title: MSCs from young (3months) treated female rats, treated with Dex

status: Public on Aug 08 2006

type: RNA

city: Tel Aviv

first: Dafna

last: Benayahu

department: Cellular and Developmental Biology, Sackler Faculty of Medicine

country: Israel

institute: Tel Aviv University

description: Cells were harvested from 6 rats. Cells were plated and after one week of culturing were trypsinized; single cell suspensions were re-cultured for 7 days and were grown inpresence of 10-8 M Dexamethasone (Dex).

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Mesenchymal Stromal Cells

extract_protocol: Total RNA was extracted from the tissue lysate using a Trizol kit.

tag: Wild type, Dex treated, female, 3m, MSCs.


title: MSCs from old (15months) treated female rats

tag: Wild type, Dex treated, female, 15m, MSCs.


title: MSCs from old (15months) untreated female rats

description: Cells were harvested from 6 rats. Cells were plated and after one week of culturing were trypsinized; single cell suspensions were re-cultured for 7 days.

tag: Wild type, untreated, female, 15m, MSCs.


title: pancreas, ethanol diet, replicate 1

status: Public on Jul 01 2006

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

country: USA

institute: University of Michigan

description: Rat pancreas, ethanol diet

data_processing: Ann Arbor quantile-normalized trimmed-mean method

source_name: pancreas

label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.

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

tag: pancreas, ethanol diet, male Wistar rat


title: pancreas, ethanol diet, replicate 2

description: Rat pancreas, ethanol diet


title: right atrium, obese 4-lean 4

status: Public on Jul 05 2006

city: Toulouse

first: Philippe

middle: V

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

country: France

institute: INSERM U1048

description: Lean rats can be homozygous or heterozygous for the leptin receptor gene (+/+ or cp/+, cp means corpulent allele and is a recessive autosomic one, + means wild type)

hyb_protocol: kit Pronto plus System 6 (Corning Incorporated and Promega Corporation)

scan_protocol: Scan with Genepix 4100 A (Axon Instrument). Image analysis by Genepix version 6 (Axon Instrument).

data_processing: background subtraction, log transformation, normalization by total mean

source_name: right atrium, obese-4

label_protocol: Reverse Transcription of 5 µg total RNA from each right atrium with Superscript enzyme (Invitrogen). Using of Cy5-dCTP from Amersham Society

growth_protocol: Animals were lodged in the Zootechnic service of the Louis Bugnard Institute. A veterinary oversees animal health and management. Temperature : 22 +/- 1 degrees. Cycles nights/days : 12 hours. Food : Teklad Global 16% Protein Rodent Diet (Harlan)

extract_protocol: General anesthesia by Isoflurane 4%. Heart extraction. Isolation of total RNA from left ventricular by : TRIzol (Invitrogen), homogeneisor Ika Ultra-Thurax T 25 (Janke and Kunkel), DNAfree (Ambion). Quality and quantity were determined by capillary electrophoresis (Agilent).

tag: Strain

value: SHHF, Gender:Male, Age:10 months old, Tissue:right atrium, Other:hypertension, metabolic syndrom, dilated cardiomyopathy starting from 10 months old

source_name: right atrium, lean 4

label_protocol: Reverse Transcription of 5 µg total RNA from each right atrium with Superscript enzyme (Invitrogen). Using of Cy3-dCTP from Amersham Society

value: SHHF, Gender:Male, Age:10 months old, Tissue:right atrium, Other:hypertension, dilated cardiomyopathy starting from 14 months old


title: right atrium, obese 5-lean 3

source_name: right atrium, obese-5

value: SHHF, Gender:Male,

tag: Age

value: 10 months old,

tag: Tissue

value: right atrium,

tag: Other

value: hypertension, metabolic syndrom, dilated cardiomyopathy starting from 10 months old

source_name: right atrium, lean-3

value: hypertension, dilated cardiomyopathy starting from 14 months old


title: MSCs from young untreated male rats

description: Cells were plated and after one week of culturing were trypsinized; single cell suspensions were re-cultured for 7 days.

tag: Wild type, untreated, male, MSCs.


title: MSCs from young (3months) untreated female rats

tag: Wild type, untreated, female, 3m, MSCs.


title: right atrium, obese 1-lean 5

source_name: right atrium, obese-1

source_name: right atrium, lean 5


title: pancreas, control diet, replicate 2

description: Rat pancreas, control diet

tag: pancreas, control diet, male Wistar rat


title: pancreas, ethanol diet, replicate 3

description: Rat pancreas, ethanol diet


title: pancreas, control diet, replicate 1

description: Rat pancreas, control diet


title: pancreas, control diet, replicate 3

description: Rat pancreas, control diet


title: KG-1 treated with various Cordyceps sinensis extract_S1_QCS1/QFB

status: Public on Jul 26 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: We applied loop design for our microarray experiments in order to reduce the systemic error.

hyb_protocol: 3 DNA array 50 Kit protocol (Genisphere)

scan_protocol: Barcode=12605193 "PMTGain=800	500" Scanner=GenePix 4000B [81963] "LaserPower=3.18	4.41" Temperature=25.38 "ScanPower=33	33"

data_processing: Data processing will be described in detail in our website http://140.114.106.30/publication/mltsai/

organism: Homo sapiens

source_name: KG-1 treated with QCS1 extract 20μl/ml, 4 days

growth_protocol: Fresh medium and Cordeceps extracts were replaced at day 2 after seeding. Cells were harvested at day 4 .

extract_protocol: Total RNA was isolated using Trizol reagent and purified by RNeasy . The quality of RNA was examined by capillary electrophoresis (Agilent chip).

treatment_protocol:
The KG-1 cells were treated with 20μl/ml of Qinghai intact Cordyceps sinensis(QCS) water extracts.

In order to evaluate the quality of microarray result, duplicated QCS extract-treated samples, denoted as QCS-1 and QCS-2, were included as internal control samples.

tag: Cell line:

tag: KG-1 is a human CD34+ hemotopoietic progenitor cell line that has been used as an in vitro cell model system for the study of dendritic cells .

tag: TCM:

tag: Cordyceps sinensis, a parasitic fungus, infects the caterpillar larva of the moth Hepilus fabricius.It is a well-known nutritious tonic and one of the most valuable Chinese herbal medicines.

source_name: KG-1 treated with QFB extract 20μl/ml, 4 days

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai fruiting body Cordyceps sinensis(QFB) water extracts.

tag: cell line:


title: coronary smooth muscle cells nebivolol replicate 3

status: Public on May 01 2006

city: Tuebingen

first: Bernhard

middle: R.

last: Brehm

address: Otfried-Mueller-Str. 10

country: Germany

institute: University of Tuebingen

description: human coronary artery smooth muscle Cells, treated with nebivolol, replicate 3

source_name: coronary smooth muscle cells (hcaSMC), treated with nebivolol for 72 hours

label_protocol: Approximately 7 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: total RNA of human coronary artery smooth muscle (hcaSMC) cultivated in SMGM-2-MV bulletkit medium were isolated after incubation with nebivolol for 72 hours using Trizol and purified with RNeasy spin columns.

tag: nebivolol treated muscle cells


title: right atrium, obese 3-lean 4

source_name: right atrium, obese-3


title: coronary smooth muscle cells nebivolol replicate 2

description: human coronary artery smooth muscle Cells, treated with nebivolol, replicate 2


title: coronary smooth muscle cells control replicate 3

description: human coronary artery smooth muscle Cells, untreated control, replicate 3

source_name: coronary smooth muscle cells (hcaSMC), treated with control medium for 72 hours

extract_protocol: total RNA of human coronary artery smooth muscle (hcaSMC) cultivated in SMGM-2-MV bulletkit medium were isolated after incubation with control medium for 72 hours using Trizol and purified with RNeasy spin columns.

tag: control, untreated muscle cells


title: coronary smooth muscle cells control replicate 2

description: human coronary artery smooth muscle Cells, untreated control, replicate 2


title: coronary smooth muscle cells metoprolol replicate 1

description: human coronary artery smooth muscle Cells, treated with metoprolol, replicate 1

source_name: coronary smooth muscle cells (hcaSMC), treated with metoprolol for 72 hours

extract_protocol: total RNA of human coronary artery smooth muscle (hcaSMC) cultivated in SMGM-2-MV bulletkit medium were isolated after incubation with metoprolol for 72 hours using Trizol and purified with RNeasy spin columns.

tag: metoprolol treated muscle cells


title: coronary smooth muscle cells metoprolol replicate 3

description: human coronary artery smooth muscle Cells, treated with metoprolol, replicate 3


title: coronary smooth muscle cells metoprolol replicate 2

description: human coronary artery smooth muscle Cells, treated with metoprolol, replicate 2


title: Growthplate: 6 week fracture

status: Public on Mar 31 2006

city: Charlotte

first: Ralph

middle: A.

last: Meyer

state: NC

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

description: growthplate from fractured femur, 6 weeks after fracture

hyb_protocol: Standard Affymetrix hybridization

scan_protocol: Affymetrix GeneArray Scanner 3000

data_processing: all genes scaled to 500

label: SAPE

source_name: SD rat proximal femoral growthplate

label_protocol: Standard Affymetrix sample preparation

treatment_protocol: Study of rat proximal femoral growthplate after mid-shaft fracture in 4 week old Sprague-Dawley female rats. Two rats were pooled for each sample. Proximal femoral growthplate was studied from the fractured femora and the intact contralateral femora.

tag: SD female rat


title: Growthplate, 3 week control

description: control growthplate from intact femur, 3 weeks after fracture


title: Growthplate: 4 week fracture

description: growthplate from fractured femur, 4 weeks after fracture


title: coronary smooth muscle cells nebivolol replicate 1

description: human coronary artery smooth muscle Cells, treated with nebivolol, replicate 1


title: coronary smooth muscle cells control replicate 1

description: human coronary artery smooth muscle Cells, untreated control, replicate 1


title: Growthplate, 6 week control

description: control growthplate from intact femur, 6 weeks after fracture


title: Growthplate: 2 week control

description: control growthplate from intact femur, 2 weeks after fracture


title: Growthplate: 2 week fracture

description: growthplate from fractured femur, 2 weeks after fracture


title: Growthplate: 4 week control

description: control growthplate from intact femur, 4 weeks after fracture


title: Growthplate: 3 week fracture

description: growthplate from fractured femur, 3 weeks after fracture


title: Growthplate: 3 day fracture

description: growthplate from fractured femur, 3 days after fracture


title: Growthplate, 1 day fracture

description: growthplate from fractured femur, 1 day after fracture


title: Growthplate: 1 week fracture

description: growthplate from fractured femur, 1 week after fracture


title: Growthplate: 1 week control

description: control growthplate from intact femur, 1 week after fracture


title: Th cells_antiCD3+antiCD28+IL12_2h_replicate 2a (U133B)

status: Public on Mar 22 2006

city: Turku

first: Riikka

middle: Johanna

last: Lund

address: Tykistökatu 6 A

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku and Åbo Akademi University

source_name: Cord blood CD4+ cells

tag: CD4+ cells isolated from randomly collected cord bloods of healthy neonates, cells pooled from different individuals


title: Growthplate: 3 day control

description: control growthplate from intact femur, 3 days after fracture


title: Th cells_antiCD3+antiCD28+IL12_6h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28+IL4_2h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_2h_replicate 2a (U133B)


title: Growthplate, 1 day control

description: control growthplate from intact femur, 1 day after fracture


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_2h_replicate 2a (U133B)


title: Growthplate: no fracture right

description: growthplate of right no-fracture control

source_name: SD rat proximal femur growthplate

treatment_protocol: Study of rat proximal femoral growthplate after mid-shaft fracture in 4 week old Sprague-Dawley female rats. Two rats pooled for each sample

tag: Sprague Dawley female rat


title: Growthplate: left no fracture

description: growthplate of left no-fracture control

treatment_protocol: Study of rat proximal femoral growthplate after mid-shaft fracture in 4 week old Sprague-Dawley female rats

tag: Intact female SD rat


title: Th cells_no treatment_0h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28+IL4_6h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_6h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28_6h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_6h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28_2h_replicate 2a (U133B)


title: Th cells_antiCD3+antiCD28+IL4_48h_replicate 1b (U133B)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_48h_replicate 1b (U133B)


title: Th cells_antiCD3+antiCD28+IL4_2h_replicate 1a (U133B)


title: Th cells_no treatment_0h_replicate 1b (U133B)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_2h_replicate 1a (U133B)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_48h_replicate 2b (U133B)


title: Th cells_antiCD3+antiCD28+IL12_48h_replicate 1b (U133B)


title: Th cells_antiCD3+antiCD28+IL12_2h_replicate 1a (U133B)


title: Th cells_antiCD3+antiCD28+IL4_48h_replicate 2b (U133B)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_48h_replicate 2b (U133B)


title: Th cells_antiCD3+antiCD28+IL12_48h_replicate 2b (U133B)


title: Th cells_no treatment_0h_replicate 2b (U133B)


title: Th cells_antiCD3+antiCD28_48h_replicate 2b (U133B)


title: Th cells_antiCD3+antiCD28_48h_replicate 1b (U133B)


title: Th cells_antiCD3+antiCD28_2h_replicate 1a (U133B)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_6h_replicate 1a (U133B)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_48h_replicate 1b (U133B)


title: Th cells_antiCD3+antiCD28_6h_replicate 1a (U133B)


title: FDB1_FI72h_FI0h_Rep_1_AMC_472

status: Public on Mar 20 2006

city: North Adelaide

first: Christopher

last: Wilkinson

state: South Australia

address: 72 King William Road

country: Australia

institute: Child Health Research Institute

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_472) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

scan_protocol: Slides were scanned with a GenePix 3000B Scanner (Axon Instruments)

data_processing: Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to spots betwen 70 and 110 pixels. Spots outside of this range were linearly decreased down to a min value of 0.1 (see LIMMA guide at www.bioconductor.org). Spots with both channels at max threshold were set to weight 0 as were spots with sizes of less than 15 pixels. Spots with a single channel maxed out were set to weights of 0.1. These weights were used during normalisation and linear modelling. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors). Print tip loess was assessed by calculating the interquartile range (IQR) of M (log2(R/G) values for each print-tip on each array. An array was flagged as having a spatial feature if at least 1 grid on the array had a IQR > 3 x standard deviation of all IQRs (all groups, all arrays). In this case 2D spatial loess normalisation was applied prior to print-tip intensity dependent loess normalisation.

organism: Mus musculus

source_name: FDB1_FI-Delta Rep 1

label_protocol: Indirect labelling using Cy-Scribe post-labelling kit (Amersham) as per the instructions (protocol available at http://www.microarray.adelaide.edu.au/protocols/cdna/)

growth_protocol: FDB1 cells were grown in Iscove's modified Dulbecco's medium supplemented with 10% fetal calf serum and 500 U/mL mIL-3. See PMID: 10607694

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow without factor for 72 hours

tag: FDB1_FI-Delta cells


title: FDB1_FI6h_V449E6h_Rep_1_AMC_469

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_469) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow without factor for 6 hours

source_name: FDB1_V449E Rep 1

tag: FDB1_V449E cells


title: Th cells_antiCD3+antiCD28+IL4_6h_replicate 1a (U133B)


title: FDB1_FI24h_V449E24h_Rep_1_AMC_465

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_465) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow without factor for 24 hours


title: FDB1_V449E12h_FI12h_Rep_1_AMC_468

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_468) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow without factor for 12 hours


title: FDB1_FI72h_V449E72h_Rep_1_AMC_461

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_461) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_6h_replicate 1a (U133B)


title: Th cells_antiCD3+antiCD28+IL12_6h_replicate 1a (U133B)


title: FDB1_V449E6h_V449E0h_Rep_1_AMC_451

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_451) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E24h_Rep_1_AMC_446

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_446) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E12h_Rep_1_AMC_448

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_448) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E48h_V449E0h_Rep_1_AMC_445

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_445) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow without factor for 48 hours


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_2h_replicate 1a (U133B)


title: FDB1_FI48h_FI0h_Rep_1_AMC_441

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_441) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

data_processing: Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to spots betwen 70 and 110 pixels. Spots outside of this range were linearly decreased down to a min value of 0.1 (see LIMMA guide at www.bioconductor.org). Spots with both channels at max threshold were set to weight 0 as were spots with sizes of less than 15 pixels. Spots with a single channel maxed out were set to weights of 0.1. These weights were used during normalisation and linear modelling. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors). Print tip loess was assessed by calculating the interquartile range (IQR) of M (log2(R/G) values for each print-tip on each array. An array was flagged as having a spatial feature if at least 1 grid on the array had a IQR > 3 x standard deviation of all IQRs (all groups, all arrays). In this case 2D spatial loess normalisation was applied prior to print-tip intensity dependent loess normalisation. 2D spatial loess WAS used on this slide


title: FDB1_GM6h_GM0h_Rep_1_AMC_439

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_439) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

source_name: FDB1_GM-CSF Rep 1

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow in 500 U/mL of mGM-CSF for 6 hours

tag: FDB1_GM-CSF cells


title: Th cells_no treatment_0h_replicate 1a (U133B)


title: FDB1_V449E0h_V449E6h_Rep_1_AMC_450

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_450) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI72h_Rep_1_AMC_471

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_471) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E6h_FI6h_Rep_1_AMC_470

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_470) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM6h_Rep_1_AMC_438

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_438) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E72h_FI72h_Rep_1_AMC_462

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_462) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI12h_V449E12h_Rep_1_AMC_467

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_467) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI12h_Rep_1_AMC_456

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_456) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI6h_FI0h_Rep_1_AMC_459

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_459) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E48h_FI48h_Rep_1_AMC_464

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_464) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI6h_Rep_1_AMC_458

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_458) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI6h_GM6h_Rep_1_AMC_427

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_427) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM12h_FI12h_Rep_1_AMC_426

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_426) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow in 500 U/mL of mGM-CSF for 12 hours


title: FDB1_FI12h_FI0h_Rep_1_AMC_457

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_457) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM6h_FI6h_Rep_1_AMC_428

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_428) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI12h_GM12h_Rep_1_AMC_425

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_425) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_FI0h_Rep_1_AMC_455

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_455) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_V449E0h_Rep_1_AMC_454

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_454) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM24h_GM0h_Rep_1_AMC_435

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_435) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow in 500 U/mL of mGM-CSF for 24 hours


title: FDB1_FI24h_FI0h_Rep_1_AMC_453

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_453) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI24h_Rep_1_AMC_452

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_452) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E24h_V449E0h_Rep_1_AMC_447

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_447) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E6h_Rep_2_AMC_420

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_420) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

source_name: FDB1_V449E Rep 2


title: FDB1_V449E12h_V449E0h_Rep_2_AMC_421

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_421) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E48h_Rep_1_AMC_444

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_444) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E72h_Rep_1_AMC_442

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_442) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E6h_V449E0h_Rep_2_AMC_419

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_419) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E48h_Rep_2_AMC_417

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_417) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E48h_V449E0h_Rep_2_AMC_418

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_418) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI48h_Rep_1_AMC_440

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_440) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM24h_FI24h_Rep_1_AMC_411

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_411) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E72h_V449E0h_Rep_1_AMC_443

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_443) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM72h_GM0h_Rep_1_AMC_414

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_414) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow in 500 U/mL of mGM-CSF for 72 hours


title: FDB1_V449E0h_V449E72h_Rep_2_AMC_415

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_415) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM48h_FI48h_Rep_1_AMC_409

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_409) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow in 500 U/mL of mGM-CSF for 48 hours


title: FDB1_FI24h_GM24h_Rep_1_AMC_410

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_410) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM12h_Rep_1_AMC_436

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_436) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM12h_GM0h_Rep_1_AMC_437

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_437) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM48h_GM0h_Rep_1_AMC_433

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_433) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM24h_Rep_1_AMC_434

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_434) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM72h_Rep_1_AMC_431

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_431) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E24h_Rep_2_AMC_424

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_424) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_GM0h_Rep_1_AMC_429

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_429) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_FI0h_Rep_1_AMC_430

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_430) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI6h_Rep_2_AMC_406

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_406) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

source_name: FDB1_FI-Delta Rep 2


title: FDB1_GM0h_GM48h_Rep_1_AMC_432

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_432) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_V449E12h_Rep_2_AMC_422

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_422) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E24h_V449E0h_Rep_2_AMC_423

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_423) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI12h_Rep_2_AMC_404

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_404) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E72h_V449E0h_Rep_2_AMC_416

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_416) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI24h_FI0h_Rep_2_AMC_403

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_403) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI72h_FI0h_Rep_2_AMC_397

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_397) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI72h_GM72h_Rep_1_AMC_413

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_413) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI72h_Rep_2_AMC_396

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_396) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI48h_GM48h_Rep_1_AMC_408

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_408) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI6h_FI0h_Rep_2_AMC_407

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_407) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI48h_FI0h_Rep_2_AMC_399

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_399) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI48h_Rep_2_AMC_398

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_398) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_FI0h_Rep_2_AMC_395

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_395) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E72h_FI72h_Rep_2_AMC_401

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_401) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI72h_V449E72h_Rep_2_AMC_400

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_400) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI48h_V449E48h_Rep_1_AMC_385

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_385) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E12h_V449E0h_Rep_1_AMC_383

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_383) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI48h_V449E48h_Rep_2_AMC_381

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_381) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_FI24h_Rep_2_AMC_378

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_378) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E24h_FI24h_Rep_1_AMC_384

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_384) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_V449E0h_Rep_1_AMC_377

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_377) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_FI0h_Rep_2_AMC_1245

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1245) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

source_name: FDB1_IL-3 Rep 2

tag: FDB1_IL-3 cells


title: FDB1_V449E12h_FI12h_Rep_2_AMC_391

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_391) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI12h_FI0h_Rep_2_AMC_379

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_379) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI6h_V449E6h_Rep_2_AMC_392

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_392) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E6h_FI6h_Rep_2_AMC_393

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_393) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM6h_FI6h_Rep_2_AMC_1243

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1243) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

source_name: FDB1_GM-CSF Rep 2


title: FDB1_V449E0h_GM0h_Rep_1_AMC_376

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_376) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI6h_GM6h_Rep_2_AMC_1242

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1242) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI24h_V449E24h_Rep_2_AMC_388

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_388) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM72h_FI72h_Rep_1_AMC_382

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_382) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI12h_V449E12h_Rep_2_AMC_390

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_390) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E48h_FI48h_Rep_2_AMC_387

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_387) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_V449E0h_Rep_2_AMC_394

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_394) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM72h_FI72h_Rep_2_AMC_1235

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1235) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM12h_Rep_2_AMC_1233

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1233) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E24h_FI24h_Rep_2_AMC_380

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_380) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI12h_GM12h_Rep_2_AMC_1240

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1240) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_V449E0h_Rep_2_AMC_375

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_375) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_GM0h_Rep_2_AMC_374

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_374) was hybridised to run 1. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI24h_GM24h_Rep_2_AMC_1219

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1219) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_GM0h_Rep_2_AMC_1223

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1223) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM72h_Rep_2_AMC_1227

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1227) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM48h_Rep_2_AMC_1220

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1220) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_FI0h_GM0h_Rep_2_AMC_1244

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1244) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM12h_FI12h_Rep_2_AMC_1241

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1241) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM24h_FI24h_Rep_2_AMC_1239

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1239) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: 3-Methylcholanthrene treated Rat (15 Day)

status: Public on Dec 22 2005

city: Madison

first: Aaron

last: Vollrath

state: WI

address: 1400 University Ave

institute: McArdle Laboratory

description: Following hybridization, the chips were scanned using Agilent Microarray scanner (model G2565BA (Agilent, Palo Alto, CA), and the data were analyzed using Agilent Feature Extraction, followed by importing the information into MySQL databases.  Normalization was performed by the LOWESS method in the Feature Extraction Software.  Dye-Swap performed on each array.

data_processing: this represent the natural log of the average of the trimmed mean for the six replicates on each of the arrays used in the dye swap

source_name: treated liver excised one day after 3-Methylcholanthrene treatement

treatment_protocol: Rats were treated with 3-methylcholanthrene (MC) (100 umol/kg) in corn oil (CO) (2 ml/kg)or were given equal volumes of CO, i.p., once daily for 4 days.

tag: Tissue

value: Liver Duration:15 Day

source_name: Vehicle-Treated Control


title: 3-Methylcholanthrene treated Rat (28 Day)

source_name: treated liver excised 28 days after 3-Methylcholanthrene treatment

value: Liver Duration:28 Days


title: FDB1_FI72h_GM72h_Rep_2_AMC_1237

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1237) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM6h_Rep_2_AMC_1234

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1234) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM12h_GM0h_Rep_2_AMC_1232

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1232) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM48h_FI48h_Rep_2_AMC_1229

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1229) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM24h_GM0h_Rep_2_AMC_1230

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1230) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM6h_GM0h_Rep_2_AMC_1228

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1228) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_GM24h_Rep_2_AMC_1231

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1231) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: MicMa267_Stanford_cDNA

status: Public on Nov 30 2005

city: Foster City

first: Yulei

last: Wang

state: CA

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

description: biopsy of breast carcinoma

hyb_protocol: cRNA hybridized at 65C overnight

scan_protocol: the hybridized arrays were scanned on an Agilent DNA microarray scanner and images analyzed by GenePix Pro v 4.1

data_processing: The Limma package (R/Bioconductor, http://www.bioconductor.org) was used to perform within array normalization (Print- tip loess normalization) and between array normalization (Median of absolute deviation normalization).

source_name: MicMa267_Stanford cDNA with Cy5

label_protocol: Amplification was performed based on the Van Gelder and Eberwine method using the MessageAmp amplification kit (Ambion) and labeling of 3 ?g total RNA per sample was carried out as previously described using incorporation of Cy5 for tumor RNA and Cy3 for reference RNA (Stratagene UHR)

tag: early stage, breast carcinoma

source_name: Universal Human Reference (Stratagene) with Cy3

tag: Universal human reference


title: FDB1_GM72h_GM0h_Rep_2_AMC_1226

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1226) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_V449E0h_GM0h_Rep_1_AMC_1225

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1225) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order

source_name: FDB1_IL-3 Rep 1


title: FDB1_GM48h_GM0h_Rep_2_AMC_1221

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1221) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_V449E0h_Rep_2_AMC_1222

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1222) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: FDB1_GM0h_V449E0h_Rep_1_AMC_1224

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1224) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: IFNb-treated MEF 2

status: Public on Dec 31 2005

city: Memphis

first: Lawrence

last: Pfeffer

state: TN

address: 930 Madison Avenue,#530

department: Pathology

institute: University of Tennessee Health Science

description: IFNb treated

source_name: MEF

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

extract_protocol: Total cellular RNA from IFNb-treated (2500 units/ml for 5 h) MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

tag: IFNb treated


title: IFNb-treated MEF 3

description: IFNb treated


title: wild-type MEF 2

description: Wild type MEF

extract_protocol: Total cellular RNA from untreated and IFN-treated (2500 units/ml for 5 h) MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

tag: Wild type


title: wild-type MEF 3

description: Wild type MEF


title: MicMa101_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa101_Stanford cDNA with Cy5


title: MicMa132_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa132_Stanford cDNA with Cy5


title: FDB1_FI48h_GM48h_Rep_2_AMC_1218

description: This sample comes a series (FDB1_GM-CSF_Series) that spanned two array print runs (slides AMC 374 - AMC 472 and AMC 1218 - 1245). Array spotting layouts were changed between print runs. This sample (AMC_1218) was hybridised to run 2. Following normalisation, all spots were re-ordered according to the print run2 order for subsequent analysis (ie to make a data matrix where cols=arrays and rows = genes).Data presented below is in print run 2 order


title: MicMa122_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa122_Stanford cDNA with Cy5


title: MicMa079_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa079_Stanford cDNA with Cy5


title: MicMa067_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa067_Stanford cDNA with Cy5


title: BJ-SPT10(C388S)-HA. Data set #3

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

description: No other details.

data_processing: Each VALUE was calculated using Affymetrix GCOS software.

label: Bioytinylated cRNAs detected by fluorescently-labelled streptavidin.

organism: Saccharomyces cerevisiae

source_name: Yeast strain BJ-SPT10(C388S)-HA

tag: Yeast strain based on BJ5459 carrying the spt10-C388S mutation (and a C-terminal 3HA tag). BJ-SPT10(C388S)-HA cells were grown in synthetic complete medium to A600 = 0.6. RNA was prepared using an RNeasy kit (Qiagen). This is #3 of three independently prepared samples.


title: BJ-SPT10(C388S)-HA. Data set #2

description: No other details.

tag: Yeast strain based on BJ5459 carrying the spt10-C388S mutation (and a C-terminal 3HA tag). BJ-SPT10(C388S)-HA cells were grown in synthetic complete medium to A600 = 0.6. RNA was prepared using an RNeasy kit (Qiagen). This is #2 of three independently prepared samples.


title: wild-type MEF 1

description: Wild type MEF

extract_protocol: Total cellular RNA from untreated MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.


title: IFNb-treated MEF 1

description: IFNb treated


title: BJ5459 spt10-C388S mutant. Data set #1

description: No other details.

source_name: Yeast cells in log phase of growth in synthetic medium.

tag: Yeast strain based on BJ5459 carrying the spt10-C388S mutation (and a C-terminal 3HA tag). BJ-SPT10(C388S)-HA cells were grown in synthetic complete medium to A600 = 0.6. RNA was prepared using an RNeasy kit (Qiagen). This is #1 of three independently prepared samples.


title: 3-Methylcholanthrene treated Rat (1 Day)

source_name: treated liver excised one day after 3-Methylcholanthrene treatemen

value: Liver

tag: Duration

value: 1 Day


title: S4-040517-SA

status: Public on Oct 30 2005

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: normal smoker

data_processing: MAS 5.0

source_name: airway epithelium, small airways, obtained by bronchoscopy and brushing

tag: male

tag: 38 yr old

tag: White


title: S3-040330-SA

description: normal smoker

tag: 48 yr old


title: S2-041129-SA

description: normal smoker

tag: female

tag: 37 yr old

tag: Black


title: S5-040803-SA

description: normal smoker

tag: 42 yr old


title: MicMa632_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa632_Stanford cDNA with Cy5


title: MicMa709_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa709_Stanford cDNA with Cy5


title: MicMa263_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa263_Stanford cDNA with Cy5


title: MicMa185_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa185_Stanford cDNA with Cy5


title: Adenoviral beta-Gal in human skeletal myoblasts

status: Public on Oct 27 2005

city: Dallas

first: G. C. Teg

last: Pipes

state: TX

address: 6000 Harry Hines Blvd

department: MBO

institute: University of Texas Southwestern Medical Center at Dallas

label: affy default

source_name: human skeletal myoblasts

tag: see the following reference

value: Cronin, E. M., Thurmond, F. A., Bassel-Duby, R., Williams, R. S., Wright, W. E., Nelson, K. D., and Garner, H. R. 2004. Protein-coated poly(L-lactic acid) fibers provide a substrate for differentiation of human skeletal muscle cells. J Biomed Mater Res A 69, 373-81.


title: Human Skeletal myoblasts infected with Adenoviral myocardin

source_name: immortalized human skeletal myoblasts

tag: see the following reference for the cell line:Cronin, E. M., Thurmond, F. A., Bassel-Duby, R., Williams, R. S., Wright, W. E., Nelson, K. D., and Garner, H. R. 2004. Protein-coated poly(L-lactic acid) fibers provide a substrate for differentiation of human skeletal muscle cells. J Biomed Mater Res A 69, 373-81.


title: MicMa148_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa148_Stanford cDNA with Cy5

tag: early stage, breast carcinoma

source_name: Universal Human Reference (Stratagene) with Cy3

tag: Universal human reference


title: 4 hour prepupae EcR mutant replicate 3

status: Public on Oct 04 2005

city: Athens

first: Robert

middle: B

last: Beckstead

state: GA

address: 119 Poultry Science Building

department: Poultry Science

institute: The University of Georgia

description: EcR mutants die during early stages of development, complicating their use for studying receptor function during metamorphosis. To circumvent this problem, we employed a transgenic system that allows heat-induced expression of double-stranded RNA corresponding to the EcR common region to disrupt EcR function at puparium formation (EcRi)

data_processing: dChip 1.2

organism: Drosophila melanogaster

source_name: whole animal

label_protocol: Approxiamately 12 ug of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Prepupae were staged relative to pupariation

extract_protocol: RNA was isolated from 10 animals using TriPure (Roche) followed by further purification with RNAeasy columns (Qiagen)

treatment_protocol: hs-EcRi-11 third instar larvae were heat-treated twice at 37°C, each time for 1 hour, at 24 hours and 18 hours prior to pupariation

tag: Transgenic animal containing a heat-inducible transgene that expresses a double-stranded RNA corresponding to the EcR common region (hs-EcRi-11)


title: mammary_16wkWT_ker70

status: Public on Oct 10 2005

city: Cleveland

first: Ruth

last: Keri

state: OH

address: 2109 Adelbert

department: Pharmacology

institute: Case Western Reserve University

description: Thoracic mammary glands were collected from three virgin wild type F1 CF-1/FVB mice at 16 weeks of age; RNA was pooled before synthesis of cDNA. This and two other distinct wild type samples were compared to mammary glands from 16 week old LH-overexpressing mice.

hyb_protocol: Preparation of Hybridization cocktails: The standard hybridization cocktail volume was 300 ul. 150 ul of 2X hybridization buffer was added (final concentrations : 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20) Herring sperm and acetylated BSA were added to a final concentration of 0.1 and 0.5mg/ml respectively. The amount of fragmentation reaction containing 15ug of cRNA was added to the cocktail and the remaining volume was made up with molecular biology grade water.  External controls (spikes): A 15 ul aliquot of a 20X mixture of in-vitro transcripts of bacterial genes BioB BioC BioD and cre  were added to the cocktail to give final concentrations of 1.5, 5, 25 and 100pM respectively. Control oligonucleotide (5 ul) was added to a final concentration of 50pM.  Hybridization: Sample Hyridization cocktails (300 ul) were removed from storage at �20C and thawed in a 45C temperature block. The samples were incubated at 45C for 5 min, incubated at 45C for 5 min and then centrifuged at 15,000g for 5 min.  Meanwhile,  the Affymetrix chip arrays were taken from their storage at 4C and allowed to come to room temperature. The chamber was filled with 1X hybridization buffer (final concentrations : 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20). The chip was then preconditioned by incubation in the hybridization oven at 45C for 10 min. The chip was removed and the chamber drained.  Sample cocktails (200 ul) were then introduced into the chamber of the chips. The ports were sealed with tough-spots stickers and placed in the hybridization oven and incubated at 45C with rotation overnight.  Next day (16hr later), the incubation was terminated and the chips removed from the oven.  Samples were retrieved from the chips and stored again in a freezer at -20C. The chips were filled with buffer A and placed in a module of Fluidics 400 wash station.  The chips were subjected to the Affymetrix  �EuKws4 ver 2� programmed series of stringent post hybridization washes, staining and post-staining washes in accordance with Affy protocols.  Upon completion of the wash series (approximately 2 hrs), the chips were removed from the Fluidics station. The chips were inspected

scan_protocol: Chips were scanned using an Agilent Gene Array scanner 2000 driven by Affymetrix MicroArray Suite 5.0.  The scanner PMT was set to the later, wide dynamic range setting.

data_processing: MAS5.0, scaled to 1500

source_name: wild type mammary gland

label_protocol: Double-stranded cDNA was made from the pooled RNA samples using the Superscript Double Stranded cDNA Synthesis kit (Invitrogen, Carlsbad, CA; cat# 11917-010) and an oligo-dT primer coupled to the T7 RNA polymerase promoter. Biotin-labeled cRNA was generated with the Enzo BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA; cat# 900182) and purified using the Qiagen RNEasy kit (cat# 74104).

extract_protocol: TRIzol (Invitrogen)


title: mammary_16wkWT_ker75

hyb_protocol: Preparation of Hybridization cocktails: The standard hybridization cocktail volume was 300 ul. 150 ul of 2X hybridization buffer was added (final concentrations : 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20) Herring sperm and acetylated BSA were added to a final concentration of 0.1 and 0.5mg/ml respectively. The amount of fragmentation reaction containing 15ug of cRNA was added to the cocktail and the remaining volume was made up with molecular biology grade water.

tag: Thoracic mammary glands were collected from three virgin wild type F1 CF-1/FVB mice at 16 weeks of age; RNA was pooled before synthesis of cDNA.


title: mammary_16wkLH_ker73

description: Thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age and pooled before synthesis of cDNA. This and two other distinct transgenic samples were compared to mammary glands from 16 week old wild type mice.

source_name: transgenic (LH-overexpressing) mammary gland

tag: thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age and pooled before synthesis of cDNA


title: MicMa146_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa146_Stanford cDNA with Cy5


title: MicMa065_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa065_Stanford cDNA with Cy5


title: 0 hour prepupae EcR mutant replicate 2


title: MicMa088_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa088_Stanford cDNA with Cy5


title: MicMa091_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa091_Stanford cDNA with Cy5


title: MicMa085_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa085_Stanford cDNA with Cy5


title: MicMa053_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa053_Stanford cDNA with Cy5


title: third instar larvae -4 hours relative to pupariation EcRi mutant replicate 3

growth_protocol: Larvae were staged by addition of 0.05% bromophenol blue and collected as actively wandering larvae with clear guts


title: 4 hour prepupae EcR mutant replicate 2


title: 0 hour prepupae EcR mutant replicate 1


title: 4 hour prepupae EcRi control replicate 2

description: Control data set for EcRi data set from the 4 hour prepupae


title: MicMa042_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa042_Stanford cDNA with Cy5


title: third instar larvae -4 hours relative to pupariation EcRi mutant replicate 1


title: third instar larvae -4 hours relative to pupariation EcRi control replicate 3

description: Control data set for EcRi data set from the third instar larvae -4 hour relative to pupariation


title: 0 hour prepupae EcRi control replicate 3

description: Control data set for EcRi data set from the 0 hour prepupae


title: NS5-040401-SA

description: normal non-smoker

source_name: airway epithelium, small airways, obtained by bronchoscopy and brushing


title: S1-030626-SA

description: normal smoker

tag: 33 yr old


title: NS3-040213-SA

description: normal non-smoker

tag: 41 yr old


title: NS4-040331-SA

description: normal non-smoker

tag: 29 yr old


title: S6-041001-SA

description: normal smoker

tag: male

tag: 36 yr old

tag: Hispanic


title: MicMa020_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa020_Stanford cDNA with Cy5


title: third instar larvae -4 hours relative to pupariation EcRi control replicate 2


title: NS2-031009-SA

description: normal non-smoker

source_name: airway epithelium, smal airways, obtained by bronchoscopy and brushing

tag: 34 yr old


title: MicMa031_Stanford_cDNA

description: biopsy of breast carcinoma

source_name: MicMa031_Stanford cDNA with Cy5


title: third instar larvae -4 hours relative to pupariation EcRi control replicate 1

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


title: NS1-030915-SA

description: normal non-smoker

tag: female


title: Organ culture cycloheximide-treated replicate 2

description: Cycloheximide treated organ cultures

label_protocol: Approximately 12 ug of total RNA was processed to produce biotinylated cRNA targest

growth_protocol: Larvae were staged by addition of 0.05% bromophenol blue to food and collected as actively wandering third instar larvae with partial blue guts (~8 hour prior to pupariation).

extract_protocol: RNA was isolated using TriPure (Roche) followed by further purification with RNAeasy (Qiagen)

treatment_protocol: Eight animals were dissected in a 9 well glass dish (Corning) and cultured in ~100 µl oxygenated Schneiders Drosophila Medium (Gibco) at 25°C. Cultures were incubated in an a styrofoam box under a constant flow of oxygen. Following an initial incubation of 1 hour, the medium was removed and replaced with fresh Schneiders Drosophila Medium plus 8.5x10-5 M cycloheximide and incubated for 6 hours at 25°C.


title: Human Skeletal myoblasts infected with Adenoviral beta-Gal

source_name: immortalized human skeletal myoblasts


title: Organ culture 20E-treated replicate 3

description: 20E treated organ cultures

treatment_protocol: Eight animals were dissected in a 9 well glass dish (Corning) and cultured in ~100 µl oxygenated Schneiders Drosophila Medium (Gibco) at 25°C. Cultures were incubated in an a styrofoam box under a constant flow of oxygen. Following an initial incubation of 1 hour, the medium was removed and replaced with fresh Schneiders Drosophila Medium plus 5x10-6 M 20-hydroxyecdysone and incubated for 6 hours at 25°C.


title: 4 hour prepupae EcR mutant replicate 1


title: Adenoviral myocardin in human skeletal myoblasts

source_name: human skeletal myoblasts

tag: see the following publication for details on the cell line:Cronin, E. M., Thurmond, F. A., Bassel-Duby, R., Williams, R. S., Wright, W. E., Nelson, K. D., and Garner, H. R. 2004. Protein-coated poly(L-lactic acid) fibers provide a substrate for differentiation of human skeletal muscle cells. J Biomed Mater Res A 69, 373-81.


title: mammary_16wkLH_ker74

description: Thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age; RNA was pooled before synthesis of cDNA. Data from this and two other distinct transgenic samples were compared to mammary glands from 16 week old wild type mice.

tag: thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age; RNA was pooled before synthesis of cDNA


title: 0 hour prepupae EcR mutant replicate 3


title: mammary_16wkWT_ker71


title: mammary_16wkLH_ker72

description: Thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age; RNA was pooled before synthesis of cDNA. This and two other distinct transgenic samples were compared to mammary glands from 16 week old wild type mice.