title: Non resistant tumor (26A-4) x Gemcitabine resistant tumor (26G-3)

source_name: Colon tumor 26A-4

source_name: Colon tumor 26G-3


title: Atm+/+ untreated C

status: Public on Dec 21 2005

type: RNA

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: Untreated Atm+/+ murine lymph node, replicate C

molecule: total RNA

organism: Mus musculus

source_name: murine lymph node


title: Atm+/+ untreated B

description: Untreated Atm+/+ murine lymph node, replicate B


title: DRG019_a

city: Beerse

first: Pieter

middle: Johan

last: Peeters

address: Turnhoutseweg 30

department: Internal Medicine

country: Belgium

institute: J&J Pharmaceutical R&D

description: Laser captured visceral sensory neurons.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

source_name: dorsal root ganglion

label_protocol: Approximately 12 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Whole ganglia were put in RLT buffer.

treatment_protocol: normal standard housing conditions

tag: BALB/c


title: Atm-/- 120 min post IR, A

description: Atm-/- murine lymph node, 120 min post-IR, replicate A


title: Atm+/+ 30 min post IR, B

description: Atm+/+ murine lymph node, 30 min post IR, replicate B


title: Atm+/+ untreated A

description: Untreated Atm+/+ murine lymph node, replicate A

source_name: Murine lymph node


title: S1_d3PDb2

city: BORDEAUX

first: Helene

last: BOEUF

country: France

description:
S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000 cells/ml in ES cell medium without LIF in the presence of 10 uM PD169316. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74Av2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.

source_name: Embryonic stem cell line


title: S1_d3b2

description:
S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000 cells/ml in ES cell medium without LIF. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74Av2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.


title: Atm-/- untreated, A

description: Atm-/- murine lymph node, untreated, replicate A


title: Atm+/+ 30 min post IR, A

description: Atm+/+ murine lymph node, 30 min post IR, replicate A


title: S1_d3PDb1


title: Gemcitabine resistant tumor (26G-1) x Non resistant tumor (26A-2)

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: One solid tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G".

source_name: Colon tumor 26G-1

source_name: Colon tumor 26A-2


title: HCjE 6 HR + 100 nM Retinoic Acid.1 Sample 1

status: Public on Dec 20 2005

city: Boston

first: Ilene

middle: K

last: Gipson

state: MA

address: 20 Staniford ST

country: USA

institute: Schepens Eye Research Institute

description: HCjE CONTROL Sample 1

data_processing: Rosetta Resolver

label: Biotin

organism: Homo sapiens

tag: Human conjunctival epithelial cell line (as described in Gipson et al, Invest Ophthalmol Vis Sci

tag: 2003;44:2496-2506) treated for 3, 6, 12, 24 or 48 hours with 100 nM retinoic acid and untreated controls (N=2 for each condition.)


title: HCjE 48 HR + 100 nM Retinoic Acid Sample 1

description: HCjE CONTROL Sample 1


title: HCjE 24 HR + 100 nM Retinoic Acid Sample 1

description: HCjE CONTROL Sample 1


title: S1_d3b1


title: HCjE 24 HR + 100 nM Retinoic Acid.2 Sample 2

description: HCjE CONTROL Sample 1


title: HCjE 3 HR + 100 nM Retinoic Acid.2 Sample 2

description: HCjE CONTROL Sample 1


title: HCjE 6 HR + 100 nM Retinoic Acid.2 Sample 2

description: HCjE CONTROL Sample 1


title: MO32_18

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

description: Myometrium tissue.

source_name: Trizol extracted total RNA from myometrium tissue.


title: HCjE 12 HR + 100 nM Retinoic Acid.2 Sample 2

description: HCjE CONTROL Sample 1


title: HCjE 12 HR + 100 nM Retinoic Acid Sample 1

description: HCjE CONTROL Sample 1


title: HCjE CONTROL Sample 1

description: HCjE CONTROL Sample 1

source_name: HCjE CONTROL Sample 1


title: HCjE  3 HR + 100 nM Retinoic Acid Sample 1

description: HCjE CONTROL Sample 1


title: MO32_17

description: Uterine fibroid tissue carrying wild-type fumarate hydratase gene.

source_name: Trizol extracted total RNA from uterine fibroid tissue.


title: MO32_15


title: 6n

description: Myometrium tissue.


title: MO32_8

description: Uterine fibroid tissue with mutated fumarate hydratase gene.


title: MO32_16

description: Myometrium tissue.


title: MO32_7


title: MO32_9


title: 51n

description: Myometrium tissue.

source_name: Trizol extracted total RNA from myometrium tissue. Trizol extracted total RNA from myometrium tissue.


title: MO32_11


title: B7n

description: Myometrium tissue.

source_name: Trizol extracted total RNA from myometrium tissue. Trizol extracted total RNA from myometrium tissue (HLRCC).


title: MO32_10


title: Atm-/- 30 min post IR, B

description: Atm-/- murine lymph node, 30 minpost-IR, replicate B


title: MO32_12

description: Myometrium tissue.

source_name: Trizol extracted total RNA from myometrium tissue (HLRCC).


title: 44n

description: Myometrium tissue.


title: Atm+/+ 120 min post IR, A

description: Atm+/+ murine lymph node, 120 min post IR, replicate A


title: 11n

description: Myometrium tissue.


title: 28n

description: Myometrium tissue.


title: 38n

description: Myometrium tissue.


title: B7m1

description: Uterine fibroid tissue with mutated  fumarate hydratase gene.


title: B7m2


title: 34n

description: Myometrium tissue.


title: B7m6


title: 4m3


title: 4n

description: Myometrium tissue.


title: 32n

description: Myometrium tissue.


title: 32m1


title: 9n

description: Myometrium tissue.


title: HCjE CONTROL.2 Sample 2

description: HCjE CONTROL Sample 1

source_name: HCjE CONTROL.2 Sample 2


title: B7m3


title: 9m5


title: 51m1


title: 9m1


title: NG026_a

source_name: nodose ganglion


title: intestine mRNAtagging exp. 3

city: Stanford

first: Florencia

last: Pauli

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-02/38265.gif; format: GIF

organism: Caenorhabditis elegans

source_name: Cy3 (channel 1): L4/YA lysate no IP amplified

source_name: Cy5 (channel 2): L4/YA lysate IP 250 amplified


title: 44m3


title: intestine mRNAtagging exp. 8

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-06/41886.gif; format: GIF

source_name: Cy3 (channel 1): YA (5/19) lysate no IP amplified

source_name: Cy5 (channel 2): YA (5/19) lysate IP amplified, 350 mM NaCl buffer


title: NG020_a


title: 4m2


title: 44m2


title: intestine mRNAtagging exp. 7

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-06/41834.gif; format: GIF

source_name: Cy3 (channel 1): YA (5/19) no IP amplified

source_name: Cy5 (channel 2): YA (5/19) IP amplified long wash


title: 11m2


title: intestine mRNAtagging exp. 1

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-01/36590.gif; format: GIF

source_name: Cy5 (channel 2): L4/YA lysate fly precleared IP amplified


title: 38m1


title: 38m5


title: 9m3


title: 38m4


title: 28m1


title: 03_add_s_2

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description:
Experiment Type:  expression profile of each tissue
Dye Swap:  red/green
Organization:  RIKEN Genome Science Centre (GSC) Yokohama Japan

scan_protocol: Image Analysis Software: DigitalGENOME (Molecularware Inc.)

data_processing: Lowess Normalisation (Genespring7.2). A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point.  This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10 otherwise the measurement was thrown out.

source_name: Tissue Type:  Adipose D

label_protocol: direct labelling of cDNA

tag: Age

value: 8 weeks

tag: Sex

value: male

tag: Strain/Cell-line

tag: Developmental stage

value: Adult

source_name: Common Reference: 17.5dpc total embryo

tag: 17.5dpc total embryo


title: 03_ade_s_2

source_name: Tissue Type:  Adipose E


title: 03_ade_a_2


title: 03_add_a_2


title: intestine mRNAtagging exp. 2

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-02/38262.gif; format: GIF

source_name: Cy3 (channel 1): L4/YA lysate 230 ug amplified no IP

source_name: Cy5 (channel 2): L4/YA lysate 500 ug amplified IP


title: 14m8

source_name: Trizol extracted total RNA from uterine fibroid tissue.


title: 11m1


title: 03_add_a_1


title: 32m4


title: 03_ade_s_1


title: intestine mRNAtagging exp. 4

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-03/39215.gif; format: GIF

source_name: Cy3 (channel 1): YA lysate 250 no IP amplified

source_name: Cy5 (channel 2): YA lysate 1000 IP amplified


title: 03_add_s_1


title: intestine mRNAtagging exp. 6

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-06/41833.gif; format: GIF

source_name: Cy3 (channel 1): YA lysate no IP amplified

source_name: Cy5 (channel 2): YA lysate IP amplified


title: intestine mRNAtagging exp. 5

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2003-05/40157.gif; format: GIF

source_name: Cy3 (channel 1): L4/YA lysate, no IP, amplified

source_name: Cy5 (channel 2): L4/YA lysate  200 ug precleared with fly extract IP amplified


title: HCjE 48 HR + 100 nM Retinoic Acid.2 Sample 2

description: HCjE CONTROL Sample 1


title: 03_adm_a_11

source_name: Tissue Type:  adipose M


title: 02_add_a_1

description:
Experiment Type: Expression profile of each tissue
Dye Swap: red/green
Organization: RIKEN Genome Science Centre (GSC) Yokohama Japan

source_name: Tissue Type: adipose-d


title: 02_add_s_2


title: 02_add_a_2


title: 02_add_s_1


title: 03_adm_a_1


title: 03_adm_s_1


title: 02_ade_s_1

source_name: Tissue Type: adipose-e


title: 03_adm_a_2


title: 02_ade_a_1


title: 02_adm_a_2

source_name: Tissue Type: adipose-m


title: 02_ade_s_2


title: 02_ade_a_2


title: 03_adm_s_11


title: 03_bo_a_1

source_name: Tissue Type:  Bone


title: 02_adm_s_1


title: 02_br_a_2

source_name: Tissue Type: Brain


title: 03_adm_s_2

source_name: Common Reference: 17.5dpc total embryo


title: 03_adm_a_22


title: 02_adm_s_2


title: 02_bo_s_1

source_name: Tissue Type: Bone


title: 02_bo_a_1


title: 02_bo_a_2


title: 02_adm_a_1


title: 03_adm_s_22


title: 02_br_a_1


title: 02_bo_s_2


title: B7m5


title: 02_ce_a_1

source_name: Tissue Type: Cereb


title: 02_br_s_1


title: 02_ce_a_2


title: 02_ce_s_2


title: 03_bo_s_11


title: 02_co_s_1

source_name: Tissue Type: Colon


title: LZ75 T42

city: Denver

first: Robert

middle: S

last: Stearman

state: CO

address: 4200 E Ninth Ave

department: Medicine/Pulmonary

institute: UCHSC

description: 42 week tumor lung

source_name: lung tissue


title: 02_co_a_1


title: 03_bo_s_2


title: 03_bo_s_22


title: LZ74 T42

description: 42 week tumor lung


title: 03_bo_a_22


title: 02_ce_s_1


title: 02_br_s_2


title: 03_bo_a_11


title: 03_bo_a_2


title: LZ73 Tq42

description: 42 week tumor lung


title: 03_bo_s_1


title: 03_br_a_3

source_name: Tissue Type:  Brain


title: 02_co_s_2


title: 02_he_a_2

source_name: Tissue Type: Heart


title: 03_br_a_4


title: LZ72 T42

description: 42 week tumor lung


title: 02_he_s_2


title: 02_he_s_1


title: 02_co_a_2


title: 02_he_a_1


title: 02_ki_a_111

source_name: Tissue Type: Kidney


title: 02_ki_a_1


title: 02_ki_a_11


title: 02_ki_a_2


title: 03_ce_a_4

source_name: Tissue Type:  cerebellum


title: 02_ki_a_22


title: 02_ki_s_1


title: 02_ki_s_2


title: 02_ki_s_22


title: LZ70 T42

description: 42 week tumor lung


title: LZ69 T42

description: 42 week tumor lung


title: LZ71 T42

description: 42 week tumor lung


title: 02_li_s_1

source_name: Tissue Type: Liver


title: LZ36 T42

description: 42 week tumor lung


title: LZ38 T42

description: 42 week tumor lung


title: LZ35 T42

description: 42 week tumor lung


title: 02_lu_a_1

source_name: Tissue Type: Lung


title: 02_li_s_2


title: 02_lu_a_2


title: 02_ki_s_111


title: 02_li_a_1


title: 03_cer10_a_1

source_name: Tissue Type:  cerebellum neonate


title: LZ39 T42

description: 42 week tumor lung


title: 03_ce_retry_a_3


title: LZ68 T42

description: 42 week tumor lung


title: 02_ki_a_222


title: 03_ce_a_1


title: 02_ki_s_11


title: 02_li_a_2


title: 03_ce_s_3


title: 03_ce_a_2


title: 03_cer10_a_2


title: 03_co_a_1

source_name: Tissue Type:  Colon


title: LZ33 T42

description: 42 week tumor lung


title: 02_lu_s_1


title: LZ32 T42

description: 42 week tumor lung


title: 02_ki_s_222


title: LZ65 A42

description: 42 week adjacent normal lung


title: 03_co_a_4


title: 03_li_a_1

source_name: Tissue Type:  Liver


title: LZ66 A42

description: 42 week adjacent normal lung


title: 02_lu_s_2


title: 9_placenta_B

description:
Experiment Type: expression profile of each tissue
Dye Swap: red/green
Organization: RIKEN Genome Science Centre

scan_protocol: Image Analysis Software: DigitalGENOME

data_processing: Lowess Normalisation (Genespring7.2). A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10 otherwise the measurement was thrown out.

source_name: Tissue Type: placenta

value: 8 Weeks


title: LZ29 T42

description: 42 week tumor lung


title: 02_n10ce_a_1

source_name: Tissue Type: Cerebellum neonate


title: 02_mu_a_1

source_name: Tissue Type: Muscle


title: 6_heart_A

source_name: Tissue Type: heart

source_name: Common Reference: 17.5dpc total embryo


title: LZ67 A42

description: 42 week adjacent normal lung


title: 03_co_a_3


title: 03_co_a_2


title: 8_cerebellum_s1

source_name: Tissue Type: cerebellum


title: 03_co_s_1


title: 02_mu_s_1


title: 9_placenta_A


title: 02_mu_a_2


title: LZ27 T42

description: 42 week tumor lung


title: LZ28 T42

description: 42 week tumor lung


title: 03_co_s_2


title: 03_lu_a_3

source_name: Tissue Type:  Lung


title: 8_cerebellum_s2


title: 5_spleen_B

source_name: Tissue Type: spleen


title: 02_n10ce_s_1


title: 02_n10ce_a_2


title: 02_n10ce_s_2


title: 02_mu_s_2


title: LZ37 A42

description: 42 week adjacent normal lung

source_name: lung tissue


title: 6_heart_B


title: 03_li_a_2


title: 03_mu_a_1

source_name: Tissue Type:  Muscle


title: LZ31 A42

description: 42 week adjacent normal lung


title: 5_spleen_A


title: 02_n10sk_a_1

source_name: Tissue Type: Skin neonate


title: 03_lu_a_4


title: LZ26 A42

description: 42 week adjacent normal lung


title: 53_embryo16_lung_A

source_name: Tissue Type: lung embryonic

value: mixed pool

value: Embryo


title: 02_n10sk_a_11


title: 03_mu_s_1


title: 03_mu_a_2


title: LZ30 Tq

description: 24-26 week tumor lung


title: 52_colon_s2

source_name: Tissue Type: colon


title: LZ11 T

description: 24-26 week tumor lung


title: 53_embryo16_lung_B


title: LZ9 T

description: 24-26 week tumor lung


title: AJ18 T

description: 24-26 week tumor lung


title: 52_colon_s1


title: 02_n10sk_s_1


title: 03_pa_a_1

source_name: Tissue Type:  Pancreas


title: 02_n10sk_a_22


title: 03_mu_s_2


title: 02_n10sk_s_11


title: 02_pa_a_1

source_name: Tissue Type: Pancreas


title: 51_muscle_A

source_name: Tissue Type: muscle


title: 03_pa_a_2


title: 03_pa_s_1


title: 03_pa_s_2


title: AJ17 T

description: 24-26 week tumor lung


title: LZ64 A42

description: 42 week adjacent normal lung


title: 4_lung_A

source_name: Tissue Type: lung


title: 02_pa_a_11


title: 51_muscle_B


title: AJ16 T

description: 24-26 week tumor lung


title: LZ10 T

description: 24-26 week tumor lung


title: 4_lung_B


title: 02_n10sk_s_22


title: AJ15 T

description: 24-26 week tumor lung


title: 03_pl_a_11

source_name: Tissue Type:  Placenta

value: embryonic

value: Pool


title: AJ14 T

description: 24-26 week tumor lung


title: 03_pl_a_2


title: 02_pa_a_22


title: AJ13 T

description: 24-26 week tumor lung


title: 02_pa_s_1


title: 02_pa_a_2


title: 01_LZ12 T

description: 24-26 week tumor lung


title: 41_olfactory_brain_s4

source_name: Tissue Type: olfactory brain


title: 02_pa_s_22


title: 41_olfactory_brain_s3


title: 3_kidney_sg2

source_name: Tissue Type: kidney


title: 03_pl_a_22


title: 3_kidney_sg1


title: AJ12 T

description: 24-26 week tumor lung


title: 40_medulla_oblongata_B

source_name: Tissue Type: medulla oblongata


title: 02_pa_s_11

source_name: Common Reference: 17.5dpc total embryo


title: 03_pl_s_11


title: 40_medulla_oblongata_A


title: 03_pl_s_1


title: 02_pa_s_2


title: LZ8 A

description: 24-26 week adjacent normal lung


title: 03_pl_s_2


title: 03_pl_a_1


title: 39_embryo11_head_s2

source_name: Tissue Type: head embryonic

value: Embyro


title: 02_pl_a_2

source_name: Tissue Type: Placenta

value: pool


title: 02_pl_a_1


title: 03_pl_s_22


title: 39_embryo11_head_s1


title: 03_si_a_1

source_name: Tissue Type:  small intestine


title: 02_pl_s_1


title: AJ9 A

description: 24-26 week adjacent normal lung

source_name: lung tissue


title: AJ10 A

description: 24-26 week adjacent normal lung


title: 02_si_a_1

source_name: Tissue Type: Small Intestine


title: 02_pl_s_2


title: 03_si_a_2


title: 03_sk_a_1

source_name: Tissue Type:  Skin


title: 37_thymus_B

source_name: Tissue Type: thymus


title: AJ7 A

description: 24-26 week adjacent normal lung


title: AJ6 A

description: 24-26 week adjacent normal lung


title: Experiment 3: 3T3-F442A adipocytes. GH 48 hr.

city: Ann Arbor

first: Jessica

last: Schwartz

state: MI

address: 1301 Catherine St.

department: Molecular and Integrative Physiology

institute: University of Michigan

description: 3T3-F442A adipocytes. GH 48 hr.

source_name: 3T3-F442A Adipocytes


title: 03_sk_a_2


title: 03_sk_a_11


title: AJ5 A

description: 24-26 week adjacent normal lung


title: AJ8 A

description: 24-26 week adjacent normal lung


title: 35_head_neonate6day_A

source_name: Tissue Type: Head 6day

value: youth


title: 02_si_a_2


title: Experiment 3: 3T3-F442A adipocytes. GH 4 hr.

description: 3T3-F442A adipocytes. GH  30 min.


title: 02_si_a_11


title: 37_thymus_A


title: 03_sp_a_2

source_name: Tissue Type:  Spleen


title: 32_head_neonate0day_A

source_name: Tissue Type: head neonate

value: Neonate


title: 35_head_neonate6day_B


title: 03_sk_a_22


title: 02_si_s_1


title: 02_si_s_11


title: 02_si_a_22


title: 30_skin_neonate0day_B

source_name: Tissue Type: skin neonate


title: 03_sp_a_1


title: 32_head_neonate0day_B


title: Experiment 3: 3T3-F442A adipocytes. GH 30 min.

description: 3T3-F442A adipocytes. GH  30 min.


title: 2_liver_B

source_name: Tissue Type: liver


title: 30_skin_neonate0day_A


title: 02_si_s_22


title: Experiment 3: 3T3-F442A adipocytes. Control 48 hr.

description: 3T3-F442A adipocytes.  Control 4 hr.


title: 02_si_s_2


title: 03_st_a_1

source_name: Tissue Type:  Stomach


title: Experiment 3: 3T3-F442A adipocytes. Control  4 h.

description: 3T3-F442A adipocytes. Control 4 hr.


title: 03_st_a_2


title: 02_sp_a_2

source_name: Tissue Type: Spleen


title: 03_te_a_1

source_name: Tissue Type:  Testis


title: 03_te_a_2

source_name: Common Reference: 17.5dpc total embryo


title: 2_liver_A


title: Experiment 3: 3T3-F442A adipocytes. Control 30 min.

description: 3T3-F442A adipocytes. Control 30 min.


title: 02_sp_a_1


title: Experiment 2: 3T3-F442A adipocytes. GH 4 hr.

description: 3T3-F442A adipocytes. GH 4 hr.


title: Experiment 2: 3T3-F442A adipocytes. GH 30 min.

description: 3T3-F442A adipocytes. GH 30 min.


title: Experiment 2: 3T3-F442A adipocytes. GH 48 hr.

description: 3T3-F442A adipocytes. GH 48 hr.


title: 03_te_s_2


title: Experiment 2: 3T3-F442A adipocytes. Control 48hr.

description: 3T3-F442A adipocytes. Control 48 hr.


title: 02_sp_s_2


title: 03_te_s_1


title: 03_th_a_1

source_name: Tissue Type:  Thymus


title: Experiment 2: 3T3-F442A adipocytes. Control 30 min.

description: 3T3-F442A adipocytes. Control 30 min.


title: 03_th_a_2


title: 02_st_a_1

source_name: Tissue Type: Stomach


title: 03_th_a_11


title: Experiment 1, 3T3-F442A adipocytes. GH 48 hr.

description: 3T3-F442A adipocytes. GH 48 hr.


title: 24_embryo15_head_A

source_name: Tissue Type: embryo head


title: 02_sp_s_1


title: 02_st_s_2


title: 03_th_a_22


title: Experiment 2: 3T3-F442A adipocytes. Control 4 hr.

description: 3T3-F442A adipocytes. Control 4 hr.


title: 02_st_s_1


title: 02_te_a_1

source_name: Tissue Type: Testis


title: 29_mammary_grand_lactate10day_A

source_name: Tissue Type: mammary gland

value: 10 day

value: female


title: 20_embryo17_head_B


title: 23_embryo13_B

source_name: Tissue Type: embryo


title: 02_st_a_2


title: 03_th_s_1


title: Experiment 1: 3T3-F442A adipocytes. GH 4 hr.

description: 3T3-F442A adipocytes. GH 4 hr.


title: 23_embryo13_A


title: 20_embryo17_head_A


title: 24_embryo15_head_B


title: 03_th_s_11


title: 02_te_a_2


title: Experiment 1: 3T3-F442A adipocytes. GH 30 min.

description: 3T3-F442A adipocytes. GH  48 hr.


title: 03_th_s_2


title: Experiment 1: 3T3-F442A adipocytes. Control 4 hr.

description: 3T3-F442A adipocytes. Control 4 hr.


title: 1_brain_s3

source_name: Tissue Type: brain


title: 18_embryo12_head_B


title: Experiment 1: 3T3-F442A adipocytes. Control 48 hr.

description: 3T3-F442A adipocytes. Control 48 hr.

source_name: 3T3-F442A Adipocytes


title: 02_te_s_2


title: 02_te_s_1


title: 03_th_s_22


title: 03_ut_a_1

source_name: Tissue Type:  Uterus


title: 18_embryo12_head_A


title: 17_embryo11_B


title: 02_th_a_1

source_name: Tissue Type: Thymus


title: 03_ut_a_2


title: 17_embryo11_A


title: Experiment 1, 3T3-F442A adipocytes. Control 30 min.

description: 3T3-F442A adipocytes. Control 30 min.


title: 02_th_s_1


title: 1_brain_s4


title: 03_ut_a_22


title: 02_ut_a_1

source_name: Tissue Type: uterus


title: 02_ut_a_2


title: 03_ut_s_11


title: 02_th_a_2


title: 03_ut_s_1


title: 14_tongue_B

source_name: Tissue Type: tongue


title: 13_stomach_A

source_name: Tissue Type: stomach


title: 13_stomach_B


title: 02_th_s_2


title: 03_ut_a_11


title: 14_tongue_A


title: LZ5 A

description: 24-26 week adjacent normal lung

source_name: lung tissue


title: Rat1_Myc_serum_apoptosis_mitochondria

type: protein

city: San Antonio

first: Yuzuru

last: Shiio

state: TX

address: 8403 Floyd Curl Dr.

department: CCRI

institute: UTHSCSA

description:
Chromatin-enriched fractions (2.5 mg each), soluble fractions (2.5 mg each), and crude mitochondrial fractions (250 ug each) were prepared as described (1,2), dissolved in the ICAT labeling buffer (0.05% SDS, 6M urea, 200 mM Tris [pH 8.3], and 5 mM EDTA), reduced with 5 mM Tris(2-carboxyethyl) phosphine (TCEP) for 30 min at 37 ºC, and labeled (Rat1/vector cell lysate: isotopically-light ICAT reagent; Rat1/Myc cell lysate: isotopically-heavy ICAT reagent). The two labeled fractions were combined, proteolyzed to peptides with trypsin, and fractionated by cation-exchange chromatography. ICAT reagent-labeled peptides were purified using the biotin tag present in the reagent and analyzed by microcapillary high performance liquid chromatography-tandem mass spectrometry (µLC-MS/MS) as described (1,3-5). MS/MS spectra were searched against the NCBI rat/mouse/human protein database. Peptide/protein identification was validated by Peptide/ProteinProphet software tools (6,7). Peptide and protein abundance ratios were calculated using ASAPRatio software tool (8).
1.  Shiio, Y., Eisenman, R. N., Yi, E. C., Donohoe, S., Goodlett, D. R., and Aebersold, R. (2003) J Am Soc Mass Spectrom 14(7), 696-703
2. Juin, P., Hueber, A. O., Littlewood, T., and Evan, G. (1999) Genes Dev 13(11), 1367-1381
3. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Nat Biotechnol 17(10), 994-999
4. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Nat Biotechnol 19(10), 946-951
5. Shiio, Y., Donohoe, S., Yi, E. C., Goodlett, D. R., Aebersold, R., and Eisenman, R. N. (2002) Embo J 21(19), 5088-5096
6. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Anal Chem 74(20), 5383-5392
7. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) Anal Chem 75(17), 4646-4658
8. Li, X. J., Zhang, H., Ranish, J. A., and Aebersold, R. (2003) Anal Chem 75(23), 6648-6657

data_processing: Supplementary data files contain peptides with PeptideProphet probability score greater than/equal to 0.5 (6,7). Peptide and protein abundance ratios were calculated using ASAPRatio software tool (8). Abundance ratios of 0, 9999, and -1 denote that acceptable peptide peak(s) were not detected for one or both of the ICAT-labeled peptide(s).

label: isotopically-heavy ICAT reagent

molecule: protein

organism: Rattus norvegicus

source_name: Rat1_Myc cells

extract_protocol: as described in J Am Soc Mass Spectrom 14:696-703, 2003.

treatment_protocol: Serum deprivation for 12 hours.

tag: Cell type

value: Rat1_Myc fibroblasts

tag: Fraction

value: Mitochondrial

label: isotopically-light ICAT reagent

source_name: Rat1_vector cells

value: Rat1_vector fibroblasts


title: 02_ut_s_2

value: 8 weeks

source_name: Common Reference: 17.5dpc total embryo


title: 02_ut_s_1


title: Rat1_Myc_serum_apoptosis_chromatin

value: Chromatin


title: 03_ut_s_2

value: Adult


title: 12_small_intestine_B

source_name: Tissue Type: small intestine

value: male


title: 12_small_intestine_A


title: Rat1_Myc_serum_apoptosis_soluble

value: Soluble


title: kid_a_auto

source_name: Tissue Type:  Kidney


title: heart_b_auto

source_name: Tissue Type:  Heart


title: 11_pancreas_B

source_name: Tissue Type: pancreas


title: 03_ut_s_22


title: kid_b_auto


title: heart_a_auto


title: comparison between cer6-2 mutant and Ler-0 wild-type plants (dye-swap of GSM87735)

city: bordeaux

first: bertrand

last: garbay

address: 146 rue leo saignat

department: estbb

institute: university bordeaux2

description: Comparison of gene expression between a wax-deficient mutant (cer6-2) and wild-type plants (Ler-0). Aerial parts of the 15-day-old plants (leaves and stems). Total RNA was purified from 20 plants of each genotype.

hyb_protocol: Agilent Arabidopsis2 oligo microarray hybridization protocol

scan_protocol: Dual-laser Microarray scanner Agilent Technologies, 10µm resolution, 100% PMT

data_processing: Agilent Feature-extraction software version A.7.5.1. Spot analysis method using Cookie Cutter, pixel outlier rejection based on IQR, non-uniformity outlier flagging on, population outlier flagging on, no background subtraction, spatial detrend on, normalization feature selection by using rank consistency filter, normalization method linear and LOWESS, multiplicative errors of 0.15 for red and 0.25 for green, additive errors of 20 for both channels

organism: Arabidopsis thaliana

source_name: Ler-0 wild-type plant

label_protocol: Agilent fluorescent Direct Label Kit

growth_protocol: 16h light/8h dark, 22°C, 80% relative humidity

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: No treatment

tag: Aerial part of 2-week-old plant

source_name: cer6-2 mutant


title: 11_pancreas_A


title: 10_testis_B

source_name: Tissue Type: testis


title: comparison between cer6-2 mutant and Ler-0 wild-type plants


title: 10_testis_A


title: NF51_b36_s90

status: Public on Dec 19 2005

type: genomic

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004)  Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).

molecule: genomic DNA

label_protocol:
DNA labeling protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

extract_protocol:
DNA isolation protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: healthy individual

tag: Tissue

value: peripheral blood, white cells

tag: Gender

source_name: male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: Pooled DNA from the blood of 10 healthy male individuals


title: 29_mammary_grand_lactate10day_B

source_name: Tissue Type: mammary gland


title: NF45_b41_s100


title: Thyroid_papillary carcinoma 77

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

institute: OSU

description: sample name in manuscript: T-PTC8

data_processing: Robust Multichip Averages

source_name: frozen surgical tissue

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: standard Trizol reagent procedures

tag: Tissue:tumor; Gender:female; Age:65  Tumor stage:T2NxMx


title: Thyroid_ unaffected_paired with PTC86T

description: sample name in manuscript: N-PTC9

value: normal thyroid; Gender:female; Age:31


title: Thyroid_papillary carcinoma 86

description: sample name in manuscript: T-PTC9

tag: Tissue:tumor; Gender:female; Age:31; Tumor stage:T4aN1bMx


title: NF63_b36_s91


title: AGD Atlantic Salmon Study Slide EB018_028

city: Victoria

first: Ben

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

description: 189 hour AGD exposed Salmo salar replicate #3

hyb_protocol: Microarray was prepared for hybridization by washing 2 x 5 min with 0.1% SDS, 5 x 1 min with MilliQ water, immersion in 95C MilliQ water for 3 min followed by drying using centrifugation (5 min, 514 x g in 50 mL tube). Array was pre-hybridized in 5X SSC, 0.1% SDS, 0.2% BSA for 1.5 h at 49C, briefly washed 2 X 20 sec in MilliQ water and dried by centrifugation. Labeled cDNAs were hybridized to pre-warmed microarray in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution, and 4 ul of Genisphere LNA dT blocker) for 16 h at 49C. Coverslips were removed in 2X SSC, 0.1% SDS at 49C. The arrays were washed 1 x 10 min at 49C (2X SSC, 0.1% SDS). All subsequent washes were at room temperature; 2 x 5 min in 2X SSC, 0.1% SDS, 2 x 5 min in 1X SSC and 2 x 5 min in 0.1X SSC and dried by centrifugation.

scan_protocol: Fluorescent array images were collected immediately for both Cy3 and Cy5 using ScanArray Express (PerkinElmer).  Image intensity data were extracted using Imagene 5.5 software (Biodiscovery).

data_processing: Only elements deemed present by Imagene software and with control values greater then the average base/proportional value were used.  Expression ratios were generated using background corrected lowess normalized data using GeneSpring 6.1 software (Silicon Genetics, Agilent Technologies, Palo Alto, Ca, USA).

organism: Salmo salar

source_name: 114 hour sham control Salmo salar fish #3

label_protocol: Labeled cDNA was generated using a SuperScript Indirect cDNA Labeling System kit (Invitrogen) according to the manufacturer's instructions. For each sample 5.0 ug of total RNA was used to generate modified cDNAs.

extract_protocol: TRIzol Reagent (Invitrogen Australia Pty Limited ) according to manufacturers protocol

tag: non infected gill arch tissue

source_name: 114 hour AGD exposed Salmo salar fish #4

tag: infected gill arch tissue


title: NF46_b36_s89


title: AGD Atlantic Salmon Study Slide EB018_034

source_name: 44 hour AGD exposed Salmo salar fish #4

source_name: 44 hour sham control Salmo salar fish #4


title: NF26_b41_s98


title: Thyroid_papillary carcinoma 71

description: sample name in manuscript: T-PTC7

tag: Tissue:tumor; Gender:male; Age:36; Tumor stage:T4aN1aM1


title: AGD Atlantic Salmon Study Slide EB018_033

source_name: 189 hour sham control Salmo salar fish #4

source_name: 189 hour AGD exposed Salmo salar fish #4


title: AGD Atlantic Salmon Study Slide EB018_007

source_name: 44 hour sham control Salmo salar fish #3

source_name: 44 hour AGD exposed Salmo salar fish #3


title: AGD Atlantic Salmon Study Slide EB018_014

source_name: 0 hour sham control Salmo salar fish#1

source_name: 0 hour AGD exposed Salmo salar fish #1


title: AGD Atlantic Salmon Study Slide EB018_030

source_name: 0 hour AGD exposed Salmo salar fish #4

source_name: 0 hour sham control Salmo salar #4


title: Thyroid_ unaffected_paired with PTC11T

description: sample name in manuscript: N-PTC1

value: normal thyroid; Gender:female; Age:48


title: NF37_b41_s99


title: Thyroid_ unaffected_paired with PTC67T

description: sample name in manuscript: N-PTC5

value: normal thyroid; Gender:female; Age:43


title: Thyroid_papillary carcinoma 67

description: sample name in manuscript: T-PTC5

tag: Tissue:tumor; Gender:female; Age:43; Tumor stage:T1N1aMx


title: AGD Atlantic Salmon Study Slide EB018_031

source_name: 114 hour AGD exposed Salmo salar fish #2

source_name: 114 hour sham control Salmo salar fish #2


title: AGD Atlantic Salmon Study Slide EB018_006

source_name: 0 hour sham control Salmo salar fish #3

source_name: 0 hour AGD exposed Salmo salar fish #3


title: Thyroid_ unaffected_paired with PTC77T

description: sample name in manuscript: N-PTC8

source_name: frozen surgical tissue

value: normal thyroid; Gender:female; Age:65


title: Thyroid_ papillary carcinoma 11

description: sample name in manuscript: T-PTC1

tag: Tissue:tumor; Gender:female; Age:48  Tumor stage:T3N1bMx


title: NF23_b41_s87

tag: normal individual

source_name: male reference DNA

tag: Pooled DNA from the blood of 10 normal male individuals


title: AGD Atlantic Salmon Study Slide EB018_004

source_name: 114 hour sham control Salmo salar fish#1

source_name: 114 hour AGD exposed Salmo salar fish #1


title: NF24_b41_s89


title: AGD Atlantic Salmon Study Slide EB018_019

source_name: 44 hour sham control Salmo salar fish #2

source_name: 44 hour AGD exposed Salmo salar fish #2


title: AGD Atlantic Salmon Study Slide EB018_005

source_name: 189 hour sham control Salmo salar fish #1

source_name: 189 hour AGD exposed Salmo salar fish #1


title: Thyroid_ unaffected_paired with PTC69T

description: sample name in manuscript: N-PTC6

value: normal thyroid; Gender:male; Age:56


title: Thyroid_papillary carcinoma 26

description: sample name in manuscript: T-PTC3

tag: Tissue:tumor; Gender

value: male; Age:43; Tumor stage:T2NxMx


title: Thyroid_ unaffected_paired with PTC50T

description: sample name in manuscript: N-PTC4

value: normal thyroid; Gender:male; Age:33


title: Thyroid_ papillary carcinoma 50

description: sample name in manuscript: T-PTC4

value: tumor; Gender:male; Age:33  Tumor stage:T1N0MX


title: AGD Atlantic Salmon Study Slide EB018_032

source_name: 189 hour AGD exposed Salmo salar fish #3

source_name: 189 hour sham control Salmo salar fish #3


title: Thyroid_ papillary carcinoma 69

description: sample name in manuscript: T-PTC6

tag: Tissue:tumor; Gender:male; Age:56; Tumor stage:T4N0M1


title: Thyroid_ unaffected_paired with PTC26T

description: sample name in manuscript: N-PTC3

value: normal thyroid; Gender:male; Age:43


title: VUMC_GT1_b28_s62

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 100 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl water and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 71% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridization was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192 no tRNA used during hybridization

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1, the Confidence value less than 0.1 or when no chromosomal mapping information was available. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their mode value.

extract_protocol:
DNA isolation protocol available via www.vumc.nl/microarrays
Also described in Weiss,M.M., Hermsen,M.A., Meijer,G.A., van Grieken,N.C., Baak,J.P., Kuipers,E.J. and van Diest,P.J. (1999) Comparative genomic hybridisation. Mol.Pathol., 52, 243-251.

tag: gastric tumor

source_name: female reference DNA

tag: Pooled DNA from the blood of 10 normal female individuals


title: VUMC_GT1_b43_s83


title: VUMC_GT1_b47_s28


title: BT474_b43_s88

growth_protocol: according to ATCC conditions

tag: BT474 (ATCC nr. HTB-20) breast tumor cell line

value: female


title: Thyroid_ unaffected_paired with PTC71T

description: sample name in manuscript: N-PTC7

tag: Tissue

value: normal thyroid; Gender:male; Age:36


title: GM07408_b42_s55

tag: Chorionic villus-derived cell line

tag: Gender

tag: ISCN

tag: as described


title: BT474_noCot1_b42_s63

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA and 50 µl of Cy5-labeled reference DNA were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridization was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192 Modification: this hybridization was done without Cot1 DNA


title: Thyroid_ unaffected_paired with PTC14T

description: sample name in manuscript: N-PTC2

value: normal thyroid; Gender:male; Age:42


title: 03 JOS 137_b9_s43

growth_protocol: described in Jonkers et al, Nature Genetics, 2001, vol. 29, 418-425

extract_protocol: described in Chung et al., Genome Research, 2004, vol.14, 188-196

tag: Strain

value: Kcre; Br2F/F; p53F/F

tag: Age

value: 23 days

value: Brca2 deficient p53 deficient mamma epithelial tumor

tag: Tumor stage

value: spleen


title: BT474_noCot1_b30_s20

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192 not Cot1 DNA used in hybridization mix

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized global to the median value of the chromosome 2 log2ratio's. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004)  Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).


title: GIS_LT1_1

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a MAUI Hybridization System (BioMicro Systems Inc., Salt Lake City, USA). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

scan_protocol: as described in Lung et al. (2005) Oncogene, vol.24, 6525–6532.

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004) Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).

tag: lung tumor

value: male

tag: normal female reference DNA


title: BT474_b44_s50


title: GIS_LT1_2


title: GM13031_b42_s54

tag: B-Lymphocyte cell line


title: BT474_100%Cot1_b30_s21

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 100 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192 100 µg Cot1 DNA used in hybridization mix

tag: Pooled DNA from the blood of 10 normal male individuals


title: MA69 glucose pulse 3 T=300 seconds

status: Public on Dec 16 2005

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description: Replicate arrays MA61 and MA81

scan_protocol: Array scanned twice Affymetrix scanner 3000

data_processing: Data processed with Affymetrix GCOS software

label: biotynilated cRNA

organism: Saccharomyces cerevisiae

source_name: glucose pulse perturbation to a chemostat culture (300 s after the pulse)

growth_protocol: Chemostat cultivation – Saccharomyces cerevisiae (CEN PK 113-7D) was cultivated in an aerobic carbon-limited chemostat culture in a 7-litres fermentor (Applikon, The Netherlands) with a working volume of 4-l on the adapted doubled mineral medium (Verduyn et al., 1992) with 27.1 g.l-1 of glucose and 1.42 g.l-1 of ethanol, to support a biomass concentration of about 15 g dry weight.l-1. The dilution rate was set to be 0.05 hr-1 and the airflow rate was set to be 200 l.hr-1. Other fermentation parameters are: a pH controlled at 5, a temperature controlled at 30˚C, an overpressure of 0.3 bar and stirrer speed of 600 rpm. The chemostat was considered to obtain its stable steady state condition 5 resident times after the end of its batch phase.

treatment_protocol: Liquid nitrogen quenching - Sampling for Microarrays - Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.

tag: Strain CEN.PK113-7D Mat a prototroph


title: VUMC_GT1_b31_s23


title: VUMC_GT1_b43_s79


title: BT474_b43_s50


title: 99 JOS 32_b9_s42


title: MA64 glucose pulse 3 T=0

description: Replicate arrays MA25 and MA56

hyb_protocol: Sampling for Microarrays - Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.

source_name: glucose pulse perturbation to a chemostat culture (initial steady state)

tag: Strain CEN.PK113-7D MAta Prototroph


title: GM01750_b42_s51

tag: fibroblast cell line


title: Thyroid_papillary carcinoma 14

description: sample name in manuscript: T-PTC2

value: tumor; Gender:male; Age:42  Tumor stage:T3NxMx


title: MA67 glucose pulse 3 T=60 seconds

description: Replicate arrays MA59

source_name: glucose pulse perturbation to a chemostat culture (60 s after the pulse

label_protocol: Sampling for Microarrays - Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.

tag: Strain CEN.PK113-7D MAta prototroph


title: MA68 glucose pulse 3 T=120 seconds

description: Replicate arrays MA60 and MA78

source_name: glucose pulse perturbation to a chemostat culture (120s after the pulse)

extract_protocol: Sampling for Microarrays - Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.

tag: Strain CEN.PK113-7D MAt a prototroph


title: MA66 glucose pulse 3 T=30 seconds

description: Replicate arrays MA58

source_name: glucose pulse perturbation to a chemostat culture (30s after the pulse)


title: BT474_10%Cot1_b30_s21

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192 10 µg Cot1 DNA used in hybridization mix

tag: BT474 (ATCC nr. HTB-20) breast tumor cell line


title: MA61 glucose pulse 2 T=300 seconds

description: Replicate arrays MA81 and MA69

source_name: glucose perturbation to a chemostat culture (300s after the pulse)

tag: Strain CENPK113-7D Mat a prototroph


title: MA58 glucose pulse 2 T=30 seconds

description: Replicate arrays MA66

source_name: glucose pulse perturbation to a chemostat culture (30 s after the pulse)


title: MA59 glucose pulse 2 T= 60 seconds

description: Replicate arrays MA67

source_name: glucose pulse perturbation to a chemostat culture (60 s after the pulse)


title: MA23 glucose pulse 2 T=330 seconds

description: Replicate array MA24

source_name: glucose pulse perturbation to a chemostat culture (330s after the pulse)

tag: Strain CEN.PK113-7D


title: MA56 Glucose pulse 2 T= 0 s

description: Replicate arrays MA25 and MA64


title: MA24 glucose pulse 1 T=330 seconds

description: Replicate array MA23

source_name: glucose pulse perturbation to a chemostat culture (330 seconds after the pulse)


title: MA60 glucose pulse 2 T=120 seconds

description: Replicate arrays MA78 and MA 68

source_name: glucose pulse perturbation to a chemostat culture (120 s after the pulse)

tag: Strain CEN.PK 113-7D Mata prototroph


title: MA81 glucose pulse 1 T= 300 seconds

description: Replicate array MA61 and MA69


title: CH2119

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the Paraventricular nucleus from 5 dehydrated animals (3 Days)

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: MessageAmpII aRNA Amplification kit (Ambion)

source_name: Paraventricular nucleus_3d dehydrated

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit  (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

value: Sprague Dawley

tag: Gender

value: Male

value: 10-12 weeks

tag: Tissue

value: Hypothalamic Paraventricular nucleus


title: MA79 glucose pulse 1 T=210 seconds

description: No duplicate

source_name: glucose pulse perturbation to a chemostat culture (210 s after the pulse

growth_protocol:
Chemostat cultivation – Saccharomyces cerevisiae (CEN PK 113-7D) was cultivated in an aerobic carbon-limited chemostat culture in a 7-litres fermentor (Applikon, The Netherlands) with a working volume of 4-l on the adapted doubled mineral medium (Verduyn et al., 1992) with 27.1 g.l-1 of glucose and 1.42 g.l-1 of ethanol, to support a biomass concentration of about 15 g dry weight.l-1. The dilution rate was set to be 0.05 hr-1 and the airflow rate was set to be 200 l.hr-1. Other fermentation parameters are: a pH controlled at 5, a temperature controlled at 30˚C, an overpressure of 0.3 bar and stirrer speed of 600 rpm. The chemostat was considered to obtain its stable steady state condition 5 resident times after the end of its batch phase.
Glucose pulse experiment - At the age of 7 dilution times, the steady state chemostat culture was perturbed by the addition of 20 ml of glucose solution (200 g/l) to the fermentor so that the residual glucose concentration was suddenly increased to about 1 g/l (5.56 mM). The glucose solution was rapidly injected by a pneumatic system (< 1 s). Samples were taken prior to the glucose pulse (steady state samples) and within 360 s transient after the perturbation.

Reference List

Verduyn,C., Postma,E., Scheffers,W.A., and van Dijken,J.P. (1992). Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8, 501-517.

treatment_protocol:
Liquid nitrogen quenching - Sampling for Microarrays - Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.
Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and Pronk,J.T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008.

tag: Strain CEN.PK113-7D Mata prototroph


title: MA25 Glucose pulse 1 T=0

description: Replicate arrays MA56 and MA64

hyb_protocol: Hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture. Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and Pronk,J.T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008.

scan_protocol: Array scan twice pixel value 3micron Wl 570 mn affymetrix scanner 3000

label: Biotynilated cRNA

label_protocol:
probe preparation  were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.
Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and Pronk,J.T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008.

extract_protocol:
Total RNA extracted as described by Piper et al (2002)
Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and Pronk,J.T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008.

treatment_protocol:
Liquid nitrogen quenching
Sampling for Microarrays - Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.
Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and Pronk,J.T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008.


title: CH2118

tag: Strain

tag: Age


title: MA78 glucose pulse 1 T=120 seconds

description: Replicate arrays MA60 and MA68

hyb_protocol: Hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.

scan_protocol: Array scanned twice with Affymetrix scanner 3000

label_protocol: probe preparation  were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.

extract_protocol: Total RNA extracted as described by Piper et al (2002)


title: CH2117


title: Ad (2nd generation) infected murine liver (5267)- 6 hpi

status: Public on Dec 15 2005

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: Sample is murine liver RNA extract after Ad (E1-E2b-E3-LacZ) infection

hyb_protocol: Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Pro 4000A scanner and image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.

data_processing: VALUE column is normalized Cy5 signal after Intensity-Dependent normalization.

source_name: Cy5 labeled Liver RNA

label_protocol: The RNA from murine liver was directly labelled with Cy5 using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labelling and hybridization protocols.

extract_protocol: RNA isolation was accomplished by homogenizing liver in liquid nitrogen, then extracting RNA using TriReagent (Molecular Research Center, Inc.). The RNA (10 µg) was purified using an RNeasy Kit (Qiagen) and assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: The RNA (10 µg) was a total RNA mix that was assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: C57/BL6 murine Liver RNA- 3 hours post-injection with a 2nd generation (E1-E2b-E3-CMVLacZ) vector.

source_name: Murine Reference RNA

tag: Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.


title: Ad infected murine liver (4093)- 3 wpi

description: Sample is murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 3 wpi.

label_protocol: The RNA from murine liver was directly labeled with Cy5 using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labelling and hybridization protocols.

tag: C57/BL6 murine Liver RNA- 3 weeks post-injection with a 1st generation (E1-E3-CMVLacZ) vector.

label_protocol: The RNA from murine liver was directly labeled with Cy3 using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labelling and hybridization protocols.


title: Ad infected murine liver (4084)- 3 dpi

description: Sample is murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 3 dpi.

tag: C57/BL6 murine Liver RNA- 3 days post-injection with a 1st generation (E1-E3-CMVLacZ) vector.

label_protocol: The RNA from murine liver was directly labelled with Cy3 using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labelling and hybridization protocols.


title: Ad infected murine liver (4092)- 3 wpi


title: Mock infected murine liver (3873)

description: Sample is murine liver RNA extract after mock infection

tag: C57/BL6 murine Liver RNA- after Mock infection with PBS


title: Ad infected murine liver (4085)- 3 dpi


title: Ad infected murine liver (4082)- 3 dpi


title: Ad infected murine liver (3862)- 3 dpi

description: Sample is murine liver RNA extract after Ad infection (E1-E2b-E3-LacZ)

tag: C57/BL6 murine Liver RNA- 3 days post-injection with a 2nd generation (E1-E2b-E3-CMVLacZ) vector.


title: Ad (2nd generation) infected murine liver (3863)- 3 wpi

tag: C57/BL6 murine Liver RNA- 3 weeks post-injection with a 2nd generation (E1-E2b-E3-CMVLacZ) vector.


title: Mock infected murine liver (790)

description: Sample is murine liver RNA extract after mock infection with 200ul of PBS.

tag: C57/BL6 murine Liver RNA- 6 hours post mock infection with PBS.


title: CH2116


title: G42-Homogenate-CingulateCortex replicate2

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: Tissue homogenate from cingulate cortex from G42 mouse (Ref. Pubmed:15509747 ).

data_processing: dCHIP PM-only method

source_name: cingulate cortex

label_protocol: Total RNA from dissociated unsorted cells was amplified and processed to produce biotinylated cRNA targets.

extract_protocol: Cingulate cortex was microdissected from 400 micron thick slice. The microdissected tissue chunks were dissociated by pronase E and trituration. 5 micro litter from 1 mL of the dissociated cells (at lest 1000 cells) was lysed in XB buffer (Arcturus). Total RNA was extracted from the lysate using PicoPure Kit (Arcturus). (Detailed protocol is available at http://mouse.bio.brandeis.edu/protocol.pdf.)

tag: tissue homogenate from cingulate cortex of G42 transgenic mouse line


title: Ad (2nd generation) infected murine liver (3866)- 3 wpi


title: CH2115

label_protocol:
Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

500ng total RNA was used initially

tag: CHARACTERISTICS


title: G42-Homogenate-CingulateCortex replicate1


title: Ad (2nd generation) infected murine liver (3864)- 3 wpi


title: Ad infected murine liver (4091)- 3 wpi


title: G42-Homogenate-CingulateCortex replicate3


title: Ad infected murine liver (3860)- 3 dpi


title: Mock infected murine liver (788)

description: Sample is murine liver RNA extract after mock infection with 200ul PBS at 6 hpi.

tag: C57/BL6 murine Liver RNA- 6 hours post-mock (PBS) injection


title: Ad infected murine liver (345)- 6 hpi

description: Sample is murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

tag: C57/BL6 murine Liver RNA- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.


title: GIN-Homogenate-CingulateCortex replicate2

description: Tissue homogenate from cingulate cortex from GIN mouse (Gad1 inhibitory ref. (pubmed id:10777798) ).

tag: tissue homogenate from cingulate cortex of GIN transgenic mouse line


title: GIN-Homogenate-CingulateCortex replicate3


title: Ad infected murine liver (3861)- 3 dpi


title: Ad infected murine liver (340)- 6 hpi

tag: C57/BL6 murine Liver- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.


title: G30-Amygdala-replicate3

description: GFP labeled neurons in amygdala.

source_name: amydgala

label_protocol: Total RNA from 63 cells was amplified and processed to produce biotinylated cRNA targets.

extract_protocol: Amygdala was microdissected from 400 micron thick slice. The microdissected tissue chunks were dissociated by pronase E and trituration. Fluorescently labeled neurons from the dissociated cells were hand-sorted under a fluorescent dissection microscope using glass pipette with 50 micron diameter and lysed in XB buffer (Arcturus). Total RNA was extracted from the lysate using PicoPure Kit (Arcturus). (Detailed protocol is available at http://mouse.bio.brandeis.edu/protocol.pdf .)

value: Mixed G30 (ref. pubmed id:15115742) & C57BL/6j

tag: Gender

tag: Tissue

value: Amygdala

tag: Cell

value: GFP labeled neurons


title: GIN-Homogenate-CingulateCortex replicate1


title: G30-Amygdala-replicate2

description: GFP labeled neurons in amygdala.

label_protocol: Total RNA from 61 cells was amplified and processed to produce biotinylated cRNA targets.

tag: Strain

tag: Age


title: YFPH-Amygdala-replicate2

description: YFP labeled neurons in amygdala.

label_protocol: Total RNA from 120 cells was amplified and processed to produce biotinylated cRNA targets.

value: Mixed YFPH (Ref. PubmedID:11086982) & C57BL/6j

value: YFP labeled neurons.


title: G30-Amygdala-replicate1

description: GFP labeled neurons in amygdala.

label_protocol: Total RNA from 44 cells was amplified and processed to produce biotinylated cRNA targets.


title: YFPH-Amygdala-replicate3

description: YFP labeled neurons in amygdala.

label_protocol: Total RNA from 111 cells was amplified and processed to produce biotinylated cRNA targets.


title: YFPH-Hippocampus-replicate3

description: Pyramidal neurons in hippocampus.

source_name: hippocampus

label_protocol: Total RNA from 43 cells was amplified and processed to produce biotinylated cRNA targets.

extract_protocol: Hippocampus was microdissected from 400 micron thick slice. The microdissected tissue chunks were dissociated by pronase E and trituration. Fluorescently labeled neurons from the dissociated cells were hand-sorted under a fluorescent dissection microscope using glass pipette with 50 micron diameter and lysed in XB buffer (Arcturus). Total RNA was extracted from the lysate using PicoPure Kit (Arcturus). (Detailed protocol is available at http://mouse.bio.brandeis.edu/protocol.pdf .)

value: Hippocampus

value: YFP labeled pyramidal neurons.


title: YFPH-Amygdala-replicate1

description: YFP labeled neurons in amygdala.

label_protocol: Total RNA from 90 cells was amplified and processed to produce biotinylated cRNA targets.


title: YFPH-SomatosensoryCortex-replicate2

description: Layer 5 pyramidal neurons in somatosensory cortex.

source_name: somatosensory cortex

label_protocol: Total RNA from 50 cells was amplified and processed to produce biotinylated cRNA targets.

extract_protocol: Somatosensory cortex was microdissected from 400 micron thick slice. The microdissected tissue chunks were dissociated by pronase E and trituration. Fluorescently labeled neurons from the dissociated cells were hand-sorted under a fluorescent dissection microscope using glass pipette with 50 micron diameter and lysed in XB buffer (Arcturus). Total RNA was extracted from the lysate using PicoPure Kit (Arcturus). (Detailed protocol is available at http://mouse.bio.brandeis.edu/protocol.pdf .)

value: Somatosensory Cortex

value: YFP labeled layer 5 pyramidal neurons.


title: YFPH-Hippocampus-replicate2

description: Pyramidal neurons in hippocampus.

label_protocol: Total RNA from 81 cells was amplified and processed to produce biotinylated cRNA targets.


title: YFPH-SomatosensoryCortex-replicate3

label_protocol: Total RNA from 34 cells was amplified and processed to produce biotinylated cRNA targets.


title: YFPH-Hippocampus-replicate1

description: Pyramidal neurons in hippocampus.

label_protocol: Total RNA from 104 cells was amplified and processed to produce biotinylated cRNA targets.


title: YFPH-SomatosensoryCortex-replicate1


title: YFPH-CingulateCortex-replicate3

description: Layer 5 pyramidal neurons in cigulate cortex.

label_protocol: Total RNA from 57 cells was amplified and processed to produce biotinylated cRNA targets.

extract_protocol: Cingulate cortex was microdissected from 400 micron thick slice. The microdissected tissue chunks were dissociated by pronase E and trituration. Fluorescently labeled neurons from the dissociated cells were hand-sorted under a fluorescent dissection microscope using glass pipette with 50 micron diameter and lysed in XB buffer (Arcturus). Total RNA was extracted from the lysate using PicoPure Kit (Arcturus). (Detailed protocol is available at http://mouse.bio.brandeis.edu/protocol.pdf .)

value: Cingulate Cortex


title: YFPH-CingulateCortex-replicate2

label_protocol: Total RNA from 105 cells was amplified and processed to produce biotinylated cRNA targets.


title: CT6-CingulateCortex-replicate1

description: Layer 6 pyramidal neurons in cigulate cortex which project to medial dorsal thalamus.

label_protocol: Total RNA from 27 cells was amplified and processed to produce biotinylated cRNA targets.

value: Layer 6 pyramidal neurons retrogradedly labeled by fluorescent beads injection into medial dorsal thalamus.


title: Ad (2nd Generation) infected murine liver (349)- 6 hpi

label_protocol: The RNA from murine liver was directly labelled with Cy5 using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labelling and hybridization protocols.

tag: C57/BL6 murine Liver RNA- 6 hours post-injection with a 2nd generation (E1-E2b-E3-CMVLacZ) vector

label_protocol: The RNA from murine liver was directly labelled with Cy3 using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labelling and hybridization protocols.

tag: Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.


title: G42-LGN replicate3

description: G42 neurons from lateral geniculate nucleus (LGN)

source_name: lateral geniculate nucleus (LGN)

label_protocol: Total RNA from 48 cells was amplified and processed to produce biotinylated cRNA targets.

extract_protocol: LGN was microdissected from 400 micron thick slice. The microdissected tissue chunks were dissociated by pronase E and trituration. Fluorescently labeled neurons from the dissociated cells were hand-sorted under a fluorescent dissection microscope using glass pipette with 50 micron diameter and lysed in XB buffer (Arcturus). Total RNA was extracted from the lysate using PicoPure Kit (Arcturus). (Detailed protocol is available at http://mouse.bio.brandeis.edu/protocol.pdf .)

value: Mixed G42 (ref. pubmed id:15509747) & C57BL/6j

value: male

value: LGN

value: GFP expressing interneurons


title: YFPH-CingulateCortex-replicate1

label_protocol: Total RNA from 74 cells was amplified and processed to produce biotinylated cRNA targets.


title: CT6-CingulateCortex-replicate2

label_protocol: Total RNA from 36 cells was amplified and processed to produce biotinylated cRNA targets.

value: males


title: CT6-CingulateCortex-replicate3

label_protocol: Total RNA from 37 cells was amplified and processed to produce biotinylated cRNA targets.


title: G42-LGN replicate2

label_protocol: Total RNA from 38 cells was amplified and processed to produce biotinylated cRNA targets.


title: G30-SomatosensoryCortex replicate2

description: G30 neurons from somatosensory cortex

label_protocol: Total RNA from 66 cells was amplified and processed to produce biotinylated cRNA targets.


title: G42-LGN replicate1


title: Ad infected murine liver (339)- 6 hpi


title: G30-SomatosensoryCortex replicate3

description: G30 neurons from somatosensory cortex

label_protocol: Total RNA from 54 cells was amplified and processed to produce biotinylated cRNA targets.


title: G30-CingulateCortex replicate3

description: G30 neurons from cingulate cortex

label_protocol: Total RNA from 64 cells was amplified and processed to produce biotinylated cRNA targets.


title: BT474_b5

description: see also Carvalho et al (2004) J.Clin.Path., vol. 57, 644-646.

scan_protocol: ScanArray Express (Perkin Elmer), default settings

data_processing: Using ImaGene as described in Carvalho et al (2004) J.Clin.Path., vol. 57, 644-646. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA). Weighted moving average values were calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004) Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.). Normalization was done global to the median value of the chromosome 2 log2ratio's.

label_protocol:
DNA labeling protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

extract_protocol:
DNA isolation protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: BT474 (ATCC nr. HTB-20) breast tumor cell line

value: female

source_name: male reference DNA

tag: Pooled DNA from the blood of 10 normal individuals


title: G30-SomatosensoryCortex replicate1

description: G30 neurons from somatosensory cortex

label_protocol: Total RNA from 41 cells was amplified and processed to produce biotinylated cRNA targets.

value: Mixed G30 (ref. pubmed id:15115742) & C57BL/6j


title: G30-CingulateCortex replicate1

description: G30 neurons from cingulate cortex

label_protocol: Total RNA from 61 cells was amplified and processed to produce biotinylated cRNA targets.

value: G30 (ref. pubmed id:15115742)transgenic mouse.


title: G42-CingulateCortex replicate2

description: G42 neurons from cingulate cortex

label_protocol: Total RNA from 35 cells was amplified and processed to produce biotinylated cRNA targets.

value: GFP expressing parvalbumin positive interneurons


title: G42-CingulateCortex replicate3

description: G42 neurons from cingulate cortex

label_protocol: Total RNA from 43 cells was amplified and processed to produce biotinylated cRNA targets.


title: G30-CingulateCortex replicate2

description: G30 neurons from cingulate cortex

label_protocol: Total RNA from 51 cells was amplified and processed to produce biotinylated cRNA targets.


title: G42-CingulateCortex replicate1

description: G42 neurons from cingulate cortex


title: GIN-CingulateCortex replicate1

description: GIN (Gad1 inhibitory ref. (pubmed id:10777798) ) neurons from cingulate cortex

label_protocol: Total RNA from 46 cells was amplified and processed to produce biotinylated cRNA targets.

value: Mixed GIN (pubmed id:10777798) & C57BL/6j

value: GFP expressing somatostatin positive interneurons


title: ca843 tfoX overexpression

first: Melanie

last: Blokesch

department: Medical School

description:
Simple annotation: gene overexpression, Gene overexpression
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65140.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Vibrio cholerae


title: ca866 tfoX overexpression exp. 2

description:
Simple annotation: gene overexpression, Gene overexpression
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65142.gif; format: GIF


title: GIN-Hippocampus replicate2

description: GIN (Gad1 inhibitory ref. (pubmed id:10777798) ) neurons from hippocampus

value: Hippocampus


title: GIN-Hippocampus replicate3

label_protocol: Total RNA from 49 cells was amplified and processed to produce biotinylated cRNA targets.


title: GIN-CingulateCortex replicate2

label_protocol: Total RNA from 32 cells was amplified and processed to produce biotinylated cRNA targets.


title: ca867  tfoX overexpression exp. 2

description:
Simple annotation: gene overexpression, Gene overexpression
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65143.gif; format: GIF


title: Mouse ES cells (MoES.C57B)

type: MPSS

city: Hayward

first: Daixing

last: Zhou

address: 25861 Industrial Blvd

department: Bioinformatics

institute: Solexa

description:
Strain: C57BL6
Mouse ES cells total RNA (MoES.C57B) received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library MoES.C57B.sig21
Cell type Mouse ES cells
Source NHGRI
RNA isolation LYNX mRNA QC passed
cDNA library:
Library 	DpnII restriction - (signature cloning using MmeI)
Sequence length	20 bp
MPSS:
runs
MoES.C57B_sig21.5639W.c-20	12/8/2005	423009	11427	QC Passed
MoES.C57B_sig21.5639W.a-20	11/29/2005	702248	14349	QC Passed
MoES.C57B_sig21.5639F.a-20	11/28/2005	524384	11923	QC Passed
MoES.C57B_sig21.5639F.b-20	11/28/2005	460522	9668	QC Passed
Run group:
Total Beads successfully sequenced - 2110163
Processed Signatures - 17724

source_name: Mouse ES cells total RNA


title: GIN-Hippocampus replicate1

label_protocol: Total RNA from 29 cells was amplified and processed to produce biotinylated cRNA targets.


title: CH1801

description: Sample represents the Neurointermediate lobe of the Pituitary from 5 dehydrated animals (3 Days)

source_name: Neurointermediate lobe _3d dehydration

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

value: Sprague Dawley

value: Male

value: 10-12 weeks

value: Neurointermediate lobe of the Pituitary


title: ca844 tfoX overexpression

description:
Simple annotation: gene overexpression, Gene overexpression
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65141.gif; format: GIF


title: vcd695 hapR mutant induced by chitin exp. 1

description:
Simple annotation: Environmental conditions, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64663.gif; format: GIF

source_name: wt induced ( 3 ug RNA)

tag: wt induced ( 3 ug RNA)

source_name: hapR  mutant  induced ( 3ug RNA)

tag: hapR  mutant  induced ( 3ug RNA)


title: Mouse ES cells (MoES.R1xx)

description:
Strain: 129
Mouse ES cells total RNA (MoES.R1xx) received from National Mouse Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library MoES.R1xx.sig21
Cell type Mouse ES cells
Source NHGRI
RNA isolation LYNX mRNA QC passed
cDNA library:
Library 	DpnII restriction - (signature cloning using MmeI)
Sequence length	20 bp
MPSS:
runs
MoES.R1xx_sig21.5638W.a-20	11/29/2005	661223	16641	QC Passed
MoES.R1xx_sig21.5638W.b-20	11/29/2005	609258	13896	QC Passed
MoES.R1xx_sig21.5638F.a-20	11/28/2005	546489	12729	QC Passed
MoES.R1xx_sig21.5638F.b-20	11/28/2005	510373	11835	QC Passed
Run group:
Total Beads successfully sequenced - 2327343
Processed Signatures - 20154


title: CH1800

label_protocol:
Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

500ng total RNA was used initially


title: vcd699 hapR mutant induced by chitin exp. 1

description: Simple annotation: Environmental conditions, Mutant


title: CH1802


title: GIN-CingulateCortex replicate3

label_protocol: Total RNA from 48 cells was amplified and processed to produce biotinylated cRNA targets.

value: GIN (pubmed id:10777798)transgenic mice.

value: Cingulate Cortex


title: CH1804


title: vcd624 hapR mutant induced by chitin exp. 2

description:
Simple annotation: Environmental conditions, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64666.gif; format: GIF

source_name: wt induced ( 2 ug RNA)

tag: wt induced ( 2 ug RNA)

source_name: hapR  mutant  induced ( 2 ug RNA)

tag: hapR  mutant  induced ( 2 ug RNA)


title: vcd693 hapR mutant induced by chitin exp. 2

description:
Simple annotation: Environmental conditions, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64665.gif; format: GIF


title: CH1803


title: IFN_16 hours_rep2

status: Public on Dec 12 2005

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Global transcriptional analysis to explore the gene expression pattern of CD8+ DCs purified from the mouse spleen and treated with IFN-gamma

hyb_protocol: Standard Affymetrix procedures (see GeneChip® Expression Analysis Technical Manual)

data_processing: Robust Multi-Array Average (RMA) procedure

source_name: CD8+ DCs purified from mouse spleen

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets according to Affymetrix Expression Analysis Technical Manual

growth_protocol: CD8+ DCs were incubated on medium alone (CTR) or with 200 U/ml of mouse IFN-gamma (IFN) for 4 or 16 hours

extract_protocol: Total RNA was extracted from incubated cells using TRIzol LS Reagent (Invitrogen Life Technologies, Carlsbad, CA). RNA samples were processed according to the Affymetrix Expression Analysis Technical Manual.

treatment_protocol: Mice were treated with 10 µg of Flt3-L for 9 days

value: 60 days

value: spleen


title: IFN_16 hours_rep1

scan_protocol: Standard Affymetrix procedures (see GeneChip® Expression Analysis Technical Manual)


title: IFN_4 hours_rep2


title: Microdissected Normal

status: Public on Dec 13 2005

city: Seoul

first: Inchul

last: Lee

address: 388-1 Poongnap-Dong, Songpa-Gu

country: South Korea

institute: University of Ulsan College of Medicine

description: normal

hyb_protocol: cRNA was hybridized to X3P array at 45℃ for 16 hrs.

scan_protocol: Scanning of the array was done by Affymetrix GeneChip Scanner3000.

data_processing: standard Affymetrix protocol

source_name: Human colon normal cell from formalin-fixed, paraffin-embedded (FFPE) samples

label_protocol: cRNA was produced by GeneChip IVT labeling kit (Affymetrix: 900449) according to manufacturer’s instruction.

extract_protocol: Total RNA was extracted using TRIzol reagent(invtrogen, Carlsbad,CA.) .  two-cycle cDNA synthesis, assays were performed using two-cycle cDNA synthesis kit (Affymetrix: 900432) according to manufacturer’s instruction.

value: Human Colon

tag: State

value: Normal

value: 3 male pooled


title: Nup2-MN ChEC DNA sample gw-probe hybridization

city: Geneva 4

first: Ulrich

middle: K.

last: Laemmli

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

description: Nup2-MN in vivo ChEC cleavage for 5 minutes at 30°C.

data_processing: VALUE was calculated as Average of the rma values of 3 independent ChEC experiments using the probesets described in the accompanying Platform.

source_name: S. cerevisiae

growth_protocol: Yeast grown in 2% raffinose as sole carbon source and induced for 1 hour with 2% galactose during logarithmic growth

tag: Gw-probes prepared from a ChEC experiments of W303 derivative expressing Nup2-MN. Nup2-MN is expressed from the endogenous NUP2 gene locus. Yeast strain was grown in logarithmic phase induced by galactose and in vivo ChEC cleavage carried out for 5 minute at 30°C.


title: IFN_4 hours_rep1

value: female


title: Control_16 hours_rep2


title: H2b-MN ChEC DNA sample gw-probe hybridization

description: H2b-MN in vivo ChEC cleavage for 1 minute on ice.

tag: Gw-probes prepared from a ChEC experiments of W303 derivative expressing H2b-MN. H2b-MN is expressed from the endogenous HTB2 gene locus. Yeast strain was grown in logarithmic phase induced by galactose and in vivo ChEC cleavage carried out for 1 minute on ice.


title: Control_16 hours_rep1


title: Microdissected Ulcerative Colitis

description: ulcerative colitis

hyb_protocol: Fragmented cRNA was hybridized to X3P array at 45℃ for 16 hrs.

source_name: Human Ulcerative Colitis cell from formalin-fixed, paraffin-embedded (FFPE) samples

value: Ulcerative Colitis

value: 2 male and 1 female pooled


title: Uncleaved ChEC DNA sample gw-probe hybridization

description: Uncleaved DNA

tag: Gw-probes prepared from a ChEC experiments without Ca2+ addition (uncleaved) in W303 yeast strain grown in logarithmic phase after galactose induction.


title: Control_4 hours_rep1

status: Public on Dec 10 2005

tag: Gender


title: VP963/DK1622, 48hr, E200, Exp#3 (5C)

city: Davis

first: Mitchell

last: Singer

address: 1 Shields Ave

department: Microbiology

institute: The University of California, Davis

description: standard protocol

data_processing: GenePix, Excel

organism: Myxococcus xanthus


title: Imbibed seeds_3day

city: Fredericton

first: Helen

middle: H

last: Tai

email: htai@nrcan.gc.ca, taihelen@yahoo.com

state: New Brunswick

address: 1350 Regent St.

department: Natural Resources Canada

institute: Canadian Forest Service

description: Affymetrix ATH1 array

source_name: Seeds imbibed for 3 days on media

growth_protocol: Seeds were germinated under 16 h light conditions.

extract_protocol: Tai, H.H., Pelletier, C., Beardmore, T. (2004) Total RNA isolation from Picea marianna dry seed. Plant Molecular Biology Reporter 22: 93.

treatment_protocol: Seeds from Arabidopsis thaliana ecotype Columbia were surface sterilized and sown on nylon membranes on Murashige and Skoog (MS) media (Murashige and Skoog, 1962) containing 0.8% agar with and without 10 mM Trichostatin A (TSA) (Sigma Chemical Co., USA) in 10 cm Petri dishes with 10 ml media/dish.

tag: Ecotype

value: Columbia

tag: Developmental Stage

value: Seeds 3 days after imbibition


title: Control_4 hours_rep2

tag: Strain

tag: Tissue


title: Imbibed seed_untreated_3days_rep2

description: replicates are from two separate treatments


title: Unimbibed seed

description: Affymetrix ATH1 array

source_name: Unimbibed seed

value: unimbibed seed


title: VP963/DK1622, 60hr, E201, Exp#3 (5C)

description: standard protocol


title: Imbibed seeds_3days_TSA

description: Affymetrix ATH1 array

source_name: Seeds imbibed for 3 days on media containing 10 micromolar Trichostatin A (TSA)

value: columbia


title: VP963/DK1622, 0hr, E199, Exp#3 (5C)

description: standard protocol


title: VP963/DK1622, 60hr, E176, Exp#2 (4)

description: standard protocol


title: Imbibed seed_untreated_3days_rep1


title: VP963/DK1622, 0hr, E174, Exp#2 (4)

description: standard protocol


title: VP963/DK1622, 0hr, E003, Exp#1 (1B)

description: standard protocol


title: Imbibed seed_TSA_3days_rep2

growth_protocol: Seeds were germinated under 16 h light conditions without stratification.

treatment_protocol: Seeds from Arabidopsis thaliana ecotype Columbia were surface sterilized and sown on nylon membranes on Murashige and Skoog (MS) media (Murashige and Skoog, 1962) containing 0.8% agar with and without 10 mM Trichostatin A (TSA) (Sigma Chemical Co., USA) in 10 cm Petri dishes with 10 ml media/dish.  Seeds were germinated under 16 h light conditions.


title: VP963/DK1622, 48hr, E175, Exp#2 (4)

description: standard protocol


title: Imbibed seed_TSA_3days_rep1


title: VP963/DK1622, 60hr, E005, Exp#1 (1B)

description: standard protocol


title: WTR40201A

status: Public on Dec 08 2005

city: Berkely

first: Sanchita

last: Bhattacharya

address: 1 Cyclotron Rd

institute: MIT

description:
Wild type _Radiated
Replicate 1

source_name: Early passage primary MEFs


title: WTR40321A

description:
Wild type _Radiated
Replicate 4


title: VP963/DK1622, 48hr, E004, Exp#1 (1B)

description: standard protocol


title: WTR40205A

description:
Wild type _Radiated
Replicate 2


title: WT40318A

description:
Wild Type
Replicate 3


title: WT40320A

description:
Wild Type
Replicate 4