title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 1 hr Rep 1

description:
Root 101 kPa 1 hr Rep1
12484_Ferl_101-A-R-2_(ATH1-121501).mas5-Signal

value: Roots

value: 10 days old plants, light grown


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 12 hrs Rep 1

status: Public on May 11 2017

type: RNA

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

country: USA

institute: University of Florida

description:
Root 101 kPa 12 hrs Rep1
12434_Ferl_101-D-R-1_(ATH1-121501).mas5-Signal

hyb_protocol: The cRNA was purified using magnetic beads and was fragmented. Following fragmentation, cRNA products (12.5 µg) were hybridized with rotation to the Affymetrix GeneChip® Arabidopsis ATH1 Genome Arrays for 16 h at 45°C.  Arrays were washed on a Fluidics Station 450 (Affymetrix) using the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: Primary data analysis was carried out using the MAS5 algorithm within the Affymetrix Expression Console software.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 12 hours

label_protocol: 100 ng of total RNA from each sample was reverse transcribed into double-stranded cDNA, from which biotin-labeled cRNA was generated using the 3′ IVT plus Kit (Affymetrix).

growth_protocol: Arabidopsis thaliana (ecotype Wassilewskija) seeds were surfaced sterilized with a five minute rinse of 70% Ethanol, a 50% bleach and Tween 20 © soak for ten minutes, followed by multiple rinses of sterile water. Seeds were then planted on vertically orientated Petri plates (10cm2) containing 0.5x MS media, 0.45% Phytagel and 2.5ppm benomyl. Plates were sealed with Micropore (3M) tape to allow air exchange. Prior to atmospheric treatments, plants were grown in an ambient pressure growth chamber at CESRF. Growth chamber conditions were: 24 hours light, 22 to 25° Celsius, 97 kPa (Guelph, ON ambient) and with ambient atmosphere.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: Experiment Unique Equipment and Environmental Conditions:   Chambers and facilities for low pressure treatments: The Low Pressure Growth Chambers (LPGC) are components of the Controlled Environment Systems Research Facility (CESRF at University of Guelph, Ontario, Canada). Temperature, air pressure, gas composition and humidity were controlled and monitored in the LPGC by the second, and data from the LPGC were collected for reporting every 5 minutes. Control pressure was set at 97kPa, which is the ambient pressure at an altitude of 1100 feet (Guelph, Ontario). The LPGC provided a constant light condition with strictly monitored, controlled temperature at 22°C to 24°C; the humidity was maintained inside the Petri plates at 95% or above.  Variations on the pressure and oxygen supplement:   At 10 days old plants were transferred to the LPGCs and were exposed to an atmosphere of 10 kPa or 97 kPa.  The 97 kPa atmosphere was composed of a partial pressure of 21 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen. The 10 kPa samples were composed of a partial pressure of 2.1 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen.  The samples were harvested at: 1 hour, 3 hours, 6 hours, 12 hours, 48 hours and 72 hours.  Each treatment of atmospheric pressures and times were replicated with three separate, concurrently run LPGC.  Each chamber in the LPGCs contained 10 plates of approximately 12 plants each.    Plant harvest: At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots.

tag: ecotype

value: Wassilewskija (WS)

tag: tissue

tag: age

tag: exposed to

value: 97 kPa pressure chamber for 12 hrs

tag: biosource type

value: RNAlater fixed_sample


title: Shoot grown at 5 kPa pressure Replica 1

data_processing: Primary data analysis was carried out using the RMA algorithm within the Affymetrix Expression Console software.

source_name: 10 day old plant transferred to 5 kPa pressure chamber for 24 hrs

growth_protocol: Plant Materials: Arabidopsis thaliana ecotype Wassilewskija (WS) was grown as previously described (Paul et al., 2001). In brief, seeds were surfaced sterilized and then planted on vertically orientated plates containing 0.5x MS media, 0.45% Phytagel and 2.5 ppm benomyl. Plants were grown for 10 days in an ambient pressure growth chamber at CESRF with 24-hour light, 22 to 25° Celsius, 97 kPa prior to low pressure treatments.

treatment_protocol: Experiment Unique Equipment and Environmental Conditions:   Chambers and facilities for low pressure treatments: The Low Pressure Growth Chambers (LPGC) are components of the Controlled Environment Systems Research Facility (CESRF at University of Guelph, Ontario, Canada). Temperature, air pressure, gas composition and humidity were controlled and monitored in the LPGC by the second, and data from the LPGC were collected for reporting every 5 minutes. Control pressure was set at 97kPa, which is the ambient pressure at an altitude of 1100 feet (Guelph, Ontario). The LPGC provided a constant light condition with strictly monitored, controlled temperature at 22°C to 24°C; the humidity was maintained inside the Petri plates at 95% or above.  Variations on the pressure and oxygen supplement:  For atmospheric treatments, The 10 day old plants were transferred to The Low Pressure Growth Chambers (LPGC) (the Controlled Environment Systems Research Facility (CESRF) at University of Guelph, Ontario, Canada) and exposed to 97 kPa, 75 kPa, 50 kPa, 25 kPa, 10 kPa, 5 kPA for 24 hours.The carbon dioxide was held constant at a partial pressure of 0.05 kPa in all treatments. Nitrogen was used as a balance of remaining gas for oxygen treatments. Each atmospheric treatment was replicated in three different chambers, and each chamber held 10 individual plates comprised of 12 plants each.   Plant harvest: At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots.

value: Shoots (entire aerial portion of the plant including hypocotyl)

value: 11 days old plants, light grown

value: 5 kPa pressure chamber for 24 hrs


title: Shoot grown at 5 kPa pressure Replica 2


title: Shoot grown at 5 kPa pressure Replica 3


title: Shoot grown at 10 kPa pressure Replica 2

source_name: 10 day old plant transferred to 10 kPa pressure chamber for 24 hrs

value: 10 kPa pressure chamber for 24 hrs


title: MDCK_LOLX2_4

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: In Situ Hybridization Kit Plus (Agilent technologies) protocols

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.0).

data_processing: Agilent Feature Extraction Software (v 10.0) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: Total RNA MDCK_LOLX2_4 cells

label_protocol: Four independent passages from stably-transfected of each analysed tranfectec cells (LOXL2, DLOXL2) and empty-pCDNA3.1 vector, used as control. Total RNA (1mg)from cell lines was isolated using Trizol reagent (Life Technologies) as indicated by the manufacturer. Purity of isolated RNA was evaluated spectrophotometrically by the A260/A280 absorbance ratio. RNA was labeled and array hybridized using the Low RNA Linear Amplification Kit and the In Situ Hybridization Kit Plus (Agilent technologies), respectively, following manufacturer’s protocol.

growth_protocol: MDCK-II cell lines were obtained from the American Type Culture Collection (LGC Standards-SLU, Barcelona, Spain) and grown in DMEM media (Gibco BRL), supplemented with 10% fetal bovine serum, 10 mmol/L glutamine (Life Technologies), 100 µg/mL ampicillin and 32 µg/mL gentamicin (or 100units/ml penicillin/streptomycin for MDA-MB-231 cells). All cell lines were grown at 37°C in a humidified 5% CO2 atmosphere. Stable transfectants were obtained from parental MDCK-II after transfection with pcDNA3-hLOXL2-Flag, pcDNA3-ΔLOXL2-Flag, Cells were grown in the presence of G418 (400 μg/ml) for 3-4 weeks and individual clones isolated with cloning rings. At least 10 independent clones were isolated from each transfection.

extract_protocol: Total RNA was using Trizol (Life Technologies, Barcelona, Spain) following the manufacturer’s protocol and subsequently treated with DNase (Promega, Barcelona, Spain). Total RNA concentration and purity was assessed using Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, NC, USA), and subsequently retro-transcribed using random hexamer primers and cDNA First Strand Synthesis kit (MRI Fermentas, Hanover, MD, USA)

tag: cell line

value: Ephitelial

source_name: Pool from MDCK pcDNA3control cells

tag: reference

value: Pool from MDCK pcDNA3 control cells


title: MDCK_LOLX2_1

source_name: Total RNA MDCK_LOLX2_1 cells


title: Shoot grown at 75 kPa pressure Replica 3

source_name: 10 day old plant transferred to 75 kPa pressure chamber for 24 hrs

value: 75 kPa pressure chamber for 24 hrs


title: Shoot grown at 75 kPa pressure Replica 4


title: Shoot grown at 75 kPa pressure Replica 2


title: MDCK_LOLX2_3

source_name: Total RNA MDCK_LOLX2_3 cells


title: Root grown at 5 kPa pressure Replica 2


title: MDCK_LOLX2_2

source_name: Total RNA MDCK_LOLX2_2 cells


title: Root grown at 5 kPa pressure Replica 1


title: Shoot grown at 75 kPa pressure Replica 1


title: Shoot grown at 10 kPa pressure Replica 3


title: siHuR.IOMM-Lee.rep6

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

country: France

institute: INSERM

hyb_protocol: One hundred ng of total RNA were used as the starting amount for microarrays experiments. 3.5 µg of labeled DNA were hybridized onto Affymetrix cartridges for 16 hours at 45°C under continuous rotation at 60 rpm. The arrays were washed and scanned according to the protocol GeneChip® Expression Wash, Stain and Scan for Cartridge Arrays (P/N 702731 Rev. 4).

scan_protocol: GeneShips were scanned using a GeneChip Scanner 3000

data_processing:
Fluorescence values corresponding to raw expression data for each sample were extracted as a whole from each Affymetrix CEL files (one file per sample) using the R oligo package with the corresponding platform definitions (pd.hugene.2.0.st). The extraction method included no normalization or background correction with the RMA algorithm. Positive and negative control probes were removed.
Raw data with no background correction, no normalization

molecule: polyA RNA

organism: Homo sapiens

source_name: Silencer Select siRNA HuR biological replicate 6

label_protocol: Gene expression experiments were performed using Affymetrix Human Genechip v.2.0 and ST Arrays using GeneChip® WT PLUS Reagent Kit, according to the standard protocol for Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2).

growth_protocol: The human anaplastic meningioma cell line IOMM-Lee (generous gift from Dr Gillespie and Dr Jensen, University of Utah, USA)  was cultured in Dulbecco’s modified Eagle’s medium (Life Technologies, Carlsbad, California, USA) supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 mg/ml streptomycin at 37°C, under 20% O2  and 5% CO2 as standard condition.

extract_protocol: Seventy-two hours after transfection of the IOMM-Lee cells with either the Silencer Select Negative Control siRNA#1 (Ambion, Life Technologies) (n=6) or Silencer Select siRNA ELAVL1 s4608 (SiHuR) (Ambion, Life Technologies) (n=6), total RNA extraction was performed using the TRIzol protocol (Invitrogen, Life Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. The quality of these RNA samples was verified independently by Nanodrop ND-1000 (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: We used siRNA Silencer Select siRNA ELAVL1 s4608 (Ambion, Life Technologies) to reduce HuR expression and used Silencer Select Negative Control siRNA#1 (Ambion, Life Technologies) as control. The efficiency of siHuR transfection was validated by Western Blot. In order to perform anchorage-dependent cell growth assay, 25,000 cells were incubated per well in 24-wells plates. Cells were transfected with 17 nM of siRNA, using RNAiMAX lipofectamin (Life Technologies), according to the manufacturer’s instructions. The number of cells per microliter was counted at 2, 4, and 6 days after transfection using LUNA Automated Cell Counter (Logos Biosystems, Annandale, USA). Each measurement was performed three times after three independent transfections (n = 9).

tag: strain

value: IOMM-Lee cells


title: Root grown at 10 kPa pressure Replica 1


title: Root grown at 75 kPa pressure Replica 3


title: Shoot grown at 10 kPa pressure Replica 1


title: Root grown at 75 kPa pressure Replica 2


title: siHuR.IOMM-Lee.rep5

description: human anaplastic meningioma cell line IOMM-Lee

source_name: Silencer Select siRNA HuR biological replicate 5


title: Root grown at 75 kPa pressure Replica 1


title: siHuR.IOMM-Lee.rep3

source_name: Silencer Select siRNA HuR biological replicate 3


title: Root grown at 50 kPa pressure Replica 2 [experiment 2]

description: Root 50 kPa Rep3 (12675_Ferl_5d-50-B_(ATH1-121501).mas5-Signal)

source_name: solid 0.5x MS media plates; 5 day old plant transferred to 50 kPa pressure chamber for 24 hours

growth_protocol: Plant Materials: Arabidopsis thaliana ecotype Wassilewskija (WS) was grown as previously described (Paul et al., 2001). In brief, seeds were surfaced sterilized and then planted on vertically orientated plates containing 0.5x MS media, 0.45% Phytagel and 2.5 ppm benomyl. Plants were grown for 5 days in an ambient pressure growth chamber at CESRF with 24-hour light, 22 to 25° Celsius, 97 kPa prior to low pressure treatments.

treatment_protocol:
Experiment Unique Equipment and Environmental Conditions:
Chambers and facilities for low pressure treatments: The Low Pressure Growth Chambers (LPGC) are components of the Controlled Environment Systems Research Facility (CESRF at University of Guelph, Ontario, Canada). Temperature, air pressure, gas composition and humidity were controlled and monitored in the LPGC by the second, and data from the LPGC were collected for reporting every 5 minutes. Control pressure was set at 97kPa, which is the ambient pressure at an altitude of 1100 feet (Guelph, Ontario). The LPGC provided a constant light condition with strictly monitored, controlled temperature at 22°C to 24°C; the humidity was maintained inside the Petri plates at 95% or above.
Variations on the pressure and oxygen supplement:
For atmospheric treatments, 5 day old plants were transferred to LPGCs and exposed to 97 kPa, 50 kPa and 50 kPa with oxygen supplemented to a partial pressure of 21 kPa (defined as 50kPa/NormOx) for 24 hours, respectively. The carbon dioxide was held constant at a partial pressure of 0.05 kPa in all treatments. Nitrogen was used as a balance of remaining gas for oxygen treatments. Each atmospheric treatment was replicated in three different chambers, and each chamber held 10 individual plates comprised of 12 plants each.
Plant harvest: At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots.

value: 5 day old plants, light grown

value: 50 kPa pressure chamber for 24 hrs


title: siHuR.IOMM-Lee.rep4

source_name: Silencer Select siRNA HuR biological replicate 4


title: Root grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 2 [experiment 2]

description: Root 50kPa/NormOx (50 kPa + 21 kPa O2) Rep2 (12681_Ferl_5d-OX1-B_(ATH1-121501).mas5-Signal)

source_name: solid 0.5x MS media plates; 5 day old plant transferred to the 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa chamber for 24 hours

value: 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa chamber for 24 hrs


title: Root grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 3 [experiment 2]

description: Root 50kPa/NormOx (50 kPa + 21 kPa O2) Rep3 (12682_Ferl_5d-OX1-C_(ATH1-121501).mas5-Signal)


title: Root grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 1 [experiment 2]

description: Root 50kPa/NormOx (50 kPa + 21 kPa O2) Rep1 (12680_Ferl_5d-OX1-A_(ATH1-121501).mas5-Signal)


title: siHuR.IOMM-Lee.rep2

source_name: Silencer Select siRNA HuR biological replicate 2


title: Root grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 3 [experiment 2]

description: Root 97 kPa Rep3 (12673_Ferl_5d-101-C_(ATH1-121501).mas5-Signal)

source_name: solid 0.5x MS media plates; 5 day old plant transferred to 97 kPa pressure chamber for 24 hours

value: 97 kPa pressure chamber for 24 hrs


title: siCtrl.IOMM-Lee.rep5

source_name: Silencer Select Negative Control biological replicate 5


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 1 hr Rep 2

description:
Shoot 101 kPa 1 hr Rep2
12485_Ferl_101-A-S-3_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 1 hour

value: Shoots

value: 97 kPa pressure chamber for 1 hr


title: siCtrl.IOMM-Lee.rep6

source_name: Silencer Select Negative Control biological replicate 6


title: siCtrl.IOMM-Lee.rep3

source_name: Silencer Select Negative Control biological replicate 3


title: Root grown at 50 kPa pressure Replica 1 [experiment 2]

description: Root 50 kPa Rep1 (12674_Ferl_5d-50-A_(ATH1-121501).mas5-Signal)

value: Wassilewskija (WS)

value: Roots


title: Root grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 1 [experiment 2]

description: Root 97 kPa Rep1 (12671_Ferl_5d-101-A_(ATH1-121501).mas5-Signal)

value: RNAlater fixed_sample


title: Root grown at 50 kPa pressure Replica 3 [experiment 2]

description: Root 50 kPa Rep3 (12676_Ferl_5d-50-C_(ATH1-121501).mas5-Signal)


title: siCtrl.IOMM-Lee.rep4

source_name: Silencer Select Negative Control biological replicate 4


title: siHuR.IOMM-Lee.rep1

source_name: Silencer Select siRNA HuR biological replicate 1


title: Shoot grown at 25 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 2

description: Shoot 25kPa/NormOx (25 kPa + 21 kPa O2) Rep2

treatment_protocol:
Experiment Unique Equipment and Environmental Conditions:
Chambers and facilities for low pressure treatments: The Low Pressure Growth Chambers (LPGC) are components of the Controlled Environment Systems Research Facility (CESRF at University of Guelph, Ontario, Canada). Temperature, air pressure, gas composition and humidity were controlled and monitored in the LPGC by the second, and data from the LPGC were collected for reporting every 5 minutes. Control pressure was set at 97kPa, which is the ambient pressure at an altitude of 1100 feet (Guelph, Ontario). The LPGC provided a constant light condition with strictly monitored, controlled temperature at 22°C to 24°C; the humidity was maintained inside the Petri plates at 95% or above.
Variations on the pressure and oxygen supplement:
For atmospheric treatments, 10 day old plants were transferred to LPGCs and exposed to 97 kPa, 50 kPa, 25 kPa, 50 kPa with oxygen supplemented to a partial pressure of 21 kPa (defined as 50kPa/NormOx), 25 kPa with oxygen supplement to a partial pressure of 21 kPa (defined as 25kPa/NormOx) and 97 kPa with reduced oxygen of 5.1 kPa (defined as 97kPa/HypOx) for 24 hours, respectively. The carbon dioxide was held constant at a partial pressure of 0.05 kPa in all treatments. Nitrogen was used as a balance of remaining gas for oxygen treatments. Each atmospheric treatment was replicated in three different chambers, and each chamber held 10 individual plates comprised of 12 plants each.
Plant harvest: At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots.

value: Shoots (entire aerial portion of the plant including hypocotyl)

value: 10 day old plants, light grown

value: 25 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa chamber for 24 hrs


title: Shoot grown at 97 kPa pressure with reduced oxygen to a partial pressure of 5.1 kPa Replica 1

description: Shoot 97kPa/HypOx (97 kPa + 5.1 kPa O2) Rep1

value: 97 kPa pressure with reduced oxygen to a partial pressure of 5.1 kPa chamber for 24 hrs


title: Shoot grown at 25 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 3

description: Shoot 25kPa/NormOx (25 kPa + 21 kPa O2) Rep3


title: Shoot grown at 97 kPa pressure with reduced oxygen to a partial pressure of 5.1 kPa Replica 2

description: Shoot 97kPa/HypOx (97 kPa + 5.1 kPa O2) Rep2


title: siCtrl.IOMM-Lee.rep2

source_name: Silencer Select Negative Control biological replicate 2


title: Root grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 2 [experiment 2]

description: Root 97 kPa Rep2 (12672_Ferl_5d-101-B_(ATH1-121501).mas5-Signal)


title: Shoot grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 3

description: Shoot 50kPa/NormOx (50 kPa + 21 kPa O2) Rep3


title: Shoot grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 4

description: Shoot 50kPa/NormOx (50 kPa + 21 kPa O2) Rep4


title: Shoot grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 2

description: Shoot 50kPa/NormOx (50 kPa + 21 kPa O2) Rep2


title: Shoot grown at 25 kPa pressure Replica 3

description: Shoot 25 kPa Rep3

source_name: Shoot grown at 25 kPa pressure

value: 25 kPa pressure chamber for 24 hrs


title: Shoot grown at 25 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 1

description: Shoot 25kPa/NormOx (25 kPa + 21 kPa O2) Rep1


title: Shoot grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 1

description: Shoot 50kPa/NormOx (50 kPa + 21 kPa O2) Rep1


title: Shoot grown at 25 kPa pressure Replica 2

description: Shoot 25 kPa Rep2


title: siCtrl.IOMM-Lee.rep1

description: human anaplastic meningioma cell line IOMM-Lee

source_name: Silencer Select Negative Control biological replicate 1


title: Shoot grown at 25 kPa pressure Replica 1

description: Shoot 25 kPa Rep1


title: Shoot grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 2

description: Shoot 97 kPa Rep2


title: Shoot grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 3

description: Shoot 97 kPa Rep3


title: Root grown at 25 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 1

description: Root 25kPa/NormOx (25 kPa + 21 kPa O2) Rep1


title: Shoot grown at 50 kPa pressure Replica 2

description: Shoot 50 kPa Rep3

source_name: Shoot grown at 50 kPa pressure


title: Shoot grown at 50 kPa pressure Replica 1

description: Shoot 50 kPa Rep1


title: Shoot grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 1

description: Shoot 97 kPa Rep1


title: Flu_pos_23

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: influenza infected patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: A venous blood sample (2.5ml) was collected at the time of enrolment into the study.  The sample was placed into PAXgene Blood RNA tubes (BD systems, NJ, USA) and was kept in storage at -20°C. RNA extraction was later performed using the standard protocol (PAXgeneTM Blood RNA kit - Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: infection

value: Influenza B

value: Blood


title: Root grown at 97 kPa pressure with reduced oxygen to a partial pressure of 5.1 kPa Replica 3

description: Root 97kPa/HypOx (97 kPa + 5.1 kPa O2) Rep3


title: Flu_pos_24


title: Shoot grown at 50 kPa pressure Replica 3

description: Shoot 50 kPa Rep3


title: Root grown at 97 kPa pressure with reduced oxygen to a partial pressure of 5.1 kPa Replica 1

description: Root 97kPa/HypOx (97 kPa + 5.1 kPa O2) Rep1


title: WT  cardiomyocytes3

city: jackson

first: lin

last: wang

state: Mississippi

address: 2501 River Oaks Blvd Apt 11 B

institute: UMMC

hyb_protocol: 1500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions.

scan_protocol: Following washing and staining with Cy3-streptavidin conjugate, the BeadChips are imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe. The intensity of the signal corresponds to the quantity of the respective mRNA in the original sample.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio (v2011.1) gene expression module (v1.9.0) to report both un-normalized and quantile normalized, background corrected gene expression signal level

label: Biotin

organism: Mus musculus

source_name: 4-6 month mice CADIOMYOCYTES

label_protocol: labeling - Expression profiling is accomplished using the Mouse WG-6  whole-genome gene expression array and direct hybridization assay (Illumina, Inc).  Initially, 500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions.

extract_protocol: Total RNA was extracted using the Invisorb RNA Kit II (Invitek, Berlin, Germany) according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol

treatment_protocol: The inducible cardiac-specific SIRT1 knockout (icSIRT1 KO) mice were generated by Tamoxifen injection (0.08 mg/g, i.p. 5 days) of CreERT2-SIRT1flox/flox (12 week old) mice

tag: gender

value: male

tag: genotype

value: Wild type

value: cardiomyocytes


title: Flu_pos_22


title: SIRT1 KO BASAL3

source_name: 4-6 month mice HEART

value: SIRT1 KO

value: heart


title: Root grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 2

description: Root 50kPa/NormOx (50 kPa + 21 kPa O2) Rep2

value: 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa chamber for 24 hrs


title: Flu_pos_20

value: Influenza A


title: WT BASAL3


title: Flu_pos_18


title: Flu_pos_21


title: Root grown at 50 kPa pressure supplemented with oxygen to a partial pressure of 21 kPa Replica 1

description: Root 50kPa/NormOx (50 kPa + 21 kPa O2) Rep1

value: Wassilewskija (WS)


title: WT ISCHEMIA(45mins)/REPERFUSION(24hours)3


title: Root grown at 25 kPa pressure Replica 2

description: Root 25 kPa Rep2

source_name: Root grown at 25 kPa pressure

value: Roots


title: Root grown at 97 kPa pressure with reduced oxygen to a partial pressure of 5.1 kPa Replica 2

description: Root 97kPa/HypOx (97 kPa + 5.1 kPa O2) Rep2

value: RNAlater fixed_sample


title: Root grown at 25 kPa pressure Replica 3

description: Root 25 kPa Rep3


title: Flu_pos_19


title: Flu_pos_16


title: SIRT1 KO cardiomyocytes3


title: Flu_pos_17


title: Root grown at 25 kPa pressure Replica 1

description: Root 25 kPa Rep1


title: SIRT1 KO ISCHEMIA(45mins)/REPERFUSION(24hours)3


title: Root grown at 50 kPa pressure Replica 3

description: Root 50 kPa Rep3

source_name: Root grown at 50 kPa pressure

value: 50 kPa pressure chamber for 24 hrs


title: Flu_pos_14


title: Flu_pos_15


title: Root grown at 50 kPa pressure Replica 2

description: Root 50 kPa Rep2

value: 10 day old plants, light grown


title: Root grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 2

description: Root 97 kPa Rep2

value: 97 kPa pressure chamber for 24 hrs


title: Root grown at 50 kPa pressure Replica 1

description: Root 50 kPa Rep1


title: Flu_pos_12


title: Flu_pos_3


title: Flu_pos_11


title: Flu_pos_7


title: Flu_pos_8


title: Flu_pos_9


title: Flu_pos_13


title: Root grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 1

description: Root 97 kPa Rep1


title: Flu_pos_10


title: hlty_ctr_15

source_name: healthy control

value: healthy control


title: Flu_pos_5


title: Root grown at control pressure, ambient pressure at an altitude of 1100 feet (Ontario, Canada) Replica 3

description: Root 97 kPa Rep3


title: Flu_pos_1


title: Flu_pos_2


title: Flu_pos_6


title: hlty_ctr_12


title: hlty_ctr_13


title: Flu_pos_4


title: Normal 5

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Standard Illumina hybridization protocol:  A total of 750ng of cRNA per sample was loaded into the Illumina Human HT-12 v4 Gene Expression BeadChip for hybridization at 58 degrees C for 17 hours.

scan_protocol: Standard Illumina scan protocol: Used Illumina iScan system

data_processing: GenomeStudio V2011.1 with GeneExpression Module V1.9.0 was used with HumanHT-12_v4_0_R2_15002873_B.bgx manifest to create a GenomeStudio project.  Matrix reports at the probe level were created with/without Average Normalization and with/without background subtraction.

source_name: Human Controls

label_protocol: Illumina TotalPrep RNA amplification kit (Illumina, San Diego, CA) was used to prepare biotinylated antisense cRNA from 500ng of high-quality total RNA

extract_protocol: Total RNA was isolated and purified from frozen tissues using the RNeasy Plus Mini Kit (Qiagen,Valencia, CA).

treatment_protocol: Fresh tissue was harvested by surgical removal from 18 children.  Upon harvesting, tissues were stored at -80 ◦C until the RNA extraction was performed.

tag: diagnosis

value: Normal

tag: subject


title: Macrocystic 7

source_name: Human Lymphatic Macrocystic Recurrent

value: Macrocystic lymphatic malformation


title: Normal 1


title: hlty_ctr_14

value: Blood


title: Normal 3


title: Macrocystic 6


title: Normal 4


title: Normal 2


title: hlty_ctr_11


title: hlty_ctr_8


title: hlty_ctr_4


title: Macrocystic 3


title: hlty_ctr_7


title: hlty_ctr_3


title: Microcystic 5

source_name: Human Lymphatic Microcystic Recurrent

value: Microcystic lymphatic malformation


title: hlty_ctr_5


title: Macrocystic 1


title: Microcystic 6


title: hlty_ctr_9


title: Macrocystic 4


title: hlty_ctr_2


title: Microcystic 1


title: hlty_ctr_6


title: Microcystic 3


title: hlty_ctr_1


title: Macrocystic 5


title: Macrocystic 2


title: hlty_ctr_10


title: Microcystic 2


title: individual 300

status: Public on May 10 2017

city: Montreal

first: Marc

last: Parisien

state: Quebec

address: 740 Dr. Penfield Avenue

department: Dentistry

country: Canada

institute: McGill University

description: Gene expression data.

hyb_protocol: The microarray hybridization was performed based on the manufacturer’s standard protocols.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 with 7G upgrade (Affymetrix, Santa Clara, CA)

data_processing: Normalization of the microarray data was done in the R statistical software, with the help of the oligo R package and the Platform Design Info for Affymetrix HTA-2_0 R  package. The Robust Multi-Array Average (RMA) algorithm was chosen for normalization, with all samples considered simultaneously.

source_name: dorsal root ganglion

label_protocol: The sample labeling was performed based on the manufacturer’s standard protocols.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs was quantified using NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Lafayette, CO) and the RNAs integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: Samples were collected post-mortem from brain-dead subjects following asystole. They consist of snap-frozen dorsal root ganglions sourced from bilateral lumbar L4 and L5 (age range: 14-89, sex ratio: 105 F / 109 M, >90% Caucasian). Samples are courtesy of the CORE/CORID repository at the university of Pittsburgh.

value: dorsal root ganglion


title: individual 299

description: Gene expression data.


title: radiation-adapted MHH-ES-1 cells

city: Houston

first: Mary

last: Shapiro

state: Texas

address: 1102 Bates St.

department: Pediatric Hematology and Oncology

institute: Baylor College of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGenome Studio

source_name: Ewing Sarcoma

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyzer.

value: radiation-adapted MHH-ES-1 cells


title: radiation-adapted A4573 cells

value: radiation-adapted A4573 cells


title: radiation-adapted SK-ES1 cells

value: radiation-adapted SK-ES1 cells


title: individual 297

description: Gene expression data.


title: wild type MHH-ES-1 cells

description: M-WT

value: wild type MHH-ES-1 cells


title: wild type A4573 cells

description: A-WT

value: wild type A4573 cells


title: individual 296

description: Gene expression data.


title: wild type SK-ES1 cells

description: SK-WT

value: wild type SK-ES1 cells


title: individual 291

description: Gene expression data.


title: individual 294

description: Gene expression data.


title: individual 293

description: Gene expression data.


title: individual 298

description: Gene expression data.


title: Microcystic 4


title: individual 287

description: Gene expression data.


title: individual 285

description: Gene expression data.


title: individual 282

description: Gene expression data.


title: individual 299

description: exon expression data

data_processing: Normalization of the microarray data was done in the R statistical software, with the help of the "oligo" R package and the "Platform Design Info for Affymetrix HTA-2_0" R  package. The Robust Multi-Array Average (RMA) algorithm was chosen for normalization, with all samples considered simultaneously.


title: individual 292

description: Gene expression data.


title: individual 288

description: Gene expression data.


title: individual 283

description: Gene expression data.


title: individual 281

description: Gene expression data.


title: individual 298

description: exon expression data


title: individual 300

description: exon expression data


title: individual 280

description: Gene expression data.


title: individual 289

description: Gene expression data.


title: individual 297

description: exon expression data


title: individual 296

description: exon expression data


title: individual 279

description: Gene expression data.


title: individual 284

description: Gene expression data.


title: individual 294

description: exon expression data


title: individual 290

description: Gene expression data.


title: individual 286

description: Gene expression data.


title: individual 293

description: exon expression data


title: individual 289

description: exon expression data


title: individual 288

description: exon expression data


title: individual 286

description: exon expression data


title: individual 285

description: exon expression data


title: individual 273

description: Gene expression data.


title: individual 284

description: exon expression data


title: individual 277

description: Gene expression data.


title: individual 290

description: exon expression data


title: individual 275

description: Gene expression data.


title: individual 292

description: exon expression data


title: individual 276

description: Gene expression data.


title: individual 268

description: Gene expression data.


title: individual 278

description: Gene expression data.


title: individual 287

description: exon expression data


title: individual 291

description: exon expression data


title: individual 281

description: exon expression data


title: individual 266

description: Gene expression data.


title: individual 282

description: exon expression data


title: individual 279

description: exon expression data


title: individual 278

description: exon expression data


title: individual 262

description: Gene expression data.


title: individual 280

description: exon expression data


title: individual 271

description: Gene expression data.


title: individual 283

description: exon expression data


title: individual 277

description: exon expression data


title: individual 267

description: Gene expression data.


title: individual 274

description: Gene expression data.


title: individual 259

description: Gene expression data.


title: individual 255

description: Gene expression data.


title: individual 257

description: Gene expression data.


title: individual 273

description: exon expression data


title: individual 272

description: Gene expression data.


title: individual 276

description: exon expression data


title: individual 270

description: Gene expression data.


title: individual 275

description: exon expression data


title: individual 270

description: exon expression data


title: individual 272

description: exon expression data


title: individual 250

description: Gene expression data.


title: individual 261

description: Gene expression data.


title: individual 274

description: exon expression data


title: individual 249

description: Gene expression data.


title: individual 271

description: exon expression data


title: individual 259

description: exon expression data


title: individual 247

description: Gene expression data.


title: individual 244

description: Gene expression data.


title: individual 267

description: exon expression data


title: individual 251

description: Gene expression data.


title: individual 252

description: Gene expression data.


title: individual 240

description: Gene expression data.


title: individual 254

description: Gene expression data.


title: individual 266

description: exon expression data


title: individual 255

description: exon expression data


title: individual 241

description: Gene expression data.


title: individual 262

description: exon expression data


title: individual 238

description: Gene expression data.


title: individual 237

description: Gene expression data.


title: individual 242

description: Gene expression data.


title: individual 243

description: Gene expression data.


title: individual 235

description: Gene expression data.


title: individual 252

description: exon expression data


title: individual 239

description: Gene expression data.


title: individual 251

description: exon expression data


title: individual 250

description: exon expression data


title: individual 247

description: exon expression data


title: individual 268

description: exon expression data


title: individual 233

description: Gene expression data.


title: individual 257

description: exon expression data


title: individual 236

description: Gene expression data.


title: individual 261

description: exon expression data


title: individual 243

description: exon expression data


title: individual 241

description: exon expression data


title: individual 234

description: Gene expression data.


title: individual 242

description: exon expression data


title: individual 249

description: exon expression data


title: individual 244

description: exon expression data


title: individual 240

description: exon expression data


title: individual 238

description: exon expression data


title: individual 229

description: Gene expression data.


title: individual 232

description: Gene expression data.


title: individual 228

description: Gene expression data.


title: individual 236

description: exon expression data


title: individual 239

description: exon expression data


title: individual 237

description: exon expression data


title: individual 234

description: exon expression data


title: individual 235

description: exon expression data


title: individual 233

description: exon expression data


title: individual 232

description: exon expression data


title: individual 254

description: exon expression data


title: individual 231

description: Gene expression data.


title: individual 223

description: Gene expression data.


title: individual 225

description: Gene expression data.


title: individual 227

description: Gene expression data.


title: individual 231

description: exon expression data


title: individual 216

description: Gene expression data.


title: individual 212

description: Gene expression data.


title: individual 229

description: exon expression data


title: individual 224

description: Gene expression data.


title: individual 218

description: Gene expression data.


title: individual 222

description: Gene expression data.


title: individual 228

description: exon expression data


title: individual 220

description: Gene expression data.


title: individual 227

description: exon expression data


title: individual 209

description: Gene expression data.


title: individual 207

description: Gene expression data.


title: individual 208

description: Gene expression data.


title: individual 224

description: exon expression data


title: individual 221

description: Gene expression data.


title: individual 211

description: Gene expression data.


title: individual 226

description: Gene expression data.


title: individual 205

description: Gene expression data.


title: individual 223

description: exon expression data


title: individual 221

description: exon expression data


title: individual 216

description: exon expression data


title: individual 218

description: exon expression data


title: individual 222

description: exon expression data


title: individual 195

description: Gene expression data.


title: individual 199

description: Gene expression data.


title: individual 207

description: exon expression data


title: individual 188

description: Gene expression data.


title: individual 190

description: Gene expression data.


title: individual 194

description: Gene expression data.


title: individual 198

description: Gene expression data.


title: individual 200

description: Gene expression data.


title: individual 193

description: Gene expression data.


title: individual 184

description: Gene expression data.


title: individual 200

description: exon expression data


title: individual 180

description: Gene expression data.


title: individual 209

description: exon expression data


title: individual 212

description: exon expression data


title: individual 211

description: exon expression data


title: individual 181

description: Gene expression data.


title: individual 156

description: Gene expression data.


title: individual 198

description: exon expression data


title: individual 225

description: exon expression data


title: individual 178

description: Gene expression data.


title: individual 155

description: Gene expression data.


title: individual 154

description: Gene expression data.


title: individual 195

description: exon expression data


title: individual 226

description: exon expression data


title: individual 185

description: Gene expression data.


title: individual 194

description: exon expression data


title: individual 220

description: exon expression data


title: individual 190

description: exon expression data


title: individual 208

description: exon expression data


title: individual 186

description: exon expression data


title: individual 153

description: Gene expression data.


title: individual 152

description: Gene expression data.


title: individual 167

description: Gene expression data.


title: individual 193

description: exon expression data


title: individual 205

description: exon expression data


title: individual 188

description: exon expression data


title: individual 180

description: exon expression data


title: individual 186

description: Gene expression data.


title: individual 179

description: exon expression data


title: individual 147

description: Gene expression data.


title: individual 146

description: Gene expression data.


title: individual 149

description: Gene expression data.


title: individual 150

description: Gene expression data.


title: individual 199

description: exon expression data


title: individual 185

description: exon expression data


title: individual 144

description: Gene expression data.


title: individual 142

description: Gene expression data.


title: individual 156

description: exon expression data


title: individual 181

description: exon expression data


title: individual 143

description: Gene expression data.


title: individual 179

description: Gene expression data.


title: individual 141

description: Gene expression data.


title: individual 140

description: Gene expression data.


title: individual 178

description: exon expression data


title: individual 153

description: exon expression data


title: individual 151

description: exon expression data


title: individual 150

description: exon expression data


title: individual 184

description: exon expression data


title: individual 155

description: exon expression data


title: individual 151

description: Gene expression data.


title: individual 136

description: Gene expression data.


title: individual 139

description: Gene expression data.


title: individual 167

description: exon expression data


title: individual 135

description: Gene expression data.


title: individual 148

description: Gene expression data.


title: individual 138

description: Gene expression data.


title: individual 154

description: exon expression data


title: individual 145

description: Gene expression data.


title: individual 134

description: Gene expression data.


title: individual 152

description: exon expression data


title: individual 147

description: exon expression data


title: individual 146

description: exon expression data


title: individual 131

description: Gene expression data.


title: individual 148

description: exon expression data


title: individual 145

description: exon expression data


title: individual 149

description: exon expression data


title: individual 130

description: Gene expression data.


title: individual 137

description: Gene expression data.


title: individual 142

description: exon expression data


title: individual 143

description: exon expression data


title: individual 140

description: exon expression data


title: individual 144

description: exon expression data


title: individual 141

description: exon expression data


title: individual 137

description: exon expression data


title: individual 129

description: Gene expression data.


title: individual 136

description: exon expression data


title: individual 139

description: exon expression data


title: individual 133

description: Gene expression data.


title: individual 133

description: exon expression data


title: individual 126

description: Gene expression data.


title: individual 128

description: exon expression data


title: individual 129

description: exon expression data


title: individual 125

description: Gene expression data.


title: individual 128

description: Gene expression data.


title: individual 124

description: Gene expression data.


title: individual 135

description: exon expression data


title: individual 123

description: Gene expression data.


title: individual 134

description: exon expression data


title: individual 130

description: exon expression data


title: individual 123

description: exon expression data


title: individual 131

description: exon expression data


title: individual 125

description: exon expression data


title: individual 122

description: exon expression data


title: individual 127

description: exon expression data


title: individual 121

description: exon expression data


title: individual 127

description: Gene expression data.


title: individual 124

description: exon expression data


title: individual 120

description: exon expression data


title: individual 115

description: exon expression data


title: individual 117

description: Gene expression data.


title: individual 116

description: exon expression data


title: individual 119

description: Gene expression data.


title: individual 115

description: Gene expression data.


title: individual 119

description: exon expression data


title: individual 121

description: Gene expression data.


title: individual 120

description: Gene expression data.


title: individual 112

description: exon expression data


title: individual 111

description: exon expression data


title: individual 117

description: exon expression data


title: individual 118

description: Gene expression data.


title: individual 116

description: Gene expression data.


title: individual 113

description: exon expression data


title: individual 109

description: exon expression data


title: individual 108

description: exon expression data


title: individual 110

description: exon expression data


title: individual 126

description: exon expression data


title: individual 118

description: exon expression data


title: individual 114

description: exon expression data


title: individual 100

description: exon expression data


title: individual 101

description: exon expression data


title: individual 102

description: exon expression data


title: individual 104

description: exon expression data


title: individual 93

description: exon expression data


title: individual 107

description: exon expression data


title: individual 92

description: exon expression data


title: individual 138

description: exon expression data


title: individual 114

description: Gene expression data.


title: individual 98

description: exon expression data


title: individual 91

description: exon expression data


title: individual 96

description: exon expression data


title: individual 111

description: Gene expression data.


title: individual 108

description: Gene expression data.


title: individual 96

description: Gene expression data.


title: individual 122

description: Gene expression data.


title: individual 113

description: Gene expression data.


title: individual 110

description: Gene expression data.


title: individual 102

description: Gene expression data.


title: individual 101

description: Gene expression data.


title: individual 112

description: Gene expression data.


title: individual 90

description: exon expression data


title: individual 98

description: Gene expression data.


title: individual 99

description: exon expression data


title: individual 109

description: Gene expression data.


title: individual 100

description: Gene expression data.


title: individual 107

description: Gene expression data.


title: individual 85

description: exon expression data


title: individual 92

description: Gene expression data.


title: individual 104

description: Gene expression data.


title: individual 94

description: exon expression data


title: individual 83

description: exon expression data


title: individual 99

description: Gene expression data.


title: individual 82

description: exon expression data


title: individual 90

description: Gene expression data.


title: individual 94

description: Gene expression data.


title: individual 93

description: Gene expression data.


title: individual 77

description: exon expression data


title: individual 86

description: exon expression data


title: individual 87

description: exon expression data


title: individual 91

description: Gene expression data.


title: individual 79

description: exon expression data


title: individual 80

description: exon expression data


title: individual 84

description: exon expression data


title: individual 81

description: exon expression data


title: individual 80

description: Gene expression data.


title: blood-d44 [II-B53]

city: Turku

first: Outi

last: Sareila

address: Tykistökatu 6 A 4

country: Finland

institute: University of Turku

hyb_protocol: 750 ng each cRNA sample was hybridized to Illumina’s Sentrix BeadChip Array MouseRef-8 v2

scan_protocol: Sentrix BeadChip Array MouseRef-8 v2 (Illumina) hybridizations were detected with Cyanine3-streptavidine. Illumina Bead Array Reader (Factor=1, PMT=521, Filter=100%) and the numerical results were extracted with Bead Studio v3.2.6 without any normalization or background subtraction.

data_processing: The microarray data was quantile-normalized and log2-transformed. Differentially regulated genes were identified using linear modeling (LIMMA packages, Bioconductor).

source_name: blood, wt, day 44 p.i.

label_protocol: From 250 ng total RNA with Ambion's Illumina Total Prep RNA Amplification kit (cat # AMIL1791), cRNA concentrations where checked with Nanodrop ND-1000 and the quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: Samples were not treated after collection

extract_protocol: In experiment I: total RNA from the spleen samples was isolated using Ambion’s Ribo Pure Kit (cat# 1924) and from the blood samples by using Ambion’s Mouse RiboPure™-Blood RNA Isolation Kit (cat# AM1951). In experiment I blood samples were purified using LiCl precipitation (Ambion, AM9480). In experiment II spleen samples were collected in RNALater (Ambion, AM7020 ) and 50 – 100 mg total RNA was isolated using Qiagen’s RNeasy mini kit (cat# 74104) with the optional DNase-treatment step (RNase-Free DNase Set, Qiagen, 79254). In experiment II blood samples were collected in RNAprotect Animal Blood Tubes (Qiagen, 76544) and RNA was isolated using Qiagen’s RNeasy Protect Animal Blood Kit (cat# 73224). All samples were treated with with Ambion’s GLOBINclear™–Mouse/Rat Kit (cat# AM1981) using 1-2 ug of blood RNA as starting material.

treatment_protocol: whole blood and total spleen samples were used without ex vivo culture or any ex vivo treatment

value: male

value: blood

tag: day postimmunization


title: individual 76

description: exon expression data


title: individual 79

description: Gene expression data.


title: blood-d44 [II-B43]

source_name: blood, Ncf1, day 44 p.i.


title: individual 74

description: exon expression data


title: individual 73

description: exon expression data


title: individual 76

description: Gene expression data.


title: individual 78

description: Gene expression data.


title: blood-d15 [II-B11]

source_name: blood, Ncf1, day 15 p.i.


title: individual 86

description: Gene expression data.


title: individual 83

description: Gene expression data.


title: individual 82

description: Gene expression data.


title: individual 72

description: exon expression data


title: blood-d15 [II-B20]

source_name: blood, wt, day 15 p.i.


title: spleen-d44 [II-S57]

source_name: spleen, wt, day 44 p.i.

value: spleen


title: individual 85

description: Gene expression data.


title: individual 81

description: Gene expression data.


title: individual 84

description: Gene expression data.


title: individual 87

description: Gene expression data.


title: individual 70

description: exon expression data


title: individual 77

description: Gene expression data.


title: individual 69

description: exon expression data


title: spleen-d15 [II-S10]

source_name: spleen, Ncf1, day 15 p.i.


title: spleen-d15 [II-S12]


title: spleen-d44 [II-S53]


title: individual 78

description: exon expression data


title: blood-d44 [II-B52]


title: individual 74

description: Gene expression data.


title: individual 71

description: Gene expression data.


title: individual 70

description: Gene expression data.


title: individual 65

description: exon expression data


title: spleen-d44 [II-S46]

source_name: spleen, Ncf1, day 44 p.i.


title: individual 75

description: Gene expression data.


title: individual 72

description: Gene expression data.


title: individual 71

description: exon expression data


title: individual 67

description: exon expression data


title: individual 75

description: exon expression data


title: individual 60

description: exon expression data


title: spleen-d15 [II-S22]

source_name: spleen, wt, day 15 p.i.


title: spleen-d44 [II-S43]


title: spleen-d15 [II-S24]


title: individual 58

description: exon expression data


title: individual 59

description: exon expression data


title: blood-d15 [II-B9]


title: individual 66

description: Gene expression data.


title: individual 57

description: exon expression data


title: individual 67

description: Gene expression data.


title: spleen-d44 [II-S45]


title: individual 59

description: Gene expression data.


title: individual 56

description: exon expression data


title: spleen-d44 [II-S52]


title: individual 69

description: Gene expression data.


title: spleen-d15 [II-S23]


title: individual 65

description: Gene expression data.


title: individual 55

description: exon expression data


title: individual 73

description: Gene expression data.


title: individual 53

description: exon expression data


title: individual 54

description: exon expression data


title: blood-d15 [II-B17]


title: blood-d44 [II-B51]


title: individual 60

description: Gene expression data.


title: individual 45

description: exon expression data


title: blood-d44 [II-B56]


title: individual 57

description: Gene expression data.


title: individual 58

description: Gene expression data.


title: individual 44

description: exon expression data


title: individual 56

description: Gene expression data.


title: individual 54

description: Gene expression data.


title: individual 50

description: exon expression data


title: individual 55

description: Gene expression data.


title: blood-d44 [II-B41]


title: blood-d44 [II-B45]


title: individual 50

description: Gene expression data.


title: blood-d15 [II-B12]


title: blood-d44 [II-B55]


title: spleen-d15 [II-S11]


title: blood-d15 [II-B23]

source_name: blood, wt, day15 p.i.


title: individual 41

description: exon expression data


title: individual 52

description: Gene expression data.


title: individual 52

description: exon expression data


title: individual 45

description: Gene expression data.


title: individual 53

description: Gene expression data.


title: individual 38

description: exon expression data


title: individual 42

description: exon expression data


title: spleen-d44 [II-S56]


title: individual 44

description: Gene expression data.


title: spleen-d44 [II-S42]


title: individual 33

description: exon expression data


title: spleen-d15 [II-S16]


title: blood-d15 [II-B21]


title: individual 43

description: exon expression data


title: individual 37

description: exon expression data


title: individual 36

description: exon expression data


title: individual 29

description: exon expression data


title: individual 27

description: exon expression data


title: spleen-d15 [II-S21]


title: blood-d15 [II-B24]


title: blood-d44 [II-B46]


title: individual 42

description: Gene expression data.


title: individual 43

description: Gene expression data.


title: individual 41

description: Gene expression data.


title: individual 38

description: Gene expression data.


title: individual 32

description: exon expression data


title: individual 37

description: Gene expression data.


title: blood-d15 [II-B16]


title: individual 31

description: exon expression data


title: blood-d44 [II-B57]


title: individual 26

description: exon expression data


title: individual 23

description: exon expression data


title: individual 30

description: exon expression data


title: individual 33

description: Gene expression data.


title: spleen-d15 [II-S14]


title: individual 29

description: Gene expression data.


title: individual 27

description: Gene expression data.


title: individual 22

description: exon expression data


title: individual 31

description: Gene expression data.


title: individual 32

description: Gene expression data.


title: blood-d15 [II-B14]


title: individual 21

description: exon expression data


title: spleen-d15 [II-S20]


title: spleen-d44 [II-S55]


title: individual 30

description: Gene expression data.


title: individual 20

description: exon expression data


title: spleen-d44 [II-S44]


title: individual 23

description: Gene expression data.


title: individual 66

description: exon expression data


title: individual 26

description: Gene expression data.


title: individual 36

description: Gene expression data.


title: blood-d44 [II-B42]

source_name: blood,Ncf1, day 44 p.i.


title: individual 20

description: Gene expression data.


title: individual 22

description: Gene expression data.


title: individual 12

description: exon expression data


title: individual 13

description: exon expression data


title: blood-d15 [II-B10]


title: individual 19

description: exon expression data


title: spleen-d15 [II-S17]


title: blood-d15 [II-B22]


title: blood-d44 [II-B44]


title: individual 8

description: exon expression data


title: individual 16

description: Gene expression data.


title: individual 19

description: Gene expression data.


title: individual 15

description: Gene expression data.


title: individual 21

description: Gene expression data.


title: individual 15

description: exon expression data


title: individual 14

description: Gene expression data.


title: spleen-d44 [II-S51]


title: spleen-d15 [II-S9]


title: individual 16

description: exon expression data


title: individual 10

description: Gene expression data.


title: blood-d44 [I-B45]


title: individual 10

description: exon expression data


title: individual 14

description: exon expression data


title: individual 13

description: Gene expression data.


title: individual 7

description: exon expression data


title: Δnsd.N+_2

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed in employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003)

organism: Fusarium fujikuroi

source_name: F. fujikuroi delta-nsd, 60 mM Gln

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown for three days in Darken medium and subsequently an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine, or 6 mM NaNO3 and grown for additional three days on a rotary shaker (180 rpm) at 28 °C.

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany) and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: Mycelium was harvested after 72h, directly frozen with liquid nitrogen and lyophilized prior to RNA extraction

tag: treatment

value: 60 mM Gln


title: Δnsd.N-_1

source_name: F. fujikuroi delta-nsd, 6 mM Gln

value: 6 mM Gln


title: individual 6

description: exon expression data


title: Δnsd.N+_1


title: blood-d15 [I-B22]


title: blood-d44 [I-B43]


title: individual 12

description: Gene expression data.


title: Δnsd.N-_2


title: spleen-d44 [II-S41]


title: individual 8

description: Gene expression data.


title: blood-d15 [I-B23]


title: Δnsd.NO_1

source_name: F. fujikuroi delta-nsd, 6 mM NaNO3

value: 6 mM NaNO3


title: wt:N+_2

source_name: F. fujikuroi wildtype, 60 mM Gln


title: blood-d15 [I-B21]


title: individual 7

description: Gene expression data.


title: spleen-d44 [I-S39]


title: blood-d15 [I-B13]


title: spleen-d44 [I-S43]


title: spleen-d15 [I-S22]


title: blood-d15 [I-B18]


title: Δnsd.NO_2


title: individual 6

description: Gene expression data.


title: wt.NO_2

source_name: F. fujikuroi wildtype, 6 mM NaNO3


title: blood-d15 [I-B9]


title: spleen-d15 [I-S23]


title: blood-d15 [I-B19]


title: wt.N-_2

source_name: F. fujikuroi wildtype, 6 mM Gln


title: wt.N+_1


title: blood-d44 [I-B41]


title: spleen-d44 [I-S35]


title: spleen-d15 [I-S19]


title: wt.N-_1


title: blood-d44 [I-B44]


title: spleen-d44 [I-S37]


title: blood-d44 [I-B40]


title: spleen-d15 [I-S17]


title: spleen-d15 [I-S16]


title: blood-d44 [I-B39]


title: spleen-d15 [I-S14]


title: spleen-d15 [I-S21]


title: spleen-d44 [I-S34]


title: blood-d44 [I-B38]


title: spleen-d44 [I-S38]


title: spleen-d44 [I-S45]


title: wt.NO_1


title: spleen-d15 [I-S15]


title: blood-d15 [I-B15]


title: blood-d15 [I-B17]


title: spleen-d15 [I-S18]


title: blood-d15 [I-B16]


title: spleen-d44 [I-S40]


title: spleen-d44 [I-S44]


title: spleen-d44 [I-S41]


title: blood-d44 [I-B35]


title: blood-d44 [I-B37]


title: blood-d44 [I-B36]


title: blood-d44 [I-B34]


title: blood-d15 [I-B11]


title: spleen-d15 [I-S9]


title: DLD-1 diploid clone 3, passage 22

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

institute: IDIBAPS / Hospital Clinic

description:
C3_P22
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

hyb_protocol: Hybridization was carried out using Agilent-026652 4x44k v2 Human Gene Expression microarrays according to the protocol, one-color microarray-based gene expression version 6.9, July 2015.

scan_protocol: Slides were scanned with the DNA microarray scanner with SureScan High-Resolution Technology (Agilent Technologies).

data_processing: Signal data were collected with the dedicated software Agilent Feature Extraction (v9.5.1). Agilent Feature Extraction files were processed and normalized ('normexp' background correction and loess normalization) using Limma R package (v3.26.9) in R.3.2.3.

source_name: DLD-1 diploid clone C3, passage 22

label_protocol: Gene expression array was performed using verified RNA with a RIN above 8 as quantified using the Bioanalyzer. All RNA samples were labeled with Cy3 using the Low Input Quick Amp Labeling Kit.

growth_protocol: DLD-1 parental cells and all subsequent clones were grown in RPMI-1640 media supplemented in 10% FBS, antibiotics and glutamine at 37°C in 5% CO2.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen, CA, USA).

treatment_protocol: Single cells were generated using FACS into 96-well plates based on size differences (i.e., forward scatter).

tag: parental cell line

tag: parental cell type

value: colorectal cell line

tag: cell type

value: epithelial cells

tag: ploidy

value: diploid

tag: clone

value: C3, passage 22


title: spleen-d15 [I-S13]

tag: tissue


title: Repeat of DLD-1 diploid clone 6

description:
C6_2
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C6


title: Repeat of DLD-1 diploid clone 1

description:
C1_R
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C1


title: Repeat of DLD-1 diploid clone 4

description:
C4_2
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C4


title: areb.100GLN_1

source_name: F. fujikuroi ΔAREB, 60 mM Gln

growth_protocol: Strains were grown for three days in Darken medium and subsequently an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional three days on a rotary shaker (180 rpm) at 28 °C.

value: mycelia

value: delta AreB

tag: nitrogen status

value: high


title: DLD-1 diploid clone 1

description:
C1
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: blood-d15 [I-B14]

source_name: blood, wt, day 15 p.i.


title: DLD-1 diploid clone 4

description:
C4_1
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: areb.100GLN_2


title: spleen-d44 [I-S33]


title: spleen-d44 [I-S36]

source_name: spleen, wt, day 44 p.i.


title: DLD-1 tetraploid clone C28 late passage

type: genomic

description:
C28_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

hyb_protocol: Hybridization was carried out using the Agilent-022060 SurePrint G3 Human CGH 4x180k microarray at 65°C for 40 hours.

data_processing: Limma R package (v3.26.9) was used for 'normexp' background correction and loess normalization in R.3.2.3.

molecule: genomic DNA

source_name: DLD-1 tetraploid clone C28 late passage

label_protocol: Sample DNA from the single-cell clones were labeled with Cy3-dUTP, and reference DNA (Promega, Madison, WI, catalog: G1471) were labeled with Cy5-dUTP using the BioPrime Array CGH genomic labeling module (Life Technologies, Carlsbad, CA).

extract_protocol: DNA was extracted using the QIAprep spin miniprep kit (Qiagen, CA, USA).

value: tetraploid

value: C28, late passage

source_name: Promega reference DNA

extract_protocol: Promega reference DNA (cat. G1471)

tag: sample type

value: reference


title: DLD-1 tetraploid clone B4 late passage

description:
B4_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B4 late passage

value: B4, late passage


title: DLD-1 diploid clone 6

description:
C6_1
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

value: male


title: areb.10GLN_1

source_name: F. fujikuroi ΔAREB, 6 mM Gln

value: low


title: areb.10GLN_2


title: DLD-1 tetraploid clone B8 late passage

description:
B8_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B8 late passage

value: B8, late passage


title: DLD-1 tetraploid clone B12 late passage

description:
B12_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B12 late passage

value: B12, late passage


title: DLD-1 tetraploid clone B9 late passage

description:
B9_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B9 late passage

value: B9, late passage


title: area.100GLN_2

source_name: F. fujikuroi ΔAREA, 60 mM Gln

value: delta AreA


title: DLD-1 tetraploid clone C28, passage 7

description:
C28_P7
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone C28, passage 7

value: colorectal cell line

value: C28, passage 7


title: spleen-d15 [I-S11]

source_name: spleen, Ncf1, day 15 p.i.

value: spleen


title: blood-d44 [I-B33]

source_name: blood, Ncf1, day 44 p.i.

value: blood


title: wt.100GLN_1

source_name: F. fujikuroi wildtype, 60 mM Gln

value: mycelia

value: wildtype


title: area.100GLN_1

value: high


title: Repeat of DLD-1 tetraploid clone C28, passage 33

description:
C28_P33_R
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone C28, passage 33

value: epithelial cells

value: tetraploid

value: C28, passage 33


title: DLD-1 diploid clone 3, passage 15

description:
C3_P15
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C3, passage 15

value: diploid

value: C3, passage 15


title: area.10GLN_1

source_name: F. fujikuroi ΔAREA, 6 mM Gln

value: low


title: DLD-1 diploid clone C2 late passage

description:
C2_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C2 late passage

value: male

value: C2, late passage

value: reference


title: DLD-1 tetraploid clone B16

description:
B16_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B16


title: DLD-1 tetraploid clone B21

description:
B21_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B21


title: DLD-1 diploid clone C1 late passage

description:
C1_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C1 late passage

value: C1, late passage

source_name: Promega reference DNA


title: DLD-1 tetraploid clone B4

description:
B4
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B4

value: colorectal cell line


title: DLD-1 tetraploid clone C28, passage 33

description:
C28_P33
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: wt.10GLN_1

source_name: F. fujikuroi wildtype, 6 mM Gln


title: DLD-1 diploid clone C3 late passage

description:
C3_late
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C3 late passage

value: C3, late passage


title: Repeat of DLD-1 tetraploid clone B9

description:
B9_R
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B9


title: DLD-1 tetraploid clone C28

description:
C28_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone C28


title: wt.10GLN_2


title: Repeat of DLD-1 tetraploid clone B8

description:
B8_R
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B8


title: DLD-1 tetraploid clone B3

description:
B3
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B3


title: DLD-1 tetraploid clone B11

description:
B11_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B11


title: DLD-1 tetraploid clone B6

description:
B6
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B6


title: area.10GLN_2

value: delta AreA


title: wt.100GLN_2

source_name: F. fujikuroi wildtype, 60 mM Gln


title: Repeat of DLD-1 tetraploid clone B4

description:
B4_R
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B8

description:
B8
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B21

description:
B21
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B12

description:
B12_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B12


title: DLD-1 tetraploid clone B19

description:
B19_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B19


title: DLD-1 tetraploid clone B9

description:
B9
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B19

description:
B19
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B8

description:
B8_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B9

description:
B9_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B16

description:
B16
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 tetraploid clone B11

description:
B11
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: cell_isolated_E15_rep2

status: Public on May 09 2017

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: Gene expression data from a single developing chick retinal cell

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip Chicken arrays using standard Affymetrix protocols at either the GeneChip Facility at Iowa State University or the University of Iowa.

scan_protocol: Affymetrix GeneChip Chicken arrays were scanned using standard protocols at either the GeneChip Facility at Iowa State University or the University of Iowa.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Gallus gallus

source_name: E15 chicken retina

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

growth_protocol: Retinas were dissected and disocciated with papain at different timepoints. There was no culture or time for growth.

extract_protocol: Individual chicken retinal cells were harvested using a pulled glass pipette and were expelled into cold lysis buffer. The total single cell RNA was reverse transcribed using Superscript III combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

treatment_protocol: Single cells were isolated and immediately placed into cell lysis buffer.

value: dissociated retina

tag: time point


title: DLD-1 tetraploid clone B6

description:
B6_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: cell_isolated_E4_rep1

source_name: E4 chicken retina


title: cell_isolated_E14_rep6

source_name: E14 chicken retina


title: cell_isolated_E14_rep2


title: DLD-1 diploid clone C2

description:
C2_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C2


title: cell_isolated_E14_rep4


title: cell_isolated_E14_rep8


title: DLD-1 tetraploid clone B12

description:
B12
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: DLD-1 diploid clone C1

description:
C1_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C1

source_name: Promega reference DNA


title: cell_isolated_E14_rep7


title: DLD-1 tetraploid clone B4

description:
B4_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B4


title: DLD-1 tetraploid clone B3

description:
B3_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.


title: cell_isolated_E9_rep3

source_name: E9 chicken retina


title: DLD-1 tetraploid clone B7

description:
B7_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 tetraploid clone B7


title: cell_isolated_E14_rep1


title: cell_isolated_E9_rep6


title: cell_isolated_E14_rep5


title: cell_isolated_E9_rep4


title: DLD-1 diploid clone C3

description:
C3_early
Epithelial adherent cell line from Dukes' type C, colorectal adenocarcinoma.

source_name: DLD-1 diploid clone C3


title: cell_isolated_E9_rep1


title: cell_isolated_E6_rep9

source_name: E6 chicken retina


title: cell_isolated_E9_rep5


title: cell_isolated_E15_rep3


title: cell_isolated_E6_rep8


title: cell_isolated_E6_rep7


title: cell_isolated_E9_rep2


title: cell_isolated_E6_rep6


title: cell_isolated_E7_rep1

source_name: E7 chicken retina


title: cell_isolated_E6_rep10


title: cell_isolated_E5_rep2

source_name: E5 chicken retina


title: cell_isolated_E6_rep5


title: cell_isolated_E6_rep2


title: cell_isolated_E3_rep3

source_name: E3 chicken retina


title: cell_isolated_E3_rep6


title: cell_isolated_E5_rep5


title: cell_isolated_E3_rep4


title: cell_isolated_E6_rep4


title: cell_isolated_E5_rep4


title: cell_isolated_E4_rep2


title: cell_isolated_E6_rep1


title: cell_isolated_E5_rep1


title: cell_isolated_E14_rep3


title: cell_isolated_E6_rep3


title: cell_isolated_E3_rep5


title: cell_isolated_E5_rep3


title: liver Cdk10KO

city: Singapore

first: Hyungwon

last: Choi

address: 14 Medical Drive, MD6 #08-01

country: Singapore

institute: National University of Singapore

hyb_protocol: Hybridization was in accordance with the Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: The chips were scanned using the BeadArray Reader 500X.

data_processing: The raw data was processed using the standard options in GenomeStudio (v1.9). Raw expression data exhibitied clear organ specific expression patterns and thus the data was log transformed (based 2) and no further normalization was applied. Differential expression analysis was performed with log2 transformed transcript-level intensity data within each organ, using EBprot software (https://sourceforge.net/projects/ebprotv2/).

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).

extract_protocol: RNA from kidney, lung, heart, brain, stomach, intestine, thymus and liver was isolated using Life Technologies' PureLink RNA mini kit. cRNA was prepared with Illumina(r) TotalPrep RNA kit according to the manufacturer's protocol.

tag: strain background

tag: genotype/variation

tag: age

value: liver


title: cell_isolated_E3_rep1


title: lung Cdk10KO

value: lung


title: liver WT

source_name: wild type_P0

value: wild type


title: intestine WT

value: intestine


title: cell_isolated_E3_rep2


title: stomach Cdk10KO

value: stomach


title: thymus WT

value: thymus


title: intestine Cdk10KO


title: lung WT


title: stomach WT


title: heart Cdk10KO

value: heart


title: thymus Cdk10KO


title: kidney WT

value: kidney


title: brain Cdk10KO

value: brain


title: heart WT


title: kidney Cdk10KO


title: brain WT


title: npr-1_neurons_24.5-28hr

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

institute: UCSF

description: a fluorescence read above 5000 intensity units in at least one npr1 sample

hyb_protocol: Labeled cRNA was hybridized to the Agilent C. elegans (V2) Gene Expression Microarray, 4x44K (design 020186, Agilent Technologies, USA) for 17 hours at 65°c in an Agilent DNA-Microarray Hybridization Oven. The arrays were later washed using the Gene Expression Wash Buffer Kit.

scan_protocol: The Microarray was scanned using the Agilent High-Resolution Microarray Scanner and the data was extracted from the resulting images using the Feature Extraction 10.7 software.

data_processing: The resulting txt files have been analyzed utilizing custom written programs in MATLAB R2013A, using routines from the Bioinformatics and Statistical toolbox.  In every individual array from a specific time point the columns of median Cy3 and Cy5 were selected and the corresponding median background of Cy3 and Cy5 was subtracted. Averaging was carried out on the 45,220 probes of the array (using the consolidation function of Microsoft Excel). This resulted in 21,268 genes in every array. Lowess normalization was carried out and flooring was performed on each of the 2 columns, set to 20 measurements. To enrich for abundant transcripts and robust changes in expression levels, data was filtered by raw data read values, requiring minimal value in at least one sample as described in the description column.

organism: Caenorhabditis elegans

label_protocol: For each sample 10 ng of purified mRNA were amplified and labeled with fluorescent dyes (Cy3 or Cy5) using the Low RNA Input Linear Amplification & Labeling kit (Agilent).

growth_protocol: To synchronize worms, we collected embryos from gravid hermaphrodites as described previously (Brenner, 1974). The collected embryos were then rotated in M9 buffer for 16 h at 21°C. We placed approximately 4800 synchronized L1 larvae in twelve 3.5 cm NGM plates seeded with 250 µl OP50 and grown them for 3 days until they reached the L4 larval stage (the 0 time point).

extract_protocol: Worms were washed 3 times with PBS and once with homogenization buffer (HB; 150 mM NaCl, 50 mM phosphate buffer pH 7.2, 1 mM EGTA, 15 mM EDTA, 0.6 mg/ml heparin sodium salt, 10% v/v glycerol, RNAsin, 1 mM DTT, 0.5% v/v Igepal (Sigma, #18896), 1:100 protease inhibitors cocktail (Sigma, #P2714). HB was treated with 1:1000 DEPC, and then RNAse free heparin sodium salt was added). Worms were resuspended in HB and homogenized using Bullet Blender (Next Advance) according to manufacturer's protocol. Worm debris was removed by centrifugation at 17,000xg for 20 min. To equilibrate the anti-FLAG beads, we washed them twice with 1 ml of 0.1M glycine, pH 3.5, following 4 washes with 500 µl of HB. All centrifuges of beads were performed at 100xg, 4°C for 3 min. We incubated amount of lysate equivalent to 50 ng of protein with 50 µl of equilibrated beads for 2 h at 4°C, then centrifuged and removed the unbound material. Beads were washed three times with 500 µl of low-salt HB buffer (LSHB; 25 mM NaCl, 20 mM phosphate buffer pH 7.2, 1 mM EGTA, 1 mM EDTA, 0.6 mg/ml heparin sodium salt, 10% v/v glycerol, RNAsin, 1mM DTT, 0.5% v/v Igepal, 1:100 protease inhibitors cocktail (Sigma, #P2714). LSHB was DEPC treated like HB). Beads were incubated with 500 µl of LSHB for 30 min. at 4°C with agitation. To elute precipitated mRNA, beads were incubated with 125 µl Trizol at 65°C for 30 min. with rotation. Elution was repeated with 15-min. incubation. Resulted RNA was purified with RNeasy minelute cleanup kit (Qiagen, #74204) following manufacturer's protocol with one change: to elute RNA, column was incubated for 1 minute with 10mM Tris pH 7.0 preheated to 65°C. The quality of precipitated mRNA was estimated using Bioanalyzer (Agilent).

treatment_protocol: The plates were put in the hypoxia chamber, 1% O2, RT. We collected the worms after 3 and 6 h exposure to 1% O2 (the 3 and 6 h time points, respectively). After 24 h in 1% O2, we placed the remaining plates in 21% O2. We collected the worms after 30 min and 4 h incubation in 21% O2 (the 24.5 h and 28 h time points, respectively). Worms were collected from plates by washing the plates 3 times with ice-cold phosphate-buffered saline (PBS, pH 7.4 supplemented with 1mM MgSO4). The resulted worm pellet was washed for additional 3 times with PBS. To crosslink mRNA with FLAG-PAB-1 in vivo, worms were treated with 1% paraformaldehyde (PFA) in PBS for 1 hour on ice with occasional agitation.

tag: strain

tag: developmental stage

value: Adult

tag: specificity

value: neurons

tag: time-point


title: glb-5;npr-1/npr-1_neurons_24hr

description: a fluorescence read above 1000 intensity units in at least one npr1 or glb5 sample


title: glb-5;npr-1_gut_0-3hr

description: a fluorescence read above 5000 intensity units in at least one gut sample

value: gut


title: glb-5;npr-1_gut_24.5-28hr


title: glb-5;npr-1_gut_6-24.5hr


title: glb-5;npr-1_neurons/gut_24hr

description: a fluorescence read above 1000 intensity units in at least one neuro or gut sample


title: npr-1_neurons_6-24.5hr


title: glb-5;npr-1_neurons/gut_3hr


title: glb-5;npr-1_gut_3-6hr


title: glb-5;npr-1/npr-1_neurons_3hr


title: npr-1_neurons_3-6hr


title: glb-5;npr-1_neurons_24.5-28hr

description: a fluorescence read above 5000 intensity units in at least one glb5 sample


title: T47D_JQ1_Rep3

status: Public on May 08 2017

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

institute: IDIBELL

description:
Gene expression after JQ1 treatment 1uM 24h
Cell line, T47D JQ1, replicate 3

hyb_protocol: Hybridization, washing and staining were performed using Agilent system instruments and protocols.

scan_protocol: After washing, microarrays were scanned using an Agilent microarray scanner (Agilent Technologies).

data_processing: Intensity values of each scanned feature were quantified using Agilent Feature Extraction Software. Background correction and quantile array normalization was performed using limma library in R software.

source_name: T47D JQ1

label_protocol: The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using Agilent protocol.

extract_protocol: RNA was extracted using Maxwell ® RSC simply RNA Cell Kit (Promega) following the manufacturer's recommendations

treatment_protocol: Cells were treated with 1uM JQ1 or vehicle (DMSO) and incubated for 24 hours at 37ºC in a humidified incubator with 5%

tag: cell line

tag: agent


title: T47D_JQ1_Rep2

description:
Gene expression after JQ1 treatment 1uM 24h
Cell line, T47D JQ1, replicate 2


title: glb-5;npr-1_neurons_6-24.5hr


title: glb-5;npr-1_neurons_0-3hr


title: npr-1_neurons_0-3hr


title: MCF7_JQ1_Rep3

description:
Gene expression after JQ1 treatment 1uM 24h
Cell line, MCF7 JQ1, replicate 3

source_name: MCF7 JQ1


title: T47D_JQ1_Rep1

description:
Gene expression after JQ1 treatment 1uM 24h
Cell line, T47D JQ1, replicate 1


title: MCF7_JQ1_Rep2

description:
Gene expression after JQ1 treatment 1uM 24h
Cell line, MCF7 JQ1, replicate 2


title: T47D_vehicle_Rep3

description:
Gene expression after vehicle (DMSO) treatment 24h
Cell line, T47D vehicle, replicate 3

source_name: T47D vehicle

value: vehicle


title: MCF7_vehicle_Rep2

description:
Gene expression after vehicle (DMSO) treatment 24h
Cell line, MCF7 vehicle, replicate 2

source_name: MCF7 vehicle


title: Macrophage M-CSF +MTX replicate 1 [M2 r1 +50nM MTX]

first: Amaya

last: Puig

address: Dr. Esquerdo 46

department: Immunology

institute: Hospital Gregorio Marañón

hyb_protocol: Standard Agilent protocols

scan_protocol: Scanned on an Agilent DNA Microarray Scaner (G2565BA)

data_processing: Scanned images and raw data were pre-processed with GeneSpring v12 (Agilent).

source_name: M-CSF +MTX Macrophage

label_protocol: 2 ug of total RNA was used to obtain cRNA. 10 ug of cRNA was labeled with Cy5-Streptavidin. All experimental procedures were performed following manufacturer instructions. Now available in http://appliedmicroarrays.com/pdf/codelink_16-assay.pdf

growth_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FCS containing either GM-CSF or M-CSF, and after an initial exposure (at day 0) to 50 nanomolar MTX

extract_protocol: Total RNA from each condition was extracted and purified using the RNasey kit (Qiagen).Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Cells were were treated with GM-CSF (1000 U/ml) or M-CSF (10 ng/ml) every 48 hours

tag: donor id

value: peripheral blood monocytes

tag: cell subtype

value: CD14+ monocytes

tag: exposed to

value: M-CSF +50 nanomolar methotrexate (MTX)


title: glb-5;npr-1_neurons_3-6hr


title: Macrophage GM-CSF replicate 1  [M1 r1-]

source_name: GM-CSF Macrophage

tag: cell type

value: GM-CSF


title: MCF7_JQ1_Rep1

description:
Gene expression after JQ1 treatment 1uM 24h
Cell line, MCF7 JQ1, replicate 1


title: Macrophage GM-CSF replicate 3 [M1 r3-]


title: Macrophage M-CSF replicate 2 [M2 r2-]

source_name: M-CSF Macrophage

value: M-CSF


title: Macrophage GM-CSF replicate 2 [M1 r2-]


title: Macrophage GM-CSF +MTX replicate 3 [M1 r3 +50nM MTX]

source_name: GM-CSF +MTX Macrophage

value: GM-CSF +50 nanomolar methotrexate (MTX)


title: MCF7_vehicle_Rep1

description:
Gene expression after vehicle (DMSO) treatment 24h
Cell line, MCF7 vehicle, replicate 1


title: Macrophage M-CSF +MTX replicate 3 [M2 r3 +50nM MTX]


title: Macrophage M-CSF replicate 1 [M2 r1-]


title: Macrophage GM-CSF +MTX replicate 2 [M1 r2 +50nM MTX]


title: MCF7_vehicle_Rep3

description:
Gene expression after vehicle (DMSO) treatment 24h
Cell line, MCF7 vehicle, replicate 3


title: T47D_vehicle_Rep1

description:
Gene expression after vehicle (DMSO) treatment 24h
Cell line, T47D vehicle, replicate 1


title: Macrophage M-CSF replicate 3 [M2 r3-]


title: T47D_vehicle_Rep2

description:
Gene expression after vehicle (DMSO) treatment 24h
Cell line, T47D vehicle, replicate 2


title: Macrophage GM-CSF +MTX replicate 1 [M1 r1 +50nM MTX]


title: Macrophage M-CSF +MTX replicate 2 [M2 r2 +50nM MTX]