title: Chip-27 RD+Vern R4blue &Para Wk12 R4red

hyb_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols. Labeled cDNAs were hybridized to a custom made 23K element microarray that contained 19,808 unigenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 unigenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates.

tag: tissue

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected from paradormant crown buds used as secondary controls, to complement 12 week ramp down treatment.


title: 120 minutes after Notch activation vs unactivated pool trial 3

status: Public on Dec 31 2012

type: RNA

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

description: 120' Notch activation trial 3

hyb_protocol: Co-hybridisation of sample vs reference control to long oligonucleotides microarrays (Flychip FL003; GEO platform accession GPL8244) was performed for 16 hours at 51°C using a GeneTac hybridisation station (Digilab Genomic Solutions Inc). Post hybridisation washes were performed according to the slide manufacturer’s recommendation.  Detailed protocols for array spotting, labelling, hybridisation and washes are available at http://www.flychip.org.uk/protocols/.

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)

data_processing: Spot finding and quantitation via the Dapple package. The R package limma (SMYTH and SPEED 2003) was used to normalize the arrays. For each array, the background intensity level of the array image was first adjusted before loess normalization was applied to the MA values of the array. The intensities of the two channels of all 72 arrays (4 replicates at 18 time points) were then quantile normalized, such that the intensities all had the same empirical distribution. Missing values arise because genes are not expressed or there is poor quality on the array.

molecule: total RNA

organism: Drosophila melanogaster

source_name: reference pool - trial 3

label_protocol: 45 µg of sample or reference pool RNA was mixed with 1.5 µM anchored oligo(dT)23 (Sigma) and incubated at 65°C for 10 minutes. Reverse transcription was performed in the presence of 1nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 20U RNAsin (Promega) with 400U SuperScript III (Life Technologies) at 46°C for 2 hours. The product was purified using Sephadex G50 columns (GE Healthcare). Samples from trials #1 and #3 were labelled with Cy5 and trails #2 and #4 as dye-swap with Cy3.

growth_protocol: DmD8 cells were cultured in Schneiders medium (Invitrogen) supplemented with 10% FBS (Sigma), 5ug/ml insulin (Sigma) and 5% penicillin / streptomycin (Sigma) according to standard protocols.

extract_protocol: RNA was extracted from cells by removing media and incubating cells in TRI-reagent (Ambion) for 5 minutes. RNA was then purified by extracting with chloroform and precipitating with isopropanol before resuspension in DEPC treated water. DNA was removed by treating with DNase (DNA-free kit - Ambion). For each trial 50 µg of the untreated RNA sample of each time point was pooled to create a trial specific reference sample.

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. For control samples, media was replaced with fresh media to mimic the addition and removal of EDTA in corresponding experimental samples.

tag: cell line

tag: time

value: pool of unactivated cells from 0-150 minutes

tag: time trial

source_name: 120' after Notch activation - trial 3

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 0 minutes before washing out EDTA using normal culture media.

value: 120 minutes after a 5 minute activation with EDTA


title: 120 minutes after Notch activation vs unactivated pool trial 1

description: 120' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 120' after Notch activation - trial 1

extract_protocol: RNA was extracted from cells by removing media and incubating cells in TRI-reagent (Ambion) for 5 minutes. RNA was then purified by extracting with chloroform and precipitating with isopropanol before resuspension in DEPC treated water. DNA was removed by treating with DNase (DNA-free kit - Ambion).


title: Ssa_Diet 6_14d_replicate 6

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

country: Canada

institute: Fisheries & Oceans Canada

hyb_protocol: Microarray hybridizations were performed using Agilent’s 4 x 44K Atlantic salmon microarray slides containing 4 grids with the same ~ 44 000 features (Design ID 025055), using a one-color approach.  All hybridizations, including washes and drying steps were carried out on a HS4800 automated hybridization station using quad chambers (Tecan, Männedorf, Switzerland). Briefly, slides were initially washed with Agilent’s aOligo aCGH Prehybridization buffer for 1 min at 65°C and injected with a 60 µl of hybridization mix containing 30 µl of fragmentation mix and 30 µl of Agilent’s 2x GEx hybridization Buffer Hi-RPM per chamber.  The injected material was hybridized for 17 hour at 65°C.  Following hybridization slides were washed twice with Agilent’s gene expression wash buffer 1 at 23°C for 1 min, twice with Agilent’s gene expression wash buffer 2 with 0.01 wash buffer additive at 37°C for 1 min and then dried under nitrogen.

scan_protocol: Microarray slides were scanned at a resolution of 5 µm using Agilent’s High Resolution Microarray Scanner (Agilent, CA, USA) using a 20-bit data format and automatic PMT adjustment.

data_processing: The resulting TIFF images were quantified using Agilent’s Feature Extraction software (Agilent, CA, USA). Numerical intensities, descriptive statistics and flag value were computed for each spot and exported in a text file. Spots were considered flagged it they were saturated, not uniform, below background levels and if the background was not uniform. Genes that had a flag on more than 1/3 of the slides used for a particular statistical analysis were filtered out.  The gProcessedSignal values (foreground value minus background value) for each spot were then log2 transformed and normalized between arrays using a median centering approach found in BRBArrayTool version 4.1.0 Beta_2 Release (developed by Dr. Richard Simon and BRB-ArrayTools Development Team).  Statistical analysis was performed on log2 transformed and normalized gProcessedSignal value.

organism: Salmo salar

source_name: Ssa_Diet 6_14d_replicate 6

label_protocol: RNA amplification and labeling for microarray was performed using the one-color Low Input Quick Amp Labeling kit (Agilent, CA, USA) and following the manufacturer’s recommendations. Briefly, 200 ng of each RNA sample was reverse transcribed, amplified and labeled using Cy3 dyes resulting in Cy3 labeled amplified RNA (aRNA). Purification of the labeled aRNA was performed using NucleoSpin RNA clean up columns (Macherey-Nagel, CA, USA) following the manufacturer’s recommendations. Following purification, labeled aRNA samples were then quantified using the NanoDrop 8000 to verify the yield of aRNA and the labeling efficiency. 1.65 µg of each purified aRNA was prepared for hybridization using the fragmentation step described in Agilent’s Low Input Quick Amp labeling kit protocol. Briefly each aRNA was fragmented by mixing 1.65 µg of aRNA in a volume of 22.8 µl, with 6 µl of 10X blocking agent and 1.2 µl of 25X fragmentation buffer and heating the mix at 60°C for 30 min.

extract_protocol: Total RNA from RNAlater preserved salmon liver samples was extracted using TRI reagent (Molecular Research Center, OH, USA) followed by column purification using the NucleoSpin RNA II (Macherey-Nagel, PA, USA) and following the manufacturer’s protocol.  An on column DNase digestion step was performed on each sample.  RNA quantification was performed using a NanoDrop 8000 (Thermo Scientific, DE, USA) and RNA quality and integrity was assessed with the Experion automated electrophoresis system (Bio-Rad, TX, USA).  Only RNA samples with RNA Quality Indicator (RQI) values above 8 were used for analysis.  RNA’s were stored at -70ºC in DEPC treated water containing an RNase inhibitor (Qiagen, ON, Canada) until needed.

tag: diet

value: Sea cucumber internal organs

value: Liver


title: Ssa_Diet 6_14d_replicate 5

source_name: Ssa_Diet 6_14d_replicate 5


title: Chip-26 Para Wk12 R4blue & RD Wk12 R4red

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

country: USA

institute: USDA-ARS

scan_protocol: Microarray hybridization was visualized using a GenePix 4000B scanner and probe intensities and background were quantified using GenePix 6.0 software (Molecular Devices, Sunnyvale, California, USA).

data_processing: A quality control value of "1" was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deleting 1% of the most intense negative/empty probe values). Intensity values of control spots (a total of 1455 spots including 3X SSC, blanks, and mouse) from MA chips were removed before bioinformatics. In this submission, the original "GPR" files include information for the control spots, while the Sample data tables include information only for the spots that were used for data analyses (a total of: 23937). Raw signal intensities of all DNA-containing spots were up-loaded into the GeneMaths XT 5.1 microarray data analysis program (Applied Maths Inc., Austin, TX, USA) for normalization following the "Layer/Normalization/Arrays" path with default settings (Offset: Average; Scaling: Standard deviation), and for statistical analysis and clustering of the dataset. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other; technical replicates within each biological replicate were averaged.

organism: Euphorbia esula

source_name: Paradormant crown buds

label_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols. Labeled cDNAs were hybridized to a custom made 23K element microarray that contained 19,808 unigenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 unigenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In this experiment, each of the four biological replicates included two technical replicates.

growth_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length. Each treatment was replicated four times, and thirty plants were used per biological replication. Prior to the start of each experiment, plants were randomly chosen from the greenhouse and acclimated in a growth chamber (PGR15 Model of Conviron, Winnipeg, Canada) for one week at 27°C, 16 h:8 h day:night photoperiod. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation.

extract_protocol: At the end of each treatment, crown bud samples were collected, flash froze in liquid N2, and stored at -80°C until RNA extraction. Crown bud samples were ground to a fine powder in liquid N2, and RNA was extracted from approximately one gram of tissue according to the pine tree RNA extraction protocol (Chang et al. 1993). RNA quality and quantity was confirmed by spectrophotometry and agarose gel electrophoresis.

tag: species

value: Leafy spurge

value: crown buds

tag: treatment

value: controls

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 12-week time point during the RDt treatment.

value: 12 weeks


title: Chip-25 RD Wk12 R4blue & RD Wk9 R4red

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 9 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 9-week time point during the RDt treatment.

value: 9 weeks


title: Ssa_Diet 6_14d_replicate 4

source_name: Ssa_Diet 6_14d_replicate 4


title: control2 [CW2011060317]

city: Boston

first: Christopher

middle: A

last: Walsh

state: MA

address: 3 Blackfan Circle

department: Genetics

institute: Children's Hospital Boston

description:
Gene expression data from cells that show a decrease in ZNF335
long term

hyb_protocol: hybridized at 45C for 16hours according to Genechip 3 IVT Express Kit User Manual

scan_protocol: Affymetrix Genechip scanner 3000 to scan the arrays

data_processing: D chip analysis

label: biotin

organism: Mus musculus

source_name: control knockdown in mouse neurons from E14.5 harvested at P0

label_protocol: labeling of RNA was done with biotinylated ribonucleotide according to Genechip 3 IVT Express Kit User Manual

extract_protocol: Qiagen total RNA kit

tag: developmental stage

tag: strain

tag: time point

value: long term (5 days post knockdown)


title: 120 minutes after Notch activation vs unactivated pool trial 2

description: 120' Notch activation trial 2 - dye swap

source_name: 120' after Notch activation - trial 2

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 120 minutes before washing out EDTA using normal culture media.

source_name: reference pool - trial 2


title: 110 minutes after Notch activation vs unactivated pool trial 4

description: 110' Notch activation trial 4 - dye swap

source_name: 110' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 110 minutes before washing out EDTA using normal culture media.

value: 110 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: control3 [CW2011082541]

description:
Gene expression data from control
short term

value: short term (1 day post knockdown)


title: Ssa_Diet 6_14d_replicate 3

source_name: Ssa_Diet 6_14d_replicate 3


title: Chip-23 RD Wk6 R4blue & RD Wk3 R4red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 6 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 6-week time point during the RDt treatment.

value: 6 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 3 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 3-week time point during the RDt treatment.

value: 3 weeks


title: Chip-24 RD Wk9 R4blue & RD Wk6 R4red

value: exposed to ramp down in temperature under constant photoperiod for 9 weeks

value: exposed to ramp down in temperature under constant photoperiod for 6 weeks


title: control2 [CW2011082540]


title: control1 [CW2011082539]


title: Ssa_Diet 6_14d_replicate 1

source_name: Ssa_Diet 6_14d_replicate 1


title: Ssa_Diet 5_56d_replicate 6

source_name: Ssa_Diet 5_56d_replicate 6

value: Herring milt


title: Chip-22 RD Wk3 R4blue & Para Wk0 R4red

value: exposed to ramp down in temperature under constant photoperiod for 3 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents paradormant crown buds (Para-0 week) used as controls.


title: 110 minutes after Notch activation vs unactivated pool trial 3

description: 110' Notch activation trial 3

source_name: reference pool - trial 3

value: pool of unactivated cells from 0-150 minutes

source_name: 110' after Notch activation - trial 3


title: 110 minutes after Notch activation vs unactivated pool trial 1

description: 110' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 110' after Notch activation - trial 1


title: SiRNA knockdown 2 [CW2011082537]

description:
Gene expression data from cells that show a decrease in ZNF335
short term

source_name: ZNF335 knockdown of cells at E14.5 harvested at P0


title: Chip-20 RD+Vern R3blue & Para Wk12 R3red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected from plants exposed to ramp down in temperature for 12 weeks under constant light, and then exposed to vernalizing cold treatment (5-7°C for 8 weeks).

value: 12 weeks, then vernalized

source_name: Paradormant crown buds


title: Chip-19 Para Wk12 R3blue & RD Wk12 R3red

value: Leafy spurge

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks


title: Chip-21 Para Wk0 R4blue & RD+Vern R3red

value: crown buds

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized


title: 100 minutes after Notch activation vs unactivated pool trial 4

description: 100' Notch activation trial 4 - dye swap

source_name: 100' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 100 minutes before washing out EDTA using normal culture media.

value: 100 minutes after a 5 minute activation with EDTA


title: 110 minutes after Notch activation vs unactivated pool trial 2

description: 110' Notch activation trial 2 - dye swap

source_name: 110' after Notch activation - trial 2

source_name: reference pool - trial 2


title: 100 minutes after Notch activation vs unactivated pool trial 3

description: 100' Notch activation trial 3

source_name: 100' after Notch activation - trial 3


title: SiRNA knockdown 3 [CW2011082538]


title: Ssa_Diet 6_14d_replicate 2

source_name: Ssa_Diet 6_14d_replicate 2

value: Sea cucumber internal organs

value: Liver


title: Ssa_Diet 5_56d_replicate 3

source_name: Ssa_Diet 5_56d_replicate 3


title: 100 minutes after Notch activation vs unactivated pool trial 1

description: 100' Notch activation trial 1

source_name: 100' after Notch activation - trial 1


title: Ssa_Diet 5_56d_replicate 4

source_name: Ssa_Diet 5_56d_replicate 4


title: SiRNA knockdown 1 [CW2011082536]


title: Chip-18 RD Wk12 R3blue & RD Wk9 R3red

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks

value: 12 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 9 weeks

value: 9 weeks


title: 100 minutes after Notch activation vs unactivated pool trial 2

description: 100' Notch activation trial 2 - dye swap

source_name: 100' after Notch activation - trial 2


title: Ssa_Diet 5_56d_replicate 5

source_name: Ssa_Diet 5_56d_replicate 5


title: Ssa_Diet 5_56d_replicate 2

source_name: Ssa_Diet 5_56d_replicate 2


title: 90 minutes after Notch activation vs unactivated pool trial 4

description: 90' Notch activation trial 4 - dye swap

source_name: 90' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 90 minutes before washing out EDTA using normal culture media.

value: 90 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: Chip-17 RD Wk9 R3blue & RD Wk6 R3red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 6 weeks

value: 6 weeks


title: slc6a4_bs_ub3

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description: Total tissue RNA (unbound) from Replicate 3

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

data_processing: GCRMA normalization within biological replicate groups.  Performed with R / Bioconductor.

label: Biotin

label_protocol: Affymetrix two cycle amplification kit, starting with 20 ng of total RNA.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice(see PMID:19013282), followed by Trizol extraction, DNAse treatment, and RNeasy-Minelute Cleanup

value: Dissected midbrain and brainstem (removed cerebellum, and took all tissue posterior to the pontine/hypothalamic junction, including superior colliculi to foramen magnum)

tag: age

value: adult(6-12 weeks)

tag: line

value: slc6a4 JD60

tag: genotype

value: Slc6a4 JD60

tag: number of mice

tag: gender

value: males and females

tag: sample type

value: Total tissue RNA (unbound)

value: mixed FVB and c57/bl6j background


title: slc6a4_bs_ub2

description: Total tissue RNA (unbound) from Replicate 2

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform


title: slc6a4_bs_ub1

description: Total tissue RNA (unbound) from Replicate 1


title: Chip-16 RD Wk6 R3blue & RD Wk3 R3red

value: Leafy spurge

value: crown buds

value: exposed to ramp down in temperature under constant photoperiod for 6 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 3 weeks

value: 3 weeks


title: Ssa_Diet 5_56d_replicate 1

source_name: Ssa_Diet 5_56d_replicate 1

value: Herring milt

value: Liver


title: 90 minutes after Notch activation vs unactivated pool trial 3

description: 90' Notch activation trial 3

source_name: reference pool - trial 3

value: pool of unactivated cells from 0-150 minutes

source_name: 90' after Notch activation - trial 3


title: slc6a4_bs_ip2

description: Trap'd serotonin neuron RNA, biological replicate 2

value: Trap'd serotonin neuron RNA


title: 90 minutes after Notch activation vs unactivated pool trial 2

description: 90' Notch activation trial 2 - dye swap

source_name: 90' after Notch activation - trial 2

value: 90 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 2


title: Ssa_Diet 5_14d_replicate 6

source_name: Ssa_Diet 5_14d_replicate 6


title: slc6a4_bs_ip3

description: Trap'd serotonin neuron RNA, biological replicate 3


title: 80 minutes after Notch activation vs unactivated pool trial 4

description: 80' Notch activation trial 4 - dye swap

source_name: 80' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 80 minutes before washing out EDTA using normal culture media.

value: 80 minutes after a 5 minute activation with EDTA


title: Chip-13 RD+Vern R2blue & Para Wk12 R2red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized

value: 12 weeks, then vernalized

source_name: Paradormant crown buds

value: controls


title: Chip-15 RD Wk3 R3blue & Para Wk0 R3red

value: exposed to ramp down in temperature under constant photoperiod for 3 weeks


title: Chip-14 Para Wk0 R3blue & RD+Vern R2red

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized


title: Chip-12 Para Wk12 R2blue & RD Wk12 R2red

source_name: Paradormant crown buds used as secondary controls, to complement 12 week ramp down treatment

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks

value: 12 weeks


title: 90 minutes after Notch activation vs unactivated pool trial 1

description: 90' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 90' after Notch activation - trial 1


title: Ssa_Diet 5_14d_replicate 5

source_name: Ssa_Diet 5_14d_replicate 5


title: Ssa_Diet 5_14d_replicate 3

source_name: Ssa_Diet 5_14d_replicate 3


title: HSC_day7, biological rep 3

city: Durham

first: Cynthia

last: Moylan

state: NC

address: 595 LaSalle Street, GSRB1, DUMC 3256

department: Gastroenterology

institute: Duke University Medical Center

description: Gene expression data from myofibroblastic HSC

hyb_protocol: Affymetrix GeneChip  hybridization Oven 645, Affymetrix (Santa Clara, CA)

scan_protocol: Affymetrix GeneChip Scanner 7G, Affymetrix (Santa Clara, CA) Fluidic station: Affymetrix GeneChip Fluidics Station 450, Affymetrx (Santa Clara, CA) Sample register: Affymetrix GeneChip Command Console Scan Control 3.0.0.1214, Affymetrix (Santa Clara, CA)

data_processing: Affymetrix Expression Console version 1.1, Affymetrix (Santa Clara, CA), RMA

label_protocol: MessageAmp Premier RNA Amplification Kit (Part Number 4385821, AM1792, 4383452), Applied Biosystems/Ambion (Austin, TX)

growth_protocol: Primary hepatic stellate cells were isolated C57BL6 mice, assessed for purity and viability and cultured for 7days.

extract_protocol:
Agilent 2100 Bioanalyzer G2939A, Agilent Technologies (Santa Clara, CA)
Nanodrop 8 spectrophotometer, Thermo Scientific/NanoDrop (Wilmington, DE)
Combination of Trizol and Rneasy columns extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Primary hepatic stellate cells were isolated from rodent liver and cultureed in DMEM with 10% fetal bovine serum and antibiotics for 7 days.

tag: cell type

value: primary hepatic stellate cells


title: Chip-11 RD Wk12 R2blue & RD Wk9 R2red

treatment_protocol: We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week). This sample represents crown buds collected at the end of 12-week time point during the RDt treatment.

tag: tissue

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 9 weeks

value: 9 weeks


title: HSC_day7, biological rep 2


title: Ssa_Diet 5_14d_replicate 1

source_name: Ssa_Diet 5_14d_replicate 1


title: 80 minutes after Notch activation vs unactivated pool trial 3

description: 80' Notch activation trial 3

tag: cell line

source_name: 80' after Notch activation - trial 3


title: 80 minutes after Notch activation vs unactivated pool trial 1

description: 80' Notch activation trial 1

tag: time

source_name: 80' after Notch activation - trial 1


title: Chip-10 RD Wk9 R2blue & RD Wk6 R2red

treatment_protocol: We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week). This sample represents crown buds collected at the end of 9-week time point during the RDt treatment.

value: Leafy spurge

value: crown buds

value: exposed to ramp down in temperature under constant photoperiod for 9 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 6 weeks

value: 6 weeks


title: Ssa_Diet 5_14d_replicate 4

source_name: Ssa_Diet 5_14d_replicate 4

value: Herring milt

value: Liver


title: Ssa_Diet 5_14d_replicate 2

source_name: Ssa_Diet 5_14d_replicate 2


title: Chip-9 RD Wk6 R2blue & RD Wk3 R2red

treatment_protocol: We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week). This sample represents crown buds collected at the end of 6-week time point during the RDt treatment.

value: exposed to ramp down in temperature under constant photoperiod for 6 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 3 weeks

value: 3 weeks


title: 80 minutes after Notch activation vs unactivated pool trial 2

description: 80' Notch activation trial 2 - dye swap

source_name: 80' after Notch activation - trial 2

value: 80 minutes after a 5 minute activation with EDTA

tag: time trial

source_name: reference pool - trial 2

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. For control samples, media was replaced with fresh media to mimic the addition and removal of EDTA in corresponding experimental samples.

value: pool of unactivated cells from 0-150 minutes


title: 70 minutes after Notch activation vs unactivated pool trial 4

description: 70' Notch activation trial 4 - dye swap

source_name: 70' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 70 minutes before washing out EDTA using normal culture media.

value: 70 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: Chip-8 Ramp Down Wk3 R2blue & Para Wk0 R2red

treatment_protocol: We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week). This sample represents crown buds collected at the end of 3-week time point during the RDt treatment.

value: exposed to ramp down in temperature under constant photoperiod for 3 weeks

source_name: Paradormant crown buds

value: controls


title: HSC_day0, biological rep 3

description: Gene expression data from early HSC

source_name: HSC


title: HSC_day0, biological rep 2

description: Gene expression data from early HSC


title: 70 minutes after Notch activation vs unactivated pool trial 3

description: 70' Notch activation trial 3

source_name: reference pool - trial 3

source_name: 70' after Notch activation - trial 3

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 0 minutes before washing out EDTA using normal culture media.


title: slc6a4_bs_ip1

description: Trap'd serotonin neuron RNA, biological replicate 1

value: Dissected midbrain and brainstem (removed cerebellum, and took all tissue posterior to the pontine/hypothalamic junction, including superior colliculi to foramen magnum)

value: adult(6-12 weeks)

value: slc6a4 JD60

value: Slc6a4 JD60

value: males and females

value: Trap'd serotonin neuron RNA

value: mixed FVB and c57/bl6j background


title: Ssa_Diet 4_56d_replicate 6

source_name: Ssa_Diet 4_56d_replicate 6

tag: diet

value: Shrimp fine meat


title: HSC_day7, biological rep 1

value: primary hepatic stellate cells


title: 70 minutes after Notch activation vs unactivated pool trial 2

description: 70' Notch activation trial 2 - dye swap

source_name: 70' after Notch activation - trial 2


title: Chip-6 Ramp Down+Vernalization R1blue & Para Wk12 R1red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. A set of plants were also exposed to vernalizing cold treatment (5-7°C for 8 weeks) after 12 weeks of ramp down in temperature under constant light. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected from plants exposed to ramp down in temperature for 12 weeks under constant light, and then exposed to vernalizing cold treatment (5-7°C for 8 weeks).

tag: species

value: Leafy spurge

value: Crown buds

value: 12 weeks, then vernalized

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. A set of plants were also exposed to vernalizing cold treatment (5-7°C for 8 weeks) after 12 weeks of ramp down in temperature under constant light. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected from paradormant crown buds used as secondary controls, to complement 12 week ramp down treatment.

value: crown buds


title: Ssa_Diet 4_56d_replicate 4

source_name: Ssa_Diet 4_56d_replicate 4

value: Liver


title: Chip-7 Para Wk0 R2blue & RD+Vern R1red

treatment_protocol: We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week). This sample represents paradormant crown buds (Para-0 week) used as controls.

tag: treatment

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized


title: HSC_day0, biological rep 1

description: Gene expression data from early HSC


title: Ssa_Diet 4_56d_replicate 5

source_name: Ssa_Diet 4_56d_replicate 5


title: Ssa_Diet 4_56d_replicate 3

source_name: Ssa_Diet 4_56d_replicate 3


title: VDRmut DC - VD3+TNFa

city: Aachen

first: Mykola

last: Goncharenko

address: Pauwelstrasse 30

department: Institute for Biomedical Technology - Cell Biology

country: Germany

institute: IBMT - Cell Biology, University Hospital, RWTH Aachen

description: cRNA labelling, array hybridisation, washing and scanning performed at the Microarray Facility of the Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany.

hyb_protocol: Chip Type: MOE430A; Chip Lot: 3001946; Protocol: EukGE-WS2; Wash A1 Temperature (C): 25; Number of Wash A1 Cycles: 10; Mixes per Wash A1 Cycle: 2; Wash B Temperature (C): 50; Number of Wash B Cycles: 4; Mixes per Wash B Cycle: 15; Stain Temperature (C): 25; First Stain Time (seconds): 600; Wash A2 Temperature (C): 25; Number of Wash A2 Cycles: 10; Mixes per Wash A2 Cycle: 4; Second Stain Time (seconds): 600; Third Stain Time (seconds): 600; Wash A3 Temperature (C): 30; Number of Wash A3 Cycles: 15; Mixes per Wash A3 Cycle: 4; Holding Temperature (C): 25; Station: 1; Module: 2.

scan_protocol: Pixel Size: 3; Filter: 570; Number of Scans: 2; Scanner Type: HP.

data_processing: Scanned GeneChip *.DAT files were processed by the Affymetrix Microarray Suite 5.0.1 analysis software. Scaling: All probe sets, TGT Value: 200; Normalisation: All probe sets.

label: Phycoerythrin (PE)

source_name: VDRmut 2-step DC - VD3 pre-treated 30 min, TNFa 4h

label_protocol:
5 ug of total RNA was used to generate cRNA using a modified protocol from the Expression Analysis Technical Manual (Affymetrix).
RNA was concentrated to >0.5 ug/ul by acid-ethanol precipitation. For the first-strand cDNA synthesis a T7-oligo(dT) primer was firstly hybridised to 8 ug of total RNA by denaturation for 10 min at 70°C, then quick-chilling on ice, followed by incubation for 2 min at 42°C. The reverse transcription reaction was performed using 200U SuperScript RT (Invitrogen) per sample for 1 h at 42°C. The second-strand cDNA synthesis reaction was carried out by firstly incubating the single-stranded cDNA with 10U of DNA ligase, 40U of DNA Polimerase I and 2U of RNase H for 2 h at 16°C, and then additionally for 5 min at 16°C with T4 DNA Polymerase in order to enhance the efficiency of the second-strand synthesis. cDNA was cleaned-up using the QIAquick Spin PCR Purification Kit (Qiagen). Buffer PB was used for binding: this allows removal of fragments smaller than 100 bp, i.e. T7-oligo(dT) primers. DNA was eluted with elution buffer (EB). Double-stranded cDNA was then concentrated again by acid-ethanol precipitation.
Synthesis of biotin-labelled cRNA was conducted using T7 Mega Script Kit (Ambion). cDNA template was incubated with dNTPs in the presence of Bio-11-CTP and Bio-11-UTP (Perkin Elmer) with the T7 RNA Polymerase. Reaction incubated for 6 h at 37°C. cRNA was purified using RNeasy Mini Kit (Qiagen). cRNA was then fragmented using the fragmentation buffer.
Further processing of probes was performed according to the recommendations of the Expression Analysis Technical Manual (Affymetrix).

growth_protocol:
Dendritic cells (DC) were generated as previously described (Hieronymus, T., T. C. Gust, R. D. Kirsch, T. Jorgas, G. Blendinger, M. Goncharenko, K. Supplitt, S. Rose-John, A. M. Muller, and M. Zenke. 2005. Progressive and controlled development of mouse dendritic cells from Flt3+CD11b+ progenitors in vitro. J Immunol 174:2552-2562).
Bone marrow was prepared from hind legs of a 9-weeks old (male) VDRmut and VDRwt control mice. Briefly, homogenised cell suspension was diluted to 2x10^6 cells/ml in RPMI 1640 medium containing 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin and streptomycin sulphate, 50 uM b-mercaptoethanol. Medium was supplemented with the following cytokines/growth factors: 20 U/ml murine SCF, 5 ng/ml hyperIL-6, 25 ng/ml Flt-3L, 40ng/ml human IGF-1 long range, 10^-6 uM dexamethasone and 25 U/ml murine GM-CSF. Cells were then cultured at 37°C in 5% CO2.
After 3 days in culture cells were applied to density gradient centrifugation using Ficoll-Hypaque (1,077g/ml) to remove dead cells and debris and to recover factor-dependent progenitor cells. Cells were washed once in complete RPMI medium and adjusted to 2x10^6 cells/ml; above listed growth factors were added again. Medium was renewed every second day and cells were adjusted to 2x10^6 cells/ml, supplementing with growth factors over again. (Cells were maintained in these conditions for 7 days.)
At day 7 of culture differentiation of DC from the proliferating progenitor cells was initiated. Cells were washed once in RPMI medium and adjusted to 2x10^6 cells/ml. Cells were seeded in new dishes and murine GM-CSF was added at final concentration of 250U/ml. Medium was renewed every second day, supplementing with 250 U/ml GM-CSF. Since cells typically carry on proliferating in the first 3-4 days of differentiation, they were adjusted to the concentration of 2x10^6 cells/ml until onset of proliferation during every medium change. After 7 days of differentiation from progenitor cells a homogenous population of DC (in suspension; beside strongly adherent macrophages) developed. Non-adherent DC were used for the experimental treatment.

extract_protocol: Total RNA was isolated with RNeasy Midi Kit including DNase digestion (Qiagen).

treatment_protocol: Dendritic cells (DC) from VDRmut and control VDRwt mice were generated as described in the Growth Protocol section. On day 7 differentiation DC were pre-treated for 30 min with 1a,25-dihydroxyvitamin D3 (VD3) at 10^-6M, or left untreated. TNFa (50 ng/ml) was added where appropriate, and cells incubated further for 4 h.

tag: Mouse strain

value: vitamin D3 receptor mutant (mut) and  wild-type (wt) (see Erben, R. G., Soegiarto, D. W., Weber, K., Zeitz, U., Lieberherr, M., Gniadecki, R., Moller, G., Adamski, J. and Balling, R., Deletion of deoxyribonucleic acid binding domain of the vitamin D receptor abrogates genomic and nongenomic functions of vitamin D. Mol Endocrinol 2002. 16:1524-1537.

tag: Gender

value: male (mut and wt); Age:9 weeks (mut and wt); Source tissue:bone marrow; Cell type:in vitro generated dendritic cells.


title: 70 minutes after Notch activation vs unactivated pool trial 1

description: 70' Notch activation trial 1

source_name: reference pool - trial 1

value: pool of unactivated cells from 0-150 minutes

source_name: 70' after Notch activation - trial 1

value: 70 minutes after a 5 minute activation with EDTA


title: Ssa_Diet 4_56d_replicate 2

source_name: Ssa_Diet 4_56d_replicate 2


title: Chip-2 Ramp Down Wk6 R1blue & Ramp Down Wk3 R1red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 6 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 6-week time point during the RDt treatment.

value: 6 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 3 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 3-week time point during the RDt treatment.

value: 3 weeks


title: Chip-3 Ramp Down Wk9 R1blue & Ramp Down Wk6 R1red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 9 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 9-week time point during the RDt treatment.

value: 9 weeks

value: exposed to ramp down in temperature under constant photoperiod for 6 weeks


title: 60 minutes after Notch activation vs unactivated pool trial 1

description: 60' Notch activation trial 1

source_name: 60' after Notch activation - trial 1

value: 60 minutes after a 5 minute activation with EDTA


title: Ssa_Diet 4_56d_replicate 1

source_name: Ssa_Diet 4_56d_replicate 1

value: Shrimp fine meat


title: Ssa_Diet 4_14d_replicate 6

source_name: Ssa_Diet 4_14d_replicate 6


title: 60 minutes after Notch activation vs unactivated pool trial 3

description: 60' Notch activation trial 3

source_name: reference pool - trial 3

source_name: 60' after Notch activation - trial 3


title: VDRmut DC - untreated

source_name: VDRmut 2-step DC - untreated


title: VDRwt DC - VD3+TNFa

source_name: VDRwt 2-step DC - VD3 pre-treated 30 min, TNFa 4h


title: VDRmut DC - TNFa

source_name: VDRmut 2-step DC - TNFa 4h


title: 50 minutes after Notch activation vs unactivated pool trial 4

description: 50' Notch activation trial 4 - dye swap

source_name: 50' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 50 minutes before washing out EDTA using normal culture media.

value: 50 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: 60 minutes after Notch activation vs unactivated pool trial 4

description: 60' Notch activation trial 4 - dye swap

source_name: 60' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 60 minutes before washing out EDTA using normal culture media.


title: VDRwt DC - TNFa

source_name: VDRwt 2-step DC - TNFa 4h


title: 60 minutes after Notch activation vs unactivated pool trial 2

description: 60' Notch activation trial 2 - dye swap

source_name: 60' after Notch activation - trial 2

source_name: reference pool - trial 2


title: Ssa_Diet 4_14d_replicate 3

source_name: Ssa_Diet 4_14d_replicate 3


title: Ssa_Diet 4_14d_replicate 5

source_name: Ssa_Diet 4_14d_replicate 5


title: Ssa_Diet 4_14d_replicate 4

source_name: Ssa_Diet 4_14d_replicate 4


title: VDRwt DC - VD3

source_name: VDRwt 2-step DC - VD3 pre-treated 30 min


title: Btau_QuilA+ASP_2878

city: Beltsville

first: Robert

middle: W

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: 7- to 10-month-old helminth‐free Holstein crossbred calves immunized with 30 μg of the native ASP fraction antigen PLUS 750 ug of QuilA adjuvant three times intramuscularly in the neck with a three‐week interval.

hyb_protocol: Hybridization was performed by NimbleGen following their standard operating protocol.

scan_protocol: Scanning was performed by NimbleGen following their standard operating protocol.

data_processing: The raw data were subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Bos taurus

source_name: fundic abomasa of calves immunized with ASP antigen + QuilA adjuvant

label_protocol: Labeling was performed by NimbleGen following their standard operating protocol (www.nimblegen.com).

growth_protocol: 7- to 10-month-old Helminth‐free Holstein crossbred calves were raised in accordance with the E.U. Animal Welfare Directives and VICH Guidelines for Good Clinical Practice. Ethical approval to conduct the studies was obtained from the Ethical Committee of the Faculty of Veterinary Medicine, Ghent University.

extract_protocol: Total RNA was extracted from tissue samples using Trizol (Invitrogen) and further purified using the RNeasy Mini kit (Qiagen). To remove contaminating genomic DNA (gDNA), on-column DNase digestion was performed using the RNase-free DNase set (Qiagen) according to the manufacturer's instructions. RNA quality was verified using an ExperionTMAutomated Electophoresis System (Bio-Rad), and concentrations were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

tag: breed

value: Holstein crossbred

tag: developmental stage

value: calf

value: fundic abomasa

value: vaccine

tag: challenge

value: Ostertagia ostertagi infection


title: Ssa_Diet 4_14d_replicate 2

source_name: Ssa_Diet 4_14d_replicate 2

value: Liver


title: Chip-1 Ramp Down Wk3 R1blue & Paradormant Wk0-R1red

source_name: Paradormant crown buds exposed to ramp down temperature under constant photoperiod for 3 weeks

value: Leafy spurge

value: crown buds

source_name: Paradormant crown buds used as controls

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents paradormant crown buds (Para-0 week) used as controls.

value: controls


title: Btau_QuilA+ASP_2148


title: VDRwt DC - untreated

source_name: VDRwt 2-step DC - untreated

value: vitamin D3 receptor mutant (mut) and  wild-type (wt) (see Erben, R. G., Soegiarto, D. W., Weber, K., Zeitz, U., Lieberherr, M., Gniadecki, R., Moller, G., Adamski, J. and Balling, R., Deletion of deoxyribonucleic acid binding domain of the vitamin D receptor abrogates genomic and nongenomic functions of vitamin D. Mol Endocrinol 2002. 16:1524-1537.

value: male (mut and wt); Age:9 weeks (mut and wt); Source tissue:bone marrow; Cell type:in vitro generated dendritic cells.


title: Btau_QuilA+ASP_2902


title: Ssa_Diet 3_56d_replicate 4

source_name: Ssa_Diet 3_56d_replicate 4

value: Herring tails


title: 50 minutes after Notch activation vs unactivated pool trial 1

description: 50' Notch activation trial 1

source_name: reference pool - trial 1

value: pool of unactivated cells from 0-150 minutes

source_name: 50' after Notch activation - trial 1


title: Ssa_Diet 3_56d_replicate 2

source_name: Ssa_Diet 3_56d_replicate 2


title: 2-step DC - AdIkBa-SR+TNFa

hyb_protocol: Protocol: EukGE-WS2; Wash A1 Temperature (C): 25; Number of Wash A1 Cycles: 10; Mixes per Wash A1 Cycle: 2; Wash B Temperature (C): 50; Number of Wash B Cycles: 4; Mixes per Wash B Cycle: 15; Stain Temperature (C): 25; First Stain Time (seconds): 600; Wash A2 Temperature (C): 25; Number of Wash A2 Cycles: 10; Mixes per Wash A2 Cycle: 4; Second Stain Time (seconds): 600; Third Stain Time (seconds): 600; Wash A3 Temperature (C): 30; Number of Wash A3 Cycles: 15; Mixes per Wash A3 Cycle: 4; Holding Temperature (C): 25; Station: 1; Module: 2; Hybridize Date: Sep 09, 2003.

scan_protocol: Pixel Size: 3; Filter: 570; Scan Date:	Sep 09, 2003; Number of Scans: 2; Scanner Type: HP.

data_processing: Scanned GeneChip *.DAT files were processed by the Affymetrix Microarray Suite 5.0.1 analysis software. Chip Files (*.CHP) contain raw data with no scaling and no normalisation.

source_name: CAR 2-step DC, AdIkBa-SR transduced, TNFa 4h

label_protocol:
8 ug of total RNA was used to generate cRNA using a modified protocol from the Expression Analysis Technical Manual (Affymetrix).
RNA was concentrated to >0.5 ug/ul by acid-ethanol precipitation. For the first-strand cDNA synthesis a T7-oligo(dT) primer was firstly hybridised to 8 ug of total RNA by denaturation for 10 min at 70°C, then quick-chilling on ice, followed by incubation for 2 min at 42°C. The reverse transcription reaction was performed using 200U SuperScript RT (Invitrogen) per sample for 1 h at 42°C. The second-strand cDNA synthesis reaction was carried out by firstly incubating the single-stranded cDNA with 10U of DNA ligase, 40U of DNA Polimerase I and 2U of RNase H for 2 h at 16°C, and then additionally for 5 min at 16°C with T4 DNA Polymerase in order to enhance the efficiency of the second-strand synthesis. cDNA was cleaned-up using the QIAquick Spin PCR Purification Kit (Qiagen). Buffer PB was used for binding: this allows removal of fragments smaller than 100 bp, i.e. T7-oligo(dT) primers. DNA was eluted with elution buffer (EB). Double-stranded cDNA was then concentrated again by acid-ethanol precipitation.
Synthesis of biotin-labelled cRNA was conducted using T7 Mega Script Kit (Ambion). cDNA template was incubated with dNTPs in the presence of Bio-11-CTP and Bio-11-UTP (Perkin Elmer) with the T7 RNA Polymerase. Reaction incubated for 6 h at 37°C. cRNA was purified using RNeasy Mini Kit (Qiagen). cRNA was then fragmented using the fragmentation buffer.
Further processing of probes was performed according to the recommendations of the Expression Analysis Technical Manual (Affymetrix).

growth_protocol:
Dendritic cells (DC) were generated as previously described (Hieronymus, T., T. C. Gust, R. D. Kirsch, T. Jorgas, G. Blendinger, M. Goncharenko, K. Supplitt, S. Rose-John, A. M. Muller, and M. Zenke. 2005. Progressive and controlled development of mouse dendritic cells from Flt3+CD11b+ progenitors in vitro. J Immunol 174:2552-2562).
Bone marrow was prepared from hind legs of a 13-weeks old (female) CAR-transgenic mouse. Briefly, homogenised cell suspension was diluted to 2x10^6 cells/ml in RPMI 1640 medium containing 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin and streptomycin sulphate, 50 uM b-mercaptoethanol. Medium was supplemented with the following cytokines/growth factors: 20 U/ml murine SCF, 5 ng/ml hyperIL-6, 25 ng/ml Flt-3L, 40ng/ml human IGF-1 long range, 1x10^-6 uM dexamethasone and 25 U/ml murine GM-CSF. Cells were then cultured at 37°C in 5% CO2.
After 3 days in culture cells were applied to density gradient centrifugation using Ficoll-Hypaque (1,077g/ml) to remove dead cells and debris and to recover factor-dependent progenitor cells. Cells were washed once in complete RPMI medium and adjusted to 2x10^6 cells/ml; above listed growth factors were added again. Medium was renewed every second day and cells were adjusted to 2x10^6 cells/ml, supplementing with growth factors over again. (Cells were maintained in these conditions for 7 days.)
At day 7 of culture differentiation of DC from the proliferating progenitor cells was initiated. Cells were washed once in RPMI medium and adjusted to 2x10^6 cells/ml. Cells were seeded in new dishes and murine GM-CSF was added at final concentration of 250U/ml. Medium was renewed every second day, supplementing with 250 U/ml GM-CSF. Since cells typically carry on proliferating in the first 3-4 days of differentiation, they were adjusted to the concentration of 2x10^6 cells/ml until onset of proliferation during every medium change. After 7 days of differentiation from progenitor cells a homogenous population of DC (in suspension; beside strongly adherent macrophages) developed. Non-adherent DC were used for the experimental treatment.

extract_protocol: Total RNA was isolated with RNeasy Midi Kit including DNase digestion (Qiagen)

treatment_protocol: Dendritic cells (DC) were generated as described in the Growth Protocol section. On day 7 differentiation DC were transduced with either AdIkBa-SR or AdOVA adenovirus at 1,500 particles/cell, or left untreated. Transductions were performed at 5x10^6 cells/ml for 2 h on a slow-rocking platform at 37°C in CO2 incubator; then diluted to 2x10^6 cells/ml and incubated for additional 18 h. TNFa (50 ng/ml) was added where appropriate, and cells incubated further for 4 h.

value: CAR; Gender:female; Age:13 weeks; Source tissue:bone marrow; Cell type:in vitro generated dendritic cells


title: Btau_QuilA+ASP_3549


title: 50 minutes after Notch activation vs unactivated pool trial 2

description: 50' Notch activation trial 2 - dye swap

source_name: 50' after Notch activation - trial 2


title: 40 minutes after Notch activation vs unactivated pool trial 4

description: 40' Notch activation trial 4 - dye swap

source_name: 40' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 40 minutes before washing out EDTA using normal culture media.

value: 40 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: 40 minutes after Notch activation vs unactivated pool trial 2

description: 40' Notch activation trial 2 - dye swap

source_name: 40' after Notch activation - trial 2

source_name: reference pool - trial 2


title: Ssa_Diet 3_56d_replicate 5

source_name: Ssa_Diet 3_56d_replicate 5


title: 40 minutes after Notch activation vs unactivated pool trial 3

description: 40' Notch activation trial 3

source_name: reference pool - trial 3

source_name: 40' after Notch activation - trial 3


title: Btau_QuilA_2149

description: 7- to 10-month-old helminth‐free Holstein crossbred calves immunized with 750 ug of QuilA adjuvant three times intramuscularly in the neck with a three‐week interval.

source_name: fundic abomasa of calves immunized with QuilA adjuvant

value: adjuvant control


title: Ssa_Diet 3_56d_replicate 6

source_name: Ssa_Diet 3_56d_replicate 6


title: 40 minutes after Notch activation vs unactivated pool trial 1

description: 40' Notch activation trial 1

source_name: 40' after Notch activation - trial 1


title: Btau_QuilA+ASP_0261

source_name: fundic abomasa of calves immunized with ASP antigen + QuilA adjuvant


title: Ssa_Diet 4_14d_replicate 1

source_name: Ssa_Diet 4_14d_replicate 1

value: Shrimp fine meat


title: 2-step DC - untreated

description: cRNA labelling, array hybridisation, washing and scanning performed at the Microarray Facility of the Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany

source_name: CAR 2-step DC, untreated


title: 2-step DC - AdIkBa-SR

source_name: CAR 2-step DC, AdIkBa-SR transduced


title: 2-step DC - TNFa

source_name: CAR 2-step DC, TNFa 4h


title: 2-step DC - AdOVA

source_name: CAR 2-step DC, AdOVA transduced


title: Btau_QuilA_2593

value: Holstein crossbred


title: Btau_QuilA_2594

value: calf


title: 2-step DC - AdOVA+TNFa

source_name: CAR 2-step DC, AdOVA transduced, TNFa 4h


title: Btau_QuilA+ASP_3556

value: fundic abomasa


title: 3aKOvsWT rep3

city: Los Angeles

first: Kevin

last: Huang

state: CA

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

description: Biological replicate 3 of 3.

hyb_protocol: Slides were hybridized at 65° for 17 hours at 4 RPMs and then washed once in Agilent Gene Expression wash buffer 1 and once in Agilent Gene Expression wash buffer 2 before a quick wash in acetonitrile.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Arrays were performed in triplicate. Probe intensities were quantile-normalized and log2-transformed across all samples.

source_name: dnmt3aKO NSCs

label_protocol: We converted the RNA into cDNA and then the cDNA into cRNA using the Agilent Low RNA Input Linear Amplification Kit (Agilent).

growth_protocol: mESCs were cultured on 0.2% gelatin-coated plate in normal mESCs medium for one passage to get rid of MEF feeder cells. When the plate was confluent, mESCs colonies were completely trypsinizated to single cells followed by washing with DMEM: F12 medium three times to wash off all serum, and then passaged to a new 0.1% gelatin-coated plate. These cells were maintained for 7 days in serum-free N2B27 medium supplemented with EGF (10 ng/ml) and bFGF (10 ng/ml). Neurosphere formation was carried out when the plate was confluent and colonies began showing partial differentiation morphology. Neurospheres were maintained in an ultra-low attachment plate with suspension culture in N2B27 medium supplemented with bFGF and EGF for a week. At the fourth day after neurospheres formation, cells were transferred to poly-L-ornithine (PO) / fibronectin (FN) coated plate and grown in N2B27 medium supplemented with bFGF and EGF. Neurospheres attached to the plate after 3-5 days and bipolar cells could be found around the attached neurospheres. These bipolar cells were termed mNSCs P0 and could be passaged with 0.025% Trypsin/EDTA followed by adding trypsin inhibitor.

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

tag: genotype

value: neural stem cells (NSCs)

source_name: WT NSCs

value: wildtype


title: Ssa_Diet 3_56d_replicate 3

source_name: Ssa_Diet 3_56d_replicate 3

value: Liver


title: Ssa_Diet 3_56d_replicate 1

source_name: Ssa_Diet 3_56d_replicate 1


title: Chip-4 Ramp Down Wk12 R1blue & Ramp Down Wk9 R1red

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected at the end of 12-week time point during the RDt treatment.

value: Leafy spurge

value: 12 weeks

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 9 weeks

value: 9 weeks


title: 50 minutes after Notch activation vs unactivated pool trial 3

description: 50' Notch activation trial 3

source_name: reference pool - trial 3

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. For control samples, media was replaced with fresh media to mimic the addition and removal of EDTA in corresponding experimental samples.

source_name: 50' after Notch activation - trial 3

value: 50 minutes after a 5 minute activation with EDTA


title: Btau_QuilA_2879

source_name: fundic abomasa of calves immunized with QuilA adjuvant

value: Ostertagia ostertagi infection


title: Ssa_Diet 3_14d_replicate 6

source_name: Ssa_Diet 3_14d_replicate 6

value: Herring tails


title: Btau_QuilA_4487


title: 3aKOvsWT rep2

description: Biological replicate 2 of 3.


title: Chip-5 Para Wk12 R1blue & Ramp Down Wk12 R1red

source_name: Paradormant crown buds used as secondary controls, to complement 12 week ramp down treatment

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected from paradormant crown buds used as secondary controls, to complement 12 week ramp down treatment.

value: crown buds

value: exposed to ramp down in temperature under constant photoperiod for 12 weeks


title: Ssa_Diet 3_14d_replicate 4

source_name: Ssa_Diet 3_14d_replicate 4


title: 35 minutes after Notch activation vs unactivated pool trial 3

description: 35' Notch activation trial 3

value: pool of unactivated cells from 0-150 minutes

source_name: 35' after Notch activation - trial 3

value: 35 minutes after a 5 minute activation with EDTA


title: Btau_QuilA_2869

value: adjuvant control


title: 35 minutes after Notch activation vs unactivated pool trial 2

description: 35' Notch activation trial 2 - dye swap

source_name: 35' after Notch activation - trial 2

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 35 minutes before washing out EDTA using normal culture media.

source_name: reference pool - trial 2


title: 30 minutes after Notch activation vs unactivated pool trial 4

description: 30' Notch activation trial 4 - dye swap

source_name: 30' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 30 minutes before washing out EDTA using normal culture media.

value: 30 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: 3aKOvsWT rep1

description: Biological replicate 1 of 3.

source_name: dnmt3aKO NSCs


title: Ssa_Diet 3_14d_replicate 3

source_name: Ssa_Diet 3_14d_replicate 3


title: 35 minutes after Notch activation vs unactivated pool trial 4

description: 35' Notch activation trial 4 - dye swap

source_name: 35' after Notch activation - trial 4


title: Lesioned_day30_1

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505A with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014879_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: hippocampus, lesioned, day30, 1

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

extract_protocol: Total RNA was extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and cleaned using the RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed by ultraviolet spectrophotometry and an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2, and a 28S:18S ratio of >1.6; the RNA integrity number (RIN) was > 8.1.

value: hippocampus

tag: strain

value: Wistar

value: male

value: 1 ul/min of FeCl3 (FeCl3 was dissolved in saline solution (100 mM, pH 2.2)) and mice were sacrificed at 30 days

tag: experimental group

value: chronic phase of injury


title: 35 minutes after Notch activation vs unactivated pool trial 1

description: 35' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 35' after Notch activation - trial 1

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 0 minutes before washing out EDTA using normal culture media.


title: 30 minutes after Notch activation vs unactivated pool trial 2

description: 30' Notch activation trial 2 - dye swap

source_name: 30' after Notch activation - trial 2


title: Ssa_Diet 3_14d_replicate 5

source_name: Ssa_Diet 3_14d_replicate 5

value: Liver


title: Lesioned_day30_3

source_name: hippocampus, lesioned, day30, 3

tag: gender


title: MTT1

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

organism: Homo sapiens

source_name: PC14(Hs), NIH 3T3(Mm), NIH 3T3(Mm)

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: protocol

value: NIH 3T3(first co-culture) and NIH 3T3(second co-culture)


title: MTT3


title: Lesioned_day30_4

source_name: hippocampus, lesioned, day30, 4

tag: tissue


title: Lesioned_day30_2

source_name: hippocampus, lesioned, day30, 2


title: 30 minutes after Notch activation vs unactivated pool trial 3

description: 30' Notch activation trial 3

source_name: reference pool - trial 3

tag: cell line

source_name: 30' after Notch activation - trial 3


title: MTT2


title: MAT3

source_name: PC14(Hs), astrocytes(Mm), NIH 3T3(Mm)

value: astrocytes(first co-culture) and NIH 3T3(second co-culture)


title: Ssa_Diet 3_14d_replicate 1

source_name: Ssa_Diet 3_14d_replicate 1

tag: time


title: Ssa_Diet 2 _56d_replicate 6

source_name: Ssa_Diet 2 _56d_replicate 6

value: Crab hepatopancreas


title: 30 minutes after Notch activation vs unactivated pool trial 1

description: 30' Notch activation trial 1

tag: time trial

source_name: 30' after Notch activation - trial 1


title: 25 minutes after Notch activation vs unactivated pool trial 2

description: 25' Notch activation trial 2 - dye swap

source_name: 25' after Notch activation - trial 2

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 25 minutes before washing out EDTA using normal culture media.

value: 25 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 2


title: MTA3

source_name: PC14(Hs), NIH 3T3(Mm), astrocytes(Mm)

value: NIH 3T3(first co-culture) and astrocytes(second co-culture)


title: Ssa_Diet 3_14d_replicate 2

source_name: Ssa_Diet 3_14d_replicate 2

tag: diet

value: Herring tails


title: 25 minutes after Notch activation vs unactivated pool trial 3

description: 25' Notch activation trial 3

source_name: 25' after Notch activation - trial 3


title: 25 minutes after Notch activation vs unactivated pool trial 4

description: 25' Notch activation trial 4 - dye swap

source_name: 25' after Notch activation - trial 4

source_name: reference pool - trial 4


title: Lesioned_day15_3

source_name: hippocampus, lesioned, day15, 3

value: 1 ul/min of FeCl3 (FeCl3 was dissolved in saline solution (100 mM, pH 2.2)) and mice were sacrificed at 15 days

value: sub-chronic phase of injury


title: MAT1


title: Lesioned_day15_2

source_name: hippocampus, lesioned, day15, 2


title: Ssa_Diet 2 _56d_replicate 5

source_name: Ssa_Diet 2 _56d_replicate 5


title: Ssa_Diet 2 _56d_replicate 4

source_name: Ssa_Diet 2 _56d_replicate 4


title: Lesioned_day15_4

source_name: hippocampus, lesioned, day15, 4


title: MAT2


title: Lesioned_day15_1

source_name: hippocampus, lesioned, day15, 1


title: VDRmut DC - VD3

source_name: VDRmut 2-step DC - VD3 pre-treated 30 min

value: vitamin D3 receptor mutant (mut) and  wild-type (wt) (see Erben, R. G., Soegiarto, D. W., Weber, K., Zeitz, U., Lieberherr, M., Gniadecki, R., Moller, G., Adamski, J. and Balling, R., Deletion of deoxyribonucleic acid binding domain of the vitamin D receptor abrogates genomic and nongenomic functions of vitamin D. Mol Endocrinol 2002. 16:1524-1537.

value: male (mut and wt); Age:9 weeks (mut and wt); Source tissue:bone marrow; Cell type:in vitro generated dendritic cells.


title: Ssa_Diet 2 _56d_replicate 1

source_name: Ssa_Diet 2 _56d_replicate 1


title: Lesioned_day5_4

source_name: hippocampus, lesioned, day5, 4

value: 1 ul/min of FeCl3 (FeCl3 was dissolved in saline solution (100 mM, pH 2.2)) and mice were sacrificed at 5 days

value: acute phase


title: 20 minutes after Notch activation vs unactivated pool trial 4

description: 20' Notch activation trial 4 - dye swap

source_name: 20' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 20 minutes before washing out EDTA using normal culture media.

value: 20 minutes after a 5 minute activation with EDTA

value: pool of unactivated cells from 0-150 minutes


title: MTA1


title: MTA2


title: 25 minutes after Notch activation vs unactivated pool trial 1

description: 25' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 25' after Notch activation - trial 1


title: Ssa_Diet 2 _56d_replicate 2

source_name: Ssa_Diet 2 _56d_replicate 2


title: Lesioned_day5_3

source_name: hippocampus, lesioned, day5, 3

value: hippocampus

value: Wistar

value: male


title: MAA3

value: astrocytes(first co-culture) and astrocytes(second co-culture)


title: Lesioned_day5_2

source_name: hippocampus, lesioned, day5, 2


title: Ssa_Diet 2 _56d_replicate 3

source_name: Ssa_Diet 2 _56d_replicate 3

value: Liver


title: MAA2


title: 20 minutes after Notch activation vs unactivated pool trial 3

description: 20' Notch activation trial 3

source_name: reference pool - trial 3

source_name: 20' after Notch activation - trial 3


title: Lesioned_day5_1

source_name: hippocampus, lesioned, day5, 1


title: Ssa_Diet 2_14d_replicate 3

source_name: Ssa_Diet 2_14d_replicate 3

value: Crab hepatopancreas


title: Ssa_Diet 2_14d_replicate 6

source_name: Ssa_Diet 2_14d_replicate 6


title: Control_4

source_name: hippocampus, control, 4

value: 1.0 ul saline

value: control


title: 20 minutes after Notch activation vs unactivated pool trial 2

description: 20' Notch activation trial 2 - dye swap

source_name: 20' after Notch activation - trial 2

source_name: reference pool - trial 2


title: Ssa_Diet 2_14d_replicate 4

source_name: Ssa_Diet 2_14d_replicate 4


title: MAA1


title: Control_3

source_name: hippocampus, control, 3


title: PC14_Fibro-2_Hs

source_name: PC14, NIH 3T3

value: co-culture of MDA-MB-231 and astrocyte cells


title: 15 minutes after Notch activation vs unactivated pool trial 4

description: 15' Notch activation trial 4 - dye swap

source_name: 15' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 15 minutes before washing out EDTA using normal culture media.

value: 15 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: 20 minutes after Notch activation vs unactivated pool trial 1

description: 20' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 20' after Notch activation - trial 1


title: PC14_Fibro-4_Hs


title: 15 minutes after Notch activation vs unactivated pool trial 2

description: 15' Notch activation trial 2 - dye swap

source_name: 15' after Notch activation - trial 2


title: Ssa_Diet 2_14d_replicate 1

source_name: Ssa_Diet 2_14d_replicate 1


title: Ssa_Diet 2_14d_replicate 5

source_name: Ssa_Diet 2_14d_replicate 5


title: 15 minutes after Notch activation vs unactivated pool trial 1

description: 15' Notch activation trial 1

source_name: 15' after Notch activation - trial 1


title: 15 minutes after Notch activation vs unactivated pool trial 3

description: 15' Notch activation trial 3

source_name: reference pool - trial 3

source_name: 15' after Notch activation - trial 3


title: PC14_Fibro-3_Hs


title: Control_2

source_name: hippocampus, control, 2


title: PC14_Astro-4_Hs

source_name: PC14, astrocytes


title: Ssa_Diet 1 (ctrl)_56d_replicate 6

source_name: Ssa_Diet 1 (ctrl)_56d_replicate 6


title: PC14_Fibro-1_Hs


title: Control_1

source_name: hippocampus, control, 1


title: Ssa_Diet 1 (ctrl)_56d_replicate 5

source_name: Ssa_Diet 1 (ctrl)_56d_replicate 5


title: Ssa_Diet 2_14d_replicate 2

source_name: Ssa_Diet 2_14d_replicate 2


title: YP00-13507

type: genomic

city: Gotenburg

first: Marta

last: Persson

address: Box 425

country: Sweden

institute: Sahlgrenska Cancer Center

hyb_protocol: Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent Human Genome CGH Microarray 44K and 244K 60-mer oligonucleotide arrays) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.

scan_protocol: The arrays were scanned on an Agilent  Microarray Confocal Scanner (G2567AA) and the images were quantified with Agilent Feature Extraction Software (v.7.5) using the intensity-dependent linear normalization method.

data_processing: Data analysis was carried out using Nexus Copy Number software v.4.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the Rank segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to p=1.0E-7 and the thresholds of log2 ratio values for gain and loss were 0.4 and −0.3, respectively; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.

molecule: genomic DNA

source_name: Mucoepidermoid carcinoma

label_protocol: 3.0 µg of genomic tumor DNA and sex-matched reference DNA (pooled peripheral blood cells from 5 normal female and male genomes) were digested with AluI and Rsa1 (Promega, Madisaon, WI) and labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA).

extract_protocol: Genomic DNA was isolated from FFPE tissue using the standard phenol-chloroform method and from fresh frozen tissue using the QIAamp DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.

treatment_protocol: Fresh frozen tumor material from 15 MECs and paraffin embedded tumor material from 13 MECs were retrieved from the department of Pathology at Haartman Institute in Helsinki, the department of pathology at Sahlgrenska University Hospital in Gothenburg and the department of Oral Pathology at Guy's Hospital in London. The tumors were classified as low grade and high grade according to the histologic classification of salivary gland tumours by WHO.

tag: fusion status

value: Neg

tag: grade

value: High Grade

source_name: Normal tissue

tag: sample type

value: reference

value: F


title: PC14_Astro-3_Hs


title: 10 minutes after Notch activation vs unactivated pool trial 4

description: 10' Notch activation trial 4 - dye swap

source_name: 10' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 10 minutes before washing out EDTA using normal culture media.

value: 10 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: YP04-5790

value: M


title: PC14_Astro-2_Hs


title: Ssa_Diet 1 (ctrl)_56d_replicate 4

source_name: Ssa_Diet 1 (ctrl)_56d_replicate 4


title: C846


title: YP00-2565


title: 10 minutes after Notch activation vs unactivated pool trial 3

description: 10' Notch activation trial 3

value: pool of unactivated cells from 0-150 minutes

source_name: 10' after Notch activation - trial 3


title: C1131

value: Pos

value: Low Grade


title: PC14_Astro-1_Hs


title: 10 minutes after Notch activation vs unactivated pool trial 1

description: 10' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 10' after Notch activation - trial 1


title: MDA231_Fibro-4_Hs

source_name: MDA-MB-231, NIH 3T3


title: 10 minutes after Notch activation vs unactivated pool trial 2

description: 10' Notch activation trial 2 - dye swap

source_name: 10' after Notch activation - trial 2

source_name: reference pool - trial 2


title: 5 minutes after Notch activation vs unactivated pool trial 4

description: 5' Notch activation trial 4 - dye swap

source_name: 5' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 5 minutes before washing out EDTA using normal culture media.

value: 5 minutes after a 5 minute activation with EDTA


title: Ssa_Diet 1 (ctrl)_56d_replicate 1

source_name: Ssa_Diet 1 (ctrl)_56d_replicate 1


title: MDA231_Fibro-3_Hs


title: C1088


title: 5 minutes after Notch activation vs unactivated pool trial 2

description: 5' Notch activation trial 2 - dye swap

source_name: 5' after Notch activation - trial 2