title: TNF Monosome Fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the TNF monosome fraction used to calculate a translation index as follows:  (TNF polysome/TNF monosome)/(control polysome/control monosome).

source_name: Primary HUVEC, Treated with TNF for 2 hours before subjecting to polysome profiling

treatment_protocol: Control cells received an equal amount of HBSS as a vehicle control for TNF-alpha.

tag: Primary HUVEC cultured on gelatin coated flasks derived from 7 different umbilical cords, isolated as described by Jaffe, et al.  Cells were grown to one day post-confluence before stimulating with TNF-alpha or vehicle for 2 hours.


title: retroperitoneal adipose tissue, Day 1, Control Rep 2

status: Public on Jul 28 2006

type: RNA

city: Lincoln

first: Chris

last: LaRosa

state: NE

address: 19th & Vine

department: Center of Biotechnology

country: USA

institute: University of Nebraska, Lincoln

description: Gene expression data from retroperitoneal adipose tissue of C57BK/6J mice fed control diet.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 420 2.0 arrays using the Hybridization Oven 640, the hybridized array washed with the Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with robust multi-array analysis RMA.  The RMA signal values wre log2 transformed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse retroperitoneal fat pad

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Two retroperitoneal fat pads excised from each of 10 mice, pooled, frozen in liquid N2 and later extracted in Trizol solution.

tag: Age

value: 9 wk old mice


title: Ad+E2 replicate1 b

city: Santa Monica

first: Edmund

middle: C

last: Chang

state: California

address: 2225 Colorado Ave

institute: Kite Pharma

description: Ad(moi10)-infected, E2-treated

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: R/Bioconductor GCRMA

organism: Homo sapiens

source_name: MCF-7 breast cancer cells

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

extract_protocol: MCF-7 cells expressing endogenous ERalpha were plated in 100mm dish in 5% CD-stripped calf serum.  Cells were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 5 or 50.  Cells were infected with adenovirus for a period of 48hr before treatment with ligand (vehicle control (veh), 10nM 17beta-estradiol (E2), or 10nM trans-hydroxytamoxifen (TOT)) for a additional period of 24hr before harvest.  Total RNA was extracted using 1mL of TRIzol (Invitrogen) per 100mm dish.

tag: Ad(moi10)-infected, E2-treated for 24hr


title: retroperitoneal adipose tissue, Day 2, CLA treat

description: Gene expression data from retroperitoneal adipose tissue of C57BK/6J mice fed 0.5% trans-10 cis-12 conjugated linoleic acid.


title: retroperitoneal adipose tissue, Day 1, Control


title: Control TNF Monosome Fraction

status: Public on Jul 27 2006

city: Salt Lake City

first: Douglas

middle: I.

last: Schmid

state: UT

department: HMBG

institute: University of Utah

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the control monosome fraction used to calculate a translation index as follows:  (TNF polysome/TNF monosome)/(control polysome/control monosome).

data_processing: The value column was generated by dividing the SIGNAL_RAW values by the median signal intensity of the entire membrane.  This was done in order to compare multiple array values.

label: alpha-33P dCTP

source_name: Primary HUVEC, Treated with TNF or vehicle for 2 hours before subjecting to polysome profiling


title: Control Polysome Fraction (TNF)

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the control polysome fraction used to calculate a translation index as follows:  (TNF polysome/TNF monosome)/(control polysome/control monosome).

source_name: Primary HUVEC, Treated with vehicle for 2 hours before subjecting to polysome profiling


title: Growth arrested control monosome fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the growth arrested monosome fraction used to calculate a translation index as follows:  (Serum polysome/Serum monosome)/(growth arrested polysome/growth arrested monosome).

source_name: Primary HUVEC, growth arrested overnight before subjecting to polysome profiling

treatment_protocol: The control cells from this experiment were given fresh medium, containing 0.1% Pooled Human Serum.

tag: Primary HUVEC cultured on gelatin coated flasks derived from 7 different umbilical cords, isolated as described by Jaffe, et al.  Cells were grown to confluence before growth arresting overnight.  The experimental cells were stimulated by adding medium containing 20% pooled human serum for 6 hours.


title: Serum stimulated monosome fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the serum monosome fraction used to calculate a translation index as follows:  (Serum polysome/Serum monosome)/(growth arrested polysome/growth arrested monosome).

source_name: Primary HUVEC, growth arrested then stimulated with serum overnight before subjecting to polysome profiling


title: Ad+veh replicate2 b

description: Ad(moi10)-infected, vehicle-treated

tag: Ad(moi10)-infected, vehicle-treated for 24hr


title: Insulin Polysome Fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the Insulin polysome fraction used to calculate a translation index as follows:  (insulin polysome/insulin monosome)/(control polysome/control monosome).

treatment_protocol: Control cells received an equal amount of HBSS as a vehicle control for Insulin.

tag: Primary HUVEC cultured on gelatin coated flasks derived from 7 different umbilical cords, isolated as described by Jaffe, et al.  Cells were grown to one day post-confluence before stimulating with Insulin or vehicle for 2 hours.


title: Histamine Monosome Fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the histamine monosome fraction used to calculate a translation index as follows:  (Histamine polysome/histamine monosome)/(control polysome/control monosome).

source_name: Primary HUVEC, Treated with Histamine for 2 hours before subjecting to polysome profiling

treatment_protocol: The control cells from this experiment received an equal amount of HBSS as a vehicle for histamine.

tag: Primary HUVEC cultured on gelatin coated flasks derived from 7 different umbilical cords, isolated as described by Jaffe, et al.  Cells were grown to one day post-confluence before stimulating with histamine or vehicle for 2 hours.


title: LPS Polysome Fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the control monosome fraction used to calculate a translation index as follows:  (histamine polysome/histamine monosome)/(control polysome/control monosome).

treatment_protocol: Control cells received an equal amount of HBSS as a vehicle control for LPS.

tag: Primary HUVEC cultured on gelatin coated flasks derived from 7 different umbilical cords, isolated as described by Jaffe, et al.  Cells were grown to one day post-confluence before stimulating with LPS or vehicle for 2 hours.


title: Serum stimulated polysome fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the serum polysome fraction used to calculate a translation index as follows:  (Serum polysome/Serum monosome)/(growth arrested polysome/growth arrested monosome).


title: Insulin Monosome Fraction


title: Control Insulin Monosome Fraction


title: retroperitoneal adipose tissue, Day 1, CLA treat, Rep_2


title: Control LPS Polysome Fraction


title: Control Insulin Polysome Fraction


title: Control Histamine Polysome Fraction

treatment_protocol: Control cells received an equal amount of HBSS as a vehicle control for histamine.

tag: Primary HUVEC cultured on gelatin-coated flasks derived from 7 different umbilical cords, isolated as described by Jaffe, et al.  Cells were grown to one day post-confluence before stimulating with histamine or vehicle for 2 hours.


title: TNF Polysome Fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the TNF polysome fraction used to calculate a translation index as follows:  (TNF polysome/TNF monosome)/(control polysome/control monosome).


title: Control LPS Monosome Fraction


title: Histamine Control Monosome Fraction


title: Histamine Polysome Fraction

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the histamine polysome fraction used to calculate a translation index as follows:  (Histamine polysome/histamine monosome)/(control polysome/control monosome).


title: LPS Monosome Fraction


title: 25 uM chlorpyrifos batch 1

city: New York

first: Sarah

last: Mense

state: NY

address: 722 West 168th Street

department: Environmental Health Sciences

institute: Columbia University

description: astrocytes from second trimester (14-19 weeks) human fetal brains

data_processing: Affymetrix Microarray Suite version 5.0

source_name: 25 uM chlorpyrifos batch 1

tag: astrocytes from second trimester human fetal brains


title: 25 uM chlorpyrifos batch 2

source_name: 25 uM chlorpyrifos batch 2


title: 25 uM cyfluthrin batch 2

source_name: 25 uM cyfluthrin batch 2


title: 25 uM cyfluthrin batch 3

source_name: 25 uM cyfluthrin batch 3


title: 1% dmso batch 3

source_name: 1% dmso batch 3


title: 1% dmso batch 1

source_name: 1% dmso batch 1


title: 25 uM chlorpyrifos batch 3

source_name: 25 uM chlorpyrifos batch 3


title: 25 uM cyfluthrin batch 1

source_name: 25 uM cyfluthrin batch 1


title: retroperitoneal adipose tissue, Day 3, CLA treat, Rep_2


title: LPS + CyP 3hr 2

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: This sample is also known as IOSI 05-057

hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400

scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000

data_processing: Affymetrix GCOS 1.2

source_name: Monocyte derived dendritic cells

label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA

growth_protocol: CD14+ cells from PBMC were cultured for five days in 6-well plates in RPMI, 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 1,000 U/ml. On day 5 monocyte-derived dendritic cells were harvested and replated at 0.5 106 cells/ml (1.5 106 cells/well).

extract_protocol: cells were harvested and lysed using TRIzol (Invitrogen).

treatment_protocol: cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 0.5 µg/ml S. abortus equi S-form LPS, pure TLR4 agonist (Alexis), together with 20 µg/ml CyP (Cyanobacterial Product) for 3h

tag: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)


title: Drosophila_acute_response_5

city: Raleigh

first: Tatiana

middle: V

last: Morozova

state: NC

address: campus box 7617

department: zoology

institute: NCSU

description: Overall design:  We collected 3-5 day old Canton S flies either without exposure to ethanol (control group), immediately after passage through the inebriometer, or from a population that had developed tolerance 2h after the initial ethanol exposure.

hyb_protocol: Following fragmentation, 10 mkg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: scale factor 2.342

label: Biotinylated cRNA

organism: Drosophila melanogaster

source_name: whole body flies, after single exposure to ethanol

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

growth_protocol: single ethanol exposure

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

treatment_protocol: single ethanol exposure

tag: 3-5 day old male Canton S flies after single exposure to ethanol


title: 1% dmso batch 2

source_name: 1% dmso batch 2


title: LPS 3hr 2

description: This sample is also known as IOSI 05-056

treatment_protocol: cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 0.5 µg/ml S. abortus equi S-form LPS, pure TLR4 agonist (Alexis), for 3h


title: LPS + CyP 3hr 1

description: This sample is also known as IOSI 05-052


title: CTR 2

description: This sample is also known as IOSI 05-054

treatment_protocol: cells were plated in fresh medium and incubated for 4h at 37°C. Cells were left untreated for additional 3h.


title: Drosophila_acute_response_4

data_processing: scale factor 2.046


title: CTR 1

description: This sample is also known as  IOSI 05-049


title: CyP 3hr 1

description: This sample is also known as IOSI 05-050

treatment_protocol: cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 20 µg/ml CyP (Cyanobacterial Product), for 3h


title: Drosophila_tolerance_1

data_processing: scale factor 2.386

source_name: whole body flies from a population that had developed tolerance 2h after the initial ethanol exposure

growth_protocol: flies exposed to ethanol twice with 2 h interval

tag: 3-5 day old male Canton S flies from a population that had developed tolerance 2h after the initial ethanol exposure


title: Drosophila_tolerance_4

data_processing: scale factor 2.590

source_name: whole body flies from a population that had developed tolerance 2h after the initial ethanol exposure.

treatment_protocol: flies exposed to ethanol twice with 2 h interval


title: retroperitoneal adipose tissue, Day 1, CLA treat

description: Gene expression data from retroperitoneal adipose tissue of C57BK/6J mice fed 0.5% trans-10 cis-12 conjugated linoleic acid.

source_name: mouse retroperitoneal fat pad


title: CyP 3hr 2

description: This sample is also known as IOSI 05-055


title: CyP 1hr 1

description: This sample is also known as IOSI 05-053

treatment_protocol: cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 20 µg/ml CyP (Cyanobacterial Product), for 1h


title: CyP 1hr 2

description: This sample is also known as  IOSI 05-058


title: Drosophila_acute_response_3

data_processing: scale factor 2.045


title: Drosophila_tolerance_3

data_processing: scale factor 2.395

tag: 3-5 day old male Canton S flies from a population that had developed tolerance 2h after the initial ethanol exposure.


title: LPS 3hr 1

description: This sample is also known as IOSI 05-051


title: Drosophila_acute_response_2

data_processing: scale factor 2.098


title: Drosophila_acute_response_1

data_processing: scale factor 2.235


title: Drosophila_control_3

data_processing: scale factor 2.567

source_name: whole body flies, control, without exposure to ethanol

growth_protocol: without exposure to ethanol

treatment_protocol: without exposure to ethanol

tag: 3-5 day old male Canton S flies without exposure to ethanol


title: Drosophila_control_4

data_processing: scale factor 2.557


title: Drosophila_tolerance_5

data_processing: scale factor 2.575


title: Drosophila_control_5

data_processing: scale factor 3.037


title: Drosophila_ control_2

data_processing: scale factor 1.951

source_name: whole body flies, control

tag: 3-5 day old male, whole body,  Canton S flies without exposure to ethanol


title: f2#359 versus pool Mouse Liver

city: Los Angeles

first: Leslie

last: Ingram-drake

state: CA

department: Medicine/MIMG/Human Genetics

institute: UCLA

description: Livers from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

data_processing: Arrays were quantified on the basis of spot intensity relative to background (Qhyb program, Rosetta), adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to an error model to determine significance (type I error).  Gene expression is reported as the ratio of the mean log10 intensity (mlratio) relative to the pool derived from 150 mice randomly selected from the F2 population. Normalized values are the reported as the ratio of the mlratio relative to the pool.

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female

source_name: pool

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: f2#357 versus pool Mouse Liver


title: Drosophila_tolerance_2

data_processing: scale factor 1.932

tag: pulation that had developed tolerance 2h after the initial ethanol exposure


title: Drosophila_control_1

description: Gene expression data from control flies without ethanol exposure

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 500. Scale factor = 2.022

source_name: whole body flies, without ethanol exposure

tag: Canton S co-isogenic control flies, without ethanol exposure, rep 1


title: f2#353 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male


title: f2#354 versus pool Mouse Liver


title: f2#356 versus pool Mouse Liver


title: f2#358 versus pool Mouse Liver


title: f2#351 versus pool Mouse Liver


title: f2#355 versus pool Mouse Liver


title: f2#348 versus pool Mouse Liver


title: f2#350 versus pool Mouse Liver


title: f2#349 versus pool Mouse Liver


title: colorectal tumor c381

city: Helsinki

first: Antti

last: Kokko

address: POBOX 63 (Haartmaninkatu 8)

department: Dept of Medical Genetics

country: Finland

institute: University of Helsinki

description: serrated colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, female, Proximal Location , Tumor Grade 2

data_processing: Affymetrix Microarray Suite version 5.0

source_name: cololrectal tumor

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

extract_protocol: colon tumor samples.Total RNA extracted from the fresh frozen tumors using Trizol reagent (GibcoBRL) an purified using RNeasy kit (Qiagen).

tag: tumor tissue


title: retroperitoneal adipose tissue, Day 4, CLA treat

data_processing: The data were analyzed with robust multi-array analysis RMA.  The RMA signal values wre log2 transformed.

tag: Age


title: f2#343 versus pool Mouse Liver


title: f2#345 versus pool Mouse Liver


title: f2#342 versus pool Mouse Liver


title: f2#340 versus pool Mouse Liver


title: f2#336 versus pool Mouse Liver


title: f2#346 versus pool Mouse Liver


title: f2#338 versus pool Mouse Liver


title: f2#339 versus pool Mouse Liver


title: f2#334 versus pool Mouse Liver


title: f2#335 versus pool Mouse Liver


title: f2#324 versus pool Mouse Liver


title: f2#341 versus pool Mouse Liver


title: f2#329 versus pool Mouse Liver


title: f2#323 versus pool Mouse Liver


title: f2#326 versus pool Mouse Liver


title: f2#320 versus pool Mouse Liver


title: f2#327 versus pool Mouse Liver


title: f2#318 versus pool Mouse Liver


title: Large Scale Identification of DNaseI Hypersensitive Regions in Genomic DNA

type: genomic

city: Seattle

first: Michael

middle: Scott

last: Kuehn

state: WA

address: 1705 NE Pacific St #K-357

department: Genome Sciences

institute: University of Washington

description:
Digestion of purified GM06990c nuclei with low levels of DNaseI results
in the release of low mw DNA fragments adjoining multiple DNaseI cut
sites.  These fragments were enriched using high speed centrifugation
through sucrose step gradients.  The small fragments were purified then
labeled using random primer extension with Cy5 labeled random heximers.

data_processing: Data values are the log ratio of red and green channel intensities, scaled by the tukey-biweight mean of array control probes

molecule: genomic DNA

source_name: GM06990c B-Lymphocytes

tag: Total genomic DNA (Control).  Fragmented by DNaseI. Labeled using primer extension with cy3 labeled random hexamers.

tag: DNaseI hypersensitive enriched fraction.  HS sites enriched by sucrose gradient fractionation.  DNA labeled using primer extension with cy5 labeled random hexamers.


title: f2#316 versus pool Mouse Liver


title: f2#322 versus pool Mouse Liver


title: f2#332 versus pool Mouse Liver


title: f2#328 versus pool Mouse Liver


title: f2#321 versus pool Mouse Liver


title: f2#312 versus pool Mouse Liver


title: f2#311 versus pool Mouse Liver


title: f2#330 versus pool Mouse Liver


title: f2#317 versus pool Mouse Liver


title: f2#303 versus pool Mouse Liver


title: f2#313 versus pool Mouse Liver


title: f2#306 versus pool Mouse Liver


title: f2#314 versus pool Mouse Liver


title: f2#294 versus pool Mouse Liver


title: f2#308 versus pool Mouse Liver


title: f2#302 versus pool Mouse Liver


title: f2#310 versus pool Mouse Liver


title: f2#296 versus pool Mouse Liver


title: f2#300 versus pool Mouse Liver


title: f2#295 versus pool Mouse Liver


title: f2#291 versus pool Mouse Liver


title: f2#325 versus pool Mouse Liver


title: f2#307 versus pool Mouse Liver


title: f2#352 versus pool Mouse Liver


title: f2#309 versus pool Mouse Liver


title: f2#305 versus pool Mouse Liver


title: f2#304 versus pool Mouse Liver


title: f2#290 versus pool Mouse Liver


title: f2#299 versus pool Mouse Liver


title: f2#281 versus pool Mouse Liver


title: f2#276 versus pool Mouse Liver


title: f2#292 versus pool Mouse Liver


title: f2#289 versus pool Mouse Liver


title: f2#277 versus pool Mouse Liver


title: f2#270 versus pool Mouse Liver


title: f2#282 versus pool Mouse Liver


title: f2#278 versus pool Mouse Liver


title: f2#271 versus pool Mouse Liver


title: f2#301 versus pool Mouse Liver


title: f2#280 versus pool Mouse Liver


title: f2#275 versus pool Mouse Liver


title: f2#272 versus pool Mouse Liver


title: f2#274 versus pool Mouse Liver


title: f2#267 versus pool Mouse Liver


title: f2#287 versus pool Mouse Liver


title: f2#268 versus pool Mouse Liver


title: f2#288 versus pool Mouse Liver


title: f2#315 versus pool Mouse Liver


title: f2#285 versus pool Mouse Liver


title: f2#265 versus pool Mouse Liver


title: f2#298 versus pool Mouse Liver


title: f2#269 versus pool Mouse Liver


title: f2#279 versus pool Mouse Liver


title: f2#263 versus pool Mouse Liver


title: f2#264 versus pool Mouse Liver


title: f2#284 versus pool Mouse Liver


title: f2#246 versus pool Mouse Liver


title: f2#257 versus pool Mouse Liver


title: f2#259 versus pool Mouse Liver


title: f2#256 versus pool Mouse Liver


title: f2#244 versus pool Mouse Liver


title: f2#254 versus pool Mouse Liver


title: f2#240 versus pool Mouse Liver


title: f2#245 versus pool Mouse Liver


title: f2#242 versus pool Mouse Liver


title: f2#249 versus pool Mouse Liver


title: f2#243 versus pool Mouse Liver


title: f2#266 versus pool Mouse Liver


title: f2#248 versus pool Mouse Liver


title: f2#250 versus pool Mouse Liver


title: f2#253 versus pool Mouse Liver


title: f2#239 versus pool Mouse Liver


title: f2#237 versus pool Mouse Liver


title: f2#247 versus pool Mouse Liver


title: f2#238 versus pool Mouse Liver


title: f2#236 versus pool Mouse Liver


title: f2#251 versus pool Mouse Liver


title: f2#261 versus pool Mouse Liver


title: f2#234 versus pool Mouse Liver


title: f2#235 versus pool Mouse Liver


title: f2#241 versus pool Mouse Liver


title: f2#347 versus pool Mouse Liver


title: f2#228 versus pool Mouse Liver


title: f2#231 versus pool Mouse Liver


title: f2#230 versus pool Mouse Liver


title: f2#233 versus pool Mouse Liver


title: f2#217 versus pool Mouse Liver


title: f2#224 versus pool Mouse Liver


title: f2#225 versus pool Mouse Liver


title: f2#219 versus pool Mouse Liver


title: f2#215 versus pool Mouse Liver


title: f2#210 versus pool Mouse Liver


title: f2#232 versus pool Mouse Liver


title: f2#216 versus pool Mouse Liver


title: f2#227 versus pool Mouse Liver


title: f2#208 versus pool Mouse Liver


title: f2#213 versus pool Mouse Liver


title: f2#214 versus pool Mouse Liver


title: f2#209 versus pool Mouse Liver


title: f2#218 versus pool Mouse Liver


title: f2#222versus pool Mouse Liver


title: f2#212 versus pool Mouse Liver


title: f2#221 versus pool Mouse Liver


title: f2#223 versus pool Mouse Liver


title: f2#203 versus pool Mouse Liver


title: f2#220 versus pool Mouse Liver


title: f2#226 versus pool Mouse Liver


title: f2#198 versus pool Mouse Liver


title: f2#192 versus pool Mouse Liver


title: f2#197 versus pool Mouse Liver


title: f2#189 versus pool Mouse Liver


title: f2#191 versus pool Mouse Liver


title: f2#190 versus pool Mouse Liver


title: f2#200 versus pool Mouse Liver


title: f2#199 versus pool Mouse Liver


title: f2#201 versus pool Mouse Liver


title: f2#185 versus pool Mouse Liver


title: f2#195 versus pool Mouse Liver


title: f2#186 versus pool Mouse Liver


title: f2#196 versus pool Mouse Liver


title: f2#182 versus pool Mouse Liver


title: f2#194 versus pool Mouse Liver


title: f2#181 versus pool Mouse Liver


title: f2#183 versus pool Mouse Liver


title: f2#179 versus pool Mouse Liver


title: f2#187 versus pool Mouse Liver


title: f2#184 versus pool Mouse Liver


title: f2#180 versus pool Mouse Liver


title: f2#207 versus pool Mouse Liver


title: f2#188 versus pool Mouse Liver


title: f2#178 versus pool Mouse Liver


title: f2#175 versus pool Mouse Liver


title: f2#176 versus pool Mouse Liver


title: brain_OFC_control C_mr217

city: Cambridge

first: Sabine

last: Bahn

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridised to Affymetrix Human Genome 133A GeneChips for 16 hours at 45oC with constant rotation at 60rpm. Chips were washed and stained according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Affymetrix HG-U133A GeneChips were scanned with the Agilent GeneArray Scanner

data_processing: The raw data (CEL files) were read into R statistical package and normalised using the robust multi-chip average (RMA) method (Irizarray et al, 'Exploration, normalization and summaries of high density oligonucleotide array probe level data', Biostatistics, 2003).

label: Biotin

source_name: human post-mortem brain tissue, healthy control

label_protocol: Double-stranded cDNA was synthesised from 5 micrograms of total RNA using Superscript II double-stranded cDNA synthesis kit (Invitrogen, USA), purified, then in-vitro transcribed and labelled using BioArray HighYield RNA transcript Labeling Kit (Enzo Life Sciences, USA)

extract_protocol: Total RNA was isolated from human postmortem brain tissue using Trizol (Invitrogen, USA) or Tri reagent (Sigma, UK) total RNA isolation kits according to the manufacturer's instructions.

value: Healthy control

tag: Age (years)

tag: Gender

value: Female

tag: Age of onset (years)

tag: Duration of illness (years)

tag: Brain pH

tag: Post mortem interval (hours)

tag: Side of brain

value: Right

tag: Fluphenazine mg. Equivalents

tag: Lithium treatment

tag: Valproate treatment

tag: Electroconvulsive therapy

tag: Suicide

value: No

tag: Drug abuse (ratings scale

value: 0 (no use) to 5 (heavy use)):1

tag: Alcohol abuse (ratings scale

value: 0 (no use) to 6 (heavy use)):0


title: f2#170 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: brain_OFC_control C_mr96

value: Left

value: 0 (no use) to 5 (heavy use)):0


title: brain_OFC_control C_mr381

value: Male


title: f2#165 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female


title: f2#169 versus pool Mouse Liver


title: f2#164 versus pool Mouse Liver


title: f2#171 versus pool Mouse Liver


title: f2#172 versus pool Mouse Liver


title: f2#162 versus pool Mouse Liver


title: f2#160 versus pool Mouse Liver


title: f2#177 versus pool Mouse Liver


title: brain_OFC_control C_mr231

tag: Age (years)


title: f2#168 versus pool Mouse Liver


title: f2#173 versus pool Mouse Liver


title: brain_OFC_control C_mr350

tag: Gender

value: 0 (no use) to 6 (heavy use)):1


title: f2#163 versus pool Mouse Liver


title: f2#159 versus pool Mouse Liver


title: f2#174 versus pool Mouse Liver


title: f2#161 versus pool Mouse Liver


title: f2#167 versus pool Mouse Liver


title: brain_OFC_control C_mr216

tag: Age of onset (years)


title: f2#158 versus pool Mouse Liver


title: f2#157 versus pool Mouse Liver


title: brain_OFC_control C_mr202

tag: Duration of illness (years)


title: f2#156 versus pool Mouse Liver


title: f2#153 versus pool Mouse Liver


title: f2#148 versus pool Mouse Liver


title: f2#149 versus pool Mouse Liver


title: f2#155 versus pool Mouse Liver


title: f2#154 versus pool Mouse Liver


title: f2#286 versus pool Mouse Liver


title: f2#146 versus pool Mouse Liver


title: f2#152 versus pool Mouse Liver


title: brain_OFC_bipolar B_mr89

source_name: human post-mortem brain tissue, bipolar disorder

value: Bipolar disorder

tag: Brain pH

value: Yes

value: 0 (no use) to 5 (heavy use)):3

value: 0 (no use) to 6 (heavy use)):2


title: brain_OFC_control C_mr169

tag: Post mortem interval (hours)

value: 0 (no use) to 5 (heavy use)):2


title: brain_OFC_bipolar B_mr421

tag: Side of brain

value: 0 (no use) to 6 (heavy use)):3


title: brain_OFC_bipolar B_mr93

tag: Fluphenazine mg. Equivalents

value: 0 (no use) to 5 (heavy use)):5


title: brain_OFC_control C_mr170

value: Healthy control

tag: Lithium treatment


title: brain_OFC_bipolar B_mr351

value: Female

tag: Valproate treatment

value: 0 (no use) to 6 (heavy use)):5


title: brain_OFC_bipolar B_mr384

value: No

tag: Electroconvulsive therapy

value: Yes (5 treatments)


title: brain_OFC_control C_mr131

tag: Suicide


title: brain_OFC_bipolar B_mr94

value: Right

tag: Drug abuse (ratings scale


title: brain_OFC_bipolar B_mr91

value: 0 (no use) to 5 (heavy use)):4

tag: Alcohol abuse (ratings scale

value: 0 (no use) to 6 (heavy use)):6


title: f2#151 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male


title: f2#147 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: f2#145 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female


title: brain_OFC_bipolar B_mr233

tag: Age (years)

value: Male

value: Left

value: 0 (no use) to 5 (heavy use)):0


title: brain_OFC_bipolar B_mr221

value: Bipolar disorder

tag: Gender

value: Yes

value: 0 (no use) to 6 (heavy use)):0


title: f2#142 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr945

tag: Age of onset (years)


title: f2#143 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr871

tag: Duration of illness (years)


title: brain_DLPFC_bipolar C_mr869

tag: Brain pH


title: brain_DLPFC_bipolar C_mr780

tag: Post mortem interval (hours)


title: brain_OFC_bipolar B_mr212

tag: Side of brain


title: brain_DLPFC_bipolar C_mr951

tag: Fluphenazine mg. Equivalents


title: f2#121 versus pool Mouse Liver


title: f2#127 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr700

tag: Lithium treatment

value: 0 (no use) to 5 (heavy use)):1

value: 0 (no use) to 6 (heavy use)):1


title: f2#122 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr701

tag: Valproate treatment


title: f2#141 versus pool Mouse Liver


title: f2#126 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr682

tag: Electroconvulsive therapy

value: 0 (no use) to 5 (heavy use)):3

value: 0 (no use) to 6 (heavy use)):4


title: brain_DLPFC_bipolar C_mr801

value: Healthy control

tag: Suicide


title: brain_DLPFC_bipolar C_mr677

value: Female

tag: Drug abuse (ratings scale


title: f2#124 versus pool Mouse Liver


title: f2#120 versus pool Mouse Liver


title: f2#128 versus pool Mouse Liver


title: f2#123 versus pool Mouse Liver


title: f2#252 versus pool Mouse Liver


title: brain_OFC_control C_mr206

value: No

tag: Alcohol abuse (ratings scale

value: 0 (no use) to 6 (heavy use)):2


title: brain_DLPFC_bipolar C_mr645

value: Right

value: 0 (no use) to 6 (heavy use)):3


title: f2#260 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male


title: brain_DLPFC_bipolar C_mr545


title: f2#117 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: brain_DLPFC_bipolar C_mr539


title: f2#119 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female


title: f2#116 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr544

tag: Age (years)


title: f2#166 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr538

tag: Gender


title: f2#125 versus pool Mouse Liver


title: f2#108 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr523

tag: Age of onset (years)


title: f2#114 versus pool Mouse Liver


title: f2#110 versus pool Mouse Liver


title: f2#111 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr521

tag: Duration of illness (years)


title: brain_DLPFC_bipolar C_mr540

tag: Brain pH


title: brain_DLPFC_bipolar C_mr532

tag: Post mortem interval (hours)


title: f2#105 versus pool Mouse Liver


title: f2#112 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr448

tag: Side of brain


title: brain_DLPFC_bipolar C_mr537

tag: Fluphenazine mg. Equivalents


title: f2#115 versus pool Mouse Liver


title: f2#109 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr444

tag: Lithium treatment


title: f2#104 versus pool Mouse Liver


title: f2#107 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr423

tag: Valproate treatment


title: brain_DLPFC_bipolar C_mr418

tag: Electroconvulsive therapy


title: brain_DLPFC_bipolar C_mr404

tag: Suicide


title: f2#93 versus pool Mouse Liver


title: f2#94 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr284

tag: Drug abuse (ratings scale


title: brain_DLPFC_bipolar C_mr407

tag: Alcohol abuse (ratings scale


title: f2#89 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr276


title: f2#92 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male


title: f2#91 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: f2#87 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female


title: brain_DLPFC_bipolar C_mr283

tag: Age (years)


title: f2#88 versus pool Mouse Liver


title: brain_DLPFC_bipolar C_mr275

tag: Gender


title: f2#84 versus pool Mouse Liver


title: f2#85 versus pool Mouse Liver


title: f2#86 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr953

tag: Age of onset (years)

value: 0 (no use) to 5 (heavy use)):Unknown


title: f2#79 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr950

tag: Duration of illness (years)


title: brain_DLPFC_bipolar B_mr943

tag: Brain pH


title: f2#81 versus pool Mouse Liver


title: f2#80 versus pool Mouse Liver


title: f2#82 versus pool Mouse Liver


title: f2#144 versus pool Mouse Liver


title: f2#78 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr867

value: Male

tag: Post mortem interval (hours)


title: brain_DLPFC_bipolar B_mr781

tag: Side of brain


title: brain_DLPFC_bipolar B_mr667

value: Left

tag: Fluphenazine mg. Equivalents


title: brain_DLPFC_bipolar B_mr678

tag: Lithium treatment


title: brain_DLPFC_bipolar B_mr777

tag: Valproate treatment


title: brain_DLPFC_bipolar B_mr946

tag: Electroconvulsive therapy

value: 0 (no use) to 6 (heavy use)):5


title: brain_DLPFC_bipolar B_mr697

value: Bipolar disorder

tag: Suicide


title: brain_DLPFC_bipolar B_mr646

value: Yes

tag: Drug abuse (ratings scale


title: f2#77 versus pool Mouse Liver


title: f2#75 versus pool Mouse Liver


title: f2#76 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr648

tag: Alcohol abuse (ratings scale

value: 0 (no use) to 6 (heavy use)):0


title: f2#73 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male


title: f2#72 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: brain_DLPFC_bipolar B_mr553


title: f2#74 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr547


title: brain_DLPFC_bipolar B_mr613


title: brain_DLPFC_bipolar B_mr520


title: brain_DLPFC_bipolar B_mr430


title: brain_DLPFC_bipolar B_mr426


title: f2#69 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female


title: f2#66 versus pool Mouse Liver


title: f2#64 versus pool Mouse Liver


title: f2#71 versus pool Mouse Liver


title: f2#68 versus pool Mouse Liver


title: f2#65 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr427

tag: Age (years)


title: brain_DLPFC_bipolar B_mr425

tag: Gender


title: brain_DLPFC_bipolar B_mr446

tag: Age of onset (years)


title: brain_DLPFC_bipolar B_mr409

tag: Duration of illness (years)


title: brain_DLPFC_bipolar B_mr403

tag: Brain pH


title: f2#67 versus pool Mouse Liver


title: f2#63 versus pool Mouse Liver


title: f2#62 versus pool Mouse Liver


title: f2#59 versus pool Mouse Liver


title: f2#60 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr304

tag: Post mortem interval (hours)

value: 0 (no use) to 6 (heavy use)):Unknown


title: brain_DLPFC_bipolar B_mr279

tag: Side of brain


title: f2#57 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr676

tag: Fluphenazine mg. Equivalents


title: f2#56 versus pool Mouse Liver


title: f2#61 versus pool Mouse Liver


title: s1n0t3r3

city: Bethesda

first: Shuibang

last: Wang

state: MD

address: 10 Center Drive

department: Critical Care Medicine Dept

institute: Clinical Center

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 180 min treatment of GSH. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

source_name: THP-1 Cells

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 180 min treatment of GSH"


title: s1n0t3r4


title: f2#53 versus pool Mouse Liver


title: f2#54 versus pool Mouse Liver


title: f2#58 versus pool Mouse Liver


title: f2#55 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr288

tag: Lithium treatment

tag: Valproate treatment


title: brain_DLPFC_bipolar B_mr282

tag: Electroconvulsive therapy

tag: Suicide


title: s1n0t3r2


title: s1n0t3r1


title: brain_DLPFC_bipolar B_mr281

tag: Drug abuse (ratings scale

tag: Alcohol abuse (ratings scale


title: f2#51 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: f2#50 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male


title: brain_DLPFC_bipolar C_mr546

tag: Age (years)

value: 0 (no use) to 5 (heavy use)):0


title: s1n0t2r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 90 min treatment of GSH. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 90 min treatment of GSH"


title: f2#52 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female


title: s1n0t2r3


title: s1n0t1r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 45 min treatment of GSH. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 45 min treatment of GSH"


title: s1n0t2r2


title: f2#47 versus pool Mouse Liver


title: f2#49 versus pool Mouse Liver


title: s1n0t1r3


title: f2#48 versus pool Mouse Liver


title: s1n1t3r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 180 min treatment of GSNO. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 180 min treatment of GSNO"


title: f2#46 versus pool Mouse Liver


title: s1n0t1r1


title: f2#45 versus pool Mouse Liver


title: s1n0t2r1


title: s1n1t3r1


title: s1n1t3r2


title: s1n0t1r2


title: f2#40 versus pool Mouse Liver


title: s1n1t3r3


title: f2#41 versus pool Mouse Liver


title: f2#39 versus pool Mouse Liver


title: f2#43 versus pool Mouse Liver


title: f2#42 versus pool Mouse Liver


title: s1n1t2r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 90 min treatment of GSNO. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 90 min treatment of GSNO"


title: f2#37 versus pool Mouse Liver


title: f2#70 versus pool Mouse Liver


title: f2#83 versus pool Mouse Liver


title: s1n1t2r2


title: f2#36 versus pool Mouse Liver


title: s1n1t2r1


title: s1n1t2r3


title: f2#35 versus pool Mouse Liver


title: s1n1t1r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 45 min treatment of GSNO. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB and then 45 min treatment of GSNO"


title: f2#34 versus pool Mouse Liver


title: s1n0t0r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D in the presence of SB"


title: f2#33 versus pool Mouse Liver


title: f2#28 versus pool Mouse Liver


title: f2#229 versus pool Mouse Liver


title: s1n1t1r1


title: s1n1t1r2


title: f2#32 versus pool Mouse Liver


title: s0n1t3r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 180 min treatment of GSNO. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 180 min treatment of GSNO"


title: s1n0t0r2


title: s1n1t1r3


title: f2#30 versus pool Mouse Liver


title: s1n0t0r1


title: s1n0t0r3


title: f2#26 versus pool Mouse Liver

description: Livers from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57B1/J6 and C3H/HeJ on ApoE null backgrounds.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: f2#29 versus pool Mouse Liver


title: f2#25 versus pool Mouse Liver


title: s0n1t3r3


title: s0n1t3r1


title: f2#24 versus pool Mouse Liver


title: s0n1t3r2


title: s0n1t2r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 90 min treatment of GSNO. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 90 min treatment of GSNO"


title: f2#27 versus pool Mouse Liver


title: f2#21 versus pool Mouse Liver


title: s0n1t1r2

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 45 min treatment of GSNO. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 45 min treatment of GSNO"


title: f2#17 versus pool Mouse Liver


title: f2#20 versus pool Mouse Liver


title: f2#19 versus pool Mouse Liver


title: f2#14 versus pool Mouse Liver


title: f2#16 versus pool Mouse Liver


title: s0n1t2r1


title: f2#15 versus pool Mouse Liver


title: f2#18 versus pool Mouse Liver


title: s0n0t3r1

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 180 min treatment of GSH. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 180 min treatment of GSH"


title: s0n1t2r3


title: s0n1t1r1


title: f2#13 versus pool Mouse Liver


title: s0n1t2r2


title: f2#10 versus pool Mouse Liver


title: s0n0t3r2


title: s0n1t1r4


title: s0n0t2r3

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 90 min treatment of GSH. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 90 min treatment of GSH"


title: s0n0t3r3


title: f2#12 versus pool Mouse Liver


title: s0n0t1r3

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 45 min treatment of GSH. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 45 min treatment of GSH"


title: f2#23 versus pool Mouse Liver


title: s0n0t2r2


title: f2#11 versus pool Mouse Liver


title: f2#7 versus pool Mouse Liver


title: s0n0t2r1

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 90 min treatment of GSH.The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."


title: f2#9 versus pool Mouse Liver


title: brain_DLPFC_bipolar B_mr420

tag: Gender

tag: Age of onset (years)

tag: Duration of illness (years)

tag: Brain pH

tag: Post mortem interval (hours)

tag: Side of brain

tag: Fluphenazine mg. Equivalents

value: Unknown

tag: Lithium treatment

tag: Valproate treatment

tag: Electroconvulsive therapy

value: Yes (60 treatments)

tag: Suicide

tag: Drug abuse (ratings scale

tag: Alcohol abuse (ratings scale


title: low temperature stress, logarithmic phase

city: Hannover

first: Burkhard

last: Tummler

address: Carl-Neuberg-Str. 1

country: Germany

institute: Medizinische Hochschule Hannover

description: Data analysis was performed with the data warehouse and interpretation software package M-CHiPS (http://www.mchips.org)

hyb_protocol: For each condition, 3 arrays were hybridised independently, two samples with a Cy3-labelled cDNA from the stress condition (tableno197 and tableno198), two samples with a Cy5-labelled control cDNA (tableno193 and tableno194), one sample with Cy5-labelled cDNA from the stress condition (tableno200) and one sample with Cy3-labelled control cDNA (tableno196). (See supplementary materials).

scan_protocol: Fluorescence signals were detected on a ScanArray5000 unit (Packard, Billerica, USA) and analysed with the GenePix software package (Axon Instruments, Union City, USA).

data_processing: stringent min-max separation criterion followed by subsequent correspondence analysis of the intensity ratios

label: Cy3, Cy5

organism: Pseudomonas putida

source_name: liquid bacterial culture

label_protocol: For labelling of the cDNA to be used for transcriptome analyses, the mRNA samples were pooled and random priming was performed on 500 ng cDNA in the presence of 15 mM dNTP (A,G,T) and 25 mM Cy3 or Cy5 labelled dCTP (Amersham-Pharmacia, Amersham, UK)

growth_protocol:
growth phase: logarithmic (OD600  0.8)
condition: control growth in liquid ABC minimal medium (pH 7.5) with 15 mM sodium benzoate at 26C

tag: strain

growth_protocol:
growth phase: logarithmic (OD600  0.8)
condition: stressed growth in liquid ABC minimal medium (pH 7.5) with 15 mM sodium benzoate at 4C


title: f2#8 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: low temperature stress, stationary phase

hyb_protocol: For each condition, 4 arrays were hybridised independently, two samples with a Cy3-labelled cDNA from the stress condition (tableno205 and tableno206), two samples with a Cy5-labelled control cDNA (tableno201 and tableno202), two samples with Cy5-labelled cDNA from the stress condition (tableno207 and tableno208) and two sample with Cy3-labelled control cDNA (tableno203 and tableno204). (See supplementary materials).

growth_protocol:
growth phase: stationary (OD600  3.0)
condition: control growth in liquid ABC minimal medium (pH 7.5) with 15 mM sodium benzoate at 26C

growth_protocol:
growth phase: stationary (OD600  3.0)
condition: stressed growth in liquid ABC minimal medium (pH 7.5) with 15 mM sodium benzoate at 4C


title: s0n0t2r4

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 90 min treatment of GSH"


title: s0n0t1r2

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 45 min treatment of GSH"


title: sodium benzoate stress, stationary phase

hyb_protocol: For each condition, 3 arrays were hybridised independently, two samples with a Cy3-labelled cDNA from the stress condition (tableno178 and tableno179), two samples with a Cy5-labelled control cDNA (tableno174 and tableno175), one sample with Cy5-labelled cDNA from the stress condition (tableno180) and one sample with Cy3-labelled control cDNA (tableno176). (See supplementary materials).

growth_protocol:
growth phase: stationary (OD600  3.0)
condition: stressed growth in liquid ABC minimal medium (pH 7.5) with 45 mM sodium benzoate at 26C


title: f2#6 versus pool Mouse Liver


title: s0n0t1r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 45 min treatment of GSH.The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."


title: s0n0t3r4

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 180 min treatment of GSH"


title: s0n0t1r1


title: sodium benzoate stress, logarithmic phase

hyb_protocol: For each condition, 3 arrays were hybridised independently, two samples with a Cy5-labelled cDNA from the stress condition (tableno172 and tableno173), two samples with a Cy3-labelled control cDNA (tableno168 and tableno169), one sample with Cy3-labelled cDNA from the stress condition (tableno170) and one sample with Cy5-labelled control cDNA (tableno167). (See supplementary materials).

growth_protocol:
growth phase: logarithmic (OD600  0.8)
condition: stressed growth in liquid ABC minimal medium (pH 7.5) with 45 mM sodium benzoate at 26C


title: f2#5 versus pool Mouse Liver


title: s0n0t0r2

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures."

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D "


title: s0n0t0r4

description: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D. The cells were collected, and total RNA was extracted, labeled and hybridized to human U133A microarrays following standard Affymetrix procedures. "


title: 0.8M urea stress, stationary phase

hyb_protocol: For each condition, 4 arrays were hybridised independently, two samples with a Cy3-labelled cDNA from the stress condition (tableno162 and tableno163), two samples with a Cy5-labelled control cDNA (tableno158 and tableno159), two samples with Cy5-labelled cDNA from the stress condition (tableno164 and tableno165) and two sample with Cy3-labelled control cDNA (tableno160 and tableno161). (See supplementary materials).

growth_protocol:
growth phase: stationary (OD600  3.0)
condition: stressed growth in liquid ABC minimal medium (pH 7.5) with 15 mM sodium benzoate and 0.8M urea at 26C


title: 0.8M urea stress, logarithmic phase

hyb_protocol: For each condition, 3 arrays were hybridised independently, two samples with a Cy3-labelled cDNA from the stress condition (tableno154 and tableno155), two samples with a Cy5-labelled control cDNA (tableno150 and tableno151), one sample with Cy5-labelled cDNA from the stress condition (tableno156) and one sample with Cy3-labelled control cDNA (tableno152). (See supplementary materials).

growth_protocol:
growth phase: logarithmic (OD600  0.8)
condition: stressed growth in liquid ABC minimal medium (pH 7.5) with 15 mM sodium benzoate and 0.8M urea at 26C


title: s0n0t0r3


title: f2#4 versus pool Mouse Liver


title: f2#3 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:Female


title: Sample7_111004_III_3+5-

status: Public on Jul 26 2006

city: Dallas

first: Eric

middle: J.

last: Hansen

state: TX

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: UT Southwestern Medical Center

description: Array hybridized with cDNA labeled with Cy5 (Iron-restricted) and Cy3 (Iron-replete).  cDNA was generated from total RNA with genome-directed primers (GDPs).

data_processing: Gene Pix Pro5.0 and Acuity 4.0

organism: Francisella tularensis

source_name: Ft LVS iron-restricted

tag: F.t. LVS grown in MH-/DF iron-restricted condition

source_name: Ft LVS iron-replete

tag: F.t. LVS grown in MH+ iron-replete condition


title: Sample2_101504_3+5-


title: f2#2 versus pool Mouse Liver


title: Sample3_102704_3+5-

tag: F. t. LVS grown in MH-/DF iron-restricted condition


title: T21_TNB_4

city: Stillwater

first: Tingting

last: Weng

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

description: To understand molecular mechanisms of the late stage of rat lung development, we investigated gene expression profiling of lungs at gestational day 18, 19, 20, 21, new born, and adult rats using in-house rat DNA microarray containing 6,000 known genes and 4,000 ESTs. A loop microarray design were used as following: D18-D19-D20-D21-NB-AD-D18.

data_processing: LOWESS normalization

label: Alexa 546

organism: Rattus norvegicus

source_name: Fetal day 21 rat lung tissue

tag: Fetal day 21 rat lung tissue labeled with alexa 546

label: Alexa 647

source_name: New born rat lung tissue

tag: New born rat lung tissue labeled with alexa 647


title: T20_T21_3

source_name: Fetal day 20 rat lung tissue

tag: Fetal day 20 rat lung tissue labeled with alexa 546

tag: Fetal day 21 rat lung tissue labeled with alexa 647


title: T18_T19_3

source_name: Fetal day 18 rat lung tissue

tag: Fetal day 18 rat lung tissue labeled with alexa 546

source_name: Fetal day 19 rat lung tissue

tag: Fetal day 19 rat lung tissue labeled with alexa 647


title: T18_T19_4


title: T21_T20_4

tag: Fetal day 20 rat lung tissue labeled with alexa 647


title: s0n0t0r1


title: T20_T19_3


title: T18_TAD_3

source_name: Adult rat lung tissue

tag: Adult rat lung tissue labeled with alexa 647


title: TNB_T21_3

tag: New born rat lung tissue labeled with alexa 546


title: TAD_TNB_3

tag: Adult rat lung tissue labeled with alexa 546


title: TNB_TAD_3


title: TNB_T21_4


title: T21_TNB_3


title: T19_T18_3

tag: Fetal day 19 rat lung tissue labeled with alexa 546

tag: Fetal day 18 rat lung tissue labeled with alexa 647


title: Sample4_102704_3+5-I


title: TNB_TAD_4


title: TAD_T18_3


title: T20_T21_2


title: f2#22 versus pool Mouse Liver

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks Gender:male

tag: Strain:C57BL/J6 and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: T19_T20_3


title: T18_T19_2


title: T21_T20_2


title: T20_T21_4


title: T20_T19_2


title: GM15816

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: RNA was extracted from lymphoblastoid cells from heterozygous carriers of Nijmegen Breakage Syndrome and non-carriers.  The cells were grown at a density of 5 x 105 cells/ ml in RPMI 1640 with 15% FBS, 100 U penicillin/ml, 100 ugm streptomycin sulfate/ml, 1% L-glutamine at 37°C in a humidified 5% CO2 chamber.

source_name: Nijmegen Breakage Syndrome carrier lymphoblastoid cell line

label_protocol: standard Affymetrix procedures

tag: Coriel cell line repository identifier


title: T19_T20_2


title: T18_TAD_2


title: T19_T18_2


title: GM15821


title: TNB_TAD_2


title: TNB_T21_2


title: T21_TNB_2


title: TAD_T18_2


title: T20_T21_1


title: T18_T19_1

tag: Fetal day 18 rat lung tissue labeled with alexa546


title: TNB_TAD_1

tag: New born rat lung tissue labled with alexa 546


title: T18_TAD_1


title: s0n1t1r3

tag: "THP-1 cells prestimulated with LPS for 4 h, followed by 30 min treatment of actinomycin D and then 45 min treatment of GSNO"


title: TAD_TNB_2

tag: New born rat lung tissue labeled with alexa 647


title: GM15820


title: GM15811


title: TNB_T21_1


title: GM15815


title: GM15810


title: T19_T18_1


title: T21_T19_1

tag: Fetal day 21 rat lung tissue labeled with alexa 546


title: TAD_TNB_1


title: T21_T20_1


title: T21_TNB_1


title: TAD_T18_1


title: T21_T20_3


title: T18_T19

description: To understand molecular mechanisms of the late stage of fetal lung development, we investigated gene expression profiling of lungs at gestational day 18, 19, 20, 21, new born, and adult rats using in-house rat DNA microarray containing 6,000 known genes and 4,000 ESTs. A loop microarray design were used.

tag: Fetal day 18 rat lung tissue labeled with Alexa 546

tag: Fetal day 19 rat lung tissue labeled with Alexa 647


title: GM12912_rep1

source_name: lymphoblastoid cell line


title: GM12912_rep2


title: T19_T20_1

tag: Fetal day 21 rat lung tissue labeled with alexa 647


title: GM12911_rep1


title: GM15841


title: GM15805


title: GM08037


title: GM08036


title: GM12911_rep2


title: TNB_TAD

tag: New born rat lung tissue labeled with Alexa 546

tag: Adult rat lung tissue labeled with Alexa 647


title: GM15806


title: GM12865_rep1


title: GM12865_rep2


title: GM12817_rep2


title: GM12817_rep1


title: GM12767_rep2


title: GM12767_rep1


title: T18_TAD

description: A loop Microarray design

source_name: Fetal day 18 lung tissue

tag: Fetal day 18 rat lung tissue labled with Alexa 546

tag: Adult rat lung tissue labled with Alexa 647


title: T20_T21

tag: Fetal day 20 rat lung tissue labeled with Alexa 546

tag: Fetal day 21 lung tissue labeled with Alexa 647


title: T20_T19

description: A loop Microarray design

source_name: Fetal day 20 lung tissue

tag: Fetal day 20 rat lung tissue labled with Alexa 546

source_name: Fetal day 19 lung tissue

tag: Fetal day 19 rat lung tissue labled with Alexa 647


title: Female STAT5b KO/Male STAT5b KO #3 from STAT5b KO study

city: Boston

first: David

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The genetic expression profile for a pool of 3 females without STAT5b expression and a pool of 3 males without STAT5b expression is given as a normalized ratio as reported from Rosetta Resolver.  The reported ratio is the average of two dye-swapped fluorescent reverse pairings.  The purpose of this comparison is to highlight the sex-specific differences in gene expression in the STAT5b KO mouse model.

data_processing: Rosetta Resolver pipeline

source_name: frozen adult female mouse liver tissue prepared using Trizol

tag: Strain

tag: Gender

tag: Tissue

value: Liver

tag: Age

value: 8-9 weeks

tag: Genotype

value: STAT5b KO

source_name: frozen adult male mouse liver tissue prepared using Trizol


title: Female STAT5b KO/Male STAT5b KO #2 from STAT5b KO study

value: Female


title: GM12740_rep2

tag: Coriel cell line repository identifier


title: T21_T20

description: A loop Microarray design

source_name: Fetal day 21 lung tissue

tag: Fetal day 21 rat lung tissue labled with Alexa 546

tag: Fetal day 20 rat lung tissue labled with Alexa 647


title: T19_T20

description: A loop Microarray design

tag: Fetal day 19 lung tissue labeled with Alexa 546

tag: Fetal day 20 lung tissue labeled with Alexa 546


title: Female STAT5b KO/Male STAT5b KO #1 from STAT5b KO study


title: TNB_T21

description: A loop Microarray design

tag: New born rat lung tissue labled with Alexa 546

tag: Fetal day 21 rat lung tissue labled with Alexa 647


title: Female STAT5b KO/Female wildtype #2 from STAT5b KO study

description: The genetic expression profile for a pool of 3 females without STAT5b expression and a pool of 3 wildtype females is given as a normalized ratio as reported from Rosetta Resolver.  The reported ratio is the average of two dye-swapped fluorescent reverse pairings.  The purpose of this comparison is to highlight the expression differences caused by the loss of STAT5b in female mouse liver gene expression.


title: T21_TNB

description: This is a loop microarray design  for fetal lung development.

tag: Fetal day 21 lung tissue labeled with Alexa546

source_name: New born lung tissue

tag: New born rat lung tissue labeled with Alexa 647


title: T19_T18

description: A loop Microarray design

tag: Fetal day 19 rat lung tissue labled with Alexa 546

tag: Fetal day 18 rat lung tissue labled with Alexa 647


title: TAD_TNB

description: A loop Microarray design

source_name: Adult lung tissue

tag: Adult rat lung tissue labled with Alexa 546

tag: New born rat lung tissue labled with Alexa 647


title: Female STAT5b KO/Female wildtype #3 from STAT5b KO study

tag: Strain

tag: Gender


title: GM07042_rep1


title: GM07042_rep2


title: GM12740_rep1


title: Female STAT5b KO/Female wildtype #1 from STAT5b KO study

tag: Tissue

tag: Age


title: Male wildtype/Male STAT5b KO #1 from STAT5b KO study

description: The genetic expression profile for a pool of 3 males and a pool of 3 males without STAT5b expression is given as a normalized ratio as reported from Rosetta Resolver.  The reported ratio is the average of two dye-swapped fluorescent reverse pairings.  The purpose of this comparison is to highlight the expression differences caused by the loss of STAT5b in male mouse liver gene expression.

tag: Genotype


title: Jurkat with Nef Biological Replicate 3

status: Public on Jul 25 2006

city: Davis

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data Jurkat cell line

data_processing: The data were analyzed with Gene Chip Operating System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method

source_name: Jurkat cell line

treatment_protocol: 10 micromolar ponasterone A

tag: Jurkat cell line transfected with SIV Nef


title: Jurkat with Nef Biological Replicate 2

description: Gene expression data Jurkat cell line


title: Male wildtype/Male STAT5b KO #3 from STAT5b KO study


title: Jurkat with Nef Biological Replicate 1

description: Gene expression data Jurkat cell line


title: GM07013_rep2

tag: Coriel cell line repository identifier


title: Male wildtype/Male STAT5b KO #2 from STAT5b KO study


title: GM07013_rep1


title: Jurkat Biological Replicate 2

description: Gene expression data Jurkat cell line

treatment_protocol: 10 micromolar pronasterone A

tag: Untransfected Jurkat cell line


title: Jurkat Biological Replicate 3

description: Gene expression data Jurkat cell line


title: Jurkat Biological Replicate 1

description: Gene expression data Jurkat cell line


title: Hardness comparison, EgSuS.8.109.gpr

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
A comparison of grain hardness between different wheat cultivars at approximately 8 DPA
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true

data_processing: Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.

organism: Triticum aestivum

source_name: Hard cultivar

tag: Hard cultivar, Biological Repl

value: 1, Technical repl:1

source_name: Soft cultivar

tag: Soft cultivar, Biological Repl


title: Hardness comparison, FaHe.8.106.gpr

description:
A comparison of grain hardness between different wheat cultivars at approximately 8 DPA
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: Hardness comparison, HeFaS.8.105.gpr


title: Hardness comparison, KuJaS.9.107.gpr


title: Hardness comparison, KuHa.9.108.gpr


title: TAD_T18

tag: Channel 1 is Alexa546 labeled cDNA of adult lung tissue

tag: Channel 2 is Alexa647 labeled cDNA of fetal day 18 lung tissue


title: Hardness comparison, CoHe.8.103.gpr


title: StratUnivRNA_2ug_5_A

city: Tampa

first: Sean

last: Yoder

state: FL

address: 12902 Magnolia Dr.

department: Molecular Genomics Core Facility

institute: Moffitt Cancer Center & Research Institute

description: Stratagene Universal Human Reference RNA

hyb_protocol: Affymetrix eukaryotic target prep

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: MAS 5.0 scaled to 500

label_protocol: Affymetrix eukaryotic target prep

extract_protocol: MAS 5.0 Signal Intensity


title: Himalaya vs 292 comparison, Hi292S_98.gpr

description:
Comparison of whole seed RNA from barley cv Himalaya and the barley Himalaya mutant 292 at approximately 15 to 20 DPA
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: true

organism: Hordeum vulgare

source_name: wild type Himalaya

tag: wild type Himalaya, Biological Repl

value: 4, Technical repl:1

source_name: Mutant 292

tag: Mutant 292, Biological Repl


title: Himalaya vs 292 comparison, Hi292_97.gpr

description:
Comparison of whole seed RNA from barley cv Himalaya and the barley Himalaya mutant 292 at approximately 15 to 20 DPA
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false

value: 3, Technical repl:1


title: Hardness comparison, CorCoS.8.104.gpr


title: StratUnivRNA_2ug_4_A

source_name: Stratagene Universal Human Reference RNA


title: Himalaya vs 292 comparison, Hi292_96.gpr

description:
Comparison of whole seed RNA from barley cv Himalaya and the barley Himalaya mutant 292 at approximately 15 to 20 DPA
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false

value: 2, Technical repl:1


title: StratUnivRNA_2ug_2_A

tag: Stratagene Universal Human Reference RNA


title: StratUnivRNA_2ug_1_A


title: 61: menin A300 from hum. Islets (4P1501 layer1)

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: ChIP DNA, menin A300 from hum. Islets (4P1501 layer1)

data_processing: Ratio of red/green

tag: Antibody:menin A300, Cell Line:hum. Islets (4P1501 layer1)

source_name: Input DNA

tag: Antibody:None, Cell Line:hum. Islets (4P1501 layer1)


title: 293: H3 K4 from HR193 (80K 40% piure)

description: ChIP DNA, H3 K4 from HR193 (80K 40% piure)

tag: Antibody:H3 K4, Cell Line:HR193 (80K 40% piure)

tag: Antibody:None, Cell Line:HR193 (80K 40% piure)


title: Grain hardness Falcon, FLR1T.12.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The late stage of development, 25-30 DPA.
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true

source_name: Falcon hard seed

tag: Falcon hard seed, Biological Repl

value: 1, Technical repl:2

source_name: Falcon soft seed

tag: Falcon soft seed, Biological Repl


title: 310: Rbbp5 from islets (HP1499)

description: ChIP DNA, Rbbp5 from islets (HP1499)

source_name: ChIP DNA, Rbbp5 from islets (HP1499)

tag: Antibody:Rbbp5, Cell Line:islets (HP1499)

tag: Antibody:None, Cell Line:islets (HP1499)


title: Himalaya vs 292 comparison, Hi292S_95.gpr

description:
Comparison of whole seed RNA from barley cv Himalaya and the barley Himalaya mutant 292 at approximately 15 to 20 DPA
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true


title: StratUnivRNA_2ug_3_A


title: 330: Rbbp5 from 90% pure islets

description: ChIP DNA, Rbbp5 from 90% pure islets

source_name: ChIP DNA, Rbbp5 from 90% pure islets

tag: Antibody:Rbbp5, Cell Line:90% pure islets

tag: Antibody:None, Cell Line:90% pure islets


title: 60: menin A300 from hum. Islets (4P1501 layer1)

source_name: ChIP DNA, menin A300 from hum. Islets (4P1501 layer1)


title: Clinical isolate #135 Up_iso135

city: Moscow

middle: Victorovich

last: Klubin

address: ul. Malaya Pirogovskaya 1a

department: Departament of molecular biology and genetics

country: Russia

institute: Research Institute of  Physico-Chemical Medicine

description: Hybridization signals were quantified with ImageQuant 5.1 software (Molecular Dynamics).

data_processing: The signals of individual spots from different arrays were normalized by comparing the signal from a gene to the total signal from all spots on the array

organism: Ureaplasma parvum

source_name: clinical isolate

tag: Clinical isolate #135


title: 289: menin from Islets H04-? (60K 50% pure)

description: ChIP DNA, menin from Islets H04-? (60K 50% pure)

tag: Antibody:menin, Cell Line:Islets H04-? (60K 50% pure)

tag: Antibody:None, Cell Line:Islets H04-? (60K 50% pure)


title: 291: MLL1 from HR193 (80K 40% piure)

description: ChIP DNA, MLL1 from HR193 (80K 40% piure)

tag: Antibody:MLL1, Cell Line:HR193 (80K 40% piure)


title: 284: Rbbp5 from HepG2

description: ChIP DNA, Rbbp5 from HepG2

source_name: ChIP DNA, Rbbp5 from HepG2

tag: Antibody:Rbbp5, Cell Line:HepG2

tag: Antibody:None, Cell Line:HepG2


title: 287: H3 K4 from HepG2

description: ChIP DNA, H3 K4 from HepG2

source_name: ChIP DNA, H3 K4 from HepG2

tag: Antibody:H3 K4, Cell Line:HepG2


title: 283: Rbbp5 from HepG2

description: ChIP DNA, Rbbp5 from HepG2


title: Clinical isolate #88 Up_iso88

tag: Clinical isolate #88


title: 290: menin from HR193 (80K 40% piure)

description: ChIP DNA, menin from HR193 (80K 40% piure)

tag: Antibody:menin, Cell Line:HR193 (80K 40% piure)


title: Grain hardness Falcon, FLR1F.12.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The late stage of development, 25-30 DPA.
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: Clinical isolate #116 Up_iso116

tag: Clinical isolate #116


title: 282: MLL1 from HepG2

description: ChIP DNA, MLL1 from HepG2

source_name: ChIP DNA, MLL1 from HepG2

tag: Antibody:MLL1, Cell Line:HepG2


title: 285: Rbbp5 from HepG2

description: ChIP DNA, Rbbp5 from HepG2


title: Clinical isolate #122 Up_iso122

tag: Clinical isolate #122


title: 280: MLL1 from HepG2

description: ChIP DNA, MLL1 from HepG2


title: Grain hardness Falcon, FLR2T.13.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The late stage of development, 25-30 DPA.
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

tag: Falcon hard seed, Biological Repl

value: 2, Technical repl:2

tag: Falcon soft seed, Biological Repl


title: 288: H3 K4 from HepG2

description: ChIP DNA, H3 K4 from HepG2


title: 281: MLL1 from HepG2

description: ChIP DNA, MLL1 from HepG2


title: Grain hardness Falcon, FLR2F.13.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The late stage of development, 25-30 DPA.
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: Clinical isolate #23 Up_iso23

tag: Clinical isolate #23


title: 286: H3 K4 from HepG2

description: ChIP DNA, H3 K4 from HepG2


title: Grain hardness Heron late, HLR1.44.gpr

description:
A comparison of Heron NIL varying in grain hardness. Samples from a late stage of endosperm development 25-30 DPA
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

source_name: Heron soft  seed

tag: Heron soft  seed, Biological Repl

source_name: Heron hard seed

tag: Heron hard seed, Biological Repl


title: Grain hardness Falcon middle, FMR2T.7.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The middle stage of development, 12-15DPA
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true


title: Grain hardness Heron late, HLR40067.gpr

description:
A comparison of Heron NIL varying in grain hardness. Samples from a late stage of endosperm development 25-30 DPA
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: false


title: Grain hardness Falcon middle, FMR2F.7A.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The middle stage of development, 12-15DPA
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: Grain hardness Falcon middle, FMR1T.06.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The middle stage of development, 12-15DPA
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: Clinical isolate #15 Up_iso15

tag: Clinical isolate #15


title: Clinical isolate #11 Up_iso11

tag: Clinical isolate #11


title: Clinical isolate #17 Up_iso17

tag: Clinical isolate #17


title: 169: Rbbp5 from HelaS3

description: ChIP DNA, Rbbp5 from HelaS3

source_name: ChIP DNA, Rbbp5 from HelaS3

tag: Antibody:Rbbp5, Cell Line:HelaS3

tag: Antibody:None, Cell Line:HelaS3


title: Grain hardness Heron late, HLR2.58.gpr

description:
A comparison of Heron NIL varying in grain hardness. Samples from a late stage of endosperm development 25-30 DPA
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: true


title: 22: menin A300 from HeLa S3

description: ChIP DNA, menin A300 from HeLa S3

source_name: ChIP DNA, menin A300 from HeLa S3

tag: Antibody:menin A300, Cell Line:HeLa S3

tag: Antibody:None, Cell Line:HeLa S3


title: 311: H3 K4 from islets (HP1499)

description: ChIP DNA, H3 K4 from islets (HP1499)

source_name: ChIP DNA, H3 K4 from islets (HP1499)

tag: Antibody:H3 K4, Cell Line:islets (HP1499)

tag: Antibody:None, Cell Line:islets (HP1499)


title: Grain hardness Heron late, HLR30066.gpr

description:
A comparison of Heron NIL varying in grain hardness. Samples from a late stage of endosperm development 25-30 DPA
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: true


title: Clinical isolate #14 Up_iso14

tag: Clinical isolate #14


title: Grain hardness Falcon middle, FMR1F.06.gpr

description:
Comparison of wheat grain texture using NIL of Falcon. The middle stage of development, 12-15DPA
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: Grain hardness Heron middle, HMR1.61.2.gpr

description:
Heron NIL for soft/hard seed. Determine the differentially expressed genes at  middle development stage, 10-15 DPA.
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

source_name: Heron soft seed

tag: Heron soft seed, Biological Repl

source_name: Heron hard

tag: Heron hard, Biological Repl


title: Grain hardness Heron middle, HMR2.42.gpr

description:
Heron NIL for soft/hard seed. Determine the differentially expressed genes at  middle development stage, 10-15 DPA.
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true


title: Grain hardness Falcon early, FER2T.11.gpr

description:
Comparison of wheat grain texture between seeds of the NIL of Falcon. Early development stage 6-8 DPA
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

tag: Falcon hard seed, Biological Repl


title: 267: menin from HepG2

description: ChIP DNA, menin from HepG2

source_name: ChIP DNA, menin from HepG2

tag: Antibody:menin, Cell Line:HepG2

source_name: Input DNA

tag: Antibody:None, Cell Line:HepG2


title: Laboratory strain of U.parvum Up_LabStr

description: Hybridization signals were quantified with ImageQuant 5.1 software (Molecular Dynamics).

source_name: laboratory strain

tag: laboratory strain of U.parvum


title: Grain hardness Heron middle, HMR3.60.gpr


title: Grain hardness Falcon early, FER1F.10.gpr

description:
Comparison of wheat grain texture between seeds of the NIL of Falcon. Early development stage 6-8 DPA
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

source_name: Falcon soft seed

tag: Falcon soft seed, Biological Repl

source_name: Falcon hard seed


title: Clinical isolate #1 Up_iso1

tag: Clinical isolates #1


title: Grain hardness Falcon early, FER2F.11.gpr

description:
Comparison of wheat grain texture between seeds of the NIL of Falcon. Early development stage 6-8 DPA
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: 167: Rbbp5 from HelaS3

description: ChIP DNA, Rbbp5 from HelaS3


title: slide42_M

status: Public on Jul 21 2006

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: RNA was isolated from eight to twenty anthers per each individual tassel using Trizol reagent (Invitrogen, Carlbad, CA) as per manufacturer's instructions. Equal amounts of RNA from one to four individuals per stage per floret type (i.e., upper or lower) were pooled randomly to generate one biological replicate. In total, 24 biological replicates (two biological replicates per stage per floret type) were generated. Approximately 100 ng of total RNA from each biological replicate were used as starting material for T7-based linear RNA amplification, performed as described by Nakazono et al. (2003). Each biological replicate yielded between 30 and 50 micrograms of amplified RNA (aRNA). Approximately 3 micrograms of aRNA for each sample was indirectly labeled with Cy dye and hybridized to the GPL3021 sample platform.

hyb_protocol: Fluorescent targets were hybridized as described in the "cDNA microarray protocol" file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Each microarray chip (48 total) was scanned six times in ascending amounts of laser power and PMT gain with a ScanArray 5000 (Packard, Meriden, CT). Three scans from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide. The values for the low, medium, and high scan intensity data sets were 5.7, 7.2 and 8.7, respectively.

data_processing: An R implementation of the lowess normalization method (Dudoit and Fridlyand, 2002) was used to normalize the two channels for each combination of slide and scan intensity. The lowess normalized data from each scan was used to conduct a mixed linear model analysis separately for each of 12,160 spots using a strategy similar to that of Wolfinger et al., (2001)

organism: Zea mays

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the mid/late-microspore (mixed) developmental stage by light microscopy

label_protocol: Fluorescent targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Only targets that contained more than 3000 picomoles of cDNA, more than 60 picomoles of Cy dye and more than one dye molecule per 50 bases were used for hybridizations.

extract_protocol: Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer's instructions

tag: Inbred line

value: Ky21;Floret:Lower;Developmental stage:Mid/late-microspore (mixed);Sample name:M/LM2L

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid/late-microspore (mixed) developmental stage by light microscopy

label_protocol: Fluorescent targets were synthesized and labeled as described in the "cDNA microarray protocol" file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Only targets that contained more than 3000 picomoles of cDNA, more than 60 picomoles of Cy dye and more than one dye molecule per 50 bases were used for hybridizations.

value: Ky21;Floret:Upper;Developmental stage:Mid/late-microspore (mixed);Sample name:M/LM2u


title: slide41_H

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the mid-microspore developmental stage by light microscopy

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid-microspore developmental stage by light microscopy


title: slide42_H


title: slide42_L


title: slide40_H

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the early microspore developmental stage by light microscopy

value: Ky21;Floret:Lower;Developmental stage:Early microspore;Sample name:EM2L

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the early microspore developmental stage by light microscopy

value: Ky21;Floret:Upper;Developmental stage:Early microspore;Sample name:EM2u


title: Grain hardness Heron middle, HMR4.59.gpr


title: 279: menin from HepG2

description: ChIP DNA, menin from HepG2


title: Grain hardness Falcon early, FER1T.10.gpr

description:
Comparison of wheat grain texture between seeds of the NIL of Falcon. Early development stage 6-8 DPA
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: slide39_L

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the tetrad developmental stage by light microscopy

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the tetrad developmental stage by light microscopy


title: 163: MLL (BL1289) from HelaS3

description: ChIP DNA, MLL (BL1289) from HelaS3

source_name: ChIP DNA, MLL (BL1289) from HelaS3

tag: Antibody:MLL (BL1289), Cell Line:HelaS3


title: 168: Rbbp5 from HelaS3

description: ChIP DNA, Rbbp5 from HelaS3

source_name: ChIP DNA, Rbbp5 from HelaS3

tag: Antibody:Rbbp5, Cell Line:HelaS3


title: slide39_M


title: slide41_L


title: slide38_M

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the dyad/tetrad (mixed) developmental stage by light microscopy

value: Ky21;Floret:Lower;Developmental stage:Dyad/tetrad (mixed);Sample name:D/T2L

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the dyad/tetrad (mixed) developmental stage by light microscopy

value: Ky21;Floret:Upper;Developmental stage:Dyad/tetrad (mixed);Sample name:D/T2u


title: slide41_M


title: slide38_H


title: slide40_L


title: slide36_H

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the meiocyte developmental stage by light microscopy


title: slide40_M


title: slide39_H


title: slide36_L


title: slide38_L


title: slide37_L

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the meiocyte developmental stage by light microscopy


title: slide35_L


title: slide37_H


title: 161: MLL (BL1289) from HelaS3

description: ChIP DNA, MLL (BL1289) from HelaS3

source_name: Input DNA

tag: Antibody:None, Cell Line:HelaS3


title: slide37_M


title: 158: 3MK4 from HelaS3

description: ChIP DNA, 3MK4 from HelaS3

source_name: ChIP DNA, 3MK4 from HelaS3

tag: Antibody:3MK4, Cell Line:HelaS3


title: slide32_H


title: slide36_M


title: slide32_M


title: slide33_H

value: Ky21;Floret:Lower;Developmental stage:Early Microspore;Sample name:EM2L


title: slide34_M


title: slide34_L


title: slide33_M


title: slide35_M


title: slide32_L


title: slide35_H


title: 137: menin A300 from HelaS3

description: ChIP DNA, menin A300 from HelaS3

source_name: ChIP DNA, menin A300 from HelaS3

tag: Antibody:menin A300, Cell Line:HelaS3


title: 136: menin A300 from HelaS3

description: ChIP DNA, menin A300 from HelaS3


title: 159: 3MK4 from HelaS3

description: ChIP DNA, 3MK4 from HelaS3


title: slide33_L


title: slide34_H


title: slide31_H


title: slide31_M


title: slide30_H


title: 101: menin A300 from HepG2

description: ChIP DNA, menin A300 from HepG2

source_name: ChIP DNA, menin A300 from HepG2

tag: Antibody:menin A300, Cell Line:HepG2


title: slide30_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid/late-microspore (mixed) developmental stage by light microscopy


title: slide31_L


title: 141: tri-meth K4 (ab8580) from HelaS3

description: ChIP DNA, tri-meth K4 (ab8580) from HelaS3

tag: Antibody:tri-meth K4 (ab8580), Cell Line:HelaS3


title: slide29_L


title: slide28_L


title: slide25_M

value: Ky21;Floret:Upper;Developmental stage:Dyad/Tetrad (mixed);Sample name:D/T2u


title: slide26_M


title: slide30_L


title: slide29_M


title: slide27_L

value: Ky21;Floret:Upper;Developmental stage:Early Microspore;Sample name:EM2u

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the Tetrad developmental stage by light microscopy


title: slide28_H

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid-microspore developmental stage by light microscopy


title: slide24_H

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the mid/late-microspore (mixed) developmental stage by light microscopy

value: Ky21;Floret:Upper;Developmental stage:Mid/late-microspore (mixed));Sample name:M/LM1u


title: slide24_M


title: slide27_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the early microspore developmental stage by light microscopy


title: slide26_H


title: slide24_L


title: slide25_L


title: slide27_H


title: slide28_M


title: slide26_L


title: 162: MLL (BL1289) from HelaS3

description: ChIP DNA, MLL (BL1289) from HelaS3


title: slide25_H


title: slide23_M

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the mid-microspore developmental stage by light microscopy


title: slide23_H


title: slide20_L

value: Ky21;Floret:Lower;Developmental stage:Dyad/tetrad (mixed);Sample name:DT1L

value: Ky21;Floret:Upper;Developmental stage:Dyad/tetrad (mixed);Sample name:D/T1u


title: slide21_H

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the tetrad developmental stage by light microscopy

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the tetrad developmental stage by light microscopy


title: slide23_L


title: slide22_L

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the early microspore developmental stage by light microscopy

value: Ky21;Floret:Lower;Developmental stage:Early microspore;Sample name:EM1L

value: Ky21;Floret:Upper;Developmental stage:Early microspore;Sample name:EM1u


title: slide22_H


title: slide29_H


title: slide21_L


title: slide19_H


title: slide20_H

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the dyad/tetrad (mixed) developmental stage by light microscopy


title: slide20_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the dyad/tetrad (mixed) developmental stage by light microscopy


title: slide11_M

value: Ky21;Floret:Lower;Developmental stage:Mid/late-microspore (mixed);Sample name:M/LM1L


title: slide22_M


title: slide19_M

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the meiocyte developmental stage by light microscopy


title: slide10_L


title: slide21_M


title: slide19_L

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the meiocyte developmental stage by light microscopy


title: slide11_L


title: slide9_H


title: slide10_H


title: slide12_M


title: slide12_L


title: slide9_M


title: slide11_H


title: slide12_H


title: slide10_M


title: slide8_M

value: Ky21;Floret:Lower;Developmental stage:Dyad/tetrad (mixed);Sample name:D/T1L


title: slide8_H


title: slide9_L


title: slide6_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid/late microspore (mixed) developmental stage by light microscopy

tag: Floret

value: Upper;

tag: Developmental stage

value: Mid/late microspore (mixed);

tag: Sample name

value: Meiocyte;


title: slide5_M

value: Ky21;Floret:Upper;Developmental stage:Mid/late microspore (mixed);Sample name:M/LM1u


title: slide7_H


title: TA-n10; normal tibialis anterior 10 month

city: Athens

first: Despina

last: Sanoudou

address: Soranou Efesiou 4

department: Molecular Biology

country: Greece

institute: Foundation for Biomedical Research, Academy of Athens

description: Wild type, snap frozen, tibialis anterior muscle, 10 month age animal

source_name: tibialis anterior muscle

extract_protocol: Standard Trizol protocol extraction. Total RNA pools from 3-5 mice were processed and hybridized to each microarray.


title: slide7_M


title: TA-n10-2; normal tibialis anterior 10 month

tag: Wild type, snap frozen, tibialis anterior muscle, 10 month age animal


title: TA-t10-2; transgenic tibialis anterior 10 month

description: Transgenic for alpha tropomyosin slow, snap frozen, tibialis anterior muscle, 10 month age animal

tag: Transgenic, snap frozen, tibialis anterior muscle, 10 month age animal


title: slide8_L


title: TA-n7-2; normal tibialis anterior 7 month

description: Wild type, snap frozen, tibialis anterior muscle, 7month age animal


title: PLT-n7; normal plantaris 7 month

description: Wild type, snap frozen, plantaris muscle, 7month age animal

source_name: plantaris muscle

tag: Wild type, snap frozen, plantaris muscle, 7 month age animal


title: PLT-t7-2; transgenic plantaris 7 month

description: Transgenic for alpha tropomyosin slow, snap frozen, plantaris muscle, 7month age animal

tag: Transgenic, snap frozen, plantaris muscle, 7month age animal


title: slide1_M

label_protocol: Fluorescent targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.  Only targets that contained more than 3000 picomoles of cDNA, more than 60 picomoles of Cy dye and more than one dye molecule per 50 bases were used for hybridizations.

value: Upper

value: Meiocyte

value: Dyad/tetrad (mixed)


title: PLT-t10; transgenic plantaris 10 month

description: Transgenic for alpha tropomyosin slow, snap frozen, plantaris muscle, 10 month age animal

tag: Transgenic, snap frozen, plantaris muscle, 10 month age animal


title: PLT-n7-2; normal plantaris 7 month


title: slide5_L


title: TA-n7; normal tibialis anterior 7 month

tag: Wild type, snap frozen, tibialis anterior muscle, 7month age animal


title: PLT-t7; transgenic plantaris 7 month


title: PLT-n10; normal plantaris 10 month

description: Wild type, snap frozen, plantaris muscle, 10 month age animal


title: slide4_M

tag: Inbred line

value: Early Microspore;

value: Mid-microspore;


title: TA-t7; transgenic tibialis anterior 7 month

description: Transgenic for alpha tropomyosin slow, snap frozen, tibialis anterior muscle, 7month age animal

tag: Transgenic, snap frozen, tibialis anterior muscle, 7month age animal


title: slide4_H


title: slide7_L


title: slide3_L

value: Ky21;Floret:Upper;Developmental stage:Early Microspore;Sample name:EM1u


title: slide2_L

value: Dyad/tetrad (mixed);

value: Tetrad;


title: GAS-t7; transgenic gastrocnemus 7 month

description: Transgenic for alpha tropomyosin slow, snap frozen, gastrocnemus muscle, 7month age animal

source_name: gastrocnemus muscle

tag: Transgenic, snap frozen, gastrocnemus muscle, 7month age animal


title: slide3_M


title: Brg1 mutant 2 cell embryo rep3

first: Hua

last: Pan

address: 415 S University Avenue

department: Department of Biology

institute: University of Pennsylvania

description: Brg1 mutant whole embryo

source_name: Brg1 mutant 2 cell embryo rep3

label_protocol: total RNA from 20 embryos was processed to produce biotinylated cRNA targets using Affy Small Sample Target Labeling Assay Version II.

extract_protocol: Total RNA from 20 embryos was extracted and purified using an Picopure kit (Arcturus).

tag: in vivo,2 cell stage, embryo


title: slide6_H


title: slide3_H


title: TA-t7-2; transgenic tibialis anterior 7 month


title: GAS-t10; transgenic gastrocnemus 10 month

description: Transgenic for alpha tropomyosin slow, snap frozen, gastrocnemus muscle, 10 month age animal

tag: Transgenic, snap frozen, gastrocnemus muscle, 10 month age animal


title: GAS-n10-2; normal gastrocnemus 10 month

description: Wild type, snap frozen, gastrocnemus muscle, 10 month age animal


title: slide4_L


title: TA-t10; transgenic tibialis anterior 10 month


title: GAS-t10-2; transgenic gastrocnemus 10 month


title: slide5_H


title: slide6_L


title: Brg1 mutant 2 cell embryo rep1

description: Brg1 mutant whole embryo

source_name: Brg1 mutant 2 cell embryo rep1


title: Brg1 mutant 2 cell embryo rep4

description: Brg1 mutant whole embryo

source_name: Brg1 mutant 2 cell embryo rep4


title: GAS-n10; normal gastrocnemus 10 month

tag: Wild type, snap frozen, gastrocnemus muscle, 10 month age animal


title: GAS-t7-2; transgenic gastrocnemus 7 month


title: slide1_H

hyb_protocol: Fluorescent targets were hybridized as described in the


title: slide2_M


title: Brg1 mutant 2 cell embryo rep2

description: Brg1 mutant whole embryo

source_name: Brg1 mutant 2 cell embryo rep2


title: wild type 2 cell embryo rep3

description: Wild type whole embryo

source_name: wild type 2 cell embryo rep3


title: slide1_L

label_protocol: Fluorescent targets were synthesized and labeled as described in the "cDNA microarray protocol" file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.  Only targets that contained more than 3000 picomoles of cDNA, more than 60 picomoles of Cy dye and more than one dye molecule per 50 bases were used for hybridizations.


title: wild type 2 cell embryo rep2

description: Wild type whole embryo

source_name: wild type 2 cell embryo rep2


title: slide2_H


title: GAS-n7; normal gastrocnemus 7 month

description: Wild type, snap frozen, gastrocnemus muscle, 7month age animal


title: GAS-n7-2; normal gastrocnemus 7 month

tag: Wild type, snap frozen, gastrocnemus muscle, 7month age animal