title: Wild type no vs high Pi conditions Replicate 3

description:
Biological replicate
Part II


title: Wild type no vs high Pi conditions Replicate 1

status: Public on Jun 29 2011

type: RNA

city: Boston

first: Xu

last: Zhou

state: MA

address: 300 Longwood Ave

department: Pediatrics

country: USA

institute: Boston Children's Hospital

description:
Biological replicate
Part II

hyb_protocol: 300 ng Cy3-labeled and 300 ng Cy5-labeled cDNA was competitively hybridized to Agilent 8×15K S. cerevisiae two-color expression microarrays (G2509F) in Agilent hybridization buffer for 17 hours at 60 °C.

scan_protocol: Microarrays were washed and scanned immediately using an Axon 4000B scanner

data_processing: The average intensity of the Cy3 and Cy5 fluorescence at each spot was then extracted using GenePix 5.1 software.  Lowess and quantile normalization were performed using the MATLAB bioinformatics toolbox before further analysis.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Wild type

label_protocol: Purified cDNA samples were then labeled with NHS-ester Cy3 or Cy5 (GE Biosciences).

growth_protocol: Monobasic potassium phosphate was added to phosphate-free medium to make high phosphate (Pi) medium containing a final concentration of 10 mM inorganic phosphate. All media were adjusted to pH 4.0 with HCl2.  Yeast strains were grown at 30 °C with shaking and cell samples were collected at early/mid-logarithmic phase (OD600 0.3 ~ 0.4).

extract_protocol: Cell cultures were added directly into cold methanol (~ -50 °C) with volume ratio of 2:3, and incubated in an ethanol-dry ice bath for at least 20 minutes.  Cells were collected by centrifugation and quickly washed with ice-cold water to remove alcohol, and resuspended in RNAlater solution (Ambion).  For each sample, 5×107 cells were used to isolate total RNA with the RNase Mini kit (Qiangen), and RNA integrity was analyzed on an agarose gel or with an Agilent bioanalyzer.  cDNA was synthesized from 10 μg total RNA with 1:1 ratio of random 10-mers and oligo-dT primers (Operon), and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma), using the Superscript III reverse transcription system (Invitrogen).  cDNA was purified with a PCR purification kit (Qiagen) after hydrolyzing RNA.

treatment_protocol: To induce the Pi starvation response, yeast cells were first grown in 10 mM Pi medium to early/mid-logarithmic phase.  Cells were then harvested by filtering and washed 2 – 3 times with no Pi medium pre-warmed to 30 °C.  Finally, cells were resuspended in pre-warmed no Pi medium and grown at 30 °C for 60 minutes.

tag: strain

tag: genotype/variation

value: Wild type

tag: protocol

value: High Pi (10 mM Pi)

tag: agent

value: inorganic phosphate

value: No Pi (0 mM Pi)

value: control


title: Brassica rapa_Leaf_BraIRRI183_Low P_Rep_2

city: Crawley

first: John

last: Hammond

state: WA

address: 35 Stirling Highway

department: School of Plant Biology

country: Australia

institute: University of Western Australia

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Brassica 95k Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then air dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 2x105k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 018073_D_F_20071106) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. gProcessedSignal values within arrays were normalized to the 50th percentile. Normalized signal values for individual probes were standardized to the median signal value for the probe across all arrays.

organism: Brassica rapa

source_name: Leaf tissue from RIL BraIRRI183, Low P

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

growth_protocol: Plants were grown from seed in individual pots (9cm x 9cm x 8cm; Desch Plantpak B.V., Waalwijk, NL) containing a moistened peat-based compost, under controlled-environment conditions. The potting mix consisted of 25% sand and 75% (v/v) compost (Shamrock medium grade sphagnum peat, Scotts UK, Bromford, UK). Unfertilised, the potting mix had an Olsen extractable P (Olsen et al., 1954) of 8 mg L-1.  The compost contained the following nutrients in sufficient amounts to prevent deficiencies as follows: NH4NO3 (0.4 g L-1), KNO3 (0.75 g L-1), ground limestone 2.25 g L-1, magnesium limestone 2.25 g L-1, and a fritted trace elements mixture containing B, Cu, Fe, Mn, Mo and Zn (WM255, Fargro Ltd, Littlehampton, UK) at 0.4 g L-1. Potting mixes were made in bulk using a paddle mixer (Model 156, St Moritz, Spalding, UK). The CE was a walk-in high specification growth room (Weiss-Gallenkamp, Loughborough, UK), set to a 16 h photoperiod using metal halide lamps, giving a photon flux density between 400 and 700 nm (PAR) of 250 µmol photons m-2 s-1 at plant height. The day/night settings for temperature and relative humidity were 18/15ºC and 76/71%.

extract_protocol: All plants were harvested 21 days after sowing. For each line at each treatment, fully-expanded leaves from 3 plants (6-leaf stage, not flowering) were sampled, snap-frozen in liquid nitrogen, freeze-dried, ground, and stored at -80°C. RNA was extracted from leaf samples using a modified TRIzol extraction method (Hammond et al., 2006). Extracted total RNA was purified using the ‘RNA Cleanup’ protocol for RNeasy columns with on-column DNase digestion to remove residual genomic DNA (Qiagen, Crawley, UK). Samples of total RNA were checked for integrity and quality using an Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Two [P]ext treatments of 9 mg L-1 (low) or 30 mg L-1 (optimal) Olsen extractable P were produced by incorporating 0.075 g and 0.45 g of sieved (mesh 500 µm) single superphosphate (SSP, 7% P) per litre of compost, and used to induce a growth response based on previous studies with Brassica (Broadley et al., 2008, 2010; Hammond et al., 2009; White et al., 2010).

tag: tissue

value: leaf

tag: ril

tag: treatment

value: Low P


title: Wild type no vs high Pi conditions Replicate 2

description:
Biological replicate
Part II


title: Mutant Cycle Replicate 3 Comparison 16

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 15

description:
Biological replicates
Part I

source_name: pho2Δ pho4Δ

value: pho2Δ pho4Δ


title: Mutant Cycle Replicate 3 Comparison 14

description:
Biological replicates
Part I


title: Brassica rapa_Leaf_BraIRRI103_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI103, Low P


title: Mutant Cycle Replicate 3 Comparison 12

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 13

description:
Biological replicates
Part I


title: Onion_Bulb_1MCP_before_curing_rep_1

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a custom Agilent 8 x 15k Onion array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and eXtended Dynamic range mode active, with Green PMT set to 100% for XDR Hi and 10% for XDR Lo).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 023780_D_F_20090803) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Allium cepa

source_name: Onion bulb, treated with 1µL L-1 1-methylcyclopropene (1-MCP) gas for 24 hours at 20ºC

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

growth_protocol: Onion seeds ‘Sherpa’ (medium pungency, medium dry matter) were drilled on sandy clay loam (Alistair Findlay’s, Cardington, Beds., UK; 1.2 x 0.3 ha) on 5 March 2008 at a rate of 57 seeds m-2 with pesticides applied as per commercial practice although remained MH-free.  Plants were machine-harvested at 100% fall-down on 17 September 2008.  Onion bulbs were stored in 72 large net bags (approx. 60 bulbs) and 24 half net bags (approx. 30 bulbs) buried amongst loose bulbs in one tonne wooden crates for batch curing at the Sutton Bridge Crop Storage Research (Lincs., UK).  Bulbs were artificially cured at either 20 or 28°C for 6 weeks as per normal commercial practice in the UK with relative humidity controlled at 65 – 75%.

extract_protocol: For each treatment,six bulbs were selected and two longitudinal wedges for each bulb were cut and snap-frozen in liquid nitrogen and stored at -80°C for RNA extraction. Total RNA was isolated according to Chang et al. (1993) with modifications. Total RNA was extracted from frozen, ground onion tissue (100 mg) homogenised in 1 mL extraction buffer (2% (w/v) CTAB (cetyl trimethylammonium bromide), 0.8 M NaCl, 20 mM Na2EDTA, 0.2 M boric acid, adjusted to pH 7.6 with TRIZMA base, β-mercaptoethanol added to 1% (v/v) just prior to use) using a pestle and mortar.  The mixture was transferred to a 2 mL microtube and incubated at 65ºC for 10 min, then allowed to return to room temperature.  Chloroform (1 mL) was added and mixed before being centrifuged at 16.2 g for 5 min at room temperature.  The aqueous phase was removed to a clean tube and an equal volume of precipitation buffer (0.5% (w/v) CTAB, 50 mM Na2EDTA, 50 mM MES (2-(N-morpholino) ethanesulfonic acid), adjusted to pH 5.8 with NaOH, and filtered through a 0.2 μM sterile filter), mixed and incubated on ice for 30 min.  Samples were centrifuged at 13 000 rpm for 20 min at 4ºC and the supernatant removed.  The pellet was resuspended in SSTE (1.0 M NaCl, 0.5% SDS, 10 mM TrisHCl (pH 8.0), 1 mM Na2EDTA (pH 8.0)) and briefly incubated at 37ºC, before being allowed to return to room temperature.  Chloroform (1 mL) was added and mixed, before being centrifuged at 13 000 rpm for 5 min at room temperature.  The aqueous phase was removed to a clean tube and an equal volume of isopropanol added and incubated on ice for 20 min.  Samples were centrifuged at 13 000 rpm for 20 min at 4ºC and the supernatant removed.  The pellet containing total nucleic acid was washed with 1 mL 70% (v/v) ethanol, then left to air dry and finally resuspended in 50 μL DEPC-treated water.  Then, 30 μL 8 M lithium chloride solution was added and the samples incubated on ice overnight to selectively precipitate RNA.  Samples were centrifuged for at 16.2 g for 30 min at 4ºC, the supernatant was removed, the pellet washed with 0.5 mL 70% ethanol and resuspended in 15 µL RNase-free water.  Sample purity and integrity were verified using the RNA 6000 Nano Assay on the Agilent 2100 BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA, USA) and then treated with Baseline Zero DNase (Epicentre, Madison, WI, USA) according to the supplier’s instructions.

treatment_protocol: The treatments were as follows; 1. 1 µL L-1 1-MCP before curing, 2. 10 µL L-1 ethylene before curing, 3. both 10 µL L-1 ethylene and 1 µL L-11-MCP before curing, 4. no treatment. Treatments were applied in water-sealed air tight polypropylene chambers (88 cm x 59 cm x 59 cm) which housed two 8 x 8 cm electric fans (Nidec Beta SL, Nidec, Japan) to circulate the gases during treatments.  Onion bulbs were treated in the chambers for 24 h at 20°C and the control bulbs held at 20°C in air.  In the treatment boxes, levels of CO2 did not rise above 0.30%.  The 1-MCP was applied by adding 1.8 g SmartFresh (0.14 %, Rohm and Haas, PA) to a 50 mL conical flask and sealed with Nescofilm (Bando Chemical Ind. Ltd., Kobe, Japan).  To release 1 µL L-1 1-MCP gas, 20 mL warm (50°C) water was injected into the conical flask through the Nescofilm using a needle and syringe prior to transfer to the chamber (Chope et al., 2007a).  Ethylene treatment (10 µL L-1) was administered by injecting 3.25 mL ethylene (100 % ethylene; SIP Analytical Ltd., Kent, UK) directly into the chamber via a tapped tube (polyvinyl chloride) followed by repeated full withdrawal-injection displacements to flush the ethylene into the chamber.  Control bulbs cured at 28°C for six weeks were placed in individual plastic trays and stored in air or 10 µL L-1 ethylene for a further 29 weeks at 0-1°C in the dark at the Research Institute of Vegetable Crops (Skierniewice, Poland).

tag: time

value: Before curring


title: Onion_Bulb_continuous_ethylene_after_storage_rep_1

source_name: Onion bulb, stored under continuous ethylene (10µL L-1) for 29 weeks at 1ºC in the dark

value: Continuous ethylene

value: After 29 weeks storage


title: Mutant Cycle Replicate 3 Comparison 11

description:
Biological replicates
Part I


title: Onion_Bulb_control_after_storage_rep_2

source_name: Onion bulb, stored under air for 29 weeks at 1ºC in the dark

value: Control


title: Mutant Cycle Replicate 3 Comparison 10

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 8

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 9

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 7

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 6

description:
Biological replicates
Part I


title: Onion_Bulb_control_after_storage_rep_1


title: Onion_Bulb_ethylene_and_1MCP_before_curing_rep_1

source_name: Onion bulb, treated with 10µL L-1 ethylene and 1µL L-1 1-methylcyclopropene (1-MCP) gas for 24 hours at 20ºC

value: Ethylene and 1-MCP


title: Onion_Bulb_1MCP_before_curing_rep_2


title: Onion_Bulb_ethylene_and_1MCP_before_curing_rep_2


title: Mutant Cycle Replicate 3 Comparison 5

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 4

description:
Biological replicates
Part I


title: Onion_Bulb_control_before_curing_rep_3

source_name: Onion bulb, control stored under air for 24 hours at 20ºC


title: Onion_Bulb_ethylene_and_1MCP_before_curing_rep_3


title: Onion_Bulb_control_before_curing_rep_2


title: Onion_Bulb_ethylene_before_curing_rep_3

source_name: Onion bulb, treated with 10µL L-1 ethylene for 24 hours at 20ºC

value: Ethylene


title: Onion_Bulb_control_after_storage_rep_3


title: Mutant Cycle Replicate 3 Comparison 1

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 3 Comparison 2

description:
Biological replicates
Part I


title: Onion_Bulb_ethylene_before_curing_rep_2


title: Onion_Bulb_1MCP_before_curing_rep_3


title: Mutant Cycle Replicate 3 Comparison 3

description:
Biological replicates
Part I


title: Onion_Bulb_continuous_ethylene_after_storage_rep_3


title: Brassica rapa_Leaf_BraIRRI076_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI076, Optimal P

value: Optimal P


title: Mutant Cycle Replicate 2 Comparison 15

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 16

description:
Biological replicates
Part I


title: Onion_Bulb_control_before_curing_rep_1


title: Mutant Cycle Replicate 2 Comparison 14

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 13

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 12

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 10

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 8

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 9

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 6

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 7

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 5

description:
Biological replicates
Part I


title: Onion_Bulb_ethylene_before_curing_rep_1


title: Onion_Bulb_continuous_ethylene_after_storage_rep_2


title: Mutant Cycle Replicate 2 Comparison 4

description:
Biological replicates
Part I


title: bodies-light_dark-ZT56-lateDay-rep1

city: Notre Dame

first: Samuel

last: Rund

state: IN

address: Galvin Life Science

department: Biological Science

institute: University of Notre Dame

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT56,  late day (44 hours after lights off at the beginning of experiment)

hyb_protocol: Sample hybridized to a Plasmodium/Anopheles Affymetrix GeneChip GeneChip expression array (Affymetrix 900511, GEO GLP1321) per manufaturer's protocol.

scan_protocol: Sample scanned on an Affymetix GeneChip Scanner 7G running Command Console version 3.0 using manufactuer's protocols.

data_processing: Expression values were normalized using the GC-RMA algorithm in GeneSpring GX11 (Agilent Technologies) against all other head or body samples.

label: Streptavidin Phycoerythrin (SAPE)

organism: Anopheles gambiae

label_protocol: Sample labeled using the Affymetrix 3'IVT Express Kit per manufaturer's protocol.

growth_protocol: Female mated, but not blood-fed Anopheles gambiae (Pimperena S form) mosquitoes were maintained at 80% humidity and 75°C in either constant dark conditions or 11 hours full light with a 1 hour dawn and one hour dusk transitions.  Experiment began with females 7-9 days old.  Zeitgeber Time (ZT) with ZT12 defined as time of lights OFF under the light:dark cycle, and ZT0 defined as end of the dawn transition. Circadian Time (CT) with CT0 defined as subjective dawn, inferred from ZT0 of the previous light:dark cycle.

extract_protocol: 20-30 mosquitoes were collected and pooled per timepoint. Heads (including mouth parts and antenae) were separated from bodies (including appendges), and RNA extracted using TRIzol reagent (2 rounds) (Invitrogen) and sodium acetate precipitation.

value: body

tag: timecollected

tag: colloquialtimeofday

value: lateDay

value: Pimperena

tag: gender

value: female

tag: lighttreatment

value: lightDarkCycle


title: bodies-light_dark-ZT56-lateDay-rep2


title: bodies-light_dark-ZT52-earlyDay-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT52,  early day (40 hours after lights off at the beginning of experiment)

value: earlyDay


title: bodies-light_dark-ZT44-lateNight-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT44,  late night (32 hours after lights off at the beginning of experiment)

value: lateNight


title: bodies-light_dark-ZT60-dusk-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT60,  dusk (48 hours after lights off at the beginning of experiment)

value: dusk


title: Mutant Cycle Replicate 2 Comparison 11

description:
Biological replicates
Part I

value: No Pi (0 mM Pi)

value: control


title: bodies-light_dark-ZT48-dawn-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT48,  dawn (36 hours after lights off at the beginning of experiment)

value: dawn


title: bodies-light_dark-ZT44-lateNight-rep2


title: bodies-light_dark-ZT52-earlyDay-rep1


title: bodies-light_dark-ZT40-earlyNight-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT40,  early night (28 hours after lights off at the beginning of experiment)

value: earlyNight


title: Mutant Cycle Replicate 2 Comparison 2

description:
Biological replicates
Part I

value: Wild type

value: High Pi (10 mM Pi)

value: inorganic phosphate


title: bodies-light_dark-ZT48-dawn-rep1


title: bodies-light_dark-ZT60-dusk-rep1


title: Mutant Cycle Replicate 2 Comparison 1

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 2 Comparison 3

description:
Biological replicates
Part I


title: bodies-light_dark-ZT40-earlyNight-rep1


title: Mutant Cycle Replicate 1 Comparison 16

description:
Biological replicates
Part I

value: pho2Δ pho4Δ


title: bodies-light_dark-ZT36-dusk-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT36,  dusk (24 hours after lights off at the beginning of experiment)


title: Mutant Cycle Replicate 1 Comparison 14

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 13

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 12

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 11

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 9

description:
Biological replicates
Part I


title: bodies-light_dark-ZT32-lateDay-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT32,  late day (20 hours after lights off at the beginning of experiment)


title: Mutant Cycle Replicate 1 Comparison 8

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 10

description:
Biological replicates
Part I


title: bodies-light_dark-ZT36-dusk-rep2


title: bodies-light_dark-ZT28-earlyDay-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT28,  early day (16 hours after lights off at the beginning of experiment)


title: Mutant Cycle Replicate 1 Comparison 15

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 7

description:
Biological replicates
Part I


title: bodies-light_dark-ZT20-lateNight-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT20,  late night (8 hours after lights off at the beginning of experiment)


title: Mutant Cycle Replicate 1 Comparison 4

description:
Biological replicates
Part I


title: bodies-light_dark-ZT12-dusk-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT12,  dusk (0 hours after lights off at the beginning of experiment)


title: bodies-light_dark-ZT24-dawn-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT24,  dawn (12 hours after lights off at the beginning of experiment)


title: Mutant Cycle Replicate 1 Comparison 5

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 6

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 2

description:
Biological replicates
Part I


title: bodies-light_dark-ZT16-earlyNight-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT16,  early night (4 hours after lights off at the beginning of experiment)


title: bodies-light_dark-ZT24-dawn-rep1


title: bodies-light_dark-ZT20-lateNight-rep1


title: heads-light_dark-ZT60-dusk-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT60,  dusk (48 hours after lights off at the beginning of experiment)

value: head


title: bodies-light_dark-ZT12-dusk-rep2

value: body


title: heads-light_dark-ZT60-dusk-rep1


title: heads-light_dark-ZT56-lateDay-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT56,  late day (44 hours after lights off at the beginning of experiment)

value: lateDay


title: bodies-light_dark-ZT28-earlyDay-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT28,  earlyl day (16 hours after lights off at the beginning of experiment)

value: Pimperena


title: bodies-light_dark-ZT16-earlyNight-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT16,  early night  (4 hours after lights off at the beginning of experiment)

value: female


title: bodies-light_dark-ZT32-lateDay-rep1

value: lightDarkCycle


title: Mutant Cycle Replicate 1 Comparison 3

description:
Biological replicates
Part I


title: Mutant Cycle Replicate 1 Comparison 1

description:
Biological replicates
Part I


title: heads-light_dark-ZT52-earlyDay-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT52,  early day (40 hours after lights off at the beginning of experiment)

value: earlyDay


title: heads-light_dark-ZT56-lateDay-rep1


title: heads-light_dark-ZT52-earlyDay-rep1


title: heads-light_dark-ZT48-dawn-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT48,  dawn (36 hours after lights off at the beginning of experiment)


title: 2dpi_Rep4

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

description: Biological replicate 4 of 4. ILTV infected chicken embryo lung cells, harvested at 2dpi.

hyb_protocol: An equal amount (825 ng) of Cy3 and Cy5 labeled cRNA probes were mixed with gene expression hybridization kit (Agilent, part No. 5188-5242) and hybridized on a 4X44K Agilent custom chicken oligo microarray (array ID: 015068). The hybridized slides were washed using a commercial kit package (Agilent).

scan_protocol: Scanned on an Genepix 4000B scanner (Molecular Devices Corporation)

data_processing: Gene Pix Pro (v 6.1) with Accuity software (v 4.0)

organism: Gallus gallus

label_protocol: 2 µg of total RNA were used for this experiment, and all procedures were followed to manufacturer's instructions.

growth_protocol: Cells were grown in a 1:1 ratio of mammary epithelial growth media (MEGM; Lonza, Rockland, ME, USA) and Dulbecco’s Modified Eagle’s Medium (DMEM, 0.45% glucose) plus 2% fetal bovine serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine in 10 cm tissue culture plates (Sarstedt Inc., Newton, NC, USA) pretreated with 0.5 % gelatin in PBS to improve cell adhesion.

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

treatment_protocol: ILTV vaccine strain was infected the chicken embryonic lung cells at three doses.

tag: developmental stage

value: embryo

value: lung


title: 3dpi_Rep4

description: Biological replicate 4 of 4. ILTV infected chicken embryo lung cells, harvested at 3dpi.


title: heads-light_dark-ZT44-lateNight-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT44,  late night (32 hours after lights off at the beginning of experiment)

value: lateNight


title: 1dpi_Rep4

description: Biological replicate 4 of 4. ILTV infected chicken embryo lung cells, harvested at 1dpi.


title: 1dpi_Rep3

description: Biological replicate 3 of 4. ILTV infected chicken embryo lung cells, harvested at 1dpi.


title: heads-light_dark-ZT44-lateNight-rep2


title: heads-light_dark-ZT48-dawn-rep2


title: 4dpi_Rep3

description: Biological replicate 3 of 4. ILTV infected chicken embryo lung cells, harvested at 4dpi.


title: heads-light_dark-ZT36-dusk-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT36,  dusk (24 hours after lights off at the beginning of experiment)

value: dusk


title: 2dpi_Rep3

description: Biological replicate 3 of 4. ILTV infected chicken embryo lung cells, harvested at 2dpi.


title: 4dpi_Rep4

description: Biological replicate 4 of 4. ILTV infected chicken embryo lung cells, harvested at 4dpi.


title: 3dpi_Rep3

description: Biological replicate 3 of 4. ILTV infected chicken embryo lung cells, harvested at 3dpi.


title: heads-light_dark-ZT32-lateDay-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT32,  late day (20 hours after lights off at the beginning of experiment)


title: heads-light_dark-ZT36-dusk-rep1


title: 2dpi_Rep2

description: Biological replicate 2 of 4. ILTV infected chicken embryo lung cells, harvested at 2dpi.


title: 4dpi_Rep1

description: Biological replicate 1 of 3. ILTV infected chicken embryo lung cells, harvested at 4dpi.


title: 3dpi_Rep2

description: Biological replicate 2 of 4. ILTV infected chicken embryo lung cells, harvested at 3dpi.


title: 3dpi_Rep1

description: Biological replicate 1 of 4. ILTV infected chicken embryo lung cells, harvested at 3dpi.


title: heads-light_dark-ZT28-earlyDay-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT28,  earlyl day (16 hours after lights off at the beginning of experiment)


title: heads-light_dark-ZT32-lateDay-rep1


title: 2dpi_Rep1

description: Biological replicate 1 of 4. ILTV infected chicken embryo lung cells, harvested at 2dpi.


title: 1dpi_Rep2

description: Biological replicate 2 of 4. ILTV infected chicken embryo lung cells, harvested at 1dpi.


title: heads-light_dark-ZT40-earlyNight-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT40,  early night (28 hours after lights off at the beginning of experiment)


title: heads-light_dark-ZT28-earlyDay-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT28,  early day (16 hours after lights off at the beginning of experiment)


title: 4dpi_Rep2

description: Biological replicate 2 of 4. ILTV infected chicken embryo lung cells, harvested at 4dpi.


title: heads-light_dark-ZT24-dawn-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT24,  dawn (12 hours after lights off at the beginning of experiment)

value: dawn


title: heads-light_dark-ZT24-dawn-rep1


title: bodies-dark_dark-CircadianTime40-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT40, subjective early night (52 hours after lights off at the beginning of experiment)

value: subjectiveEarlyNight

value: constantDark


title: bodies-dark_dark-CircadianTime44-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT44, subjective late night (56 hours after lights off at the beginning of experiment)

value: subjectiveLateNight


title: bodies-dark_dark-CircadianTime36-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT36, subjective dusk (48hours after lights off at the beginning of experiment)

value: subjectiveDusk


title: 1dpi_Rep1

description: Biological replicate 1 of 4. ILTV infected chicken embryo lung cells, harvested at 1dpi.


title: heads-light_dark-ZT12-dusk-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT12,  dusk (0 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime32-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT32, subjective late day (44 hours after lights off at the beginning of experiment)

value: subjectiveLateDay


title: bodies-dark_dark-CircadianTime48-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT48, subjective dawn (60 hours after lights off at the beginning of experiment)

value: subjectiveDawn


title: bodies-dark_dark-CircadianTime48-rep2

value: body


title: bodies-dark_dark-CircadianTime36-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT36, subjective dusk (48 hours after lights off at the beginning of experiment)


title: heads-light_dark-ZT20-lateNight-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT20,  late night (8 hours after lights off at the beginning of experiment)

value: head


title: heads-light_dark-ZT16-earlyNight-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT16,  early night (4 hours after lights off at the beginning of experiment)

value: earlyNight

value: Pimperena


title: heads-light_dark-ZT12-dusk-rep1

value: female

value: lightDarkCycle


title: bodies-dark_dark-CircadianTime24-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT24, subjective dawn (36 hours after lights off at the beginning of experiment)


title: heads-light_dark-ZT20-lateNight-rep2


title: bodies-dark_dark-CircadianTime44-rep1


title: bodies-dark_dark-CircadianTime20-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT20, subjective late night (32 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime12-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT12, subjective dusk (24 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime16-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT16, subjective early night  (28 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime24-rep1


title: bodies-dark_dark-CircadianTime40-rep2


title: bodies-dark_dark-CircadianTime28-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT28, subjective early day (40 hours after lights off at the beginning of experiment)

value: subjectiveEarlyDay


title: bodies-dark_dark-CircadianTime20-rep2


title: bodies-dark_dark-CircadianTime32-rep2


title: bodies-dark_dark-CircadianTime28-rep2


title: bodies-dark_dark-CircadianTime12-rep1


title: bodies-dark_dark-CircadianTime8-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT8, subjective late day (20 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime16-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT16, subjective early night (28 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime44-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT44, subjective late night (56 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime4-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT4, subjective early day (16 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime48-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT48, subjective dawn (60 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime0-rep2

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT0, subjective dawn (12 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime44-rep1


title: heads-dark_dark-CircadianTime40-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT40, subjective early night (52 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime40-rep2


title: heads-dark_dark-CircadianTime32-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT32, subjective late day (44 hours after lights off at the beginning of experiment)


title: bodies-dark_dark-CircadianTime4-rep1


title: bodies-dark_dark-CircadianTime-rep1


title: bodies-dark_dark-CircadianTime8-rep1

description: Female Anopheles gambiae bodies from mosquitoes reared under constant dark conditions. Collected at CT8, subjective late day  (20 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime28-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT28, subjective early day (40 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime20-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT20, subjective late night (32 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime36-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT36, subjective dusk (48hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime24-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT24, subjective dawn (36 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime32-rep2


title: heads-dark_dark-CircadianTime48-rep1


title: heads-dark_dark-CircadianTime20-rep1


title: heads-dark_dark-CircadianTime24-rep2


title: heads-dark_dark-CircadianTime12-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT12, subjective dusk (24 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime16-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT16, subjective early night (28 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime8-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT8, subjective late day (20 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime36-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT36, subjective dusk (48 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime16-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT16, subjective early night  (28 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime12-rep2


title: heads-dark_dark-CircadianTime8-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT8, subjective late day  (20 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime28-rep1


title: heads-dark_dark-CircadianTime4-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT4, subjective early day (16 hours after lights off at the beginning of experiment)


title: rmc low nitrogen 3

city: St. Louis

first: Dan

last: Ruzicka

state: MO

address: 975 N. Warson Rd.

institute: Donald Danforth Plant Science Center

hyb_protocol: Follow Affymetrix suggested standard method;  wash and stain protocol: mini_euk2v3-450, with fluidics station 450

scan_protocol: Genechipscanner 3000 with 7G upgrade, Software: GCOS v1.4

data_processing: Signal intenisty data were summarized with MAS5.0 algorithm, log2 transformed and processed with JMP genomics 4.0 software.  The probelist was filtered for expressed genes based on Affmetrix expression console sofware PMA designation.  ANOVA analysis was performed on all expressed genes to identify significantly differential probesets.

label: biotin

organism: Solanum lycopersicum

source_name: rmc root, 24h 6.5ppm ammonium treatment

label_protocol: RNA samples were prepared for microarray analysis using the MessageAmp Premier RNA Amplification Kit (Ambion, Foster City CA) with 200 ng total RNA as input

growth_protocol: 8 week old tomato plants were transplanted into field soil at Durst Farm, Yolo County CA and grown for an additional 5 weeks.

extract_protocol: 24 hours post-treatment, patch roots were excised, washed, and frozen.  RNA was extracted using a modified Qiagen Rneasy extraction kit

treatment_protocol: ammonium and control treatments were injected into discrete soil patches

tag: genotype

value: rmc

value: low nitrogen

value: root


title: heads-dark_dark-CircadianTime0-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under constant dark conditions. Collected at CT0, subjective dawn (12 hours after lights off at the beginning of experiment)


title: heads-dark_dark-CircadianTime0-rep1

value: subjectivesubjectiveDawn


title: rmc low nitrogen 4


title: rmc high nitrogen 4

source_name: rmc root, 24h 65ppm ammonium treatment

value: high nitrogen


title: rmc high nitrogen 5


title: rmc high nitrogen 3


title: rmc low nitrogen 1


title: rmc high nitrogen 2


title: rmc control 3

source_name: rmc root, 24h water treatment

value: water


title: rmc control 5


title: rmc control 4


title: rmc low nitrogen 5


title: heads-light_dark-ZT40-earlyNight-rep2

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT40,  early night (28 hours after lights off at the beginning of experiment)


title: rmc low nitrogen 2


title: wild type high nitrogen 4

source_name: wildtype root, 24h 100uM ammonium treatment

value: wild type


title: wild type high nitrogen 5


title: wild type high nitrogen 3


title: rmc control 1


title: wild type high nitrogen 2


title: heads-dark_dark-CircadianTime4-rep1

value: constantDark


title: rmc control 2


title: wild type low nitrogen 5

source_name: wildtype root, 24h 10uM ammonium treatment


title: wild type high nitrogen 1


title: rmc high nitrogen 1


title: wild type low nitrogen 4


title: No-PK control

type: genomic

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

hyb_protocol: Approximately 10 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Primary data analyses were carried out using the Affymetrix microarray Suite version 5.0 software to obtain hybridization intensity, fold change value, change P-value, and detection P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using three criteria. First, the reliability of strength of signal was judged by detection P-value of each locus (P ≥ 0.025). Second, the reliability of binding ratio was judged by change P-value (P  ≥ 0.025). Third, clusters consisting of at least three contiguous loci that filled the above two criteria were selected, because it was known that a single site of protein–DNA interaction will result in immunoprecipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors.
Locus identification, raw signal intensity, detection P-value, value, signal log ratio, and change p-value as obtained using the Affymetrix microarray Suite version 5.0 software.

molecule: genomic DNA

source_name: PK ChIP DNA from SY2080, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 10 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in YPD to mid-log phase at 25°C

extract_protocol: ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-PK monoclonal antibody SV5-Pk1 (AbD, Serotec) and anti-Flag monoclonal antibody M2 (Sigma-Aldrich) were used for ChIP.

value: MATa ade2-1 ura3  leu2-3,112  his3-11,15 can1-100 GAL+ PSI+

tag: cell cycle stage

value: asynchronous

tag: sample type

value: IP fraction

label: Biotin

source_name: Input DNA from SY2080, asynchronous culture

value: input


title: wild type low nitrogen 3


title: wild type low nitrogen 2


title: No-FLAG control

source_name: FLAG ChIP DNA from SY2201, asynchronous culture

value: MATa ade2-1 ura3  leu2-3,112  his3-11,15 can1-100 ura3::URA3/GPD-TK(7X) GAL+ PSI+

source_name: Input DNA from SY2201, asynchronous culture


title: Sub2 asyn

description:
Sub2 asyn IP.CEL
Sub2 asyn SUP.CEL

data_processing:
Primary data analyses were carried out using the Affymetrix microarray Suite version 5.0 software to obtain hybridization intensity, fold change value, change P-value, and detection P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using three criteria. First, the reliability of strength of signal was judged by detection P-value of each locus (P ≥ 0.025). Second, the reliability of binding ratio was judged by change P-value (P  ≥ 0.025). Third, clusters consisting of at least three contiguous loci that filled the above two criteria were selected, because it was known that a single site of protein–DNA interaction will result in immunoprecipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors.
Results files description: Locus identification, raw signal intensity, detection P-value, value, signal log ratio, and change p-value as obtained using the Affymetrix microarray Suite version 5.0 software.

source_name: FLAG ChIP DNA from SY2201 SUB2-FLAG, asynchronous culture

value: MATa ade2-1 ura3  leu2-3,112  his3-11,15 can1-100 ura3::URA3/GPD-TK(7X) GAL+ PSI+ SUB2-FLAG

value: Sub2 ChIP fraction

source_name: Input DNA from SY2201 SUB2-FLAG, asynchronous culture


title: Rrm3-WT asyn

description:
RrM3-WT asyn IP.CEL
RrM3-WT asyn SUP.CEL

source_name: FLAG ChIP DNA from SY2201 RRM3-FLAG, asynchronous culture

value: MATa ade2-1 ura3  leu2-3,112  his3-11,15 can1-100 ura3::URA3/GPD-TK(7X) GAL+ PSI+ RRM3-FLAG

value: Rrm3 ChIP fraction

source_name: Input DNA from SY2201 RRM3-FLAG, asynchronous culture


title: Rrm3-hpr1∆ asyn

description:
Rrm3-hpr1∆ asyn IP.CEL
Rrm3-hpr1∆ asyn SUP.CEL

source_name: FLAG ChIP DNA from SY2201 RRM3-FLAG hpr1∆, asynchronous culture

source_name: Input DNA from SY2201 RRM3-FLAG hpr1∆, asynchronous culture


title: wild type low nitrogen 1


title: heads-light_dark-ZT16-earlyNight-rep1

description: Female Anopheles gambiae heads from mosquitoes reared under 12hr light:12hr dark conditions. Collected at ZT16,  early night  (4 hours after lights off at the beginning of experiment)

value: head

value: earlyNight

value: Pimperena

value: female

value: lightDarkCycle


title: Rpb3 asyn

description:
Rpb3 asyn IP.CEL
Rpb3 asyn SUP.CEL

source_name: PK ChIP DNA from SY2080 RPB3-PK, asynchronous culture

value: MATa ade2-1 ura3  leu2-3,112  his3-11,15 can1-100 RPB3::rpb3-6PKTRP1 GAL+ PSI+

value: Rpb3 ChIP fraction

source_name: Input DNA from SY2080 RPB3-PK, asynchronous culture


title: Hpr1 S

description:
Hpr1 S IP.CEL
Hpr1 S SUP.CEL
Cells were released from G1 into 0.2 M HU. Samples were collected after 1hr and processed for ChIP.

source_name: FLAG ChIP DNA from SY2201 HPR1-FLAG, S-phase culture

value: MATa ade2-1 ura3  leu2-3,112  his3-11,15 can1-100 ura3::URA3/GPD-TK(7X) GAL+ PSI+ HPR1-FLAG

value: S

value: Hpr1 ChIP fraction

source_name: Input DNA from SY2201 HPR1-FLAG, S-phase culture


title: wild type control 2

source_name: wildtype root, 24h water treatment

value: wild type

value: water

value: root


title: wild type control 3


title: wild type control 5


title: wild type control 1


title: Hpr1 G1

description:
Hpr1 G1 IP.CEL
Hpr1 G1 SUP.CEL
Cell synchronization in G1 was accomplished by treatment of exponentially growing cells with 3µg/ml alpha-factor pheromone for 2.5 h

source_name: FLAG ChIP DNA from SY2201 HPR1-FLAG, G1 arrested culture

source_name: Input DNA from SY2201 HPR1-FLAG, G1 arrested culture

value: input


title: Hpr1 G2

description:
Hpr1 G2 IP.CEL
Hpr1 G2 SUP.CEL
Cells were released from G1 and arrested in G2/M by treatment with 15 mg/ml Nocodazole. Samples were collected after 3 hr and processed for ChIP.

source_name: FLAG ChIP DNA from SY2201 HPR1-FLAG, G2 arrested culture

source_name: Input DNA from SY2201 HPR1-FLAG, G2 arrested culture


title: Hpr1 asyn

description:
HPR1 asyn IP.CEL
HPR1 asyn SUP.CEL

source_name: FLAG ChIP DNA from SY2201 HPR1-FLAG, asynchronous culture

value: asynchronous

source_name: Input DNA from SY2201 HPR1-FLAG, asynchronous culture


title: wild type control 4


title: CD71 positive erythroblasts sorted from the bone marrow of mice expressing a mutant RPS19, rep3

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description:
Gene expression data from CD71 positive erythroblasts sorted from the bone marrow of mice expressing a mutant RPS19
DB6_K196_BM_11

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cRNAs was hybridized to The Affymetrix Mouse 430A GeneChips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Gene Chip Operating software 1.2 (GCOS 1.2, Affymetrix).

data_processing: CEL files generated by the Affymetrix GCOS program were imported into the Affymetrix Expression Console program and an RMA (Robust Microarray Analysis) normalization was performed to generate the .chp files.

organism: Mus musculus

label_protocol: Per RNA labeling, 5 micrograms of total RNA was used in conjunction with the Affymetrix recommended protocol One-Cycle Target Labeling and Control Reagents (Catalog# 900493).

growth_protocol: CD71 positive erythroblasts sorted from the bone marrow of wild type mice and mice expressing a mutant RPS19 (RPS19R62W) transgene

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

value: FVB/N

value: mutant RPS19

value: bone marrow

tag: cell type

value: CD71 positive erythroblasts


title: 350617

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
NC48h1 vs. 3p48h1
Date:2008/07/17

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Homo sapiens

label_protocol: Ambion protocol.

extract_protocol: Total RNA was extracted using TRIZOL reagent.

tag: cell line

value: HaCaT

value: keratinocyte

tag: transfection

value: pre-miR-NC

tag: transfection time

tag: label

tag: extract

tag: sample

tag: subject

tag: tissue derivation

value: epidermis

tag: replicate


title: CD71 positive erythroblasts sorted from the bone marrow of mice expressing a mutant RPS19, rep2

description:
Gene expression data from CD71 positive erythroblasts sorted from the bone marrow of mice expressing a mutant RPS19
DB5_K187_BM_10

tag: strain

tag: genotype/variation

tag: tissue


title: drought effect_swap_Replicate2

city: Seibersdorf

first: Silvia

last: Fluch

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

country: Austria

institute: Austrian Research Centers GmbH

description: Biological replicate 2 out of 3

hyb_protocol: For hybridization the probes were mixed with hybridisation buffer (Amersham Biosciences) and Formamide at the ratio of 1:1:2 (v/v), respectively. Hybridizations were carried out using a Tecan HS 400 Hybridization Station (Tecan Austria GmbH, Austria) at 42°C for 15 h. The arrays were washed with 1x SSC for 30sec at RT, 1x SSC, 0,2% SDS for 20min at 50°C, 0,1x SSC, 0,2% SDS for 10min at RT and 0,2x SSC twice for 5min at RT.

scan_protocol: Microarray images were acquired on a Tecan LS 200 Scanner (Tecan Austria GmbH, Austria).

data_processing: Quantitation of signals was done using GenePix® Pro 5.0 software (Axon Instruments, Foster City, US, California). Differentially expressed clones were selected by pair-wise comparison of the samples from control using the GeneSpring version 7.2 (Agilent Technologies, Redwood City, CA, USA) where a one-way ANOVA was performed for drought effect.

label: AlexaFluor® 555

organism: Populus nigra

source_name: root

label_protocol: 5 μg of total RNA was reverse transcribed using Anchored Oligo(dT)20 Primer, amino-modified nucleotides and SuperScriptTM  RT (Superscript Plus indirect cDNA labeling System,  Invitrogen, Carlsbad, US California) according to manufacturer instructions. The first-strand cDNA was purified using the Qiagen PCR Purification Kit and subsequently coupled to AlexaFluor® 555 or AlexaFluor® 647 reactive Dye. The fluorescently labelled probes were purified using the same kit as written above.

growth_protocol: A clone of Populus nigra (E10), originating from a natural stand in Eferding (Upper Austria; Longitude: 14°05´, Latitude: 48°18´), was multiplied via cuttings in January 2005. Cuttings were rooted in small pots in standard soil and cultivated in greenhouse for 12 weeks. After this time the plants were well established they were transferred into bigger pots (Ø 30cm) and grown for further 6 weeks till the shoots were approx. 50cm in length. The plants were exposed to natural daily sunlight; humidity of the air was 67%. The daily temperature cycle was 18°C between 6 p.m. and 6 a.m. and 22°C between 6 a.m. and 6 p.m.

extract_protocol: The method of Chang et al. (1993) was used to extract RNA from roots of 3 control and 3 drought-treated poplar leaves.

treatment_protocol: The poplar plants were in the first week of July 2005 split into two groups. Pots were watered till saturation at the beginning of experiment. Water stress was applied by withholding water, while the control plants were kept well watered. Water content and conductivity of the substrate was measured using a Theta Probe ML2 (Delta-T DeviceLTd.) connected with an Infield 7 Data Logger (UMS GmbH München). The conductivity values measured of stressed plants dropped to maximum 10%. Roots were washed, dried using paper towels and frozen immediately in liquid nitrogen. Samples were stored at -80°C until analysis.  The poplar plants (exposed to natural daily sunlight; humidity of the air 67%; daily temperature cycle 18°C between 6 p.m. and 6 a.m. and 22°C between 6 a.m. and 6 p.m) were in the first week of July 2005 split into two groups. Pots were watered till saturation at the beginning of experiment. Water stress was applied by withholding water, while the control plants were kept well watered. Water content and conductivity of the substrate was measured using a Theta Probe ML2 (Delta-T DeviceLTd.) connected with an Infield 7 Data Logger (UMS GmbH München). The conductivity values measured of stressed plants dropped to maximum 10%. Roots were washed, dried using paper towels and frozen immediately in liquid nitrogen. Samples were stored at -80°C until analysis.

value: roots

tag: stress

label: AlexaFluor® 647

value: drought-treated


title: CD71 positive erythroblasts sorted from the bone marrow WT mice, rep2

description:
Gene expression data from CD71 positive erythroblasts sorted from the bone marrow WT mice
DB2_WT_9


title: CD71 positive erythroblasts sorted from the bone marrow of mice expressing a mutant RPS19, rep1

description:
Gene expression data from CD71 positive erythroblasts sorted from the bone marrow of mice expressing a mutant RPS19
DB4_J97_BM_4


title: Gastric cancer tissue samples (FFPE)_B 67

status: Public on Jun 28 2011

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: A pool of DNA from blood of normal individuals

hyb_protocol: As described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Bluefuse software version 3.4 (BlueGnome, Cambridge, UK) was used for automatic feature extraction. Spots were excluded when the quality flag was below 1 or the confidence value was below 0.1. Log2 tumor to normal ratio was calculated for each clone and median block normalization was used to normalize the data.

source_name: Gastric cancer

label_protocol: Labeling was done by random priming (Bioprime DNA Labeling System, Invitrogen, Breda, The Netherlands)

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51. DNA was isolated using commercially available DNA isolation kits (QIAamp DNA mini kit; Qiagen, Westburg, Leusden, The Netherlands and QIAamp microkit; Qiagen, Hilden, Germany).

value: Gastric cancer

tag: gender

value: male

tag: race

value: Caucasian SA patient

tag: msi status

value: MSS

source_name: female reference DNA

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: 352930

description:
NC48h2 vs. 3p48h2
Date:2008/07/17

tag: cell type


title: drought effect_Replicate1

description: Biological replicate 1 out of 3


title: CD71 positive erythroblasts sorted from the bone marrow WT mice, rep1

description:
Gene expression data from CD71 positive erythroblasts sorted from the bone marrow WT mice
DB1_WT_9

value: wild type


title: drought effect_Replicate2

description: Biological replicate 2 out of 3


title: 353508

description:
3p48h1 vs. NC48h1
Date:2008/07/17

tag: cell line


title: Gastric cancer tissue samples (FFPE)_B 61

value: female

source_name: male reference DNA

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: CD71 positive erythroblasts sorted from the bone marrow WT mice, rep3

description:
Gene expression data from CD71 positive erythroblasts sorted from the bone marrow WT mice
DB3_WT_9

value: FVB/N


title: Gastric cancer tissue samples (FFPE)_B 66

value: MSI-H


title: Gastric cancer tissue samples (FFPE)_B 65


title: Gastric cancer tissue samples (FFPE)_B 60


title: Gastric cancer tissue samples (FFPE)_B 64


title: Gastric cancer tissue samples (FFPE)_B 59


title: drought effect_Replicate3

description: Biological replicate 3 out of 3


title: drought effect_swap_Replicate3

description: Biological replicate 3 out of 3


title: Gastric cancer tissue samples (FFPE)_B 62


title: Gastric cancer tissue samples (FFPE)_B 63


title: 353514

description:
3p48h2 vs. NC48h2
Date:2008/07/17

tag: transfection


title: Gastric cancer tissue samples (FFPE)_S 56

value: native SA patient


title: Gastric cancer tissue samples (FFPE)_S 55


title: Gastric cancer tissue samples (FFPE)_S 57


title: Gastric cancer tissue samples (FFPE)_S 58


title: drought effect_swap_Replicate1

description: Biological replicate 1 out of 3


title: Gastric cancer tissue samples (FFPE)_S 54


title: Gastric cancer tissue samples (FFPE)_S 52


title: Gastric cancer tissue samples (FFPE)_S 53

value: MSI-L


title: Gastric cancer tissue samples (FFPE)_S 50


title: Gastric cancer tissue samples (FFPE)_S 51


title: Gastric cancer tissue samples (FFPE)_S 45


title: Gastric cancer tissue samples (FFPE)_S 46


title: Gastric cancer tissue samples (FFPE)_UK 31

value: UK patient


title: Gastric cancer tissue samples (FFPE)_S 44


title: Gastric cancer tissue samples (FFPE)_S 41


title: Gastric cancer tissue samples (FFPE)_S 34


title: Gastric cancer tissue samples (FFPE)_UK 33


title: Gastric cancer tissue samples (FFPE)_UK 32


title: Gastric cancer tissue samples (FFPE)_S 35


title: Gastric cancer tissue samples (FFPE)_S 38


title: Gastric cancer tissue samples (FFPE)_S 36


title: Gastric cancer tissue samples (FFPE)_S 40


title: Gastric cancer tissue samples (FFPE)_S 43


title: Gastric cancer tissue samples (FFPE)_S 39


title: Gastric cancer tissue samples (FFPE)_S 49


title: Gastric cancer tissue samples (FFPE)_UK 29


title: Gastric cancer tissue samples (FFPE)_S 47


title: Gastric cancer tissue samples (FFPE)_S 42


title: Gastric cancer tissue samples (FFPE)_S 48


title: Gastric cancer tissue samples (FFPE)_UK 30


title: Aged Female Rabbit Cardioplegia Heart vs. Aged Female Rabbit Control Heart

first: James

middle: D

last: McCully

address: 77 Avenue Louis Pasteur

department: Cardiothoracic Surgery

institute: BIDMC/Harvard Medical School

hyb_protocol: Contro heart samples were labeled with Cy3-dUTP and  experimental hearts samples (Global ischemia and cardioplegia) were  labeled with Cy5-dUTP and then  combined with 30 uL hybridization solution (stock solution containing 100 uL DIG EasyHyb hybridization solution (Roche), 5 uL yeast tRNA (10 mg/mL), 5 uL human COT1 DNA, 5 uL Poly-dA, and 5 uL salmon sperm DNA (10 mg/mL).  In the case of Global Ischemia vs. Cardioplegia, Global ischemia samples were labeled with Cy3-dUTP and  Cardioplegia  heart samples  were  labeled with Cy5-dUTP and then  combined with 30 uL hybridization solution. The probe solution was hybridized to the arrayed slide at 37 C overnight.  The following day, slides were  washed first with 1x SSC to remove the cover slip (Hybri-Slips, Sigma) , then 3 successive washes of 1x SSC / 0.1% SDS for 15 minutes each at 50 oC, followed by a rinse with 1x SSC.  The slides were dried in individual 50 mL conical tubes and centrifuged at 500 rpm to remove excess fluid.

scan_protocol: Scanning of the slides was performed using the GMS 418 scanner (Affymetrix) at 532 nm (Cy3) and 635 nm (Cy5).

data_processing: Local background was subtracted from the fluorescent value Cluster Analysis. All treatments were compared to Control to account for constitutive gene expression. Raw scanned images of Cy3 and Cy5 fluorescence were processed using Axon 4000A microarray scanner with GenePix analysis software using Ro etta Resolver (Molecular Devices Corp, Sunnyvale CA.). Dye swap was treated as technical replicates to account for dye effect error. Fold change criteria was used together with p-values to identify gene expression changes. p values were calculated based on dye swap results. Computational biology was performed using Spotfire Decision Site 8.1 (Spotfire, Somerville, MA).  Functional annotation cluster analysis was performed using DAVID 2007 functional annotation bioiformatics microarray analysis (http://david.abcc.ncifcrf.gov/).

organism: Oryctolagus cuniculus

source_name: New Zealand White rabbits (aged female, > 32 months ; 6 to 8 kg)

label_protocol: Total RNA was isolated separately from Control, Global ischemia and Cardioplegia treated  New Zealnad White Rabbit heart tissue using Trizol reagent (Gibco BRL- Life Technologies), according to the manufacturer’s protocol.  Integrity of the RNA was determined by 1% agarose gel containing 3% formaldehyde, 0.02 M MOPS pH 7.4 (3-[N-morpholino] propanesulfonic acid) and 0.001 M disodium EDTA (ethylenediamine tetraacetic acid).RNA (35 ug) from control and experimental groups was used separately for first strand cDNA synthesis using an oligo-dT primer (0.5ug /uL). Following incubation at 65 oC for 5 min. the reaction was  put on ice and the following added:  4uL first strand buffer; 2uL 0.1M DTT;  2uL 10X low dTTP–dNTP (5 mM dATP, dCTP, dGTP, and 2 mM dTTP); 2uL CyanineX-dUTP (1 mM ; Cyanine3; Cy3 for control; green and Cyanine5; Cy5 for experimental; Amersham, Pharmacia Biotech); 1uL RNasin and 1uL of Superscript II (GIBCO) and incubated at 42 oC  for 30 min. then and another 1uL Superscript II added and the reaction allowed to continue a further 40 min. at 42 oC. The reaction was stopped with the addition of  2.5 uL 500 mM EDTA and heating to 65 oC for 1 min. The RNA template was hydrolyzed with the addition of 5 uL 1M NaOH and incubation at 65 oC for 10 min. and then neutralized by adding 12.5 uL 1M Tris pH 7.5 immediately to neutralize the pH. The labeled cDNA probes were purified by gel exclusion chromatography (ProbeQuant G-50, Amersham) and the volume reduced to 5-10 uL using a Speedvac.

extract_protocol: Total heart (atria and ventricles) RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: In situ blood perfused cardiopulmonary bypass (CPB): Rabbits were sedated with acepromazine (0.75 mg/kg IM (intramuscular)) and a 21-gage butterfly catheter was placed in the ear and looped and secured in place with tape and vet wrap. Ketamine (35 mg/kg) and xylazine (2.5 mg/kg) IV and were administered via the catheter  which was also used intra-operatively to administer heparin (3 mg/kg IV), lidocaine (1% solution, 5 ml) and Lactated Ringer’s solution (10 mL/kg/hr).   The surgical site was shaved and prepped with Betadine solution and 70% isopropyl alcohol, each applied in triplicate and patted dry with sterile gauze pads and the entire animal was draped with sterile towels (except for the surgical sites). The larynx was anesthetized with a 1% lidocaine solution and the rabbit was intubated with an uncuffed endotracheal tube (pediatric size 2-0 or 3-0 ID ) and the rabbit was placed on mechanical ventilation (oxygen 40%; tidal volume = 18 ml/kg; ventilation rate 16-18 breaths/min). Proper endotracheal tube placement was verified by auscultation and observation of condensation of the end of the tube. General anesthesia was induced with 3.0% isoflurane and maintained at 1.5% for the duration of the surgical procedure. The animal was secured on the operating room table using soft restraints.   Cardiopulmonary Bypass:  A medial sternotomy was performed and the heart was exposed and the pericardial sac opened. The cardiopulmonary bypass circuit was achieved using a Prolene (6-0) cardiovascular suture to form a single purse-string layer in the ascending aorta. An incision was made  within the purse-string to allow insertion of an  aortic cannula (3.3 mm). The cannula was secured with a purse-string tourniquet. A 14 Fr venous cannula was inserted in the right atrium via the auricular appendage. The cardiopulmonary circuit consisted of a roller pump (American Optical Corp., Southbridge, MA) and a neonate membrane oxygenator (Sorin Group USA, St. Louis, MO). The circuit was primed with whole blood obtained from a donor rabbit. During cardiopulmonary bypass when oxygenation was no longer occurring via ventilator, propofol (0.5 – 0.7 mg/kg/min IV) was continuously infused via the marginal ear vein.  Blood Donor Rabbits  Donor rabbits were sedated and anesthetized as described above. A medial sternotomy was performed and the heart was exposed, a large bore needle was inserted into the heart and blood was withdrawn into a 60 ml syringe. The heart was then removed and the animal died by exsanguination. The blood was collected in blood bags containing citric acid (Baxter, Deerfield, IL) and used immediately to prime the cardiopulmonary bypass circuit . The blood volume in the priming solution was calculated for the final hematocrit of the priming volume to be 18-20%.  Mannitol (15%) and sodium bicarbonate (20 mEq/1) were added for pH adjustment. Blood gases and hematocrit were monitored every 10-15 minutes using a Corning 238 pH/blood gas analyzer and a Corning 270 CO-oximeter (Chiron Diagnostics, Emeryville, CA).   Treatment Groups:  Three treatment groups were investigated. Control treatment animals were sedated, anesthetized and received a sternotomy; the aorta, right atrium\auricular appendage and the apex were sham-manipulated in the same manner as for global ischemia and cardioplegia hearts. Control hearts received no ischemia or cardioplegia. Control hearts were removed from the animal following 180 minutes (30 minutes equilibrium, 30 minutes sham ischemia and 120 minutes sham reperfusion). Global ischemia hearts received 30 minutes of global ischemia. Global ischemia was achieved by crossclamping of the aorta. Cardioplegia hearts received cold blood cardioplegia (Deaconess Surgical Associates (DSA) solution (K+, 60 mM; MgSO4 , 8 mM; dextrose, 2.5 mM; THAM (tris(hydroxymethyl) aminomethane), 10 mM in normal (0.9%) saline and 50 uM diazoxide) mixed (1:4; v:v) with cold blood). Diazoxide (DZX) was dissolved in dimethyl sulfoxide (DMSO, Fisher Scientific Co., Fair Lawn, NJ) before being added to DSA cardioplegia. The final concentration of DMSO was less than 0.1%. DMSO was added to control and global ischemia hearts at the same concentration. Cardioplegia was administered antegradely through the aortic root (20 ml/kg) to induce cardiac arrest. Following 30 minutes of cardioplegia the crossclamp was released, the cardiopulmonary bypass was ceased and the hearts were reperfused for 120 minutes.   Langendorff Perfusion:  To ensure that the heart tissue did not contain blood, a possible source of contamination in subsequent molecular isolation and analysis, following 120 minutes of reperfusion the heart was excised from the animal and placed in an ice-cold bath of 4oC Krebs-Ringer solution containing; NaCl 100 mM, KCl 4.7 mM, KH2PO4 1.1 mM, MgSO4 1.2 mM, NaHCO3 25 mM, CaCl2 1.7 mM, glucose 11.5 mM, pyruvic acid 4.9 mM, and fumaric acid 5.4 mM and equilibrated with 95% O2 and 5% CO2 (pH 7.4 at 37oC), where spontaneous beating ceased within a few seconds. The aorta was cannulated with a polyethylene cannula, and the heart was subjected to Langendorff retrograde perfusion for 10 minutes through the aortic root with Krebs-Ringer solution to remove all blood. Langendorff perfusion was performed at a constant pressure of 75 cm H2O in a water-jacketed chamber with myocardial temperature maintained at 37oC. The blood free heart was removed from perfusion and the atria and large vessels removed. The heart was then quick frozen in liquid nitrogen and then stored in liquid nitrogen prior to the isolation of myocardial RNA and proteins.  RNA and Protein Isolation:  Total tissue RNA was isolated and quality and purity was assessed by spectrophotometric analysis and agarose gel electrophoresis.  Total tissue ventricular myocardial protein was isolated and quality and purity was assessed by poly-acrylamide gel electrophoresis.

tag: age

value: > 32 months

tag: weight

value: 6 to 8 kg

value: Total heart (atria and ventricles)

tag: treatment

value: Cardioplegia

value: Control


title: Aged Female Rabbit Cardioplegia Heart vs. Aged Female Rabbit Global Ischemia Heart

value: Global Ischemia


title: Gastric cancer tissue samples (FFPE)_UK 28

value: Gastric cancer

value: male


title: Gastric cancer tissue samples (FFPE)_S 37

value: MSS


title: Aged Female Rabbit Global Ischemia Heart vs. Aged Female Rabbit Cardioplegia Heart


title: Aged male Rabbit Cardioplegia Heart vs. Aged male Rabbit Global Ischemia Heart

source_name: New Zealand White rabbits (aged male, > 32 months ; 6 to 8 kg)


title: Aged Female Rabbit Control Heart vs. Aged Female Rabbit Cardioplegia Heart


title: Aged Female Rabbit Control Heart vs.Aged Female Rabbit Global Ischemia Heart


title: Aged Female Rabbit Global Ischemia Heart vs. Aged Female Rabbit Control Heart


title: Gastric cancer tissue samples (FFPE)_UK 27

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: Gastric cancer tissue samples (FFPE)_UK 19


title: Gastric cancer tissue samples (FFPE)_UK 18

value: female


title: Gastric cancer tissue samples (FFPE)_UK 26


title: Mature Female Rabbit Cardioplegia Heart vs. Mature Female Rabbit Control Heart

source_name: New Zealand White rabbits (female, 15-20 weeks; 3 to 4 kg)

value: 15-20 weeks

value: 3 to 4 kg


title: Gastric cancer tissue samples (FFPE)_UK 24


title: Gastric cancer tissue samples (FFPE)_UK 25


title: Gastric cancer tissue samples (FFPE)_UK 22


title: Gastric cancer tissue samples (FFPE)_UK 20


title: Aged male Rabbit Global Ischemia Heart vs. Aged male Rabbit Cardioplegia Heart


title: Mature Female Rabbit Control Heart vs. Mature Female Rabbit Cardioplegia Heart


title: Gastric cancer tissue samples (FFPE)_UK 23


title: Aged male Rabbit Control Heart vs. Aged male Rabbit Cardioplegia Heart


title: Aged male Rabbit Cardioplegia Heart vs. Aged male Rabbit Control Heart


title: CH34_Zn_0.8mM_rep2

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: induction with 0.8mM zinc (II)

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit's protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices©, USA).

data_processing: Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fitted to al linear model and moderated t-statistics were calculated using empirical Bayes method. P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Cupriavidus metallidurans CH34

source_name: non-induced culture

label_protocol: Ten micrograms of RNA were reverse transcribed following the instructions provided with the Pronto kit (Promega, United States). Two color labeling, green for control samples and red for condition (metal challenge) samples, was performed using respectively Cy™3-dCTP and Cy™5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: Cultivating C. metallidurans CH34 for studying the gene expression during a defined chemical compound stress was done in by first inoculating 40 ml TrisMMM-gluconate with 500 microliter of a stationary C. metallidurans CH34 culture. These subcultures were allowed to grow until a cell density of 5.108 [CFU.ml-1] was reached. Cell density was controlled by regular OD600 measurements on aliquots of growing C. metallidurans CH34 subcultures with a biological spectrophotometer (biophotometer, Eppendorf). A bacterial density of 5.108 [CFU.ml-1] corresponds with an OD600 value of 0.5. This cell density in trisMMM-gluconate medium is typical reached after 20 hours of incubation at 30°C.

extract_protocol: Total RNA extraction was performed using the SV Total RNA Isolation system (Promega Corporation). The RNA isolation protocol used was optimized for RNA-extraction from C. metallidurans CH34 bacterial cells. A -80°C frozen bacterial pellet (approx 109 cells) was unfrozen at room temperature suspended in 100 microliter of RNA-stabilizing solution (RNAlater®, Ambion Inc.) and maintained at room temperature for approximately one hour. Afterwards, this cell suspension was centrifuged for 2 minute at 10 000 g and the supernatants was discarded. Lysis of the bacterial cell walls of C. metallidurans CH34 was performed by resuspending the recovered bacterial pellet in a solution containing 3 [mg.ml-1] (i.e. ≥ 120 000 [units.ml-1]) lysozyme (Sigma-Aldrich®)at room temperature. The lysis reaction was stopped after ten minutes. After this lysis, the standard microbial RNA isolation protocol of SV Total RNA Isolation system was resumed according to the centrifugation method. The quantity of extracted RNA was measured using a NanoDrop™ 1000 spectrophotometer (Thermo Scientific, USA). The RNA quality was determined with a bioanalyzer (Agilent 2100 Electrophoresis Bioanalyzer, Agilent Technologies). Only extracted RNA with a RNA integrity number (RIN-number) of higher than 8 was accepted for further micro array gene expression analysis

treatment_protocol: After growth, the subculture was divided in two equal portions of 20 ml in two new falcon tubes. One tube was used as condition (i.e. challenged with the defined amount of a chemical compound – see samples) while the other flask served as control (i.e. same amount of sterile water added). Immediately after addition, the tubes were incubated at the same conditions as before for the needed duration for chemical compound challenges (i.e. 30 min). After this challenge, each 20 ml culture was immediately subdivided in 10 eppendorfs of 2 ml, and the cells were harvested by centrifugation for 1 minute at 10 000 g. Supernatans was removed and the eppendorfs containing only the centrifuged bacterial pellets (each containing ca. 109 bacterial cells) were flash frozen by immersion into liquid nitrogen. Pellets were kept frozen at -80°C at all times. Each challenge condition (i.e. each of the different tested chemical compounds) was performed in biological quadruplicate, using 4 independent bacterial cultures.

tag: metal

source_name: induction with 0.8mM zinc (II)

value: 0.8mM zinc (II)


title: Mature Female Rabbit Global Ischemia Heart vs. Mature Female Rabbit Cardioplegia Heart


title: Aged male Rabbit Global Ischemia Heart vs. Aged male Rabbit Control Heart


title: Gastric cancer tissue samples (FFPE)_UK 17

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: CH34_Tl_0.05mM_rep2

description: induction with 0.05mM thallium (I)

source_name: induction with 0.05mM thallium (I)

value: 0.05mM thallium (I)


title: Aged male Rabbit Control Heart vs. Aged male Rabbit Global Ischemia Heart


title: Gastric cancer tissue samples (FFPE)_UK 21

value: UK patient


title: CH34_Zn_0.8mM_rep1

description: induction with 0.8mM zinc (II)


title: Mature Female Rabbit Cardioplegia Heart vs. Mature Female Rabbit Global Ischemia Heart


title: Mature Female Rabbit Global Ischemia Heart vs. Mature Female Rabbit Control Heart


title: CH34_Tl_0.05mM_rep1

description: induction with 0.05mM thallium (I)


title: Gastric cancer tissue samples (FFPE)_UK 16


title: CH34_Tl_0.05mM_rep3

description: induction with 0.05mM thallium (I)


title: CH34_Sr_10mM_rep1

description: induction with 10mM strontium (II)

source_name: induction with 10mM strontium (II)

value: 10mM strontium (II)


title: CH34_Se_1mM_rep2

description: induction with 1mM selenite (IV)

source_name: induction with 1mM selenite (IV)

value: 1mM selenite (IV)


title: CH34_Sr_10mM_rep2

description: induction with 10mM strontium (II)


title: Mature Female Rabbit Control Heart vs. Mature Female Rabbit Global Ischemia Heart

description:
Rabbit Set 2 Slide 11.gpr (not provided by submitter)
Rabbit Set 2 Slide 12.gpr (not provided by submitter)

value: Total heart (atria and ventricles)


title: Gastric cancer tissue samples (FFPE)_UK 15


title: CH34_Se_1mM_rep1

description: induction with 1mM selenite (IV)


title: CH34_Pb_0.4mM_rep2

description: induction with 0.4mM lead (II)

source_name: induction with 0.4mM lead (II)

value: 0.4mM lead (II)


title: Gastric cancer tissue samples (FFPE)_UK 13


title: Gastric cancer tissue samples (FFPE)_UK 14


title: CH34_Ni_0.6mM_rep1

description: induction with 0.6mM nickel (II)

source_name: induction with 0.6mM nickel (II)

value: 0.6mM nickel (II)


title: CH34_Pb_0.4mM_rep1

description: induction with 0.4mM lead (II)


title: Mature male Rabbit Cardioplegia Heart vs. Mature male Rabbit Global Ischemia Heart

source_name: New Zealand White rabbits (male, 15-20 weeks; 3 to 4 kg)

value: Cardioplegia

value: Global Ischemia


title: CH34_Mn_10mM_rep3

description: induction with 10mM manganese (II)

source_name: induction with 10mM manganese (II)

value: 10mM manganese (II)


title: CH34_Sr_10mM_rep3

description: induction with 10mM strontium (II)


title: Mature male Rabbit Global Ischemia Heart vs. Mature male Rabbit Control Heart

value: male

value: Control


title: rtt106-del-TSA

city: Nanjing

first: Yakun

last: Wan

address: Sipailou #2

country: China

institute: Southeast University

description: Two color microarrays, comparing RNA from the experimental conditions (deletion mutations grown in YPD, WT and deletion mutations grown in YPD with TSA treatment) to RNA from the control WT cells grown in glucose-containing medium (YPD), were performed using Agilent whole-genome S. cerevisiae arrays.

hyb_protocol: Agilent yeast gene expression array protocol

data_processing: Log2 of the average mRNA abundance ratios are reported. Differentially expressed genes were identified by maximum-likelihood analysis (λ>25) and significantly affected genes in the experimental conditions were identified by a change in expression of two-fold or more compared to the expression in the relevant WT strains. Significantly differentially expressed genes were analyzed as previously described in (Wan, Y. et al. NAR, 2010) by using Excel (Microsoft) for chromosome position analysis.

source_name: control

growth_protocol: The strains were cultured at 30°C in YPD (1% yeast extract, 2% peptone, 2% glucose) media. For TSA treatments, WT and deletion mutants were grown to mid-log phase (OD600=0.5), TSA (Sigma-Aldrich) was then added to the yeast cultures at a final concentration of 10 μM and cells were cultured for additional hour.

extract_protocol: Total RNA was isolated by hot acid phenol extraction protocol as previously described in Wan, Y. et al. MCB, 2009

value: untreated

source_name: deletion and treatment

value: TSA


title: vps75-del-TSA

scan_protocol: Agilent yeast gene expression array protocol


title: Mature male Rabbit Control Heart vs. Mature male Rabbit Global Ischemia Heart

value: 15-20 weeks

value: 3 to 4 kg


title: vps75-del

label_protocol: Agilent yeast gene expression array protocol

value: wild type

source_name: deletion


title: Gastric cancer tissue samples (FFPE)_UK 11

source_name: Gastric cancer

value: Gastric cancer

value: female

value: MSS

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: CH34_Mn_10mM_rep2

description: induction with 10mM manganese (II)


title: CH34_Ni_0.6mM_rep2

description: induction with 0.6mM nickel (II)


title: Gastric cancer tissue samples (FFPE)_UK 12

value: UK patient

source_name: female reference DNA

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: CH34_Mn_10mM_rep1

description: induction with 10mM manganese (II)


title: Gastric cancer tissue samples (FFPE)_UK 10


title: Gastric cancer tissue samples (FFPE)_UK 9

source_name: male reference DNA


title: CH34_Hg_1.3uM_rep2

description: induction with 1.3uM mercury (II)

source_name: induction with 1.3uM mercury (II)

value: 1.3uM mercury (II)


title: rtt106-del


title: CH34_Hg_1.3uM_rep1

description: induction with 1.3uM mercury (II)


title: CH34_Hg_1.3uM_rep3

description: induction with 1.3uM mercury (II)


title: nap1-del-TSA


title: nap1-del


title: Gastric cancer tissue samples (FFPE)_UK 8


title: CH34_Cu_0.1mM_rep1

description: induction with 0.1mM copper (II)

source_name: induction with 0.1mM copper (II)

value: 0.1mM copper (II)


title: CH34_Cu_0.1mM_rep2

description: induction with 0.1mM copper (II)

source_name: non-induced culture


title: CH34_Cs_30mM_rep3

description: induction with 30mM cesium (I)

source_name: induction with 30mM cesium (I)

value: 30mM cesium (I)


title: CH34_Cs_30mM_rep2

description: induction with 30mM cesium (I)


title: CH34_Cr_0.1mM_rep2

description: induction with 0.1mM chromate (VI)

source_name: induction with 0.1mM chromate (VI)

value: 0.1mM chromate (VI)


title: CH34_Cr_0.1mM_rep3

description: induction with 0.1mM chromate (VI)


title: CH34_Cs_30mM_rep1

description: induction with 30mM cesium (I)


title: CH34_Co_10mM_rep3

description: induction with 10mM cobalt (II)

source_name: induction with 10mM cobalt (II)

value: 10mM cobalt (II)


title: chz1-del-TSA


title: Gastric cancer tissue samples (FFPE)_UK 6

value: male


title: asf1-del-TSA

value: untreated


title: chz1-del-glucose

value: glucose


title: CH34_Cr_0.1mM_rep1

description: induction with 0.1mM chromate (VI)


title: wt-TSA

source_name: treated

value: TSA


title: CH34_Co_10mM_rep1

description: induction with 10mM cobalt (II)


title: CH34_Co_10mM_rep2

description: induction with 10mM cobalt (II)


title: Gastric cancer tissue samples (FFPE)_UK 5


title: Gastric cancer tissue samples (FFPE)_UK 4


title: asf1-del


title: Gastric cancer tissue samples (FFPE)_UK 7


title: CH34_Cd_0.6mM_rep2

description: induction with 0.6mM cadmium (II)

source_name: induction with 0.6mM cadmium (II)

value: 0.6mM cadmium (II)


title: Gastric cancer tissue samples (FFPE)_UK 3


title: CH34_Cd_0.6mM_rep1

description: induction with 0.6mM cadmium (II)


title: CH34_Au_0.5umM_rep3

description: induction with 0.5umM gold (III)

source_name: induction with 0.5umM gold (III)

value: 0.5umM gold (III)


title: CH34_Au_0.5umM_rep2

description: induction with 0.5umM gold (III)


title: Gastric cancer tissue samples (FFPE)_UK 2

value: Gastric cancer


title: Gastric cancer tissue samples (FFPE)_UK 1


title: CH34_As_0.5mM_rep3

description: induction with 0.5mM arsenickel (II)te (III)

value: 0.5mM arsenickel (II)te (III)


title: CH34_Au_0.5umM_rep1

description: induction with 0.5umM gold (III)


title: CH34_As_0.5mM_rep2

source_name: induction with 0.5mM arsenickel (II)te (III)


title: Wildtype 5mil rep2

city: Milano

first: Riccardo

middle: Lorenzo

last: Rossi

state: MI

address: Via Trivulzio 10

department: Integrative Biology

country: Italy

institute: Fondazione INGM

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol, with Illumina iScan System.

data_processing: The data were normalised using quantile normalisation with BeadStudio 3.0

source_name: HeLa (5 millions) transfected with mock plasmid, wild type sample, array replica2

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Quiagen miRneasy kit , in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: HeLa


title: KD 5mil rep2

source_name: HeLa (5 millions) transfected with Hmgb1-shRNA plasmid, KD sample, array replica2


title: CH34_Ag_0.25uM_rep3

description: induction with 0.25uM silver (I)

source_name: induction with 0.25uM silver (I)

value: 0.25uM silver (I)


title: CH34_Ag_0.25uM_rep1

description: induction with 0.25uM silver (I)


title: CH34_Ag_0.25uM_rep2

description: induction with 0.25uM silver (I)


title: KD 500K rep2

source_name: HeLa (500K) transfected with Hmgb1-shRNA plasmid, KD sample, array replica2


title: CH34_As_0.5mM_rep1


title: Space flight Sample -  biological replicate 3

description: gene expression data from bacteria cultured in space flight conditions

hyb_protocol: Samples were hybridized, washed, stained, and scanned as described in the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

data_processing: Raw Affymetrix data were pre-processed using the Affy package in BioConductor as follows: (i) background correction based on the robust multichip average (RMA) convolution model (Irizarry et al., 2003), (ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), (iii) summarization of multiple probe intensities for each probe set to one expression value per gene using RMA (Irizarry et al., 2003). To test for differential expression between the spaceflight and ground control cultures, the Bayesian adjusted t-statistics was used as implemented in the LIMMA package (version 2.5.15) (Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg, 1995). Microarray analysis was performed on all three biological replicates.

organism: Pseudomonas aeruginosa PAO1

source_name: Space flight sample

label_protocol:
Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression protocol. Briefly, random hexamers (Invitrogen) were added to 10 microgram of RNA along with
in vitro-transcribed Bacillus subtilis control spikes. cDNA was synthesized using Superscript III (Invitrogen) and the following conditions: 25°C for 10 min, 37°C for 60 min, and 70°C for 10 min. RNA was removed by alkaline treatment and subsequent neutralization. The cDNA was purified by using a QIAquick PCR purification kit (QIAGEN) and eluted in 40 microl of elution buffer (QIAGEN). The cDNA was then fragmented by using 0.6 U DNase I (Amersham) per microg cDNA
at 37°C for 10 min. The fragmented cDNA was end labeled with biotin-ddUTP by using a BioArray terminal labeling kit (Enzo) per the manufacturer’s instructions. A gel shift mobility assay was performed using NeutrAvadin (Pierce) on a 5% polyacrylamide gel stained with SYBR green (Roche) to ensure complete fragmentation and labeling.

growth_protocol: P. aeruginosa PAO1 was grown in LB medium containing 25 µg/ml gentamicin in the spaceflight hardware (see below) to avoid growth of any contaminants. The bacterial inoculum 1.5 x 10+8 CFU/ml was suspended in 0.5 ml phosphate buffered saline (PBS)

extract_protocol: Total RNA was isolated using the RNeasy minikit (Qiagen) per the manufacturer’s instructions.

treatment_protocol: A derivative of the wild type P. aeruginosa PAO1 (ATCC 15692) was used for the spaceflight experiment, which contained a gentamicin resistance cassette. The gentamicin-resistant strain was constructed through homologous recombination as described previously (Schweizer, 1993). P. aeruginosa PAO1 was grown in LB medium containing 25 µg/ml gentamicin in the spaceflight hardware (see below) to avoid growth of any contaminants. The bacterial inoculum 1.5 x 108 CFU/ml in the spaceflight hardware was suspended in 0.5 ml phosphate buffered saline (PBS) (Invitrogen), and remained viable but -static during launch and until nine days into the flight. Here after, growth was initiated by the addition of LB as described below. Cells were fixed in-flight using the RNA and protein fixative RNA Later II (Ambion). At 2.5 hours after Shuttle landing at the Kennedy Space Center (KSC), samples were recovered and subsequently used for whole genome transcriptional microarray and proteomic analysis. In each case, the flight culture samples were compared with culture samples grown under identical conditions on the ground at KSC using coordinated activation and termination times (by means of real-time communications with the Shuttle astronauts) in an insulated room that maintained identical temperature and humidity levels as those on the Shuttle (Orbital Environment Simulator).

tag: culture

value: bacteria cultured during space flight

tag: atcc


title: KD 5mil rep1

source_name: HeLa (5 millions) transfected with Hmgb1-shRNA plasmid, KD sample, array replica1


title: M16_WT_0h, biological rep4

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

description:
M16
Wildtype, untreated.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99°C for 5 minutes, then 42°C for 5 minutes, and centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing: RMA normalization using Expression Console.

source_name: Spleen, wildtype, untreated

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Shh mutant phenotypes were manually identified as wild-type or mutants. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: phenotype

value: wildtype

value: spleen


title: M13_WT_Oh, biological rep1

description:
M13
Wildtype, untreated.

tag: strain


title: Wildtype 500K rep2

source_name: HeLa (500K) transfected with mock plasmid, wild type sample, array replica2


title: M12_WT_CASP, biological rep4

description:
M12
Wildtype, septic.

source_name: Spleen, wildtype, septic

value: colon ascendens stent peritonitis (CASP)


title: Wildtype 500K rep1

source_name: HeLa (500K) transfected with mock plasmid, wild type sample, array replica1


title: Wildtype 5mil rep1

source_name: HeLa (5 millions) transfected with mock plasmid, wild type sample, array replica1


title: FOG1+/+ Meg, biological rep3

city: Philadelphia

first: Yuhuan

last: Wang

state: PA

address: 3615 Civic Center Blvd

institute: The Children's Hospital of Philadelphia

hyb_protocol: Probes were hybridized to Affymetrix Mouse Genome 430 2.0 Array GeneChips.

scan_protocol: All samples were amplified, labeled, hybridized, and scanned at the Penn Microarray Facility (University of Pennsylvania) according to manufacturer’s protocol.

data_processing: The raw data (.CEL files) were processed by MAS5.0, using the xps package at the University of Pennsylvania Microarray Facility. The signals for the 3 replicates of each probe set were averaged. Averaged signals between Ki/Ki and WT samples were computed for comparative analyses (fold changes). Annotations were extracted from affymatrix database. Results and annotations were merged into Microsoft Excel.

source_name: FOG1+/+ Meg

label_protocol: RNA was amplified using the WT-Ovation Pico System from NuGEN. Sense transcript (ST)-cDNA was generated using the WT-Ovation Exon Module. ST-cDNA was subsequently fragmented and 3’ labeled with biotin using the WT-Ovation Biotin Module V2 (NuGEN).

growth_protocol: Mouse Megs were differentiated from fetal liver cells in IMDM medium with thrompoietin

extract_protocol: Total RNA was extracted from Megs using Rneasy Plus kit  according to the manufacturer's instructions.

tag: background strain

value: mixed C57BL/6xSv129 background

tag: genotype/variation

value: fetal liver

value: megakaryocyte


title: M14_WT_0h, biological rep2

description:
M14
Wildtype, untreated.

tag: tissue


title: M15_WT0h, biological rep3

description:
M15
Wildtype, untreated.


title: FOG1+/- Meg, biological rep2

source_name: FOG1+/- Meg


title: FOG1+/- Meg, biological rep1


title: KD 500K rep1

source_name: HeLa (500K) transfected with Hmgb1-shRNA plasmid, KD sample, array replica1


title: FOG1-/- ki/ki Meg, biological rep2

source_name: FOG1-/- ki/ki Meg

value: FOG1-/- ki/ki


title: M11_WT_CASP, biological rep3

description:
M11
Wildtype, septic.


title: FOG1-/- ki/ki Meg, biological rep1


title: FOG1-/- ki/ki Meg, biological rep3