title: Halobacterium H2O2 exposure experiment, Array 9029

description: No H2O2 control sample grown in standard conditions and sampled 40 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

source_name: Halobacterium NRC1, no H2O2 control, 40 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 40 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 40 minutes post mock EMS treatment


title: Halobacterium H2O2 exposure experiment, Array 9082

status: Public on Jan 03 2008

type: RNA

city: Seattle

first: Marc

last: Facciotti

state: WA

address: 1441 North 34th Street

country: USA

institute: Institute for Systems Biology

description: H2O2 treated sample grown in standard conditions and sampled 0 minutes post H2O2 treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-51

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

label: Alexa 547

molecule: total RNA

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC1, EMS treated sample 0 minutes post H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 50mM H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 0 minutes post 30min H2O2 treatment.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

label: Alexa 647

source_name: Standard mid-log Halobacterium NRC-1 reference sample.

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.

tag: Halobacterium NRC-1 grown in standard growth media


title: Halobacterium H2O2 exposure experiment, Array 9084

description: H2O2 treated sample grown in standard conditions and sampled 10 minutes post H2O2 treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-53

source_name: Halobacterium NRC1, EMS treated sample 10 minutes post H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 50mM H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 10 minutes post 30min H2O2 treatment.


title: Halobacterium H2O2 exposure experiment, Array 9085

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54

tag: H2O2 treated sample grown in standard conditions and sampled 10 minutes post H2O2 treatment


title: Halobacterium H2O2 exposure experiment, Array 9043

description: No H2O2 control sample grown in standard conditions and sampled 60 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-47

label: Alexa 532

source_name: Halobacterium NRC1, no H2O2 control, 60 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 60 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 60 minutes post mock EMS treatment


title: Halobacterium H2O2 exposure experiment, Array 9045

description: No H2O2 control sample grown in standard conditions and sampled 120 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-49

source_name: Halobacterium NRC1, no H2O2 control, 120 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 120 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 120 minutes post mock EMS treatment


title: Halobacterium H2O2 exposure experiment, Array 9044

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-48


title: Halobacterium H2O2 exposure experiment, Array 9027

description: No H2O2 control sample grown in standard conditions and sampled 30 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-42

source_name: Halobacterium NRC1, no H2O2 control, 30 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 30 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 30 minutes post mock EMS treatment


title: Halobacterium H2O2 exposure experiment, Array 9041

description: No H2O2 control sample grown in standard conditions and sampled 50 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-45

source_name: Halobacterium NRC1, no H2O2 control, 50 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 50 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 50 minutes post mock EMS treatment


title: Halobacterium H2O2 exposure experiment, Array 9026

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-41


title: Halobacterium H2O2 exposure experiment, Array 9025

description: No H2O2 control sample grown in standard conditions and sampled 20 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

source_name: Halobacterium NRC1, no H2O2 control, 20 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 20 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 20 minutes post mock EMS treatment


title: Halobacterium H2O2 exposure experiment, Array 9006

description: No H2O2 control sample grown in standard conditions and sampled 0 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

source_name: Halobacterium NRC1, no H2O2 control, 0 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 0 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 0 minutes post mock EMS treatment


title: Halobacterium H2O2 exposure experiment, Array 9022

description: No H2O2 control sample grown in standard conditions and sampled 10 minutes post mock H2O2 treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37

source_name: Halobacterium NRC1, no H2O2 control, 10 minutes post mock H2O2 dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of H2O2, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 10 minutes post 30min mock H2O2 treatment.

tag: No H2O2 control sample grown in standard conditions and sampled 10 minutes post mock EMS treatment


title: Halobacterium NRC-1 dark diurnal experiment 1, 16.0 hours post entrainment, Array 7367

description: Halobacterium NRC-1 dark diurnal experiment 1, 16.0 hours post entrainment versus standard reference.

source_name: Halobacterium NRC-1 dark diurnal experiment 1, 16.0 hours post entrainment.

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

growth_protocol: Halobacterium NRC-1 were grown in aerobic conditions (shaking at 100RPM) at 42degrees C  and entrained for 72 hours with 12:12hr light:dark cycle at a light intensity of 150µE/M^2/sec. and sampled in darkness16.0 minutes post entrainment.

tag: Halobacterium NRC-1 dark diurnal experiment 1 with cells grown at 42degrees C in aerobic conditions and entrained for 72 hours with 12:12hr light:dark cycle and sampled in darkness.0_h hours post entrainment.

tag: Halobacterium NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).


title: Halobacterium H2O2 exposure experiment, Array 9028

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-43


title: Halobacterium H2O2 exposure experiment, Array 9024

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39


title: Halobacterium EMS exposure experiment, Array 8188

description: EMS treated sample grown in standard conditions and sampled 40 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-60

source_name: Halobacterium NRC1, EMS treated sample 40 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 40 minutes post 30min EMS treatment.

label: Alexa 546


title: Halobacterium EMS exposure experiment, Array 8192

description: EMS treated sample grown in standard conditions and sampled 50 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-62

source_name: Halobacterium NRC1, EMS treated sample 50 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 50 minutes post 30min EMS treatment.


title: Halobacterium EMS exposure experiment, Array 8194

description: EMS treated sample grown in standard conditions and sampled 60 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-64

source_name: Halobacterium NRC1, EMS treated sample 60 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 60 minutes post 30min EMS treatment.


title: Halobacterium H2O2 exposure experiment, Array 9021

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36


title: Halobacterium EMS exposure experiment, Array 8196

description: EMS treated sample grown in standard conditions and sampled 120 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-66

source_name: Halobacterium NRC1, EMS treated sample 120 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 120 minutes post 30min EMS treatment.


title: Halobacterium H2O2 exposure experiment, Array 9023

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38


title: Halobacterium EMS exposure experiment, Array 8187

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-59

tag: EMS treated sample grown in standard conditions and sampled 40 minutes post EMS treatment


title: Halobacterium EMS exposure experiment, Array 8189

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-61

tag: EMS treated sample grown in standard conditions and sampled 50 minutes post EMS treatment


title: Halobacterium EMS exposure experiment, Array 8186

description: EMS treated sample grown in standard conditions and sampled 30 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-58

source_name: Halobacterium NRC1, EMS treated sample 30 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 30 minutes post 30min EMS treatment.


title: Halobacterium EMS exposure experiment, Array 8184

description: EMS treated sample grown in standard conditions and sampled 20 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-56

source_name: Halobacterium NRC1, EMS treated sample 20 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 20 minutes post 30min EMS treatment.


title: Halobacterium EMS exposure experiment, Array 8193

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-63

tag: EMS treated sample grown in standard conditions and sampled 60 minutes post EMS treatment


title: Halobacterium EMS exposure experiment, Array 8195

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-65

tag: EMS treated sample grown in standard conditions and sampled 120 minutes post EMS treatment


title: U937 cells treated with mild hyperthermia (treatment-1)

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: Human lymphoma U937 cells were treated with mild hyperthermia (41°C for 30 min) and followed by incubation for 3 h at 37°C.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: biotin

organism: Homo sapiens

source_name: Human lymphoma U937 cells

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: Human lymphoma U937 cells

tag: mild hyperthermia


title: Halobacterium EMS exposure experiment, Array 8181

description: EMS treated sample grown in standard conditions and sampled 10 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54

source_name: Halobacterium NRC1, EMS treated sample 10 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 10 minutes post 30min EMS treatment.

source_name: Standard mid-log Halobacterium NRC-1 reference sample.

tag: Halobacterium NRC-1 grown in standard growth media


title: U937 cells treated with mild hyperthermia (control-2)

description: Human lymphoma U937 cells were cultured at 37°C (non-treatment; control).

tag: control


title: U937 cells treated with mild hyperthermia (treatment-2)


title: Halobacterium EMS exposure experiment, Array 8185

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-57

tag: EMS treated sample grown in standard conditions and sampled 30 minutes post EMS treatment

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.


title: Halobacterium EMS exposure experiment, Array 8179

description: EMS treated sample grown in standard conditions and sampled 0 minutes post EMS treatment versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-52

source_name: Halobacterium NRC1, EMS treated sample 0 minutes post EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the presence of 100mM EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 0 minutes post 30min EMS treatment.


title: Samples from Pool L2 Shrimp were exposed to thermal stress and then Sampled at T2 (Hyb 24 Cy5)

city: Charleston

first: Enrique

last: de la Vega

state: SC

address: 331 Fort Johnson Road

department: Biochemistry

institute: Medical University of South Carolina

description: Samples from Pool L2. Shrimp were exposed to thermal stress and then sampled at T2

hyb_protocol: Human Cot1 DNA [(10 μg), (Invitrogen)], and 2 μg of poly dA (Roche) were added to the purified probe mix and dried prior to resuspending in 30 μl of 4X SSC (0.6 M sodium chloride and 60 mM sodium citrate), 40% deionized formamide and 0.1% sodium dodecyl sulfate (SDS). Following incubation at 95°C for 5 min, and then 45°C for 90 min, the labelled probe mix was loaded onto the microarray chip, and hybridisation was carried out for 16 h at 45°C. Following hybridisation, the microarray chip was washed twice with 0.2X SSC, 0.05% SDS and 2 more times with 0.2X SSC. Slides were finally dried by centrifugation at 600 rpm for 5 min.

scan_protocol: Cy3 and Cy5 fluorescence hybridized to the cDNA elements spotted onto the microarray chip was detected with a GMS 418 Array Scanner (Genetic Microsystems) using Imagene 4.2 software (BioDiscovery, Inc.) and the default parameters.

data_processing: Only genes with a signal to noise ratio (computed by dividing the backgroundcorrected intensities by the standard deviation of the background pixels) greater than 1.0, scored in both dyes and with at least 24 readings across the 24 slides were used in this study. The VALUE data included in this table was calculated by base-2 logarithm transforming (Log2) the value obtained by subtracting signal_median - background_median. Signal intensities were base-2 logarithm (log2) transformed and normalized by a multivariate mixed-model approach as previously described (Reverter et. al. 2005. Bioinformatics 21: 1112-1120) using the following equation: Only genes with a signal to noise ratio (computed by dividing the backgroundcorrected intensities by the standard deviation of the background pixels) greater than 1.0, scored in both dyes and with at least 24 readings across the 24 slides were used in this study. Signal intensities were base-2 logarithm (log2) transformed and normalized by a multivariate mixed-model approach as previously described (Reverter et. al. 2005. Bioinformatics 21: 1112-1120) using the following equation. yE = XEßE + ZE1cE + ZE2aE + ZE3dE + ZE4tE + eE Where: y is the vector of all the intensity signals (N= 202 636), background corrected and base-2 log transformed X is the incidence matrix relating signals in y with systematic fixed effects in ß including array slide, printing block and fluorescent dye channel ZE1 is the incidence matrix relating y with random effects in c corresponding to the clones (N= 2841) printed on the array that passed the filtering criteria ZE2 is the incidence matrix relating y with random effects in a corresponding to the three-way interaction of clone by array and printing block ZE3 is the incidence matrix relating y with random effects in d corresponding to the interaction of clone by the two fluorescent dye channels ZE4 is the incidence matrix relating y with random effects in t corresponding to the interaction of clone by the 12 experimental treatment conditions e is the random error associated with signals in y. The variance components were estimated by restricted maximum likelihood (REML) using VCE 4 software (available at Eildert Groeneveld's web page at the Institute for Animal Breeding Mariensee). The fitting of the above model provided BLUP (Best Linear Unbiased Prediction) solutions that were the basis for the normalization methods.

organism: Penaeus monodon

source_name: hemocytes from Penaeus monodon exposed to environmental stressors

label_protocol: cDNA labeling was performed as previously described (Woods et al. 2004, Development 131: 2921-2933). Amplified RNA (2μg) were reverse transcribed using an oligo dT18 primer (50 μM), 1.25 mM dNTP mix (Biotech International) with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma), 10 mM dithiothreitol (DTT), 600 units of Superscript III ® (Invitrogen), and 60 units of RNAse out (Invitrogen) in a 30 μl reaction volume. RNA was hydrolyzed by the addition of 3 μl of 1 M NaOH and 3 μl of 0.5 M ethylene-diamine-tetraacetate (EDTA) followed by heating to 65°C for 15 min. The solution was neutralized by the addition of 3 μl of 1 M HCl. Following synthesis, aminoallyllabeled cDNA (aa-cDNA) was purified using the Millipore Montage PCR cleanup kit following the manufacturer’s instructions, dried down and the pellet resuspended in 4.5 μl of freshly prepared 100 mM sodium carbonate (pH 9.0). A total of 100 ng of Cy3 or Cy5 reactive dyes (resuspended in 4.5 μl DMSO) (Amersham) were added to the respective aa-cDNAs and the coupling reaction allowed to proceed at room temperature for 1.5 h in the dark. Unincorporated dyes were removed from the reaction by the addition of 4 M hydroxylamine. Cy3- and Cy5-labelled cDNA was then combined and purified using a Qiagen QIAquick PCR cleanup kit

extract_protocol: Total RNA was extracted from haemocytes by homogenisation in Trizol-LS(Life Technologies) and then amplified using the Message Amp II® aRNA amplification kit (Ambion®) following the manufacturer’s instructions for one-round amplification.

tag: Samples used in this experiment came from hemocytes of juvenile Penaeus monodon originating from a hatchery in North Queensland, Australia. This hatchery uses wild caught broodstock for its operation.


title: Halobacterium EMS exposure experiment, Array 8180

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-53

tag: EMS treated sample grown in standard conditions and sampled 10 minutes post EMS treatment


title: Halobacterium EMS exposure experiment, Array 8183

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-55

tag: EMS treated sample grown in standard conditions and sampled 20 minutes post EMS treatment


title: Samples from Pool A Shrimp immediately after acclimation and before any stress (Hyb 24 Cy3)

description: Samples from Pool A. Shrimp immediately after acclimation and before any stress


title: Samples from Pool K2 Shrimp exposed to thermal stress and Sampled at T3 (Hyb 23 Cy5)

description: Samples from Pool K2. Shrimp exposed to thermal stress and sampled at T3


title: Samples from Pool L2 Shrimp exposed to thermal stress and Sampled at T2 (Hyb 23 Cy3)

description: Samples from Pool L2. Shrimp exposed to thermal stress and sampled at T2


title: Halobacterium EMS exposure experiment, Array 8178

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-51

tag: EMS treated sample grown in standard conditions and sampled 0 minutes post EMS treatment


title: U937 cells treated with mild hyperthermia (control-1)


title: Samples from Pool H2 Shrimp exposed to hypoxic stress and Sampled at T3 (Hyb 20 Cy5)

description: Samples from Pool H2. Shrimp exposed to hypoxic stress and sampled at T3


title: Samples from Pool J2 Shrimp exposed to thermal stress and Sampled at T4 (Hyb 21 Cy3)

description: Samples from Pool J2. Shrimp exposed to thermal stress and sampled at T4


title: Halobacterium EMS exposure experiment, Array 8177

description: No EMS control sample grown in standard conditions and sampled 120 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-50

source_name: Halobacterium NRC1, no EMS control, 120 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 120 minutes post 30min mock EMS treatment.


title: Halobacterium EMS exposure experiment, Array 8175

description: No EMS control sample grown in standard conditions and sampled 60 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-48

source_name: Halobacterium NRC1, no EMS control, 60 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 60 minutes post 30min mock EMS treatment.


title: Samples from Pool I2 Shrimp exposed to hypoxic stress and Sampled at T4 (Hyb 21 Cy5)

description: Samples from Pool I2. Shrimp exposed to hypoxic stress and sampled at T4


title: Samples from Pool J2 Shrimp exposed to thermal stress and Sampled at T4 (Hyb 22 Cy5)


title: Halobacterium EMS exposure experiment, Array 8176

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-49

tag: No EMS control sample grown in standard conditions and sampled 120 minutes post mock EMS treatment


title: Samples from Pool K2 Shrimp exposed to thermal stress and Sampled at T3 (Hyb 22 Cy3)


title: Samples from Pool G2 Shrimp exposed to hypoxic stress and Sampled at T2 (Hyb19 Cy5)

description: Samples from Pool G2. Shrimp exposed to hypoxic stress and sampled at T2


title: Halobacterium EMS exposure experiment, Array 8173

description: No EMS control sample grown in standard conditions and sampled 50 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-46

source_name: Halobacterium NRC1, no EMS control, 50 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 50 minutes post 30min mock EMS treatment.


title: Samples from Pool H2 Shrimp exposed to hypoxic stress and Sampled at T3 (Hyb19 Cy3)


title: Samples from Pool I2 Shrimp exposed to hypoxic stress and Sampled at T4 (Hyb20 Cy3)


title: Halobacterium EMS exposure experiment, Array 8174

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-47

tag: No EMS control sample grown in standard conditions and sampled 60 minutes post mock EMS treatment


title: Samples from Pool G2 Shrimp exposed to hypoxic stress and Sampled at T2 (Hyb 18 Cy3)


title: Samples from Pool F2 Shrimp exposed to osmotic stress and Sampled at T2 (Hyb 17 Cy3)

description: Samples from Pool F2. Shrimp exposed to osmotic stress and sampled at T2


title: Halobacterium EMS exposure experiment, Array 8172

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-45

tag: No EMS control sample grown in standard conditions and sampled 50 minutes post mock EMS treatment


title: Halobacterium EMS exposure experiment, Array 8170

description: No EMS control sample grown in standard conditions and sampled 40 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-43

source_name: Halobacterium NRC1, no EMS control, 40 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 40 minutes post 30min mock EMS treatment.


title: Includes Samples from D2 osmotic T4 (Hyb15Cy3)

description: includes samples from D2 osmotic T4


title: Samples from pool D2 osmotic challenge at T4 (Hyb16Cy5)

description: samples from pool D2 osmotic challenge at T4


title: Halobacterium EMS exposure experiment, Array 8171

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

tag: No EMS control sample grown in standard conditions and sampled 40 minutes post mock EMS treatment


title: Samples from Pool F2 Shrimp exposed to osmotic stress and Sampled at T2 (Hyb18 Cy5)


title: Samples from pool E2 osmotic challenge at T3 (Hyb16Cy3)

description: samples from pool E2 osmotic challenge at T3


title: Samples from Pool E2 Shrimp exposed to osmotic stress and Sampled at T3 (Hyb 17 Cy5)

description: Samples from Pool E2. Shrimp exposed to osmotic stress and sampled at T3


title: Includes Samples from control group pool C2 at T4 (Hyb15Cy5)

description: includes samples from control group pool C2 at T4


title: Halobacterium EMS exposure experiment, Array 8169

description: No EMS control sample grown in standard conditions and sampled 30 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-42

source_name: Halobacterium NRC1, no EMS control, 30 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 30 minutes post 30min mock EMS treatment.


title: Includes Samples from control group pool C2 at T4 (Hyb14Cy3)


title: Includes Samples from control group pool C2 at T2T3 (Hyb14Cy5)

description: includes samples from control group pool C2 at T2T3


title: TCDD Low1

city: Eggenstein-Leopoldshafen

first: Jessica

last: Legradi

state: Baden-Wuerttemberg

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics ITG

country: Germany

institute: Karlsruhe Institute of Technology

description: This file contains all technological and biological replicates (i.e. from the same and different biological source, repspectively) that were performed with this particular toxin at this particular concentration.  The Dye-Swap Designe was utilised.

hyb_protocol: 1) Removal of unincorporated nucleotides over Microcon 30 spin columns (Millipore, Bedford, MA). 2) The concentrated probes were hybridized to the microarray in 1xDIG Easy-Hyb buffer (Hoffmann-La Roche, Basel, CH) overnight at 42 C. 3) Cover slips were removed from the slides by flushing with 4xSSC. 4) Slides were washed in pre-warmed wash buffer 1 (2xSSC, 0.1% SDS) for 5 minutes at 42 C. 5) Washing in buffer 2 (0.1xSSC, 0.1% SDS) for 10 minutes at room temperature. 6) Washing in 0.1xSSC four times for 1 min at room temperature. 7) The slides were briefly dipped into 0.01xSSC at room temperature. 8) Centrifugation for 7 min at 800 rpm in an Eppendorf 5810R centrifuge.

scan_protocol: 1) Scanned on an GenePix 4000B dual-laser scanner from Molecular Devices 2) Both channels (532 nm for Cy3 and 635 nm for Cy5) were scanned in parallel 3) Data was stored as 16-bit TIFF files 4) The channels for Cy3 and Cy5 were balanced in each scan for approximately the same intensity profile. 5) Each array was scanned three times (low, medium and high scan) with different signal amplification factors (voltage settings of the photomultiplier tubes), but with the same laser power. 6) Raw data was retrieved with GenePix Pro 6.0 software from Axon Instruments . 7) Data processing was performed 8) The absolute intensity values span the range from 0 to 65536. 9) The scans were performed with a resolution of 10 um.

data_processing: 1) Raw data are retrieved with GenePix  2) Quality control on spot level  3) Local background correction.  4) Averaging of the two spots for each gene.  5) Consensus signals are calculated from low, medium and high scan based on a Least Squares Algorithm.  6) Log transformation.  7) locally weighted regression smoother (LOESS).  8) Scaling to a common MAD.  9) t-test  10) adjustment of p-values for multiplicity  11) Quality control on array level.

molecule: polyA RNA

organism: Danio rerio

source_name: mRNA from zebrafish embryos that were exposed to TCDD Low1

label_protocol: Labeled cDNA was synthesized from 1-2 ug mRNA using the Amersham direct cDNA labeling kit (Amersham Europe, Freiburg, Germany).

growth_protocol: as described in Westerfield 1993

extract_protocol: 1) Total RNA was isolated using the Nucleospin RNA L Kit (Macherey-Nagel, Dueren, Germany).  2) mRNA was extracted with the Ambion Purist Kit (Austin, TX).

treatment_protocol: Acrylamide (CH2=CHCONH2), Aroclor 1254 (PCB), Arsenic(III) Oxide (As2O3), tBHQ (tert-Butylhydroquinone (CH3)3CC6H3-1,4-(OH)2),  Cadmiumchloride (CdCl2.2H2O), 4-Chloroaniline (ClC6H4NH2), DDT (1,1-Bis-(4-Chlorphenyl)-2,2,2-Trichlorethan (ClC6H4)2CHCCl3), Lead (II)chloride (PbCl2), Methylmercurychloride (CH3ClHg), TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) and Valproic acid (CH3(CH2)4CO2H) were purchased from Sigma-Aldrich. Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. Embryos were grown in embryo medium (60 ug/ml Instant Ocean, Red Sea Fish Pharm Ltd.) Different numbers of embryos were exposed to the chemicals: between 4 to 24 hpf (600 embryos), 24 to 48 hpf (400 embryos) and 96 to 120 hpf (200 embryos). Embryo medium alone (Cd, Hg, Pb, As, VA, AA) or 0.2 % ethanol in embryo medium (tBHQ , 4CA, PCB, DDT) or 0.5% DMSO, 28mg/l toluene in embryo medium (TCDD) were used as vehicle controls. The toxin concentrations were adjusted in such a way that embryo death was minimal. The few dead embryos were discarded before preparation of RNA.

tag: whole body mRNA

tag: Strains

value: 200-800 zebrafish from AB*,AB2O2,AB2O2 Golden and AB2O2 Leo

source_name: mRNA from zebrafish embryos that were not exposed to a toxic environment


title: Includes Samples  from pool A Shrimp after acclimation Sampled at T1 (Hyb13 Cy5)

description: includes samples  from pool A. Shrimp after acclimation sampled at T1


title: Samples from Pool D1 Shrimp exposed to osmotic stress at T4 (Hyb 3 Cy3)

description: Samples from Pool D1. Shrimp exposed to osmotic stress at T4

extract_protocol: otal RNA was extracted from haemocytes by homogenisation in Trizol-LS(Life Technologies) and then amplified using the Message Amp II® aRNA amplification kit (Ambion®) following the manufacturer’s instructions for one-round amplification.


title: Halobacterium EMS exposure experiment, Array 8168

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-41

tag: No EMS control sample grown in standard conditions and sampled 30 minutes post mock EMS treatment


title: TCDD 48h

source_name: mRNA from zebrafish embryos that were exposed to TCDD 48h

extract_protocol:
1) Total RNA was isolated using the Nucleospin RNA L Kit (Macherey-Nagel, Dueren, Germany).
2) mRNA was extracted with the Ambion Purist Kit (Austin, TX).


title: Halobacterium EMS exposure experiment, Array 8167

description: No EMS control sample grown in standard conditions and sampled 20 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

source_name: Halobacterium NRC1, no EMS control, 20 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 20 minutes post 30min mock EMS treatment.


title: Includes Samples from pool B2 Control shrimp Sampled at T2 + T3 (Hyb 13 Cy3)

description: includes samples from pool B2. Control shrimp sampled at T2 + T3


title: Samples from pool A Shrimp after acclimation and Sampled at T1 (Hyb 12 Cy3)

description: Samples from pool A. Shrimp after acclimation and sampled at T1

label: Cy 3


title: Halobacterium EMS exposure experiment, Array 8165

description: No EMS control sample grown in standard conditions and sampled 10 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38

source_name: Halobacterium NRC1, no EMS control, 10 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 10 minutes post 30min mock EMS treatment.


title: TCDD Low2

source_name: mRNA from zebrafish embryos that were exposed to TCDD Low2


title: Samples from Pool L1 Shrimp exposed to thermal stress and Sampled at T2 (Hyb 12 Cy 5)

description: Samples from Pool L1. Shrimp exposed to thermal stress and sampled at T2

hyb_protocol: Human Cot1 DNA [(10 μg), (Invitrogen)], and 2 μg of poly dA (Roche) were added to the purified probe mix and dried prior to resuspending in 30 μl of 4X SSC (0.6 M sodium chloride and 60 mM sodium citrate), 40% deionized formamide and 0.1% sodium dodecyl sulfate (SDS). Following incubation at 95°C for 5 min, and then 45°C for 90 min, the labelled probe mix was loaded onto the microarray chip, and hybridisation was carried out for 16 h at 45°C. Following hybridisation, the microarray chip was washed twice with 0.2X SSC, 0.05% SDS and 2 more times with 0.2X SSC. Slides were finally dried by centrifugation at 600 rpm for 5 min.

label: Cy 5


title: Samples from Pool B1 Control shrimp at T2 + T3 (Hyb 2 Cy5)

description: Samples from Pool B1. Control shrimp at T2 + T3


title: Valproic acid 48h

source_name: mRNA from zebrafish embryos that were exposed to Valproic acid 48h


title: Halobacterium EMS exposure experiment, Array 8164

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37

tag: No EMS control sample grown in standard conditions and sampled 10 minutes post mock EMS treatment


title: Samples from Pool L1 Shrimp exposed to thermal stress and Sampled at T2 (Hyb 11 Cy 3)


title: Samples from pool K1 Shrimp exposed to thermal stress and Sampled at T3 (Hyb 11 Cy 5)

description: Samples from pool K1. Shrimp exposed to thermal stress and sampled at T3


title: New Cadmium

source_name: mRNA from zebrafish embryos that were exposed to New Cadmium


title: Samples from Pool J1 Shrimp exposed to thermal stress and Sampled at T4 (Hyb 10 Cy 5)

description: Samples from Pool J1. Shrimp exposed to thermal stress and sampled at T4


title: Valproic acid 24h

source_name: mRNA from zebrafish embryos that were exposed to Valproic acid 24h


title: TCDD

source_name: mRNA from zebrafish embryos that were exposed to TCDD


title: Halobacterium EMS exposure experiment, Array 8166

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39

tag: No EMS control sample grown in standard conditions and sampled 20 minutes post mock EMS treatment

source_name: Standard mid-log Halobacterium NRC-1 reference sample.


title: Samples from Pool I1 Shrimp exposed to Hypoxic stress and Sampled at T4 (Hyb 9 Cy 5)

description: Samples from Pool I1. Shrimp exposed to Hypoxic stress and sampled at T4

source_name: hemocytes from Penaeus monodon exposed to environmental stressors


title: Samples from pool H1 Shrimp exposed to hypoxic stress and Sampled at T3 (Hyb 8 Cy 5)

description: Samples from pool H1. Shrimp exposed to hypoxic stress and sampled at T3

label_protocol: cDNA labeling was performed as previously described (Woods et al. 2004, Development 131: 2921-2933). Amplified RNA (2μg) were reverse transcribed using an oligo dT18 primer (50 μM), 1.25 mM dNTP mix (Biotech International) with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma), 10 mM dithiothreitol (DTT), 600 units of Superscript III ® (Invitrogen), and 60 units of RNAse out (Invitrogen) in a 30 μl reaction volume. RNA was hydrolyzed by the addition of 3 μl of 1 M NaOH and 3 μl of 0.5 M ethylene-diamine-tetraacetate (EDTA) followed by heating to 65°C for 15 min. The solution was neutralized by the addition of 3 μl of 1 M HCl. Following synthesis, aminoallyllabeled cDNA (aa-cDNA) was purified using the Millipore Montage PCR cleanup kit following the manufacturer’s instructions, dried down and the pellet resuspended in 4.5 μl of freshly prepared 100 mM sodium carbonate (pH 9.0). A total of 100 ng of Cy3 or Cy5 reactive dyes (resuspended in 4.5 μl DMSO) (AmcDNA labeling was performed as previously described (Woods et al. 2004, Development 131: 2921-2933). Amplified RNA (2μg) were reverse transcribed using an oligo dT18 primer (50 μM), 1.25 mM dNTP mix (Biotech International) with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma), 10 mM dithiothreitol (DTT), 600 units of Superscript III ® (Invitrogen), and 60 units of RNAse out (Invitrogen) in a 30 μl reaction volume. RNA was hydrolyzed by the addition of 3 μl of 1 M NaOH and 3 μl of 0.5 M ethylene-diamine-tetraacetate (EDTA) followed by heating to 65°C for 15 min. The solution was neutralized by the addition of 3 μl of 1 M HCl. Following synthesis, aminoallyllabeled cDNA (aa-cDNA) was purified using the Millipore Montage PCR cleanup kit following the manufacturer’s instructions, dried down and the pellet resuspended in 4.5 μl of freshly prepared 100 mM sodium carbonate (pH 9.0). A total of 100 ng of Cy3 or Cy5 reactive dyes (resuspended in 4.5 μl DMSO) (Amersham) were added to the respective aa-cDNAs and the coupling reaction allowed to proceed at room temperature for 1.5 h in the dark. Unincorporated dyes were removed from the reaction by the addition of 4 M hydroxylamine. Cy3- and Cy5-labelled cDNA was then combined and purified using a Qiagen QIAquick PCR cleanup kitersham) were added to the respective aa-cDNAs and the coupling reaction allowed to proceed at room temperature for 1.5 h in the dark. Unincorporated dyes were removed from the reaction by the addition of 4 M hydroxylamine. Cy3- and Cy5-labelled cDNA was then combined and purified using a Qiagen QIAquick PCR cleanup kit


title: Halobacterium EMS exposure experiment, Array 8163

description: No EMS control sample grown in standard conditions and sampled 0 minutes post mock EMS treatment versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36

source_name: Halobacterium NRC1, no EMS control, 0 minutes post mock EMS dose.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 0 minutes post 30min mock EMS treatment.


title: Samples from Pool J1 Shrimp exposed to thermal stress and Sampled at T4 (Hyb 9 Cy 3)


title: Mixture (Publication)

source_name: mRNA from zebrafish embryos that were exposed to Mixture (Publication)


title: Samples from pool G1 Shrimp exposed to hypoxic stress and Sampled at T2 (Hyb 7 Cy 5)

description: Samples from pool G1. Shrimp exposed to hypoxic stress and sampled at T2


title: Samples from Pool I1 Shrimp exposed to hypoxic stress and Sampled at T4 (Hyb 8 Cy 3)

description: Samples from Pool I1. Shrimp exposed to hypoxic stress and sampled at T4


title: Valproic acid

source_name: mRNA from zebrafish embryos that were exposed to Valproic acid


title: Samples from Pool K1 Shrimp exposed to thermal stress and Sampled at T3 (Hyb 10 Cy 3)

description: Samples from Pool K1. Shrimp exposed to thermal stress and sampled at T3


title: Halobacterium EMS exposure experiment, Array 8162

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

tag: No EMS control sample grown in standard conditions and sampled 0 minutes post mock EMS treatment


title: Fat line hypothalamus, week 7

type: other

city: College Park

first: Tom

middle: E

last: Porter

state: MD

address: Building #142

department: Animal and Avian Sciences

institute: University of Maryland

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled fat week 1 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

scan_protocol: The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

data_processing: The two images from each slide were processed with Spotfinder version 2.2.4 (The Institute for Genomic Research, Rockville, MD) using the following settings:  Otsu thresholding algorithm (minimum spot size 3 and maximum spot size 25); keep flagged values; keep raw data; and quality control filter set so 50% cutoff equals background plus 1 standard deviation.  Data were normalized using Microarray Data Analysis System (MIDAS) version 2.18 (The Institute for Genomic Research).  In MIDAS, channel A and B flags and channel A and B background checking were used, and the signal-to-noise threshold was set at 3.0.  Data from the Cy3 channel were first Lowess (LocFit) normalized by pin (block) using a smoothing parameter of 0.33 with Cy5 as the reference and then sujected to standard deviation regularization first by pin (block) then by slide with Cy5 as the reference.  A cross file cutoff of 25% was used, so that at least 4 of the 32 slides for a given spot had to pass quality control checks

molecule: other

organism: Gallus gallus

label_protocol: 20 micrograms of total RNA were converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion), and Cy3-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA.  Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences).

growth_protocol: Standard broiler chicken growth protocol. Hypothalami were rapidly excised, frozen in liquid nitrogen and stored at –75 °C until RNA extraction.

extract_protocol: Total RNA was extracted with the RNeasy Midi Kit according to the manufacturer's protocol (Qiagen, Valencia, CA).

tag: Log Ratio [log2(normalized Cy3/raw Cy5)]

source_name: Reference pool of hypothalamic total RNA from fat and lean lines, week 1, 3, 5, and 7

tag: raw Cy5


title: TCDD 24h

description: This file contains all technological and biological replicates (i.e. from the same and different biological source, repspectively) that were performed with this particular toxin at this particular concentration.  The Dye-Swap Designe was utilised.

source_name: mRNA from zebrafish embryos that were exposed to TCDD 24h


title: Fat line hypothalamus, week 5


title: Samples from Pool H1 Shrimp exposed to hypoxic stress and Sampled at T3 (Hyb 7 Cy 3)

description: Samples from Pool H1. Shrimp exposed to hypoxic stress and sampled at T3


title: Methyl mercury Low2

source_name: mRNA from zebrafish embryos that were exposed to Methyl mercury Low2


title: Samples from pool F1 Shrimp exposed to osmotic stress and Sampled at T2 (Hyb 6 Cy 5)

description: Samples from pool F1. Shrimp exposed to osmotic stress and sampled at T2


title: Methyl mercury Low1

source_name: mRNA from zebrafish embryos that were exposed to Methyl mercury Low1

source_name: mRNA from zebrafish embryos that were not exposed to a toxic environment


title: Samples from pool G1 Shrimp exposed to hypoxic stress and Sampled at T2 (Hyb 6 Cy 3)


title: Lead chloride

source_name: mRNA from zebrafish embryos that were exposed to Lead chloride


title: Fat line hypothalamus, week 3


title: Samples from Pool E1 Shrimp exposed to osmotic stress and Sampled at T3 (Hyb 5 Cy 5)

description: Samples from Pool E1. Shrimp exposed to osmotic stress and sampled at T3


title: Fat line hypothalamus, week 1


title: PCB 5d

source_name: mRNA from zebrafish embryos that were exposed to PCB 5d


title: Lean line hypothalamus, week 7


title: Samples from Pool F1 Shrimp exposed to osmotic stress and Sampled at T2 (Hyb 5 Cy 3)

description: Samples from Pool F1. Shrimp exposed to osmotic stress and sampled at T2


title: Samples from Pool D1 Shrimp were exposed to Osmotic stress and Sampled at T4 (Hyb 4 Cy5)

description: Samples from Pool D1. Shrimp were exposed to Osmotic stress and sampled at T4


title: Lean line hypothalamus, week 5


title: Samples from Pool C1 Control shrimp at T4 (Hyb 3 Cy5)

description: Samples from Pool C1. Control shrimp at T4


title: Samples from Pool C1 Control shrimp at T4 (Hyb 2 Cy3)


title: Samples from Pool E1 Shrimp were exposed to osmotic stress and Sampled at T3 (Hyb 4 Cy3)

description: Samples from Pool E1. Shrimp were exposed to osmotic stress and sampled at T3


title: Lead chloride Low

source_name: mRNA from zebrafish embryos that were exposed to Lead chloride Low


title: t-BHQ 5d

source_name: mRNA from zebrafish embryos that were exposed to t-BHQ 5d


title: Samples from Pool A immediately after acclimation T1 (Hybridization 1 Cy5)

label_protocol: DNA labeling was performed as previously described (Woods et al. 2004, Development 131: 2921-2933). Amplified RNA (2μg) were reverse transcribed using an oligo dT18 primer (50 μM), 1.25 mM dNTP mix (Biotech International) with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma), 10 mM dithiothreitol (DTT), 600 units of Superscript III ® (Invitrogen), and 60 units of RNAse out (Invitrogen) in a 30 μl reaction volume. RNA was hydrolyzed by the addition of 3 μl of 1 M NaOH and 3 μl of 0.5 M ethylene-diamine-tetraacetate (EDTA) followed by heating to 65°C for 15 min. The solution was neutralized by the addition of 3 μl of 1 M HCl. Following synthesis, aminoallyllabeled cDNA (aa-cDNA) was purified using the Millipore Montage PCR cleanup kit following the manufacturer’s instructions, dried down and the pellet resuspended in 4.5 μl of freshly prepared 100 mM sodium carbonate (pH 9.0). A total of 100 ng of Cy3 or Cy5 reactive dyes (resuspended in 4.5 μl DMSO) (Amersham) were added to the respective aa-cDNAs and the coupling reaction allowed to proceed at room temperature for 1.5 h in the dark. Unincorporated dyes were removed from the reaction by the addition of 4 M hydroxylamine. Cy3- and Cy5-labelled cDNA was then combined and purified using a Qiagen QIAquick PCR cleanup kit


title: Lean line hypothalamus, week 3


title: whole crab early premoult (Cy3) compared with late premoult (Cy5) rep 3 right

city: Maroochydore DC

first: Anna

middle: Viktoria

last: Kuballa

state: Queensland

address: University of the Sunshine Coast

department: Faculty of Science, Health and Education

country: Australia

institute: University of the Sunshine Coast

description:
Clones were spotted in duplicate on each array (once on the left and once on the right side), providing a technical replicate within each array, analysis of each side of the slide occured individually thus each array has 2 separate data entries, one for the left and right).
Microarray data analysis was performed by Emphron Informatics (Chapel Hill, Qld, Australia), this information (differentail gene expression data) is provided in a separate supplementary file.

hyb_protocol: cDNA was labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

scan_protocol: Microarray slides were scanned using a white-light ArrayWorx Biochip Reader (Applied Precision, LLC, Issaquah, Washington, USA).  ImaGene (BioDiscovery Inc., El Segundo, CA, USA) was then used to process images and create spot intensity reports, while CloneTracker (Biodiscovery Inc.) was used to generate gene ID mapping files and assign gene identification.  Final intensity reports were retrieved as raw spot intensities in tab-delimited files.

data_processing: The data in the VALUE column were not normalized.  The VALUE column contains the log ratios of the raw values for signal intensity for both channels (i.e. Cy3 Signal Mean / Cy5 Signal Mean).

organism: Portunus pelagicus

source_name: whole crab early premoult

label_protocol: 10 ug of total RNA (pooled from 3 individuals) was converted to cDNA then labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

growth_protocol: Crabs were individually housed in a flowthrough system at an ambient water temperature of 24oC and fed a commercial diet twice daily

extract_protocol: Whole crabs were snap frozen and ground under liquid nitrogen.  Total RNA was isolated from each sample using Trizol reagent as recommended by the manufacturer (Invitrogen Life Technologies, Carlsbad, CA, USA).  RNA was DNase treated using RQ1 RNase free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer.

tag: 3 individual whole crabs (pooled equally) sampled at the early premoult stage of the moult cycle

source_name: whole crab late premoult

tag: 3 individual whole crabs (pooled equally) sampled at the late premoult stage of the moult cycle


title: Methyl mercury 48h

source_name: mRNA from zebrafish embryos that were exposed to Methyl mercury 48h


title: Lean line hypothalamus, week 1


title: Methyl mercury 24h

source_name: mRNA from zebrafish embryos that were exposed to Methyl mercury 24h


title: whole crab early premoult (Cy3) compared with late premoult (Cy5) rep 2 right


title: whole crab intermoult (Cy3) compared with early premoult (Cy5) rep 3 right

source_name: whole crab intermoult

tag: 3 individual whole crabs (pooled equally) sampled at the intermoult stage of the moult cycle


title: whole crab early premoult (Cy3) compared with late premoult (Cy5) rep 1 left


title: whole crab early premoult (Cy3) compared with late premoult (Cy5) rep 1 right


title: whole crab early premoult (Cy3) compared with late premoult (Cy5) rep 2 left


title: whole crab intermoult (Cy3) compared with early premoult (Cy5) rep 2 right


title: Methyl mercury

source_name: mRNA from zebrafish embryos that were exposed to Methyl mercury


title: Samples from Pool B1 control treatment at T2 and T3 (Hyb 1 Cy3)

description: samples from Pool B1 control treatment at T2 and T3

data_processing:
Only genes with a signal to noise ratio (computed by dividing the backgroundcorrected intensities by the standard deviation of the background pixels) greater than 1.0, scored in both dyes and with at least 24 readings across the 24 slides were used in this study.
The VALUE data included in this table was calculated by base-2 logarithm transforming (Log2) the value obtained by subtracting signal_median - background_median.
Signal intensities were base-2 logarithm (log2) transformed and normalized by a multivariate mixed-model approach as previously described (Reverter et. al. 2005. Bioinformatics 21: 1112-1120) using the following equation:
Only genes with a signal to noise ratio (computed by dividing the backgroundcorrected intensities by the standard deviation of the background pixels) greater than 1.0, scored in both dyes and with at least 24 readings across the 24 slides were used in this study. Signal intensities were base-2 logarithm (log2) transformed and normalized by a multivariate mixed-model approach as previously described (Reverter et. al. 2005. Bioinformatics 21: 1112-1120) using the following equation.

yE = XEßE + ZE1cE + ZE2aE + ZE3dE + ZE4tE + eE

Where:

y is the vector of all the intensity signals (N= 202 636), background corrected and base-2 log transformed
X is the incidence matrix relating signals in y with systematic fixed effects in ß including array slide, printing block and fluorescent dye channel
ZE1 is the incidence matrix relating y with random effects in c corresponding to the clones (N= 2841) printed on the array that passed the filtering criteria
ZE2 is the incidence matrix relating y with random effects in a corresponding to the three-way interaction of clone by array and printing block
ZE3 is the incidence matrix relating y with random effects in d corresponding to the interaction of clone by the two fluorescent dye channels
ZE4 is the incidence matrix relating y with random effects in t corresponding to the interaction of clone by the 12 experimental treatment conditions
e is the random error associated with signals in y.
The variance components were estimated by restricted maximum likelihood (REML) using VCE 4 software (available at   Eildert Groeneveld's web page at the Institute for Animal Breeding Mariensee).  The fitting of the above model provided BLUP (Best Linear Unbiased Prediction) solutions that were the basis for the normalization methods.

source_name: hemocytes from Penaeus monodon exposed to environmental stressors

label_protocol: cDNA labeling was performed as previously described (Woods et al. 2004, Development 131: 2921-2933). Amplified RNA (2μg)  were reverse transcribed using an oligo dT18 primer (50 μM), 1.25 mM dNTP mix (Biotech International) with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma), 10 mM dithiothreitol (DTT), 600 units of Superscript III ® (Invitrogen), and 60 units of RNAse out (Invitrogen) in a 30 μl reaction volume. RNA was hydrolyzed by the addition of 3 μl of 1 M NaOH and 3 μl of 0.5 M ethylene-diamine-tetraacetate (EDTA) followed by heating to 65°C for 15 min. The solution was neutralized by the addition of 3 μl of 1 M HCl. Following synthesis, aminoallyllabeled cDNA (aa-cDNA) was purified using the Millipore Montage PCR cleanup kit following the manufacturer’s instructions, dried down and the pellet resuspended in 4.5 μl of freshly prepared 100 mM sodium carbonate (pH 9.0). A total of 100 ng of Cy3 or Cy5 reactive dyes (resuspended in 4.5 μl DMSO) (Amersham) were added to the respective aa-cDNAs and the coupling reaction allowed to proceed at room temperature for 1.5 h in the dark. Unincorporated dyes were removed from the reaction by the addition of 4 M hydroxylamine. Cy3- and Cy5-labelled cDNA was then combined and purified using a Qiagen QIAquick PCR cleanup kit

tag: Samples used in this experiment came from hemocytes of juvenile Penaeus monodon originating from a hatchery in North Queensland, Australia.  This hatchery uses wild caught broodstock for its operation.


title: whole crab intermoult (Cy3) compared with early premoult (Cy5) rep 1 right


title: whole crab early premoult (Cy3) compared with late premoult (Cy5) rep 3 left


title: whole crab intermoult (Cy3) compared with early premoult (Cy5) rep 2 left


title: whole crab intermoult (Cy3) compared with early premoult (Cy5) rep 1 left


title: whole crab intermoult (Cy3) compared with early premoult (Cy5) rep 3 left


title: whole crab ecdysis (Cy3) compared with postmoult (Cy5) rep 3 right

source_name: whole crab ecdysis

tag: 3 individual whole crabs (pooled equally) sampled at ecdysis

source_name: whole crab postmoult

tag: 3 individual whole crabs (pooled equally) sampled at the postmoult stage of the moult cycle


title: Cadmium chloride Low 2

source_name: mRNA from zebrafish embryos that were exposed to Cadmium chloride Low 2


title: whole crab ecdysis (Cy3) compared with postmoult (Cy5) rep 2 left

description: Clones were spotted in duplicate on each array (once on the left and once on the right side), providing a technical replicate within each array, analysis of each side of the slide occured individually thus each array has 2 separate data entries one for the left and right.  Microarray data analysis was performed by Emphron Informatics (Chapel Hill, Qld, Australia), this information (differential gene expression data) is provided in a separate supplementary file.

data_processing: The data in the VALUE column was not normalized.  The VALUE column contains the log ratios of the raw values for signal intensity for both channels (i.e. Cy3 Signal Mean / Cy5 Signal Mean).

growth_protocol: Crabs were individually housed in a flowthrough system at an ambient water temperature of 24oC and fed a commercial diet, twice daily.


title: Cadmium chloride Low1

source_name: mRNA from zebrafish embryos that were exposed to Cadmium chloride Low1


title: DDT 24h

source_name: mRNA from zebrafish embryos that were exposed to DDT 24h


title: whole crab late premoult (Cy3) compared with ecdysis (Cy5) rep 3 right


title: whole crab ecdysis (Cy3) compared with postmoult (Cy5) rep 1 left


title: Blind test 9

source_name: mRNA from zebrafish embryos that were exposed to Blind test 9

source_name: mRNA from zebrafish embryos that were not exposed to a toxic environment


title: whole crab ecdysis (Cy3) compared with postmoult (Cy5) rep 2 right


title: whole crab ecdysis (Cy3) compared with postmoult (Cy5) rep 1 right


title: DDT 48h

source_name: mRNA from zebrafish embryos that were exposed to DDT 48h


title: Blind test 6

source_name: mRNA from zebrafish embryos that were exposed to Blind test 6


title: Blind test 4

source_name: mRNA from zebrafish embryos that were exposed to Blind test 4


title: Blind test 5

source_name: mRNA from zebrafish embryos that were exposed to Blind test 5


title: Blind test 3

source_name: mRNA from zebrafish embryos that were exposed to Blind test 3


title: Blind test 8

source_name: mRNA from zebrafish embryos that were exposed to Blind test 8


title: Blind test 7

source_name: mRNA from zebrafish embryos that were exposed to Blind test 7


title: whole crab late premoult (Cy3) compared with ecdysis (Cy5) rep 2 right

source_name: whole crab late premoult


title: whole crab late premoult (Cy3) compared with ecdysis (Cy5) rep 2 left


title: Cadmium chloride 24h

source_name: mRNA from zebrafish embryos that were exposed to Cadmium chloride 24h


title: whole crab postmoult (Cy3) compared with intermoult (Cy5) rep 3 left

source_name: whole crab intermoult


title: whole crab ecdysis (Cy3) compared with postmoult (Cy5) rep 3 left

source_name: whole crab ecdysis


title: whole crab late premoult (Cy3) compared with ecdysis (Cy5) rep 1 right


title: Cadmium chloride 48h

source_name: mRNA from zebrafish embryos that were exposed to Cadmium chloride 48h


title: Blind test 2

source_name: mRNA from zebrafish embryos that were exposed to Blind test 2


title: whole crab postmoult (Cy3) compared with intermoult (Cy5) rep 3 right

source_name: whole crab postmoult


title: whole crab late premoult (Cy3) compared with ecdysis (Cy5) rep 1 left


title: Cadmium chloride

source_name: mRNA from zebrafish embryos that were exposed to Cadmium chloride


title: Blind test 16

source_name: mRNA from zebrafish embryos that were exposed to Blind test 16


title: Blind test 14

source_name: mRNA from zebrafish embryos that were exposed to Blind test 14

source_name: mRNA from zebrafish embryos that were not exposed to a toxic environment


title: whole crab postmoult (Cy3) compared with intermoult (Cy5) rep 1 right

description: Clones were spotted in duplicate on each array (once on the left and once on the right side), providing a technical replicate within each array, analysis of each side of the slide occured individually thus each array has 2 separate data entries, one for the left and right). Microarray data analysis was performed by Emphron Informatics (Chapel Hill, Qld, Australia), this information (differential gene expression data) is provided in a separate supplementary file.


title: DDT

source_name: mRNA from zebrafish embryos that were exposed to DDT


title: Blind test 13

source_name: mRNA from zebrafish embryos that were exposed to Blind test 13


title: Blind test 15

source_name: mRNA from zebrafish embryos that were exposed to Blind test 15


title: whole crab postmoult (Cy3) compared with intermoult (Cy5) rep 2 right


title: Lead chloride 5d

source_name: mRNA from zebrafish embryos that were exposed to Lead chloride 5d


title: postmoult(Cy3) compared with intermoult(Cy5) rep 1 left

tag: 3 individual whole crabs pooled (in equal amounts) sampled at the postmoult stage of the moult cycle

tag: 3 individual whole crabs pooled (in equal amounts) sampled at the intermoult stage of the moult cycle


title: whole crab late premoult (Cy3) compared with ecdysis (Cy5) rep 3 left


title: unexposed_rep2

status: Public on Jan 02 2008

city: College Station

first: Ginger

middle: E.

last: Carney

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

description: Males were randomly pooled in groups of approximately 12 individuals for RNA extraction.

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing:
Data were analyzed 3 different ways:

VALUE [dCHIP PMMM]: All 6 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM procedure under default parameters.

VALUE2 [dCHIP_PMonly]: All 6 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM_only procedure under default parameters.

VALUE3 [GCOS]: Expression values were computed using the recommended settings in GCOS version 1.2. All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0).

organism: Drosophila melanogaster

source_name: male body_5min

label_protocol: Standard Affymetrix

growth_protocol: Stocks were maintained on cornmeal/sugar media at 25o.

extract_protocol: Standard Trizol (Invitrogen) extraction.

treatment_protocol: Virgin males were raised in groups of 20 or fewer flies at 25o. They were transferred to individual vials on day 3. On day 4 they were mock-exposed and observed for 5 min.

tag: Strain

value: Canton-S

tag: Gender

value: male

tag: Age

value: 4 days


title: exposed_rep3

description: Only males who who demonstrated robust courtship but did not mate in the 5-min window were collected. Males were randomly pooled in groups of approximately 12 individuals for RNA extraction.

treatment_protocol: Virgin males were raised in groups of 20 or fewer flies at 25o. They were transferred to individual vials on day 3. On day 4 they were exposed to a virgin female fly and observed for 5 min.


title: unexposed_rep1


title: exposed_rep1


title: unexposed_rep3


title: Dicer-conditional ES cell line

status: Public on Oct 31 2007

city: Cambridge

first: J. Mauro

last: Calabrese

state: MA

address: 40 Ames Street

institute: MIT

description: To better understand Dicer function, and the potential mechanisms by which RNAi contributes to pluripotency, short RNA expression was profiled from 4 ES cell libraries: 2 made from a Dicer-conditional ES cell line before and several months after deletion of Dicer, and 2 made before and 5 days after demethylation of J1 ES cells with 5-aza-deoxycytidine.

data_processing:
Sequences were extracted from 454 reads that had 10 nt of perfect match to the ligated adaptors (measuring from the 3' end of the 5' adaptor and 5' end of the 3' adaptor).
Contributed here are the unannotated sequence data from each library, including those sequences that did not match the mouse genome or any known non-coding RNAs.

organism: Mus musculus

source_name: Dicer-conditional ES cell line

extract_protocol: Trizol, PAGE purify 16-30 nt fraction

treatment_protocol: control

tag: Dicer-conditional ES cell line


title: exposed_rep2


title: p53 family members in myogenic differentiation mock 24 h

status: Public on Oct 16 2006

city: Wuerzburg

first: Christof

last: Burek

address: Josef-schneider-Str. 2

department: Pathologie

institute: Universitaet Wuerzburg

description: mock 24 h after differentiation

hyb_protocol: standard Affymetrix procedures

scan_protocol: tandard Affymetrix procedures

data_processing: normalization on target 500

label: Biotin

source_name: C2C12 myoblast

label_protocol: Approximately 5 ?g of total RNA was processed to produce biotinylated cRNA targets.

tag: mock 24 h


title: Blind test 12

source_name: mRNA from zebrafish embryos that were exposed to Blind test 12

tag: whole body mRNA

tag: Strains


title: Dicer-deleted ES cell line

data_processing:
Sequences were extracted from 454 reads that had 10 bp of perfect match to the ligated adaptors (measuring from the 3' end of the 5' adaptor and 5' end of the 3' adaptor).
Contributed here are the unannotated sequence data from each library, including those sequences that did not match the mouse genome or any known non-coding RNAs.

source_name: Dicer-deleted ES cell line

extract_protocol: Trizol, PAGE purification of 16-30 nt fraction

treatment_protocol: Dicer-deleted ES cell line

tag: Dicer-deleted ES cell line


title: AD933M

status: Public on Oct 13 2006

city: Montreal

first: Olivier

middle: Charles

last: Maes

state: Quebec

address: 3999 Cote Ste Catherine

department: Bloomfield Centre for Research in Aging

country: Canada

institute: Lady Davis Institute for Medical Research

description: peripheral blood mononuclear cell

hyb_protocol: Nadon, Mohr, and Becker, National Institute on Aging microarray facility--resources for gerontology research. Journals of Gerontology Series A-Biological Sciences & Medical Sciences, 2005. 60(4): p. 413-5, PMID: 15933377, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15933377

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

data_processing: Array-Pro Analyzer 4.5 software (Media Cybernetics). Data acquisition was made using the option net intensity.

label: alpha 32P dCTP

source_name: peripheral blood

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

extract_protocol: Lacelle et al., J Gerontol A Biol Sci Med Sci, 2002. 57(7): p. B285-7, PMID: 12084799, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=12084799

tag: Sporadic Alzheimer's Disease, Male


title: p53 family members in myogenic differentiation mock 6 h

description: mock control 6 h after differentiation

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

tag: mock 6 h


title: AD911M

description: peripheral blood mononuclear cell


title: whole crab postmoult (Cy3) compared with intermoult (Cy5) rep 2 left

description: Clones were spotted in duplicate on each array (once on the left and once on the right side), providing a technical replicate for each array, analysis of each side of the slide occured individually thus each array has 2 separate data entries one for the left and right.  Microarray data analysis was performed by Emphron Informatics (Chapel Hill, Qld, Australia), this information (differential gene expression data) is provided in a separate supplementary file.

source_name: whole crab intermoult


title: Blind test 10

source_name: mRNA from zebrafish embryos that were exposed to Blind test 10


title: p53 family members in myogenic differentiation DeltaNp73 6h

description: DeltaNp73 6h after differentiation

tag: DeltaNp73 6h


title: Arsenic oxide Low

source_name: mRNA from zebrafish embryos that were exposed to Arsenic oxide Low


title: Blind Test 1

source_name: mRNA from zebrafish embryos that were exposed to Blind Test 1


title: p53 family members in myogenic differentiation DeltaNp72 24h

description: DeltaNp72 24h after differentiation

tag: DeltaNp72 24h


title: Blind test 11

source_name: mRNA from zebrafish embryos that were exposed to Blind test 11


title: p53 family members in myogenic differentiation mock 0 h

description: 0h after onset of differentiation

scan_protocol: standard Affymetrix procedures

tag: mock 0 h


title: AD1022M

description: peripheral blood mononuclear cell


title: ADR1032M

description: peripheral blood mononuclear cell


title: NEC946M

description: peripheral blood mononuclear cell

tag: Normal elderly control, Male


title: NEC923M

description: peripheral blood mononuclear cell


title: NEC917M

description: peripheral blood mononuclear cell


title: NECR830M

description: peripheral blood mononuclear cell


title: AD1038F

description: peripheral blood mononuclear cell

tag: Sporadic Alzheimer's Disease, Female


title: AD2R622M

description: peripheral blood mononuclear cell


title: AD940F

description: peripheral blood mononuclear cell


title: AD906M

description: peripheral blood mononuclear cell


title: p53 family members in myogenic differentiation DeltaNp73 0 h

description: DeltaNp73 0 h after differentiation

tag: DeltaNp73 0 h


title: NEC1044M

description: peripheral blood mononuclear cell


title: NEC990F

description: peripheral blood mononuclear cell

tag: Normal elderly control, Female


title: ADR386M

description: peripheral blood mononuclear cell


title: NEC994F

description: peripheral blood mononuclear cell


title: NEC1016F

description: peripheral blood mononuclear cell


title: AD962F

description: peripheral blood mononuclear cell


title: AD1049F

description: peripheral blood mononuclear cell


title: AD1064F

description: peripheral blood mononuclear cell


title: NEC991F

description: peripheral blood mononuclear cell


title: AD2R411F

description: peripheral blood mononuclear cell


title: NEC947M

description: peripheral blood mononuclear cell


title: ADR430F

description: peripheral blood mononuclear cell


title: NEC948M

description: peripheral blood mononuclear cell


title: NEC984F

description: peripheral blood mononuclear cell


title: NEC988F

description: peripheral blood mononuclear cell


title: Arsenic oxide

source_name: mRNA from zebrafish embryos that were exposed to Arsenic oxide


title: NECR787F

description: peripheral blood mononuclear cell


title: 4-Chloroaniline

source_name: mRNA from zebrafish embryos that were exposed to 4-Chloroaniline

source_name: mRNA from zebrafish embryos that were not exposed to a toxic environment


title: 4-Chloroaniline 24h

source_name: mRNA from zebrafish embryos that were exposed to 4-Chloroaniline 24h


title: 4-Chloroaniline 48h

source_name: mRNA from zebrafish embryos that were exposed to 4-Chloroaniline 48h


title: WT - Cre Treated - 0.5 hrs - repeat 1 - Cy3 - mAdbID:62541

status: Public on Oct 02 2006

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

description: mAdb experiment ID: 62541

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: WT Primary Hepatocytes - Pooled -Cy5

label_protocol: Cy5 Sample Labeling Protocol - generic

growth_protocol:
Cell Culture Protocol
Media: 1:1 DMEM and HAM's F12 supplemented with ITS
Other: Primary hepatocytes were seeded at 2x106 in 10 cm dishes in the plating medium supplemented with 10% FBS . After 4 hours, the plating medium was replaced to serum-free medium. The following day cells were treated with 50 ng/ml of rhHGF for 0.5, 2, 12 and 24 h. Triplicate cell cultures were established from three individual mice.

extract_protocol:
Extraction Protocol
Extraction method: Trizol protocol

tag: Strain

value: 9-10 weeks

tag: Tissue

value: liver

tag: Developmental stage

value: adult

tag: Cell type

value: Primary hepatocytes

source_name: WT - Cre Control - treated 0.5 hr - Cy3

label_protocol: Cy3 Sample Labeling Protocol - generic

treatment_protocol:
Treatment type: compound
Agent: HGF (Hepatocyte Growth Factor)
Treatment dose: 50 nM
Treatment time: 0.5 hour

tag: Genotype/Genetic variation Alb-Cre +/-


title: KO - knock-out Treated - 24 hrs - repeat 1 - Cy3 - mAdbID:61776

description: mAdb experiment ID: 61776

tag: Gender

tag: Age

source_name: KO - Met knock-out -treated 24 hr - Cy3

treatment_protocol:
Treatment type: compound
Agent: HGF (Hepatocyte Growth Factor)
Treatment dose: 50 nM
Treatment time: 24 hour

tag: Genotype/Genetic variation gene knock out

tag: Genotype/Genetic variation

value: Alb-Cre +/-; Met Fl/Fl


title: KO - knock-out Treated - 2 hrs - repeat 1 - Cy3 - mAdbID:62610

description: mAdb experiment ID: 62610

source_name: KO - Met knock-out -treated 2 hr - Cy3

treatment_protocol:
Treatment type: compound
Agent: HGF (Hepatocyte Growth Factor)
Treatment dose: 50 nM
Treatment time: 2 hour


title: Acrylamide 5d

source_name: mRNA from zebrafish embryos that were exposed to Acrylamide 5d

tag: whole body mRNA

tag: Strains


title: WT - Cre Treated - 2 hrs - repeat 1 - Cy3 - mAdbID:62605

description: mAdb experiment ID: 62605

source_name: WT - Cre Control - treated 2 hr - Cy3


title: WT - Cre Treated - 2 hrs - repeat 3 - Cy3 - mAdbID:62607

description: mAdb experiment ID: 62607


title: KO - knock-out Treated - 0.5 hrs - repeat 1 - Cy3 - mAdbID:62496

description: mAdb experiment ID: 62496

source_name: KO - Met knock-out -treated 0.5 hr - Cy3


title: WT - Cre Treated - 0.5 hrs - repeat 2 - Cy3 - mAdbID:62542

description: mAdb experiment ID: 62542


title: WT - Cre Treated - 0.5 hrs - repeat 3 - Cy3 - mAdbID:62543

description: mAdb experiment ID: 62543


title: WT - Cre Treated - 2 hrs - repeat 2 - Cy3 - mAdbID:62606

description: mAdb experiment ID: 62606


title: WT - Cre Treated - 24 hrs - repeat 1 - Cy3 - mAdbID:61769

description: mAdb experiment ID: 61769

source_name: WT - Cre Control - treated 24 hr - Cy3

value: Transgenic-heterozygous for Cre recombinase


title: KO - knock-out Treated - 24 hrs - repeat 2 - Cy3 - mAdbID:61777

description: mAdb experiment ID: 61777


title: KO - knock-out Treated - 0.5 hrs - repeat 2 - Cy3 - mAdbID:62530

description: mAdb experiment ID: 62530


title: KO - knock-out Treated - 12 hrs - repeat 3 - Cy3 - mAdbID:61764

description: mAdb experiment ID: 61764

source_name: KO - Met knock-out -treated 12 hr - Cy3


title: KO - knock-out Treated - 2 hrs - repeat 2 - Cy3 - mAdbID:62611

description: mAdb experiment ID: 62611


title: KO - knock-out Treated - 12 hrs - repeat 1 - Cy3 - mAdbID:61762

description: mAdb experiment ID: 61762


title: KO - knock-out Treated - 0.5 hrs - repeat 3 - Cy3 - mAdbID:62537

description: mAdb experiment ID: 62537


title: KO - knock-out Treated - 12 hrs - repeat 2 - Cy3 - mAdbID:61763

description: mAdb experiment ID: 61763


title: WT - Cre Treated - 12 hrs - repeat 1 - Cy3 - mAdbID:61756

description: mAdb experiment ID: 61756

source_name: WT - Cre Control - treated 12 hr - Cy3


title: KO - knock-out Untreated - 0 hrs - repeat 2 - Cy3 - mAdbID:61727

description: mAdb experiment ID: 61727

source_name: KO - Met knock-out - Untreated - Cy3


title: MNG-27 (14 day hindlimb suspended rats treated with ALCAR)_HS+ALCAR P

status: Public on Jun 07 2006

city: Bari

first: Maria Nicola

last: Gadaleta

address: via Orabona 4

department: Department of Biochemistry and Molecular Biology

country: Italy

institute: University of Bari, Italy

description: Acetyl-L-carnitine (ALCAR)-treated 14-day suspended rats.RNA was isolated from cryosections using RNeasy kit (Qiagen). 3 microgram total RNA was subjected to microarray analysis.

hyb_protocol: According the instructions supplied with AtlasTM Rat 1.2 cDNA arrays (Clontech Laboratories).

scan_protocol: The raw signal and local background of each probe spot on the membrane, given as the sum of pixels, was estimated with AIDA Array Easy software (Raytest Schweiz A.G., Urdorf, Switzerland) using the “local dot ring” mode as described in Wittwer et al., FASEB J 2002 Jun;16(8):884-6.

data_processing: HS+ALCAR P; the data are normalized vs. the total sum of signals.

organism: Rattus norvegicus

source_name: soleus muscle, 3-month-old female pathogen-free Wistar rats

label_protocol: 3 μg of isolated RNA was reverse-transcribed using the specific primers supplied with AtlasTM Rat 1.2 cDNA arrays (Clontech Laboratories) and 200 units of Superscript III reverse transcriptase (Invitrogen).

extract_protocol: Total RNA was extracted from pooled 25 μm-thick cryostat sections of the muscle using modified RNeasy mini-protocol for skeletal muscle (Qiagen) as described in Wittwer et al., FASEB J 2002 Jun;16(8):884-6.

tag: Extracted molecule total RNA


title: MNG-28 (14 day hindlimb suspended rats treated with ALCAR)_HS+ALCAR R

data_processing: HS+ALCAR R; the data are normalized vs. the total sum of signals.


title: WT - Cre Treated - 12 hrs - repeat 3 - Cy3 - mAdbID:61758

description: mAdb experiment ID: 61758


title: MNG-22 (14 day hindlimb suspended rats treated with ALCAR)_HS+ALCAR D

data_processing: HS+ALCAR D; the data are normalized vs. the total sum of signals.


title: MNG-21 (ALCAR-treated control rats)_ALCAR S

description: Acetyl-L-carnitine (ALCAR)-treated control rats.RNA was isolated from cryosections using RNeasy kit (Qiagen). 3 microgram total RNA was subjected to microarray analysis.

data_processing: ALCAR S; the data are normalized vs. the total sum of signals.


title: MNG-20 (ALCAR-treated control rats)_ALCAR Q

data_processing: ALCAR Q; the data are normalized vs. the total sum of signals.


title: MNG-18 (ALCAR-treated control rats)_ALCAR N

data_processing: ALCAR N; the data are normalized vs. the total sum of signals.


title: WT - Cre Untreated - 0 hrs - repeat 1 - Cy3 - mAdbID:61715

description: mAdb experiment ID: 61715

source_name: WT - Cre Control - Untreated - Cy3


title: MNG-25 (14 day hindlimb suspended rats treated with ALCAR)_HS+ALCAR I

data_processing: HS+ALCAR I; the data are normalized vs. the total sum of signals.


title: MNG-17 (ALCAR-treated control rats)_ALCAR M

data_processing: ALCAR M; the data are normalized vs. the total sum of signals.


title: MNG-23 (14 day hindlimb suspended rats treated with ALCAR)_HS+ALCAR E

data_processing: HS+ALCAR E; the data are normalized vs. the total sum of signals.


title: MNG-24 (14 day hindlimb suspended rats treated with ALCAR)_HS+ALCAR H

data_processing: HS+ALCAR H; the data are normalized vs. the total sum of signals.


title: MNG-26 (14 day hindlimb suspended rats treated with ALCAR)_HS+ALCAR L

data_processing: HS+ALCAR L; the data are normalized vs. the total sum of signals.


title: MNG-16 (ALCAR-treated control rats)_ALCAR G

data_processing: ALCAR G; the data are normalized vs. the total sum of signals.


title: MNG-19 (ALCAR-treated control rats)_ALCAR O

data_processing: ALCAR O; the data are normalized vs. the total sum of signals.


title: MNG-15 (ALCAR-treated control rats)_ALCAR F

data_processing: ALCAR F; the data are normalized vs. the total sum of signals.


title: KO - knock-out Treated - 24 hrs - repeat 3 - Cy3 - mAdbID:54822

description: mAdb experiment ID: 54822


title: WT - Cre Treated - 12 hrs - repeat 2 - Cy3 - mAdbID:61757

description: mAdb experiment ID: 61757


title: KO - knock-out Untreated - 0 hrs - repeat 1 - Cy3 - mAdbID:61726

description: mAdb experiment ID: 61726


title: WT - Cre Treated - 24 hrs - repeat 2 - Cy3 - mAdbID:54726

description: mAdb experiment ID: 54726


title: WT - Cre Untreated - 0 hrs - repeat 2 - Cy3 - mAdbID:61716

description: mAdb experiment ID: 61716


title: KO - knock-out Treated - 2 hrs - repeat 3 - Cy3 - mAdbID:51964

description: mAdb experiment ID: 51964


title: WT - Cre Treated - 24 hrs - repeat 3 - Cy3 - mAdbID:54725

description: mAdb experiment ID: 54725


title: KO - knock-out Untreated - 0 hrs - repeat 3 - Cy3 - mAdbID:51962

description: mAdb experiment ID: 51962


title: WT - Cre Untreated - 0 hrs - repeat 3 - Cy3 - mAdbID:54711

description: mAdb experiment ID: 54711


title: MNG-11 (14-day hindlimb suspended rats)_HS04

description: 14-day hindlimb suspended rats.RNA was isolated from cryosections using RNeasy kit (Qiagen). 3 microgram total RNA was subjected to microarray analysis.

data_processing: HS04; the data are normalized vs. the total sum of signals.


title: MNG-8 (14-day hindlimb suspended rats)_HS01

description:
14-day hindlimb suspended rats.
RNA was isolated from cryosections using RNeasy kit (Qiagen). 3 microgram total RNA was subjected to microarray analysis.

hyb_protocol: According the instructions supplied with AtlasTM Rat 1.2 cDNA arrays (Clontech Laboratories)

data_processing: HS01; the data are normalized vs. the total sum of signals.

label_protocol: 3 μg of isolated RNA was reverse-transcribed using the specific primers supplied with AtlasTM Rat 1.2 cDNA arrays (Clontech Laboratories) and 200 units of Superscript III reverse transcriptase (Invitrogen)


title: MNG-5 (14 days age control)_CT7

description:
cage control rats.
RNA was isolated from cryosections using RNeasy kit (Qiagen). 3 microgram total RNA was subjected to microarray analysis.

data_processing: CT7; the data are normalized vs. the total sum of signals.


title: MNG-3 (14 days age control)_CT5

description:
cage control rats.
RNA was isolated from cryosections using RNeasy kit (Qiagen). 3 microgram total RNA was subjected to microarray analysis

data_processing: CT5; the data are normalized vs. the total sum of signals.


title: MNG-1 (14 days age control)_CT2

hyb_protocol: According to instruction supplied in AtlasTM Rat 1.2 cDNA arrays (Clontech Laboratories)

scan_protocol: The raw signal and local background of each probe spot on the membrane, given as the sum of pixels, was estimated with AIDA Array Easy software (Raytest Schweiz A.G., Urdorf, Switzerland) using the “local dot ring” mode as described in Wittwer et al., FASEB J. 2002 Jun;16(8):884-6.

data_processing: CT2; the data are normalized vs. the total sum of signals.

extract_protocol: Total RNA was extracted from pooled 25 μm-thick cryostat sections of the muscle using modified RNeasy mini-protocol for skeletal muscle (Qiagen) as described in Wittwer et al., FASEB J. 2002 Jun;16(8):884-6.


title: MNG-4 (14 days age control)_CT6

data_processing: CT6; the data are normalized vs. the total sum of signals.


title: MNG-10 (14-day hindlimb suspended rats)_HS03

data_processing: HS03; the data are normalized vs. the total sum of signals.


title: MNG-6 (14 days age control)_CT9

data_processing: CT9; the data are normalized vs. the total sum of signals.


title: MNG-13 (14-day hindlimb suspended rats)_HS06

data_processing: HS06; the data are normalized vs. the total sum of signals.


title: MNG-14 (14-day hindlimb suspended rats)_HS07

data_processing: HS07; the data are normalized vs. the total sum of signals.


title: MNG-12 (14-day hindlimb suspended rats)_HS05

data_processing: HS05; the data are normalized vs. the total sum of signals.


title: MNG-9 (14-day hindlimb suspended rats)_HS02

data_processing: HS02; the data are normalized vs. the total sum of signals.


title: MNG-7 (14 days age control)_CT10

data_processing: CT10; the data are normalized vs. the total sum of signals.