title: MCF7 5'DFUR+NBTI 24h exp2.Cy3

status: Public on Jul 13 2006

type: RNA

city: Barcelona

first: Miriam

last: Molina-Arcas

address: Av. Diagonal, 645

department: Bioquimica i Biologia Molecular

country: Spain

institute: Universitat de Barcelona

description: Sample RNA was labelled with Cy3 and human Universal RNA with Cy5. RNA was extracted and amplified (PMID: 14522886). Hibridation and Scanning protocol (PMID: 12414529)

scan_protocol: Scannarray 5000 XL (PMID:12414529)

molecule: total RNA

organism: Homo sapiens

source_name: universal control

label_protocol: Three ug of the amplified RNA was labelled with fluorescent Cy5, as described (PMID: 12414529)

tag: Universal Human RNA (Stratagene, La Jolla, CA, USA)

source_name: MCF7 5'DFUR+NBTI 24h

label_protocol: Three ug of the amplified RNA was labelled with fluorescent Cy3, as described (PMID: 12414529)

growth_protocol: MCF7 cells were seeded 20.000 cel/ml and were cultured in DMEM medium supplemented with 10% foetal bovine serum (GIBCO-BRL), 2mM glutamine and a mixture of antibiotics

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Quiagen, Hilden, Germany). T7-amplified RNA was synthesized as described elsewhere (PMID: 14522886)

treatment_protocol: MCF7 cells were treated with 5'DFUR 250uM + NBTI 100nM for 90 min. RNA was extracted at 24 hours.

tag: MCF7 cell line RNA


title: MCF7 ctrl 4h exp2.Cy3

description: Sample RNA was labelled with Cy5 and human Universal RNA with Cy3. RNA was extracted and amplified (PMID: 14522886). Hibridation and Scanning protocol (PMID: 12414529)

source_name: Universal control

extract_protocol: T7-amplified RNA was synthesized as described elsewhere (PMID: 14522886)

source_name: MCF7 ctrl 4h


title: MCF7 5'DFUR+NBTI 4h exp1.Cy3

source_name: MCF7 5'DFUR+NBTI 4h

treatment_protocol: MCF7 cells were treated with 5'DFUR 250uM + NBTI 100nM for 90 min. RNA was extracted 4 hours after the beginning of treatment


title: MCF7 NBTI 24h exp1.Cy3

source_name: MCF7 NBTI 24h

treatment_protocol: MCF7 cells were treated with NBTI 100nM for 90 min. RNA was extracted at 24 hours


title: MCF7 5'DFUR+NBTI 4h exp2.Cy3

treatment_protocol: MCF7 cells were treated with 5'DFUR 250uM+NBTI 100nM for 90 min. RNA was extracted 4 hours after the beginning of treatment


title: MCF7 5'DFUR 24h exp2.Cy3

source_name: MCF7 5'DFUR 24h

treatment_protocol: MCF7 cells were treated with 5'DFUR for 90 min. RNA was extracted at 24 hours.


title: MCF7 5'DFUR 24h exp1.Cy3

treatment_protocol: MCF7 cells were treated with 5'DFUR 250uM for 90 min. RNA was extracted at 24 hours


title: MCF7 ctrl 24h exp1.Cy3

source_name: MCF7 ctrl 24h

treatment_protocol: MCF7 cells were treated with NBTI 100nM for 90 min. RNA was extracted 4 hours after the beginning of treatment


title: MCF7 NBTI 4h exp2.Cy3

source_name: MCF7 NBTI 4h

treatment_protocol: MCF7 cells were treated with NBTI 100nM for 90 min. RNA was extracted 24 hours after the beginning of treatment


title: MCF7 ctrl 4h exp1.cy3


title: MCF7 NBTI 24h exp2.Cy3

treatment_protocol: MCF7 cells were treated with NBTI 100nM for 90 min. RNA was extracted at 24 hours.


title: MCF7 5'DFUR+NBTI 4h exp2.cy5


title: MCF7 ctrl 24h exp2.CY3


title: MCF7 5'DFUR 24h exp2.cy5


title: MCF7 5'DFUR+NBTI 24h exp1.Cy3

treatment_protocol: MCF7 cells were treated with 5'DFUR 250uM +NBTI 100nM for 90 min. RNA was extracted at 24 hours


title: MCF7 NBTI 24h exp1.cy5


title: MCF7 5'DFUR 4h exp1.cy5

description: Sample RNA was labelled with Cy5 and human Universal RNA with Cy3.

scan_protocol: Scannarray 5000 XL (PMID: 12414529)

source_name: MCF7 5'DFUR 4h

label_protocol: Three ug of the amplified RNA was labelled with fluorescent Cy5 , as described (PMID: 12414529)

growth_protocol: MCF7 cells were seeded 20.000 cel/cm2 and were cultured in DMEM medium supplemented with 10%  foetal bovine serum (GIBCO-BRL), 2mM glutamine and a mixture of antibiotics

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen, Hilden, Germany). T7-amplified RNA was synthesized as described elsewhere (PMID: 14522886 )

treatment_protocol: MCF7 cells were treated with 5'DFUR 250 microM for 90 min. RNA was extracted 4 hours from the beginning of treatment.


title: MCF7 5'DFUR 24h exp1.cy5

treatment_protocol: MCF7 cells were treated with 5'DFUR 250 uM for 90 min. RNA was extracted at 24 hours.


title: MCF7 5'DFUR 4h exp2.Cy3

treatment_protocol: MCF7 cells were treated with 5'DFUR 250uM for 90 min. RNA was extracted 4 hours after the beginning of treatment


title: MCF7 5'DFUR 4h exp1.Cy3

treatment_protocol: MCF7 cells were treated with 5'DFUR for 90 min. RNA was extracted 4 hours after the beginning of treatment


title: MCF7 NBTI 4h exp1.Cy3


title: MCF7 5'DFUR+NBTI 24h exp2.cy5

treatment_protocol: MCF7 cells were treated with 5'DFUR 250uM+NBTI 100nM for 90 min. RNA was extracted at 24 hours


title: MCF7 NBTI 24h exp2.cy5


title: NLS10_1GHd

status: Public on Jul 08 2006

city: Potomac Falls

first: Agnieszka

middle: Maria

last: Lichanska

state: VA

country: USA

institute: Tessarae, LLC

description: Experiment Type=time course

scan_protocol: Image Analysis Software=Imagene 5.2

data_processing: Lowess normalization

organism: Mus musculus

label_protocol: Alexa indirect labeling - Green dye incorporation=13.3 bases/dye molecule

treatment_protocol: human growth hormone, 100 ng/ml

tag: Amount of probe=402 ng

tag: Common Reference (Yes/No, ID)=Yes, Ambion embryonic RNA

tag: Sample Source=cell-line

tag: Time=1 hours

source_name: Ambion embryonic RNA

label_protocol: Alexa indirect labeling - Red dye incorporation=17.9 bp/dye molecule


title: MCF7 ctrl 24h exp2.cy5


title: MCF7 5'DFUR 4h exp2.cy5

treatment_protocol: MCF7 cell were treated with 5'DFUR 250uM for 90 min. RNA was extracted 4 hours after the beginning of treatment


title: WT10_1GHd

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=15.8 bases/dye molecule


title: NLS10_1GHc

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=12.8 bases/dye molecule

tag: Amount of probe=504 ng

label_protocol: Alexa indirect labeling - Red dye incorporation=19.8 bp/dye molecule


title: NLS10_0GHb

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=16 bases/dye molecule

tag: Time=0 hours

label_protocol: Alexa indirect labeling - Red dye incorporation=19.3 bp/dye molecule


title: NLS10_0GHc

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=13.7 bases/dye molecule


title: MCF7 5'DFUR+NBTI 24h exp1.cy5

treatment_protocol: MCF7 cells were treated with 5'DFUR 250 uM+ NBTI 100nM for 90 min. RNA was extracted at 24 hours.


title: E08_80

status: Public on Jul 06 2006

city: Brussels

first: Bart

last: Scherens

address: Av. E. Gryson, 1

department: Microbiology

country: Belgium

institute: IRMW-ULB

description: scan at high laser power and high PMT gain to detect the faintest spots

data_processing: VALUE = Log Ratio (635 /532), NO normalization

organism: Saccharomyces cerevisiae

source_name: gln3∆-gat1∆ (03167b) on M.Pro

tag: gln3∆-gat1∆ (03167b) on M.Pro

source_name: WT (BY4700) on M.Pro

tag: WT (BY4700) on M.Pro


title: E10_80

source_name: WT (BY4700) on M.Gln

tag: WT (BY4700) on M.Gln

source_name: ure2∆ (4709∆URE2) on M.Gln

tag: ure2∆ (4709∆URE2) on M.Gln


title: E06_40

description: scan at low laser power and a PMT gain avoiding saturation

source_name: WT (BY4700) after 2h shift from M.Gln to M.Pro


title: E04_80


title: E06_80

tag: WT (BY4700) after 2h shift from M.Gln to M.Pro


title: E08_40


title: WT10_1GHc

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=19.2 bases/dye molecule


title: MCF7 ctrl 4h exp2.cy5


title: MCF7 5'DFUR+NBTI 4h exp1.cy5

treatment_protocol: MCF7 cells were treated with 5'DFUR 250 microM + NBTI 100nM for 90 min. RNA was extracted 4 hours from the beginning of treatment.

extract_protocol: T7-amplified RNA was synthesized as described elsewhere (PMID: 14522886 )


title: 2nd spleen 24h LPS

status: Public on Jul 12 2006

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

description: Total RNA from human spleen (donor 2). treated with LPS for 24hrs.

source_name: human spleen


title: MCF7 ctrl 24h exp1.cy5

source_name: universal control


title: E09_80

source_name: gln3∆-gat1∆ (03167b) after 2h shift from M.Gln to M.Pro


title: MCF7 ctrl 4h exp1.cy5

description:
Sample RNA was labelled with Cy5 and human Universal RNA with Cy3.
RNA was extracted and amplified (PMID: 14522886 ). Hibridation and scannig protocol (PMID: 12414529)


title: 3rd spleen 48h LPS

status: Public on Jun 12 2006

description: Total RNA from human spleen (donor 3). treated with LPS for 48hrs.


title: WT10_0GHd

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=15.3 bases/dye molecule


title: E07_100

source_name: gln3∆-gat1∆ (03167b) M.Gln + rapamycin (20 min)

source_name: WT (BY4700) on M.Gln + rapamycin (20 min)


title: E07_50

tag: gln3∆-gat1∆ (03167b) M.Gln + rapamycin (20 min)

tag: WT (BY4700) on M.Gln + rapamycin (20 min)


title: E09_30

tag: gln3∆-gat1∆ (03167b) after 2h shift from M.Gln to M.Pro


title: PBMC 48hrs APS

description: Total RNA from human PBMC.treated with APS for 48hrs

data_processing: Normalized by all genes on array

source_name: human PBMC

tag: PBMC


title: PBMC 48hs Control

description: Total RNA from human PBMC for 48hrs control

data_processing: Normalized by all genes in array

source_name: PBMC

tag: Human PBMC


title: WT10_0GHb

description: Experiment Type=time course


title: WT10_1GHb

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=15.6 bases/dye molecule


title: NLS10_0GHd

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=15.1 bases/dye molecule


title: NLS10_1GHb

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=15.5 bases/dye molecule


title: E05_30

description: Scan at low laser power and a PMT gain avoiding saturation

source_name: gln3∆-gat1∆ (03167b) on M.Gln

tag: gln3∆-gat1∆ (03167b) on M.Gln


title: WT10_0GHc

description: Experiment Type=time course

label_protocol: Alexa indirect labeling - Green dye incorporation=14.2 bases/dye molecule

tag: Common Reference (Yes/No, ID)=Yes, Ambion Embryonic RNA


title: E01_30


title: E01_80

description: Scan at high laser power and high PMT gain to detect the faintest spots


title: E04_40


title: E10_40


title: 3rd spleen 24h VI-28

description: Total RNA from human spleen (donor 3). treated with VI-28 for 24hrs


title: 2nd spleen 24h control

description: Total RNA from human spleen (donor 2).


title: 2nd spleen 48h VI-28

description: Total RNA from human spleen (donor 2) , treated with VI-28 for 48hrs.


title: PBMC 24hrs control

description: Total RNA from human PBMC 24hrs control


title: 2nd spleen 48h control

description: Total RNA from human spleen (donor 2).


title: PBMC 24hrs VI-28

description: Total RNA from human PBMC, treated with VI-28 for 24hrs.


title: 1st spleen 48h Aps

description: Total RNA from human spleen (donor 1) treated with APS for 48rs.


title: PBMC-APS-24Hrs

description: Total RNA from human PBMC treated with APS for 24hrs


title: E02_50


title: E05_80

description: high laser power and high PMT (Photo Multiplier Tube) gain to detect the faintest spots


title: E03_30


title: E03_80

description: Scan at high laser power and high PMT (Photo Multiplier Tube) gain to detect the faintest spots


title: untreated moDC

status: Public on Jun 30 2006

city: Berlin

first: Reinhard

last: Wanner

address: Arnimallee 22

department: Inst. of Molecular Biology and Bioinformatics

country: Germany

institute: Charite-CBF

description: Expression profile of untreated monocyte-derived dendritic cells of one donor. Note that data in files "D19-treated moDC" and in "control D-treated moDC" stem from the same donor.

scan_protocol: GenChip Scanner 3000

data_processing: GCOS 1.2

label: biotinylated UTP/CTP; SAPE-solution; biotinylated goat anti-streptavidin; 2nd SAPE-solution;

source_name: Dendritic cells generated in vitro from monocytes by supplementing culture media with rhIL-4 and rhGM-CSF

tag: anonymous healthy blood donor


title: 3rd spleen 48h VI-28+PB

description: Total RNA from human spleen (donor 3). treated with VI-28 and polymyxin B for 48hrs.


title: PBMC 48HRS VI-28

description: Total RNA from human PBMC . Treated with VI-28 for 48hrs.


title: 3rd spleen 48h VI-28

description: Total RNA from human spleen (donor 3). treated with VI-28 for 48hrs.


title: 3rd spleen 48h control

description: Total RNA from human spleen (donor 3).


title: Saccharomyces cerevisiae Sgu52 YPD Sgu52 NS24 Array_A

status: Public on Jan 01 2006

city: Florence

first: Duccio

last: Cavalieri

address: Viale Pieraccini 6

department: Department of Pharmacology

country: Italy

institute: University of Florence

description: Some hybridizations were performed in duplicates on the same microarrays. Two complete sets of PCR products were printed on the same glass slide and under a single cover slip. These duplicates are labeled Array_A and Array_B. Since these are not complete technical replicates, they were averaged in Landry et al. (Gene, accepted) following the normalization and prior to statistical analysis. Replicate indicates a complete independent hybridization.

data_processing: Spots of bad quality were given negative flags. Nonnormalized ratios are provided.

molecule: polyA RNA

source_name: Saccharomyces cerevisiae Sgu52 in YPD

label_protocol: See Townsend, Cavalieri and Hartl 2003

extract_protocol: See Townsend, Cavalieri and Hartl 2003

tag: Saccharomyces cerevisiae Sgu52 in YPD

source_name: Saccharomyces cerevisiae Sgu52 in NS24

tag: Saccharomyces cerevisiae Sgu52 in NS24


title: Saccharomyces cerevisiae Sgu52 YPD Sgu52 SWM Array_A

source_name: Saccharomyces cerevisiae Sgu52 in SWM

tag: Saccharomyces cerevisiae Sgu52 in SWM


title: Saccharomyces cerevisiae Sgu52 NS4 Sgu52 YPD Array_A

source_name: Saccharomyces cerevisiae Sgu52 in NS4

tag: Saccharomyces cerevisiae Sgu52 in NS4


title: 3rd spleen 24h VI-28+PB

description: Total RNA from human spleen (donor 3). treated with VI-28 and polymyxin B.


title: Saccharomyces cerevisiae Sgu52 SWM Sgu52 NS24 Array_A


title: 3rd spleen 24h LPS

description: Total RNA from human spleen (donor 3). treated with LPS for 24hrs.


title: 3rd spleen 24h control

description: Total RNA from human spleen (donor 3).


title: Saccharomyces cerevisiae Sgu52 NS4 Sgu52 SWM Array_A


title: D19-treated moDC

description: Expression profile of monocyte-derived dendritic cells of one donor after treatment with the CpG-oligonucleotide D19. Note that data in files "control D-treated moDC" and in "untreated moDC" stem from the same donor.


title: control D-treated moDCs

description: Expression profile of monocyte-derived dendritic cells of one donor after treatment with the non-CpG oligonucleotide control D. Note that data in files "D19-treated moDC" and in "untreated moDC" stem from the same donor.


title: E02_100

description: scan at high laser power and high PMT gain to detect the faintest spots


title: 2nd spleen 24h VI-28

description: Total RNA from human spleen (donor 2), treated with VI-28


title: Saccharomyces cerevisiae Sgu52 NS4 Sgu52 SWM Array_B


title: 2nd spleen 48h LPS

description: Total RNA from human spleen (donor 2), treated with LPS for 48hrs.


title: 1st spleen 48h VI-28

description: Total RNA from human spleen (donor 1) treated with VI-28 for 48hrs.


title: 1st spleen 48h control

description: Total RNA from human spleen (donor 1).


title: Saccharomyces cerevisiae Sgu421 YPD Sgu421 SWM

source_name: Saccharomyces cerevisiae Sgu421 in YPD

tag: Saccharomyces cerevisiae Sgu421 in YPD

source_name: Saccharomyces cerevisiae Sgu421 in SWM

tag: Saccharomyces cerevisiae Sgu421 in SWM


title: Saccharomyces cerevisiae Sgu421 YPD BY4743 YPD Replicate2_Array_B

source_name: Saccharomyces cerevisiae BY4743 in YPD

tag: Saccharomyces cerevisiae BY4743 in YPD


title: Saccharomyces cerevisiae Sgu52 YPD BY4743 YPD Replicate1


title: Saccharomyces cerevisiae Sgu421 SWM Sgu421 NS4 Array_B

source_name: Saccharomyces cerevisiae Sgu421 in NS4

tag: Saccharomyces cerevisiae Sgu421 in NS4


title: Saccharomyces cerevisiae Sgu52 YPD BY4743 YPD


title: Saccharomyces cerevisiae Sgu421 SWM Sgu421 NS4 Array_A


title: Saccharomyces cerevisiae Sgu52 YPD Sgu52 SWM Array_B


title: Saccharomyces cerevisiae Sgu421 SWM Sgu421 NS24 Array_B

source_name: Saccharomyces cerevisiae Sgu421 in NS24

tag: Saccharomyces cerevisiae Sgu421 in NS24


title: Saccharomyces cerevisiae Sgu52 SWM Sgu52 NS4 Array_B


title: Saccharomyces cerevisiae Sgu52 YPD Sgu52 NS24 Array_B


title: Saccharomyces cerevisiae Sgu52 SWM Sgu52 NS4 Array_A


title: Saccharomyces cerevisiae Sgu52 SWM Sgu52 NS24 Array_B


title: Saccharomyces cerevisiae Sgu407 YPD Sgu407 SWM Array_B

source_name: Saccharomyces cerevisiae Sgu407 in YPD

tag: Saccharomyces cerevisiae Sgu407 in YPD

source_name: Saccharomyces cerevisiae Sgu407 in SWM

tag: Saccharomyces cerevisiae Sgu407 in SWM


title: Saccharomyces cerevisiae Sgu407 YPD Sgu407 SWM Array_A


title: Saccharomyces cerevisiae Sgu52 NS4 Sgu52 YPD Array_B


title: Saccharomyces cerevisiae Sgu407 SWM Sgu407 NS4 Array_B

source_name: Saccharomyces cerevisiae Sgu407 in NS4

tag: Saccharomyces cerevisiae Sgu407 in NS4


title: Saccharomyces cerevisiae Sgu52 NS24 EM93 NS24 Array_A

source_name: Saccharomyces cerevisiae EM93 in NS24

tag: Saccharomyces cerevisiae EM93 in NS24


title: Saccharomyces cerevisiae Sgu407 SWM Sgu407 NS4 Array_A


title: Saccharomyces cerevisiae Sgu407 NS4 Sgu407 YPD Array_A


title: Saccharomyces cerevisiae Sgu52 NS24 EM93 NS24 Array_B


title: Saccharomyces cerevisiae Sgu407 NS4 Sgu407 YPD Array_B


title: Saccharomyces cerevisiae Sgu421 YPD BY4743 YPD Array_A


title: Saccharomyces cerevisiae Sgu421 YPD BY4743 YPD Replicate1_Array_A


title: Saccharomyces cerevisiae Sgu421 YPD BY4743 YPD Array_B


title: Saccharomyces cerevisiae Sgu421 SWM Sgu421 NS24 Array_A


title: Saccharomyces cerevisiae Sgu407 NS24 Sgu421 NS24 Array_B

source_name: Saccharomyces cerevisiae Sgu407 in NS24

tag: Saccharomyces cerevisiae Sgu407 in NS24


title: Saccharomyces cerevisiae Sg60 YPD Sg60 NS24 Array_B

source_name: Saccharomyces cerevisiae Sg60 in YPD

tag: Saccharomyces cerevisiae Sg60 in YPD

source_name: Saccharomyces cerevisiae Sg60 in NS24

tag: Saccharomyces cerevisiae Sg60 in NS24


title: Saccharomyces cerevisiae Sgu421 NS4 Sgu421 YPD Array_B


title: Saccharomyces cerevisiae Sg60 SWM Sg60 NS4 Array_B

source_name: Saccharomyces cerevisiae Sg60 in SWM

tag: Saccharomyces cerevisiae Sg60 in SWM

source_name: Saccharomyces cerevisiae Sg60 in NS4

tag: Saccharomyces cerevisiae Sg60 in NS4


title: Saccharomyces cerevisiae Sg60 SWM Sg60 NS4 Array_A


title: Saccharomyces cerevisiae Sgu421 NS4 Sgu421 YPD Array_A


title: Saccharomyces cerevisiae Sgu421 NS24 Ds288c NS24 Array_B

source_name: Saccharomyces cerevisiae Ds288c in NS24

tag: Saccharomyces cerevisiae Ds288c in NS24


title: Saccharomyces cerevisiae Sg60 YPD Sg60 NS24 Array_A


title: Saccharomyces cerevisiae Sgu421 NS24 Ds288c NS24 Array_A


title: Saccharomyces cerevisiae Sg60 SWM Sg60 NS24 Array_A


title: Saccharomyces cerevisiae Sg60 SWM Sg60 NS24 Array_B


title: Saccharomyces cerevisiae Sg60 NS24 Sgu407 NS24 Array_B


title: Saccharomyces cerevisiae Sg60 NS4 Sg60 YPD Array_B


title: Saccharomyces cerevisiae Sg60 NS4 Sg60 YPD Array_A


title: Saccharomyces cerevisiae Ds288c YPD BY4743 YPD Array_A

source_name: Saccharomyces cerevisiae Ds288c in YPD

tag: Saccharomyces cerevisiae Ds288c in YPD


title: Saccharomyces cerevisiae Sgu407 YPD BY4743 YPD Array_A


title: Saccharomyces cerevisiae Sgu407 YPD BY4743 YPD Array_B


title: Saccharomyces cerevisiae Sgu407 YPD Sgu407 NS24


title: Saccharomyces cerevisiae Sgu407 SWM Sgu407 NS24 Array_A


title: Saccharomyces cerevisiae Sgu407 SWM Sgu407 NS24 Array_B


title: Saccharomyces cerevisiae Ds288c YPD Ds288c SWM

source_name: Saccharomyces cerevisiae Ds288c in SWM

tag: Saccharomyces cerevisiae Ds288c in SWM


title: Saccharomyces cerevisiae Ds288c YPD Ds288c NS24


title: Saccharomyces cerevisiae Ds288c SWM Ds288c SWM Array_A


title: Saccharomyces cerevisiae Sgu407 NS24 Sgu421 NS24 Array_A


title: Saccharomyces cerevisiae Ds288c NS24 Sgu52 NS24 Array_B

source_name: Saccharomyces cerevisiae Sgu52 in NS24

tag: Saccharomyces cerevisiae Sgu52 in NS24


title: Saccharomyces cerevisiae Ds288c SWM Ds288c NS24 Array_B


title: Saccharomyces cerevisiae Sg60 YPD BY4743 YPD Array_B


title: Saccharomyces cerevisiae Ds288c NS4 Ds288c YPD Array_A

source_name: Saccharomyces cerevisiae Ds288c in NS4

tag: Saccharomyces cerevisiae Ds288c in NS4


title: Saccharomyces cerevisiae Ds288c NS4 Ds288c YPD Array_B


title: Saccharomyces cerevisiae EM93 YPD BY4743 YPD Array_A

source_name: Saccharomyces cerevisiae EM93 in YPD

tag: Saccharomyces cerevisiae EM93 in YPD

source_name: Saccharomyces cerevisiae BY4743 in YPD

tag: Saccharomyces cerevisiae BY4743 in YPD


title: Saccharomyces cerevisiae EM93 YPD EM93 NS24 Array_A


title: Saccharomyces cerevisiae EM93 YPD EM93 SWM Array_B

source_name: Saccharomyces cerevisiae EM93 in SWM

tag: Saccharomyces cerevisiae EM93 in SWM


title: Saccharomyces cerevisiae EM93 YPD EM93 NS24 Array_B


title: Saccharomyces cerevisiae EM93 NS24 Sg60 NS24 Array_B


title: Saccharomyces cerevisiae EM93 NS4 EM93 YPD Array_A

source_name: Saccharomyces cerevisiae EM93 in NS4

tag: Saccharomyces cerevisiae EM93 in NS4


title: Saccharomyces cerevisiae Sg60 YPD Sg60 SWM Array_B


title: Saccharomyces cerevisiae Sg60 YPD Sg60 SWM Array_A


title: Saccharomyces cerevisiae Sg60 YPD BY4743 YPD Array_A


title: Saccharomyces cerevisiae Sg60 YPD Sg60 NS24 Replicate1_Array_A


title: Saccharomyces cerevisiae Sg60 YPD Sg60 NS24 Replicate1_Array_B


title: Saccharomyces cerevisiae BY4743 YPD EM93 YPD Replicate1_Array_A


title: Saccharomyces cerevisiae BY4743 YPD EM93 YPD Array_B


title: Saccharomyces cerevisiae Sg60 NS24 Sgu407 NS24 Array_A


title: Saccharomyces cerevisiae Ds288c YPD BY4743 YPD Array_B


title: Saccharomyces cerevisiae Ds288c YPD Ds288c NS4 Array_B


title: Saccharomyces cerevisiae Ds288c NS4 Ds288c SWM


title: Saccharomyces cerevisiae Ds288c SWM Ds288c SWM Array_B


title: Saccharomyces cerevisiae Ds288c YPD Ds288c NS4 Array_A


title: Saccharomyces cerevisiae Ds288c SWM Ds288c NS24 Array_A


title: cDNA array +10wt/+3wt set2

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

description: Comparison of gene expression profiles of +10 DPA and +3 DPA wide-type upland cotton ovules

data_processing: All microarrays were scanned with a ScanArray Express scanner using the ScanArray 2.0 software (Packard Bioscience, Meriden, CT) and analyzed using the GenePix Pro 4.0 software (Axon Instruments, Foster City, CA). We quantified signal intensities of individual spots from the 16-bit TIFF images using GenePix Pro 4.0 (Axon Instruments). Since extensive expression pattern shift was recorded in mRNA populations of late developmental stages, such as the 10dpa/3dpa sample pair shown in Fig. 1C, we applied a linear normalization strategy (van de Peppel et al., 2003) instead of the nonlinear global-intensity-based LOWESS program used for most genome-wide microarrays (Yang et al., 2002). Expression ratios were collected only on those spots with signal intensity >800 in at least one dye channel on the microarray slides. Experimental parameters will be included in supplementary file.

organism: Gossypium hirsutum

source_name: +10 DPA wide-type cotton ovule

tag: Extracted total RNA from +10 DPA wide-type cotton ovules

source_name: +3 DPA wide-type cotton ovule

tag: Extracted total RNA from +3 DPA wide-type cotton ovules


title: cDNA array +3wt/+3wt set1 (self-to-self)

description: Self-to-self hybridizations of genes from +3 DPA wild-type upland cotton ovules to confirm reproducibility of array data.


title: Saccharomyces cerevisiae Ds288c NS24 Sgu52 NS24 Array_A


title: cDNA array +3wt/-3wt set2

description: Comparison of gene expression profiles of +3 DPA and -3 DPA wild-type upland cotton ovules.

source_name: -3 DPA wide-type cotton ovule

tag: Extracted total RNA from -3 DPA wide-type cotton ovules


title: cDNA array +3wt/+3wt set2 (self-to-self)


title: Saccharomyces cerevisiae EM93 YPD EM93 SWM Array_A


title: Saccharomyces cerevisiae EM93 NS4 EM93 SWM


title: Saccharomyces cerevisiae EM93 NS4 EM93 YPD Array_B


title: Saccharomyces cerevisiae EM93 YPD BY4743 YPD Array_B


title: Saccharomyces cerevisiae EM93 SWM EM93 NS24 Array_B

source_name: Saccharomyces cerevisiae EM93 in NS24

tag: Saccharomyces cerevisiae EM93 in NS24


title: Saccharomyces cerevisiae EM93 NS24 Sg60 NS24 Array_A


title: Saccharomyces cerevisiae EM93 SWM EM93 NS24 Array_A


title: C. elegans_2_3

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: pRF4: is a transformation marker.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

organism: Caenorhabditis elegans

source_name: egl-15::gfp; pRF4

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: No heat shock treatment


title: C. elegans_3_3

description: pRF4: is a transformation marker.


title: C. elegans_3_1

description: pRF4: is a transformation marker.

source_name: egl-15::gfp; pHS::hlh-8 pHS::hlh-2 pRF4

tag: no heat shock treatment


title: C. elegans_2-1

description: pRF4: is a transformation marker.


title: C. elegans_1_3

description: pRF4: is a transformation marker.


title: C. elegans_1_2

description: pRF4: is a transformation marker.

tag: heat shock treatment


title: Saccharomyces cerevisiae BY4743 YPD EM93 YPD Replicate_2


title: Saccharomyces cerevisiae BY4743 YPD EM93 YPD Replicate1_Array_B


title: cDNA array +3wt/-3wt set3 (dye-swap)


title: cDNA array +3wt/-3wt set3


title: MGd_50uM_Zn_2

city: Los Angeles

first: Mazen

last: Karaman

state: CA

address: 2250 Alcazar St IGM/CSC 240

department: Institute for Genetic Medicine

institute: University of Southern California

description: B-cell lymphoma cell line

data_processing: GCOS

label: Biotin

source_name: Ramos cells

tag: Treated with 10uM Motexafin gadolinium and 50uM Zinc for 4 hrs -- replicate #2


title: Saccharomyces cerevisiae BY4743 YPD EM93 YPD Array_A


title: MGd_50uM_Zn_1

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium and 50uM Zinc for 4 hrs -- replicate #1


title: cDNA array +3wt/-3wt set2 (dye-swap)


title: MGd_25uM_Zn_1

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium and 25uM Zinc for 4 hrs -- replicate #1


title: MGd_25uM_Zn_3

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium and 25uM Zinc for 4 hrs -- replicate #3


title: cDNA array +3wt/+3wt set3 (self-to-self)


title: cDNA array +3wt/-3wt set1 (dye-swap)


title: C. elegans_3_4

description: pRF4: is a transformation marker.

tag: With heat shock treatment


title: cDNA array +3wt/-3wt set1


title: C. elegans_2_2 (2)

description: pRF4: is a transformation marker.


title: C. elegans_2_2

description: pRF4: is a transformation marker.


title: C. elegans_1_4

description: pRF4: is a transformation marker.


title: C. elegans_2_4

description: pRF4: is a transformation marker.


title: Mannitol_1

description: Ramos B-cell lymphoma cell line

source_name: Ramos Cells

tag: Treated with 5% mannitol for 4 hrs -- replicate #1


title: MGd_50uM_Zn_3

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium and 50uM Zinc for 4 hrs -- replicate #3


title: Mannitol_2

description: Ramos B-cell lymphoma cell line

tag: Treated with 5% mannitol for 4 hrs -- replicate #2


title: KYSE890cDNA_2

status: Public on Dec 31 2005

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

description: Expression profiles of esophageal cancer cell line established and given from Kyoto University. Reference sample is a non-cancerous esophageal epithelial cell strain HEEC-1.


title: KYSE1190cDNA_2


title: KYSE1170cDNA_2


title: 50uM_Zn_1

description: B-cell lymphoma cell line

tag: Treated with 50uM Zinc for 4 hrs -- replicate #1


title: 50uM_Zn_2

description: B-cell lymphoma cell line

tag: Treated with 50uM Zinc for 4 hrs -- replicate #2


title: MGd_2

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium for 4 hrs -- replicate #2


title: 25uM_Zn_3

description: B-cell lymphoma cell line

tag: Treated with 25uM Zinc for 4 hrs -- replicate #3


title: MGd_1

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium for 4 hrs -- replicate #1


title: 50uM_Zn_3

description: B-cell lymphoma cell line

tag: Treated with 50uM Zinc for 4 hrs -- replicate #3


title: KYSE770cDNA_2


title: MGd_25uM_Zn_2

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium and 25uM Zinc for 4 hrs -- replicate #2


title: C. elegans_1_1

description: pRF4: is a transformation marker.

tag: no heat shock treatment


title: KYSE590cDNA_1


title: KYSE520cDNA_2


title: KYSE770cDNA_1


title: MGd_3

description: B-cell lymphoma cell line

tag: Treated with 10uM Motexafin gadolinium for 4 hrs -- replicate #3


title: 25uM_Zn_2

description: B-cell lymphoma cell line

tag: Treated with 25uM Zinc for 4 hrs -- replicate #2


title: 25uM_Zn_1

description: Ramos B-cell lymphoma cell line

tag: Treated with 25uM Zinc for 4 hrs -- replicate #1


title: Mannitol_3

description: Ramos B-cell lymphoma cell line

tag: Treated with 5% mannitol for 4 hrs -- replicate #3


title: KYSE1250cDNA_2


title: KYSE350cDNA_1


title: KYSE890cDNA_1


title: KYSE850cDNA_2


title: KYSE1190cDNA_1


title: KYSE2270cDNA_2


title: KYSE1170cDNA_1


title: KYSE2270cDNA_1


title: KYSE1250cDNA_1


title: KYSE410cDNA_2


title: KYSE180cDNA_1


title: KYSE220cDNA_1


title: KYSE180cDNA_2


title: KYSE850cDNA_1


title: KYSE590cDNA_2


title: KYSE890oligo

description: RNA was extracted from an esophageal cancer cell line KYSE30 established and given from Kyoko University. Target cRNA was prepared and hybridized to commercially available CodeLink Human 20K oligonucleotide array as manufacturers recomended. The raw image data was analyzed using CodeLink Expression Analysis ver.2.3 Software (Amersham).  Data for each array was normalized using a global normalization method.

source_name: esophageal cancer cell line


title: KYSE1170oligo

description: RNA was extracted from an esophageal cancer cell line established and given from Kyoto University. Target cRNA was prepared and hybridized to commercially available CodeLink Human 20K oligonucleotide array as manufacturers recomended. The raw image data was analyzed using CodeLink Expression Analysis ver.2.3 Software (Amersham).  Data for each array was normalized using a global normalization method.


title: KYSE850oligo


title: KYSE510cDNA_1


title: KYSE510cDNA_2


title: KYSE520cDNA_1


title: KYSE30cDNA_1

description: Expression profiles of esophageal cancer cell line established and given from Kyoto University. Reference sample is a non-cancerous esophageal epithelial cell strain HEEC-1


title: KYSE520oligo


title: KYSE510oligo


title: KYSE410oligo


title: KYSE450cDNA_2


title: KYSE410cDNA_1


title: KYSE450cDNA_1


title: KYSE350cDNA_2


title: KYSE350oligo


title: KYSE220cDNA_2


title: KYSE220oligo


title: KYSE200cDNA_2


title: KYSE200oligo


title: KYSE170cDNA_1


title: KYSE150cDNA_2


title: KYSE140cDNA_2


title: KYSE200cDNA_1


title: KYSE170cDNA_2


title: KYSE140cDNA_1


title: Cold-shock_replicate_2

status: Public on Dec 01 2005

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

country: Canada

institute: University of Toronto

description:
Array Number:  12981823
The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = cold hardening

hyb_protocol: Hybridizations were performed as in Neal et al., 2003.  The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 14.5 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA).

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10 um scan: Cy3(543 nm) 100-75, Cy5(633 nm) 100-70 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.

data_processing: Data were normalized using the Lowess algorithm implemented in GeneTraffic DUO while ignoring the flagged values.  Refer to the manuscript for further discussion of data handling.

organism: Drosophila melanogaster

source_name: dp males, untreated

label_protocol: The direct labeling protocol was performed as described by Neal et al., 2003.

growth_protocol: Flies were cultured in a standard yeast sucrose medium, at 25ºC in a 12 h light/ 12 h darkness (L: D, 8 am to 8 pm) photoperiod.  Newly emerged adults were removed from bottles after eclosion and transferred to fresh medium on which they were allowed to feed and oviposit for 1-2 days.  Adult males (< 2 days post eclosion)  were selected and transferred to fresh food bottles for 5 more days before being treated.

extract_protocol: RNA was isolated with TRIzol as described in Riedl et al., 2005.

treatment_protocol: Control flies were maintained at 25ºC in the treatment vessel for the duration of the experimental procedure.  The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

tag: Strain

value: dp cn bw cl

tag: Age

value: 6-7 days post-eclosion

tag: Sex

value: Male

tag: Tissue

value: Whole organism

source_name: dp males, 2 h cold shock at 0ºC, 30 min recovery

treatment_protocol: Flies were treated for 2 h at 0 +/- 0.5ºC, followed by a 30 min recovery at 25ºC (during the light portion of their photoperiod).  The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: KYSE150cDNA_1


title: KYSE30cDNA_2


title: KYSE2270oligo


title: Cold-shock_replicate_3

description:
Array Number:  12981838
The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = cold hardening

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10 um scan: Cy3(543 nm) 100-74, Cy5(633 nm) 100-72 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.


title: hsf4_vs_dp_hyb_1

description:
Array Number:  12281337
The data in the file is not normalized.  The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = neuromuscular junction
Keywords = heat stress
Keywords = thermotolerance

hyb_protocol: Hybridizations were performed as in Neal et al., 2003.  The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 16 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA).

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings:  10 um scan:  Cy3 (543 nm) 100-72, Cy5 (633 nm) 100-65 (laser power-PMT Gain).  Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.

data_processing: Data were normalized using the Lowess algorith implemented in GeneTraffic DUO while ignoring the flagged values.  Refer to the manuscript for further discussion of data handling.

source_name: dp larvae, untreated

label_protocol: The direct labeling protocol was performed as described by Neal et al., 2005.

growth_protocol: D. melanogaster strains were grown on standard yeast-agar medium supplemented with 0.05% (w/v) bromophenol blue at 25ºC with a 12 h/12 h light/dark cycle.  Adult flies were allowed to lay eggs for 3 days on fresh media and wandering third instar larvae were collected upon their emergence from the food during the illuminated period.  Staging was verified by the blue-gut method (Maroni and Stamey, 1983).

extract_protocol: RNA was isolated with TRIzol as described in Riedl at al., 2005.

treatment_protocol: Approximately 30 larvae were collected in 2 mL screwcap plastic vials and were returned to the 25ºC incubator for 90 min.  Larvae were snap-frozen in liquid nitrogen immediately following the treatment.

tag: Stage

value: Late third instar

tag: Stage Determination

value: blue-gut method

source_name: hsf4 larvae, untreated

value: cn bw hsf4


title: KYSE1250oligo

description: RNA was extracted from an esophageal cancer cell lineestablished and given from Kyoto University. Target cRNA was prepared and hybridized to commercially available CodeLink Human 20K oligonucleotide array as manufacturers recomended. The raw image data was analyzed using CodeLink Expression Analysis ver.2.3 Software (Amersham).  Data for each array was normalized using a global normalization method.


title: F203 HS swap dye

status: Public on Oct 24 2005

city: Columbia

first: Sachin

middle: S

last: Bhusari

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: Univ of Missouri

description: Only replicate for this sample.

hyb_protocol: hybridised overnight in waterbath at 65*c.

scan_protocol: scaned using Axon scanner and image analysed using genepix software.

data_processing: normalized log2(ch2/ch1) using plant control spots.

source_name: mice liver, chronic HS, 2 wks

label_protocol: indirect amino-allyl lebeling.

extract_protocol: RNAquious-Midi kit, Ambion inc, Austin, Tx.

treatment_protocol: exposed mice from 27 to 40d of age (2wks) to chronic heat stress at 34*c.

tag: ICR strain mice, Female, 27d age, liver tissue.

source_name: Universal mouse reference RNA

tag: RNA extracted from 11 different cell lines.


title: KYSE450oligo


title: KYSE770oligo


title: M233 HS 3rd rep swap dye

description: this is the 3rd rep for this biological sample.

scan_protocol: Scanned using Axon Genepix scanner and intensities captured using Genepix software.

data_processing: log2(ch1/ch2) normalized using external plant control spikes.

label_protocol: used indirect labeling protocol using aa-dUPT.

extract_protocol: RNA extracted using RNAqueous- Midi kit (Ambion inc, Austin, Texas).

treatment_protocol: Mice were exposed to chronic heat stress for a period of 2 weeks.

tag: RNA extracted from 11 different mouse cell lines.

source_name: Male Mice liver, chronic heat stress, 2 wks,

label_protocol: indirect amino-allyl labeling protocol.

tag: ICR stain mice, Male, 27 days old, liver tissue.


title: KYSE1190oligo


title: KYSE150oligo


title: M242 HS 1st rep

description: this is the 1st rep for this biological sample.

source_name: Mice liver, chronic HS, 2 wks

tag: ICR strain mice, Female, age

value: 27d, liver tissue.


title: KYSE30oligo


title: KYSE170oligo


title: dp_heat_shock_hyb_2

description:
Array Number:  12281361
The data in the file is not normalized.  The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = neuromuscular junction
Keywords = heat stress
Keywords = thermotolerance

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings:  10 um scan:  Cy3 (543 nm) 100-72, Cy5 (633 nm) 100-62 (laser power-PMT Gain).  Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.

source_name: dp larvae, heat shock

treatment_protocol: Approximately 30 larvae were collected in 2 mL screwcap plastic vials and were heat shocked in an air incubator at 36ºC for 60 min and were returned to the 25ºC incubator for 30 min.  Larvae were snap-frozen in liquid nitrogen immediately following the treatment.


title: KYSE140oligo


title: F241 HS swap dye

description: Only replicate for this sample.

tag: ICR strain mice, Female, 27d old, liver tissue.

tag: Total RNA extracted from 11 different mouse cell lines.


title: KYSE590oligo


title: KYSE180oligo


title: Pilot_cold-shock_experiment.

description:
Array Number:  12291544
The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = cold hardening

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10 um scan: Cy3(543 nm) 100-65, Cy5(633 nm) 100-58 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.


title: hsf4_vs_dp_hyb_2

description:
Array Number:  12292176
The data in the file is not normalized.  The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = neuromuscular junction
Keywords = heat stress
Keywords = thermotolerance


title: ras2a22_rep1

status: Public on Oct 01 2005

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: RAS2a22 dominant-negative mutant

hyb_protocol: Samples were stained by with streptavidin-conjugated phycoerythrin, then washed.

data_processing: normalized with bulk-signal scaling

source_name: RAS2a22 mutant

growth_protocol: SC medium

extract_protocol: Hot-acid phenol preparation

tag: Strain SR753


title: ira2_rep2

description: IRA2 gene deletion

source_name: IRA2 gene deletion

tag: Strain SR563

value: MATa/alpha  ira2::HIS3/ira2::LEU2  ura3-52/ura3-52  leu2::hisG/leu2::hisG  his3::hisG/his3::hisG  pRS316


title: ras2v19_rep1

description: RAS2v19 dominant-active mutant

source_name: RAS2v19 mutant

tag: Strain SR453

value: MATa/alpha  ura3‑52/ura3‑52  pRS316‑RAS2V19


title: hsf4_heat_shock_hyb_2

description:
Array Number:  12281302
The data in the file is not normalized.  The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = neuromuscular junction
Keywords = heat stress
Keywords = thermotolerance

source_name: hsf4 larvae, heat shock


title: Cold-shock_replicate_1

description:
Array Number:  12695370
The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = cold hardening

hyb_protocol: Hybridizations were performed as in Neal et al., 2003.  The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 15.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA).

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10 um scan: Cy3(543 nm) 100-68, Cy5(633 nm) 100-70 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.

tag: 5-7 day malesStrain


title: hsf4_heat_shock_hyb_1

description:
Array Number:  12281106
The data in the file is not normalized.  The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = neuromuscular junction
Keywords = heat stress
Keywords = thermotolerance

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings:  10 um scan:  Cy3 (543 nm) 100-74, Cy5 (633 nm) 90-67 (laser power-PMT Gain).  Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.

tag: Strain


title: M233 HS 1st Rep

source_name: Liver, chronic heat stress, 2 weeks

tag: ICR strain mice used. Mice were heat stressed at 34*c for 2 weeks. Liver used to extract RNA. This is a Male, 27d old mice.

label: labeled with Cy3.

tag: this RNA was extracted from 11 different mouse cell lines bought from Stratagene.


title: ras2v19_rep2

description: RAS2v19 dominant-active mutant

value: MATa/alpha  ura3-52/ura3-52  pRS316-RAS2V19


title: M242 HS 2nd rep

description: this is the 2nd replicate of this biological specimen.

scan_protocol: scanned using Axon genepix scanner and software.

data_processing: Normalized log2(ch1/ch2) using external plant control spikes.

source_name: Mice liver, chronic heat stress, 2wks

label_protocol: indirect amino-allyl labeling.

extract_protocol: RNAqueous-Midi, Ambion inc (Austin, Tx).

treatment_protocol: mice exposed to 2 weeks of chronic heat stress at 34*c.

tag: ICR mice, Female, 27d old, liver tissue,

tag: RNA extracted from 11 different mice cell lines.


title: F241 HS 1st rep

description: Only replicate for this sample.

data_processing: normalized log2(ch1/ch2) using plant control spots.

source_name: mice liver, 2 wks chronic HS

tag: ICR strain mice, Female, 27d age, liver tissue


title: M256 HS 1st rep

description: Only replicate for this sample.

tag: ICR strain mice, Male, 27d old, liver tissue.


title: ira1RA_rep2

description: IRA1 point mutant, replaces active arginine with alanine

source_name: Ira1RA mutation

tag: Strain SR954

value: MATa/alpha  ira1::HIS3/ira1::LEU2  ura3‑52/ura3‑52  leu2::hisG/leu2::hisG  his3::hisG/his3::hisG  pRS316‑IRA1RA


title: ira1RA_rep1


title: ras2a22_rep2

description: RAS2a22 dominant-negative mutant


title: F222 HS 1st Rep

source_name: Mouse liver, chronic heat stress at 34*c, 2 weeks

tag: ICR strain mice, Female, 27 day age, liver tissue, 2 wks heat stressed.


title: M233 HS 2nd Rep

description: this is the 2nd rep for this biological sample.

source_name: Mouse liver,  chronic Heat stress, 2 weeks

tag: ICR mice, Male, 27d old, liver tissue used for RNA extraction.

tag: The total RNA was extracted from 11 different mouse cell lines.


title: M242 HS 3rd rep swap dye

description: this is the 3rd replicate of this biological specimen.

data_processing: Normalized log2(ch2/ch1) using external plant control spikes.

source_name: mice liver, chronic heat stress, 2wks

tag: ICR mice, Female, 27d old, liver tissue.

tag: RNA extracted from 11 different cell lines.


title: dp_heat_shock_hyb_1

description:
Array Number:  12281243
The data in the file is not normalized.  The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = neuromuscular junction
Keywords = heat stress
Keywords = thermotolerance

hyb_protocol: Hybridizations were performed as in Neal et al., 2003.  The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 17 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA).

scan_protocol: Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings:  10 um scan:  Cy3 (543 nm) 100-71, Cy5 (633 nm) 100-66 (laser power-PMT Gain).  Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction.

source_name: dp larvae, untreated

tag: Stage

tag: Stage Determination

tag: Tissue


title: M256 HS swap dye

description: Only replicate for this sample.

source_name: Mice liver, chronic Heat stress, 2 wks

tag: RNA extracted from 11 different mouse cell lines.


title: F222 HS 3rd rep dye swap

source_name: Universal mouse reference RNA

tag: ICR strain mice, Female, age

value: 27d, Tissue:liver.


title: ira2_rep1

description: IRA2 gene deletion

tag: Strain SR563


title: F222 HS 2nd rep

source_name: Mice liver, chronic heat stress, 2 wks

tag: ICR stain of mice, Female, 27d old mice, liver tissue, chronic Heat stress at 34*c for 2wks


title: ira1_rep2

description: IRA1 gene deletion

source_name: IRA1 gene deletion

tag: Strain SR595

value: MATa/alpha  ira1::HIS3/ira1::LEU2  ura3-52/ura3-52  leu2::hisG/leu2::hisG  his3::hisG/his3::hisG  pRS316


title: 1mM_cAMP

description: Cellular synthesis and degradation of cAMP impeded by Ras1, Ras2, Pde2 loss-of-function mutants, 1 mM exogenous cAMP in SC medium.

source_name: 1 mM exogenous cAMP concentration and ras1/ras2/pde2 deletion

tag: Strain SR957

value: MATa/alpha  ras1::HIS3/ras1::HIS3  ras2delta/ras2delta  pde2::kanR/ pde2::kanR  ura3-52/ura3-52 leu2::hisG/leu2::hisG  his3::hisG/his3::hisG  TRP1+/trp1::hisG


title: ira1_rep1

description: IRA1 gene deletion


title: H3K36me2 ChIP in set2 delete strain rep8

type: mixed

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

description: set2 delete (AS4) cells

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysi

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were normalized

molecule: genomic DNA

source_name: input cells

label_protocol: Input DNA was labeled using Cy3

growth_protocol: set2 delete (AS4) strain cells were grown to OD of 0.8-1, fixed and DNA was purified after reversing crosslinks

extract_protocol: Fixed cells were washed and lysed using bead beater and sonicated to get the extract

tag: set2 delete (AS4) cells

molecule: other

source_name: ChIP DNA IP using H3K36me2

label_protocol: DNA was purified after reversing cross links using qiagen

extract_protocol: Extract was used for IP with H3K36me2 Ab.

tag: H3K36me2 ChIP


title: Yeast cells rep2

description: AS4 cells

growth_protocol: AS4 strain cells were grown to OD of 0.8-1, fixed and DNA was purified after reversing crosslinks

tag: AS4 cells


title: 0.5mM_cAMP

description: Cellular synthesis and degradation of cAMP impeded by Ras1, Ras2, Pde2 loss-of-function mutants, 0.5 mM exogenous cAMP in SC medium.

source_name: 0.5 mM exogenous cAMP concentration and ras1/ras2/pde2 deletion


title: 0mM_cAMP_rep2

description: Cellular synthesis and degradation of cAMP impeded by Ras1, Ras2, Pde2 loss-of-function mutants.

source_name: 0 mM exogenous cAMP concentration and ras1/ras2/pde2 deletion

tag: Strain SR959

value: MATa/alpha  ras1::HIS3/ras1::HIS3  ras2delta/ras2delta  pde2::kanR/ pde2::kanR  ura3-52/ura3-52 leu2::hisG/leu2::hisG  his3::hisG/his3::hisG  TRP1+/trp1::hisG  pRS315


title: 2mM_cAMP_rep2

description: Cellular synthesis and degradation of cAMP impeded by Ras1, Ras2, Pde2 loss-of-function mutants, 2 mM exogenous cAMP in SC medium.

source_name: 2 mM exogenous cAMP concentration and ras1/ras2/pde2 deletion


title: 2mM_cAMP_rep1


title: wild_type_rep2

description: Wild-type

source_name: wild type

tag: Strain SR1187

value: MATa/alpha ura3-52/ura3-52 pRS316


title: 0mM_cAMP_rep1


title: wild_type_rep1

description: Wild-type


title: H3K36me2 ChIP in set2 delete  rep2

description: set2 delete (AS4) cells


title: wild_type_rep3

description: Wild type


title: wild_type_rep4

description: Wild type


title: H3K36me2 ChIP in set2 delete rep1

description: set2 delete (AS4) cells


title: Yeast cells rep8b

description: AS4 cells


title: Yeast cells rep5

description: AS4 cells


title: H3K36me2 ChIP in set2 delete strain rep7

description: set2 delete (AS4) cells


title: Yeast cells rep1

description: AS4 cells


title: H3K36me2 ChIP in set2 delete strain rep4

description: set2 delete (AS4) cells


title: Yeast cells H4-myc log rep1

description: H4-myc cells

growth_protocol: H4-myc strain cells were grown to OD of 0.8-1, fixed and DNA was purified after reversing crosslinks

tag: H4-myc cells

source_name: ChIP DNA IP using myc antibody for the myc tagged histone H4

extract_protocol: Extract was used for IP with myc Ab.

tag: H4-myc ChIP


title: H3K36me2 ChIP in set2 delete strain rep3

description: set2 delete (AS4) cells


title: H3K36me2 ChIP in set2 delete strain rep6

description: set2 delete (AS4) cells


title: Yeast cells H4-myc t=15 Myc ChIP rep1

description: H4-myc cells

source_name: t=15 input cells

growth_protocol: H4-myc strain cells were grown to OD of 0.8-1, cells were put in media at 37C for 15min ,fixed and DNA was purified after reversing crosslinks

source_name: t=15 ChIP DNA IP using H3K36me2


title: Yeast cells H4-myc t=0 Myc ChIP rep2

description: H4-myc cells

source_name: t=0 input cells

source_name: t=0 ChIP DNA IP using H3K36me2


title: Yeast cells rep6b

description: AS4 cells


title: Yeast cells rep3

description: AS4 cells


title: H3K36me2 ChIP in set2 delete rep5

description: set2 delete (AS4) cells


title: Yeast cells rep7a

description: AS4 cells


title: Yeast cells H4-myc t=0 Myc ChIP rep1

description: H4-myc cells


title: Yeast cells t=0 H4-myc rep1

description: H4-myc cells


title: Yeast cells rep6a

description: AS4 cells


title: Yeast cells H4-myc log rep2

description: H4-myc cells


title: Yeast cells rep8a

description: AS4 cells


title: Yeast cells rep7b

description: AS4 cells


title: Yeast cells H4-myc t=15 Myc ChIP rep3

description: H4-myc cells


title: Yeast cells t=0 H4-myc rep2

description: H4-myc cells


title: Yeast cells H4-myc t=15 Myc ChIP rep2

description: H4-myc cells


title: Yeast cells rep4

description: AS4 cells


title: WT

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

institute: The University of Tokyo

description: 10-day-old mice were sacrificed, and their back skin was peel off.  Skins were cut in small pieces with scissors and homogenized Isogen (Nippon Gene, Tokyo).

data_processing: target intensity=100

source_name: non-transgenic (wild type) mice

tag: organism; wild type mice litter mate

tag: strain; mixed background

tag: tissue; skin

tag: gender; mixed (2 females and 2 males)

tag: age; 10 day old


title: CD4R6D1_I-23

status: Public on Sep 30 2005

city: Corvallis

first: Edwards

last: Allen

state: OR

address: 3021 Ag Life Sciences Building

department: Botany and Plant Pathology

institute: Oregon State University

description: Col-0 control for dcl1-7 inflorescence samples

data_processing: RMA-normalized Signal intensity

organism: Arabidopsis thaliana

source_name: inflorescence stages 1 to 12

tag: Inflorescence stages 1-12.  RNA was extracted using TRIzol, purified using Qiagen RNA Midi Kit, and labeled using Ambion MessageAmp.


title: Yeast cells  t=0 rep4

description: AS4 cells

tag: AS4 cell


title: Yeast cells  t=0 rep3

description: AS4 cells


title: CD4R6D1_I-22


title: CD4R6D1_I-26

description: dcl1-7 inflorescence


title: CD4R6D1_I-25

description: dcl1-7 inflorescence


title: CD4R6D1_I-24


title: CD4R6D1_I-16

description: dcl4-2 inflorescence

source_name: Inflorescence stages 1 to 12


title: K14Ahr

source_name: transgenic mice expressing constitutive active form of AhR in keratinocytes

tag: organism; AhR-CA transgenic mice

tag: gender; mixed (3 females and 2 males)


title: CD4R6D1_I-17

description: dcl4-2 inflorescence


title: CD4R6D1_L-10

description: dcl1-7 leaf

source_name: rosette leaves 5 to 8

tag: Rosette leaves 5 to 8.  RNA was extracted using TRIzol, purified using Qiagen RNA Midi Kit, and labeled using Ambion MessageAmp.


title: CD4R6D1_I-27

description: dcl1-7 inflorescence


title: CD4R6D1_I-20

description: rdr6-15 inflorescence


title: CD4R6D1_I-19

description: rdr6-15 inflorescence


title: CD4R6D1_L-9

description: rdr6-15 leaf


title: CD4R6D1_L-12

description: dcl1-7 leaf


title: CD4R6D1_I-15

description: Col-0 control for dcl4-2, and rdr6-15 inflorescence samples


title: CD4R6D1_L-11

description: dcl1-7 leaf


title: CD4R6D1_L-7

description: rdr6-15 leaf


title: CD4R6D1_L-6

description: dcl4-2 leaf


title: CD4R6D1_I-13


title: CD4R6D1_I-21

description: rdr6-15 inflorescence


title: CD4R6D1_L-5

description: dcl4-2 leaf


title: CD4R6D1_L-4

description: dcl4-2 leaf


title: CD4R6D1_L-8

description: rdr6-15 leaf


title: CD4R6D1_I-14


title: CD4R6D1_L-3

description: Col-0 control for dcl1-7, dcl4-2, and rdr6-15 leaf samples


title: CD4R6D1_L-1


title: Yeast cells  H4-myc log rep3

description: H4-myc cells


title: CD4R6D1_L-2


title: TM_12 mouse breast tumor

status: Public on Sep 13 2005

type: genomic

city: San Francisco

first: Graeme

last: Hodgson

department: Neurological Surgery

institute: UCSF

description: Mouse breast tumor

hyb_protocol: Hodgson et al.(2001) Nat Genet, 29, 459-64.

source_name: Mouse breast tumor

tag: Mouse strain FVB/N

source_name: Normal mouse spleen


title: MT_634_701_BT mouse breast tumor

description: Mouse breast tumor

scan_protocol: Hodgson et al.(2001) Nat Genet, 29, 459-64.


title: DB4_7887_BT1 mouse breast tumor

description: Mouse breast tumor

data_processing: Hodgson et al.(2001) Nat Genet, 29, 459-64.


title: MT_634_705_BT mouse breast tumor

description: Mouse breast tumor

label_protocol: Hodgson et al.(2001) Nat Genet, 29, 459-64.


title: MT_634_702_BT mouse breast tumor

description: Mouse breast tumor

extract_protocol: Hodgson et al.(2001) Nat Genet, 29, 459-64.


title: TM_11 mouse breast tumor

description: Mouse breast tumor


title: MT_634_700_BT mouse breast tumor

description: Mouse breast tumor


title: DB4_7909_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_8232_BT1 mouse breast tumor

description: Mouse breast tumor


title: DB4_7477_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_8235_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_4105_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_4091_BT2 mouse breast tumor

description: Mouse breast tumor


title: DB4_7443_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_6388_BT2 mouse breast tumor

description: Mouse breast tumor


title: YD5_8233_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_8223_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_4092_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_6390_BT2 mouse breast tumor

description: Mouse breast tumor


title: YD5_8224_BT1 mouse breast tumor

description: Mouse breast tumor


title: DB4_7442_BT2 mouse breast tumor

description: Mouse breast tumor


title: YD5_8225_BT2 mouse breast tumor

description: Mouse breast tumor


title: YD5_6391_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_4058_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_0475_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_0473_BT mouse breast tumor

description: Mouse breast tumor


title: CD4R6D1_I-18

description: dcl4-2 inflorescence


title: YB2_6821_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_4104_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_5387_BT2 mouse breast tumor

description: Mouse breast tumor


title: YB2_8858 mouse breast tumor

description: Mouse breast tumor


title: YD5_2763_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_8868_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_8662_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_2818_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_3279_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_2810_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_#2 mouse breast tumor

description: Mouse breast tumor


title: TM_18 mouse breast tumor

description: Mouse breast tumor


title: YB2_2817_BT mouse breast tumor

description: Mouse breast tumor


title: TM_9 mouse breast tumor

description: Mouse breast tumor


title: YB2_2805_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_#1 mouse breast tumor

description: Mouse breast tumor


title: YD5_9547_BT mouse breast tumor

description: Mouse breast tumor


title: TM_15 mouse breast tumor

description: Mouse breast tumor


title: TM_16 mouse breast tumor

description: Mouse breast tumor


title: YD5_3376_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_4014_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_7554_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_4090_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_7541_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_7536_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_2808_BT2 mouse breast tumor

description: Mouse breast tumor


title: YD5_1116_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_7542_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_7553_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_3296_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_#3 mouse breast tumor

description: Mouse breast tumor


title: MT_8608 mouse breast tumor

description: Mouse breast tumor


title: DB4_5699 mouse breast tumor

description: Mouse breast tumor


title: DB4_1987 mouse breast tumor

description: Mouse breast tumor


title: YB2_2161 mouse breast tumor

description: Mouse breast tumor


title: MT_8607 mouse breast tumor

description: Mouse breast tumor


title: TM_9 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_925 mouse breast tumor

description: Mouse breast tumor


title: MT_7487 mouse breast tumor

description: Mouse breast tumor


title: TM_756 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_430 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_382 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_520 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_1597 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_15 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_14 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_728 mouse breast tumor

description: Mouse breast tumor


title: TM_5906 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_386 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_354 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_388 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_298 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_12 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_1249 mouse breast tumor

description: Mouse breast tumor


title: MT_7905 mouse breast tumor

description: Mouse breast tumor


title: DB4_5707 mouse breast tumor

description: Mouse breast tumor


title: TM_8 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_16 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_11 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_1498 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_1134 mouse breast tumor

description: Mouse breast tumor


title: MT_8607 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_18 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_10 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_8608 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_1248 mouse breast tumor

description: Mouse breast tumor


title: MT_634_705_BT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_7905 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_8062 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_634_701_BT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_634_702_BT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_8413 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_634_62_MT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_634_63_MT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_7909_HB mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_7487 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YD5_6388_BT1 mouse breast tumor

description: Mouse breast tumor


title: MT_634_700_BT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YD5_8867 mouse breast tumor

description: Mouse breast tumor


title: DB4_925 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_7909_BT1 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_634_64_MT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_634_61_MT mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_7887_HB mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YD5_8225_BT1 mouse breast tumor

description: Mouse breast tumor


title: DB4_7887 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_7477_BT1 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YD5_4068_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_5455_BT mouse breast tumor

description: Mouse breast tumor


title: YD5_4090_BT2 mouse breast tumor

description: Mouse breast tumor


title: YD5_4071_BT1 mouse breast tumor

description: Mouse breast tumor


title: YD5_4072_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB7_98076_BT2 mouse breast tumor

description: Mouse breast tumor


title: DB4_7477_HB mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YB8_2874 mouse breast tumor

description: Mouse breast tumor


title: YB7_5889 mouse breast tumor

description: Mouse breast tumor


title: DB4_7443_HB mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_7443_BT1 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YB7_4644_BT mouse breast tumor

description: Mouse breast tumor


title: YB7_5497_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB6_1357_BT mouse breast tumor

description: Mouse breast tumor


title: YB5_8387_BT mouse breast tumor

description: Mouse breast tumor


title: DB4_7442_HB mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YB6_7203_BT mouse breast tumor

description: Mouse breast tumor


title: DB4_7442_BT2 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_7439_BT2 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_6101 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_5699 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YB5_3406_BT1 mouse breast tumor

description: Mouse breast tumor


title: DB4_728 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_7439_HB mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: YB2_7551_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_7634_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB2_3276_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB3_1365_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_9439_BT1 mouse breast tumor

description: Mouse breast tumor


title: YB5_2070_BT mouse breast tumor

description: Mouse breast tumor


title: DB4_5707 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_8413 mouse breast tumor

description: Mouse breast tumor


title: YB2_#2a_BT mouse breast tumor

description: Mouse breast tumor


title: YB2_3276_BT2 mouse breast tumor

description: Mouse breast tumor


title: TM_14 mouse breast tumor

description: Mouse breast tumor


title: DB4_1987 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: TM_8 mouse breast tumor

description: Mouse breast tumor


title: YB2_0457_BT mouse breast tumor

description: Mouse breast tumor


title: TM_10 mouse breast tumor

description: Mouse breast tumor


title: YB8_8875_BT mouse breast tumor

description: Mouse breast tumor


title: DB4_1249 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: MT_8410 mouse breast tumor

description: Mouse breast tumor


title: PA2384-OD 2.1 replicate 2

status: Public on Sep 07 2005

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Pseudomonas aeruginosa mutant

organism: Pseudomonas aeruginosa

label_protocol: standard Affymetrix procedures

growth_protocol: Batch cultures of P. aeruginosa wild type PAO1 and isogenic PA2384 mutant were grown in iron-limited minimal medium C in the computer-controlled bioreactor system. Samples were harvested at different growth stages with OD600 of 0.2, 1.3 and 2.1, respectively.

extract_protocol: RNA was immediately stabilized with RNAprotect Bacteria Reagent (Qiagen). Samples were stored at -70 oC. Total RNA was extracted with RNeasy mini kit following the protocol recommended by the manufacturer (Qiagen), treated with a DNA-free kit (Ambion) to remove residual chromosomal DNA.

tag: PA2384 mutant


title: WT-OD2.1 replicate 2

description: Pseudomonas aeruginosa wilde type

tag: wilde type


title: MT_634_64_MT mouse breast tumor

description: Mouse breast tumor


title: WT-OD1.3 replicate 2

description: Pseudomonas aeruginosa wilde type


title: DB4_7439_BT2 mouse breast tumor

description: Mouse breast tumor


title: MT_634_63_MT mouse breast tumor

description: Mouse breast tumor


title: MT_634_62_MT mouse breast tumor

description: Mouse breast tumor


title: DB4_8062_BT mouse breast tumor

description: Mouse breast tumor


title: MT_8410 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: DB4_1248 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: PA2384-OD 1.3 replicate 2

description: Pseudomonas aeruginosa mutant


title: PA2384-OD 2.1 replicate 1

description: Pseudomonas aeruginosa mutant


title: WT-OD1.3 replicate 1

description: Pseudomonas aeruginosa wilde type

tag: wild type


title: WT-OD2.1 replicate 1

description: Pseudomonas aeruginosa wilde type


title: WT-OD0.2 replicate 2

description: Pseudomonas aeruginosa wilde type


title: PA2384-OD0.2 replicate 2

description: Pseudomonas aeruginosa mutant


title: PA2384-OD1.3 replicate 1

description: Pseudomonas aeruginosa mutant


title: DB4_1134 mouse breast tumor hybridized to UCSF_mouse_288_v1.0

description: Mouse breast tumor


title: WT-OD0.2 replicate 1

description: Pseudomonas aeruginosa wilde type


title: MT_634_61_MT mouse breast tumor

description: Mouse breast tumor


title: DB4_6101 mouse breast tumor

description: Mouse breast tumor


title: PA2384-OD0.2 replicate 1

description: Pseudomonas aeruginosa PA2384 mutant

growth_protocol: Samples were harvested at different growth stages with OD600 of 0.2, 1.3 and 2.1, respectively.

treatment_protocol: Batch cultures of P. aeruginosa wild type PAO1 and isogenic PA2384 mutant were grown in iron-limited minimal medium C in the computer-controlled bioreactor system.


title: H3K14Ac Replicate 3 vs input | array 9_38

status: Public on Sep 01 2005

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 25 ul Abcam rabbit anti-H3K14Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios were calculated to produce the values given in the data table.

source_name: aRNA-amplifed MNase digested DNA

label_protocol: The cDNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

tag: Strain

source_name: H3K14Ac ChIP, 25 ul Ab, IVT #506


title: H4K8Ac Replicate 2 vs input | array 9_63

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 2 ul Abcam rabbit anti-H4K8Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K8Ac ChIP, 2 ul Ab, IVT #485


title: H3K4Me2 Replicate 3 vs input | array 9_35

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 6 ul Abcam rabbit anti-H3K4Me2 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me2 ChIP, 6 ul Ab, IVT #503


title: H3K14Ac Replicate 4 vs input | array 8_58

source_name: H3K14Ac ChIP, 25 ul Ab, IVT #539


title: H4K16Ac Replicate 2 vs input | array 8_69

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 4 ul Abcam rabbit anti-H4K16Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K16Ac ChIP, 4 ul Ab, IVT #481


title: H3K4Me1 Replicate 3 vs input | array 9_43

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 25 ul Abcam rabbit anti-H3K4Me1 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me1 ChIP, 25 ul Ab, IVT #520


title: H3K4Me3 Replicate 3 vs input | array 9_36

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 4 ul Abcam rabbit anti-H3K4Me3 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me3 ChIP, 4 ul Ab, IVT #504


title: H3K4Me3 Replicate 4 vs input | array 8_55

source_name: H3K4Me3 ChIP, 4 ul Ab, IVT #536


title: H4K16Ac Replicate 3 vs input | array 9_37

source_name: H4K16Ac ChIP, 4 ul Ab, IVT #505


title: H4K16Ac Replicate 3 vs input | array 8_70


title: anti-Ac Replicate 4 vs input | array 8_62

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 25 ul Abcam rabbit anti-anti-Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: anti-Ac ChIP, 25 ul Ab, IVT #543


title: H4K5Ac Replicate 4 vs input | array 8_57

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 9 ul Abcam rabbit anti-H4K5Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K5Ac ChIP, 9 ul Ab, IVT #538


title: H4K16Ac Replicate 4 vs input | array 8_56

source_name: H4K16Ac ChIP, 4 ul Ab, IVT #537


title: H2AK7Ac Replicate 4 vs input | array 8_85

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 3 ul Abcam rabbit anti-H2AK7Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H2AK7Ac ChIP, 3 ul Ab, IVT #540


title: H2BK16Ac Replicate 2 vs input | array 8_83

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 25 ul Abcam rabbit anti-H2BK16Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H2BK16Ac ChIP, 25 ul Ab, IVT #489


title: Mock Replicate 3 vs input | array 8_84

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 15X ul Abcam rabbit anti-Mock was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: Mock ChIP, 15X ul Ab, IVT #527


title: H4K5Ac Replicate 3 vs input | array 9_44

source_name: H4K5Ac ChIP, 9 ul Ab, IVT #521


title: Mock Replicate 3 vs input | array 8_74

source_name: aRNA-amplifed MNase digested DNA


title: H4K16Ac Replicate 4 vs input | array 9_68


title: Mock Replicate 3 vs input | array 8_77


title: Mock Replicate 3 vs input | array 9_66


title: H3K4Me3 Replicate 1 vs input | array 9_46

source_name: H3K4Me3 ChIP, 4 ul Ab, IVT #437


title: H4K8Ac Replicate 4 vs input | array 8_60

source_name: H4K8Ac ChIP, 2 ul Ab, IVT #541


title: H2AK7Ac Replicate 3 vs input | array 9_39

source_name: H2AK7Ac ChIP, 3 ul Ab, IVT #507


title: H4K5Ac Replicate 3 vs input | array 8_73


title: anti-Ac Replicate 3 vs input | array 9_40

source_name: anti-Ac ChIP, 25 ul Ab, IVT #510


title: H2BK16Ac Replicate 1 vs input | array 9_48

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 10 ul Abcam rabbit anti-H2BK16Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H2BK16Ac ChIP, 10 ul Ab, IVT #469


title: H2AK7Ac Replicate 4 vs input | array 8_59


title: H3K4Me1 Replicate 4 vs input | array 8_53

source_name: H3K4Me1 ChIP, 25 ul Ab, IVT #534


title: H3K9Ac Replicate 2 vs input | array 8_48

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 16 ul Abcam rabbit anti-H3K9Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K9Ac ChIP, 16 ul Ab, IVT #488


title: H4K8Ac Replicate 4 vs input | array 9_69


title: H2BK16Ac Replicate 2 vs input | array 8_49


title: H3K9Ac Replicate 3 vs input | array 9_41

source_name: H3K9Ac ChIP, 16 ul Ab, IVT #511


title: MM-094_2

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description:
gene expression profiles of purified plasma cells (PCs) obtained from MM-004 patient.
Keywords = Gene expression profiling
Keywords = Multiple myeloma
Keywords = TC classification
Keywords = Cyclin D
Keywords = IGH translocation

data_processing: After scanning, the CEL files were processed using standard Robust Multi-Array average (RMA) procedure to generate gene expression intensity values. Detection calls were calculated using the default parameters of Affymetrix MAS 5.0 software package.

label: biotin-labeled UTP and CTP

source_name: CD138+ plasma cells obtained from bone marrow of MM patient

tag: for full details see Table 1, Appendix_A from Agnelli, et al., "Molecular classification of multiple myeloma

value: a distinct transcriptional profile characterizes patients expressing CCND1 and negative for 14q32 translocations", J Clin Onc, in press


title: MM-092_2


title: H2AK7Ac Replicate 2 vs input | array 8_46

source_name: H2AK7Ac ChIP, 3 ul Ab, IVT #484


title: MM-087_2


title: anti-Ac Replicate 2 vs input | array 8_47

source_name: anti-Ac ChIP, 25 ul Ab, IVT #487


title: MM-083_2


title: MM-082_2


title: H3K4Me1 Replicate 3 vs input | array 6_92

source_name: H3K4Me1 ChIP, 25 ul Ab, IVT #520


title: MM-089_2


title: H4K8Ac Replicate 1 vs input | array 8_39

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 5 ul Abcam rabbit anti-H4K8Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K8Ac ChIP, 5 ul Ab, IVT #460


title: MM-077_2


title: H3K14Ac Replicate 2 vs input | array 8_45

source_name: H3K14Ac ChIP, 25 ul Ab, IVT #483


title: H3K14Ac Replicate 1 vs input | array 8_37

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 20 ul Abcam rabbit anti-H3K14Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K14Ac ChIP, 20 ul Ab, IVT #458


title: MM-072_2


title: MM-078_2


title: H4K5Ac Replicate 1 vs input | array 8_40

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 10 ul Abcam rabbit anti-H4K5Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K5Ac ChIP, 10 ul Ab, IVT #461


title: H3K9Ac Replicate 1 vs input | array 8_38

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 8 ul Abcam rabbit anti-H3K9Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: aRNA-amplifed MNase digested DNA

source_name: H3K9Ac ChIP, 8 ul Ab, IVT #459


title: MM-079_2


title: H3K4Me3 Replicate 2 vs input | array 8_42

source_name: H3K4Me3 ChIP, 4 ul Ab, IVT #488


title: MM-074_2


title: H4K16Ac Replicate 2 vs input | array 8_43

source_name: H4K16Ac ChIP, 4 ul Ab, IVT #481


title: H3K4Me1 Replicate 1 vs input | array 8_36

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 20 ul Abcam rabbit anti-H3K4Me1 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me1 ChIP, 20 ul Ab, IVT #452


title: H4K12Ac Replicate 1 vs input | array 6_87

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 10 ul Abcam rabbit anti-H4K12Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K12Ac ChIP, 10 ul Ab, IVT #463


title: MM-069_2


title: H3K4Me3 Replicate 5 vs input | array 6_29

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 4 or 8 ul Abcam rabbit anti-H3K4Me3 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me3 ChIP, 8 ul Ab, IVT #414


title: MM-067_2


title: MM-068_2


title: H4K5Ac Replicate 2 vs input | array 8_44

source_name: H4K5Ac ChIP, 9 ul Ab, IVT #482


title: H4K12Ac Replicate 3 vs input | array 6_94

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 15 ul Abcam rabbit anti-H4K12Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K12Ac ChIP, 15 ul Ab, IVT #509


title: H3K4Me2 Replicate 1 vs input | array 8_35

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 4 ul Abcam rabbit anti-H3K4Me2 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me2 ChIP, 4 ul Ab, IVT #451


title: H3K4Me2 Replicate 2 vs input | array 8_41

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 6 ul Abcam rabbit anti-H3K4Me2 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me2 ChIP, 6 ul Ab, IVT #479


title: H4K12Ac Replicate 2 vs input | array 6_90

source_name: H4K12Ac ChIP, 15 ul Ab, IVT #486


title: H3K4Me1 Replicate 2 vs input | array 6_88

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 25 ul Abcam rabbit anti-H3K4Me1 was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K4Me1 ChIP, 25 ul Ab, IVT #478


title: MM-066_2

source_name: CD138+ plasma cells obtained from bone marrow of MM patient


title: MM-063_2


title: MM-056_2


title: MM-064_2


title: MM-052_2


title: MM-040_2


title: MM-048_2


title: MM-043_2


title: MM-049_2


title: MM-054_2


title: MM-037_2


title: MM-050_2


title: MM-045_2


title: MM-055_2


title: MM-038_2


title: MM-042_2


title: MM-031_2


title: MM-035_2


title: MM-032_2


title: MM-039_2


title: MM-036_2


title: MM-027_2


title: MM-070_2


title: MM-030_2


title: MM-047_2


title: MM-021_2


title: MM-034_2


title: MM-016_2


title: MM-033_2


title: MM-019_2


title: MM-025_2


title: MM-026_2


title: MM-014_2


title: MM-015_2


title: MM-004_2


title: Coffee Se

status: Public on Aug 15 2005

city: Campinas

first: Jorge

middle: Maurício Costa

last: Mondego

state: SP

address: Cidade Universitária Zeferino Vaz s/n

department: Genetics and Evolution

country: Brazil

institute: UNICAMP

description:
Susceptible coffee plants infested with coffee leaf miner. Leaves were collected after seven days of infestation. Larvae have ecloded from the egg.
Keywords = coffee
Keywords = coffee leaf miner
Keywords = biotic stress
Keywords = nylon arrays
Keywords = subtracted cDNA library

organism: Coffea

source_name: Leaves from coffee plants


title: Wildtype Salmonella treatment for 4hr triplicate 3

status: Public on Jul 31 2005

city: Atlanta

first: Hui

last: Zeng

state: GA

address: 1600 Clifton Rd. MS:G16

department: Influenza Branch

institute: Centers for disease control

description: After scanning, the data analysis were proformed by Biodiscovery softwares and Cluster/TreeView.

hyb_protocol: The labelled cDNA were cleaned up, pooled, and hybridized to the array chips.

scan_protocol: Both channels were scanned separately and imput softwares GeneSight from Biodiscovery Inc.

data_processing: normalization, background substract, transformation, t-test

source_name: Reference total RNA

label_protocol: Reverse transcription labelling

tag: High quality RNA pool from ten human cell	lines.

source_name: Treated sample

label_protocol: Reverse Transcription

extract_protocol: TRizol

tag: T84 cells were treated with Wildtype Salmonella for	4hr


title: Coffee Sc

description:
Susceptible coffee plants not infested with coffee leaf miner.
Keywords = coffee
Keywords = coffee leaf miner
Keywords = biotic stress
Keywords = nylon arrays
Keywords = subtracted cDNA library


title: Wildtype Salmonella treatment for 5hr triplicate 1


title: Wildtype Salmonella treatment for 6hr triplicate 1


title: Coffee Re

description:
Resistant coffee plants infested with coffee leaf miner. Leaves were collected after seven days of infestation. Larvae have ecloded from the egg.
Keywords = coffee
Keywords = coffee leaf miner
Keywords = biotic stress
Keywords = nylon arrays
Keywords = subtracted cDNA library


title: Wildtype Salmonella treatment for 5hr triplicate 2

tag: T84 cells were treated with Wildtype Salmonella for 4hr


title: Wildtype Salmonella treatment for 6hr triplicate 2


title: Coffee Ro

description:
Resistant coffee plants infested with coffee leaf miner. Leaves were collected after three days of infestation. Eggs have not hatched yet.
Keywords = coffee
Keywords = coffee leaf miner
Keywords = biotic stress
Keywords = nylon arrays
Keywords = subtracted cDNA library


title: parous+MNU mammary gland

city: Osaka

first: Norihisa

last: Uehara

institute: Kansai Medical University

description: Pregnant and age-matched virgin (AMV) Lewis rats (10 animals each) were used for the experiments. After parturition (at 87 days of age), parous animals were allowed to nurse their offspring for 21 days. At 108 days of age, the litters were removed, and the parous animals underwent 28 days of postlactational involution. At 136 days of age, parous and AMV rats (5 animals each) were sacrificed, and the remaining animals (5 parous and 5 AMV rats) received a single 50 mg/kg dose of Nmethyl-N-nitrosourea (MNU) by an intraperitoneal route. Three weeks after MNU administration, both parous and AMV rats (age, 157 days) were sacrificed.

organism: Rattus norvegicus

source_name: parous mammary gland (3weeks after MNU-treatment)


title: AMV mammary gland

description: Pregnant and age-matched virgin (AMV) Lewis rats (10 animals each) were used for the experiments. After parturition (at 87 days of age), parous animals were allowed to nurse their offspring for 21 days. At 108 days of age, the litters were removed, and the parous animals underwent 28 days of postlactational involution. At 136 days of age, parous and AMV rats (5 animals each) were sacrificed, and the remaining animals (5 parous and 5 AMV rats) received a single 50 mg/kg dose of N-methyl-N-nitrosourea (MNU) by an intraperitoneal route. Three weeks after MNU administration, both parous and AMV rats (age, 157 days) were sacrificed.

source_name: virgin mammary glsnd (136 days of age)


title: parous mammary gland

description: Pregnant Lewis rats (5 animals) were used. After parturition (at 87 days of age), parous animals were allowed to nurse their offspring for 21 days. At 108 days of age, the litters were removed, and the parous animals underwent 28 days of postlactational involution. At 136 days of age, parous rats (5 animals) were sacrificed.

source_name: parous mammary gland (136 days of age)


title: Wildtype Salmonella treatment for 6hr triplicate 3


title: Coffee Rc

description:
Resitant coffee plants not infested with coffee leaf miner.
Keywords = coffee
Keywords = coffee leaf miner
Keywords = biotic stress
Keywords = nylon arrays
Keywords = subtracted cDNA library


title: AMV+MNU mammary gland

source_name: virgin mammary gland (3weeks after MNU-treatment)


title: Wildtype Salmonella treatment for 5hr triplicate 3


title: Coffee So

description:
Susceptible coffee plants infested with coffee leaf miner. Leaves were collected after three days of infestation. Eggs have not hatched yet.

Keywords = coffee
Keywords = coffee leaf miner
Keywords = biotic stress
Keywords = nylon arrays
Keywords = subtracted cDNA library


title: H2A.Z Replicate 2 vs input | array 11_156

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 10 ul rabbit anti-H2A.Z was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: aRNA-amplifed MNase digested DNA

source_name: H2A.Z ChIP, 10 ul Ab, IVT #655


title: H3K18Ac Replicate 1 vs input | array 11_137

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 3 ul rabbit anti-H3K18Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K18Ac ChIP, 3 ul Ab, IVT #636


title: H2A.Z Replicate 2 vs input | array 11_155


title: H4K16Ac_Grunstein Replicate 2 vs input | array 11_132

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 5 ul Grunstein rabbit anti-H4K16Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H4K16Ac Grunstein ChIP, 5 ul Ab, IVT #641


title: Wildtype Salmonella treatment for 4hr triplicate 2


title: Wildtype Salmonella treatment for 4hr triplicate 1


title: H4K16Ac_Grunstein Replicate 2 vs input | array 11_133


title: Wildtype Salmonella treatment for 3hr triplicate 1


title: Wildtype Salmonella treatment for 3hr triplicate 2


title: H3K18Ac Replicate 1 vs input | array 11_122


title: Wildtype Salmonella treatment for 3hr triplicate 3


title: Wildtype Salmonella treatment for 2hr triplicate 2


title: TNF treatment for 6hr triplicate 2

tag: T84 cells were treated with TNF for	4hr


title: Wildtype Salmonella treatment for 2hr triplicate 3


title: Wildtype Salmonella treatment for 2hr triplicate 1


title: Wildtype Salmonella treatment for 1hr triplicate 2


title: Wildtype Salmonella treatment for 1hr triplicate 3


title: TNF treatment for 5hr triplicate 3


title: H3K18Ac Replicate 2 vs input | array 11_139

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 5 ul rabbit anti-H3K18Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

source_name: H3K18Ac ChIP, 5 ul Ab, IVT #642


title: Wildtype Salmonella treatment for 1hr triplicate 1


title: TNF treatment for 5hr triplicate 2

tag: T84 cells were treated with TNF for 4hr


title: TNF treatment for 6hr triplicate 1


title: TNF treatment for 5hr triplicate 1


title: H2A.Z Replicate 1 vs input | array 11_130

source_name: H2A.Z ChIP, 10 ul Ab, IVT #637


title: TNF treatment for 4hr triplicate 1


title: TNF treatment for 4hr triplicate 3


title: TNF treatment for 3hr triplicate 3


title: TNF treatment for 4hr triplicate 2


title: TNF treatment for 6hr triplicate 3


title: TNF treatment for 3hr triplicate 2


title: H3K18Ac Replicate 2 vs input | array 11_131


title: H2A.Z Replicate 2 vs input | array 11_127