Scan Time : 11:32:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Trisome 14

value: Tris XIV (A18349)


title: Fig S2: Tris VIII (A18347) DNA (swap)

description: Fig S2: Tris VIII (A18347) DNA (swap)

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-12 Scan Time : 11:28:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Trisome 8

value: Tris VIII (A18347)


title: Fig S2: Dis XIV pdr5 (A15568) DNA (swap)

description: former name: Disome 14.2delta pdr5 (channels originally misassigned)

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-23 Scan Time : 09:52:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 8.1.1.1
Datafile type : Agilent result file

value: Dis XIV pdr5 (A15568)


title: Cold stress, biological rep 1

city: New Delhi

first: Akhilesh

middle: K.

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

institute: University of Delhi South Campus

description: 7-day-old light-grown rice seedlings kept at 4 ± 1 degree celsius for 3 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using script EukGE-WS2v5.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChipOperating Software (GCOS 1.2.1) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Oryza sativa

source_name: 7-day-old light-grown rice seedlings

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

growth_protocol: Rice seeds were disinfected with 0.1% HgCl2 for 1 h, thoroughly washed with RO (reverse-osmosis) water and soaked overnight in RO water. Seedlings were grown in RO water, at 28±1 degree celsius for 7 days, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark.

extract_protocol: Extraction of total RNA was performed using Trizol, according to the manufacturer's instructions

treatment_protocol: Seedlings were kept at 4±1 degree celsius for 3 h

tag: Supspecies

value: indica, Variety:IR64


title: Cold stress, biological rep 3


title: Fig S2: Dis II pdr5 (A15552) DNA (swap)

description: former name: Disome 2.3 delta pdr5.A

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-10 Scan Time : 09:54:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis II pdr5 (A15552)


title: Fig S2: Dis VIII pdr5 (A15558) DNA (swap)

description: former name: Disome 8.2 delta pdr5 (channels originally misassigned)

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-10 Scan Time : 10:02:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis VIII pdr5 (A15558)

source_name: Wild type


title: Fig S2: Tris XV (A18350) DNA (swap)

description: Fig S2: Tris XV (A18350) DNA (swap)

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-12 Scan Time : 11:32:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Trisome 15

value: Tris XV (A18350)


title: Fig S2: Tris XI (A18348) DNA (swap)

description: Fig S2: Tris XI (A18348) DNA (swap)

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-12 Scan Time : 11:31:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Trisome 11

value: Tris XI (A18348)