title: Dp Mutant #2

status: Public on Apr 27 2008

type: RNA

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

country: USA

institute: United States EPA

description: gene expression data from Dpa2/Dpa4 null mutant embryos (8-10hrs) selected using the COPASTM SELECT system from Dpa2/CyO[Kr-GFP] crossed to Dpa4/CyO[Kr-GFP]

hyb_protocol: Affymetrix direction.  Details are in Cayirlioglu, P.et al (2003). Transcriptional repressor functions of Drosophila E2F1 and E2F2 cooperate to inhibit genomic DNA synthesis in ovarian follicle cells. Mol Cell Biol 23, 2123-34.

scan_protocol: Affymetrix direction using a Hewlett-Packard GeneArray scanner.

data_processing: Affymetrix GeneChip microarray suite 5.0 software was used for washing, scanning, and calculating expression summaries.

label: biotin-streptavidin-R-phycoerythrin

molecule: total RNA

organism: Drosophila melanogaster

source_name: Dpa2/Dpa4 null mutant embryos (8-10hrs) were selected using the COPASTM SELECT system from Dpa2/CyO[Kr-GFP] crossed to Dpa4/CyO[Kr-GFP]

label_protocol: During the washing, the cRNA probe was labeled with R-phycoerythrin streptavidin.  Details are in Cayirlioglu, P.et al (2003). Transcriptional repressor functions of Drosophila E2F1 and E2F2 cooperate to inhibit genomic DNA synthesis in ovarian follicle cells. Mol Cell Biol 23, 2123-34.

treatment_protocol: RNA was obtained from approximately 200 to 700 embryos per sample.  For each cross, 2 h embryo collections were aged for 8 to 14 h at 25oC, quick frozen in an ethanol/dry ice mixture, and stored at -80oC.  The RNA was prepared for microarray analysis as described Cayirlioglu, P.et al (2003). Transcriptional repressor functions of Drosophila E2F1 and E2F2 cooperate to inhibit genomic DNA synthesis in ovarian follicle cells. Mol Cell Biol 23, 2123-34.

tag: no additional


title: dnE2F #2

description: gene expression data from 8 to 10 hour old embryos from Arm-Gal4 crossed to E2f1336-805 (a dominant negative form of E2f1 lacking the DNA binding domain)

extract_protocol: Affymetrix direction.  Details are in Cayirlioglu, P.et al (2003). Transcriptional repressor functions of Drosophila E2F1 and E2F2 cooperate to inhibit genomic DNA synthesis in ovarian follicle cells. Mol Cell Biol 23, 2123-34.


title: Dp Mutant #1


title: yw #2

description: gene expression data from 8 to 10 hour old embryos from Arm-Gal4 crossed to yw


title: yw 14-16 hrs #2

description: gene expression data from 14 to 16 hour old embryos from Arm-Gal4 crossed to yw


title: E2F #1

description: gene expression data from 8 to 10 hour old embryos from Arm-Gal4 crossed to E2f1/Dp


title: E2F2 #1

description: gene expression data from 8 to 10 hour old embryos from Arm-Gal4 crossed to E2f2/Dp


title: yw 14-16 hrs #1

source_name: 14 to 16 hour old embryos from Arm-Gal4 crossed to yw


title: Rbf #1

description: gene expression data from 8 to 10 hour old embryos from Arm-Gal4 crossed to Rbf1


title: E2F2 #2

source_name: 8 to 10 hour old embryos from Arm-Gal4 crossed to E2f2/Dp


title: Rbf #2

source_name: 8 to 10 hour old embryos from Arm-Gal4 crossed to Rbf1


title: E2F 8-10 hrs mutant  #1

description: gene expression data from E2f17172/E2f191 null mutant embryos (8-10hrs) selected using the COPASTM SELECT system from E2f17172/TM3[Kr-GFP] x E2f191/TM3[Kr-GFP]

source_name: E2f17172/E2f191 null mutant embryos (8-10hrs) were selected using the COPASTM SELECT system from E2f17172/TM3[Kr-GFP] x E2f191/TM3[Kr-GFP]


title: E2F 8-10 hrs mutant  #2


title: yw #1

source_name: 8 to 10 hour old embryos from Arm-Gal4 crossed to yw


title: E2F 14-16 hrs mutant #1

description: gene expression data from 14-16 hr E2f17172/E2f191 null mutant embryos hand selected from E2f17172/TM3[Kr-GFP] x E2f191/TM3[Kr-GFP] based on the absence of fluorescent Bolwig’s organs in Kr-GFP balanced stocks using a Zeiss stereomicroscope equipped with epifluorescence.

source_name: 14-16 hr E2f17172/E2f191 null mutant embryos were hand selected from E2f17172/TM3[Kr-GFP] x E2f191/TM3[Kr-GFP] based on the absence of fluorescent Bolwig’s organs in Kr-GFP balanced stocks using a Zeiss stereomicroscope equipped with epifluorescence.


title: E2F #2

source_name: 8 to 10 hour old embryos from Arm-Gal4 crossed to E2f1/Dp


title: E2F 14-16 hrs mutant #2


title: dnE2F #1

source_name: 8 to 10 hour old embryos from Arm-Gal4 crossed to E2f1336-805 (a dominant negative form of E2f1 lacking the DNA binding domain)


title: zebrafish-35hpf-cd41-sorted-GFP-neg-9_repl-4

status: Public on Apr 26 2008

city: Boston

first: Gerhard

middle: J

last: Weber

state: MA

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Children's Hospital Boston, Harvard Medical School

description: Gene expression data from sorted zebrafish GFP negative cell populations at 35hours post fertilization.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Danio rerio

source_name: transgenic zebrafish embryos at 35hpf

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

growth_protocol: Embryos were obtained by pairwise matings of adult transgenic fish, raised at 28 ºC.

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

treatment_protocol:
gata1-GFP+/+(12 somites),  lmo2-GFP+/+ (12 somites and 35 hpf)1 and cd41-GFP+/+ (35 hpf)2 cells were separated from GFP-/- cells by flow cytometry at the indicated stages.  Sorting was based on propidium iodide exclusion, forward scatter, and GFP fluorescence, using a FACSVantage flow cytometer (Beckton Dickinson).  Sorted cell populations were run twice to optimize cell purity.  Total RNA from cell-sorted populations was extracted with TRIzol reagent (Invitrogen) and purified on RNeasy resins (Qiagen) according to the manufacturer’s recommendations.  Total RNA was subjected to two rounds of linear amplification (Ambion) and hybridized to Affymetrix zebrafish Gene Chips, according to Affymetrix guidelines. After staining with a streptavidin-phycoerythrin conjugate (Molecular Probes), the fluorescence of bound RNA was quantitated by using a Gene Chip scanner (Affymetrix). The raw expression data were calculated and, after pairing of GFP+/+ and GFP-/- samples, statistically analyzed using methods implemented in Bioconductor’s “affy” package and available custom scripts 3,4.
references:
1.	Zhu, H. et al. Regulation of the lmo2 promoter during hematopoietic and vascular development in zebrafish. Dev Biol 281, 256-69 (2005).
2.	Lin, H. F. et al. Analysis of thrombocyte development in CD41-GFP transgenic zebrafish. Blood 106, 3803-10 (2005).
3.	Choe, S. E., Boutros, M., Michelson, A. M., Church, G. M. & Halfon, M. S. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 6, R16 (2005).
4.	Weber, G. J. et al. Mutant-specific gene programs in the zebrafish. Blood 106, 521-30 (2005).

tag: strain background

value: AB. Genotype:cd41-GFP transgenic, isolated GFP negative cells

tag: Age

value: 35 hours post fertilization


title: zebrafish-35hpf-cd41-sorted-GFP-pos+6_repl-2

description: Gene expression data from sorted zebrafish GFP positive cell populations at 35hours post fertilization.

value: AB. Genotype:cd41-GFP transgenic, isolated GFP positive cells


title: zebrafish-35hpf-cd41-sorted-GFP-pos+8_repl-3


title: zebrafish-35hpf-cd41-sorted-GFP-neg-6_repl-2


title: zebrafish-35hpf-cd41-sorted-GFP-pos+9_repl-4


title: zebrafish-35hpf-cd41-sorted-GFP-neg-8_repl-3


title: LEC jaundice Ra2606

status: Public on Apr 25 2008

city: Toulouse

first: Françoise

last: Guéraud

address: 180, Chemin de Tounefeuille BP3, Cedex 9

department: UMR1089 INRA-ENVT

country: France

institute: Institut National de la Recherche Agronomique (INRA)

description:
LEC rat is an inbread mutant strain of rat with hereditary hepatitis isolated from randomly bred Long Evans rats originating from Kobe University and maintened at Hokkaido University (Japan)
D-penicillamine is a copper chelating agent that it is shown to prevent hepatitis developing in LEC rats

hyb_protocol: 8 hours at 42ºC in the automatic hybridization machine discovery from Ventana. After hybridization, slides were washed twice in Ribowash buffer for 5 minutes with agitation and then once with 0.1xSSC buffer

scan_protocol: Scanning with Genepix 400A microarray scanner (Axon Instruments). Image analysis was made by Genepix Pro V6 software, each spot was evaluated and selectioned to be analysed by Bioplot software (Biochips Platform website, Genopole Toulouse Midi Pyrenees, INSA Toulouse).

data_processing: Background substraction with lowess allowed value 10, log transformation and Lowess normalization

organism: Rattus norvegicus

source_name: Total RNA from Log Evans Cinnamon-like rat liver, strong hepatitis, labeled with Cyanine-3

label_protocol: Reverse transcription of 5 µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260 and 550 nm

growth_protocol: Animals were maintened in metabolic cages from 6 weeks old until sacrifice. Under Institutional Animal Care and Use Commitee Guidlines. Temperature: 22 ºC. Cycles night/day: 12 hours. Food: AIN93 ad libitum

extract_protocol: Sacrifice by exsanguination under ether anesthesia. Liver was excised, washed in physiological saline solution, immersed in RNA later and stored at -80ºC. Isolation of total RNA from liver samples following the instructions from Qiagen RNeasy mini kit. Quality and quantity were determined by capilary electrophoresis (RNA 6000 nano assay, Agilent)

tag: Strain

value: LEC (Long Evans Cinnamon-like)

tag: Gender

value: Male

value: 11 weeks old

tag: Treatment

tag: Tissue

value: liver

tag: Other

value: abnormal liver histology and abnormal transaminases and bilirubin plasma levels (ALT=1184±344.71 U/l, AST=725.77±207.97 U/l, tBil=106.69±228.01 µmol/l )

source_name: Total RNA from D-penicillamine-treated Long Evans Cinnamon-like rat liver labeled with Cyanine-5

label_protocol: Reverse transcription of 5 µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260 and 650 nm

growth_protocol: Animals were maintened in metabolic cages frome 6 weeks old until sacrifice. Under Institutional Animal Care and Use Commitee Guidlines. Temperature: 22 ºC. Cycles night/day: 12 hours. Food: AIN93 ad libitum

treatment_protocol: D-penicillamine 100mg/kg/day in drinking water, from 6 weeks old until sacrifice at 13 weeks old

value: 13 weeks old

value: D-penicillamine 100mg/kg/day

value: normal liver histology and normal transaminases and bilirubin plasma levels (ALT < 77 U/l, AST < 140 U/l, tBil < 3 µmol/l )


title: LEC jaundice Ra1703


title: LEC slight jaundice Ra1303

source_name: Total RNA from Log Evans Cinnamon-like rat liver, slight hepatitis, labeled with Cyanine-5

value: abnormal liver histology and abnormal transaminases and bilirubin plasma levels (ALT=584.3±120 U/l, AST=479±144 U/l, tBil=106.98±64.69 µmol/l )

source_name: Total RNA from D-penicillamine-treated Long Evans Cinnamon-like rat liver labeled with Cyanine-3


title: LEC slight jaundice Ra2106

source_name: Total RNA from Log Evans Cinnamon-like rat liver, slight hepatitis, labeled with Cyanine-3


title: LEC jaundice Ra2706

source_name: Total RNA from Log Evans Cinnamon-like rat liver, strong hepatitis, labeled with Cyanine-5

value: 10 weeks old

value: abnormal liver histology and abnormal transaminases and bilirubin plasma levels (ALT=1184±344.71 U/l, AST=725±207.97 U/l, tBil=369.69±228.01 µmol/l )


title: LEC slight jaundice Ra2306


title: LEC Normal 9w Ra2506

source_name: Total RNA from Log Evans Cinnamon-like rat liver, normal liver, labeled with Cyanine-5

value: 9 weeks old


title: LEC slight jaundice Ra0401


title: zebrafish-35hpf-cd41-sorted-GFP-neg-3_repl-1


title: LEC Normal 9w Ra3207

source_name: Total RNA from Log Evans Cinnamon-like rat liver, normal liver, labeled with Cyanine-3


title: LEC slight jaundice Ra1603


title: zebrafish-35hpf-cd41-sorted-GFP-pos+3_repl-1


title: LEC Normal 9w Ra0201


title: LEC Normal 9w Ra3407

description:
LEC rat is an inbread mutant strain of rat with hereditary hepatitis isolated from randmly bred Long Evans rats originating from Kobe University and maintened at Hokkaido University (Japan)
D-penicillamine is a copper chelating agent that it is shown to prevent hepatitis developing in LEC rats


title: LEC Normal 6w Ra2906

value: 6 weeks old

value: normal liver histology and normal transaminases and bilirubin plasma levels (ALT < 77 U/l, AST < 140 U/l, tBil < 3  µmol/l )


title: LEC Normal 6w Ra3106


title: LEC Normal 6w Ra0702


title: LEC Normal 9w Ra2406


title: LEC slight jaundice Ra0601

value: 12 weeks old


title: LEC jaundice Ra0501


title: LEC Normal 6w Ra3006


title: LEC Normal 6w Ra0502

label_protocol: Reverse transcription of 5 µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260 and 550  nm

value: normal liver histology and normal transaminases and bilirubin plasma levels (ALT  <  77 U/l, AST  <  140 U/l, tBil < 3  µmol/l )

label_protocol: Reverse transcription of 5 µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260 and 650  nm


title: LEC Normal 9w Ra0101


title: LEC jaundice Ra1503


title: LEC Normal 6w Ra0602


title: Prachatice parent 5

status: Public on Apr 17 2008

city: Maastricht

first: Danitsja

middle: Maria

last: van Leeuwen

address: PO Box 616

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

description: Blood collected from Prachatice parents which live in an area with low levels of air pollution

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Scanning on ScanArrayExpress (Perkin Elmer). All slides were scanned with set laser power at 100% and photomultiplier gain at 55% for Cy5 and 60% for Cy3 channel based on previous establishment of ideal scan settings

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) andf included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of Cy5 (test) with Cy3 (common reference) sample

organism: Homo sapiens

source_name: human whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow

label_protocol: Agilent Low RNA Input Linear Amplification system according to the manufacturer's instructions.

growth_protocol: No growth protocols were used as RNA was extracted from blood without any ex vivo performances.

extract_protocol: Total RNA isolation with PAXgene Blood RNA system according to manufacturer's instructions. Additional DNAse treatment and concentration of material with Qiagens MinElute system according to manufacturer's instructions.

treatment_protocol: Blood collection into PAXgene RNA vacutainers.

tag: whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow from Prachatice individual

source_name: common reference sample compsed of total RNAs isolated from whole blood from 20 Prachatice children


title: Prachatice parent 6

tag: whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow


title: Prachatice parent 10


title: Prachatice parent 1


title: Prachatice parent 11


title: Prachatice parent 12


title: Teplice parent 11

description: Blood collected from Teplice parents which live in an area with high levels of air pollution

tag: whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow from Teplice individual


title: Prachatice parent 7


title: Prachatice parent 9


title: Prachatice parent 4


title: Teplice parent 12


title: Teplice parent 8


title: Teplice parent 10


title: Teplice parent 4


title: Teplice parent 1


title: Teplice parent 3


title: Prachatice parent 2


title: Prachatice child 24

description: Blood collected from Prachatice children which live in an area with low levels of air pollution


title: Prachatice child 23


title: Prachatice child 21


title: Prachatice parent 3


title: Prachatice child 22


title: Teplice parent 5


title: Prachatice child 20


title: Teplice parent 2


title: Prachatice child 19


title: Teplice parent 6


title: Teplice parent 9


title: Prachatice child 15


title: Prachatice child 14


title: Prachatice child 13


title: Prachatice child 17


title: Prachatice child 10


title: Prachatice child 12


title: Prachatice child 8


title: Prachatice child 11


title: Prachatice child 9


title: Prachatice child 7


title: Prachatice child 5


title: Prachatice child 3


title: Prachatice child 4


title: Teplice child 23

description: Blood collected from Teplice children which live in an area with high levels of air pollution


title: Prachatice child 2


title: Prachatice child 1


title: Prachatice child 6


title: Teplice child 22


title: Teplice child 20


title: Teplice child 19


title: Teplice child 16


title: Teplice child 18


title: Teplice child 17


title: Teplice child 21


title: Teplice child 15


title: Teplice child 13


title: Teplice child 12


title: Teplice child 8


title: Teplice child 14


title: Teplice child 9


title: Teplice child 6


title: Teplice child 7


title: Teplice child 11


title: Teplice child 4


title: Teplice child 1


title: Teplice child 5


title: Teplice child 2


title: Teplice child 3


title: Sample 3106c, cell line 3106

status: Public on Apr 15 2008

city: pittsburgh

first: Naftali

last: Kaminski

state: PA

address: 3459 5th Avenue

department: Pulmonary, Allergy and Critical Care Medicine

institute: University of Pittsburgh Medical Center

description: Male

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Rhesus Macaque Genome 49 format Arrays

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner

data_processing: The data were analyzed with Affymetrix GCOS software, Statistical analysis was performed using Scoregene gene expression package at the Computational Molecular Biology website of The Hebrew University,and data visualization was performed using Genexpress (Stanford University), Spotfire Decision Site 8.0 (Spotfire Inc. Göteborg, Sweden) and Treeview (Eisen lab).

organism: Macaca mulatta

source_name: embryonic stem cell line 3106

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Inner cell mass (ICM) cells were isolated from expanded blastocysts using immunosurgery. First, the zona pellucidas were removed by exposure to acid Tyrode’s media (Specialty Media, Phillipsburg, NJ) for 30-45 seconds. The ICM was next isolated by exposure first to anti-monkey antiserum [1:3, Sigma, St. Louis MO] for 15-20 min at 37° C and then transferred to guinea pig complement [1:3; Biomeda, Foster City, CA] for an additional 15-20 min at 37°C. This destroys the outer trophectoderm, leaving the ICM cells intact. Mechanical pipetting with a 75 ìm tip was used to dissociate the ICM, prior to washing and plating onto mitomycin C-treated mouse embryonic fibroblasts (MEF; Specialty Media) in 80% Knockout Media; 20% Knockout Serum Replacer; 1mM L-glutamine; 0.1mM Nonessential Amino Acids; 1% Penicillin/Streptomycin; 12ng/mL of bFGF; 10ng/mL of Activin A and 10ng/mL hLIF (All components from Invitrogen except hLIF, Chemicon and Activin A, Sigma). After 10 to 14 days, sections of expanded ICM with characterisitic ESC morphology (tightly packed cells with high nuclear:cytoplasm ratio and prominent nucleoli) are dissociated with a fine glass capillary and colony pieces transferred to new MEF for expansion with culture media changed every 48 hours.

treatment_protocol: Non-human primate ESCs were isolated by scraping colonies with good morphology

tag: parent ID M106F88


title: Sample 3806b, cell line 3806

description: Female

source_name: embryonic stem cell line 3806

tag: parent ID M106F32


title: Prachatice child 18


title: Sample 3806a, cell line 3806

description: Female


title: Sample 3006c, cell line 3006

description: Female

source_name: embryonic stem cell line 3006


title: Sample 3806c, cell line 3806

description: Female


title: Sample 3006a, cell line 3006

description: Female


title: Sample 3106a, cell line 3106

description: Male


title: Sample 3006b, cell line 3006

description: Female


title: Sample 2706c, cell line 2706

description: Male

source_name: embryonic stem cell line 2706


title: Sample 2406a, cell line 2406

description: Female

source_name: embryonic stem cell line 2406

tag: parent ID M106F77


title: Sample 2706a, cell line 2706

description: Male


title: Sample 2406e, cell line 2406

description: Female


title: Sample 2706b, cell line 2706

description: Male


title: Sample 906c, cell line 906

description: Male

source_name: embryonic stem cell line 906

tag: parent ID M36F183


title: Sample 2906d, cell line 2906

description: Female

source_name: embryonic stem cell line 2906


title: Sample 2406d, cell line 2406

description: Female


title: Sample 906a, cell line 906

description: Male


title: Sample 306a, cell line 306

description: Male

source_name: embryonic stem cell line 306

tag: parent ID M106F244


title: Sample 306b, cell line 306

description: Male


title: Sample 906d, cell line 906

description: Male


title: Sample 306c, cell line 306

description: Male


title: LEC jaundice Ra1403

source_name: Total RNA from Log Evans Cinnamon-like rat liver, strong hepatitis, labeled with Cyanine-3

source_name: Total RNA from D-penicillamine-treated Long Evans Cinnamon-like rat liver labeled with Cyanine-5


title: Sample 106d, cell line 106

description: Male

source_name: embryonic stem cell line 106


title: Sample 206c, cell line 206

description: Female

source_name: embryonic stem cell line 206


title: Prachatice parent 8


title: Sample 106a, cell line 106

description: Male


title: Neuro2a control siRNA

status: Public on Apr 09 2008

city: Kisarazu

first: Kazuhide

last: Imai

state: Chiba

address: 2-6-7 Kazusa-Kamatari

country: Japan

institute: Chiba Industry Advancement Center

description: Gene expression data on Affymetrix GeneChip Mouse Genome 430 2.0 Array from Neuro2a cells transfected with  control (non-specific) siRNA

hyb_protocol: Using standard Affymetrix protocols (Affymetrix 1999 Genechip Expression Technical Manual, Affymetrix Santa Clara USA)

data_processing: Using Affymetrix global scaling (TGT 100) and MAS5 algorithm

organism: Mus musculus

source_name: Neuro2a, a murine neuroblastoma cells

extract_protocol: Total RNA isolation was performed with Trizol reagent.

treatment_protocol: Neuro2a cells were treated with control (non-specific) siRNA

tag: murine neuroblastoma Neuro2a cells


title: Neuro2a siRNA against mKIAA1583 (Tmem132a)

scan_protocol: Using standard Affymetrix protocols (Affymetrix 1999 Genechip Expression Technical Manual, Affymetrix Santa Clara USA)

treatment_protocol: Neuro2a cells were treated with siRNA against mKIAA1583 (Tmem132a)


title: Disease_4_T12

status: Public on Apr 03 2008

city: San Francisco

first: Sergio

last: Baranzini

state: CA

address: 513 Parnassus Ave

department: Neurology

institute: University of California San Francisco

description: Disease animal

hyb_protocol: Hybridization onto glass slides containing 16,496 spotted 60- to 70-mer oligonucleotides, followed by washing and scanning was performed at the Gladstone microarray core facility at the University of California (San Francisco, CA).

scan_protocol: Scanning was performed at the Gladstone microarray core facility at the University of California (San Francisco, CA).

data_processing: Lowess normalized ratios as calculated by BRB array Tools Software (NIH)

source_name: Disease animal #4, timepoint 12

label_protocol: Samples were hydrolyzed by adding 10 micro liters of 0.1 N NaOH, neutralized with 25 micro liters of 1 M HEPES, and precipitated with 3 M sodium acetate and ethanol. Resuspension in 0.05 M sodium bicar- bonate was followed by 1 h incubation with either N-hydroxysuccinimide ester Cy3 or Cy5 fluorescent dyes (Amersham Biosciences). Probes were quenched by the addition of 4 M hydroxylamine and neutralized with 100 mM sodium acetate. Final probe cleanup was conducted using the QIA- Quick PCR purification kit (Qiagen). We followed a common reference design in which each Cy3-labeled spinal cord probe was combined with a Cy5-labeled probe derived from a pool of brain and spleen RNA. Hybrid- ization onto glass slides containing 16,496 spotted 60- to 70-mer oligonu- cleotides, followed by washing and scanning was performed at the Glad- stone microarray core facility at the University of California (San Francisco, CA).

extract_protocol: Spinal cords were removed from RNA later and homogenized in TRIzol (Invitrogen Life Technologies) using an electric homogenizer

tag: Disease animal

source_name: Common reference RNA pool

extract_protocol: cDNA was synthesized from 15 micrograms of total RNA using Superscript II RT (Invitrogen Life Technologies) and a modified dNTP mix containing dUTP

tag: RNA from lymph node


title: Disease_4_T11

description: Disease animal

source_name: Disease animal #4, timepoint 11


title: Disease_4_T8R2

description: Disease animal

source_name: Disease animal #4, timepoint 8, replicate 2


title: Sample 106c, cell line 106

description: Male


title: Disease_4_T10

description: Disease animal

source_name: Disease animal #4, timepoint 10


title: Disease_4_T6R2

description: Disease animal

source_name: Disease animal #4, timepoint 6, replicate 2


title: Disease_4_T5

description: Disease animal

source_name: Disease animal #4, timepoint 5


title: Disease_4_T7

description: Disease animal

source_name: Disease animal #4, timepoint 7


title: Sample 206a, cell line 206

description: Female


title: Disease_4_T9

description: Disease animal

source_name: Disease animal #4, timepoint 9


title: Disease_4_T4

description: Disease animal

source_name: Disease animal #4, timepoint 4


title: Disease_3_T10

description: Disease animal

source_name: Disease animal #3, timepoint 10


title: Disease_3_T11R2

description: Disease animal

source_name: Disease animal #3, timepoint 11, replicate 2


title: Disease_3_T9

description: Disease animal

source_name: Disease animal #3, timepoint 9


title: Teplice parent 7

source_name: human whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow

source_name: common reference sample compsed of total RNAs isolated from whole blood from 20 Prachatice children


title: Disease_4_T1

description: Disease animal

source_name: Disease animal #4, timepoint 1


title: Disease_4_T0RB

description: Disease animal

source_name: Disease animal #4, timepoint 0, replicate B


title: Disease_3_T12R2

description: Disease animal

source_name: Disease animal #3, timepoint 12, replicate 2


title: Disease_3_T13

description: Disease animal

source_name: Disease animal #3, timepoint 13

source_name: Common reference RNA pool


title: Disease_3_T8R2

description: Disease animal

source_name: Disease animal #3, timepoint 8, replicate 2


title: Disease_4_T3R2

description: Disease animal

source_name: Disease animal #4, timepoint 3, replicate 2


title: Disease_3_T6R2

description: Disease animal

source_name: Disease animal #3, timepoint 6, replicate 2


title: Disease_3_T5

description: Disease animal

source_name: Disease animal #3, timepoint 5


title: Disease_3_T4R2

description: Disease animal

source_name: Disease animal #3, timepoint 4, replicate 2


title: Prachatice child 16


title: Disease_3_T7

description: Disease animal

source_name: Disease animal #3, timepoint 7


title: Disease_3_T1

description: Disease animal

source_name: Disease animal #3, timepoint 1


title: Disease_2_T8

description: Disease animal

source_name: Disease animal #2, timepoint 8


title: Disease_2_T12

description: Disease animal

source_name: Disease animal #2, timepoint 12


title: Disease_2_T5

description: Disease animal

source_name: Disease animal #2, timepoint 5


title: Disease_2_T9R2

description: Disease animal

source_name: Disease animal #2, timepoint 9, replicate 2


title: Disease_2_T4

description: Disease animal

source_name: Disease animal #2, timepoint 4


title: Disease_2_T10R2

description: Disease animal

source_name: Disease animal #2, timepoint 10, replicate 2


title: Disease_2_T1

description: Disease animal

source_name: Disease animal #2, timepoint 1


title: Disease_2_T11

description: Disease animal

source_name: Disease animal #2, timepoint 11


title: Disease_2_T6R2

description: Disease animal

source_name: Disease animal #2, timepoint 6, replicate 2


title: Disease_3_T0

description: Disease animal

source_name: Disease animal #3, timepoint 0

source_name: Common reference RNA pool


title: Disease_1_T12

description: Disease animal

source_name: Disease animal #1, timepoint 12


title: Disease_1_T11

description: Disease animal

source_name: Disease animal #1, timepoint 11


title: Disease_1_T10R2

description: Disease animal

source_name: Disease animal #1, timepoint 10, replicate 2


title: Disease_3_T2

description: Disease animal

source_name: Disease animal #3, timepoint 2


title: Disease_2_T0

description: Disease animal

source_name: Disease animal #2, timepoint 0


title: Teplice child 10

source_name: human whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow

source_name: common reference sample compsed of total RNAs isolated from whole blood from 20 Prachatice children


title: Disease_2_T3

description: Disease animal

source_name: Disease animal #2, timepoint 3


title: Disease_1_T7

description: Disease animal

source_name: Disease animal #1, timepoint 7


title: Disease_1_T3

description: Disease animal

source_name: Disease animal #1, timepoint 3


title: Disease_1_T5

description: Disease animal

source_name: Disease animal #1, timepoint 5


title: Disease_1_T6

description: Disease animal

source_name: Disease animal #1, timepoint 6


title: Disease_1_T0

description: Disease animal

source_name: Disease animal #1, timepoint 0


title: Disease_1_T4

description: Disease animal

source_name: Disease animal #1, timepoint 4


title: Sample 3106b, cell line 3106

description: Male

source_name: embryonic stem cell line 3106


title: Control_2_T11

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 11

tag: Control animal, adjuvent injected


title: Disease_1_T9

description: Disease animal

source_name: Disease animal #1, timepoint 9

source_name: Common reference RNA pool


title: Control_2_T10R2

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 10, replicate 2


title: Control_2_T12

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 12


title: Disease_1_T13R2

description: Disease animal

source_name: Disease animal #1, timepoint 13, replicate 2


title: Disease_1_T8

description: Disease animal

source_name: Disease animal #1, timepoint 8


title: Control_2_T3

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 3


title: Control_2_T5R2

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 5, replicate 2


title: Control_2_T6

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 6


title: Control_2_T4R2

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 4, replicate 2


title: Control_2_T7

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 7


title: Control_1_T12

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 12


title: Control_1_T6R2

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 6, replicate 2


title: Control_2_T8R2

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 8, replicate 2


title: Control_1_T4

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 4


title: Control_2_T2

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 2


title: dye-swap experiment between shoot submarged in water for 72hours and non-treated shoot 2

status: Public on Apr 01 2008

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

description: 10 days old shoot13' is control sample. 'shoot submarged in water for 48hours' is target sample, and is same as sample of sample name FS48hrs_self. The data of sample treated for 24 hours are GSM45503 and 45502

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 8.1.1.1
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Japonica Group

source_name: shoot submarged in water for 72hours

label_protocol:
Kit: Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Linear Amplification kit standard protocol

growth_protocol:
growth: hydroponic culture
growth enviroment: growth chamber study
Growth substrates: 1/5000 diluted Hyponex (10-3-3) solution
light condition: 16hrs day length
temperature: 28 degreeC

extract_protocol:
Separation technique: Trimming
Extraction source: Frozen
Kit: RNeasy Midi Kit
Manufacturer: QIAGEN
Manual: QIAGEN
Kit: OligotexTM-dt30 <Super> mRNA Purification kit (From Total RNA)
Manufacturer: TaKaRa
Manual: TaKaRa

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: 72 hours

tag: cultivar

value: Nipponbare

value: shoot

tag: stage

value: LP.03 three leaves visible

tag: age

value: 10 days after sowing

source_name: 10 days old shoot13


title: Control_1_T10

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 10

source_name: Common reference RNA pool


title: dye-swap experiment between shoot submarged in water for 72hours and non-treated shoot 1

description: 10 days old shoot13' is control sample. 'shoot submarged in water for 72hours' is target sample, and is same as sample of sample name FS72hrs_self. The data of sample treated for 24 hours are GSM45503 and 45501

tag: Tissue


title: dye-swap experiment between laid-down shoot submarged in water for 6 hours and non-treated shoot 1

description: 10 days old shoot12' is control sample. laid-down shoot submarged in water for 6 hours' is target sample, and is same as sample of sample name FL06hrs_self. The data of sample treated for 24 hours are GSM45503 and 45504

source_name: 10 days old shoot12

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: lay down
stress factor: 6 hours


title: Control_2_T1

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 1


title: dye-swap experiment between laid-down shoot submarged in water for 48 hours and non-treated shoot 1

description: 10 days old shoot12' is control sample. laid-down shoot submarged in water for 48 hours' is target sample, and is same as sample of sample name FL48hrs_self. The data of sample treated for 24 hours are GSM45503 and 45504

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: lay down
stress factor: 48 hours


title: dye-swap experiment between shoot treated 25% PEG for 9hours and non-treated shoot 1

description: 10 days old shoot3' is control sample, and is same as sample of sample name shoot_self4. 'shoot treated with 25% polyethylene glycol 6000 for 9 hours' is target sample, and is same as sample of sample name Drt09hrs_self. The data of sample treated for 24 hours are GSM45725 and 45726

source_name: 10 days old shoot3

treatment_protocol:
aboitic factor: drought environment
stress factor: 25% polyethylene glycol 6000
stress factor: 9 hours


title: dye-swap experiment between shoot treated 25% PEG for 9hours and non-treated shoot 2

source_name: shoot treated with 25% polyethylene glycol 6000 for 9 hours


title: dye-swap experiment between shoot submarged in water for 48hours and non-treated shoot 1

description: 10 days old shoot13' is control sample. 'shoot submarged in water for 48hours' is target sample, and is same as sample of sample name FS48hrs_self. The data of sample treated for 24 hours are GSM45503 and 45501

source_name: shoot submarged in water for 48hours

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: 48 hours


title: dye-swap experiment between shoot submarged in water for 48hours and non-treated shoot 2


title: Disease_1_T2R2

description: Disease animal

source_name: Disease animal #1, timepoint 2, replicate 2


title: dye-swap experiment between shoot treated 10 degreeC for 72hours and non-treated shoot 1

description: 10 days old shoot4' is control sample, and is same as sample of sample name shoot_self4. 'shoot treated with 10 degreeC for 72 hours' is target sample, and is same as sample of sample name cold72hrs_self. The data of sample treated for 24 hours are GSM45729 and 45731

source_name: 10 days old shoot4

treatment_protocol:
aboitic factor: cold temperature regimen
stress factor: 10 degree C
stress factor: 72 hours


title: dye-swap experiment between laid-down shoot submarged in water for 6 hours and non-treated shoot 2


title: Control_1_T13

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 13


title: Control_1_T11

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 11


title: dye-swap experiment between shoot treated 10 degreeC for 72hours and non-treated shoot 2

source_name: shoot treated with 10 degreeC for 72 hours


title: dye-swap experiment between shoot treated 25% PEG for 1hour and non-treated shoot 1

description: 10 days old shoot3' is control sample, and is same as sample of sample name shoot_self4. 'shoot treated with 25% polyethylene glycol 6000 for 1 hour' is target sample, and is same as sample of sample name Drt01hr_self. The data of sample treated for 24 hours are GSM45725 and 45726

treatment_protocol:
aboitic factor: drought environment
stress factor: 25% polyethylene glycol 6000
stress factor: 1 hour


title: dye-swap experiment between laid-down shoot submarged in water for 48 hours and non-treated shoot 2


title: Control_1_T1

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 1


title: dye-swap experiment between shoot treated 10 degreeC for 48hours and non-treated shoot 1

description: 10 days old shoot4' is control sample, and is same as sample of sample name shoot_self4. 'shoot treated with 10 degreeC for 48 hours' is target sample, and is same as sample of sample name cold48hrs_self. The data of sample treated for 24 hours are GSM45729 and 45731

treatment_protocol:
aboitic factor: cold temperature regimen
stress factor: 10 degree C
stress factor: 48 hours


title: Control_1_T2

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 2


title: dye-swap experiment between shoot treated 10 degreeC for 48hours and non-treated shoot 2

source_name: shoot treated with 10 degreeC for 48 hours


title: dye-swap experiment between regenerated plant and shoot 1

description: 10 days old shoot7' is control sample, and is same as sample of sample name shoot_self7. 'regenerated plant from callus' is target sample, and is same as sample of sample name Reg_plant_self

source_name: 10 days old shoot7

source_name: regenerated plant from callus

growth_protocol:
growth: in vitro culture
growth enviroment: growth chamber study
Growth substrates: hormone-free medium
light condition: 16hrs day length
temperature: 28 degreeC
reference: Kyozuka and Shimamoto (1991) Transformation and regeneration of rice protoplasts. In K Lindsey, ed, Plant Tissue Culture Manual B1.

tag: Tissues

value: cultured callus

value: incubation for 52 days


title: dye-swap experiment between green callus and shoot 1

description: 10 days old shoot7' is control sample, and is same as sample of sample name shoot_self7. 'green callus incubated on re-differential induced medium' is target sample, and is same as sample of sample name Grn_callus_self

growth_protocol:
growth: in vitro culture
growth enviroment: growth chamber study
Growth substrates: redifferentiation medium
light condition: continuous light
temperature: 30 degreeC
reference: Kyozuka and Shimamoto (1991) Transformation and regeneration of rice protoplasts. In K Lindsey, ed, Plant Tissue Culture Manual B1.

value: plantlet regeneration (early)

value: incubation for 42 days


title: Control_2_T13

description: Control animal, adjuvent injected

source_name: Control animal #2, timepoint 13


title: dye-swap experiment between panicle and shoot 2

description: 10 days old shoot1' is control sample, and is same as sample of sample name shoot_self1. 'panicle before heading' is target sample, and is same as sample of sample name panicle_self

source_name: panicle before heading

growth_protocol:
growth: soil environment
growth enviroment: field study
light condition: not controlled

value: inflorescence

value: booting stage

source_name: 10 days old shoot1


title: dye-swap experiment between propagated callus and shoot 2

description: 10 days old shoot5' is control sample, and is same as sample of sample name shoot_self5. 'propagated callus' is target sample, and is same as sample of sample name Prop_callus_self

source_name: propagated callus

growth_protocol:
growth: in vitro culture
growth enviroment: growth chamber study
Growth substrates: callus induction medium
light condition: continuous light
temperature: 30 degreeC
reference: Kyozuka and Shimamoto (1991) Transformation and regeneration of rice protoplasts. In K Lindsey, ed, Plant Tissue Culture Manual B1.

value: in-vitro culture stage

value: incubation for 21 days

source_name: 10 days old shoot5


title: dye-swap experiment between root and shoot 2

description: 10 days old shoot1' is control sample, and is same as sample of sample name shoot_self1. '10 days old root' is target sample, and is same as sample of sample name root_self

source_name: 10 days old root

value: root


title: dye-swap experiment between mature leaf and shoot 1

description: 10 days old shoot1' is control sample, and is same as sample of sample name shoot_self1. 'mature leaf' is target sample, and is same as sample of sample name mature-leaf_self

source_name: mature leaf

value: flag leaf


title: dye-swap experiment between apical meristem and shoot 1

description: 10 days old shoot5' is control sample, and is same as sample of sample name shoot_self5. 'apical meristem' is target sample, and is same as sample of sample name meristem_self

source_name: apical meristem

value: shoot apex


title: dye-swap experiment between apical meristem and shoot 2


title: dye-swap experiment between germination seed and shoot 1

description: 10 days old shoot6' is control sample, and is same as sample of sample name shoot_self6. 'germinated seed' is target sample, and is same as sample of sample name Germ-seed_self

source_name: 10 days old shoot6

source_name: germinated seed

growth_protocol:
growth: hydroponic culture
growth enviroment: growth chamber study
Growth substrates: 1/5000 diluted Hyponex (10-3-3) solution
light condition: continuous dark
temperature: 28 degreeC

value: whole plant

value: coleoptile emergence

value: 4 days after sowing


title: dye-swap experiment between propagated callus and shoot 1

value: Nipponbare

value: shoot


title: Self-Hyb_FL48hrs

description: submarge and lay-down stress, self-hybridization

source_name: laid-down shoot submarged in water for 48 hours

value: LP.03 three leaves visible

value: 10 days after sowing


title: Self-Hyb_FS24hrs

description: submarge stress, self-hybridization

source_name: shoot submarged in water for 24hours

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: 24 hours


title: Self-Hyb_Salt24hrs

description: salt stress, self-hybridization

source_name: shoot treated with 150mM NaCl for 24 hours

treatment_protocol:
aboitic factor: salt regimen
stress factor: 150mM NaCl
stress factor: 24 hours


title: dye-swap experiment between mature leaf and shoot 2


title: Self-Hyb_Os24hrs

description: Osmotic stress, self-hybridization

source_name: shoot treated with 260mM mannitol for 24 hours

treatment_protocol:
aboitic factor: abiotic environment
stress factor: 260mM mannitol
stress factor: 24 hours


title: Self-Hyb_FS48hrs

description: submarge stress, self-hybridization

source_name: shoot submarged in water for 48hours


title: dye-swap experiment between root and shoot 1


title: Self-Hyb_FS72hrs

description: submarge stress, self-hybridization

source_name: shoot submarged in water for 72hours


title: Self-Hyb_FL6hrs

source_name: laid-down shoot submarged in water for 6 hours


title: Self-Hyb_FL24hrs

source_name: laid-down shoot submarged in water for 24 hours

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: lay down
stress factor: 24 hours


title: dye-swap experiment between germination seed and shoot 2


title: Control_1_T5

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 5

source_name: Common reference RNA pool


title: Control_1_T9R2

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 9, replicate 2


title: Control_1_T3

description: Control animal, adjuvent injected

source_name: Control animal #1, timepoint 3


title: Self-Hyb_drt09hrs

description: drought stress, self-hybridization

source_name: shoot treated with 25% polyethylene glycol 6000 for 9 hours


title: Self-Hyb_drt01hr

description: drought stress, self-hybridization

source_name: shoot treated with 25% polyethylene glycol 6000 for 1 hour


title: Self-Hyb_cold24hrs

description: cold stress, self-hybridization

source_name: shoot treated with 10 degreeC for 24 hours

treatment_protocol:
aboitic factor: cold temperature regimen
stress factor: 10 degree C
stress factor: 24 hours


title: Self-Hyb_germ_seed

description: self-hybridization


title: Self-Hyb_cold72hrs

description: cold stress, self-hybridization

source_name: shoot treated with 10 degreeC for 72 hours


title: Self-Hyb_prop_callus

description: Callus originated from primary callus, self-hybridization

source_name: propagated callus

value: cultured callus


title: dye-swap experiment between shoot treated 25% PEG for 1hour and non-treated shoot 2

source_name: 10 days old shoot3


title: Self-Hyb_mature-leaf

description: self-hybridization

source_name: mature leaf


title: Self-Hyb_grn_callus

description: Callus originated from callus incubated on re-differential induced medium, color of callus is green, self-hybridization

source_name: green callus incubated on re-differential induced medium

value: plantlet regeneration (early)


title: Self-Hyb_reg_plant

description: Plantlet generated from green green callus incubated on re-differential induced medium., self-hybridization

source_name: regenerated plant from callus

value: incubation for 52 days


title: Self-Hyb_shoot6

description: Technical replicate 6 of 7., self-hybridization

source_name: 10 days old shoot6


title: Self-Hyb_shoot4

description: Technical replicate 4 of 7., self-hybridization

source_name: 10 days old shoot4


title: Self-Hyb_root

description: self-hybridization

source_name: 10 days old root


title: Self-Hyb_shoot7

description: Technical replicate 7 of 7., self-hybridization

source_name: 10 days old shoot7


title: Self-Hyb_shoot5

description: Technical replicate 5 of 7., self-hybridization

source_name: 10 days old shoot5


title: Self-Hyb_cold48hrs

description: cold stress, self-hybridization

source_name: shoot treated with 10 degreeC for 48 hours


title: Self-Hyb_meristem

description: self-hybridization

source_name: apical meristem


title: Self-Hyb_shoot1

description: Technical replicate 1 of 7., self-hybridization

source_name: 10 days old shoot1


title: Self-Hyb_ Prim_callus

description: Callus originated from scutellum, self-hybridization

source_name: primary callus

value: incubation for 7 days

value: callus promotion


title: Self-Hyb_shoot2

description: Technical replicate 2 of 7., self-hybridization

source_name: 10 days old shoot2


title: Self-Hyb_shoot3

description: Technical replicate 3 of 7., self-hybridization


title: Self-Hyb_panicle

description: self-hybridization

source_name: panicle before heading

value: inflorescence

value: booting stage


title: dye-swap experiment between shoot laid down for 24 hours and non-treated shoot 1

description: 10 days old shoot10' is control sample, and is same as sample of sample name shoot_self10. 'shoot laid down for 24 hours' is target sample, and is same as sample of sample name L24hrs_self.

source_name: 10 days old shoot10

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

extract_protocol:
Separation technique: Trimming
Extraction source: Frozen
Kit: RNeasy Midi Kit
Manufacturer: QIAGEN
Manual: QIAGEN

source_name: shoot laid down for 24 hours

treatment_protocol:
aboitic factor: abiotic environment
stress factor: lay down
stress factor: 24 hours


title: dye-swap experiment between laid-down shoot submarged in water for 24 hour and non-treated shoot 2

description: 10 days old shoot10' is control sample, and is same as sample of sample name shoot_self10. 'laid-down shoot submarged in water for 1 hour' is target sample, and is same as sample of sample name FS01hrs_self.


title: dye-swap experiment between laid-down shoot submarged in water for 1 hour and non-treated shoot 1

description: 10 days old shoot10' is control sample, and is same as sample of sample name shoot_self10. 'laid-down shoot submarged in water for 1 hour' is target sample, and is same as sample of sample name FL01hrs_self.

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: lay down
stress factor: 1 hour


title: dye-swap experiment between shoot submarged in water for 1hour and non-treated shoot 2

source_name: shoot submarged in water for 1hour

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: 1 hour


title: dye-swap experiment between panicle and shoot 3

description: 10 days old shoot9' is control sample, and is same as sample of sample name shoot_self9. 'panicle before heading2' is target sample.

source_name: 10 days old shoot9

source_name: panicle before heading2


title: dye-swap experiment between germination seed and shoot 4

description: 10 days old shoot8' is control sample, and is same as sample of sample name shoot_self8. 'germinated seed2' is target sample, and is same as sample of sample name Germ-seed_self2

source_name: germinated seed2

source_name: 10 days old shoot8


title: dye-swap experiment between laid-down shoot submarged in water for 24 hours and non-treated shoot 4

description: 10 days old shoot9' is control sample, and is same as sample of sample name shoot_self9. 'laid-down shoot submarged in water for 24 hour2' is target sample..

source_name: laid-down shoot submarged in water for 24 hours2

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: lay down
stress factor: 24 hour


title: dye-swap experiment between shoot submarged in water for 24 hours and non-treated shoot 3

description: 10 days old shoot10' is control sample, and is same as sample of sample name shoot_self10. 'shoot submarged in water for 24 hours2' is target sample.

source_name: shoot submarged in water for 24 hours2

treatment_protocol:
aboitic factor: flood water
stress factor: flood
stress factor: 24 hour


title: Self-Hyb_shoot8

description: Technical replicate 1 of 4., self-hybridization


title: dye-swap experiment between shoot submarged in water for 1hour and non-treated shoot 1


title: dye-swap experiment between llaid-down shoot submarged in water for 24 hours and non-treated shoot 3


title: Self-Hyb_FL01hr

description: submarge and lay-down stress, self-hybridization

source_name: laid-down shoot submarged in water for 1 hours


title: Self-Hyb_FS01hr

description: submarge stress, self-hybridization

source_name: shoot submarged in water for 1hours


title: Self-Hyb_germ_seed2

description: self-hybridization


title: dye-swap experiment between shoot submarged in water for 24 hours and non-treated shoot 4


title: dye-swap experiment between germination seed and shoot 3


title: dye-swap experiment between primary callus and shoot 2

description: 10 days old shoot5' is control sample, and is same as sample of sample name shoot_self5. 'primary callus' is target sample, and is same as sample of sample name Prim_callus_self

value: in-vitro culture stage

source_name: 10 days old shoot5


title: Self-Hyb_shoot9

description: Technical replicate 2 of 4., self-hybridization


title: Self-Hyb_shoot11

description: Technical replicate 4 of 4, self-hybridization

source_name: 10 days old shoot11


title: dye-swap experiment between primary callus and shoot 1


title: Self-Hyb_shoot10

description: Technical replicate 3 of 4., self-hybridization


title: dye-swap experiment between panicle and shoot 1

description: 10 days old shoot1' is control sample, and is same as sample of sample name shoot_self1. 'panicle before heading' is target sample, and is same as sample of sample name panicle_self

source_name: 10 days old shoot1


title: HS11-139 aTEA 40 uM 12 hour treatment for MDA-MB-435 cells

status: Public on Mar 17 2008

city: Austin

first: Weiping

last: Yu

state: TX

address: 1 University Station

department: Microbiology

institute: The University of Texas at Austin

data_processing: Data generated by GenePix 5.0 software.

molecule: polyA RNA

source_name: vehicle treated MDA-MB-435 cells

extract_protocol: Messenger RNA was isolated using the FastTRack 2.0 kit (Invitrogen, Carlsbad, CA).

tag: vehicle (ethanol) treated MDA-MB-435 cells

source_name: aTEA 40 uM 12 hour treated MDA-MB-435 cells


title: Germfree-4 (GF4) villi cells cy5-cy3

status: Public on Mar 04 2008

city: Urbana

first: H

middle: Rex

last: Gaskins

state: IL

address: 1207 W Gregory Dr

department: Animal Sciences

institute: UIUC

description: The hybridization chamber was disassembled and the LifterSlip™ was removed by immersing the array in 2X SSC, 0.1% SDS (at 42 °C) until the LifterSlip™ moved freely away from the slide. The arrays were placed in 2X SSC, 0.1% SDS for 5 min at 42 °C. Subsequently the arrays were placed in 0.1X SSC, 0.1% SDS for 10 min at room temperature followed by 0.1X SSC for 1 min at room temperature. The arrays were then rinsed in 0.01X SSC for 10 sec or less and dried by centrifugation.

hyb_protocol: Porcine oligonucleotide set represents 13,297 porcine cDNAs and ESTs. A reference design was used in which each of the experimental samples was cohybridized with the reference sample that contained equal amounts of all the RNA samples used in the experiment, which allowed the treatment of fluorescence ratios as measurements of relative expression. Single-spotted oligos were printed on GAPS II slides (Corning, Corning, NY) at the W. M. Keck Center for Comparative and Functional Genomics, University of Illinois. Before hybridization, the arrays were plunged in 0.2% SDS water and immediately agitated vigorously for 2 min, washed three times in successive jars of distilled water and rinse in 100% ethanol. The arrays were then incubated in 5X SSC, 0.1% SDS, 1% BSA in a Coplin jar for 45 to 60 min at 42 °C, washed by immersing in 5 successive Coplin jars of deionized distilled water (RICCA Chemical Company, Arlington, TX), rinsed in 100% isopropanol, to ensure that the SDS is completely removed from the arrays and subsequently dried by centrifugation. An array was placed into a Corning Hybridization Chamber (Sigma) and 80 μl of the leveled solution was applied to a slide and covered with a LifterSlip™ (Erie Scientific, Portsmouth, NH). The chamber was then assembled and submerged in a 42 °C water bath for 48 h.

scan_protocol: Following hybridization and washing, slides were scanned immediately for both dye channels with an Axon 4000B (Molecular Devices, Union City, CA) dual-laser confocal scanner and images were processed using GenePix v6.0 software (Molecular Devices).

data_processing: Median foreground intensities (F) and median background intensities (B) were generated to construct the data matrix. Data were filtered out when the following criteria were satisfied: (I) removal of low intensity spots when F-B < M + 2 MAD, where M is the median of the negative control spots (blank or buffer spots); MAD is the median absolute deviation, (II) removal of saturated spots with very high intensity, and (III) removal of spots flagged by GenePix.  Data were normalized using the regional lowess normalization (rlowess) method from the MAANOVA package and analyzed by Proc GLM in SAS (version 8.2).  To avoid type I error of least square means, Proc multtest was conducted to generate a false discovery rate value (FDR). FDR adjustments balance type I and type II error rates. Genes were considered to be differentially expressed when P ≤ 0.05.

organism: Sus scrofa

source_name: Germfree-4 villi cells cy5

label_protocol: The amplified anti-sense (aRNA) was labeled with Cy3 or Cy5 dyes. Each of the 16 cell populations was reversed labeled with Cy3 and Cy5 to account for dye labeling bias, resulting in 32 target samples for microarray hybridization. Cy3 and Cy5 dyes were resuspended in 45 μl dimethyl sulfoxide (DMSO, Sigma) and stored at – 80 °C in a light protected area. For the labeling reaction, 5-7 μg of amino-allyl tagged aRNA was dried in a SpeedVac and 5 μl of 0.1 M Na2CO3 (pH, 9.0) and 5 μl of dye (Cy3 or Cy5) dissolved in DMSO were added to the dried sample. The mixture was then incubated in the dark for 75 min and unincorporated dye was removed with a modified protocol based on the Qiagen Mini Elute Kit (Qiagen, Valencia, CA) with a total elution volume of 50 µl for each sample.  The sample was then dried in a SpeedVac for 50 min to dryness followed by adding 10 µl of RNase free water.  To decrease the fragment size to 60-200 bases, 1 µL of fragmentation buffer (Ambion) was added to the sample and heated to 70 °C for 15 min. Stop solution (1 µl) was added to terminate the reaction. A blocking mixture containing 2 µl of poly d(A) and 20 µl of Porcine HyblocTM (Applied Genetics Laboratories, Inc, Melbourne, FL) were added to 12 µl probe and incubated at 100 °C for 1 min then snap cool on ice for 2 min. Subsequently, the mixture was centrifuged to dryness in a SpeedVac and 80 µl of the hybridization buffer (20% formamide, 5X Denhardts, 6x SSC, 0.1 % SDS, 25 µg/ml tRNA, and RNase free water) was added to each dried sample. The probe was warmed to 42 °C for 5 min and maintained at this temperature until hybridization.

extract_protocol: Total RNA was isolated from laser captured villus and crypt cells using the PicoPureTM RNA isolation Kit (Arcturus) according to manufacturer’s recommendations. Briefly, 20 μl of extraction buffer was placed into the LCM assembly microcentrifuge tube and incubated for 30 min at 42 °C. After incubation, the assembly was briefly centrifuged to collect the extraction fluid into the microcentrifuge tube. The fluid was then loaded onto a spin column, washed several times, and the total cellular RNA was eluted as 10 μl volume. RNA from each sample was subjected to 2 rounds of amplification using the RiboAmpTM RNA linear amplification kit (Arcturus). Subsequently, RNA was reverse-transcribed into cDNA incorporating a T7 promoter. The cDNA was eluted with 16 μl of elution buffer and in vitro transcribed into amplified anti-sense RNA with a T7 RNA polymerase incorporating amino-allyl-UTP (Ambion, Austin, TX).

tag: aRNA labeled with cy5

source_name: reference sample

tag: aRNA labeled with cy3


title: Germfree-3 (GF3) villi cy5-cy3

source_name: Germfree-3  villi cy5


title: Germfree-1 (GF1) villi cells cy5-c3

source_name: Germfree-1 (GF1) villi cells cy5

source_name: pooled sample


title: Germfree-4 (GF4) villi cells cy3-cy5

source_name: Germfree-4  villi cells cy3


title: HS9-169 aTEA 40 uM 12 hour treatment for MDA-MB-435 cells

tag: aTEA 40 uM 12 hour treated MDA-MB-435 cells


title: HS11-135 aTEA 40 uM 12 hour treatment for MDA-MB-435 cells


title: Conventional16 (CONV16) villi cells cy3-cy5

source_name: Conventional16 (CONV16) villi cells cy3

source_name: pooled reference sample


title: Conventional-15 (CONV15) cy5-cy3 villi cells

source_name: Conventional-15  villi cells cy5

source_name: pooled raference sample


title: Conventional-16 (CONV16) villi cells cy5-cy3

source_name: Conventional-16 villi cells cy5


title: Germfree-1 (GF1) villi cells cy3-cy5

source_name: Germfree-1  villi cells cy3


title: Germfree-3 (GF3) villi cells cy3-cy5

source_name: Germfree-3 villi cells cy3


title: Conventional-14 (CONV14) villi cells cy3-cy5

source_name: Conventional-14  villi cells


title: HS9-170 aTEA 40 uM 12 hour treatment for MDA-MB-435 cells


title: Conventional-14 (CONV14) villi cells cy5-cy3


title: Conventional-13 (CONV13) villi cells cy5-cy3

source_name: Conventional-13 villi cells


title: Germfree-3 (GF-3)  crypt cells cy5-cy3

source_name: Germ free aRNA

source_name: pooled sample Cy3

tag: reference aRNA labeled cy3


title: Germfree-2 (GF2) villi cells cy3-cy5

source_name: Germfree-2 villi cells cy3


title: Conventional-13 (CONV13) villi cells cy3-cy5


title: HS9-074 aTEA 40 uM 12 hour treatment for MDA-MB-435 cells

source_name: vehicle treated MDA-MB-435 cells

source_name: aTEA 40 uM 12 hour treated MDA-MB-435 cells


title: dye-swap experiment between panicle and shoot 4

source_name: panicle before heading2

source_name: 10 days old shoot9


title: Conventional-15 (CONV15) villi cells cy3-cy5

source_name: reference sample


title: Germfree crypt 4 cy3-cy5

description: The hybridization chamber was disassembled and the LifterSlip™ was removed by immersing the array in 2X SSC, 0.1% SDS (at 42 °C) until the LifterSlip™ moved freely away from the slide. The arrays were placed in 2X SSC, 0.1% SDS for 5 min at 42 °C. Subsequently the arrays were placed in 0.1X SSC, 0.1% SDS for 10 min at room temperature followed by 0.1X SSC for 1 min at room temperature. The arrays were then rinsed in 0.01X SSC for 10 sec or less and dried by centrifugation. Following hybridization and washing, slides were scanned immediately for both dye channels with an Axon 4000B (Molecular Devices, Union City, CA) dual-laser confocal scanner and images were processed using GenePix v6.0 software (Molecular Devices).

source_name: Germfree crypt 4


title: Germfree-4 (GF4) crypt cells cy5-cy3

source_name: Germfree crypt cells

source_name: reference pooled sample


title: Conventional crypt 16 cy3-cy5

type: other

description: Porcine oligonucleotide set represents 13,297 porcine cDNAs and ESTs. A reference design was used in which each of the experimental samples was cohybridized with the reference sample that contained equal amounts of all the RNA samples used in the experiment, which allowed the treatment of fluorescence ratios as measurements of relative expression. Single-spotted oligos were printed on GAPS II slides (Corning, Corning, NY) at the W. M. Keck Center for Comparative and Functional Genomics, University of Illinois. Before hybridization, the arrays were plunged in 0.2% SDS water and immediately agitated vigorously for 2 min, washed three times in successive jars of distilled water and rinse in 100% ethanol. The arrays were then incubated in 5X SSC, 0.1% SDS, 1% BSA in a Coplin jar for 45 to 60 min at 42 °C, washed by immersing in 5 successive Coplin jars of deionized distilled water (RICCA Chemical Company, Arlington, TX), rinsed in 100% isopropanol, to ensure that the SDS is completely removed from the arrays and subsequently dried by centrifugation. An array was placed into a Corning Hybridization Chamber (Sigma) and 80 μl of the leveled solution was applied to a slide and covered with a LifterSlip™ (Erie Scientific, Portsmouth, NH). The chamber was then assembled and submerged in a 42 °C water bath for 48 h. he hybridization chamber was disassembled and the LifterSlip™ was removed by immersing the array in 2X SSC, 0.1% SDS (at 42 °C) until the LifterSlip™ moved freely away from the slide. The arrays were placed in 2X SSC, 0.1% SDS for 5 min at 42 °C. Subsequently the arrays were placed in 0.1X SSC, 0.1% SDS for 10 min at room temperature followed by 0.1X SSC for 1 min at room temperature. The arrays were then rinsed in 0.01X SSC for 10 sec or less and dried by centrifugation. Slides were scanned immediately for both dye channels with an Axon 4000B (Molecular Devices, Union City, CA) dual-laser confocal scanner and images were processed using GenePix v6.0 software (Molecular Devices).

data_processing: Median foreground intensities (F) and median background intensities (B) were generated to construct the data matrix. Data were filtered out when the following criteria were satisfied: (I) removal of low intensity spots when F-B < M + 2 MAD, where M is the median of the negative control spots (blank or buffer spots); MAD is the median absolute deviation, (II) removal of saturated spots with very high intensity, and (III) removal of spots flagged by GenePix.  Data were normalized using the regional lowess normalization (rlowess) method from the MAANOVA package and analyzed by Proc GLM in SAS (version 8.2). To avoid type I error of least square means, Proc multtest was conducted to generate a false discovery rate value (FDR). FDR adjustments balance type I and type II error rates. Genes were considered to be differentially expressed when P ≤ 0.05.

molecule: other

source_name: Conventional crypt

label_protocol: Cy3 and Cy5 dyes were resuspended in 45 μl dimethyl sulfoxide (DMSO, Sigma) and stored at – 80 °C in a light protected area. For the labeling reaction, 5-7 μg of amino-allyl tagged aRNA was dried in a SpeedVac and 5 μl of 0.1 M Na2CO3 (pH, 9.0) and 5 μl of dye (Cy3 or Cy5) dissolved in DMSO were added to the dried sample. The mixture was then incubated in the dark for 75 min and unincorporated dye was removed with a modified protocol based on the Qiagen Mini Elute Kit (Qiagen, Valencia, CA) with a total elution volume of 50 µl for each sample.  The sample was then dried in a SpeedVac for 50 min to dryness followed by adding 10 µl of RNase free water.  To decrease the fragment size to 60-200 bases, 1 µL of fragmentation buffer (Ambion) was added to the sample and heated to 70 °C for 15 min. Stop solution (1 µl) was added to terminate the reaction. A blocking mixture containing 2 µl of poly d(A) and 20 µl of Porcine HyblocTM (Applied Genetics Laboratories, Inc, Melbourne, FL) were added to 12 µl probe and incubated at 100 °C for 1 min then snap cool on ice for 2 min. Subsequently, the mixture was centrifuged to dryness in a SpeedVac and 80 µl of the hybridization buffer (20% formamide, 5X Denhardts, 6x SSC, 0.1 % SDS, 25 µg/ml tRNA, and RNase free water) was added to each dried sample. The probe was warmed to 42 °C for 5 min and maintained at this temperature until hybridization.

extract_protocol: RNA from each sample was subjected to 2 rounds of amplification using the RiboAmpTM RNA linear amplification kit (Arcturus). Subsequently, RNA was reverse-transcribed into cDNA incorporating a T7 promoter. The cDNA was eluted with 16 μl of elution buffer and in vitro transcribed into amplified anti-sense RNA with a T7 RNA polymerase incorporating amino-allyl-UTP (Ambion, Austin, TX). The amplified anti-sense (aRNA) was labeled with Cy5 dye.

extract_protocol: RNA from each sample was subjected to 2 rounds of amplification using the RiboAmpTM RNA linear amplification kit (Arcturus). Subsequently, RNA was reverse-transcribed into cDNA incorporating a T7 promoter. The cDNA was eluted with 16 μl of elution buffer and in vitro transcribed into amplified anti-sense RNA with a T7 RNA polymerase incorporating amino-allyl-UTP (Ambion, Austin, TX). The amplified anti-sense (aRNA) was labeled with Cy3 dye.


title: Conventional crypt 16 cy5-cy3

hyb_protocol: Porcine oligonucleotide set represents 13,297 porcine cDNAs and ESTs. A reference design was used in which each of the experimental samples was cohybridized with the reference sample that contained equal amounts of all the RNA samples used in the experiment, which allowed the treatment of fluorescence ratios as measurements of relative expression. Single-spotted oligos were printed on GAPS II slides (Corning, Corning, NY) at the W. M. Keck Center for Comparative and Functional Genomics, University of Illinois. Before hybridization, the arrays were plunged in 0.2% SDS water and immediately agitated vigorously for 2 min, washed three times in successive jars of distilled water and rinse in 100% ethanol. The arrays were then incubated in 5X SSC, 0.1% SDS, 1% BSA in a Coplin jar for 45 to 60 min at 42 °C, washed by immersing in 5 successive Coplin jars of deionized distilled water (RICCA Chemical Company, Arlington, TX), rinsed in 100% isopropanol, to ensure that the SDS is completely removed from the arrays and subsequently dried by centrifugation. An array was placed into a Corning Hybridization Chamber (Sigma) and 80 μl of the leveled solution was applied to a slide and covered with a LifterSlip™ (Erie Scientific, Portsmouth, NH). The chamber was then assembled and submerged in a 42 °C water bath for 48 h. he hybridization chamber was disassembled and the LifterSlip™ was removed by immersing the array in 2X SSC, 0.1% SDS (at 42 °C) until the LifterSlip™ moved freely away from the slide. The arrays were placed in 2X SSC, 0.1% SDS for 5 min at 42 °C. Subsequently the arrays were placed in 0.1X SSC, 0.1% SDS for 10 min at room temperature followed by 0.1X SSC for 1 min at room temperature. The arrays were then rinsed in 0.01X SSC for 10 sec or less and dried by centrifugation.

scan_protocol: Slides were scanned immediately for both dye channels with an Axon 4000B (Molecular Devices, Union City, CA) dual-laser confocal scanner and images were processed using GenePix v6.0 software (Molecular Devices).


title: Self-Hyb_L24hrs

description: lay-down stress, self-hybridization

source_name: shoot laid down for 24 hours


title: Self-Hyb_drt24hrs

description: drought stress, self-hybridization

source_name: shoot treated with 25% polyethylene glycol 6000 for 24 hours

treatment_protocol:
aboitic factor: drought environment
stress factor: 25% polyethylene glycol 6000
stress factor: 24 hours


title: Germfree crypt 2 cy3-cy5

source_name: Germfree crypt RNA

tag: Germfree crypt aRNA labeled with cy3


title: Conventional crypt 13 cy5-cy3

source_name: Conventional Crypt

tag: The amplified anti-sense (aRNA) was labeled with Cy5 (F635)

source_name: Reference Sample

tag: The amplified anti-sense (aRNA) was labeled with Cy3 (F532)


title: Germfree crypt cy5-cy3

source_name: Germfree crypt

tag: Germfree crypt aRNA labeled with cy5


title: Conventional crypt 13 cy3-cy5


title: Germfree crypt 1 cy3-cy5

source_name: Germfree crypt 1 cy3


title: PACAP treated vs control-repeat 1 - mAdbID:61428

status: Public on Mar 01 2008

city: Bethesda

first: Babru

middle: Bahan

last: Samal

state: MD

address: 9000 Rockville Pike

department: SMN

institute: NIMH/NIH

description: mAdb experiment ID: 61428

hyb_protocol: Hybridization Protocol Other: Total RNA (15-50 ug in 15.5 ul) was incubated with amino-modified random primer (2 ug/ul, 2 ul) and RNase inhibitor (5 units/ul, 1 ul) at 70C for 10 min. Primer-RNA solution was then incubated at 42C for 2 h with the reverse transcriptase mix containing 5X first-strand buffer, 50X aadUTP/dNTPs (25 mM dATP, 25 mM dGTP, 25 mM dCTP, 15 mM dTTP and 10 mM aminoallyl dUTP), 0.1 M DDT, and Superscript II reverse transcriptase. The cDNAs were labeled with NHS-ester Cy3 and Cy5 dye in the presence of 1 M sodium bicarbinate. Array slides placed in a hybridization chamber (Corning, Corning, NY) were incubated at 42C for 16-24 h, and successively washed with 0.5x SSC, 0.01% SDS, and 0.06X SSC at room temperature for 10 min each.

scan_protocol: Scanning Protocol Other: Arrays were scanned with a GenePix 4000A scanner (Axon, Foster City, CA), and the resulting images were analyzed using IPlab (Fairfax, VA) and a FileMaker Pro 5 (Santa Clara, CA) relational database designed by Zedong Chen, NHGRI.

data_processing: Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

organism: Bos taurus

source_name: BCC control 1

label_protocol:
Cy3 Label Protocol
Other: The cDNA were labeled with NHS-ester Cy3 dye in the presence of 1 M sodium bicarbonate.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted with Trizol Reagent (Invitrogen) and purfied using RNeasy Mini Kit (Qiagen, Valencia, CA).

value: brain

tag: Cell type

value: chromaffin cells

source_name: BCC treated 1

label_protocol:
Cy5 Label Protocol
Other: The cDNA were labeled with NHS-ester Cy5 dye in the presence of 1 M sodium bicarbonate.

treatment_protocol:
Treatment type: compound
Treatment dose: 100 ng/ml
Treatment time: 6 hr
Treatment temperature: 37 C
In-vivo treatment: The bovine chromaffin cells were treated with 100 ng/ml PACAP in vitro for 6 hours.


title: Germfree crypt 1 cy5-cy3

source_name: aRNA labeled with cy5 fron germfree pig


title: PACAP treated vs control-repeat 4 - mAdbID:61430

description: mAdb experiment ID: 61430

source_name: BCC control 4

source_name: BCC treated 4


title: PACAP treated vs control-repeat 3 - mAdbID:61429

description: mAdb experiment ID: 61429

source_name: BCC control 3

source_name: BCC treated 3


title: dye-swap experiment between green callus and shoot 2

description: 10 days old shoot7' is control sample, and is same as sample of sample name shoot_self7. 'green callus incubated on re-differential induced medium' is target sample, and is same as sample of sample name Grn_callus_self

value: incubation for 42 days

source_name: 10 days old shoot7


title: WT/KO-repeat 6 - mAdbID:42789

description: mAdb experiment ID: 42789

source_name: MAG Control 6

value: adrenal gland

tag: genotype/variation

value: 129XC57BL6 PACAP +/+ F2

source_name: MAG KO 6

tag: genotype/variation gene knock out

value: 129XC57BL6 PACAP -/- F2


title: Conventional crypt 14 cy3-cy5

source_name: Conventional crypt

tag: The amplified anti-sense (aRNA) was labeled with Cy3

source_name: reference sample (pooled sample)

tag: The amplified anti-sense (aRNA) was labeled with Cy5


title: PACAP treated vs control-repeat 2 - mAdbID:61427

description: mAdb experiment ID: 61427

source_name: BCC control 2

source_name: BCC treated 2


title: hSc_normal_LEY vs. hSc_reference pool

city: Amsterdam

first: Marcel

last: Kwa

email: m.s.kwa@amc.uva.nl, m.s.kwa@wxs.nl

address: Meibergdreef 9

institute: Academic Medical Center, Univ. Amsterdam

description:
Congenital demyelinating neuropathies are a group of neurological disorders that involve either lack of myelin synthesis or progressive loss of myelinated nerve fibers, leading to peripheral nerve dysfunction. Genetic analyses have mapped up to 30 different loci of which 21 genes have been identified. Normal function of the encoded proteins and disease mechanisms remain elusive.
Schwann cells carrying the genetic defect in the diseased nerve are not capable of either synthesizing or maintaining myelin synthesis. Comparing this population with the population obtained from a healthy nerve may therefore identify essential cellular processes or (early) pathways affecting myelin formation or maintenance. Schwann cells can be expanded in vitro by stimulation with mitogens to obtain almost pure (95-99%) cell populations. Genes expressed late in the differentiation program leading to (defects in) myelination will not be expressed and thereby not detected by this approach.

hyb_protocol: Hybridization was according to the protocol of Agilent ServiceXS B.V. Wassenaarseweg 72 2333 AL Leiden the Netherlands reference AXS0512293

scan_protocol: Protocol_Name 44k (Read Only) Scan_ScannerName Agilent Technologies Scanner G2505B US23502317

data_processing:
Data were generated using Agilent Feature Extraction software (FE version 7.5) with background correction option "No background" and "spatial detrend". All other software settings were standard/default.
Quality control of the microarrays was performed using methods available from Bioconductor (Gentleman et al. 2004) packages (marray, arrayQuality) in the statistical software package R (http://www.r-project.org/). By inspecting the intensities of negative and positive controls, spatial effects, M/A plots, and signal-to-noise distributions no strange effects could be found.

label: Cy3 (green)

source_name: cultured Schwann cells isolated from sural nerve biopsy

label_protocol: 500 ng of total RNA was used to generate labeled cRNA using the Low RNA input Fluorescent Linear Amplification Kit (Agilent, Santa Clara , CA, USA). After labeling cRNA yield was determined by Nanodrop and ranged between 43-160 ng/µl. Cyanine-3/Cyanine-5 incorporation was determined by wavescan analysis. Labeling and Hybridization were according to the protocol of Agilent.

growth_protocol: We established primary human Schwann cell lines from sural nerve biopsies (normal, NDRG1, CTDP1 and PMP22 mutations) or medial plantar nerves (PMP22 duplication) dissected out of amputation material as described (Hanemann et al., 1998; Rutkowski et al., 1995) with a few modifications (see below). Normal biopsies were taken from subjects with suspected vasculitic neuropathies or morbus Hansen, but without known mutations in myelin genes. All normal subjects’ biopsies proved to be normal after pathological examination and were therefore designated normal. No obvious differences in Schwann cell morphology or immunoreactivity between the different cell lines were observed. One cell line was established from an HSMN-Lom patient with a mutation (Arg148Stop) in NDRG1 (Kalaydjieva et al., 2000). Two cell lines were generated from patients with HMSN1A. One had a PMP22 duplication and the other a PMP22 Leu16Pro mutation. The Schwann cell line harboring the PMP22 duplication was generated from the median plantar nerve. We generated two different primary lines from two CCFDN patients carrying the same mutation. All mutations were verified by sequence analysis. Schwann cells were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco) supplemented with: 10% FCS, 10 nM recombinant human beta1-heregulin177-244 (a gift from Genentech, Inc., South San Fransisco, USA), 2.5 μg/ml insulin, 0.5 mM IBMX (3-isobutyl-1-methylxanthine, ICN, Costa Mesa, USA), 0.5 μM forskolin (ICN), 100 Units/ml penicillin and 100 μg/ml streptomycin. All plasticware was coated with 5 µg/ml Laminin (Roche). Until the first passage 0.25 μg/ml phytohaemoagglutinin (PHA-M, Sigma) was included. Schwann cultures were further purified by Thy-1.1/complement mediated lysis (Brockes et al., 1979, Kwa et al. 2003). Alternatively, anti-Fibroblast Microbeads were used for fibroblast depletion by magnetic cell sorting (MACS) according to the instructions of the manufacturer (Miltenyi Biotech, Auburn, USA). Cultures were expanded up to 106 cells and aliquots of early passage numbers were stored frozen in culture medium supplemented with 10% DMSO. Routinely, cells could be cultured up to 15 passages, with a doubling time of 2-3 weeks, but in this study we did not use cells with passage numbers higher than 10. Every 3-4 days half of the total volume culture medium was displaced. Schwann cell purity (95-99%) and fibroblast contamination were routinely monitored by immune fluorescence using Schwann cell markers S100beta, glial fibrillary acidic protein (GFAP), p75 low-affinity neurotrophin receptor (NGFR). Antibodies to fibroblast marker SMA (smooth muscle actin) only stained a low percentage (<5%) of the cells.

extract_protocol: Schwann cells were grown to 50-70% confluency in duplicate 225cm2 flasks, harvested and RNA was extracted twice with TrizolTM (Invitrogen) in two independent separate batches. For microarray analysis, total Schwann cell RNA Trizol extraction was followed by an extra DNA removal by NucleospinR RNA-L columns according to the instructions of the manufacturer (Machery-Nagel, Düren, Germany). Total RNA purity and integrity was assayed on a 2100 Bioanalyzer Nano (Agilent, Santa Clara , CA, USA).

tag: Normal subject (lab code LEY) without any known mutations causing neuropathy. All normal subjects’ biopsies proved to be normal after pathological examination and were therefore designated normal.

label: Cy5 (red)

source_name: cultured Schwann cells from six sural nerve and one plantar nerve biopsies

tag: reference pool, mix of all samples in this series


title: hSc_HMSN1A_JIMa vs. hSc_reference pool

tag: Patient (labcode JIM, replicate a) with hereditary motor and sensory neuropathy type 1A (HMSN1A), also known as Charcot-Marie-Tooth disease type 1A (CMT1A).

tag: The causative mutation is a mutation (Leu16Pro) in the gene encoding Peripheral myelin protein 22 (PMP22).


title: hSc_HMSN1A_BARb vs. hSc_reference pool

source_name: cultured Schwann cells isolated from medial plantar nerve amputation

tag: Patient (labcode BAR, replicate b) with hereditary motor and sensory neuropathy type 1A (HMSN1A), also known as Charcot-Marie-Tooth disease type 1A (CMT1A).

tag: The causative mutation is a duplication of the gene encoding Peripheral myelin protein 22 (PMP22)


title: hSc_CCFDN_BONb vs. hSc_reference pool

hyb_protocol: Hybridization was according to the protocol of Agilent ServiceXS B.V. Wassenaarseweg 72 2333 AL Leiden reference AXS0512293

tag: Patient (labcode BON, replicate a) with congenital cataracts and facial dysmorphism neuropathy (CCFDN) syndrome. The causative is mutation in c-terminal domain phosphatase 1 (CTDP1 IVS6+389C>T).


title: BS21110106_01 (mutant, 2%xyl, c2-A0.5)

city: Martinsried

first: Christoph

last: Schaab

address: Fraunhoferstrasse 20

country: Germany

institute: GPC Biotech AG

description: Second time point repleted cells.

hyb_protocol: We used three arrays with duplicate features for each hybridisation. These arrays contained the same clones but had differences in batch preparation, e.g. different robot runs or different PCR aliquots. Arrays were initially prehybridised for at least 2 h and then hybridised for 20 h at 50°C in a buffer containing 50% formamide, 63SSC, 7% SDS and 50mMNaphosphate, pH 7.5. The typical hybridisation volume was 50 ml. After hybridisation, arrays were washed twice for 15 min in Washing buffer I (23 SSC, 0.5% SDS) and then twice for 15 min in Washing buffer II (0.13 SSC, 0.5% SDS). Before wrapping with SaranWrap, excess liquid was removed by placing membranes on Whatman paper for a few seconds.

scan_protocol: Arrays were exposed for 100 h to Fuji BAS-IP MS 2025 plates and scanned at 25 mm resolution on a Fuji BAS-5000 phosphorimager (Raytest, Germany) (13,14). The acquired images were then analysed with a publicly available image analysis package VisualGrid. The diameter of the circular area used to quantify the spots, the node mask, was 27 pixels, which corresponds to 675 mm. The VisualGrid generates a text-file format output that was further used for data processing and analysis.

data_processing:
Data processing included the following steps: subtraction of
local background, correction for the neighbourhood effect
(when required) and normalisation. Calculation of the background
was based on the empty dots present in each block. The
local background of a block was taken as a mean value of the
empty dots located in the block and in the neighbouring
blocks. Normalisation was important to compensate for differences
caused by different labelling efficiencies of RNA samples. The mean
signal intensity of all features was set to `one' for all
experiments. In addition, the normalised signals from the six
replicas (three replica arrays times two duplicates) were used
to calculate the mean and standard error for every clone.

organism: Bacillus subtilis

source_name: tagD - mutant - 2% xylose - cycle 2, A600=0.5

label_protocol:
Four aliquots of the RNA sample each containing 2 µg of total RNA were prepared. Each aliquot
was handled as independently as possible. They were mixed
with 0.6 mg of random hexamers (dN)6 heated at 70°C for
3 min and chilled on ice. The volume was adjusted to 20 ml
with buffer according the SuperScript II manufacturer's
protocol (Life Technologies, UK). The labelling reaction
contained a final concentration of 1 mM each dATP, dGTP,
dTTP, 50 mCi 33P-dCTP (corresponding to ~0.5 mM) and
100 U SuperScript II. After 1 h incubation at 42°C, probes
were purified on mini Quick Spin DNA columns (Roche,
Germany) followed by denaturation in 0.5 M NaOH at 65°C
for 20 min, neutralisation with 1 M Na-phosphate buffer at
pH 7.5 and pooling of all four aliquots. The typical incorporation
rate was ~70% and we estimate that the amount of
synthesised cDNA is ~30 ng.

growth_protocol: pre culture grown with 2% xylose, then cells were washed and diluted to an A600 of 0.05; cells were then grown to an A600 of 0.5 with 2% xylose; then cells were again diluted to an A600 of 0.05 and grown yet again to an A600 of 0.5 in the presence of 2% xylose.

extract_protocol:
For RNA preparation, 10 ml of the culture was harvested by
centrifugation at 3,000 x g. After cells were harvested, cell pellets
were immediately resuspended in 450 µl of lysis buffer
(1% [vol/vol] beta-mercaptoethanol and 1 mM EDTA in RLT buffer
[Qiagen, Hilden, Germany]). This suspension was transferred to a
FastPrep tube (Qbiogene, Carlsbad, Calif.) prefilled with 400 µl
of glass beads (diameter, 106 µm; acid washed; Sigma), 500 µl of
citric acid-saturated phenol, and 200 µl of chloroform. The tube was
processed in a FP120 FastPrep cell disrupter (Qbiogene) for 45 s at
6.5 m/s. The slurry was then transferred to a Phase-Lock tube (2 ml,
heavy; Eppendorf, Hamburg, Germany) and spun for 10 min in a
microcentrifuge. Ethanol (250 µl) was added to the supernatant,
and the RNA was purified from this mixture on an RNeasy column
(Qiagen), according to the instructions of the manufacturer. At this
stage three replicates of each sample in equal amounts were pooled
to give a total RNA amount of 100 µg. The prepurified and pooled
RNAs were digested with RNase-free DNase I (Roche, Basel,
Switzerland), and cleanup was performed with RNeasy columns
(Qiagen). Quality control of each RNA sample included
spectrophotometric analysis and formaldehyde gel
electrophoresis. Furthermore, each RNA was subjected to reverse
transcription-PCR. Amplification of the transcript in the presence of
reverse transcriptase served as an indicator of the integrity of the
RNA, while reverse transcription-PCR without the addition of reverse
transcriptase was performed to verify the absence of any genomic DNA.

tag: Strain

tag: xylose inducible conditional tagD mutant


title: hSc_HMSN1A_BARa vs. hSc_reference pool

tag: Patient (labcode BAR, replicate a) with hereditary motor and sensory neuropathy type 1A (HMSN1A), also known as Charcot-Marie-Tooth disease type 1A (CMT1A).


title: Self-Hyb_redif_callus

description: Callus originated from propagated callus, color of callus is white, self-hybridization

source_name: callus incubated on re-differential induced medium

tag: cultivar

value: Nipponbare

tag: Tissues

tag: stage

tag: age

value: incubation for 35 days


title: BS21110102_01 (mutant, 2%xyl, c1-A0.5)

description: First time point repleted cells.

source_name: tagD - mutant - 2% xylose - cycle 1, A600=0.5

growth_protocol: pre culture grown with 2% xylose, then cells were washed and diluted to an A600 of 0.05; cells were then grown to an A600 of 0.5 with 2% xylose.


title: dye-swap experiment between laid-down shoot submarged in water for 1 hour and non-treated shoot 2

description: 10 days old shoot10' is control sample, and is same as sample of sample name shoot_self10. 'laid-down shoot submarged in water for 1 hour' is target sample, and is same as sample of sample name FL01hrs_self.

tag: Tissue

value: shoot

value: LP.03 three leaves visible

value: 10 days after sowing

source_name: 10 days old shoot10


title: hSc_normal_ETTa vs. hSc_reference pool

source_name: cultured Schwann cells isolated from a sural nerve biopsy

tag: Normal subject (lab code ETT, replicate a) without any known mutations causing neuropathy. All normal subjects’ biopsies proved to be normal after pathological examination and were therefore designated normal.


title: hSc_HMSN1A_JIMb vs. hSc_reference pool

tag: Patient (labcode JIM, replicate b) with hereditary motor and sensory neuropathy type 1A (HMSN1A), also known as Charcot-Marie-Tooth disease type 1A (CMT1A).


title: Conventional crypt 15cy3 -cy5

source_name: Conventional epithelial crypt RNA

tag: Conventional epithelial crypt RNA (aRNA labeled with cy3)

source_name: reference pooled sample cy5

tag: aRNA labeled with cy5


title: WT/KO-repeat 2 - mAdbID:42785

description: mAdb experiment ID: 42785

source_name: MAG Control 2

tag: genotype/variation

source_name: MAG KO 2

tag: genotype/variation gene knock out


title: hSc_normal_ETTb vs. hSc_reference pool

tag: Normal subject (lab code ETT, replicate b) without any known mutations causing neuropathy. All normal subjects’ biopsies proved to be normal after pathological examination and were therefore designated normal.

tag: reference pool, mix of all samples in this series


title: Germfree crypt 3 cy3-cy5

source_name: Germfree crypt RNA

tag: aRNA labeled with cy3

source_name: reference sample


title: Conventional crypt 14 cy5-cy3

source_name: Conventional crypt

tag: The amplified anti-sense (aRNA) was labeled with Cy5

tag: The amplified anti-sense (aRNA) was labeled with Cy3


title: WT/KO-repeat 1 - mAdbID:42784

description: mAdb experiment ID: 42784

source_name: MAG Control 1

source_name: MAG KO 1


title: WT/KO-repeat 4 - mAdbID:42787

description: mAdb experiment ID: 42787

source_name: MAG Control 4

source_name: MAG KO 4


title: hSc_normal_AAL vs. hSc_reference pool

tag: Normal subject (lab code AAL) without any known mutations causing neuropathy. All normal subjects’ biopsies proved to be normal after pathological examination and were therefore designated normal.

source_name: cultured Schwann cells from six sural nerve and one plantar nerve biopsies


title: WT/KO-repeat 3 - mAdbID:42786

description: mAdb experiment ID: 42786

source_name: MAG Control 3

source_name: MAG KO 3


title: BS21110002_01 (tagD-mutant, 0%xyl, c1-A0.5)

description: First time point depleted cells.

source_name: tagD - mutant - 0 (control) - cycle 1, A600=0.5

growth_protocol: pre culture grown with 2% xylose, then cells were washed and diluted to an A600 of 0.05; cells were then grown to an A600 of 0.5 without any xylose.

tag: Strain

tag: xylose inducible conditional tagD mutant


title: Conventional crypt 15 cy5-cy3

source_name: reference pooled sample


title: hSc_CCFDN_BONa vs. hSc_reference pool

source_name: cultured Schwann cells isolated from sural nerve biopsy

growth_protocol: We established primary human Schwann cell lines from sural nerve biopsies (normal, NDRG1, CTDP1 and PMP22 mutations) or medial plantar nerves (PMP22 duplication, Table 1)) dissected out of amputation material as described (Hanemann et al., 1998; Rutkowski et al., 1995) with a few modifications (see below). Normal biopsies were taken from subjects with suspected vasculitic neuropathies or morbus Hansen, but without known mutations in myelin genes. All normal subjects’ biopsies proved to be normal after pathological examination and were therefore designated normal. No obvious differences in Schwann cell morphology or immunoreactivity between the different cell lines were observed. One cell line was established from an HSMN-Lom patient with a mutation (Arg148Stop) in NDRG1 (Kalaydjieva et al., 2000). Two cell lines were generated from patients with HMSN1A. One had a PMP22 duplication and the other a PMP22 Leu16Pro mutation. The Schwann cell line harboring the PMP22 duplication was generated from the median plantar nerve. We generated two different primary lines from two CCFDN patients carrying the same mutation. All mutations were verified by sequence analysis. Schwann cells were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco) supplemented with: 10% FCS, 10 nM recombinant human beta1-heregulin177-244 (a gift from Genentech, Inc., South San Fransisco, USA), 2.5 μg/ml insulin, 0.5 mM IBMX (3-isobutyl-1-methylxanthine, ICN, Costa Mesa, USA), 0.5 μM forskolin (ICN), 100 Units/ml penicillin and 100 μg/ml streptomycin. All plasticware was coated with 5 µg/ml Laminin (Roche). Until the first passage 0.25 μg/ml phytohaemoagglutinin (PHA-M, Sigma) was included. Schwann cultures were further purified by Thy-1.1/complement mediated lysis (Brockes et al., 1979, Kwa et al. 2003). Alternatively, anti-Fibroblast Microbeads were used for fibroblast depletion by magnetic cell sorting (MACS) according to the instructions of the manufacturer (Miltenyi Biotech, Auburn, USA). Cultures were expanded up to 106 cells and aliquots of early passage numbers were stored frozen in culture medium supplemented with 10% DMSO. Routinely, cells could be cultured up to 15 passages, with a doubling time of 2-3 weeks, but in this study we did not use cells with passage numbers higher than 10. Every 3-4 days half of the total volume culture medium was displaced. Schwann cell purity (95-99%) and fibroblast contamination were routinely monitored by immune fluorescence using Schwann cell markers S100beta, glial fibrillary acidic protein (GFAP), p75 low-affinity neurotrophin receptor (NGFR). Antibodies to fibroblast marker SMA (smooth muscle actin) only stained a low percentage (<5%) of the cells.

tag: Patient (labcode BON, replicate a) with congenital cataracts and facial dysmorphism neuropathy (CCFDN) syndrome. The causative is mutation in c-terminal domain phosphatase 1 (CTDP1 IVS6+389C>T).


title: hSc_CCFDN_MARa vs. hSc_reference pool

tag: Patient (labcode MAR, replicate a) with congenital cataracts and facial dysmorphism neuropathy (CCFDN) syndrome. The causative is mutation in c-terminal domain phosphatase 1 (CTDP1 IVS6+389C>T).


title: WT/KO-repeat 5 - mAdbID:42788

description: mAdb experiment ID: 42788

source_name: MAG Control 5

tag: Tissue

source_name: MAG KO 5


title: hSc_CCFDN_MARb vs. hSc_reference pool

tag: Patient (labcode MAR, replicate b) with congenital cataracts and facial dysmorphism neuropathy (CCFDN) syndrome. The causative is mutation in c-terminal domain phosphatase 1 (CTDP1 IVS6+389C>T).


title: C3H_Skin_72h

status: Public on Dec 30 2007

city: Chiba

first: Shuhei

last: Noda

address: Anagawa 4-9-1

department: Frontier research center

institute: National institute of radiological sciences

description: In channel 2, total RNA was purified and pooled from 3 mice. Skin was taken as full layers.

hyb_protocol: cDNA Microarray Kit Protocol (Double barcoded slide) Version 7.0, Publication Number:  G4100-98000

scan_protocol: Agilent Microarray Scanner User Manual (6.3, 5th edition, December 2003), Publication Number:  G2566-90009 10µm resolution, 100% PMT

data_processing: Feature Extraction Software (Agilent Technologies)

source_name: control RNA mixture

label_protocol: Agilent Fluorescent Direct Label Kit Protocol (June 2003 Rev 2.1), Publication Number:  G2555-98003_JUNE_2003

tag: Ten of First Choice total RNA (Ambion, Inc.) derived from ten organs(midterm embryo, thymus, ovary, testicle, spleen, lung, heart, liver, kidney, brain) were equally mixed.

treatment_protocol: Seventy two hours after local irrradiation (hind leg, 30Gy)

tag: 'Strain

value: C3H/HeMs', 'Gender:female', 'Age:12~13 week'


title: C3H_Skin_1h

treatment_protocol: One hour after local irrradiation (hind leg, 30Gy)


title: C3H_Skin_12h

treatment_protocol: Twelve hours after local irrradiation (hind leg, 30Gy)


title: C3H_Skin_NoIrradiation

treatment_protocol: No treatment


title: B6_Skin_72h

value: C57BL6/J', 'Gender:female', 'Age:12~13 week'


title: A/J_Skin_12h

value: A/J', 'Gender:female', 'Age:12~13 week'


title: B6_Skin_12h


title: B6_Skin_1h


title: C3H_Lung_12h

description: In channel 1, total RNA was purified and pooled from 3 mice

treatment_protocol: Twelve hour after local irrradiation (thorax, 10Gy)


title: A/J_Skin_72h


title: B6_Skin_NoIrradiation


title: B6_Lung_72h

treatment_protocol: Seventy two hour after local irrradiation (thorax, 10Gy)


title: A/J_Skin_1h


title: C3H_Lung_NoIrradiation


title: C3H_Lung_72h


title: B6_Lung_1h

treatment_protocol: One hour after local irrradiation (thorax, 10Gy)