title: Control GFP RNAi, day 6, biological replicate 1

city: Singapore

first: Vinsensius

middle: B

last: Vega

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Gene expression data from Control GFP shRNA treated E14 embryonic stem cells, day 6

hyb_protocol: 1.5 ug of cRNA were hybridized to Illumina Mouse-6 Expression BeadChip v1.1 for 20 hr at 58oC on Ilumina Hybridization Oven.

scan_protocol: Illumina Mouse-6 Expression BeadChip v1.1 were washed and stained with streptavidin-Cy3 before scanning using the Illumina Bead Reader.

data_processing: The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.

source_name: E14 mouse embryonic stem (ES) cells

label_protocol: Biotinylated cRNA were prepared from 500 ng of total RNA according to the standard protocol (TotalPrep RNA Amplification Kit, Instruction Manual, Catalog #IL1791, Illumina).

growth_protocol: Mouse ES cells were cultured at 37°C with 5% CO2. Mouse ES cells were maintained on gelatin-coated dishes in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purified with RNeasy minikit (Qiagen).

treatment_protocol: Transfection of GFP shRNA plasmid was performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s

tag: Control GFP shRNA (targeting GFP transcript) transfected E14 mouse embryonic stem cells


title: Esrrb RNAi, day 6, biological replicate 3

status: Public on Jan 15 2009

type: RNA

description: Gene expression data from Esrrb shRNA treated E14 embryonic stem cells, day 6

label: Biotin

molecule: total RNA

organism: Mus musculus

treatment_protocol: Transfection of Esrrb shRNA plasmid was performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s

tag: Esrrb shRNA (targeting Esrrb transcript) transfected E14 mouse embryonic stem cells


title: Esrrb RNAi, day 4, biological replicate 3

description: Gene expression data from Esrrb shRNA treated E14 embryonic stem cells, day 4


title: LWset2_Col-0_mock_9h

city: St Paul

first: lin

last: wang

state: MN

address: 350 Cargill building, 1500 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

description: Col-0 infiltrated with water, harvested 9h after infiltration in setLWset2 experiment.

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)

scan_protocol: Slide was scanned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing:
Note that each Sample corresponds to two GPR files (we use low PMT and high PMT, then combine them).

The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. KTset1_Col-0_hrcC_03h, KTset1_Col-0_hrcC_09h, KTset1_coi1_hrcC_03h, KTset1_coi1_hrcC_09h, KTset1_dde2_hrcC_03h, KTset1_dde2_hrcC_09h, KTset1_ein2_hrcC_03h, KTset1_ein2_hrcC_09h, KTset1_Col-0_mock_03h, KTset1_Col-0_mock_09h, KTset1_mpk3_hrcC_03h, KTset1_mpk3_hrcC_09h, KTset1_pad4_hrcC_03h, KTset1_pad4_hrcC_09h, KTset1_sid2_hrcC_03h, KTset1_sid2_hrcC_09h, KTset2_Col-0_hrcC_03h, KTset2_Col-0_hrcC_09h, KTset2_coi1_hrcC_03h, KTset2_coi1_hrcC_09h, KTset2_dde2_hrcC_03h, KTset2_dde2_hrcC_09h, KTset2_ein2_hrcC_03h, KTset2_ein2_hrcC_09h, KTset2_Col-0_mock_03h, KTset2_Col-0_mock_09h, KTset2_mpk3_hrcC_03h, KTset2_mpk3_hrcC_09h, KTset2_pad4_hrcC_03h, KTset2_pad4_hrcC_09h, KTset2_sid2_hrcC_03h, KTset2_sid2_hrcC_09h, KTset3_Col-0_hrcC_03h, KTset3_Col-0_hrcC_09h, KTset3_coi1_hrcC_03h, KTset3_coi1_hrcC_09h, KTset3_dde2_hrcC_03h, KTset3_dde2_hrcC_09h, KTset3_ein2_hrcC_03h, KTset3_ein2_hrcC_09h, KTset3_Col-0_mock_03h, KTset3_Col-0_mock_09h, KTset3_mpk3_hrcC_03h, KTset3_mpk3_hrcC_09h, KTset3_pad4_hrcC_03h, KTset3_pad4_hrcC_09h, KTset3_sid2_hrcC_03h, KTset3_sid2_hrcC_09h, LWset1_SALK-023199_hrcC_09h, LWset1_Col-0_hrcC_09h, LWset1_Col-0_mock_09h, LWset2_SALK-023199_hrcC_09h, LWset2_Col-0_hrcC_09h, LWset2_Col-0_mock_09h, LWset3_SALK-023199_hrcC_09h, LWset3_Col-0_hrcC_09h, LWset3_Col-0_mock_09h, LWset1_Col-0_mock_03h, LWset1_Col-0_hrcC_03h, LWset1_SALK-023199_hrcC_03h, LWset2_Col-0_mock_03h, LWset2_Col-0_hrcC_03h, LWset2_SALK-023199_hrcC_03h, LWset3_SALK-023199_hrcC_03h, LWset3_Col-0_mock_03h, and LWset3_Col-0_hrcC_03h were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 9h

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.

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

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 9h later.

tag: Genotype

tag: Tissue

value: leaves

tag: Age

value: 4 week-old

tag: Treatment

value: water

tag: Time point


title: Esrrb RNAi, day 6, biological replicate 1


title: Esrrb RNAi, day 4, biological replicate 2


title: LWset2_SALK_023199_hrcC_3h

description: SALK_023199 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setLWset2 experiment.

source_name: Arabidopsis thaliana SALK_023199, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 3h later.


title: Esrrb RNAi, day 6, biological replicate 2


title: Control GFP RNAi, day 6, biological replicate 3


title: Control GFP RNAi, day 4, biological replicate 3

description: Gene expression data from Control GFP shRNA treated E14 embryonic stem cells, day 4


title: LWset2_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setLWset2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 9h later.


title: LWset2_Col-0_mock_3h

description: Col-0 infiltrated with water, harvested 3h after infiltration in setLWset2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 3h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 3h later.


title: Esrrb RNAi, day 4, biological replicate 1


title: Control GFP RNAi, day 6, biological replicate 2


title: LWset2_Col-0_hrcC_3h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setLWset2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: LWset1_Col-0_mock_9h

description: Col-0 infiltrated with water, harvested 9h after infiltration in setLWset1 experiment.


title: Control GFP RNAi, day 4, biological replicate 2


title: Esrrb RNAi, day 2, biological replicate 1

description: Gene expression data from Esrrb shRNA treated E14 embryonic stem cells, day 2


title: Esrrb RNAi, day 2, biological replicate 3


title: LWset1_SALK_023199_hrcC_9h

description: SALK_023199 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setLWset1 experiment.

source_name: Arabidopsis thaliana SALK_023199, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: LWset1_SALK_023199_hrcC_3h

description: SALK_023199 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setLWset1 experiment.


title: Esrrb RNAi, day 2, biological replicate 2


title: Control GFP RNAi, day 4, biological replicate 1


title: control 20 min after KCl replicate 1

type: genomic

city: Boston

first: Tae-Kyung

last: Kim

state: MA

address: 300 Longwood avenue, CLS building 12260

department: Neurology

institute: Children's Hospital

description: control ChIP from neurons depolarized by KCl for 20 minutes

hyb_protocol: 12 ug of the Cy5-labeled ChIP sample and 12 ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems).After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems) and dried by centrifugation.

scan_protocol: The arrays were scanned at 5-μm resolution using the GenePix 4000B scanner (Axon Instruments)

data_processing: Signal intensity data was extracted from the scanned images of each array using NimbleScan, NimbleGen’s data extraction software. Subsequently, scaled log2-ratio values from each probe were obtained (log2[ChIP signal intensity/input signal intensity]). The log2-ratio was computed and scaled to center these values around zero. Scaling was performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: control_20min after KCL (IP)

label_protocol: DNA sample (1 μg) was denatured in the presence of 5'-Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

growth_protocol: Hippocampal neurons from E18 Long-Evans rats were isolated. Neurons were maintained for 7 days in Neurobasal Medium (Invitrogen, Gaithersburg, MD) containing B27 Supplement (2%; Invitrogen), penicillin-streptomycin (50 µg/ml penicillin, 50 U/mL streptomycin; Sigma, St. Louis, MO) and glutamine (1mM; Sigma).

extract_protocol: Typically 20-40 million hippocampal neurons were used for a single ChIP experiment. To cross-link protein-DNA complexes, media was removed from neuronal cultures and crosslinking-buffer (0.1 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 25 mM Hepes-KOH, pH 8.0) containing 1% paraformaldehyde was added for 10 minutes at room temperature. Cross-linking was quenched by adding 125 mM glycine for 5 minutes at RT. Cells were then rinsed 3 times in ice-cold PBS containing complete protease inhibitor cocktail tablets (Roche Diagnostics, Mannheim, Germany) and collected by scraping. Cells were pelleted and either stored at -80 oC until use or immediately processed. Cell pellets were lysed by 20 cell pellet volumes (CPVs) of L1 buffer (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, pH 8.0, 10 % Glycerol, 0.5 % NP-40, 0.25 % Triton X-100, complete protease inhibitor cocktail) for 10 min at 4 oC.  Nuclei were then pelleted by centrifugation at 3000 rpm for 10 min at 4 oC. The isolated nuclei were rinsed with 20 CPVs of L2 buffer (200 mM NaCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 10 mM Tris-HCl, pH 8.0, complete protease inhibitor cocktail) for 10 min at RT and re-pelleted.  Next, 4 CPVs of L3 buffer (1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 10 mM Tris-HCl, pH 8.0, complete protease inhibitor cocktail) were added to the nuclei and sonication was carried out using a Misonix 3000 Sonicator (Misonix, Farmingdale, NY) set at a power setting of 7.5 (equivalent to 24 watts). 16 pulses of 15 seconds each were delivered at this setting, which resulted in genomic DNA fragments with sizes ranging from 200 bp to 2 kb. Insoluble materials were removed by centrifugation at 20,000 relative centrifugal force for 10 min at 4 oC. The supernatant was transferred to a new tube and the final volume of the resulting nuclear lysate was adjusted to 1 mL by adding L3 buffer supplemented with 0.3 M NaCl, 1 % Triton X-100, 0.1 % Deoxycholate.

treatment_protocol: For KCl depolarization of neurons, TTX (1 µM; Calbiochem, La Jolla, CA) and AP5 (100 µM; Tocris, Ellisville, MO) were added prior to stimulation to reduce basal neuronal activity and neurons were depolarized by adding 31% depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES) to the culture media for the indicated amounts of time.

tag: primary rat hippocampal neurons

tag: ChIP by pre-blocked MEF2D antibody (control)

source_name: control_20min after KCL (Input)

tag: input genomic DNA


title: Control GFP RNAi, day 2, biological replicate 3

description: Gene expression data from Control GFP shRNA treated E14 embryonic stem cells, day 2


title: Control GFP RNAi, day 2, biological replicate 2


title: LWset1_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setLWset1 experiment.


title: LWset1_Col-0_hrcC_3h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setLWset1 experiment.


title: Control GFP RNAi, day 2, biological replicate 1

treatment_protocol: Transfection of GFP shRNA plasmid was performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. Oligonucleotides were cloned into pSUPER.puro (Bgl II and Hind III sites, Oligoengine), which expresses 19-nucleotide hairpin-type shRNAs with a 9-nucleotide loop. 1.5 ?g of plasmid was transfected into ES cells in 6 well dishes for total RNA extraction.


title: control 2 hr after KCl replicate 2

description: control ChIP from neurons depolarized by KCl for 2 hr

source_name: control_2hr after KCL (IP)

source_name: control_2hr after KCL (Input)


title: control 2 hr after KCl replicate 1


title: MEF2D binding in quiescent neurons replicate 1

description: MEF2D ChIP from quiescent neurons

source_name: MEF2D_untreated (IP)

tag: ChIP by MEF2D antibody

source_name: MEF2D_untreated (Input)


title: LWset1_Col-0_mock_3h

description: Col-0 infiltrated with water, harvested 3h after infiltration in setLWset1 experiment.


title: control in quiescent neurons replicate 2

description: control ChIP from quiescent neurons

source_name: control_untreated (IP)

source_name: control_untreated (Input)


title: MEF2D binding 2 hr after KCl replicate 2

description: MEF2D ChIP from neurons depolarized by KCl for 2 hr

source_name: MEF2D_2hr after KCL (IP)

source_name: MEF2D_2hr after KCL (Input)


title: MEF2D binding 20 min after KCl replicate 1

description: MEF2D ChIP from neurons depolarized by KCl for 20 minutes

source_name: MEF2D_20min after KCL (IP)

source_name: MEF2D_20min after KCL (Input)


title: KTset3_sid2-2_hrcC_3h

description: sid2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana sid2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: control in quiescent neurons replicate 1

description: control ChIP from quiescent neurons


title: KTset3_sid2-2_hrcC_9h

description: sid2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana sid2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: Pou5f1-GFP MEF, biological replicate 2

description: Gene expression data from MEF cells

source_name: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven  by Pou5f1 promoter

growth_protocol: MEFs were cultured at 37°C with 5% CO2. MEFs were maintained in 15% FBS-DMEM containing 20 ?g ml-1 gentamicin.

tag: Pou5f1-GFP transgenic mice were from the Jackson Laboratory, Stock No 004654. Pou5f1-GFP MEFs were prepared from E13.5  embryos obtained from the intercross between male Pou5f1-GFP mice and female wild-type C57BL/6J mice.


title: KTset3_pad4-1_hrcC_9h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: KTset3_pad4-1_hrcC_3h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: KTset3_mpk3_hrcC_9h

description: mpk3 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: MEF2D binding 20 min after KCl replicate 2


title: KTset3_mpk3_hrcC_3h

description: mpk3 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: Pou5f1-GFP MEF, biological replicate 1

description: Gene expression data from MEF cells


title: MEF2D binding 2 hr after KCl replicate 1


title: KTset3_ein2-1_hrcC_9h

description: ein2-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana ein2-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: MEF2D binding in quiescent neurons replicate 2

description: MEF2D ChIP from quiescent neurons


title: iPS  OSE #T8, biological replicate 2

description: Gene expression data from mouse iPS cells

source_name: mouse induced pluripotent cells (iPS)

growth_protocol: Mouse iPS cells were cultured at 37°C with 5% CO2. Mouse iPS cells were maintained on mitomycin C-treated MEF feeders in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon).

tag: OSE-induced iPS


title: KTset3_ein2-1_hrcC_3h

description: ein2-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana ein2-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: Actin-GFP MEF, biological replicate 1

description: Gene expression data from MEF cells

source_name: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven  by Actin promoter.

tag: Actin-GFP transgenic mice were from the Jackson Laboratory, Stock No 003516. Actin-GFP MEFs were prepared from E13.5  embryos obtained from the intercross between male Actin-GFP mice and female wild-type CD1 mice.


title: iPS  OSE #T9, biological replicate 1


title: iPS  OSE #T9, biological replicate 2


title: iPS  OSCE #13, biological replicate 2

tag: OSCE-induced iPS


title: iPS  OSE #T8, biological replicate 1


title: iPS  OSCE #13, biological replicate 1


title: KTset3_dde2-2_hrcC_9h

description: dde2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana dde2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: control 20 min after KCl replicate 2

description: control ChIP from neurons depolarized by KCl for 20 minutes

source_name: control_20min after KCL (IP)

source_name: control_20min after KCL (Input)


title: KTset3_dde2-2_hrcC_3h

description: dde2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana dde2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: KTset3_Col-0_mock_9h

description: Col-0 infiltrated with water, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 9h


title: iPS OSCE #8, biological replicate 1


title: iPS OSCK, biological replicate 2

tag: OSCK-induced iPS


title: KTset3_Col-0_mock_3h

description: Col-0 infiltrated with water, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 3h


title: delta-pbf1 delta-pbf2 cells at T20, replicate #3

city: Worcester

first: Cong

last: Zhu

address: 364 Plantation Street

department: Program in Gene Function and Expression

institute: UMass Medical School

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 300.

data_processing: MAS 5

label: biotin

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells 20 min after heat shock

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

growth_protocol: S. cerevisiae cells were grown @ 25 ºC to O.D. 600 of 0.3~04, in triplicate.

extract_protocol: RiboPure kit were used to extract total RNA. Total RNAs were further purified using Qiagen RNAeasy Mini kit.

treatment_protocol: Half of the cells were collected at T0 and half of the cells were subjected to 25 ºC-->37 ºC heat shock and cells were collected after 20 min, as samples T20.

tag: delta-pbf1 delta-pbf2


title: ES cells, biological replicate 2

description: Gene expression data from mouse ES cells

source_name: R1 mouse embryonic stem (ES) cells

growth_protocol: Mouse ES cells were cultured at 37°C with 5% CO2. Mouse ES cells were maintained on mitomycin C-treated MEF feeders in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon).

tag: R1 mouse ES cells


title: delta-pbf1 delta-pbf2 cells at T20, replicate #2


title: delta-pbf1 delta-pbf2 cells at T0, replicate #3

source_name: S. cerevisiae cells before heat shock


title: delta-pbf1 delta-pbf2 cells at T20, replicate #1


title: iPS OSCK, biological replicate 1


title: delta-pbf1 delta-pbf2 cells at T0, replicate #2


title: delta-pbf1 delta-pbf2 cells at T0, replicate #1


title: KTset3_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: KTset3_Col-0_hrcC_3h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: KTset3_coi1-1_hrcC_9h

description: coi1-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana coi1-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: KTset3_coi1-1_hrcC_3h

description: coi1-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset3 experiment.

source_name: Arabidopsis thaliana coi1-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: delta-pbf2 cells at T20, replicate #2


title: delta-pbf2 cells at T0, replicate #3


title: delta-pbf2 cells at T20, replicate #1


title: delta-pbf2 cells at T20, replicate #3


title: delta-pbf2 cells at T0, replicate #2


title: KTset2_sid2-2_hrcC_9h

description: sid2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana sid2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: delta-pbf2 cells at T0, replicate #1


title: KTset2_pad4-1_hrcC_9h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: KTset2_pad4-1_hrcC_3h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: delta-pbf1 cells at T0, replicate #3


title: delta-pbf1 cells at T20, replicate #1


title: delta-pbf1 cells at T20, replicate #3


title: delta-pbf1 cells at T0, replicate #2


title: delta-pbf1 cells at T20, replicate #2


title: KTset2_sid2-2_hrcC_3h

description: sid2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana sid2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: iPS  OSCE #8, biological replicate 2

source_name: mouse induced pluripotent cells (iPS)


title: KTset2_Col-0_mock_9h

description: Col-0 infiltrated with water, harvested 9h after infiltration in setKTset2 experiment.


title: KTset2_dde2-2_hrcC_3h

description: dde2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset2 experiment.


title: KTset2_ein2-1_hrcC_9h

description: ein2-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana ein2-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: BY4741 cells at T20, replicate #3


title: delta-pbf1 cells at T0, replicate #1


title: KTset2_Col-0_mock_3h

description: Col-0 infiltrated with water, harvested 3h after infiltration in setKTset2 experiment.


title: KTset2_mpk3_hrcC_9h

description: mpk3 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: ES cells, biological replicate 1


title: KTset2_mpk3_hrcC_3h

description: mpk3 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: KTset2_ein2-1_hrcC_3h

description: ein2-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana ein2-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: KTset2_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset2 experiment.


title: KTset2_dde2-2_hrcC_9h

description: dde2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset2 experiment.

source_name: Arabidopsis thaliana dde2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: KTset2_Col-0_hrcC_3h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset2 experiment.


title: KTset1_sid2-2_hrcC_9h

description: sid2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset1 experiment.


title: KTset1_mpk3_hrcC_3h

description: mpk3 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset1 experiment.


title: KTset1_mpk3_hrcC_9h

description: mpk3 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset1 experiment.


title: BY4741 cells at T0, replicate #3


title: KTset1_Col-0_hrcC_3h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset1 experiment.


title: KTset1_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset1 experiment.


title: KTset1_ein2-1_hrcC_3h

description: ein2-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset1 experiment.


title: KTset1_Col-0_mock_9h

description: Col-0 infiltrated with water, harvested 9h after infiltration in setKTset1 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 9h


title: KTset1_Col-0_mock_3h

description: Col-0 infiltrated with water, harvested 3h after infiltration in setKTset1 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 3h


title: KTset1_ein2-1_hrcC_9h

description: ein2-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset1 experiment.


title: KTset1_dde2-2_hrcC_3h

description: dde2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset1 experiment.

source_name: Arabidopsis thaliana dde2-2, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: KTset1_pad4-1_hrcC_3h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset1 experiment.


title: KTset1_pad4-1_hrcC_9h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset1 experiment.


title: KTset1_sid2-2_hrcC_3h

description: sid2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset1 experiment.


title: KTset2_coi1-1_hrcC_3h

description: coi1-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset2 experiment.


title: KTset2_coi1-1_hrcC_9h

description: coi1-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset2 experiment.


title: BY4741 cells at T20, replicate #2

source_name: S. cerevisiae cells 20 min after heat shock


title: KTset1_coi1-1_hrcC_3h

description: coi1-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setKTset1 experiment.


title: Actin-GFP MEF, biological replicate 2

description: Gene expression data from MEF cells

source_name: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven  by Actin promoter.


title: KTset1_coi1-1_hrcC_9h

description: coi1-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset1 experiment.

source_name: Arabidopsis thaliana coi1-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: KTset1_dde2-2_hrcC_9h

description: dde2-2 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setKTset1 experiment.


title: BY4741 cells at T20, replicate #1


title: BY4741 cells at T0, replicate #2

source_name: S. cerevisiae cells before heat shock


title: MD 52ne 8 DPA Biological Replicate 2, Technical Replicate 1 (_39_2)

status: Public on Jan 14 2009

city: New Orleans

first: Doug

last: Hinchliffe

state: LA

address: 1100 Robert E Lee Blvd

department: Southern Regional Research Center

institute: USDA-ARS

hyb_protocol: For each aRNA probe labeled with either Cy5 or Cy3, 2ug was used for the hybridization.  The slides were prehybridized in 5X SSC, 0.1% SDS, and 0.1 mg/ml BSA (Fraction V) at 42oC for 45 minutes and then submerged in 0.1X SSC for 5 minutes three times, followed by a final submersion in ddH2O for 30 seconds.  The slides were dried by centrifugation at 1000 X g for 5 minutes.  The probe hybridization buffer consisted of 35% formamide, 5X SSC, 0.1% SDS, and 0.1 mg/ml sheared fish testes DNA.  All hybridizations were carried out at 42oC for 16 hours in a Genetix 10-slide Hybridization Chamber (Genetix, New Milton, England).  Following hybridization, slides were washed in 2X SSC, 0.1% SDS at 42oC for 5 minutes, then washed twice in 1X SSC at room temperature for 3 minutes, then washed twice in 0.1X SSC at room temperature for 2 minutes, and finally washed once in 0.05X SSC for 30 seconds.  After drying by centrifugation, the slides were treated with DyeSaver2 (Genisphere Inc., Hatfield, PA, USA) as per the manufacturer’s protocol to prevent ozone-mediated degradation of the Cy5 dye.

scan_protocol: Slides were scanned in a GenePix 4000B microarray scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at 10mm resolution using the GenePix Pro 6.0 software package.

data_processing: Data quality was evaluated using the data distribution and ratio analysis tools.  The data was normalized within arrays using Loess normalization and across arrays by median standardization (Dudoit et al., 2002).  The normalized expression levels were further evaluated for quality using correlation and principal components analyses.  The normalized expression levels were then analyzed in individual gene-specific models.  The gene-specific models were fit in JMP® Genomics using mixed models analysis (Wolfinger et al., 2001).  The germplasm lines, developmental stage (DPA), the interaction between germplasm line and developmental stage, and dye channel were the fixed effects.  The array effect was considered as a random effect.

organism: Gossypium hirsutum

source_name: Germplasm Line MD 52ne

label_protocol: RNA amplification and labeling was performed using the Amino Allyl MessageAmpTM aRNA Amplification Kit (Ambion, Austin, TX USA) as per the manufacturer’s protocol.  In each amplification reaction, 1000ng of total RNA was used for starting material.  The in vitro transcription reaction for synthesizing amplified RNA (aRNA) was performed for 12 hours.

growth_protocol: Cotton plants were grown in commericial field plots in Stoneville, MS.

extract_protocol: Total RNA was extracted and an on-column DNase I digestion performed using the Sigma Spectrum Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) as per the manufacturer’s protocol.

treatment_protocol: RNA amplification and labeling was performed using the Ambion Amino Allyl MessageAmpTM II aRNA Amplification Kit as per the manufacturer’s protocol.  In each amplification reaction, 1000ng of total RNA was used for starting material.  The in vitro transcription reaction for synthesizing amplified RNA (aRNA) was performed for 12 hours.  Probe aRNA was indirectly labeled by dye-coupling with Cy3 or Cy5 fluorescent dyes for hybridization to the cotton oligionucleotide gene chips.

value: 8 DPA

value: Immature Cotton Fiber Cells


title: MD 90ne 24 DPA Biological Replicate 1, Technical Replicate 2 (_38_2)

source_name: Germplasm Line MD 90ne

value: 24 DPA


title: BY4741 cells at T0, replicate #1


title: MD 52ne 8 DPA Biological Replicate 1, Technical Replicate 2 (_38_1)


title: MD 52ne 24 DPA Biological Replicate 1, Technical Replicate 1 (_33_1)


title: MD 52ne 8 DPA Biological Replicate 2, Technical Replicate 2 (_40_1)


title: MD 52ne 24 DPA Biological Replicate 2, Technical Replicate 2 (_36_2)


title: MD 52ne 24 DPA Biological Replicate 1, Technical Replicate 1 (_29_2)


title: MD 52ne 24 DPA Biological Replicate 2, Technical Replicate 2 (_32_1)


title: MD 52ne 8 DPA Biological Replicate 1, Technical Replicate 1 (_37_2)


title: MD 52ne 24 DPA Biological Replicate 1, Technical Replicate 2 (_34_2)


title: MD 90ne 24 DPA Biological Replicate 2, Technical Replicate 1 (_39_1)


title: MD 90ne 24 DPA Biological Replicate 2, Technical Replicate 1 (_35_2)


title: MD 52ne 24 DPA Biological Replicate 2, Technical Replicate 1 (_31_2)


title: MD 90ne 24 DPA Biological Replicate 2, Technical Replicate 2 (_40_2)


title: MD 52ne 24 DPA Biological Replicate 2, Technical Replicate 1 (_35_1)


title: MD 52ne 24 DPA Biological Replicate 1, Technical Replicate 2 (_30_1)


title: MD 90ne 24 DPA Biological Replicate 1, Technical Replicate 1 (_37_1)


title: MD 90ne 24 DPA Biological Replicate 1, Technical Replicate 1 (_33_2)


title: MD 90ne 24 DPA Biological Replicate 2, Technical Replicate 2 (_36_1)


title: MD 90ne 20 DPA Biological Replicate 2, Technical Replicate 2 (_32_2)

value: 20 DPA


title: MD 90ne 24 DPA Biological Replicate 1, Technical Replicate 2 (_34_1)


title: MD 90ne 20 DPA Biological Replicate 2, Technical Replicate 1 (_31_1)


title: MD 52ne 20 DPA Biological Replicate 2, Technical Replicate 2 (_28_2)


title: MD 90ne 20 DPA Biological Replicate 1, Technical Replicate 2 (_30_2)


title: MD 90ne 20 DPA Biological Replicate 1, Technical Replicate 1 (_29_1)


title: MD 90ne 20 DPA Biological Replicate 2, Technical Replicate 1 (_27_2)


title: MD 90ne 20 DPA Biological Replicate 2, Technical Replicate 2 (_28_1)


title: MD 52ne 20 DPA Biological Replicate 2, Technical Replicate 1 (_27_1)


title: MD 90ne 20 DPA Biological Replicate 1, Technical Replicate 2 (_26_1)


title: MD 52ne 20 DPA Biological Replicate 1, Technical Replicate 2 (_26_2)


title: MD 52ne 16 DPA Biological Replicate 2, Technical Replicate 1 (_19_1)

value: 16 DPA


title: MD 52ne 20 DPA Biological Replicate 2, Technical Replicate 2 (_24_1)


title: MD 90ne 16 DPA Biological Replicate 1, Technical Replicate 2 (_22_2)


title: MD 90ne 16 DPA Biological Replicate 2, Technical Replicate 1 (_23_1)


title: MD 52ne 20 DPA Biological Replicate 1, Technical Replicate 2 (_22_1)


title: MD 52ne 16 DPA Biological Replicate 1, Technical Replicate 2 (_18_2)


title: MD 90ne 16 DPA Biological Replicate 2, Technical Replicate 2 (_24_2)


title: MD 90ne 16 DPA Biological Replicate 2, Technical Replicate 1 (_19_2)


title: MD 90ne 20 DPA Biological Replicate 1, Technical Replicate 1 (_25_2)


title: MD 52ne 16 DPA Biological Replicate 2, Technical Replicate 1 (_15_2)


title: MD 90ne 16 DPA Biological Replicate 1, Technical Replicate 1 (_21_1)


title: MD 52ne 16 DPA Biological Replicate 1, Technical Replicate 1 (_17_1)


title: MD 90ne 16 DPA Biological Replicate 2, Technical Replicate 2 (_20_1)


title: MD 52ne 16 DPA Biological Replicate 2, Technical Replicate 2 (_20_2)


title: MD 52ne 16 DPA Biological Replicate 2, Technical Replicate 2 (_16_1)


title: MD 52ne 20 DPA Biological Replicate 1, Technical Replicate 1 (_25_1)


title: MD 90ne 16 DPA Biological Replicate 1, Technical Replicate 1 (_17_2)


title: MD 52ne 20 DPA Biological Replicate 1, Technical Replicate 1 (_21_2)


title: MD 52ne 20 DPA Biological Replicate 2, Technical Replicate 1 (_23_2)


title: MD 90ne 16 DPA Biological Replicate 1, Technical Replicate 2 (_18_1)


title: MD 90ne 12 DPA Biological Replicate 1, Technical Replicate 2 (_14_2)

value: 12 DPA


title: MD 52ne 16 DPA Biological Replicate 1, Technical Replicate 2 (_14_1)


title: MD 90ne 12 DPA Biological Replicate 2, Technical Replicate 1 (_15_1)


title: MD 90ne 12 DPA Biological Replicate 2, Technical Replicate 2 (_16_2)


title: MD 52ne 16 DPA Biological Replicate 1, Technical Replicate 1 (_13_2)


title: MD 90ne 12 DPA Biological Replicate 1, Technical Replicate 1 (_13_1)


title: MD 90ne 12 DPA Biological Replicate 2, Technical Replicate 2 (_12_1)


title: MD 52ne 12 DPA Biological Replicate 2, Technical Replicate 1 (_11_1)


title: MD 52ne 12 DPA Biological Replicate 1, Technical Replicate 2 (_10_2)


title: MD 90ne 12 DPA Biological Replicate 2, Technical Replicate 1 (_11_2)


title: MD 52ne 12 DPA Biological Replicate 1, Technical Replicate 1 (_9_1)


title: MD 52ne 12 DPA Biological Replicate 2, Technical Replicate 2 (_8_1)


title: MD 90ne 12 DPA Biological Replicate 1, Technical Replicate 1 (_9_2)


title: MD 52ne 12 DPA Biological Replicate 2, Technical Replicate 2 (_12_2)


title: MD 90ne 12 DPA Biological Replicate 1, Technical Replicate 2 (_10_1)


title: MD 90ne 8 DPA Biological Replicate 1, Technical Replicate 2 (_6_2)


title: MD 90ne 8 DPA Biological Replicate 2, Technical Replicate 2 (_8_2)


title: MD 52ne 12 DPA Biological Replicate 2, Technical Replicate 1 (_7_2)


title: MD 52ne 12 DPA Biological Replicate 1, Technical Replicate 2 (_6_1)


title: MD 90ne 8 DPA Biological Replicate 2, Technical Replicate 1 (_7_1)


title: TNF-a treated chondrocytes, biological replicate 1

city: London

first: Jason

middle: Scott

last: Rockel

state: Ontario

address: The University of Western Ontario

department: Anatomy and Cell Biology

country: Canada

institute: CIHR Group in Skeletal Development and Remodeling

hyb_protocol: Following cRNA fragmentation, cRNA were hybridized to GeneChip RAT230 2.0 arrays and stained using the Affymetrix Fluidics 450 station as per manufacturers instructions (Expression Analysis Technical Manual, 2005-2006, Affymetrix)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Data was analyzed using Genespring GX 7.3 (Agilent).  Values were transformed using RMA.  Raw expression values <0.01 were set to 0.01 and the normalization per chip was set to the 50th percentile. Genes were normalized to DMSO control within each biological replicate.

source_name: Primary chondrocytes derived from the femoral condyles of neonatal rats, pre-treated with DMSO for 30 min followed by TNF-a for 24h.

label_protocol: Biotinylated cRNA was prepared as per standard Affymetrix protocol using 10mg of total RNA to start (Expression Analysis Technical Manual, 2005-2006, Affymetrix)

growth_protocol: Chondrocytes were isolated from the femoral condyles of neonatal (one day old) rats and plated onto tissue culture plastic at a density of ~2.5 x 104 cells/cm2.  Cells were grown in culture until confluence was reached, typcially 6-7 days.  Media used was RPMI-1640 supplimented with 5% fetal bovine serum (FBS), 100 U/ml Penicillin, 100 g/ml streptomycin and 1% HEPES buffer.  The media was changed every 3 days.

extract_protocol: Total RNA was collected by Trizol followed by Qiagen Rneasy mini clean-up, as per manufacturers' instructions.

treatment_protocol: Chondrocytes were incubated in serum free media overnight.  The next day, chondrocytes were treated with DMSO or U0126 for 30 minutes prior to addition of vehicle (BSA) or TNF-a (30 ng/ml) for 24 h.

tag: Strain:Sprague Dawley, Age:neonatal, Tissue:rat femoral condyle, Cell:chondrocytes, Contidion

value: Cell Culture/In vitro


title: MD 52ne 12 DPA Biological Replicate 1, Technical Replicate 1 (_5_2)


title: U0126 and TNF-a-treated chondrocytes, biological replicate 1

source_name: Primary chondrocytes derived from the femoral condyles of neonatal rats, pre-treated with U0126 for 30 min followed by TNF-a for 24h.


title: MD 90ne 8 DPA Biological Replicate 2, Technical Replicate 2 (_4_1)


title: MD 52ne 8 DPA Biological Replicate 1, Technical Replicate 2 (_2_2)


title: MD 90ne 8 DPA Biological Replicate 2, Technical Replicate 1 (_3_2)


title: U0126 and TNF-a-treated chondrocytes, biological replicate 2

source_name: Primary chondrocytes derived from the femoral condyles of neonatal rats, pre-treated withU0126 for 30 min followed by TNF-a for 24h.


title: MD 90ne 8 DPA Biological Replicate 1, Technical Replicate 1 (_5_1)


title: TNF-a treated chondrocytes, biological replicate 2


title: Mouse SAGE lung tissue HMD_9801

type: SAGE

anchor: NlaIII

city: Research Triangle Park

first: Kathy

last: Boon

state: NC

address: 111 TW Alexander Dr

department: Division of Intramural Research

institute: NHLBI/NIEHS

description: Frozen lung tissue from C57BL/6 adult mice that were prenatally exposed to diets with increased (HMD) methyl-donor content, with the mice gestated on a HMD developing an allergic disease phenotype according to a high eosinophil count in lavage fluid (Hollingsworth et al., American Journal of Respiratory and Critical Care Medicine 2008, (Abstracts Issue):A.

data_processing: Tag sequences were extracted from sequence files using the SAGE 2000 software.

source_name: Mouse lung tissue

extract_protocol: Total RNA was extracted from frozen lung tissue using the RNAgents total RNA isolation system (Promega, Madison, WI, USA).

tag: Lung tissue from a pool of two C57/BL6 mice prenatally exposed to a diet high in methyl-donor content and an allergic disease phenotype.


title: MD 52ne 8 DPA Biological Replicate 2, Technical Replicate 2 (_4_2)

tag: Tissue


title: MD 52ne 8 DPA Biological Replicate 2, Technical Replicate 1 (_3_1)

tag: Age


title: Synechocystis PCC6803, pooled RNA, sample 2_2

city: Freiburg

first: Jan

last: Mitschke

address: Schaenzlestr. 1

department: Biologie III

country: Germany

institute: University of Freiburg

description:
Biological replicate 2 of 2.
Technical replicate 2 of 2 (dye-swap).

hyb_protocol: For RNA hybridizations, the labelled RNA mix was fragmented and hybridized as described by the manufacturer's instructions for Agilent one-color microarrays with 3 to 5.5 µg of labeled RNA. Hybridization of labelled genomic DNA was performed similar to RNA hybridization, but omitting the fragmentation step in the Agilent protocol. For DNA hybridization, 0.5 to 3.8 µg of labeled DNA were used.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 9.5.3 and the modified protocol GE2-v5_95_Feb07 for Cy5 labelled arrays and the protocol GE1-v5_95_Feb07 for Cy3 labelled arrays.

data_processing: The raw data were normalized and rescaled. The normalization method “normalizeByReference” (Huber et. al. 2006) from the Bioconductor package “tilingArray” was used. This method offers a probe-specific background correction and scaling method that employs empirical probe response parameters determined from reference hybridizations (DNA samples).  The raw data from the DNA hybridizations are in the GSE14410_DNA_1.txt and GSE14410_DNA_2.txt files, available on the Series GSE14410 record.

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis PCC6803, pooled RNA, all treatments

label_protocol: The RNA mix was labeled directly, without cDNA synthesis in 5 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 or Cy5 according to the manufacturer's protocol. DNA was fragmented by 3h incubation at 95°C in H2O and Cy3 labeled with the Kreatech kit mentioned before.

growth_protocol: Standard growth conditions: Liquid cultures of Synechocystis 6803 were grown at 30°C in BG11 (20mM TES pH 7.6) medium under continuous illumination with white light of 50 μmol of photons•m–2•s–1 and a continuous stream of air. For array hybridization, a pooled RNA sample was generated by mixing equal amounts of RNA from all treatments.

extract_protocol: Synechocystis 6803 cells were collected by rapid filtration (Pall Supor 800 Filter, 0,8 µm). Filters with cells were dissolved in 1 ml TRIzol (Invitrogen) per 40 ml culture, immediately frozen in liquid nitrogen and incubated 15 min at 65 °C in a water bath. Further RNA isolation followed the manufacturer’s protocol.

treatment_protocol: Different growth and stress conditions were applied to exponentially growing cultures of Synechocystis 6803 as follows: For high light stress, light intensity was shifted from 50 to 500 μmol of photons•m–2•s–1, samples were collected 30, 60 and 180 min after the shift. For low light conditions, light intensity was shifted from 100 to 10 μmol of photons•m–2•s–1, samples were collected 30, 60 and 180 min after the shift. For iron and nitrogen stress, cells were collected by centrifugation and washed twice with iron-free (replacing ammonium iron (III) citrate with di-ammonium hydrogen citrate) or nitrogen-free (omitting sodium nitrate from the medium) BG11 medium. For iron stress, cells were harvested after 20 and 45 h, for nitrogen stress after 12.5 and 20 h. Heat and cold stress were applied by a temperature shift from 30 °C to 42 °C, respectively 15 °C. For heat stress, sample collection occurred after 20 and 60 min, for cold stress after 30 and 120 min. Another culture was harvested after 12 h incubation in the dark. For stationary phase, a culture was harvested at an OD750 of 3.5.

tag: Pooled RNA sample.

tag: Equal amounts of RNA from all treatments.


title: MD 90ne 8 DPA Biological Replicate 1, Technical Replicate 2 (_2_1)


title: Mouse SAGE lung tissue LMD_9495

description: Frozen lung tissue from C57BL/6 adult mice that were prenatally exposed to diets with decreased (LMD) methyl-donor content, with the mice gestated on a LMD  not developing an allergic disease phenotype according to the low eosinophil counts in lavage fluid (Hollingsworth et al., American Journal of Respiratory and Critical Care Medicine 2008, (Abstracts Issue):A.

tag: Lung tissue from a pool of two C57BL/6 mice subjected prenatally to a diet low in methyl-donor content.


title: U0126-treated chondrocytes, biological replicate 1

source_name: Primary chondrocytes derived from the femoral condyles of neonatal rats, pre-treated with U0126 for 30 min followed by vehicle (BSA) for 24h.


title: MD 90ne 8 DPA Biological Replicate 1, Technical Replicate 1 (_1_2)


title: Aerobic pH 9.0 rep 3

status: Public on Jan 13 2009

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

description: Gene expression profiles of Bacillus subtilis strain AG174 were compared as a function of steady-state external pH during growth with aeration.  Aerated overnight cultures were diluted 1:500 and incubated in 250 mL baffled flasks containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 6.0, pH 7.0, and pH 9.0.  Tubes were incubated at 37°C with aeration (260 rpm) to an optical density at 600 nm of 0.2.  For each of the three pH conditions, RNA was isolated from five independent cultures.

hyb_protocol: Affymetrix standard procedures

scan_protocol: Affymetrix standard procedures

data_processing: Affymetrix GCOS software

organism: Bacillus subtilis

source_name: Bacillus subtilis strain AG174

label_protocol: Labeled cDNA was prepared and hybridized to Affymetrix Antisense Bacillus subtilis arrays by standard procedures.

growth_protocol: Overnight cultures were diluted 1:500 and incubated in 250 mL baffled flasks containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 6.0, pH 7.0, and pH 9.0.  Cultures were incubated at 37°C with aeration (260 rpm) to an optical density at 600 nm of 0.2. Five replicate cultures were grown at each pH.

extract_protocol: RNA was isolated using RNAprotect (Qiagen) and the RNeasy Kit.

treatment_protocol: Growth at pH 9.0

tag: Bacillus subtilis strain AG174


title: U0126-treated chondrocytes, biological replicate 2


title: Synechocystis PCC6803, pooled RNA, sample 1_2

description:
Biological replicate 2 of 2.
Technical replicate 1 of 2.


title: Synechocystis PCC6803, pooled RNA, sample 2_1

description:
Biological replicate 1 of 2.
Technical replicate 2 of 2 (dye-swap).


title: Aerobic pH 7.0 rep 4

treatment_protocol: Growth at pH 7.0


title: Aerobic pH 7.0 rep 2


title: Aerobic pH 9.0 rep 5

source_name: Bacillus subtilis AG174

tag: Bacillus subtilis AG174


title: Aerobic pH 9.0 rep 4


title: DMSO-treated chondrocytes, biological replicate 1

source_name: Primary chondrocytes derived from the femoral condyles of neonatal rats, pre-treated with DMSO for 30 min followed by vehicle (BSA) for 24h.


title: MD 52ne 8 DPA Biological Replicate 1, Technical Replicate 1 (_1_1)


title: Aerobic pH 7.0 Rep 1


title: Aerobic pH 9.0 rep 1


title: Aerobic pH 7.0 rep 5


title: 33655

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

hyb_protocol: Hybridized overnight (16 hr) to Rhesus macaque GeneChips

scan_protocol: Affymetrix 3000 scanner at the excitation wavelength of 488 nm

data_processing: Data processed with dChip software. Invariant set normalization and model-based expression with PM only probesets

organism: Macaca mulatta

source_name: oropharynx, SIV infected

label_protocol: cDNA copies of the mRNA synthesized by reverse transcription, and used as a template for the synthesis of biotin-labeled cRNA in an in vitro transcription (IVT) reaction

extract_protocol: protocols and reagents in Qiagen RNeasy kit

tag: SIV infected, adult male


title: DMSO-treated chondrocytes, biological replicate 2


title: Aerobic pH 6.0 rep 5

treatment_protocol: Growth at pH 6.0


title: Aerobic pH 9.0 rep 2


title: 30327

source_name: oropharynx tissue, uninfected

tag: uninfected, adult male


title: Aerobic pH 7.0 rep 3


title: Aerobic pH 6.0 rep_4


title: Synechocystis PCC6803, pooled RNA, sample 1_1

description:
Biological replicate 1 of 2.
Technical replicate 1 of 2.


title: 34816

source_name: oropharynx, uninfected


title: 33832


title: 35182


title: Aerobic pH 6.0 rep 1

description: Gene expression profiles of Bacillus subtilis strain AG174 were compared as a function of steady-state external pH during growth with aeration.  Aerated overnight cultures were diluted 1:500 and incubated in 250 mL baffled flasks containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 6.0, pH 7.0, and pH 9.0.  Tubes were incubated at 37°C with aeration (260 rpm) to an optical density at 600 nm of 0.2.    For each of the three pH conditions, RNA was isolated from five independent cultures.


title: Aerobic pH 6.0 rep 3


title: F55T24R2

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

description: Family 55 Time 24 Replicate 2

hyb_protocol: Each slide hybridized with 90-μl mixture containing 20 μg of Cy3-coupled aRNA in hybridization buffer [50% formamide, 2.4% SDS, 4xSSPE, 2.5x Denhardt’s solution, plus 1 µg Cot-DNA and 1 µg polydATP].  Hybridizations were conducted at 50°C in a humidified hybridization oven (Boekel   Inslide-Outtm, Boekel, Festerville, PA) for 12 h.

scan_protocol: ScanArray Express (Perkin Elmer, Boston, MA) microarray scanner, 70% PMT gain and 90% laser power.The QuantArray software package (Perkin Elmer, Boston, MA) was used to acquire raw fluorescence data, background, and spot quality information from the scanned images using the included Histogram spot segmentation method.  Each spot image was visually inspected for overall quality, and damaged spots were excluded prior to statistical analysis.

data_processing: We transformed the entire dataset using a variance stabilization normalization method (vsn; Huber et al. 2002).  All spots were included in the transformation.  Spot pairs were excluded whose average intensity across the 60 slides was less than 6 for at least 1 of the sampling times, and we excluded all unsequenced spots.  We omitted flagged spots prior to statistical analysis.

organism: Magallana gigas

source_name: Family 55 Time 24

label_protocol: 1 microgram of antisense RNA was labeled with Cy3 dye according to the protocol for the Amino Allyl MessageAmp™ Kit (Ambion, Inc., Austin, TX).

extract_protocol: Each sample contaiend 50 mg gill from three individuals of each family.  Total RNA were extracted using the Qiagen miniprep system and on-column DNAse treatment.  Total RNA were used as template for synthesizing antisense RNA using the Amino Allyl MessageAmp™ Kit (Ambion, Inc., Austin, TX).  Each reaction included RNA standards:  100 ng chlorophyll A/B binding protein (Genbank #CO059871) RNA, 10 ng photosystem core protein (Genbank #CO062297) RNA, 1 ng flavodoxin (Genbank #CO065421) RNA, and 0.1 ng photolyase (Genbank #CO064781) RNA.

treatment_protocol: heat shocked 40C, 1 hour

tag: Gill

tag: High-surviving family

tag: 2.5 years of age

tag: 24 hours after heat shock


title: F55T3R2

description: Family 55 Time 3 Replicate 2

source_name: Family 55 Time 3

tag: 3 hours after heat shock


title: F55T24R1

description: Family 55 Time 24 Replicate 1


title: F55T6R3

description: Family 55 Time 6 Replicate 3

source_name: Family 55 Time 6

tag: 6 hours after heat shock


title: F55T3R3

description: Family 55 Time 3 Replicate 3


title: F55T6R2

description: Family 55 Time 6 Replicate 2


title: F25T24R3

description: Family 25 Time 24 Replicate 3

source_name: Family 25 Time 24


title: F55T0R1

description: Family 55 Time 0 Replicate 1

source_name: Family 55 Time 0

tag: Before heat shock


title: F55T0R2

description: Family 55 Time 0 Replicate 2


title: F55T0R3

description: Family 55 Time 0 Replicate 3


title: F55T1R1

description: Family 55 Time 1 Replicate 1

source_name: Family 55 Time 1

tag: 1 hour after heat shock


title: F55T1R2

description: Family 55 Time 1 Replicate 2


title: F25T6R1

description: Family 25 Time 6 Replicate 1

source_name: Family 25 Time 6


title: F55T6R1

description: Family 55 Time 6 Replicate 1


title: F25T6R3

description: Family 25 Time 6 Replicate 3


title: F25T6R2

description: Family 25 Time 6 Replicate 2


title: F25T3R3

description: Family 25 Time 3 Replicate 3

source_name: Family 25 Time 3


title: F25T3R2

description: Family 25 Time 3 Replicate 2


title: F55T24R3

description: Family 55 Time 24 Replicate 3


title: F25T24R1

description: Family 25 Time 24 Replicate 1


title: F25T24R2

description: Family 25 Time 24 Replicate 2


title: F25T3R1

description: Family 25 Time 3 Replicate 1


title: F55T3R1

description: Family 55 Time 3 Replicate 1


title: F55T1R3

description: Family 55 Time 1 Replicate 3


title: Aerobic pH 6.0 rep 2


title: F25T1R3

description: Family 25 Time 1 Replicate 3

source_name: Family 25 Time 1


title: F6T6R1

description: Family 6 Time 6 Replicate 1

source_name: Family 6 Time 6

tag: Low-surviving family


title: F10T1R3

description: Family 10 Time 1 Replicate 3

source_name: Family 10 Time 1


title: F10T1R1

description: Family 10 Time 1 Replicate 1


title: F10T1R2

description: Family 10 Time 1 Replicate 2


title: F6T6R2

description: Family 6 Time 6 Replicate 2


title: F6T6R3

description: Family 6 Time 6 Replicate 3


title: F6T3R3

description: Family 6 Time 3 Replicate 3

source_name: Family 6 Time 3


title: F6T24R1

description: Family 6 Time 24 Replicate 1

source_name: Family 6 Time 24


title: F10T6R2

description: Family 10 Time 6 Replicate 2

source_name: Family 10 Time 6


title: F6T3R2

description: Family 6 Time 3 Replicate 2


title: F10T6R1

description: Family 10 Time 6 Replicate 1


title: F10T24R2

description: Family 10 Time 24 Replicate 2

source_name: Family 10 Time 24


title: F6T24R2

description: Family 6 Time 24 Replicate 2


title: F10T24R3

description: Family 10 Time 24 Replicate 3


title: F6T3R1

description: Family 6 Time 3 Replicate 1


title: F10T6R3

description: Family 10 Time 6 Replicate 3


title: F10T24R1

description: Family 10 Time 24 Replicate 1


title: F25T0R1

description: Family 25 Time 0 Replicate 1

source_name: Family 25 Time 0


title: F25T0R2

description: Family 25 Time 0 Replicate 2


title: F25T1R1

description: Family 25 Time 1 Replicate 1


title: F6T1R3

description: Family 6 Time 1 Replicate 3

source_name: Family 6 Time 1


title: F6T1R2

description: Family 6 Time 1 Replicate 2


title: F6T1R1

description: Family 6 Time 1 Replicate 1


title: F25T0R3

description: Family 25 Time 0 Replicate 3


title: F6T24R3

description: Family 6 Time 24 Replicate 3


title: F25T1R2

description: Family 25 Time 1 Replicate 2


title: F10T0R2

description: Family 10 Time 0 Replicate 2

source_name: Family 10 Time 0


title: F6T0R3

description: Family 6 Time 0 Replicate 3

source_name: Family 6 Time 0


title: F10T0R3

description: Family 10 Time 0 Replicate 3


title: F6T0R1

description: Family 6 Time 0 Replicate 1


title: F6T0R2

description: Family 6 Time 0 Replicate 2


title: F10T0R1

description: Family 10 Time 0 Replicate 1


title: ap2-o disruptant ookinete culture 12h NO.105

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

description: P. berghei ap2-o disruptant ookinete culture 12h

hyb_protocol: Agilent Hybridization Protocol

scan_protocol: Scanned using Agilent microarray scanner

data_processing: Data were extracted with Agilent Feature Extraction 9.1 Software

organism: Plasmodium berghei

source_name: Plasmodium berghei ap2-o disruptant ookinete culture 12h

label_protocol: Agilent Low RNA Input Linear Amplification Protocol

extract_protocol: Total RNA Isolation System (Promega)


title: ap2-o disruptant ookinete culture 12h NO.104

tag: Plasmodium berghei ap2-o disruptant ookinete culture 12h


title: ap2-o disruptant ookinete culture 12h NO.103


title: Animal exposed to novel environment, animal #2

status: Public on Jan 12 2009

first: Steven

middle: Willem

last: Flavell

address: CLS 12260, 300 Longwood Avenue

institute: Children's Hospital Boston

description: Expression profiling to identify genes upregulated in response to exposure to a novel environment

hyb_protocol: Standard Affymetrix hybridization procedures.

scan_protocol: Standard Affymetrix scanning procedures.

data_processing: Raw CEL files were normalized using RMAexpress.

source_name: Rat forebrain, after three hours exposure to novel environment

label_protocol: Labeled cRNA prepared according to standard Affymetrix procedures

growth_protocol: Six-week old, male Long Evans rats were housed individually for several days

extract_protocol: Trizol extraction followed by RNEasy Mini Cleanup

treatment_protocol: Six animals were moved into a novel environment containing objects of different shapes and colors for three hours


title: F10T3R1

description: Family 10 Time 3 Replicate 1

source_name: Family 10 Time 3


title: F10T3R3

description: Family 10 Time 3 Replicate 3


title: F10T3R2

description: Family 10 Time 3 Replicate 2


title: WT ookinete culture 12h NO.101

description: P. berghei WT ookinete 12h

source_name: Plasmodium berghei WT ookinete culture 12h


title: WT ookinete culture 12h NO.102

description: P. berghei WT ookinete 12h

tag: Plasmodium berghei WT ookinete culture 12h


title: Control animal, animal #4

source_name: Rat forebrain, control condition


title: Animal exposed to novel environment, animal #6


title: Control animal, animal #2


title: Animal exposed to novel environment, animal #1


title: Animal exposed to novel environment, animal #5


title: WT ookinete culture 12h NO.100

description: P. berghei WT ookinete 12h


title: MEF2-VP16-ER, 1 hrs 4OHT, Biol Rep3

description: Expression profiling in hippocampal neurons to identify activity-regulated genes controlled by MEF2

source_name: Hippocampal neurons, MEF2-VP16-ER, 1 hours 4OHT

growth_protocol: Hippocampal neurons were grown in dissociated culture for 10 days in vitro.

extract_protocol: Rneasy Micro Kit from Qiagen

treatment_protocol: On day in vitro 3, neurons were transduced with lentiviruses expressing either either control MEF2deltaDBD-VP16-ER or MEF2-VP16-ER.  On day in vitro 10, 4OHT was applied for 0, 1 or 2.5 hours.


title: Control animal, animal #3


title: Control animal, animal #6


title: Animal exposed to novel environment, animal #3


title: Control animal, animal #1


title: Control animal, animal #5


title: MEF2-VP16-ER, 2.5 hrs 4OHT, Biol Rep3

source_name: Hippocampal neurons, MEF2-VP16-ER, 2.5 hours 4OHT


title: MEF2-VP16-ER, 0 hrs 4OHT, Biol Rep3

source_name: Hippocampal neurons, MEF2-VP16-ER, 0 hours 4OHT


title: Animal exposed to novel environment, animal #4


title: Control, 2.5 hrs 4OHT, Biol Rep3

source_name: Hippocampal neurons, MEF2deltaDBD-VP16-ER, 2.5 hours 4OHT


title: MEF2-VP16-ER, 1 hrs 4OHT, Biol Rep2


title: Control, 1 hrs 4OHT, Biol Rep3

source_name: Hippocampal neurons, MEF2deltaDBD-VP16-ER, 1 hours 4OHT


title: MEF2-VP16-ER, 2.5 hrs 4OHT, Biol Rep2


title: Control, 0 hrs 4OHT Biol Rep3

source_name: Hippocampal neurons, MEF2deltaDBD-VP16-ER, 0 hours 4OHT


title: NEC942M

city: Montreal

first: Olivier

middle: Charles

last: Maes

state: Quebec

address: 3999 Cote Ste Catherine

department: Bloomfield Centre for Research in Aging

institute: Lady Davis Institute for Medical Research

description: peripheral blood mononuclear cell

hyb_protocol: Nadon, Mohr, and Becker, National Institute on Aging microarray facility--resources for gerontology research. Journals of Gerontology Series A-Biological Sciences & Medical Sciences, 2005. 60(4): p. 413-5

scan_protocol: Hybridization intensities were measured by a Storm PhosphorImager (Molecular Dynamics)

data_processing: Array-Pro Analyzer 4.5 software (Media Cybernetics). Data acquisition was made using the option net intensity. Net intensity corrected with mean intensity from background calculated by a biquadratic polynomial.

label: alpha 32P dCTP

organism: Homo sapiens

source_name: peripheral blood

label_protocol: 3 µg of total RNA was processed into radioactive cDNA targets

extract_protocol: Lacelle et al., J Gerontol A Biol Sci Med Sci, 2002. 57(7): p. B285-7

tag: Normal elderly control, Female


title: NEC843M

description: peripheral blood mononuclear cell


title: MEF2-VP16-ER, 0 hrs 4OHT, Biol Rep2


title: Control, 0 hrs 4OHT Biol Rep1


title: Control, 2.5 hrs 4OHT, Biol Rep2


title: MEF2-VP16-ER, 2.5 hrs 4OHT, Biol Rep1


title: Control, 1 hrs 4OHT, Biol Rep2


title: Control, 1 hrs 4OHT, Biol Rep1


title: Ser5P RNA Pol II EtOH

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: See the NimbleGen website

hyb_protocol: See the NimbleGen website

scan_protocol: See the NimbleGen website

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team). All data processing scripts are available upon request. The log2 ratio data from each of the arrays was subjected to lowess normalization.

source_name: Ser5P RNA Pol II, EtOH treated

label_protocol: See the NimbleGen website

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against Ser5P RNA Pol II. The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.

tag: MCF7 cells

source_name: Input DNA

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The DNA was then amplified by LM-PCR.


title: MEF2-VP16-ER, 1 hrs 4OHT, Biol Rep1


title: Control, 2.5 hrs 4OHT, Biol Rep1


title: MEF2 RNAi, 6 hrs KCl, Biol Rep3

source_name: Hippocampal neurons, MEF2A and MEF2D shRNAs, 6 hours KCl depolarization

treatment_protocol: On day in vitro 3, neurons were transduced with lentiviruses expressing either control or MEF2-specific shRNAs.  On day in vitro 10, AP5 and TTX were applied to neurons for one hour, after which 55mM extracellular KCl was applied for 0, 1 or 6 hours.


title: Control, 1 hrs KCl, Biol Rep3

source_name: Hippocampal neurons, control shRNAs, 1 hours KCl depolarization


title: Control, 0 hrs 4OHT Biol Rep2


title: MEF2 RNAi, 0 hrs KCl, Biol Rep3

source_name: Hippocampal neurons, MEF2A and MEF2D shRNAs, 0 hours KCl depolarization


title: NELFA EtOH

description: See the NimbleGen website

source_name: NELFA ChIP, EtOH treated

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against NELFA. The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.


title: RNA Pol II E2 Rep2

description: See the NimbleGen website

source_name: RNA Pol II ChIP, E2 treated

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against RNA Pol II. The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.


title: RNA Pol II E2 Rep1

description: See the NimbleGen website


title: Control, 0 hrs KCl, Biol Rep3

source_name: Hippocampal neurons, control shRNAs, 0 hours KCl depolarization


title: MEF2 RNAi, 1 hrs KCl, Biol Rep3

source_name: Hippocampal neurons, MEF2A and MEF2D shRNAs, 1 hours KCl depolarization


title: MEF2 RNAi, 6 hrs KCl, Biol Rep2


title: MEF2-VP16-ER, 0 hrs 4OHT, Biol Rep1


title: Control, 1 hrs KCl, Biol Rep2


title: Control, 6 hrs KCl, Biol Rep2

source_name: Hippocampal neurons, control shRNAs, 6 hours KCl depolarization


title: Control, 6 hrs KCl, Biol Rep3


title: MEF2 RNAi, 6 hrs KCl, Biol Rep1


title: MEF2 RNAi, 0 hrs KCl, Biol Rep1


title: MEF2 RNAi, 0 hrs KCl, Biol Rep2


title: MEF2 RNAi, 1 hrs KCl, Biol Rep1


title: Control, 1 hrs KCl, Biol Rep1


title: Control, 6 hrs KCl, Biol Rep1


title: MEF2 RNAi, 1 hrs KCl, Biol Rep2


title: Control, 0 hrs KCl, Biol Rep2


title: Control, 0 hrs KCl, Biol Rep1


title: RNA Pol II EtOH Rep2

description: See the NimbleGen website

source_name: RNA Pol II ChIP, EtOH treated


title: Fibroblast_HFF1p8

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

country: France

institute: University Hospital of Montpellier

description: Human embryonic stem cells (hESC) samples were compared to somatic tissues, human mature oocytes samples were compared to somatic tissues, then the hESC and the mature oocyte signatures were interesected to define an oocyte/hESC signature.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: human foreskin fibroblasts at passage 8

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.

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

tag: subconfluent culture of human foreskin fibroblasts cell line from ATCC, at passage 8. HFF were cultured in in 85% DMEM, 15% fetal calf serum.


title: MCF7_1ug

source_name: Breast adenocarcinoma cell line MCF7 (1ug)

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'standard protocol', starting from 1 microgram total RNA.

tag: subconfluent breast adenocarcinoma cell line MCF7. Sample labelling starting with 1 microgram total RNA.


title: Liver_infected_4weeks_rep1

status: Public on Jan 10 2009

city: Herston

first: Melissa

middle: Louise

last: Burke

state: QLD

address: 300 Herston Road

department: Division of Infectious Diseases and Immunology

country: Australia

institute: Queensland Institute of Medical Research

description: Gene expression in the liver of C57BL/6 mice 4 weeks post infection with Schistosoma japonicum

hyb_protocol: cRNA was hybridised to Illumina mouse-6 v1.1 expression beadchips according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing: Data was analysed using BeadStudio and Genespring GX

source_name: Liver homogenate, infected, 4 weeks

label_protocol: cRNA was synthesised from 250ng of pooled total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

extract_protocol: Total RNA was extracted from 100mg of liver tissue or purified schistosome eggs by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Mice were euthanized and their livers were perfused with chilled PBS. Liver tissue was collected and stored in RNAlater for microarray analysis or frozen for egg extraction

tag: Strain

tag: Gender

value: Female

tag: Age

value: 6 weeks

tag: Tissue

value: Liver

tag: Treatment

value: 4 weeks post infection 20 cercariae


title: MCF7_5ug

source_name: Breast adenocarcinoma cell line MCF7 (5ug)

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'standard protocol', starting from 5 microgram total RNA.

tag: Subconfluent breast adenocarcinoma cell line MCF7. Sample labelling starting with 5 microgram total RNA.


title: Liver_infected_7weeks_rep2

description: Gene expression in the liver of C57BL/6 mice 7 weeks post infection with Schistosoma japonicum

source_name: Liver homogenate, infected, 7 weeks

value: 7 weeks post infection 20 cercariae


title: Schistosome_Eggs_rep2

description: Cross reactivity of Schistosoma japonicum egg gene expression with mouse genes

organism: Schistosoma japonicum

source_name: Schistosoma japonicum Eggs

tag: Stain

value: Chinese mainland Anhui population

value: mixed

value: Parasite Egg

value: Purified from livers of infected ARC SWISS mice by collagenase digest


title: Liver_infected_7weeks_rep1


title: Schistosome_Eggs_rep1


title: Liver_infected_6weeks_rep2

description: Gene expression in the liver of C57BL/6 mice 6 weeks post infection with Schistosoma japonicum

source_name: Liver homogenate, infected, 6 weeks

value: 6 weeks post infection 20 cercariae


title: HEPG2_5ug

source_name: hepatocellular carcinoma cell line HEPG2 (5ug)

tag: subconfluent hepatocellular carcinoma cell line HEPG2. Sample labelling starting with 5 microgram total RNA.


title: Chlorhexidine diacetate_60min_replicate2

city: Fort Meade

first: Chantal

middle: Wheko

last: Nde

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description: Chlorhexidine diacetate treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2.

organism: Pseudomonas aeruginosa

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated P. auruginosa cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.  Then, we added 0.008 mM chlorhexidine diacetate immediately after OD600 reached 0.8.

extract_protocol: Total RNA was isolated at 60 min after OD600 reached 0.8 using the Rneasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: Chlorhexidine diacetate (0.008mM)

tag: PA01 Wild type


title: Chlorhexidine diacetate_60min_replicate3

description: Chlorhexidine diacetate treatment


title: Liver_uninfected_control_rep2

description: Gene expression in the liver of normal C57BL/6 mice

source_name: Liver homogenate, uninfected

value: uninfected


title: Chlorhexidine diacetate_10min_replicate1

description: Chlorhexidine diacetate treatment

extract_protocol: Total RNA was isolated at 10 min after OD600 reached 0.8 using the Rneasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s protocol.


title: Chlorhexidine diacetate_60min_replicate1

description: Chlorhexidine diacetate treatment


title: Fibroblast_HFF__SM3_p6

source_name: human foreskin fibroblasts at passage 6

tag: subconfluent culture of a human foreskin fibroblasts cell line obtained at the Institute for Research in Biotherapy, at passage 6. Donor was three years old. HFF were cultured in in 85% DMEM, 15% fetal calf serum.


title: IL-2+IL-21 (Cy5) versus IL-2(Cy3) Do#3

city: Nantes

first: Emmanuel

last: Scotet

address: 9 quai moncousu

institute: INSERM

description: PIQOR Immunology Microarray Service from Miltenyi Biotec

hyb_protocol: Hybridization performed overnight using the a-Hyb Hybridization station according to the PIQOR User Manual

scan_protocol: Fluorescence signals detected using the laser scanner ScanArray Lite (PerkinElmer Life Sciences)

data_processing:
Mean signal and mean local background intensities were obtained for each spot of the microarray images using the ImaGene's software (Biodiscovery). Low-quality spots were flagged and excluded from data analysis. Unflagged spots were analysed with the PIQORTM Analyzer software. The PIQOR Analyzer allows automated data processing of the raw datatext files derived from the ImaGene software. This includes background subtraction to obtain the net signal intensity, data normalization, and calculation of the Cy5/Cy3 ratios. As an additional quality filtering step, only spots/genes are taken into account for the calculation of the Cy5/Cy3 ratio that have at least in one channel a signal intensity that is at least 2-fold higher than the mean background.
The PIQOR Analyzer calculates all normalized mean Cy5/Cy3 ratios of the four replicates per gene.

label_protocol: Sample labelling performed according to the PIQOR User Manual

growth_protocol: Cells grown in RPMI supp. 10 % FCS

extract_protocol:
RNA extacted by using Nucleospin RNA II from Macherey-Nagel
Amplification T7-based (1 microgram total RNA)
Quantity/Integrity checked by using Agilent 2100 Bioanalyzer

tag: Human T cells Vgamma9Vdelta2

tag: Amplified from human fresh PBMC for 3 weeks with IL-2 (60 ng/ml) and IL-21 (30 ng/ml) and soluble phospoantigen

tag: T cells purified by using a MACS pan gamma delta kit (positive selection)

tag: Amplified from human fresh PBMC for 3 weeks with IL-2 (60 ng/ml) and soluble phospoantigen


title: Chlorhexidine diacetate_10min_replicate2

description: Chlorhexidine diacetate treatment


title: no treatment_0min_replicate3

description: No treatment

source_name: Pseudomonas aeruginosa_no treatment

growth_protocol: (i) we initiated P. aeruginosa cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking

extract_protocol: Total RNA was isolated at 0 min after OD600 reached 0.8 using the Rneasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: No treatment


title: Chlorhexidine diacetate_10min_replicate3

description: Chlorhexidine diacetate treatment


title: Liver_uninfected_control_rep1


title: no treatment_0min_replicate2

description: No treatment


title: RNA Pol II EtOH Rep1

description: See the NimbleGen website

tag: MCF7 cells

source_name: Input DNA


title: IL-2+IL-21 (Cy5) versus IL-2(Cy3) Do#2


title: no treatment_0min_replicate1

description: No treatment


title: ThB1_T24_+TGF

status: Public on Jan 09 2009

city: Brussels

first: Sophie

last: Lucas

address: avenue Hippocrate 74

country: Belgium

institute: de Duve Institute

description:
Gene expression data from Thelper clone, activated T=24 hrs in the presence of TGFb
Experiment_number: II: Th activated in the presence or absence of TGFb

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS5.0) 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: CD4 Thelper clone, activated T=24 hrs in the presence of TGFb

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA.

growth_protocol: Culture medium was IMDM supplemented with 10% human serum, L-arginine, L-asparagine, L-glutamine and methyl-tryptophane (200 microM). Treg and Th clones from hemochromatosis patient LB2050 were derived from flow cytometry-sorted CD4+CD25+ or CD4+CD25- PBMCs. Cells were seeded in limiting dilution conditions and stimulated weekly or bi-weekly with 1 microg/ml anti-CD3 antibody (Orthoclone OKT3, Janssen-Cilag), in the presence of 130 IU/ml of recombinant human IL-2 (Proleukin, Chiron), and irradiated feeder cells (5E05/ml allogeneic PBMCs and 5E05/ml cells of an allogeneic EBV-transformed B cell line). For long term maintenance of Treg clones, culture conditions were modified to increase the concentrations of IL-2 (1000 IU/ml) and irradiated allogeneic PBMCs (1E06/ml), and to include IL-4 (0,5 ng/ml) and IL-7 (10 ng/ml). Treg and Th clones from vaccinated melanoma patient EB81 were isolated in similar conditions from the TILs of a lymph node metastasis, except for anti-tumor clone Th B1, which was isolated from a Mixed Lymphocyte-Tumor Culture as previously described.

extract_protocol: RNA was extracted using Tripure isolation reagent (Roche) according to the manufacturer’s instructions.

treatment_protocol: Cells were seeded in wells coated with 1 microg/ml anti-CD3 (Orthoclone OKT3, Janssen-Cilag), in the presence of 1 microg/ml soluble anti-CD28 (BD Pharmingen)

tag: From melanoma patient EB81


title: ThA2_T24_+TGF_rep2

description:
Gene expression data from Thelper clone, activated T=24 hrs in the presence of TGFb
Experiment_number: IV: Th activated in the presence or absence of TGFb

tag: From hemochromatosis patient LB2050


title: ThB1_T24_-TGF

description:
Gene expression data from Thelper clone, activated T=24 hrs in the absence of TGFb
Experiment_number: II: Th activated in the presence or absence of TGFb

source_name: CD4 Thelper clone, activated T=24 hrs in the absence of TGFb


title: ThA2_T24_-TGF_rep2

description:
Gene expression data from Thelper clone, activated T=24 hrs in the absence of TGFb
Experiment_number: IV: Th activated in the presence or absence of TGFb


title: ThA2_T41_Ctrl

description:
Gene expression data from Thelper clone, activated T=41 hrs in the presence of a control Th clone
Experiment_number: III: Suppressed Th versus control Th

source_name: CD4 Thelper clone, activated T=41 hrs in the presence of a control Th clone


title: ThB1_T6_+TGF

description:
Gene expression data from Thelper clone, activated T=6 hrs in the presence of TGFb
Experiment_number: II: Th activated in the presence or absence of TGFb

source_name: CD4 Thelper clone, activated T=6 hrs in the presence of TGFb


title: ThA2_T41_Supp

description:
Gene expression data from Thelper clone, activated T=41 hrs in the presence of a suppressive Treg clone
Experiment_number: III: Suppressed Th versus control Th

source_name: CD4 Thelper clone, activated T=41 hrs in the presence of a suppressive Treg clone


title: ThA2_T6_+TGF


title: ThA2_T24_-TGF_rep1

description:
Gene expression data from Thelper clone, activated T=24 hrs in the absence of TGFb
Experiment_number: II and IV: Th activated in the presence or absence of TGFb


title: ThA2_T24_Ctrl

description:
Gene expression data from Thelper clone, activated T=24 hrs in the presence of a control Th clone
Experiment_number: III: Suppressed Th versus control Th

source_name: CD4 Thelper clone, activated T=24 hrs in the presence of a control Th clone


title: ThA2_T24_+TGF_rep1

description:
Gene expression data from Thelper clone, activated T=24 hrs in the presence of TGFb
Experiment_number: II and IV: Th activated in the presence or absence of TGFb


title: ThB1_T24

description:
Gene expression data from Thelper clone, activated T=24 hrs
Experiment_number: I: Treg versus Th

source_name: CD4 Thelper clone, activated T=24 hrs


title: TregB3_T0

description:
Gene expression data from Treg clone, resting
Experiment_number: I: Treg versus Th

source_name: CD4 Treg clone, resting


title: ThB1_T0

description:
Gene expression data from Thelper clone, resting
Experiment_number: I: Treg versus Th

source_name: CD4 Thelper clone, resting


title: TregB3_T24

description:
Gene expression data from Treg clone, activated T=24 hrs
Experiment_number: I: Treg versus Th

source_name: CD4 Treg clone, activated T=24 hrs


title: ThA2_T24_Supp

description:
Gene expression data from Thelper clone, activated T=24 hrs in the presence of a suppressive Treg clone
Experiment_number: III: Suppressed Th versus control Th

source_name: CD4 Thelper clone, activated T=24 hrs in the presence of a suppressive Treg clone


title: ThB1_T6_-TGF

description:
Gene expression data from Thelper clone, activated T=6 hrs in the absence of TGFb
Experiment_number: II: Th activated in the presence or absence of TGFb

source_name: CD4 Thelper clone, activated T=6 hrs in the absence of TGFb


title: ThA2_T24


title: ThA2_T6_-TGF


title: Liver_infected_6weeks_rep1

description: Gene expression in the liver of C57BL/6 mice 6 weeks post infection with Schistosoma japonicum

source_name: Liver homogenate, infected, 6 weeks

tag: Strain


title: ThA2_T0


title: TregB1_T24


title: TregB1_T0


title: TregA1_T0


title: Liver_infected_4weeks_rep2

description: Gene expression in the liver of C57BL/6 mice 4 weeks post infection with Schistosoma japonicum

source_name: Liver homogenate, infected, 4 weeks

tag: Gender


title: Jade1 ChIP-chip

city: Stanford

first: Tiffany

last: Hung

address: 371 SERRA MALL

institute: Stanford University

description: ChIP chip samples hybridized on HG17 Encode Tiling Array

hyb_protocol: standard manufacturer's protocol

scan_protocol: scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocol

data_processing: processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction

source_name: Input Chromatin DNA

label_protocol: Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension)

growth_protocol: DMEM + 10% FBS

extract_protocol: ChIP samples collected as in http://www.genomecenter.ucdavis.edu/farnham/pdf/FarnhamLabChIP%20Protocol.pdf

tag: 1% formaldehyde crosslinked, sheared (~500bp) chromatin DNA from Hela cells

source_name: ChIP DNA


title: Jade1 deltaPHD mutant ChIP-chip

treatment_protocol: Doxorubicin 400 ng/ul, 4 hours


title: 14-day-old seedling, rep 3

status: Public on Jan 08 2009

city: Shanghai

first: Bin

last: Han

address: 500 Cao Bao Road

country: China

institute: National Center for Gene Research，Chinese Academy of Sciences

description: 14-day-old light-grown rice seedlings

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChipOperating Software (1.4) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa

source_name: 14-day-old 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: Seedlings were grown in a growth chamber with a daily photoperiodic cycle of 14 h light and 10 h dark at about 28-30 degree celsius

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

treatment_protocol: Control

tag: Japonica, variety

value: ZhongHua 11


title: 14-day-old seedling, heat shock, rep 2

description: 14-day-old light-grown rice seedlings

source_name: 14-day-old rice seedlings, heat shock treatment

treatment_protocol: 42 degree celsius for 3 h


title: Normal, biological rep 19

city: Columbus

first: Kellie

middle: J.

last: Archer

address: 1841 Neil Ave

department: Division of Biostatistics

institute: Ohio State University

description: Gene expression using RMA method

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

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.

data_processing: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

source_name: Normal liver tissue

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: Fresh tissue specimens were collected from the consented patients in the operating room and processed immediately after extraction to minimize RNA degradation. Liver tissue samples were collected in liquid nitrogen or RNA later solution (Ambion, Inc, Austin, TX), and stored at -80°C until use.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).

treatment_protocol: Five mm frozen section slides were made and stained with H&E for Pathologist evaluation to determine tumor content. After Pathologist evaluation, normal/necrotic tissue was macrodissected. Twenty 20 mm sections were performed in a 15 ml tube with 10 ml of Trizol.

tag: Tissue

value: Normal


title: Normal, biological rep 11

description: Gene expression using RMA method


title: Normal, biological rep 15

description: Gene expression using RMA method


title: Normal, biological rep 17

description: Gene expression using RMA method


title: Normal, biological rep 16

description: Gene expression using RMA method


title: Normal, biological rep 10

description: Gene expression using RMA method


title: Jade1 deltaPHD mutant ChIP-chip (+ Doxorubicin)


title: 14-day-old seedling, heat shock, rep 1

description: 14-day-old light-grown rice seedlings


title: Normal, biological rep 9

description: Gene expression using RMA method


title: TregA1_T24


title: Normal, biological rep 13

description: Gene expression using RMA method


title: 14-day-old seedling, heat shock, rep 3

description: 14-day-old light-grown rice seedlings


title: 14-day-old seedling, rep 1

description: 14-day-old light-grown rice seedlings


title: Normal, biological rep 12

description: Gene expression using RMA method


title: Jade1 + Doxorubicin ChIP-chip

tag: Hela cell line stably expressing FLAG-Jade1


title: Normal, biological rep 7

description: Gene expression using RMA method


title: Normal, biological rep 18

description: Gene expression using RMA method


title: Normal, biological rep 5

description: Gene expression using RMA method


title: Normal, biological rep 8

description: Gene expression using RMA method


title: Normal, biological rep 6

description: Gene expression using RMA method


title: Normal, biological rep 4

description: Gene expression using RMA method


title: Normal, biological rep 14

description: Gene expression using RMA method


title: cirrhosis, biological rep 40

description: Gene expression using RMA method

source_name: liver tissue with cirrhosis

value: cirrhosis


title: Normal, biological rep 1

description: Gene expression using RMA method


title: cirrhosis, biological rep 39

description: Gene expression using RMA method


title: Normal, biological rep 2

description: Gene expression using RMA method


title: HCC, biological rep 47

description: Gene expression using RMA method

source_name: liver tissue with HCC

value: HCC


title: cirrhosis, biological rep 38

description: Gene expression using RMA method


title: Normal, biological rep 3

description: Gene expression using RMA method


title: cirrhosisHCC, biological rep 2

description: Gene expression using RMA method

source_name: liver tissue with cirrhosisHCC

value: cirrhosisHCC


title: cirrhosis, biological rep 37

description: Gene expression using RMA method


title: cirrhosis, biological rep 36

description: Gene expression using RMA method


title: HCC, biological rep 46

description: Gene expression using RMA method


title: 14-day-old seedling, rep 2

description: 14-day-old light-grown rice seedlings


title: cirrhosisHCC, match HCC rep 44-2

description: Gene expression using RMA method


title: cirrhosis, biological rep 34

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 43

description: Gene expression using RMA method


title: cirrhosis, biological rep 30

description: Gene expression using RMA method


title: cirrhosis, biological rep 35

description: Gene expression using RMA method


title: cirrhosis, biological rep 31

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 45

description: Gene expression using RMA method


title: HCC, biological rep 44

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 44

description: Gene expression using RMA method


title: HCC, biological rep 41

description: Gene expression using RMA method


title: cirrhosis, biological rep 27

description: Gene expression using RMA method


title: HCC, biological rep 45

description: Gene expression using RMA method


title: cirrhosis, biological rep 28

description: Gene expression using RMA method


title: cirrhosis, biological rep 25

description: Gene expression using RMA method


title: cirrhosis, biological rep 26

description: Gene expression using RMA method


title: HCC, biological rep 42

description: Gene expression using RMA method


title: HCC, biological rep 43

description: Gene expression using RMA method