title: Melanoma (AF100KHINDIIIWM3211)

description: Melanoma


title: Melanoma (AF100KHINDIIIWM983)

status: Public on Nov 02 2007

type: genomic

city: King of Prussia

first: Joel

last: Greshock

state: PA

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

country: USA

institute: GlaxoSmithKline

description: Melanoma

hyb_protocol: Hybridizations were performed according to the standard manufacturer's describe in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix.

scan_protocol: Scanning was done using an Affymetrix 3000 microarray scanner.  Specifications can be found in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix

data_processing: Image files were analyzed using the dChip software.  A panel of chips (n = 12)  assayed with germline DNA served as a reference in order to calculate a test/reference ratio.  The ratios were then subject global normalization that assumed that the median copy number is  diploid (2n; log2 Ratio = 0).

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: WM983 Cell Line

label_protocol: 250 ng Genomic DNA was biotinylated as described by manufacturer (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).

growth_protocol: Cells were grown in in RPMI 1640 supplemented with 10% heat-inactivated FBS

extract_protocol: Genomic DNA was isolated from cultured cells with Mini DNeasy kit (Qiagen, Inc.)

tag: Melanoma


title: Germline DNA derived from normal individual (AFFY100KXBAREF3)

data_processing: Raw Intensity values were calculated using the dChip sofware package.

source_name: Germline3 Cell Line

extract_protocol: Genomic DNA was isolated from cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.


title: Melanoma (AG185KWM35)

description: Melanoma

hyb_protocol: Hybridization and assay treatment were carried out acccording to the manufacturer's recommendations

scan_protocol: Assay was scanned with an Agilent Microarray scanner

data_processing: Background corrected Test/Reference intensity ratios were calculated using the Agilent Inc. feature extraction software.  They were then subject global normalization that assumed that the median copy number is  diploid (2n; log2 Ratio = 0).

source_name: WM35 Cell Line

label_protocol: 2 ug of genomic DNA were labeled with the Enzo Genomic DNA Labeling Kit (Enzo Life Sciences)

source_name: Lymphocyte derived pooled male (Promega, Inc.)


title: Melanoma (AG185K1205LU)

description: Melanoma

source_name: 1205Lu Cell Line

tag: Lymphocyte derived pooled male (Promega, Inc.)


title: Germline DNA derived from normal individual (AFFY100KXBAREF1)

source_name: Germline1 Cell Line


title: Germline DNA derived from normal individual (AFFY100KXBAREF10)

source_name: Germline10 Cell Line


title: Melanoma (AG185KWM88)

description: Melanoma

source_name: WM88 Cell Line


title: Germline DNA derived from normal individual (AFFY100KXBAREF4)

source_name: Germline4 Cell Line


title: Germline DNA derived from normal individual (AFFY100KXBAREF2)

source_name: Germline2 Cell Line


title: Melanoma (AF100KHINDIIIWM3248)

description: Melanoma

source_name: WM3248 Cell Line


title: Germline DNA derived from normal individual (AFFY100KXBAREF9)

source_name: Germline9 Cell Line


title: Melanoma (AF500KSTY451LU)

description: Melanoma

source_name: 451LU Cell Line


title: Melanoma (AF100KHINDIIIWM1366)

description: Melanoma

source_name: WM1366 Cell Line


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF2)


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF4)


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF1)


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF3)


title: Melanoma (AF100KHINDIIIWM88)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF5)

source_name: Germline5 Cell Line


title: Melanoma (AF500KSTYWM793B)

description: Melanoma

source_name: WM793B Cell Line


title: Melanoma (AF500KSTYWM983C2)

description: Melanoma

source_name: WM983C Cell Line


title: Melanoma (AF500KNSP501MEL)

description: Melanoma

source_name: 501MEL Cell Line


title: Melanoma (AF500KSTYWM32482)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF6)

source_name: Germline6 Cell Line


title: Melanoma (AF500KSTYWM882)

description: Melanoma


title: Melanoma (AF500KSTYWM13662)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF7)

source_name: Germline7 Cell Line


title: Melanoma (AF500KSTYWM239A)

description: Melanoma

source_name: WM239A Cell Line


title: Melanoma (AF500KSTYWM122)

description: Melanoma

source_name: WM122 Cell Line


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF8)

source_name: Germline8 Cell Line


title: Melanoma (AF500KNSPWM882)

description: Melanoma


title: Melanoma (AF500KNSPWM793B)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF9)


title: Melanoma (AF500KSTYUACC62)

description: Melanoma

source_name: UACC62 Cell Line


title: Melanoma (AF500KSTYUACC257)

description: Melanoma

source_name: UACC257 Cell Line


title: Melanoma (NG1500K1205LU)

description: Melanoma

scan_protocol: Assay was scanned with an Axon microarray scanner (Axon, Inc.)

data_processing: Background corrected Test/Reference intensity ratios were calculated using Genepix software (Axon Instruments, Inc).  They were then subject global normalization that assumed that the median copy number is  diploid (2n; log2 Ratio = 0).

source_name: 1205Lu Cell Line

label_protocol: 1 ug Genomic DNA was labeled with dye-labeled 9 mers and Klenow.  Labeled DNA was isolated using ethanol precipitation


title: Melanoma (AG185KWM3248)

description: Melanoma

source_name: Lymphocyte derived pooled male (Promega, Inc.)


title: Melanoma (NG1500KWM983)

description: Melanoma

source_name: WM983 Cell Line


title: Melanoma (AF500KNSPWM983C2)

description: Melanoma


title: Melanoma (AF500KSTY501MEL)

description: Melanoma


title: Melanoma (AF500KNSPWM122)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF10)

source_name: Germline10 Cell Line


title: Melanoma (AF500KNSPWM13662)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF11)

source_name: Germline11 Cell Line


title: Melanoma (AF500KNSPWM32112)

description: Melanoma

source_name: WM3211 Cell Line


title: Melanoma (AF500KSTYSKMEL5)

description: Melanoma

source_name: SKMEL5 Cell Line


title: Melanoma (AF500KNSPUACC257)

description: Melanoma


title: Melanoma (NG1500KWM35)

description: Melanoma

source_name: WM35 Cell Line


title: Melanoma (NG1500KWM3248)

description: Melanoma

source_name: WM3248 Cell Line


title: Melanoma (NG1500KWM1366)

description: Melanoma

source_name: WM1366 Cell Line


title: Melanoma (AF500KNSP451LU)

description: Melanoma

source_name: 451LU Cell Line


title: Melanoma (AF500KNSPUACC62)

description: Melanoma


title: Melanoma (NG1500KWM88)

description: Melanoma

source_name: WM88 Cell Line


title: Melanoma (AF500KNSPSKMEL28)

description: Melanoma

source_name: SKMEL28 Cell Line


title: Melanoma (NG1500KWM3211)

description: Melanoma


title: Melanoma (AF100KHINDIII1205LU)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KHINDIIIREF12)

source_name: Germline12 Cell Line


title: Melanoma (AF500KSTYSKMEL28)

description: Melanoma


title: Melanoma (AF500KSTYMEWO)

description: Melanoma

source_name: MEWO Cell Line


title: Melanoma (AF500KNSPMALME3M)

description: Melanoma

source_name: MALME3M Cell Line


title: Melanoma (AF500KNSPM14)

description: Melanoma

source_name: M14 Cell Line


title: Melanoma (AF500KSTYMALME3M)

description: Melanoma


title: Melanoma (AF500KNSPSKMEL5)

description: Melanoma


title: Melanoma (AF500KSTYM14)

description: Melanoma


title: Melanoma (AF500KSTYWM32112)

description: Melanoma


title: Melanoma (AF500KNSPWM3211)

description: Melanoma


title: Melanoma (AF500KNSPWM3248)

description: Melanoma


title: Melanoma (AF500KNSPWM983)

description: Melanoma


title: Melanoma (AG244KWM88)

description: Melanoma


title: Melanoma (AF500KNSPWM35)

description: Melanoma


title: Melanoma (AF500KSTYWM3211)

description: Melanoma


title: Melanoma (AG244K451LU)

description: Melanoma


title: Melanoma (AF500KSTYWM35)

description: Melanoma


title: Melanoma (AF500KNSPWM88)

description: Melanoma


title: Melanoma (AF500KNSPSKMEL2)

description: Melanoma

source_name: SKMEL2 Cell Line


title: Melanoma (AG244K501MEL)

description: Melanoma

source_name: 501MEL Cell Line

source_name: Lymphocyte derived pooled male (Promega, Inc.)


title: Melanoma (AF500KNSP1205LU)

description: Melanoma

source_name: 1205Lu Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149456)

source_name: NA12717 Cell Line

extract_protocol: Genomic DNA was isolated from cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.


title: Melanoma (AG244KWM793B)

description: Melanoma

source_name: WM793B Cell Line


title: Melanoma (AF500KNSPWM239A)

description: Melanoma

source_name: WM239A Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149455)

source_name: NA12716 Cell Line


title: Melanoma (AF500KNSPWM1366)

description: Melanoma


title: Melanoma (AF500KNSPWM32482)

description: Melanoma

source_name: WM3248 Cell Line


title: Melanoma (AF500KSTYWM983)

description: Melanoma

source_name: WM983 Cell Line


title: Melanoma (AF500KSTY1205LU)

description: Melanoma


title: Melanoma (AG244KWM983C)

description: Melanoma

source_name: WM983C Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149454)

source_name: NA12707 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149453)

source_name: NA12264 Cell Line


title: Melanoma (AG244KWM3211)

description: Melanoma

source_name: WM3211 Cell Line


title: Melanoma (AF500KSTYWM3248)

description: Melanoma


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149451)

source_name: NA12057 Cell Line


title: Melanoma (AG244KWM239A)

description: Melanoma


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149450)

source_name: NA12056 Cell Line


title: Melanoma (AF500KSTYWM1366)

description: Melanoma

source_name: WM1366 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149449)

source_name: NA11832 Cell Line


title: Melanoma (AF500KSTYSKMEL2)

description: Melanoma

source_name: SKMEL2 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149448)

source_name: NA11831 Cell Line


title: Melanoma (AG244KWM122)

description: Melanoma

source_name: WM122 Cell Line

source_name: Lymphocyte derived pooled male (Promega, Inc.)


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149456)

source_name: NA12717 Cell Line


title: Melanoma (AG244KUACC62)

description: Melanoma

source_name: UACC62 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149445)

source_name: NA10851 Cell Line


title: Melanoma (AG244KWM3248)

description: Melanoma

source_name: WM3248 Cell Line


title: Melanoma (AF500KSTYWM88)

description: Melanoma

source_name: WM88 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149450)


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149455)

source_name: NA12716 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149447)

source_name: NA10863 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149452)

source_name: NA12234 Cell Line


title: Melanoma (AG244KMALME3M)

description: Melanoma

source_name: MALME3M Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149453)

source_name: NA12264 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149454)

source_name: NA12707 Cell Line


title: Melanoma (AG244KSKMEL28)

description: Melanoma

source_name: SKMEL28 Cell Line


title: Melanoma (AG244KUACC257)

description: Melanoma

source_name: UACC257 Cell Line


title: Melanoma (AF500KNSPMEWO)

description: Melanoma

source_name: MEWO Cell Line


title: Melanoma (AG44KWM3211)

description: Melanoma

source_name: WM3211 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149449)

source_name: NA11832 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149451)

source_name: NA12057 Cell Line


title: Melanoma (AG44K1205LU)

description: Melanoma

source_name: 1205Lu Cell Line

source_name: Lymphocyte derived pooled male (Promega, Inc.)


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149448)

source_name: NA11831 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KNSPSC149446)

source_name: NA10855 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149452)


title: Melanoma (AG244KSKMEL2)

description: Melanoma

source_name: SKMEL2 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149446)


title: Melanoma (AG44KWM35)

description: Melanoma

source_name: WM35 Cell Line


title: Melanoma (AG244KMEWO)

description: Melanoma


title: Melanoma (AG244KWM1366)

description: Melanoma

source_name: WM1366 Cell Line


title: Melanoma (AG244KM14)

description: Melanoma

source_name: M14 Cell Line


title: Melanoma (AG244KSKMEL5)

description: Melanoma

source_name: SKMEL5 Cell Line


title: Melanoma (AG44KWM88)

description: Melanoma

source_name: WM88 Cell Line


title: Melanoma (AG44KWM3248)

description: Melanoma

source_name: WM3248 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149447)

source_name: NA10863 Cell Line


title: Cell line derived germline DNA from human diversity panel (AFFY500KSTYSC149445)

source_name: NA10851 Cell Line


title: Melanoma (AG44KWM1366)

description: Melanoma


title: LTH x Guy11 48h-1

status: Public on Nov 01 2007

type: RNA

city: Tsukuba

first: Tomoaki

last: Kato

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

description:
Keyword : Oryza sativa
Keyword : Magnaporthe grisea
Guy11 is a wild type of the Magnaporthe grisea.

hyb_protocol: Kit : in situ hybridization kit plus Manufacture : Agilent Technologies

scan_protocol: Scanner : Agilent DNA microarray scanner Manufacture: Agilent Technologies

data_processing: Feature Extraction ver 9.1 (Agilent Technologies)

molecule: total RNA

organism: Oryza sativa

source_name: Mock infection

label_protocol:
kit : Low input RNA linear amplification kit
Manufacture : Agilent Technologies

growth_protocol: Ten rice seeds (Oryza sativa L. cv. LTH) were sown in a pot that has been filled with a commercial soil mixture (Bonsol type 1; Sumitomo Chemical, Osaka, Japan). The pot was then submerged in water inside a container and was kept in a greenhouse at 28 degreeC under natural sunlight for 14 days.

extract_protocol:
kit : RNeasy mini kit
Manufacture : Qiagen

treatment_protocol: Fourteen days old rice plants were sprayed with conidia-free water and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 48hpi.

tag: cultivar

value: LTH

tag: Age

value: 14 days

tag: Tissue

value: Leaf

source_name: Guy11 infection

treatment_protocol: Fourteen days old rice plants were sprayed with Guy11 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 48hpi.

value: A wild type of the Magnaporthe grisea.


title: LTH x mst12 24h-2

description:
Keyword : Oryza sativa
Keyword : Magnaporthe grisea
Mst12 is a mutant of the Magnaporthe grisea, which is indispensable to development of penetration peg.

treatment_protocol: Fourteen days old rice plants were sprayed with conidia-free water and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 24hpi.

source_name: mst12 infection

treatment_protocol: Fourteen days old rice plants were sprayed with mst12 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 24hpi.

value: A mutant of the transcriptional factor mst12, that is indispensable to development of penetration peg.


title: Melanoma (AG44KWM983)

description: Melanoma

source_name: WM983 Cell Line


title: LTH x mst12 48h-3

treatment_protocol: Fourteen days old rice plants were sprayed with mst12 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 48hpi.


title: LTH x mgb1 48h-3

description:
Keyword : Oryza sativa
Keyword : Magnaporthe grisea
Mgb1 is a mutant of the Magnaporthe grisea, which is impaired in the surface recognition and consequently in the initiation of appressorium formation.

source_name: mgb1 infection

treatment_protocol: Fourteen days old rice plants were sprayed with mgb1 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 48hpi.

value: A null mutant of the heterotrimeric G-protein b-subunit, which is impaired in the surface recognition and consequently in the initiation of appressorium formation.


title: LTH x Guy11 24h-1

treatment_protocol: Fourteen days old rice plants were sprayed with Guy11 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 24hpi.


title: 12m x mst12 48h-3

growth_protocol: Ten rice seeds (Oryza sativa L. cv. IRBL12-M) were sown in a pot that has been filled with a commercial soil mixture (Bonsol type 1; Sumitomo Chemical, Osaka, Japan). The pot was then submerged in water inside a container and was kept in a greenhouse at 28 degreeC under natural sunlight for 14 days.


title: LTH x mst12 24h-3


title: LTH x Guy11 24h-3


title: LTH x mgb1 24h-1

treatment_protocol: Fourteen days old rice plants were sprayed with mgb1 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 24hpi.


title: LTH x mgb1 48h-1


title: LTH x mgb1 24h-3


title: 12m x mst12 48h-1


title: LTH x mgb1 48h-2

source_name: mock infection


title: LTH x mgb1 24h-2


title: 12m x mst12 48h-2


title: LTH x mst12 24h-1


title: LTH x Guy11 48h-2

hyb_protocol: in situ hybridization kit plus Manufacture : Agilent Technologies


title: LTH x mst12 48h-2


title: 12m x Guy11 48h-2


title: 12m x mst12 24h-2


title: 12m x mst12 24h-1


title: LTH x Guy11 24h-2


title: LTH x Guy11 48h-3


title: 12m x mst12 24h-3


title: 12m x Guy11 48h-1


title: LTH x mst12 48h-1


title: Male lung, infected, 15 days p.i. (rep1)

status: Public on Oct 30 2007

city: Baltimore

first: Sabra

middle: Lynn

last: Klein

state: MD

address: 615 North Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins Bloomberg School of Public Health

description: sham = gonadally intact

hyb_protocol: 10ug fragmented, biotinylated cRNA was hybridized to RAE230A GeneChips for 16hours at 45oC and 60rpm.  The signal amplification protocol for washing/staining was performed in a FS450 automated fluidics station according to Affymetrix protocol.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

data_processing: The data were analyzed with GCOS 1.4 software.  All probe sets scaling was performed with a target signal value of 500.  No normalization was performed.

organism: Rattus norvegicus

label_protocol: 7.5 ug pooled total RNA was processed according to the Affymetrix Technical manual Rev3 protocol.  Biotinylated cRNA was prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit.

extract_protocol: Total RNA was extracted from individual lungs homogenized in TRIZOL. Pools of 2 individuals' RNA were subsequently prepared and processed, creating 3 separate pools per treatment group.

tag: Strain

value: Long Evans; Sex:Male; Age:>80 days; Tissue:Lungs; Infection Status:15 days p.i. with Seoul virus


title: Male lung, infected, 3 days p.i. (rep3)

description: sham = gonadally intact

source_name: Male lung, infected, 3 days p.i. (rep3)

value: Long Evans; Sex:Male; Age:>80 days; Tissue:Lungs; Infection Status:3 days p.i. with Seoul virus


title: Male lung, infected, 40 days p.i. (rep3)

description: sham = gonadally intact

value: Long Evans; Sex:Male; Age:>80 days; Tissue:Lungs; Infection Status:40 days p.i. with Seoul virus


title: d9012

status: Public on Oct 31 2007

city: Cambridge

first: Ahmed

middle: Ashour

last: Ahmed

address: Robinson Way

department: Oncology, University of Cambridge

country: United Kingdom

institute: Cancer Research UK Cambridge Research Institute

description:
Human paclitaxel-resistant (SKOV-3TR) ovarian cancer cell line and the
parent SKOV-3 cell line were grown in RPMI medium containing 10% fetal
calf serum. The experiment was done to compare the expression
differences between the parent SKOV-3 cell line and the derived SKOV-3TR
cell line.

Cells were plated in T75 flasks. They were cultured until they were
80% confluent and harvested by trypsinization followed by pelleting of
the cells. All RNA isolation was accomplished with the Tri-Reagent
(SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The
RNA (50 ug) was annealed with a random hexamer primer, and
reverse-transcribed into cDNA with Powerscript (Clontech) reverse
transcriptase for 2h at 42 degrees in the presence of amino-allyl
dUTP.

The cDNA from SKOV-3 RNA and SKOV-3TR RNA was covalently coupled
separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50
mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were
combined and purified with a QIAquick PCR purification kit and
hybridized to the microarray using the Hybrite chamber (Vysis).

Fluorescent array images were collected for both Cy3 and Cy5 with a
ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum
laser power and photo-multiplier tube voltage of 50 to
60%. Segmentation was performed using the histogram method of the
QuantArray (Perkin Elmer) package. Data was transformed into log base
2 expression ratios and normalized using scaled loess normalization.


title: d9018


title: Male lung, infected, 3 days p.i. (rep1)

description: sham = gonadally intact

source_name: Male lung, infected, 3 days p.i. (rep1)


title: 12m x mgb1 48h-3

value: a null mutant of the heterotrimeric G-protein b-subunit, which is impaired in the surface recognition and consequently in the initiation of appressorium formation.


title: Male lung, infected, 40 days p.i. (rep2)

description: sham = gonadally intact


title: Male lung, infected, 15 days p.i. (rep2)

description: sham = gonadally intact


title: 12m x Guy11 24h-3


title: Male lung, infected, 3 days p.i. (rep2)

description: sham = gonadally intact

source_name: Male lung, infected, 3 days p.i. (rep2)


title: 12m x Guy11 24h-1


title: Male lung, uninfected (rep3)

description: sham = gonadally intact

source_name: Male lung, uninfected (rep3)

value: Long Evans; Sex:Male; Age:>80 days; Tissue:Lungs; Infection Status:uninfected


title: d9019

description:
Human paclitaxel-resistant (SKOV-3TR) ovarian cancer cell line and the
parent SKOV-3 cell line were grown in RPMI medium containing 10% fetal
calf serum. The experiment was done to compare the expression
differences between the parent SKOV-3 cell line and the derived SKOV-3TR
cell line.

Cells were plated in T75 flasks. They were cultured until they were
80% confluent and harvested by trypsinization followed by pelleting of
the cells. All RNA isolation was accomplished with the Tri-Reagent
(SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The
RNA (50 ug) was annealed with a random hexamer primer, and
reverse-transcribed into cDNA with Powerscript (Clontech) reverse
transcriptase for 2h at 42 degrees in the presence of amino-allyl
dUTP.

The cDNA from SKOV-3 RNA and SKOV-3TR RNA was covalently coupled
separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50
mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were
combined and purified with a QIAquick PCR purification kit and
hybridized to the microarray using the Hybrite chamber (Vysis).

Fluorescent array images were collected for both Cy3 and Cy5 with a
ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum
laser power and photo-multiplier tube voltage of 50 to
60%. Segmentation was performed using the histogram method of the
QuantArray (Perkin Elmer) package. Data was transformed into log base
2 expression ratios and normalized using scaled loess normalization.


title: Male lung, uninfected (rep2)

description: sham = gonadally intact

source_name: Male lung, uninfected (rep2)


title: d9011


title: Male lung, infected, 15 days p.i. (rep3)

description: sham = gonadally intact


title: Male lung, infected, 40 days p.i. (rep1)

description: sham = gonadally intact


title: 12m x mgb1 48h-2


title: 12m x mgb1 48h-1


title: 12m x mgb1 24h-1

treatment_protocol: Fourteen days old rice plants were sprayed with conidia-free water and inoculated in a dew chamber at 25°C for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 24hpi.

treatment_protocol: Fourteen days old rice plants were sprayed with mgb1 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25°C for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 24hpi.


title: Male lung, uninfected (rep1)

description: sham = gonadally intact

source_name: Male lung, uninfected (rep1)


title: Female lung, infected, 40 days p.i. (rep3)

description: sham = gonadally intact

value: Long Evans; Sex:Female; Age:>80 days; Tissue:Lungs; Infection Status:40 days p.i. with Seoul virus


title: 12m x Guy11 24h-2


title: 12m x mgb1 24h-2


title: 12m x mgb1 24h-3


title: Female lung, infected, 40 days p.i. (rep2)

description: sham = gonadally intact


title: Female lung, infected, 15 days p.i. (rep2)

description: sham = gonadally intact

value: Long Evans; Sex:Female; Age:>80 days; Tissue:Lungs; Infection Status:15 days p.i. with Seoul virus


title: Female lung, infected, 40 days p.i. (rep1)

description: sham = gonadally intact


title: Control_short-term

status: Public on Oct 29 2007

city: Manchester

first: Nick

last: Mitsios

address: Chester Street

institute: Manchester Metropolitan University

description: RNA from three stroke patients was pooled.

hyb_protocol: The protocol recommended by Clontech in their Atlas 1.2 microarray kit was used without any modification. Briefly, cDNA was 32P-labelled and applied to the array for overnight hybridisation at 68oC.

scan_protocol: Following washing, the array was exposed to a phosphorimaging plate for 12-72 hours and data analysis was performed using the AtlasImage 1.5 software.

data_processing: The results were normalized using two housekeeping genes, ubiquitin and glyceraldehyde 3-phosphate dehydrogenase (GAPDH).

molecule: polyA RNA

source_name: Brain

label_protocol: The protocol recommended by Clontech in their Atlas 1.2 microarray kit was used without any modification. Briefly, RNA was reverse-transcribed to cDNA, 32P-labelled and applied to the array for overnight hybridisation at 68oC.

extract_protocol: RNA was extracted according to the manufacturer’s protocols (BD Biosciences, Oxfordshire, UK) and its quality was measured spectrophotometically. The protocol recommended by Clontech in their Atlas 1.2 microarray kit was used without any modification.

tag: Gender

value: Mixed


title: Female lung, infected, 15 days p.i. (rep3)

description: sham = gonadally intact


title: Female lung, infected, 3 days p.i. (rep3)

description: sham = gonadally intact

value: Long Evans; Sex:Female; Age:>80 days; Tissue:Lungs; Infection Status:3 days p.i. with Seoul virus


title: Female lung, infected, 15 days p.i. (rep1)

description: sham = gonadally intact


title: Female lung, infected, 3 days p.i. (rep2)

description: sham = gonadally intact


title: Female lung, infected, 3 days p.i. (rep1)

description: sham = gonadally intact


title: Female lung, uninfected (rep2)

description: sham = gonadally intact

source_name: Female lung, uninfected (rep2)

value: Long Evans; Sex:Female; Age:>80 days; Tissue:Lungs; Infection Status:uninfected


title: Stroke_mid-term

value: mixed


title: Stroke_long-term


title: Control_mid-term


title: Stroke_short-term


title: Control_long-term


title: Female lung, uninfected (rep3)

description: sham = gonadally intact

source_name: Female lung, uninfected (rep3)


title: Thoracic aorta age 15mo rep 4

city: Indianapolis

first: Steven

middle: J

last: Miller

state: IN

address: 1001 West 10th Street

department: Surgery

institute: Indiana University School of Medicine

description: Gene expression data form thoracic aorta

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RGU34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: Rat thoracic aorta at age 15 mo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The descending thoracic aorta (1 cm) was isolated and excised from 4 rats of each age in randomized order and the tissue was preserved in RNAlater. Tissue was weighed, disrupted by using a bead homogenizer (FastPrep System®; QBIOgene, Carlsbad, CA) and total RNA was purified by using an RNeasy® Fibrous Tissue Mini Kit (Qiagen, Valencia, CA).

tag: Fischer 344/Brown Norway F1 hybrid

tag: Thoracic Aorta from male, age 15 months


title: Thoracic aorta age 15mo rep 3


title: Thoracic aorta age 28mo rep 4

source_name: Rat thoracic aorta at age 28 mo

tag: Thoracic Aorta from male, age 28 months


title: Thoracic aorta age 28mo rep 1


title: Thoracic aorta age 28mo rep 2


title: Thoracic aorta age 15mo rep 1


title: Thoracic aorta age 28mo rep 3


title: Thoracic aorta age 15mo rep 2


title: Female lung, uninfected (rep1)

description: sham = gonadally intact

source_name: Female lung, uninfected (rep1)


title: Inoculated 120 hours KR12001

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

description:
Keyword = rice
Keyword = bacterial leaf blight disease response

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of Agilent DNA Microarray Scanner

data_processing: Feature Extraction software Version 8.1 from Agilent Technologies

organism: Oryza sativa Indica Group

source_name: 120 hr_IR24_Replication1

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown under Growth chambers and leaf samples were harvested on 23 DAS.

extract_protocol: Total RNA was extracted by Qiagen Rneasy Plant Maxi Kit according to manufacturers protocol

treatment_protocol: Leaves were inoculated with Xanthomonas oryzae pv oryzae by clip inoculation method (inoculated)

tag: Leaf samples from inoculated plants of IR24 collected at 120 hrs after inoculation

source_name: 120 hr_Ajaya_Replication1

tag: Leaf samples from inoculated plants of Ajaya collected at 120 hrs after inoculation


title: Inoculated 6 hours KR06002

source_name: 6 hrs_Ajaya_Replication 2

growth_protocol: Plants were grown under Growth chambers and leaf samples were harvested on 18 DAS.

tag: Leaf samples from inoculated plants of Ajaya collected at 6 hrs after inoculation

source_name: 6 hrs_IR24_Replication 2

tag: Leaf samples from inoculated plants of IR24 collected at 6 hrs after inoculation


title: Thoracic aorta age 6mo rep 3

source_name: Rat thoracic aorta at age 6 mo

tag: Thoracic Aorta from male, age 6 months


title: Inoculated 120 hours KR12002

source_name: 120_Ajaya_Replication 2

source_name: 120_IR24_Replication 2


title: Thoracic aorta age 6mo rep 2


title: Thoracic aorta age 3mo rep 1

source_name: Rat thoracic aorta at age 3 mo

tag: Thoracic Aorta from male, age 3 months


title: Thoracic aorta age 6mo rep 1


title: Thoracic aorta age 6mo rep 4


title: Thoracic aorta age 3mo rep 4


title: Thoracic aorta age 3mo rep 3


title: Thoracic aorta age 3mo rep 2


title: Uninoculated KRCR001

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plant Maxi Kit according to manufacturers protocol.

treatment_protocol: No treatment (un-inoculated)

tag: Leaf samples from un-inoculated control plants of IR24

tag: Leaf samples from un-inoculated control plants of Ajaya


title: Inoculated 6 hours KR06001

source_name: 6 hr_IR24_Replication1

treatment_protocol: Leaves inoculated with Xanthomonas oryzae pv oryzae pthogen by clip inoculation method (inoculated)

source_name: 6 hr_Ajaya_Replication1


title: ACY_PLACEBO_108

status: Public on Oct 25 2007

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Human laser captured benign prostate epithelial cells ACY_PLACEBO_108 from Human hybridized against Placebo Pool

hyb_protocol: Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Nelson PS, Pritchard C, Abbott D, and Clegg N. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases. Nucleic Acids Res 2002;30:218-220 and Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.

scan_protocol: Fluorescence array images were collected using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA) and processed as we have previously described in True L, Coleman I, Hawley S, et al. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A 2006;103:10991-10996.

data_processing: Changes in gene expression were evaluated using the Statistical Analysis of Microarray (SAM) program (http://www-stat.stanford.edu/_tibs/SAM/) to perform a one-sample t-test assessing the effect of Acyline treatment on gene expression (22). An FDR (false discovery rate) of less than 5% was considered significant. Quantile normalization was performed in Bioconductor (23) to allow single channel comparison of the absolute signal intensities in the experimental channel across different arrays in the same experiment.

source_name: Placebo Pool

label_protocol: cDNA probe pairs were prepared from samples obtained in the Acyline trial by amino-allyl reverse transcription using 2 µg of amplified RNA from the microdissected samples and 2µg of amplified RNA from a benign prostate reference standard. The reference was created by pooling equal amounts of RNA amplified from the microdissected placebo-treated prostate epithelial samples.  Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.

extract_protocol: Prostate samples embedded in OCT were used for laser capture microdissection (LCM). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.v

tag: Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_PLACEBO_108 treated with placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_PLACEBO_108. Prostate T

value: 2.3 (1.9) ng/g; Testosterone Treatment:N; Serum T:202 ng/ml; Prostate DHT:13.3 (2.1) ng/g; Treatment:placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily); Acyline Treatment:N; Serum DHT:27 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_PLACEBO_108;


title: ACY_T_103

description: Human laser captured benign prostate epithelial cells ACY_T_103 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_T_103 treated with "medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"

extract_protocol: Prostate samples embedded in OCT were used for laser capture microdissection (LCM). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.

tag: Human laser captured benign prostate epithelial cells ACY_T_103. Prostate T

value: 1.0 (0.5) ng/g; Testosterone Treatment:Y; Serum T:137 ng/ml; Prostate DHT:4.8 (1.3) ng/g; Treatment:"medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"; Acyline Treatment:Y; Serum DHT:55 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_T_103;


title: ACY_111

description: Human laser captured benign prostate epithelial cells ACY_111 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_111 treated with medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_111. Prostate T

value: 0.5 (0.3) ng/g; Testosterone Treatment:N; Serum T:22 ng/ml; Prostate DHT:1.8 (0.3) ng/g; Treatment:medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily); Acyline Treatment:Y; Serum DHT:11 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_111;


title: Early Onset Breast Cancer Patient 8020

status: Public on Oct 23 2007

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

hyb_protocol: DNA was prepared for hybridisation to the Human BAC Array 1400 (Spectral Genomics, USA), according to the manufacturer’s instructions. In brief, DNA was combined with SG proprietary Hybridisation Buffer I and isopropanol precipitated. DNA was resuspended in 10 mL water and 60 mL Hybridisation Buffer II and hybridised at 37uC for 16 h in the presence of 26SSC, 50% formamide (pH 7.5). Arrays were washed sequentially in 26SSC/50% deionised formamide (pH 7.5), 26SSC/0.1% NP-40 (pH 7.5) and 0.2 SSC (pH 7.5) for 20, 20 and 10min, respectively.

scan_protocol: Arrays were scanned in an Axon 4000B scanner using GenePix v3.1 acquisition software (Molecular Devices, USA).

data_processing: Spot data were median normalised, and included in the analysis only if the spot was flagged above background as calculated by GenePix before duplicate spot pairs were averaged, a single tumour/normal ratio of 1.2 was considered as gain and 0.8 as loss.

source_name: Early Onset Breast Cancer Patient_8020 Tumour DNA

label_protocol: DNA was amplified by one round of DOP PCR followed by a second DOP PCR reaction in the presence of amino-ally dUTP (Sigma-Aldrich, USA). Normal and tumour DNA was labelled by incubation with CyScribe Cy5 and Cy3 reactive dyes (Amersham Biosciences, UK).

extract_protocol: Tissue was microdissected from paraffin-embedded, formalin-fixed (PEFF) sections and digested with proteinase K.

tag: All patients were from a cohort of 116 cases of early-onset invasive breast carcinoma (i.e., diagnosed below 40 years of age), taken from a population-based registry (The Australian Breast Cancer Family Study).

source_name: Normal Female

extract_protocol: DNA was taken from peripheral blood lymphocytes using a Progenome kit (Progen).

tag: Deidentified normal healthy female with no visible by conventional comparative genomic hybridisation.


title: Early Onset Breast Cancer Patient 3304

source_name: Early Onset Breast Cancer Patient_3304 Tumour DNA


title: Early Onset Breast Cancer Patient 3345

source_name: Early Onset Breast Cancer Patient_3345 Tumour DNA


title: Early Onset Breast Cancer Patient 3267

source_name: Early Onset Breast Cancer Patient_3267 Tumour DNA


title: Saccharomyces cerevisiae oligo microarray_rep3

status: Public on Oct 24 2007

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

description: p-anisaldehyde effect on yeast

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in  hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.hybridization solution was denatured at 95? for 3 min prior to loading onto a microarray.then,hybridizing at a rotation speed of 8 rpm and a temperature of 42? overnight and washed with two consecutive solutions.

scan_protocol: LuxScanTM 3.0 software

data_processing: A space- and intensity-dependent normalization based on a LOWESS program,For further statistical analyses, The Significance Analysis of Microarrays (SAM ) add-in to Microsoft Excel was used to  compare the replicate arrays experiments.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae_p-anisaldehyde

label_protocol: cDNA products subjected to transcription reactions .Klenow enzyme labeling strategy was adopted after reverse transcription.

growth_protocol: (i)S. cerevisiae strain L1190 was grown overnight at 200 rpm in a rotary shaker at 28°C . (ii) fresh YPD broth was inoculated with an overnight culture to an initial OD600 of 0.05. The S. cerevisiae cells were grown at 28°C at 200 rpm to an OD600 of 0.6.(iii) Subsequently, p-anisaldehyde stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the culture. Then, the yeast cells  were further incubated for a certain time at 28°C.

extract_protocol: Total RNA was extracted by a hot acidic phenol method.(Collart,M.A. & Oliviero, S. (1995). Preparation of yeast RNA.In Short Protocols in Molecular Biology, 3rd edn, (Ausubel F., Brent R., Kingston, R. T., Moode, D. D, Seidman, J. G., Smith, J. A. et al., Eds), pp. 13-46-13-47. John Wiley and Sons, Inc., New York, NY)

treatment_protocol: plant medcine (p-anisaldehyde)

tag: strain L1190 (refer to the previous study done by liang zhang et al,2002,JAC)

source_name: Saccharomyces cerevisiae_DMSO

growth_protocol: (i)S. cerevisiae strain L1190 was grown overnight at 200 rpm in a rotary shaker at 28°C . (ii) fresh YPD broth was inoculated with an overnight culture to an initial OD600 of 0.05. The S. cerevisiae cells were grown at 28°C at 200 rpm to an OD600 of 0.6.(iii) Subsequently,DMSO was added to the culture. Then, the yeast cells  were further incubated for a certain time at 28°C.

treatment_protocol: DMSO


title: Early Onset Breast Cancer Patient 3650

source_name: Early Onset Breast Cancer Patient_3650 Tumour DNA


title: Saccharomyces cerevisiae oligo microarray_rep2

description: p-anisaldehyde effect on yeast


title: ACY_107

description: Human laser captured benign prostate epithelial cells ACY_107 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_107 treated with medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_107. Prostate T

value: 0.8 (0.6) ng/g; Testosterone Treatment:N; Serum T:10 ng/ml; Prostate DHT:3.0 (0.7) ng/g; Treatment:medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily); Acyline Treatment:Y; Serum DHT:4 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_107;


title: ACY_T_101

description: Human laser captured benign prostate epithelial cells ACY_T_101 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_T_101 treated with "medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"

tag: Human laser captured benign prostate epithelial cells ACY_T_101. Prostate T

value: 1.2 (0.5) ng/g; Testosterone Treatment:Y; Serum T:586 ng/ml; Prostate DHT:7.3 (1.7) ng/g; Treatment:"medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"; Acyline Treatment:Y; Serum DHT:104 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_T_101;


title: ACY_T_112

description: Human laser captured benign prostate epithelial cells ACY_T_112 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_T_112 treated with "medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"

tag: Human laser captured benign prostate epithelial cells ACY_T_112. Prostate T

value: 1.5 (0.7) ng/g; Testosterone Treatment:Y; Serum T:886 ng/ml; Prostate DHT:8.7 (2.0) ng/g; Treatment:"medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"; Acyline Treatment:Y; Serum DHT:341 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_T_112;


title: Early Onset Breast Cancer Patient 8013

source_name: Early Onset Breast Cancer Patient_8013 Tumour DNA


title: ACY_T_104

description: Human laser captured benign prostate epithelial cells ACY_T_104 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_T_104 treated with "medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"

tag: Human laser captured benign prostate epithelial cells ACY_T_104. Prostate T

value: 1.8 (1.4) ng/g; Testosterone Treatment:Y; Serum T:275 ng/ml; Prostate DHT:6.4 (2.4) ng/g; Treatment:"medical castration with Acyline as in group 2 plus testosterone gel (100 mg topically daily, Testim 1%, Auxilium Pharmaceuticals, Norristown, PA)"; Acyline Treatment:Y; Serum DHT:57 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_T_104;


title: Uninoculated KRCR002


title: ACY_109

description: Human laser captured benign prostate epithelial cells ACY_109 from Human hybridized against Placebo Pool

source_name: Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_109 treated with medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_109. Prostate T

value: 0.3 (0.2) ng/g; Testosterone Treatment:N; Serum T:18 ng/ml; Prostate DHT:0.6 (0.3) ng/g; Treatment:medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily); Acyline Treatment:Y; Serum DHT:13 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_109;


title: ACY_PLACEBO_113

description: Human laser captured benign prostate epithelial cells ACY_PLACEBO_113 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_PLACEBO_113 treated with placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_PLACEBO_113. Prostate T

value: 1.3 (1.1) ng/g; Testosterone Treatment:N; Serum T:383 ng/ml; Prostate DHT:5.6 (1.7) ng/g; Treatment:placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily); Acyline Treatment:N; Serum DHT:88 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_PLACEBO_113;


title: ACY_PLACEBO_105

description: Human laser captured benign prostate epithelial cells ACY_PLACEBO_105 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_PLACEBO_105 treated with placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_PLACEBO_105. Prostate T

value: 1.4 (1.2) ng/g; Testosterone Treatment:N; Serum T:256 ng/ml; Prostate DHT:6.8 (3.2) ng/g; Treatment:placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily); Acyline Treatment:N; Serum DHT:29 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_PLACEBO_105;


title: Early Onset Breast Cancer Patient 3208

source_name: Early Onset Breast Cancer Patient_3208 Tumour DNA


title: ACY_PLACEBO_115

description: Human laser captured benign prostate epithelial cells ACY_PLACEBO_115 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_PLACEBO_115 treated with placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_PLACEBO_115. Prostate T

value: 2.4 (2.3) ng/g; Testosterone Treatment:N; Serum T:587 ng/ml; Prostate DHT:11.3 (7.0) ng/g; Treatment:placebo vehicle injections (on day 0 and 14) and placebo gel (topically daily); Acyline Treatment:N; Serum DHT:23 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_PLACEBO_115;


title: Early Onset Breast Cancer Patient 3135

source_name: Early Onset Breast Cancer Patient_3135 Tumour DNA

source_name: Normal Female


title: ACY_106

description: Human laser captured benign prostate epithelial cells ACY_106 from Human hybridized against Placebo Pool

source_name: Human laser captured benign prostate epithelial cells ACY_106 treated with medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily)

tag: Human laser captured benign prostate epithelial cells ACY_106. Prostate T

value: 0.6 (0.3) ng/g; Testosterone Treatment:N; Serum T:53 ng/ml; Prostate DHT:2.3 (0.9) ng/g; Treatment:medical castration with Acyline (300ug/kg subcutaneously on days 0 and 14) plus placebo gel (topically daily); Acyline Treatment:Y; Serum DHT:10 ng/ml; Tissue:laser captured benign prostate epithelial cells; Specimen ID:ACY_106;


title: Early Onset Breast Cancer Patient 3169

source_name: Early Onset Breast Cancer Patient-3169 Tumour DNA


title: Early Onset Breast Cancer Patient 3169met

source_name: Early Onset Breast Cancer Patient_3169met Tumour DNA


title: Early Onset Breast Cancer Patient 3760

source_name: Early Onset Breast Cancer Patient_3760 Tumour DNA


title: Early Onset Breast Cancer Patient 3218

source_name: Early Onset Breast Cancer Patient_3218 Tumour DNA


title: Early Onset Breast Cancer Patient 3579

source_name: Early Onset Breast Cancer Patient_3579 Tumour DNA


title: Early Onset Breast Cancer Patient 3266

source_name: Early Onset Breast Cancer Patient_3266 Tumour DNA


title: Early Onset Breast Cancer Patient 3743

source_name: Early Onset Breast Cancer Patient_3743 Tumour DNA


title: Early Onset Breast Cancer Patient 3586

source_name: Early Onset Breast Cancer Patient_3586 Tumour DNA


title: Early Onset Breast Cancer Patient 3253

source_name: Early Onset Breast Cancer Patient_3253 Tumour DNA


title: Early Onset Breast Cancer Patient 3752

source_name: Early Onset Breast Cancer Patient_3752 Tumour DNA


title: Early Onset Breast Cancer Patient 3236

source_name: Early Onset Breast Cancer Patient_3236 Tumour DNA


title: Saccharomyces cerevisiae oligo microarray_rep1

description:
p-anisaldehyde effect on yeast
p-anisaldehyde effect on yeast

source_name: Saccharomyces cerevisiae_p-anisaldehyde

source_name: Saccharomyces cerevisiae_DMSO


title: Early Onset Breast Cancer Patient 3545

source_name: Early Onset Breast Cancer Patient_3545 Tumour DNA


title: Early Onset Breast Cancer Patient 3138

source_name: Early Onset Breast Cancer Patient_3138 Tumour DNA


title: Early Onset Breast Cancer Patient 3692

source_name: Early Onset Breast Cancer Patient_3692 Tumour DNA

source_name: Normal Female


title: Early Onset Breast Cancer Patient 3252

source_name: Early Onset Breast Cancer Patient_3252 Tumour DNA


title: Early Onset Breast Cancer Patient 3250

source_name: Early Onset Breast Cancer Patient_3250 Tumour DNA


title: Early Onset Breast Cancer Patient 3330

source_name: Early Onset Breast Cancer Patient_3330 Tumour DNA


title: Early Onset Breast Cancer Patient 3172

source_name: Early Onset Breast Cancer Patient_3172 Tumour DNA


title: Early Onset Breast Cancer Patient 3589

source_name: Early Onset Breast Cancer Patient_3589 Tumour DNA


title: Rsd timecourse slide 4.1

status: Public on Oct 22 2007

city: Ikoma

first: Naotake

last: Ogasawara

state: Nara

institute: Nara Institute of Science and Technology

description: RNA was isolated from MC4100 delta rsd cells, carrying plasmid pACYC Rsd and a control ‘no rsd’ plasmid pACYC delta BS, grown in LB media to stationary phase

hyb_protocol: Prehybridization of the array slides was performed for 4h in filtered prehybridization solution [25% formamide, 5x SSC, 10mg l-1 BSA (fraction V), 0.1% SDS] at 42℃. Slides were briefly washed in ethanol and dried by centrifugation at 1000g for 5 min. Hybridization of the probe was performed using hybridization solution (25% formamide, 5x SSC, 0.1% SDS, 0.1µg poly(A) ml-1, 1x Denhardt's solution and 80pmol Cy3 and Cy5 combined probe). The hybridization solution containing the Cy-Dye-labelled cDNA was heated to 95℃ for 3 min, Hybridization is performed by dvalytix hybridaization macine.

scan_protocol: After hybridization, slides were washed in wash buffer I (2x SSC/0.1% SDS) for 2min at 42℃, in wash buffer II (0.2x SSC) for 2min at room temperature and then twice in wash buffer III (0.05x SSC) for 2min at room temperature. All washes were done with vigorous shaking of the microarray slides. The slides were dried by centrifugation at 1000g for 5min, and then analysed using an Fuji FLA-8000 scanner and Array gauge ver.2.0 software (Fuji film)

data_processing: Normalization is performed by TREBAX, using MA-plots. MA-plots can reveal the spot artifacts globally and show the intensity-dependent logarithmic ratio of raw microarray data. In MA-plots, we calculate two parameters, average of logarithmic transferred intensity As=(log(Ts)+log(Rs))/2 and logarithmic ratio of intensity Ms=log(Ts/Rs) Here, Ts and Rs are the intensity of target and control experiments for sth spot, respectively.By plotting values of As on the abscissa and Ms on the ordinate of a coordinate system, it is possible to evaluate the bias error with respects to the average logarithmic intensities. Normalized log ratio M’’s is estimated as the difference between Ms and baseline M’s. Here, using a relation between Ms and As, (Ms=f(As)+es, es is the difference between Ms and f(As) for gene s) by MA plot; the baseline for sth spot is estimated by M’=f(A). The genes whose signal intensity is regarded as zero are eliminated in the present analysis. With this methodology, it is assumed that there is no large error due to expression intensity in the majority of the spots and that expression change does not occur on the majority of the spots.

organism: Escherichia coli

source_name: delta BS

label_protocol: Cyscribe Kit

growth_protocol: LB

extract_protocol: Qiagen RNeasy mini Kit

tag: Strain

value: MC4100 delta rsd pACYC delta BS

tag: stationary phase

source_name: Rsd

value: MC4100 delta rsd pACYC Rsd


title: WT vs GCN2 Exp3

city: Valencia

first: Jose

middle: Ramón

last: Murguía

state: Valencia

address: Ingeniero fausto Elio

country: Spain

institute: IBMCP

description: Spots with spotting or hybridisation defects, as well as spots whose median intensity did not reach a certain threshold (background-substracted feature median intensity higher than two times local background median intensity, in both  channels), were flagged and not considered for further analysis.

hyb_protocol: Microarrays were hybridized according to UltraGAPS manual (Corning). Slides were prehybridized in 1% BSA, 5 x SSC, 0.1% SDS for 45 min at 42ºC, washed using water and dried prior to hibridization. Labeled probes were resuspended in 50% formamide, 5 x SSC, 0.1% SDS, 0.2 ug/uL salmon sperm DNA and hybridized overnight at 42ºC using a Hyb4 hybridization station (Genomic Solutions). Following hybridization, slides were sequentially washed with 2 x SSC, 0.1% SDS; then in 0.1 x SSC, 0.1% SDS and finally in 0.1 x SSC, and dried.

scan_protocol: Slide was scanned using an Axon 4000B microarray scanner (Molecular Devices), at 10 um resolution. PMT gains was adjusted so that the ratio of pixels intensity in both channels was 1.0 Image adquisition and processing was performed using GenePix 6.0 software (Molecular Devices)

data_processing:
Replicates with valid data were merged using Acuity software
Slide was normalized by Lowess. VALUE column corresponds to the ratio of  medians Cy5/Cy3, lowess-normalized, in log scale.

source_name: GCN2c mutant strain in log phase culture

label_protocol: Fluorescent labeled cDNA was prepared from purified total RNA by the indirect method. Briefly, aminoallyl-cDNA was synthesised from 30 ug of total RNA using SuperScript II (InvitroGen) and poly-dT primer. Following removal of unincorporated nucleotides using Qiaquick columns (Qiagen), the reaction products were coupled to  Cy5 NHS-ester fluorescent dye (GE). Cy-labelled probes were further purified using Qiaquick columns and lyophilized.

growth_protocol: Cells were grown at 28ºC in YPD rich medium until Ab660=0.6. 50 mL of yeast culture was harvested by centrifugation and washed with cold water. dried cell pellet was kept at -80ºC until RNA purification.

extract_protocol: Dried cell pellet was resuspended in 350 uL TCES buffer and 350 uL phenol:chloroforme:isoamylalcohol (25:24:1), together with 0.6 mL of 0.5 mm glass beads. Cells were vortex and centrifuged 5 min at 12.000 rpm, and upper phase was recovered and re-extracted using 0.3 mL chloloforme. RNA was precipitated overnight in 6 M LiCl, centrifuged 15 min, washed with 70% ethanol and resuspended in 30 uL water. RNA was purified using RNAeasy columns from Qiagen.

tag: Strain BY4741, gcn2::GCN2c (M719V-E1537G) constitutively active GCN2 kinase mutant

source_name: WT strain in log phase culture

label_protocol: Fluorescent labeled cDNA was prepared from purified total RNA by the indirect method. Briefly, aminoallyl-cDNA was synthesised from 30 ug of total RNA using SuperScript II (InvitroGen) and poly-dT primer. Following removal of unincorporated nucleotides using Qiaquick columns (Qiagen), the reaction products were coupled to  Cy3 NHS-ester fluorescent dye (GE). Cy-labelled probes were further purified using Qiaquick columns and lyophilized.

extract_protocol: Dried cell pellet was resuspended in 350 uL TCES buffer and 350 uL phenol:chloroforme:isoamylalcohol (25:24:1), together with 0.6 mL of 0.5 mm glass beads. Cells were vortex and centrifuged 5 min at 12.000 rpm, and upper phase was recovered and re-extracted using 0.3 mL chloloforme. RNA was precipitated overnight in 6 M LiCl, centrifuged 15 min, washed with 70% ethanol and resuspended in 30 uL water.RNA was purified using RNAeasy columns from Qiagen

tag: Strain BY4741, WT


title: Rsd timecourse slide 3.1

description: RNA was isolated from MC4100 delta rsd cells, carrying plasmid pACYC Rsd and a control ‘no rsd’ plasmid pACYC delta BS, grown in LB media to OD 1.1

tag: OD


title: WT vs GCN2 Exp4

data_processing:
Replicates with valid data were merged using Acuity software
Slide was normalized by Lowess. VALUE column corresponds to the ratio of  medians Cy3/Cy5, lowess-normalized, in log scale.

tag: strain BY4741, WT


title: WT vs GCN2 Exp2


title: Rsd timecourse slide 4.2


title: Rsd timecourse slide 3.2


title: Rsd timecourse slide 2.2

description: RNA was isolated from MC4100 delta rsd cells, carrying plasmid pACYC Rsd and a control ‘no rsd’ plasmid pACYC delta BS, grown in LB media to OD 0.9


title: WT vs GCN2 Exp1


title: Rsd timecourse slide 2.1


title: J1a12 vs rpoN - 3000188445L

first: Tie

last: Koide

address: 1441 N 34th street

institute: Institute for Systems Biology

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)]

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization

organism: Xylella fastidiosa

source_name: rpoN- (cy3)

label_protocol: 20ug of total RNA was reverse transcribed and labeled using Superscript Plus Indirect cDNA Labeling System (Invitrogen). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

growth_protocol: Xylella fastidiosa strain J1a12 rpoN- was grown in Periwinkle wilt broth plus 0.5% glucose (PWG) containing 10 ug/ml ampicillin at 25oC for 7 days.

extract_protocol: Total RNA was isolated with Trizol and residual DNA was removed by treatment with 0.03U of RQ1 RNAse-free DNAse I (Promega) and 40U RNAse inhibitor RNAsin (Promega). The integrity of the RNA was checked by agarose gel electrophoresis and the lack of residual DNA was checked by PCR.

treatment_protocol: mutant rpoN-

tag: rpoN- (cy3)

growth_protocol: Xylella fastidiosa strain J1a12 was grown in Periwinkle wilt broth plus 0.5% glucose(PWG) at 25oC for 7 days.

treatment_protocol: wild type strain J1a12


title: J1a12 vs rpoN - 3000188437R


title: J1a12 vs rpoN - 3000188444R


title: J1a12 vs rpoN - 3000188445R


title: Rsd timecourse slide 1.2

description: RNA was isolated from MC4100 delta rsd cells, carrying plasmid pACYC Rsd and a control ‘no rsd’ plasmid pACYC delta BS, grown in LB media to OD 0.4


title: J1a12 vs rpoN - 3000188437L


title: J1a12 vs rpoN - 3000188444L


title: Rsd timecourse slide 1.1


title: ARD084

status: Public on Oct 20 2007

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16279.gif
Disease State: AIS-3
Cell Line: labioscrotal skin
Sex/Mating type: 46,XY

hyb_protocol: not provided

scan_protocol: not provided

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)

source_name: mixed reference (CRG + FR)

label_protocol: not provided

extract_protocol: not provided

tag: mixed reference (CRG + FR)

tag: LabeledExtract

source_name: ARD084 (PAIS3), 14 days DMEM F12, 15% FCS, Go, against mixed reference


title: ARD1097, CAIS, F, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17534.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

source_name: mixed reference (FR + CRG)

tag: mixed reference (FR + CRG)


title: ARD291a, CAIS, F, GOF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16489.gif
Disease State: CAIS
Cell Line: gonadal fibroblasts
Sex/Mating type: 46,XY

source_name: mixed reference (FR +CRG)

tag: mixed reference (FR +CRG)

source_name: ARD291,14 days DMEMF12, 12.9% FCS, G0

tag: ARD291,14 days DMEMF12, 12.9% FCS, G0


title: ARD1004, CAIS, F, GOF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17207.gif
Disease State: CAIS
Cell Line: gonadal fibroblasts
Sex/Mating type: 46,XY

source_name: ARD1004, 14 days DMEM F12, 12.9% FCS, Go


title: ARD659

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16879.gif
Disease State: AIS-4
Cell Line: localization not well documented
Sex/Mating type: 46,XY

source_name: ARD659, PAIS4, 14 days DMEM F12, 15% FCS, Go


title: ARD339

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16568.gif
Disease State: AIS-3
Cell Line: foreskin
Sex/Mating type: 46,XY

source_name: ARD339, PAIS3,DEME F12, 15% FCS, 14 days, Go


title: ARD842, CAIS, F, GOF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16237.gif
Cell Line: gonadal fibroblasts
Disease State: CAIS
Sex/Mating type: 46,XY

source_name: ARD842, CAIS 14 days DMEM F12, 12.9% FCS, Go, against mixed reference


title: ARD402, CAIS, F, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16449.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

source_name: ARD 402 14 days DMEM F12, 12.9% FCS, Go, against mied reference


title: N-33a, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16529.gif
Disease State: normal male
Cell Line: foreskin
Sex/Mating type: 46,XY

source_name: mixed reference

tag: mixed reference

source_name: nGSF33, 14 days DMEM F12, 12.9% FCS, G0

tag: nGSF33, 14 days DMEM F12, 12.9% FCS, G0


title: DS-2, N-1, NORM, nsGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57217.gif
Disease State: normal male
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 13:27:56; Parameter PMT Volts = 730; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 9038; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 13:27:56; Parameter PMT Volts = 850; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 9020; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.36; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference Lot:1130623

tag: Stratagene Reference Lot:1130623


title: ARD377, AIS4, F, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17177.gif
Disease State: AIS-4
Cell Line: labia majora
Sex/Mating type: 46,XY

source_name: ARD377, PAIS, 14 days DMEM F12, 12.9% FCS, G0


title: DS-2, ARD682a, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55050.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.35; Parameter Scan Time = 10:25:51; Parameter PMT Volts = 690; Parameter Scan Date = 2004-05-14; Parameter Pixel Size = 10; Parameter Laser on time = 7872; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.35; Parameter Scan Time = 10:25:51; Parameter PMT Volts = 800; Parameter Scan Date = 2004-05-14; Parameter Pixel Size = 10; Parameter Laser on time = 7854; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Strategene Reference Lot:1130623

tag: Strategene Reference Lot:1130623


title: ARD557a, CAIS, F, GOF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17054.gif
Disease State: CAIS
Cell Line: gonadal fibroblasts
Sex/Mating type: 46,XY

source_name: ARD557, 14 days DMEM F12, 12.9% FCS, Go

tag: ARD557, 14 days DMEM F12, 12.9% FCS, Go


title: ARD682, CAIS, F, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17056.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

source_name: ARD682, CAIS, 14 days DMEM F12, 12.9% FCS, Go


title: ARD527

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16537.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

source_name: mixed reference (CRG + FR)

source_name: ARD527, PAIS2, 14 days in DMEM F12, 15% FCS, G0


title: ARD411, CAIS, F, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17528.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

source_name: mixed reference (FR + CRG)

source_name: ARD411, 14 days DMEM F12, 12.9% FCS, Go

tag: ARD411, 14 days DMEM F12, 12.9% FCS, Go


title: ARD446

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16280.gif
Cell Line: localization not well documented
Disease State: AIS-2
Sex/Mating type: 46,XY

source_name: ARD446(PAIS2),14 days DMEM F12, 15% FCS, Go


title: ARD465, CAIS, F, GSF, mosaicism

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16471.gif
Disease State: CAIS, somatic mosaicism
Cell Line: labia majora
Sex/Mating type: 46,XY

source_name: ARD465,14 days of DMEM F12, 12.9% FCS, Go


title: ARD380

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17499.gif
Disease State: AIS-4
Cell Line: localization not well documented
Sex/Mating type: 46,XY

source_name: ARD380, DMEM F12, 14 days, 15% FCS, G0

tag: ARD380, DMEM F12, 14 days, 15% FCS, G0


title: DS-2, N-9, NORM, nsGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57247.gif
Disease State: normal male
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 12:41:27; Parameter PMT Volts = 690; Parameter Scan Date = 2004-10-07; Parameter Pixel Size = 10; Parameter Laser on time = 9093; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 12:41:27; Parameter PMT Volts = 750; Parameter Scan Date = 2004-10-07; Parameter Pixel Size = 10; Parameter Laser on time = 9075; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.36; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference Lot: 1130623

tag: Stratagene Reference Lot


title: N-57, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16248.gif
Disease State: normal male
Cell Line: foreskin
Sex/Mating type: 46,XY

source_name: nGSF57, 14 days DMEM F12, 12.9% FCS, G0, against mixed reference


title: DS-2, ARD1097b, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57672.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.67; Parameter Scan Time = 11:35:34; Parameter PMT Volts = 730; Parameter Scan Date = 2004-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 9859; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.67; Parameter Scan Time = 11:35:34; Parameter PMT Volts = 840; Parameter Scan Date = 2004-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 9841; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.32; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference Lot.-Nr. 1130623

tag: Stratagene Reference Lot.-Nr. 1130623


title: DS-2, N-5, NORM, nsGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57352.gif
Disease State: normal male
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 5520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.46; Parameter Scan Time = 14:41:00; Parameter PMT Volts = 710; Parameter Scan Date = 2004-10-26; Parameter Pixel Size = 10; Parameter Laser on time = 9483; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.46; Parameter Scan Time = 14:41:00; Parameter PMT Volts = 790; Parameter Scan Date = 2004-10-26; Parameter Pixel Size = 10; Parameter Laser on time = 9465; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.36; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus


title: ARD082

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16548.gif
Disease State: AIS-3
Cell Line: foreskin
Sex/Mating type: 46,XY

source_name: ARD082, PAIS3, 14 days DMEM F12, 15% FCS, Go


title: DS-2, ARD411b, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57685.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.57; Parameter Scan Time = 12:24:45; Parameter PMT Volts = 720; Parameter Scan Date = 2004-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 9909; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.57; Parameter Scan Time = 12:24:45; Parameter PMT Volts = 810; Parameter Scan Date = 2004-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 9891; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.36; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus


title: DS-2, ARD1097a, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55667.gif
Cell Line: labia majora
Disease State: CAIS
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 14:34:15; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 8000; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 14:34:15; Parameter PMT Volts = 830; Parameter Scan Date = 2004-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 7983; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus


title: DS-2, ARD306, AIS2,sGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59776.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 11:41:55; Parameter PMT Volts = 710; Parameter Scan Date = 2005-02-01; Parameter Pixel Size = 10; Parameter Laser on time = 12171; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 11:41:55; Parameter PMT Volts = 770; Parameter Scan Date = 2005-02-01; Parameter Pixel Size = 10; Parameter Laser on time = 12153; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.33; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Ref. Lot: 1130623

tag: Stratagene Ref. Lot

source_name: RNA 144

tag: RNA 144


title: ARD774

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17574.gif
Cell Line: scrotal fibroblasts
Disease State: AIS-2
Sex/Mating type: 46,XY

source_name: ARD774, 14 days DMEM F12, 15% FCS, Go

tag: ARD774, 14 days DMEM F12, 15% FCS, Go


title: DS-2, ARD402a, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56126.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 750, 4600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 14:10:41; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 7976; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 14:10:41; Parameter PMT Volts = 820; Parameter Scan Date = 2004-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 7958; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference Lot:1130623

source_name: RNA 068

tag: RNA 068


title: DS-2, ARD411a, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55048.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 400, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.52; Parameter Scan Time = 10:23:33; Parameter PMT Volts = 690; Parameter Scan Date = 2004-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 7917; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.64; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.52; Parameter Scan Time = 10:23:33; Parameter PMT Volts = 840; Parameter Scan Date = 2004-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 7899; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

tag: LabeledExtract


title: DS-2, ARD515, 5RD, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51595.gif
Disease State: "AIS-3"  (5 alpha reductase type II deficiency)
Cell Line: foreskin
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 6000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.56; Parameter Scan Time = 10:11:25; Parameter PMT Volts = 680; Parameter Scan Date = 2004-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 7701; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.56; Parameter Scan Time = 10:11:25; Parameter PMT Volts = 820; Parameter Scan Date = 2004-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 7683; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus


title: DS-2, N-8, NORM, nsGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57880.gif
Disease State: normal male
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 5230; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.10; Parameter Scan Time = 13:32:18; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-26; Parameter Pixel Size = 10; Parameter Laser on time = 9415; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.64; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.10; Parameter Scan Time = 13:32:18; Parameter PMT Volts = 700; Parameter Scan Date = 2004-10-26; Parameter Pixel Size = 10; Parameter Laser on time = 9397; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.35; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus


title: DS-2, ARD527, AIS2, sGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59222.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.56; Parameter Scan Time = 13:51:41; Parameter PMT Volts = 700; Parameter Scan Date = 2004-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 11773; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.64; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.56; Parameter Scan Time = 13:51:41; Parameter PMT Volts = 780; Parameter Scan Date = 2004-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 11755; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.37; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference Lot. 1130623

tag: Stratagene Reference Lot. 1130623

source_name: RNA 133

tag: RNA 133


title: ARD531, CAIS, F, GOF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16232.gif
Cell Line: gonadal fibroblasts
Disease State: CAIS
Sex/Mating type: 46,XY

source_name: mixed reference (CRG+ FR)

tag: mixed reference (CRG+ FR)

source_name: ARD531, CAIS, 14days DMEMF12, 12.9% FCS, G0 (confluency) , against mixed reference


title: DS-3, N-1, NORM, nlGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63690.gif
Disease State: normal female
Cell Line: labia minora
Sex/Mating type: 46,XX

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 34.99; Parameter Scan Time = 13:57:04; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-15; Parameter Pixel Size = 10; Parameter Laser on time = 13823; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 34.99; Parameter Scan Time = 13:57:04; Parameter PMT Volts = 800; Parameter Scan Date = 2005-06-15; Parameter Pixel Size = 10; Parameter Laser on time = 13805; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.24; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Ref. Lot.-Nr. 1130623

tag: Stratagene Ref. Lot.-Nr. 1130623