title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 9

status: Public on Dec 01 2010

type: RNA

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

country: USA

institute: Iowa State University

description: To better understand the impact of intracellular carriage of E. coli O157:H7 within a ruminant protozoa, global transcript levels of strain EDL933 cells grown under within Acanthamoeba were compared to cells grown in ATCC PYG712 using microarrays.

hyb_protocol: From each paired sample, 1.5 μg of labeled cDNA was combined, dried-down, resuspended in 60 μl Pronto! cDNA/long oligonucleotide hybridization solution (Corning), incubated at 95°C for 5 min and centrifuged at 13,000 × g for 2 min at room temperature. This solution was then pipetted on a freshly pre-hybridized microarray slide, covered with a 22 x 60 mm HybriSlip (Grace Bio Labs, Bend, OR), placed in a Corning hybridization chamber, and incubated in a 42°C water bath for 12 to 16 h. Array pre-hybridization was conducted using sodium borohydride as previously described (Raghavachari, et al., 2003). Slides were washed according to Corning’s UltraGAPS protocol and dried by centrifugation.

scan_protocol: Scanning, image segmentation, and normalization were conducted as previously described (Madsen, et al., 2006).

data_processing: Mixed model analysis was conducted as previously described (Madsen, et al., 2006) excluding slide region and slide-by-region interaction effects. The value column was not used for analysis or in publication. The normalized values for duplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the RNA samples. [mean log transformed median centered lowess normalized signal intensity]

molecule: total RNA

organism: Escherichia coli

label_protocol: Targets were generated from 10 µg of DNase treated total RNA as follows. Ten µg of total RNA was combined with 1 μl of 10 µg/μl random hexamers (Integrated DNA Technologies) and ddH20 was added to bring the total reaction volume to 15.5 μl. Samples were incubated at 70°C for 10 min followed by 10 min incubation on ice. After incubation, 14.5 μl of a reaction mix (6 μl of 5x First Strand Buffer, 1.2 μl of 25x aa-dUTP/dNTP mix (Fermentas, Glen Burnie, MD), 3 μl 0.1M DTT, 2 μl Superscript III 200U/ μl (Invitrogen Corp., Carlsbad, CA), 2.4 μl RNase-free water) was added and reactions were incubated at 42°C for at least 2 hrs. After incubation, RNA was immediately hydrolyzed by incubation with 3 μl 0.1 M ETDA and 3.5 μl 0.1 M NaOH at 65°C for 10 min. The pH was neutralized with the addition of 36.5 μl of 500 mM HEPES (pH 7.0). Reactions were purified using the Mo Bio UltraClean PCR Clean-Up Kit (MO BIO Laboratories, Inc., Carlsbad, CA), quantified using the ND-1000 spectrophotometer, dried-down, and resuspended in 10 μl RNase-free water and 1.5 μl sodium bicarbonate (pH 8.7). After 10 min, 6 μl of Cy 3 (catalog number PA25001) or Cy 5 (catalog number PA23001) (GE Healthcare, Piscataway, NJ) were added according the microarray experimental design, and samples were incubated at room temperature for 3 h. Dyes were prepared by resuspending a single tube of dye in 72 μl of DMSO and storing in 6 μl aliquots at -70°C until use. Dye coupled reactions were purified in the same manner as cDNA synthesis reactions. Frequency of dye incorporation and yield was determined using the ND-1000 spectrophotometer.

extract_protocol: RNA was isolated from samples using the RNeasy Mini Kit (Qiagen). Prior to lysis all samples were incubated for 30 min on ice in RNA stop solution (0.1% SDS, 1% Acidic phenol, 19% ethanol, ice cold). The lysis and digestion protocol was followed with two 50 μl ddH20 elutions. Each sample was treated with 2 μl of DNase (Ambion, Austin, TX) at 37°C for 30 min. Samples were purified and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA), and the quantity and purity were determined using an ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Samples were determined to be free of contaminating genomic DNA by absence of a band on a DNA electrophoresis gel after 30 rounds of PCR.

tag: growth condition

value: Inside Acanthamoeba

source_name: Escherichia coli O157:H7 EDL933 Outside Control

value: Outside Control


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 7


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 8


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 5


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 6


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 2


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 7

data_processing: "Images were quantified, log transformed, background subtracted and normalized as described in [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166]. Spot-specific mean signals were corrected for local background by subtracting spot-specific median background intensities. The natural logarithm of the background-corrected signals from a single scan was adjusted by an additive constant so that all scans of the same array-by-dye combination would have a common median. The median of these adjusted-log-background-corrected signals across multiple scans was then computed for each spot to obtain one value for each combination of spot, array, and dye channel. These data for the two dye channels on any given array were normalized using LOWESS normalization to adjust for intensity-dependent dye bias [Dudoit, S., Y. H. Yang, M. J. Callow, and T. P. Speed. 2000. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.].

label: Cy 3

source_name: Escherichia coli O157:H7 EDL933 Aerobic

extract_protocol: RNA was isolated from samples using the RNeasy Mini Kit (Qiagen). The lysis and digestion protocol was followed with two 50 μl ddH20 elutions. Each sample was treated with 2 μl of DNase (Ambion, Austin, TX) at 37°C for 30 min. Samples were purified and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA), and the quantity and purity were determined using an ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Samples were determined to be free of contaminating genomic DNA by absence of a band on a DNA electrophoresis gel after 30 rounds of PCR.

tag: Escherichia coli O157:H7 EDL933

label: Cy 5


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 6


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 4


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 3


title: Escherichia coli O157:H7 EDL933 Rumen Fluid vs. Control Slide 7

description: To better understand the impact of rumen fluid treatment on E. coli O157:H7, global transcript levels of strain EDL933 cells grown under anaerobiasis were resupsended in heat clarified rumen fluid or fresh LB for 15 min were compared using microarrays.

source_name: Escherichia coli O157:H7 EDL933 Rumen Fluid treatment

tag: escherichia coli o157

value: H7 EDL933

source_name: Escherichia coli O157:H7 EDL933 Control


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 8


title: BreastCancer-722 (miRNA)

city: Oslo

first: Hilde

last: Johnsen

address: Montebello

department: Genetics

country: Norway

institute: Norwegian Radium Hospital

description:
BC-M-722
This breast tumor sample has previously been assayed in Series GSE3985.

hyb_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.1.5

scan_protocol: Scanning on Agilent scanner G2565A.

data_processing: Feature Extraction (FE) v9.5.3.1 was used to extract signals. The Sample VALUEs represent log2 75th percentile-normalized signal intensities.

organism: Homo sapiens

source_name: Breast Primary Tumor

extract_protocol: TRIzol, following manufactors protocol

treatment_protocol: fresh frozen in liquid nitrogen

tag: tissue

value: breast

tag: disease state

value: breast primary tumor

tag: breast cancer subtype

value: Lum B

tag: tp53 mutation status

value: WT

tag: death status

value: Alive

tag: disease free survival time (months)

tag: estrogen receptor status

value: Positive

tag: her2 (fish) status

value: Negative


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 3

scan_protocol: Scanning, image segmentation, and normalization were conducted as previously described (Madsen, et et.,2006).


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 1


title: Escherichia coli O157:H7 EDL933 Rumen Fluid vs. Control Slide 5


title: Escherichia coli O157:H7 EDL933 Rumen Fluid vs. Control Slide 2


title: Escherichia coli O157:H7 EDL933 Rumen Fluid vs. Control Slide 4


title: Escherichia coli O157:H7 EDL933 Rumen Fluid vs. Control Slide 6


title: Escherichia coli O157:H7 EDL933 Rumen Fluid vs. Control Slide 1


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 5


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 2


title: Escherichia coli O157:H7 EDL933 Rumen Fluid vs. Control Slide 3


title: Escherichia coli O157:H7 EDL933 Anaerobic vs. Aerobic Slide 4


title: BreastCancer-632 (miRNA)

description:
BC-M-632
This breast tumor sample has previously been assayed in Series GSE3985.

label_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.1.5

value: Lum A


title: BreastCancer-630 (miRNA)

description:
BC-M-630
This breast tumor sample has previously been assayed in Series GSE3985.

value: Basal


title: BreastCancer-627 (miRNA)

description:
BC-M-627
This breast tumor sample has previously been assayed in Series GSE3985.

value: Normal-like

value: Mut

value: Dead of BC


title: BreastCancer-709 (miRNA)

description:
BC-M-709
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-579 (miRNA)

description:
BC-M-579
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-570 (miRNA)

description:
BC-M-570
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-551 (miRNA)

description:
BC-M-551
This breast tumor sample has previously been assayed in Series GSE3985.

value: Dead of other disease than BC


title: BreastCancer-512 (miRNA)

description:
BC-M-512
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-493 (miRNA)

description:
BC-M-493
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-470 (miRNA)

description:
BC-M-470
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-457 (miRNA)

description:
BC-M-457
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-451 (miRNA)

description:
BC-M-451
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-488 (miRNA)

description:
BC-M-488
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-476 (miRNA)

description:
BC-M-476
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-406 (miRNA)

description:
BC-M-406
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-430 (miRNA)

description:
BC-M-430
This breast tumor sample has previously been assayed in Series GSE3985.

value: Dead cause not registered


title: BreastCancer-371 (miRNA)

description:
BC-M-371
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-388 (miRNA)

description:
BC-M-388
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-391 (miRNA)

description:
BC-M-391
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-378 (miRNA)

description:
BC-M-378
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-381 (miRNA)

description:
BC-M-381
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-363 (miRNA)

description:
BC-M-363
This breast tumor sample has previously been assayed in Series GSE3985.

value: not classified


title: BreastCancer-373 (miRNA)

description:
BC-M-373
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-359 (miRNA)

description:
BC-M-359
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-357 (miRNA)

description:
BC-M-357
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-338 (miRNA)

description:
BC-M-338
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-341 (miRNA)

description:
BC-M-341
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-321 (miRNA)

description:
BC-M-321
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-355 (miRNA)

description:
BC-M-355
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-318 (miRNA)

description:
BC-M-318
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-308 (miRNA)

description:
BC-M-308
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-309 (miRNA)

description:
BC-M-309
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-300 (miRNA)

description:
BC-M-300
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-298 (miRNA)

description:
BC-M-298
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-277 (miRNA)

description:
BC-M-277
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-283 (miRNA)

description:
BC-M-283
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-275 (miRNA)

description:
BC-M-275
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-247 (miRNA)

description:
BC-M-247
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-234 (miRNA)

description:
BC-M-234
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-246 (miRNA)

description:
BC-M-246
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-264 (miRNA)

description:
BC-M-264
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-245 (miRNA)

description:
BC-M-245
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-240 (miRNA)

description:
BC-M-240
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-267 (miRNA)

description:
BC-M-267
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-269 (miRNA)

description:
BC-M-269
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-263 (miRNA)

description:
BC-M-263
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-232 (miRNA)

description:
BC-M-232
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-223 (miRNA)

description:
BC-M-223
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-221 (miRNA)

description:
BC-M-221
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-220 (miRNA)

description:
BC-M-220
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-218 (miRNA)

description:
BC-M-218
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-222 (miRNA)

description:
BC-M-222
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-201 (miRNA)

description:
BC-M-201
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-209 (miRNA)

description:
BC-M-209
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-185 (miRNA)

description:
BC-M-185
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-163 (miRNA)

description:
BC-M-163
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-150 (miRNA)

description:
BC-M-150
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-122 (miRNA)

description:
BC-M-122
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-148 (miRNA)

description:
BC-M-148
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-139 (miRNA)

description:
BC-M-139
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-146 (miRNA)

description:
BC-M-146
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-119 (miRNA)

description:
BC-M-119
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-112 (miRNA)

description:
BC-M-112
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-144 (miRNA)

description:
BC-M-144
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-101 (miRNA)

description:
BC-M-101
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-106 (miRNA)

description:
BC-M-106
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-098 (miRNA)

description:
BC-M-098
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-083 (miRNA)

description:
BC-M-083
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-086 (miRNA)

description:
BC-M-086
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-091 (miRNA)

description:
BC-M-091
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-089 (miRNA)

description:
BC-M-089
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-085 (miRNA)

description:
BC-M-085
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-088 (miRNA)

description:
BC-M-088
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-079 (miRNA)

description:
BC-M-079
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-075 (miRNA)

description:
BC-M-075
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-080 (miRNA)

description:
BC-M-080
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-071 (miRNA)

description:
BC-M-071
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-066 (miRNA)

description:
BC-M-066
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-065 (miRNA)

description:
BC-M-065
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-069 (miRNA)

description:
BC-M-069
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-068 (miRNA)

description:
BC-M-068
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-067 (miRNA)

description:
BC-M-067
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-064 (miRNA)

description:
BC-M-064
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-053 (miRNA)

description:
BC-M-053
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-057 (miRNA)

description:
BC-M-057
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-044 (miRNA)

description:
BC-M-044
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-042 (miRNA)

description:
BC-M-042
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-034 (miRNA)

description:
BC-M-034
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-031 (miRNA)

description:
BC-M-031
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-019 (miRNA)

description:
BC-M-019
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-024 (miRNA)

description:
BC-M-024
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-020 (miRNA)

description:
BC-M-020
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-023 (miRNA)

description:
BC-M-023
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-022 (miRNA)

description:
BC-M-022
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-017 (miRNA)

description:
BC-M-017
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-018 (miRNA)

description:
BC-M-018
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-014 (miRNA)

description:
BC-M-014
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-015 (miRNA)

description:
BC-M-015
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-003 (miRNA)

description:
BC-M-003
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-002 (miRNA)

description:
BC-M-002
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-627 (mRNA)_114Sample dataset

description:
BC-M-627
This breast tumor sample has previously been assayed in Series GSE3985.

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5

data_processing:
Feature Extraction (FE) v9.5.3.1 was used to extract signals.  Data were log2 transformed, non-uniform spots were excluded, and when averaging replicated probes, population outliers were excluded. Probes that are missing on more than 10 arrays were excluded.
Data in Sample tables were not normalized across samples. We did a further processing of the 114 mRNA samples: RMA normalization and averaging per Gene Symbol in our analysis.  See supplementary file (GSE19536_final_processed_mRNAdata.txt) on GSE19536 record.

value: Breast

value: Breast Primary Tumor


title: BreastCancer-722 (mRNA)_114Sample dataset

description:
BC-M-722
This breast tumor sample has previously been assayed in Series GSE3985.

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5


title: BreastCancer-488 (mRNA)_114Sample dataset

description:
BC-M-488
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-709 (mRNA)_114Sample dataset

description:
BC-M-709
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-630 (mRNA)_114Sample dataset

description:
BC-M-630
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-539 (mRNA)_114Sample dataset

description:
BC-M-539
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-430 (mRNA)_114Sample dataset

description:
BC-M-430
This breast tumor sample has previously been assayed in Series GSE3985.

value: dead but cause not registered


title: BreastCancer-632 (mRNA)_114Sample dataset

description:
BC-M-632
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-451 (mRNA)_114Sample dataset

description:
BC-M-451
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-357 (mRNA)_114Sample dataset

description:
BC-M-357
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-512 (mRNA)_114Sample dataset

description:
BC-M-512
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-388 (mRNA)_114Sample dataset

description:
BC-M-388
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-381 (mRNA)_114Sample dataset

description:
BC-M-381
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-551 (mRNA)_114Sample dataset

description:
BC-M-551
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-371 (mRNA)_114Sample dataset

description:
BC-M-371
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-476 (mRNA)_114Sample dataset

description:
BC-M-476
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-406 (mRNA)_114Sample dataset

description:
BC-M-406
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-579 (mRNA)_114Sample dataset

description:
BC-M-579
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-493 (mRNA)_114Sample dataset

description:
BC-M-493
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-570 (mRNA)_114Sample dataset

description:
BC-M-570
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-341 (mRNA)_114Sample dataset

description:
BC-M-341
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-359 (mRNA)_114Sample dataset

description:
BC-M-359
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-355 (mRNA)_114Sample dataset

description:
BC-M-355
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-363 (mRNA)_114Sample dataset

description:
BC-M-363
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-457 (mRNA)_114Sample dataset

description:
BC-M-457
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-373 (mRNA)_114Sample dataset

description:
BC-M-373
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-378 (mRNA)_114Sample dataset

description:
BC-M-378
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-470 (mRNA)_114Sample dataset

description:
BC-M-470
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-338 (mRNA)_114Sample dataset

description:
BC-M-338
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-335 (mRNA)_114Sample dataset

description:
BC-M-335
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-318 (mRNA)_114Sample dataset

description:
BC-M-318
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-263 (mRNA)_114Sample dataset

description:
BC-M-263
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-321 (mRNA)_114Sample dataset

description:
BC-M-321
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-308 (mRNA)_114Sample dataset

description:
BC-M-308
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-309 (mRNA)_114Sample dataset

description:
BC-M-309
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-283 (mRNA)_114Sample dataset

description:
BC-M-283
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-285 (mRNA)_114Sample dataset

description:
BC-M-285
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-267 (mRNA)_114Sample dataset

description:
BC-M-267
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-264 (mRNA)_114Sample dataset

description:
BC-M-264
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-245 (mRNA)_114Sample dataset

description:
BC-M-245
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-269 (mRNA)_114Sample dataset

description:
BC-M-269
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-240 (mRNA)_114Sample dataset

description:
BC-M-240
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-300 (mRNA)_114Sample dataset

description:
BC-M-300
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-275 (mRNA)_114Sample dataset

description:
BC-M-275
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-298 (mRNA)_114Sample dataset

description:
BC-M-298
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-234 (mRNA)_114Sample dataset

description:
BC-M-234
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-232 (mRNA)_114Sample dataset

description:
BC-M-232
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-246 (mRNA)_114Sample dataset

description:
BC-M-246
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-247 (mRNA)_114Sample dataset

description:
BC-M-247
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-314 (mRNA)_114Sample dataset

description:
BC-M-314
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-277 (mRNA)_114Sample dataset

description:
BC-M-277
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-221 (mRNA)_114Sample dataset

description:
BC-M-221
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-334 (mRNA)_114Sample dataset

description:
BC-M-334
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-209 (mRNA)_114Sample dataset

description:
BC-M-209
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-223 (mRNA)_114Sample dataset

description:
BC-M-223
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-222 (mRNA)_114Sample dataset

description:
BC-M-222
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-201 (mRNA)_114Sample dataset

description:
BC-M-201
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-210 (mRNA)_114Sample dataset

description:
BC-M-210
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-218 (mRNA)_114Sample dataset

description:
BC-M-218
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-220 (mRNA)_114Sample dataset

description:
BC-M-220
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-089 (mRNA)_114Sample dataset

description:
BC-M-089
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-190 (mRNA)_114Sample dataset

description:
BC-M-190
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-087 (mRNA)_114Sample dataset

description:
BC-M-087
This breast tumor sample has previously been assayed in Series GSE3985.

source_name: Lymph node metastasis (not Breast Primary Tumor)


title: BreastCancer-139 (mRNA)_114Sample dataset

description:
BC-M-139
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-157 (mRNA)_114Sample dataset

description:
BC-M-157
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-197 (mRNA)_114Sample dataset

description:
BC-M-197
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-167 (mRNA)_114Sample dataset

description:
BC-M-167
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-122 (mRNA)_114Sample dataset

description:
BC-M-122
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-185 (mRNA)_114Sample dataset

description:
BC-M-185
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-148 (mRNA)_114Sample dataset

description:
BC-M-148
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-144 (mRNA)_114Sample dataset

description:
BC-M-144
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-163 (mRNA)_114Sample dataset

description:
BC-M-163
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-091 (mRNA)_114Sample dataset

description:
BC-M-091
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-112 (mRNA)_114Sample dataset

description:
BC-M-112
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-119 (mRNA)_114Sample dataset

description:
BC-M-119
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-101 (mRNA)_114Sample dataset

description:
BC-M-101
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-107 (mRNA)_114Sample dataset

description:
BC-M-107
This breast tumor sample has previously been assayed in Series GSE3985.

value: Lymph node metastasis (not Breast Primary Tumor)


title: BreastCancer-088 (mRNA)_114Sample dataset

description:
BC-M-088
This breast tumor sample has previously been assayed in Series GSE3985.

value: Lum B


title: BreastCancer-106 (mRNA)_114Sample dataset

description:
BC-M-106
This breast tumor sample has previously been assayed in Series GSE3985.

value: WT


title: BreastCancer-098 (mRNA)_114Sample dataset

description:
BC-M-098
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-146 (mRNA)_114Sample dataset

description:
BC-M-146
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-150 (mRNA)_114Sample dataset

description:
BC-M-150
This breast tumor sample has previously been assayed in Series GSE3985.

value: Alive


title: BreastCancer-100 (mRNA)_114Sample dataset

description:
BC-M-100
This breast tumor sample has previously been assayed in Series GSE3985.

value: Positive


title: BreastCancer-132 (mRNA)_114Sample dataset

description:
BC-M-132
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-085 (mRNA)_114Sample dataset

description:
BC-M-085
This breast tumor sample has previously been assayed in Series GSE3985.

value: Negative


title: BreastCancer-079 (mRNA)_114Sample dataset

description:
BC-M-079
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-080 (mRNA)_114Sample dataset

description:
BC-M-080
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-083 (mRNA)_114Sample dataset

description:
BC-M-083
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-069 (mRNA)_114Sample dataset

description:
BC-M-069
This breast tumor sample has previously been assayed in Series GSE3985.

value: Lum A


title: BreastCancer-075 (mRNA)_114Sample dataset

description:
BC-M-075
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-067 (mRNA)_114Sample dataset

description:
BC-M-067
This breast tumor sample has previously been assayed in Series GSE3985.

value: Basal


title: BreastCancer-071 (mRNA)_114Sample dataset

description:
BC-M-071
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-064 (mRNA)_114Sample dataset

description:
BC-M-064
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-044 (mRNA)_114Sample dataset

description:
BC-M-044
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-042 (mRNA)_114Sample dataset

description:
BC-M-042
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-065 (mRNA)_114Sample dataset

description:
BC-M-065
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-057 (mRNA)_114Sample dataset

description:
BC-M-057
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-066 (mRNA)_114Sample dataset

description:
BC-M-066
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-022 (mRNA)_114Sample dataset

description:
BC-M-022
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-086 (mRNA)_114Sample dataset

description:
BC-M-086
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-053 (mRNA)_114Sample dataset

description:
BC-M-053
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-018 (mRNA)_114Sample dataset

description:
BC-M-018
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-015 (mRNA)_114Sample dataset

description:
BC-M-015
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-024 (mRNA)_114Sample dataset

description:
BC-M-024
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-031 (mRNA)_114Sample dataset

description:
BC-M-031
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-034 (mRNA)_114Sample dataset

description:
BC-M-034
This breast tumor sample has previously been assayed in Series GSE3985.

value: Normal-like


title: BreastCancer-023 (mRNA)_114Sample dataset

description:
BC-M-023
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-019 (mRNA)_114Sample dataset

description:
BC-M-019
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-003 (mRNA)_114Sample dataset

description:
BC-M-003
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-709 (mRNA)_115Sample dataset

description:
BC-M-709
This breast tumor sample has previously been assayed in Series GSE3985.

data_processing:
Feature Extraction (FE) v9.5.3.1 was used to extract signals.  Data were log2 transformed, non-uniform spots were excluded, and when averaging replicated probes, population outliers were excluded. Probes that are missing on more than 10 arrays were excluded.
Quantile normalization done in R using normalizeBetweenArrays from the limma library.  Missing values imputed using LLS imputation (R: LLSimpute from the pcaMethod library with k=20).

value: Mut


title: BreastCancer-020 (mRNA)_114Sample dataset

description:
BC-M-020
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-002 (mRNA)_114Sample dataset

description:
BC-M-002
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-722 (mRNA)_115Sample dataset

description:
BC-M-722
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-014 (mRNA)_114Sample dataset

description:
BC-M-014
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-632 (mRNA)_115Sample dataset

description:
BC-M-632
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-630 (mRNA)_115Sample dataset

description:
BC-M-630
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-017 (mRNA)_114Sample dataset

description:
BC-M-017
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-579 (mRNA)_115Sample dataset

description:
BC-M-579
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-627 (mRNA)_115Sample dataset

description:
BC-M-627
This breast tumor sample has previously been assayed in Series GSE3985.

value: Dead of BC


title: BreastCancer-551 (mRNA)_115Sample dataset

description:
BC-M-551
This breast tumor sample has previously been assayed in Series GSE3985.

value: Dead of other disease than BC


title: BreastCancer-388 (mRNA)_115Sample dataset

description:
BC-M-388
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-378 (mRNA)_115Sample dataset

description:
BC-M-378
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-373 (mRNA)_115Sample dataset

description:
BC-M-373
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-539 (mRNA)_115Sample dataset

description:
BC-M-539
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-570 (mRNA)_115Sample dataset

description:
BC-M-570
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-512 (mRNA)_115Sample dataset

description:
BC-M-512
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-476 (mRNA)_115Sample dataset

description:
BC-M-476
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-430 (mRNA)_115Sample dataset

description:
BC-M-430
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-068 (mRNA)_114Sample dataset

description:
BC-M-068
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-451 (mRNA)_115Sample dataset

description:
BC-M-451
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-470 (mRNA)_115Sample dataset

description:
BC-M-470
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-359 (mRNA)_115Sample dataset

description:
BC-M-359
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-341 (mRNA)_115Sample dataset

description:
BC-M-341
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-457 (mRNA)_115Sample dataset

description:
BC-M-457
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-334 (mRNA)_115Sample dataset

description:
BC-M-334
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-488 (mRNA)_115Sample dataset

description:
BC-M-488
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-391 (mRNA)_115Sample dataset

description:
BC-M-391
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-406 (mRNA)_115Sample dataset

description:
BC-M-406
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-314 (mRNA)_115Sample dataset

description:
BC-M-314
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-381 (mRNA)_115Sample dataset

description:
BC-M-381
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-363 (mRNA)_115Sample dataset

description:
BC-M-363
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-355 (mRNA)_115Sample dataset

description:
BC-M-355
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-371 (mRNA)_115Sample dataset

description:
BC-M-371
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-318 (mRNA)_115Sample dataset

description:
BC-M-318
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-335 (mRNA)_115Sample dataset

description:
BC-M-335
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-285 (mRNA)_115Sample dataset

description:
BC-M-285
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-357 (mRNA)_115Sample dataset

description:
BC-M-357
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-338 (mRNA)_115Sample dataset

description:
BC-M-338
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-321 (mRNA)_115Sample dataset

description:
BC-M-321
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-309 (mRNA)_115Sample dataset

description:
BC-M-309
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-308 (mRNA)_115Sample dataset

description:
BC-M-308
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-300 (mRNA)_115Sample dataset

description:
BC-M-300
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-275 (mRNA)_115Sample dataset

description:
BC-M-275
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-264 (mRNA)_115Sample dataset

description:
BC-M-264
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-283 (mRNA)_115Sample dataset

description:
BC-M-283
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-247 (mRNA)_115Sample dataset

description:
BC-M-247
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-263 (mRNA)_115Sample dataset

description:
BC-M-263
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-246 (mRNA)_115Sample dataset

description:
BC-M-246
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-269 (mRNA)_115Sample dataset

description:
BC-M-269
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-277 (mRNA)_115Sample dataset

description:
BC-M-277
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-267 (mRNA)_115Sample dataset

description:
BC-M-267
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-298 (mRNA)_115Sample dataset

description:
BC-M-298
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-240 (mRNA)_115Sample dataset

description:
BC-M-240
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-245 (mRNA)_115Sample dataset

description:
BC-M-245
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-232 (mRNA)_115Sample dataset

description:
BC-M-232
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-234 (mRNA)_115Sample dataset

description:
BC-M-234
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-221 (mRNA)_115Sample dataset

description:
BC-M-221
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-210 (mRNA)_115Sample dataset

description:
BC-M-210
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-222 (mRNA)_115Sample dataset

description:
BC-M-222
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-201 (mRNA)_115Sample dataset

description:
BC-M-201
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-218 (mRNA)_115Sample dataset

description:
BC-M-218
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-185_new (mRNA)_115Sample dataset

description:
BC-M-185 (new)
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-493 (mRNA)_115Sample dataset

description:
BC-M-493
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-223 (mRNA)_115Sample dataset

description:
BC-M-223
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-106 (mRNA)_115Sample dataset

description:
BC-M-106
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-148 (mRNA)_115Sample dataset

description:
BC-M-148
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-119 (mRNA)_115Sample dataset

description:
BC-M-119
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-163 (mRNA)_115Sample dataset

description:
BC-M-163
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-139 (mRNA)_115Sample dataset

description:
BC-M-139
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-157 (mRNA)_115Sample dataset

description:
BC-M-157
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-101 (mRNA)_115Sample dataset

description:
BC-M-101
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-144 (mRNA)_115Sample dataset

description:
BC-M-144
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-167 (mRNA)_115Sample dataset

description:
BC-M-167
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-197 (mRNA)_115Sample dataset

description:
BC-M-197
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-122 (mRNA)_115Sample dataset

description:
BC-M-122
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-150 (mRNA)_115Sample dataset

description:
BC-M-150
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-107_new (mRNA)_115Sample dataset

description:
BC-M-107 (new)
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-100 (mRNA)_115Sample dataset

description:
BC-M-100
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-220 (mRNA)_115Sample dataset

description:
BC-M-220
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-146 (mRNA)_115Sample dataset

description:
BC-M-146
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-209 (mRNA)_115Sample dataset

description:
BC-M-209
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-132 (mRNA)_115Sample dataset

description:
BC-M-132
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-190 (mRNA)_115Sample dataset

description:
BC-M-190
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-091 (mRNA)_115Sample dataset

description:
BC-M-091
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-112 (mRNA)_115Sample dataset

description:
BC-M-112
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-098 (mRNA)_115Sample dataset

description:
BC-M-098
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-087 (mRNA)_115Sample dataset

description:
BC-M-087
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-088 (mRNA)_115Sample dataset

description:
BC-M-088
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-089 (mRNA)_115Sample dataset

description:
BC-M-089
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-086 (mRNA)_115Sample dataset

description:
BC-M-086
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-080 (mRNA)_115Sample dataset

description:
BC-M-080
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-071 (mRNA)_115Sample dataset

description:
BC-M-071
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-067 (mRNA)_115Sample dataset

description:
BC-M-067
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-064 (mRNA)_115Sample dataset

description:
BC-M-064
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-083 (mRNA)_115Sample dataset

description:
BC-M-083
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-085 (mRNA)_115Sample dataset

description:
BC-M-085
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-075 (mRNA)_115Sample dataset

description:
BC-M-075
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-068 (mRNA)_115Sample dataset

description:
BC-M-068
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-066 (mRNA)_115Sample dataset

description:
BC-M-066
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-065 (mRNA)_115Sample dataset

description:
BC-M-065
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-042 (mRNA)_115Sample dataset

description:
BC-M-042
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-057 (mRNA)_115Sample dataset

description:
BC-M-057
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-069 (mRNA)_115Sample dataset

description:
BC-M-069
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-079 (mRNA)_115Sample dataset

description:
BC-M-079
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-020 (mRNA)_115Sample dataset

description:
BC-M-020
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-017 (mRNA)_115Sample dataset

description:
BC-M-017
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-044 (mRNA)_115Sample dataset

description:
BC-M-044
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-034_new (mRNA)_115Sample dataset

description:
BC-M-034 (new)
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-023 (mRNA)_115Sample dataset

description:
BC-M-023
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-031 (mRNA)_115Sample dataset

description:
BC-M-031
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-019 (mRNA)_115Sample dataset

description:
BC-M-019
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-053 (mRNA)_115Sample dataset

description:
BC-M-053
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-022 (mRNA)_115Sample dataset

description:
BC-M-022
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-024 (mRNA)_115Sample dataset

description:
BC-M-024
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-015 (mRNA)_115Sample dataset

description:
BC-M-015
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-002 (mRNA)_115Sample dataset

description:
BC-M-002
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-018 (mRNA)_115Sample dataset

description:
BC-M-018
This breast tumor sample has previously been assayed in Series GSE3985.


title: BreastCancer-014 (mRNA)_115Sample dataset

description:
BC-M-014
This breast tumor sample has previously been assayed in Series GSE3985.


title: NIEL with array type Medicago from Affymetrix

status: Public on Oct 28 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Identification of genes from the model legume Medicago truncatula whose expression is affected by the plant nitrogen status, with or without inoculation with the symbiotic bacteria Sinorhizobium meliloti. - Comparison of the supernodulant, nitrogen-insensitive, sunn-2 mutant with the A17 wild type genotype.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Medicago truncatula

source_name: NIEL

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: root - Plants were grown hydroponically. The nutrient solution contained 1 mM KNO3, 1 mM KH2PO4, 1 mM MgSO4, 250 µM CaCl2, 0.1 mM Na-Fe-EDTA, 50 µM KCl, 50 µM H3BO3, 5µM MnSO4, 1 µM ZnSO4, 1 µM CuSO4, 0.1 µM Na6Mo7O24, pH adjusted to 6 with KOH. Plants were cultivated in growth chamber with the following environmental parameters: light/dark cycle 8/16h, light intensity 250 µmol.s-1.m-2 PAR, temperature 22degres/20degres, 70 per cent hygrometry. The nutrient solution was renewed once a week.

treatment_protocol: Name:Limited_NI - limited nitrogen supply - growth conditions,nitrogen:time 2week . N supply : one part of the root system is deprived of N and the other part is supplied with 0.5mM NO3-

tag: strain

value: wild-type A17

tag: age


title: NIDS with array type Medicago from Affymetrix

source_name: NIDS

treatment_protocol: Name:Sufficient_NI - sufficient nitrogen supply - growth conditions,nitrogen:time 2week . N supply: one part of the root system is deprived of N and the other part is supplied with 10mM NH4NO3


title: NIFL with array type Medicago from Affymetrix

source_name: NIFL


title: SBS with array type Medicago from Affymetrix

source_name: SBS

value: sunn-2 mutant


title: SBL with array type Medicago from Affymetrix

source_name: SBL


title: SAL with array type Medicago from Affymetrix

source_name: SAL


title: NIES with array type Medicago from Affymetrix

source_name: NIES


title: NIDL with array type Medicago from Affymetrix

source_name: NIDL


title: SCS with array type Medicago from Affymetrix

source_name: SCS


title: SAS with array type Medicago from Affymetrix

source_name: SAS


title: ICL with array type Medicago from Affymetrix

source_name: ICL

treatment_protocol: Name:Limited_I - limited nitrogen supply - growth conditions,nitrogen:time 2week . N supply : one part of the root system is deprived of N and the other part is supplied with 0.5mM NO3-


title: IAS with array type Medicago from Affymetrix

source_name: IAS

treatment_protocol: Name:Sufficient_I - sufficient nitrogen supply - growth conditions,nitrogen:time 2week . N supply: one part of the root system is deprived of N and the other part is supplied with 10mM NH4NO3


title: IBL with array type Medicago from Affymetrix

source_name: IBL


title: SCL with array type Medicago from Affymetrix

source_name: SCL


title: IBS with array type Medicago from Affymetrix

source_name: IBS


title: ICS with array type Medicago from Affymetrix

source_name: ICS


title: IAL with array type Medicago from Affymetrix

source_name: IAL


title: Liver_female_dex_rep1

status: Public on Oct 02 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Quality control checks of total RNA from each biological sample was made using an Agilent 2100 Bioanalyzer (Agilent Technologies). Three replicate microarrays were completed for each group (male vehicle, male dexamethasone, female vehicle and female dexamethasone) for a total of 12 microarrays. Each microarray was hybridized using a pooled RNA sample, and each pool was created from equal amounts of total RNA from three independent RNA samples, representing individual animals (n=9 animals per group). This approach provides appropriate biological replication within the constraints of a limiting number of microarrays (C. Kendziorski, R. A. Irizarry, K. S. Chen, J. D. Haag, M. N. Gould, Proc Natl Acad Sci U S A 102, 4252 Mar 22, 2005). Gene expression analysis was conducted using Agilent Whole Genome Rat 4x44 multiplex format oligo arrays (014879) (Agilent Technologies) Each array included 60-mer oligonucleotide probes for over 41,000 genes and transcripts

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.1).  The resulting data were imported into Rosetta Resolver (v7.1) and log10 intensities were exported.

organism: Rattus norvegicus

source_name: liver, dexamethasone (1mg/Kg i.p.), 6 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Tissues were homogenized and total RNA from tissues were extracted by using the RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. All samples were treated with the RNase-free DNase set (Qiagen). The integrity of the RNA samples was checked by resolving the total RNA on an agarose gel and visualizing the 18S and 28S ribosomal bands after staining the gel with ethidium bromide. Samples were aliquoted and frozen at -80C

tag: Strain:Sprague-dawley, Gender

value: Female, Age:8-10 weeks, Adrenalectomized, Tissue:liver, Cycle:Diestrous 1


title: Liver_female_dex_rep3


title: Liver_female_veh_rep3

source_name: liver, vehicle, 6 hours


title: Liver_male_dex_rep3

value: Male, Age:8-10 weeks, Adrenalectomized, Tissue:liver


title: Liver_female_veh_rep1


title: Liver_female_veh_rep2


title: Liver_female_dex_rep2


title: Liver_male_veh_rep3


title: Liver_male_dex_rep1


title: Liver_male_dex_rep2


title: Liver_male_veh_rep2


title: Liver_male_veh_rep1


title: Mouse liver_PND7_26

status: Public on Oct 01 2010

first: Hongzu

last: Ren

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

description: gene expression data from developing mouse liver

hyb_protocol: Samples were hybridized according to the Affymetrix protocol

scan_protocol: Affymetrix protocol using a GeneChip scanner 3000

data_processing: Affymetrix GeneChip microarray suite software was used for washing and scanning. The version of GCOS used was 1.4.0.036. Statistically significant genes were calculated in Rosetta Resolver using the gene-specific error model and one-way ANOVA with a FDR less than or equal to 0.05 followed by a post-hoc test for significance.

label: biotin

organism: Mus musculus

source_name: liver sample from a PND7 mouse

label_protocol: Samples were labeled according to the Affymetrix protocol

extract_protocol: Total RNA was isolated using the TriReagent procedure (Molecular Research Center, Cincinnati, OH) and the Qiagen Rneasy mini RNA cleanup protocol (Qiagen, Valencia, CA)

treatment_protocol: Timed-pregnant dams were purchased from Charles River Laboratory (Raleigh, NC) and acclimated for 1 week. Mice were housed (1 per cage) in polycarbonate cages on Alpha-dri bedding. Animal facilities were controlled for temperature (20-24C) and relative humidity (40-60%), and kept under a 12-h light-dark cycle. The basal diet was pellet chow (LabDiet 5001, PMI Nutrition International LLC, Brentwood, MO) and tap water was provided ad libitum. Pregnant dams were sacrificed at GD19 and male pups were sacrificed by decapitation. Mice from additional litters at ages PND7, PND32, and PND67 were sacrificed using CO2 asphyxiation. Livers were removed, weighed and sections from the left and median lobes were fixed in formalin, embedded, sectioned, and stained with H&E. The remainder of the liver was cubed and stored at -80°C until RNA isolation.

value: liver

tag: developmental stage

value: PND7 mouse


title: Mouse liver_PND7_30


title: Mouse liver_PND32_37

source_name: liver sample from a PND32 mouse

value: PND32 mouse


title: Mouse liver_PND32_40


title: Mouse liver_PND67_47

source_name: liver sample from a PND67 mouse

value: PND67 mouse


title: Mouse liver_PND67_49

data_processing: Affymetrix GeneChip microarray suite software was used for washing and scanning.The version of GCOS used was 1.4.0.036. Statistically significant genes were calculated in Rosetta Resolver using the gene-specific error model and one-way ANOVA with a FDR less than or equal to 0.05 followed by a post-hoc test for significance.


title: Mouse liver_PND7_29


title: Mouse liver_GD19_10

source_name: liver sample from a GD19 mouse

value: GD19 mouse


title: Mouse liver_GD19_18


title: Mouse liver_PND67_45


title: Mouse liver_GD19_4


title: Mouse liver_PND32_34


title: Mouse liver_PND67_46


title: Mouse liver_PND32_33


title: Mouse liver_PND7_31


title: Mouse liver_GD19_5


title: SigmaLPS3_24hrsCy5

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

hyb_protocol: Agilent hyb reagents and protocol.

scan_protocol: Agilent scanner - default settings.

data_processing: Feature Extraction Version A.7.5.1

source_name: Universal mouse reference RNA

label_protocol: Aminoallyl labeling (TIGR protocol).

growth_protocol: RAW 264.7 cells were maintained in RPMI 1640 supplemented with 10% FBS and 200 μg/ml gentamicin (Invitrogen Life Technologies).  For stimulation of the RAW 264.7 cell, cells were plated in 6-well culture plates (3 x 10^6/well) overnight. The overnight growth was performed to allow resting before stimulation.

extract_protocol: Cells were harvested 6 or 24 hours post-treatment and RNA was extracted using Trizol and following manufacturers protocols (Invitrogen Life Technologies)

treatment_protocol: Cells were washed twice with Opti-MEM (Invitrogen Life Technologies) and stimulated with  50 ng/ml Escherichia coli 0111:B4 Ultrapure LPS (List Biological Laboratories) or 0111:B4 LPS (Sigma)

tag: sample type

value: Stratagene cat number 740100

tag: cell line

value: RAW264.7 macrophages

tag: treatment

value: Sigma LPS

tag: amount

tag: time

value: 24 hrs


title: SigmaLPS3_6hrsCy3


title: SigmaLPS2_24hrsCy3


title: Media6_24hrsCy5

value: media control


title: SigmaLPS1_6hrsCy3


title: SigmaLPS2_6hrsCy5


title: Media6_6hrsCy5

value: 6 hrs


title: SigmaLPS2_24hrsCy5


title: SigmaLPS2_6hrsCy3


title: Media6_24hrsCy3


title: SigmaLPS1_24hrsCy5


title: SigmaLPS3_6hrsCy5


title: SigmaLPS1_6hrsCy5


title: Media5_6hrsCy3


title: SigmaLPS3_24hrsCy3


title: SigmaLPS1_24hrsCy3


title: Media5_24hrsCy5


title: Media5_6hrsCy5


title: NIFS with array type Medicago from Affymetrix

source_name: NIFS


title: Media4_6hrCy3


title: Media4_24hrsCy5


title: Media3_6hrsCy5


title: Media3_24hrsCy3


title: Media3_6hrsCy3


title: Media3_24hrsCy5


title: Media4_24hrsCy3


title: Media5_24hrsCy3


title: Media2_6hrsCy5


title: Media2_6hrsCy3


title: BreastCancer-003 (mRNA)_115Sample dataset

description:
BC-M-003
This breast tumor sample has previously been assayed in Series GSE3985.

source_name: Breast Primary Tumor

tag: tissue

value: Breast

value: Breast Primary Tumor

value: Lum A

value: WT

value: Alive

value: Positive

value: Negative


title: Media2_24hrsCy5


title: Media1_24hrsCy3


title: LIST_LPS3_24hrsCy5

value: Ultrapure LPS (LIST)


title: LIST_LPS3_24hrsCy3


title: LIST_LPS3_6hrsCy3


title: Media1_6hrsCy5


title: LIST_LPS2_24hrsCy3


title: LIST_LPS2_6hrsCy5


title: LIST_LPS3_6hrsCy5


title: Media2_24hrsCy3


title: LIST_LPS1_6hrsCy5


title: Media1_6hrsCy3


title: LIST_LPS2_6hrsCy3


title: Media1_24hrsCy5


title: LIST_LPS2_24hrsCy5


title: LIST_LPS1_24hrsCy3


title: LIST_LPS1_6hrsCy3


title: LIST_LPS1_24hrsCy5


title: EBFko-3

status: Public on Sep 30 2010

city: Rochester

first: Kay

middle: L

last: Medina

state: MN

address: 200 1st Street SW

department: Immunology

institute: Mayo Clinic

description: lymphoid specified

hyb_protocol: Bio cRNA hybridized to Affymetrix 430 2.0 arrays per manufacturer's instructions.

scan_protocol: Arrays scanned using Affymetrix GeneChip Scanner 3000.

data_processing: GCRMA normalization followed by ANOVA analysis of variance performed to identify statistically significant differentially expressed genes (parametric test, variances not assumed equal by Welch t-test, p-value cutoff 0.05). Data from the three individual EBFko, Pax5ko, or RAG2ko samples was merged during the GC-RMA normalization to generate only a single GC-RMA normalized file for each cell type. GC-RMA data available on Series record.

source_name: EBFko

label_protocol: Total RNA converted to cDNA using Superscript cDNA synthesis kit. Double stranded cDNA purified by phase lock gel with phenol chloroform extraction. Purified cDNA in vitro transcribed into biotin cRNA using Affymetric labeling reagent.

growth_protocol: EBFko and Pax5 ko cell grown in standard culture medium's supplemented with 10ng/ml of recombinant human Flt3-ligand and 10ng/ml recombinant mouse IL-7. RAG2ko cells grown in 10ng/ml recombinant mouse IL-7.

extract_protocol: RNA extract using Qiagen kit per manufacturer's instructions. Integrity of the RNA was evaluated using the Agilent 2100 bioanalyzer.

treatment_protocol: no treatments performed

value: EBF deficient


title: Pax5ko-3

description: B lineage specified

value: Pax5 deficient


title: RAG2ko-1

description: B lineage committed

value: RAG2 deficient


title: EBFko-2

description: lymphoid specified


title: Pax5ko-2

description: B lineage specified


title: RAG2ko-3

description: B lineage committed


title: Pax5ko-1

description: B lineage specified


title: RAG2ko-2

description: B lineage committed


title: EBFko-1

description: lymphoid specified


title: 6259-3163-Cy3

status: Public on Sep 21 2010

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

country: Germany

institute: German Cancer Research Center (DKFZ)

description: log2 ratio Cy5/Cy3

hyb_protocol: Array platform: 70 mer oligonucleotides (Human Oligo Set 4.0; Operon, Cologne, Germany). Pretreatment of slides: 2 min in 0.2perc SDS; 2 min in ddH2O at RT; 2 min in ddH2O at 95C, followed by 1 min centrifugation at 1000 rpm. Application of preheated (60 min 60C, 10 min 70C), dye-labeled cDNA in Ultra-Hyb hybridization buffer on microarrays in a GeneTAC Hybridization Station. Hybridization for 40h at 42C with gentle agitation. Wash steps: 36C; 5 min 0.5xSSC, 0.1perc SDS; 3 min 0.05xSSC, 0.1perc SDS; 20s 0.05xSSC; 20s 0.05xSSC, 0.1perc Tween20.

scan_protocol: Scanning of hybridized microarrays at 5 um resolution and variable PMT voltage to obtain maximal signal intensities with < 0.1perc probe saturation, a count ratio of 0.8.1.2 (Cy5/Cy3) and maximal congruence of histogram curves using a GenePix 4000B microarray scanner (Axon Instruments, Union City, USA).

data_processing: Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002).

source_name: culture type: control

label_protocol: Sample labelling by Klenow reaction using Cy3- or Cy5-labeld dUTP. Purification of labelled samples on Microcon YM-30 filter columns. Addition of blocking reagents: 25 ug Cot-1 DNA, 25 ug poly-A RNA, and 75 ug yeast tRNA.

extract_protocol: Total RNA isolation by Trizol extraction and purification on RNeasy Mini spin columns. Amplification of RNA by first- and second-strand cDNA synthesis. In vitro transcription of extracted cDNA by RiboMAX Large Scale RNA Production System T7.

tag: sex

value: M

value: control

value: in old annotation control was named 'co'

tag: time point

value: 0 days

source_name: culture type: HCo

value: sample

value: HCo

value: 3 days


title: 6467-3165-Cy3

description: log2 ratio Cy5/Cy3

value: F


title: 6469-3167-Cy3

description: log2 ratio Cy5/Cy3


title: 14616-14665-Cy3

description: log2 ratio Cy5/Cy3

hyb_protocol: Array platform: 70 mer oligonucleotides (Human Oligo Set 4.0; Operon, Cologne, Germany). Pretreatment of slides: 20 min at 50C in slide blocking mix (0,3perc Ethanolamine; 0,1perc SDS, 0,1M Tris pH 9.0); 2 min at RT in ddH2O, briefly at 95C in ddH2O. Application of preheated (30 min at 60C), dye-labeled cDNA in SureHyb-chambers of Agilent Hybridization Station. Hybridization for 23h at 42C with 4 rpm rotation speed. Wash steps: 4 min 0.5xSSC, 0.1perc SDS; 3 min 0.05xSSC, 0.1perc SDS; 2 min 0.05xSSC; 30 sec 0.05xSSC, 0.05perc Tween20.

source_name: culture type: CD

value: B-CLL 58

value: CD

value: 1 days


title: 14655-14659-Cy3

description: log2 ratio Cy5/Cy3

value: B-CLL 61


title: 14619-14663-Cy5

description: log2 ratio Cy5/Cy3

value: B-CLL 59


title: 13100-13102-Cy3

description: log2 ratio Cy5/Cy3

source_name: culture type: CM

value: B-CLL 48

value: CM

value: 2 days


title: 14652-14661-Cy5

description: log2 ratio Cy5/Cy3

value: B-CLL 60


title: 6469-3167-Cy5

description: log2 ratio Cy5/Cy3


title: 6257-2954-Cy5

description: log2 ratio Cy5/Cy3

value: M


title: 6257-2954-Cy3

description: log2 ratio Cy5/Cy3

value: control


title: 14652-14661-Cy3

description: log2 ratio Cy5/Cy3


title: 14655-14659-Cy5

description: log2 ratio Cy5/Cy3


title: 14619-14663-Cy3

description: log2 ratio Cy5/Cy3


title: 6257-2955-Cy5

description: log2 ratio Cy5/Cy3

value: in old annotation control was named 'co'


title: 13100-13102-Cy5

description: log2 ratio Cy5/Cy3

value: 0 days


title: 14616-14665-Cy5

description: log2 ratio Cy5/Cy3

value: sample


title: PPC1_non-target shRNA_replicate 3

status: Public on Sep 01 2010

city: Shreveport

first: Shari

last: Meyers

state: LA

address: 1501 Kings Highway

department: Biochemistry and Molecular Biology

institute: LSU Health Sciences Center-Shreveport

description: gene expression in non-target shRNA-expressing PPC1 cells

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: prostate cancer cell line, non-target control

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Lentiviral infected PPC1 cells were maintained in RPMI containing 10% fetal calf serum, pen/strep, L-glutamine and 1 microgram/ml puromycin. Cells were subcultured 1:2 every 3 to 4 days.

extract_protocol: Total RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Asynchronously growing NT and CBFbeta knockdown cells were used for the RNA isolation.

value: prostate cancer, PPC1


title: 12618-12620-Cy3

description: log2 ratio Cy5/Cy3

value: B-CLL 46


title: PPC1_CBFbeta shRNA replicate 3

description: gene expression in CBFbeta shRNA-expressing PPC1 cells

source_name: prostate cancer cell line, CBFbeta knockdown


title: PPC1_CBFbeta shRNA replicate 2


title: U937 transfected with GFP-PRWT,9 hours post infection, replicate 2

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

hyb_protocol: 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.

scan_protocol: Gene chips were scanned using GS3000.

data_processing: To perform inter-array comparisons, the raw data for each array were scaled to an average intensity of 1,500 with Affymetrix Microarray Suite software and the (MAS5) statistical algorithm. Probesets were filtered to remove those that did not have at least 2 present calls in at least 1 of the groups (GFP, GFP-PR, GFP-PR_2VR). The remaining probesets were subjected to ANOVA, with differentially expressed genes defined at a significance level of p<0.01. MAS5-generated signal intensities were normalized to z-scores for hierarchical clustering and heatmap creation only. Statistical analysis, hierarchical clustering, and creation of heat maps were performed with Spotfire software (Spotfire, Somerville, MA).

source_name: U937 cell line

label_protocol: Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug 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: Transfection of pEGFP, pEGFP-PRWT and pEGFP-PR2VR in U937 cells was performed by electroporation (BTX).

value: U937 cells

tag: transfectant

value: transfected with plasmid containing wild type PML-RARα cDNA (pEGFP-PRWT )


title: U937 transfected with GFP-PRWT,6 hours post infection, replicate 1


title: PPC1_non-target shRNA_replicate 2


title: U937 transfected with GFP-PR2VR, 9 hours post infection, replicate 2

value: transfected with plasmid containing wild type PML-RARα cDNA (pEGFP-PR2VR )


title: PPC1_non-target shRNA_replicate 1


title: U937 transfected with control GFP, 9 hours post transfection, replicate 2

value: transfected with plasmid containing control GFP


title: U937 transfected with GFP-PRWT,6 hours post infection, replicate 2


title: U937 transfected with GFP-PR2VR, 6 hours post infection, replicate 1


title: U937 transfected with GFP-PR2VR, 6 hours post infection, replicate 2


title: PPC1_CBFbeta shRNA replicate 1


title: U937 transfected with control GFP, 6 hours post transfection, replicate 2


title: U937 transfected with GFP-PRWT,9 hours post infection, replicate 1


title: U937 transfected with control GFP, 6 hours post transfection, replicate 1


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_3798

status: Public on Aug 31 2010

city: Toronto

first: Boyko

last: Kabakchiev

state: Ontario

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

country: Canada

institute: Mount Sinai Hospital

hyb_protocol: Samples were hybridized using Affymetrix GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Probesets lacking annotation information were removed from further analysis. Raw data were background corrected, log transformed, and quantile normalized using a robust multi-array average (RMA) algorithm in R. All 40 samples were scaled using the R function “scale” (http://www.r-project.org/), and then correlated with a binary intravenous-corticosteroid therapy response variableusing the local-pooled error (LPE) method for detection of significance while controlling for batch effects.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: peripheral blood, 3 days on IVCS therapy

label_protocol: Samples were labeled using Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay - 100 ng Total RNA Labeling Protocol

extract_protocol: Total RNA was extracted from all samples using the PAXgene Blood RNA Kit (QIAGEN).

treatment_protocol: Blood samples were collected in PAXgene tubes (PreAnalytiX, QIAGEN) and were incubated at room temperaturte between 2 and 24 hours priot to being frozen at -20°C. Samples were then stored at -80°C until extraction.

value: peripheral blood

tag: age (in years)

value: No

tag: batch


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2203


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_3698


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2487


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2417

value: second line therapy


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2356


title: U937 transfected with control GFP, 9 hours post transfection, replicate 1


title: U937 transfected with GFP-PR2VR, 9 hours post infection, replicate 1


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2543


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2261


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2580


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2349


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2642

value: Yes

value: discharged


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_3131


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2403


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_3056


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_3062


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2972


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2908


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_3239


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2365


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_3609


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2486


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2446


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2370


title: peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_2451


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_3230


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2113


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_3353


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_3605


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2466


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2371


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2518


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2366


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2123


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2545


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_3274


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2372


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2986


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2354


title: Phloem 3B

status: Public on Aug 01 2010

city: corvallis

first: palitha

last: dharmawardhana

state: OR

address: 321 richarson hall,OSU

institute: OSU

description: Nimblegen pipeline

hyb_protocol: Nimblegen pipeline

scan_protocol: Nimblegen pipeline

data_processing: Nimblegen pipeline, RMA normalization algorithm.

organism: Populus trichocarpa

source_name: Phloem scrapings from an actively growing tree

label_protocol: Nimblegen pipeline

tag: tissue type

tag: tissue source

value: Populus trichocarpa Nisqually-1


title: Xylem 2C

description: Nimblegen pipeline

organism: Populus tremula x Populus alba

source_name: Xylem scrapings from an actively growing tree

value: Populus tremula X Populus alba hybrid


title: Xylem 2A

description: Nimblegen pipeline

value: Xylem scrapings from an actively growing tree


title: RTC1

description: Nimblegen pipeline

source_name: Roots from tissue culture

value: Roots from tissue culture


title: Xylem 1C

description: Nimblegen pipeline


title: Xylem 2B

description: Nimblegen pipeline


title: peripheral blood collected on day 3 from a pediatric responder to IVCS therapy SID_2384


title: RFF2

description: Nimblegen pipeline

source_name: Roots from field trees

value: Roots from field trees


title: AxB2

description: Nimblegen pipeline

source_name: Axillary buds

value: Axillary buds


title: AxB1

description: Nimblegen pipeline


title: Xylem 1B

description: Nimblegen pipeline


title: ApB2

description: Nimblegen pipeline

source_name: Shoot apex

value: Shoot apex


title: ApB1

description: Nimblegen pipeline


title: YFB2

description: Nimblegen pipeline

source_name: Female floral bud initials

value: Female floral bud initials

value: Populus trichocarpa


title: Phloem 3A

description: Nimblegen pipeline

value: Phloem scrapings from an actively growing tree


title: YMB2

description: Nimblegen pipeline

source_name: Male floral bud initials

value: Male floral bud initials


title: Xylem 1A

description: Nimblegen pipeline


title: YMB1

description: Nimblegen pipeline


title: G43h2

description: Nimblegen pipeline

source_name: Seedling 43 hr post-imbibition

value: Seedling 43 hr post-imbibition


title: Con-2 vs 0.625-3

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description: Hybridizations conducted using Balanced, Interwoven Loop Design: 2 Dyes Swaps and 4 total technical replicates

hyb_protocol: Products of the cDNA synthesis reactions were combined according to dye-swap assignments and hybridized onto microarrays.  Two µL of blocking agent, locked nucleic acid (LNA) dT Blocker (Genisphere) was included in each hybridization.  RNA sample probes were hybridized at 55ºC overnight (~16h) then washed for 20 min in 60ºC 2x SSC including 0.2% SDS, 20 min in 2x SSC at room temperature, and 20 min in 0.2x SSC also at room temperature.  Slides were then spin dried and subsequently hybridized to A647 and Cy3 labeled secondary hybridization probes in 100 µL hybridization buffer with 1 µL of Anti-Fade Reagent for 4h at 60ºC.  Microarrays were washed as described above only at 15 minute wash intervals and spin dried.  Slides were stored for no more than 1 week in a darkened desiccation chamber prior to microarray scanning.

scan_protocol: Microarrays were scanned at 5μm using a VersArray Chipreader™ (Bio-Rad, Hercules, CA).  Grids were manually fit to microarray spots for each image file and both positive and negative controls were flagged prior to spot analysis.  Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from the analysis

data_processing: Summary data consisted of LOWESS-normalized Cy3:A647 ratio values calculated using background-normalized median-signal intensities.  The statistical analysis was conducted using Bayesian Analysis of Gene Expression Levels (BAGEL) software version 3.62 (Townsend and Hartl, 2002).  Non-overlapping 97.5% confidence intervals (C.I.) among treatments were established a priori as statistically significant differences in expression.

organism: Pimephales promelas

source_name: Control, replicate 2

label_protocol: Microarray experiments were conducted using a balanced interwoven-loop design using Cyanine-3 (Cy3) and A647.  The experiment compared controls with 0.625, 2.5, 5 and 10 mg/L RDX-exposed fish with each condition including 3 biological replicates.  Hybridizations included four technical replicates and two dye swaps per biological replicate resulting in a total of 30 micorarrays assayed.  Probes for microarray hybridizations were prepared from 600 ng total RNA / sample following the Genisphere®, Array 900™ Alexa Fluor 647 and Cy3 secondary hybridization labeling protocol (Genisphere, Hatfield, PA) according to manufacturer’s instructions.

growth_protocol: Fish for each treatment were reared in a 25L aquarium where water quality parameters including temperature, dissolved oxygen, pH, ammonia concentration, hardness, and alkalinity were measured at the initiation and termination of each bioassay.  During the bioassays, temperature, dissolved oxygen, and pH were measured on days 1, 2 and then every other day until bioassay termination.

extract_protocol: RNeasy® Mini RNA extraction kits (Qiagen, Valencia, CA) were used for total RNA extractions.  RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) with RNA 6000 Nano LabChips® RNA. Only samples with a 28s/18s ratio {greater than or equal to} 1.4 and RNA integrity number (RIN) {greater than or equal to} 6 were used for downstream applications.  The majority of RNA samples greatly exceeded these minimum requirements.    Total RNA was utilized for cDNA library construction, microarray analysis and RT-qPCR.

treatment_protocol: Fathead minnows were exposed to RDX in a 10d dose-series experiment (0.625, 1.25, 2.5, 5.0, or 10 mg/L) which included an acetone-spike control (1% acetone).  Each experimental treatment included 8 replicate fish.

tag: agent

value: none, control

value: Fathead minnow brain tissue

source_name: RDX 0.625, replicate 3

value: RDX

tag: dose


title: Con-2 vs 0.625-4

source_name: RDX 0.625, replicate 4


title: Con-1 vs 0.625-3

source_name: Control, replicate 1


title: 5-5 vs 10-2

source_name: RDX 5, replicate 5

source_name: RDX 10, replicate 2


title: YFB1

description: Nimblegen pipeline


title: 10-4 vs Con-1

source_name: RDX 10, replicate 4


title: RFF1

description: Nimblegen pipeline


title: Con-4 vs 0.625-2

source_name: Control, replicate 4

source_name: RDX 0.625, replicate 2


title: 10-2 vs Con-4


title: G43h1

description: Nimblegen pipeline


title: 10-4 vs Con-2


title: 10-3 vs Con-4

source_name: RDX 10, replicate 3


title: Con-1 vs 0.625-2


title: 10-3 vs Con-1


title: 5-4 vs 10-3

source_name: RDX 5, replicate 4


title: 10-2 vs Con-2


title: 5-2 vs 10-3

source_name: RDX 5, replicate 2


title: 5-5 vs 10-4


title: 2.5-3 vs 5-2

source_name: RDX 2.5, replicate 3


title: 5-2 vs 10-2


title: 2.5-2 vs 5-5

source_name: RDX 2.5, replicate 2


title: Con-4 vs 0.625-4


title: 2.5-3 vs 5-5


title: 2.5-2 vs 5-4


title: 5-4 vs 10-4


title: 2.5-1 vs 5-2

source_name: RDX 2.5, replicate 1


title: 2.5-1 vs 5-4


title: 0.625-3 vs 2.5-3


title: 0.625-4 vs 2.5-1


title: 0.625-4 vs 2.5-3


title: 0.625-3 vs 2.5-2


title: 0.625-2 vs 2.5-2


title: 13757355 - Col0-ld-2 vs cat2xcad2-ld-2

status: Public on Jul 22 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

description:
ch1: arabidopsis thaliana (columbia)  mutant (cat2xcad2) - harvest date: 07-07-08
ch2: arabidopsis thaliana (columbia)  - harvest date: 07-07-08
How does glutathione content or reduction state affect H2O2-induced changes in the transcriptome?

hyb_protocol: cat2xcad2-ld-2 Cy5 / Col0-ld-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media=soil hygrometry=70% Temperature=25°C  Light=200 µmol/m2/s long day=16h photoperiod.

treatment_protocol: no treatment

tag: genetic background

value: Columbia

tag: genotype

value: mutant (cat2xcad2) -

tag: harvest date

value: wild type


title: 13757357 - Col0-ld-2 vs cytGR-ld-2

description:
ch1: arabidopsis thaliana (columbia)  mutant (cytgr) - harvest date: 07-07-08
ch2: arabidopsis thaliana (columbia)  - harvest date: 07-07-08
How does glutathione content or reduction state affect H2O2-induced changes in the transcriptome?

hyb_protocol: cytGR-ld-2 Cy5 / Col0-ld-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: mutant (cytgr) -