title: 98KM1178, normal

status: Public on Feb 28 2008

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42036.gif

hyb_protocol: not provided

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

organism: Homo sapiens

source_name: CRH

label_protocol: RNA from AML specimens was labeled with Cy5-dUTP using an anchored poly(dT) primer during first strand reverse transcription (Superscript II).  A universal reference RNA (pooled from 11 cell lines) was labeled identically but with Cy3-dUTP.; Protocol Type = Labeling; Performer: Lars,,Bullinger

extract_protocol: Normal karyotype acute myeloid leukemia (NK-AML) specimens comprise Ficoll gradient purified mononuclear cells (>80% blasts) from diagnostic peripheral blood or bone marrow.  Total RNA was isolated from stored, frozen mononuclear AML-cell pellets using Trizol reagent, and RNA quality assessed by gel electrophoresis.; Protocol Type = Extract preparation; Performer: Lars,,Bullinger

tag: normal karyotype acute myeloid leukemia


title: Agilent 244k Chip 1

status: Public on Feb 29 2008

type: genomic

city: Houston

first: Omar

last: Alvi

state: TX

address: 1 Baylor Plaza

department: Human Genome Sequencing Center

country: USA

institute: Baylor College of Medicine

description: CNV data for JW (Agilent Human Genome CGH 244K Array)

hyb_protocol: Experimental and reference targets for each hybridization were purified, pooled and incubated with human Cot-1 DNA (Invitrogen) and Blocking Agent (Agilent Technologies, Inc.)

scan_protocol: Slides were scanned into image files using an Axon microarray scanner (GenePix 4000B from Axon Instruments, Union City, CA, USA)

data_processing: Data was analyzed using the CGH Analytics software (Agilent Technologies, Inc.)

molecule: genomic DNA

source_name: JW DNA extracted from blood

label_protocol: The labelling reaction was performed with Bioprime CGH labelling Module (Invitrogen) at 378C for 2 hours in the presence of Cy5-dCTP following standard Agilent protocal

extract_protocol: DNA extracted from blood using FlexiGene DNA kit from Qiagen

tag: Blood from JW

source_name: Reference DNA extracted from standard reference Caucasian male blood

label_protocol: The labelling reaction was performed with Bioprime CGH labelling Module (Invitrogen) at 378C for 2 hours in the presence of  Cy3-dCTP (PerkinElmer) following standard Agilent protocal

tag: Blood from standard reference Caucasian male


title: AML 22

type: RNA

state: CA

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33564.gif

molecule: total RNA

tag: universal reference RNA (pooled from 11 cell lines)

source_name: AML 22


title: 98PB987, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42034.gif


title: 99PB311, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42038.gif


title: AML 55

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33563.gif

source_name: AML 55


title: 99KM302, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42039.gif


title: RNA: 99PB1142, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41310.gif


title: AML 30

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33064.gif

source_name: AML 30


title: AML 11

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33646.gif

source_name: AML 11


title: 98PB834, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42033.gif


title: AML 64

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33066.gif

source_name: AML 64


title: 00KM856, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42749.gif


title: Co-hybridization of Adenovirus type 40 and 41 on June 27 2006

city: East Lansing

first: Mark

last: Wong

state: MI

address: 3 Natural Resources

department: Crops and Soil Sciences

description: Arrays were scanned and washed at several different wash temperatures to ensure that probe signals behaved appropriately and were not artifacts of the hybridization.

hyb_protocol: Hybridization was carried out in 50 ul hybridization buffer at 20 degrees Celsius using a microfluidic hybridization wash station. Hybridization was allowed to proceed for at least 17 hours before washing and scanning.

scan_protocol: Arrays were scanned in a Genepix 4000B microarray scanner at PMT values of appoximately 700.

data_processing: Signal values were derived from the RAW data files by extracting the median foreground intensity for both channels for each given spot.

organism: Human adenovirus 40

source_name: Adenovirus type 40

label_protocol: Total nucleic acid extract was treated with DPN II restriction enzyme for 1 hr. Labeled with Cy3 using Klenow fragment and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.

extract_protocol: Viral DNA extracted using QIAGEN viral RNA extraction kit following manufacturer's protocol.

treatment_protocol: Viral DNA was directly extracted from ATCC vial after resuspending in DMEM.

tag: Cy3 labeled Adenovirus type 40 from ATCC number VR-931

organism: Human adenovirus 41

source_name: Adenovirus type 41

label_protocol: Total nucleic acid extract was treated with DPN II restriction enzyme for 1 hr. Labeled with Cy5 using Klenow fragment and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.

tag: Cy5 labeled Adenovirus type 41 from ATCC number VR-930


title: Poliovirus hybridization on July 13 2006

data_processing: Signal values were derived from the RAW data files by extracting the median foreground intensity for each given spot.

organism: Enterovirus C

source_name: Lab strain poliovirus LS-C-1

label_protocol: Total RNA was labeled with Cy3 using Sensicript III reverse transcriptase and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.

growth_protocol: BGM cells propagated in DMEM supplemented with 10% Fetal Bovine Serum.

extract_protocol: RNA extracted using QIAGEN viral RNA extraction kit following manufacturer's protocol.

tag: RNA extraction and labeling of poliovirus strain LS-C-1 grown on Buffalo Green Monkey cells. Viruses harvested <24 hrs post infection.


title: 98PB199, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42032.gif


title: AML 7

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33649.gif

source_name: AML 7


title: 02KM1746, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44124.gif


title: 01PB694, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43266.gif


title: 00PB1729, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42752.gif


title: Poliovirus hybridization on July 6 2006

source_name: Laboratory strain Poliovirus LS-C-1

label_protocol: Total RNA was labeled with Cy3 using Klenow Fragment and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.


title: AML 9

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32815.gif

source_name: AML 9


title: 99KM831, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42538.gif


title: AML 102

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33161.gif

source_name: AML 102


title: AML 94

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33568.gif

source_name: AML 94


title: 01PB1574, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44120.gif


title: 01PB1806, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42883.gif


title: 01KM1171, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42875.gif


title: 01KM1396, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42881.gif


title: 01PB1096, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42873.gif


title: 01PB943, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42871.gif


title: 01PB1072, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42872.gif


title: 02KM697, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43816.gif


title: 02KM2732, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44115.gif


title: Co-hybridization of Adenovirus type 40 and 41 on June 28 2006

description: Arrays were scanned and washed at several different wash temperatures to ensure that probe signals behaved appropriately and were not artifacts of the hybridization.


title: 02KM255, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43813.gif


title: 03KM1301, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62634.gif

source_name: aCR (Stratagene)


title: 01KM1717, 46,XY[13]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62631.gif


title: 00KM1316, 46,XY[4]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62629.gif


title: 02PB302, 46,XY[20]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63145.gif


title: 00KM331, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42645.gif

source_name: CRH


title: Poliovirus hybridization on July 14 2006


title: 02PB422, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43814.gif


title: 01KM1517, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62628.gif


title: 01PB2625, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43795.gif


title: 00KM2370, 46,XY[18]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63146.gif


title: 02KM4, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43801.gif


title: 00KM1797, 46,XX[11]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62623.gif


title: 99KM758, 46,XY

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62655.gif


title: 99PB1458, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42642.gif


title: 99KM1241, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42641.gif


title: 00KM184, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42644.gif


title: 99PB1308, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62621.gif


title: 00PB7, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42643.gif


title: 03KM894, 46,XX[13]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62632.gif


title: 03KM2531, 46,XX[13]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62680.gif


title: 01KM3019, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43799.gif


title: 01KM3062, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43800.gif


title: 00KM468, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62681.gif


title: 00KM2221, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42869.gif


title: 02PB2565, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43865.gif


title: 4hours_E2_vs_Ctrl_1st_expt

city: Atlanta

first: Caleb

last: Kallen

state: GA

address: 1639 Pierce Drive, WMB 4211

department: Gynecology and Obstetrics

institute: Emory University School of Medicine

description: 4 hours E2 (10nM) vs Ctrl (vehicle) 1st expt

hyb_protocol: The OHU21K human oligonucleotide array (Yale's Keck Facility), was hybridized at 64oC in a hybridization buffer comprised of 2.83 x SSC, Polyadenylic acid 0.5 mg/ul (Sigma), and 0.18% SDS.

scan_protocol: The arrays were washed and scanned in an Axon 4000 array scanner as described (Rifkin et al, 2003).

data_processing: Intensity values for cDNAs were generated with GenePix (v.4.0), background intensities were subtracted, and values were multiplied by a correction factor to normalize for labeling differential between the channels.  Data were ratio normalized and NET Signal Noise filtered (Yale Microarray Database), then corrected for intensity-dependent bias with a Lowess function in MAANOVA (R/maanova, Version 0.98.8).  Bayesian analysis of gene expression levels (BAGEL) (Townsend and Hartl, 2002) generated expression estimates for all time points by running WinABAGEL v.3.6 at default settings on all microarray datasets, where significant (p < 0.01) probes were defined relative to the control samples in at least one time point.

molecule: polyA RNA

source_name: control

label_protocol: labeling using the Powerscript fluorescent labeling kit (BD Biosciences) and monofunctional Cy3 and Cy5 dyes (Amersham /Pharmacia) per manufacturer's protocol.

extract_protocol: total RNA was isolated using Trizol (Invitrogen) per the manufacturer's instructions, Poly-A mRNA was purified from total RNA and cDNAs were prepared from 2 mg Poly-A RNA

treatment_protocol: MCF7 cells (ATCC) were grown as described (Carroll et al, 2005) and cells were changed to E2-depleted, phenol-free media for 72 hours prior to E2 treatments.

tag: Ctrl

source_name: E2 treated


title: 4hours_E2_vs_Ctrl_3rd_expt

description: 4 hours E2 (10nM) vs Ctrl (vehicle) 3rd expt


title: 4hours_E2_vs_Ctrl_2nd_expt

description: 4 hours E2 (10nM) vs Ctrl (vehicle) 2nd expt


title: 00PB1872, 46,XX[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62678.gif


title: 98PB944, 46,XY

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62658.gif


title: 24_hours_E2_vs_Ctrl_4th_expt

description: 24 hours E2 (10nM) vs Ctrl (vehicle)_4th expt


title: 02KM883, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43860.gif


title: 03KM3230, 46,XX[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62675.gif


title: 24_hours_E2_vs_Ctrl_3rd_expt

description: 24 hours E2 (10nM) vs Ctrl (vehicle)_3rd expt


title: 4hours_E2_vs_Ctrl_4th_expt

description: 4 hours E2 (10nM) vs Ctrl (vehicle) 4th expt


title: 02PB786, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43859.gif


title: 01KM1521, 46,XX[13]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62679.gif


title: 99KM279, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63384.gif


title: 99PB992, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60253.gif


title: copy of 24_hours_E2_vs_Ctrl_2nd_expt

description: 24 hours E2 (10nM) vs Ctrl (vehicle)_2nd expt


title: 03KM442, 46,XY[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63381.gif


title: 12_hours_E2_vs_Ctrl 3rd expt

description: 12 hours E2 vs Ctrl (10124)


title: 24_hours_E2_vs_Ctrl

description: 24 hours E2 (10nM) vs Ctrl (vehicle)


title: 99PB940, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62657.gif


title: 98PB345, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62656.gif


title: 99KM139, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63371.gif


title: 12_hours_E2_vs_Ctrl_2nd_expt

description: 12 hours E2 vs Ctrl (9887)


title: 02KM114, 46,XY[15]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62676.gif


title: 00KM1572, 46,XX [15]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63081.gif


title: 12_hours_E2_vs_Ctrl

description: 12 hours E2 vs Ctrl (9749)


title: 00KM432, 46,XX[20](D|sseldorf)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62622.gif


title: 99KM208, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63382.gif


title: 01PB2622, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43796.gif


title: 03KM3189, 46,XX[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63369.gif


title: 02PB3311, 46,XY[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63366.gif


title: 03KM3217, 46,XX[18]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63291.gif


title: 03KM3557, 46,XY[14]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63368.gif


title: 03KM2735, 46,XX[16]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63370.gif


title: 03PB165, 46,XY[15]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63383.gif


title: C57Bl/6J No8

city: Norfolk

first: yumi

last: imai

state: VA

address: 799W Olney Road, LH 2156

institute: Eastern Virginia Medical School

description: Microarray analyses were performed on quadruplicate RNA samples of pancreatic islets from AKR and Bl6 mice placed on high-fat diet for 3 months. Pancreases from two mice were combined to yield one sample of islet RNA. All protocols were conducted as described in the Affymetrix GeneChips Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA) using 5 μg total RNA and GeneChip Mouse Expression Arrays MOE 430 (Affymetrix).

hyb_protocol: as per Affimetrix protocol

scan_protocol: as per Affimetrix protocol

data_processing: ArrayAssist Lite version 3.1 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” marginal flags were also calculated.

label: as per Affimetrix protocol

organism: Mus musculus

source_name: pancreatic islet ftom high fat fed C57Bl/6J

label_protocol: as per Affimetrix protocol

extract_protocol: Qiagen RNa easy kit

tag: C57Bl6/J, 4 months old  male, on high fat diet for 3 months, pancretic islets


title: C57Bl/6J No6


title: 03PB2769, 46,XX[17]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63290.gif


title: C57Bl/6J No5

description: Microarray analyses were performed on quadruplicate RNA samples of pancreatic islets from AKR and Bl6 mice placed on high-fat diet for 3 months. Pancreases from two mice were combined to yield one sample of islet RNA.


title: 01KM441, 46,XY[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63079.gif


title: C57Bl/6J No7


title: 03KM2384, 46,XX[16]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63292.gif


title: 01PB360, 46,XX[9]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63078.gif


title: 03KM1144, 46,XX[10]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62275.gif


title: 01PB2118, 46,XY[25] in Gvttingen

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63287.gif


title: AKR/J No4

source_name: pancreatic islet ftom high fat fed AKR/J

tag: AKR/J, 4 months old  male, on high fat diet for 3 months, pancretic islets


title: 03KM253, 46,XY[13]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63367.gif


title: 03KM2111, 46,XX[11]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63289.gif


title: 02PB492, 46,XX[16]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63187.gif


title: 02KM2809, 46,XX[9]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63288.gif


title: 02KM494, 46,XX[10]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63191.gif


title: AKR/J No1

tag: AKR/J male , age 4 month, on high fat diet for 3 months, pancreatic islet


title: 02PB1826, 46,XY[9]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63189.gif


title: AKR/J No3


title: 99PB377, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63077.gif


title: AML 17

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26042.gif

source_name: AML 17


title: 03PB1812, 46,XX[13]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63185.gif


title: 02KM3077, 46,XX[10]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62856.gif


title: 02PB1577, 46,XY[20] in Kiel

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63188.gif


title: AKR/J No2

description: Microarray analyses were performed on quadruplicate RNA samples of pancreatic islets from AKR and Bl6 mice placed on high-fat diet for 3 months. Pancreases from two mice were combined to yield one sample of islet RNA.


title: 02PB3193, 46,XX[11]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63001.gif


title: 02PB2479, 46,XX[15]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63034.gif


title: 99PB126, 46,XY

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63386.gif


title: 03KM25, 46,XY[37] in Kiel

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/62999.gif


title: AML 35

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26043.gif

source_name: AML 35


title: 01KM2574, 46,XY

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63035.gif


title: 02KM2951, 46,XY[15]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62855.gif


title: 02PB3375, 46,XX[15]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63002.gif


title: 03KM2434, 46,XX[10]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62745.gif


title: 03KM1761, 46,XX[11]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62744.gif


title: 03KM2101, 46,XX[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62852.gif


title: 01KM486, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56548.gif


title: 03KM1689, 46,XX[5]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62743.gif


title: 03KM273, 46,XX[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63033.gif


title: 03KM1676, 46,XX[14]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62805.gif


title: 03KM104, 46,XX[10]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63030.gif


title: 01KM2453, 46,XX[20], keine Metaph.

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62746.gif


title: 03PB1447, 46,XY in Kiel

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62803.gif


title: 03KM804, 46,XY[18]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63000.gif


title: 98KM1477, 46,XX

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63031.gif


title: 02KM2188, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47489.gif


title: 00KM2459, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47465.gif


title: 98KM1558, 46,XY

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63032.gif


title: 01KM2148, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47478.gif


title: Human ileum villus epithelium P4

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: The specimens were free of macroscopic signs of disease or inflammation

hyb_protocol: 16 hr at 55rpm in an Affymetrix hybridization oven at 45C

scan_protocol: 100 format, Affymetrix scanner 3000

data_processing: GCOS

label: biotin

source_name: Ileal tissue biopsies

label_protocol: Affymetrix 2-cycle amplification and labeling protocol

extract_protocol: Qiagen RNA extraction protocol with proteinase K digestion of cellular extract

tag: Sample was obtained from individual undergoing surgery for colon cancer, bowel obstruction, or other non-inflammatory conditions. Fixed overnight in 4% (w/v) paraformaldehyde


title: Human ileum crypt epithelium P3


title: 01KM321, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47466.gif


title: 03KM1094, 46,XY[12]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62806.gif


title: 98KM1251, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47453.gif


title: Human ileum crypt epithelium P2


title: Human ileum crypt epithelium P1


title: 02KM1932, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47493.gif


title: 98KM585, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47463.gif


title: Human ileum villus epithelium P2


title: 00PB262, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47458.gif


title: p1.04s26b03scpr031211.gpr

status: Public on Feb 27 2008

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

description: Cy5 =  Aburtoni33MaT(C3-15)-030708brain01 Cy3 = Aburtoni26MaNT(C1-5)-030708brain01 hybed by SCP Renn on 20031211

hyb_protocol: The samples were combined with hybridization buffer (~2 _ SSC, ~0.35 mg/ml poly (dA) poly(dT), ~15 mM HEPES and ~0.15% SDS) and hybridized to the microarray at 65 degrees 12-16 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=650_570 ScanPower=100_100

data_processing: After removing ""flagged"" and bad spots, only those spots were used whose average intensity was at least two standard deviations above the average background. Arrays were background corrected (method minimal) and normalized in R/Bioconductor with  loess (within arrays only) and intensity ratios were calculated.

organism: Haplochromis burtoni

label_protocol: The RNA (2 ug) as annealed with primer (5 ug each poly dT 12-18 with 5 ug random hexamer oligonucleotides), and reverse transcribed with Superscript II reverse trancriptase for 2h at 42_C in the presence of amino-allyl-dUTP/dNTP mix (2.5 mM each dATP, dCTP, dGTP, 1.5 mM dTTP and 10 mM amino-allyl dUTP). RNA was hydrolyzed (~0.2M NAOH) and the cDNA was rinsed and concentrated on a YM-30 filter.

extract_protocol: Individual whole brains were dissected and stored in RNAlater at -20. Brains were homogenized (Tissue Tearor) in trizol and the RNA was extracted using a standard Trizol extraction protocol.

treatment_protocol: normal mixed population tank

tag: T-male

tag: NT-male


title: 02KM2278, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47491.gif


title: 02PB1568, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47492.gif


title: AML 10

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32545.gif

source_name: AML 10


title: AML 12

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32556.gif

source_name: AML 12


title: Human ileum villus epithelium P1

source_name: Ieal tissue biopsies


title: p1.04s22a03scpr031211.gpr

description: Cy5 =  Aburtoni15Fab(A1-f2)-030708brain01 Cy3 = Aburtoni26MaNT(C1-5)-030708brain01 hybed by SCP Renn on 20031211

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=640_530 ScanPower=100_100

tag: brooding female


title: Human ileum villus epithelium P3


title: 02KM896, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47484.gif


title: 99KM8, 46,XY

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63385.gif


title: p1.04s25b03scpr031211.gpr

description: Cy5 =  Aburtoni24MaT(C1-3)-030708brain01 Cy3 = Aburtoni30MaNT(A2-9)-030708brain01 hybed by SCP Renn on 20031211

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=640_570 ScanPower=100_100


title: p1.04s28b03scpr031119.gpr

description: Cy5 =  Aburtoni30MaNT(A2-9)-030708brain01 Cy3 = Aburtoni18Fab(C1-f5)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=690_700 ScanPower=33_33


title: p1.04s45a03scpr031119.gpr

description: Cy5 =  Aburtoni39MaNT(C3-23)-030708brain01 Cy3 = Aburtoni17Fab(B1-f4)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=700_600 ScanPower=33_33


title: p1.04s23b03scpr031211.gpr

description: Cy5 =  Aburtoni39MaNT(C3-23)-030708brain01 Cy3 = Aburtoni17Fab(B1-f4)-030708brain01 hybed by SCP Renn on 20031211

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=620_570 ScanPower=100_100


title: p1.04s25a03scpr031211.gpr

description: Cy5 =  Aburtoni18Fab(C1-f5)-030708brain01 Cy3 = Aburtoni30MaNT(A2-9)-030708brain01 hybed by SCP Renn on 20031211


title: p1.04s24a03scpr031211.gpr

description: Cy5 =  Aburtoni33MaT(C3-15)-030708brain01 Cy3 = Aburtoni15Fab(A1-f2)-030708brain01 hybed by SCP Renn on 20031211

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=600_600 ScanPower=100_100


title: p1.04s22b03scpr031211.gpr

description: Cy5 =  Aburtoni15Fab(A1-f2)-030708brain01 Cy3 = Aburtoni38MaT(C3-22)-030708brain01 hybed by SCP Renn on 20031211

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=630_600 ScanPower=100_100


title: p1.04s47b03scpr031119.gpr

description: Cy5 =  Aburtoni33MaT(C3-15)-030708brain01 Cy3 = Aburtoni39MaNT(C3-23)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=660_680 ScanPower=33_33


title: p1.04s44b03scpr031119.gpr

description: Cy5 =  Aburtoni38MaT(C3-22)-030708brain01 Cy3 = Aburtoni37MaNT (B1-21)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=630_640 ScanPower=33_33

source_name: Aburtoni37MaNT (B1-21)-030708brain01


title: 99PB1321, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47457.gif


title: p1.04s45b03scpr031119.gpr

description: Cy5 =  Aburtoni19Fab(C3-f6)-030708brain01 Cy3 = Aburtoni24MaT(C1-3)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=650_680 ScanPower=33_33


title: p1.04s44a03scpr031119.gpr

description: Cy5 =  Aburtoni21Fab(A2-f8)-030708brain01 Cy3 = Aburtoni32MaT(B3-13)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=660_660 ScanPower=33_33


title: p1.04s23a03scpr031211.gpr

description: Cy5 =  Aburtoni39MaNT(C3-23)-030708brain01 Cy3 = Aburtoni38MaT(C3-22)-030708brain01 hybed by SCP Renn on 20031211

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=620_600 ScanPower=100_100


title: 03KM1554, 46,XY [17]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62804.gif


title: AML 113

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32449.gif

source_name: AML 113


title: 02PB2243, normal

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47490.gif


title: p1.04s38b04scpr031119.gpr

description: Cy5 =  Aburtoni19Fab(C3-f6)-030708brain01 Cy3 = Aburtoni39MaNT(C3-23)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=700_660 ScanPower=33_33


title: p1.04s34b03scpr031119.gpr

description: Cy5 =  Aburtoni32MaT(B3-13)-030708brain01 Cy3 = Aburtoni18Fab(C1-f5)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=770_640 ScanPower=33_33


title: p1.04s36b03scpr031119.gpr

description: Cy5 =  Aburtoni30MaNT(A2-9)-030708brain01 Cy3 = Aburtoni24MaT(C1-3)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=640_700 ScanPower=33_33


title: p1.04s35a03scpr031119.gpr

description: Cy5 =  Aburtoni37MaNT (B1-21)-030708brain01 Cy3 = Aburtoni32MaT(B3-13)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=680_670 ScanPower=33_33


title: p1.04s36a03scpr031119.gpr

description: Cy5 =  Aburtoni24MaT(C1-3)-030708brain01 Cy3 = Aburtoni17Fab(B1-f4)-030708brain01 hybed by SCP Renn on 20031119


title: p1.04s28a03scpr031119.gpr

description: Cy5 =  Aburtoni24MaT(C1-3)-030708brain01 Cy3 = Aburtoni27MaNT(C1-6)-030708brain01 hybed by SCP Renn on 20031119


title: p1.04s42a03scpr031117.gpr

description: Cy5 =  Aburtoni37MaNT (B1-21)-030708brain01 Cy3 = Aburtoni16Fab(A3-f3)-030708brain01 hybed by SCP Renn on 20031117


title: p1.04s42b03scpr031117.gpr

description: Cy5 =  Aburtoni17Fab(B1-f4)-030708brain01 Cy3 = Aburtoni35MaT(B1-18)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=670_660 ScanPower=33_33


title: p1.04s29a03scpr031117.gpr

description: Cy5 =  Aburtoni40MaT(C2-24)-030708brain01 Cy3 = Aburtoni30MaNT(A2-9)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=680_660 ScanPower=33_33


title: p1.04s41b03scpr031117.gpr

description: Cy5 =  Aburtoni32MaT(B3-13)-030708brain01 Cy3 = Aburtoni34MaNT(C3-16)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=660_650 ScanPower=33_33


title: p1.04s41a03scpr031117.gpr

description: Cy5 =  Aburtoni18Fab(C1-f5)-030708brain01 Cy3 = Aburtoni33MaT(C3-15)-030708brain01 hybed by SCP Renn on 20031117


title: p1.04s34a03scpr031119.gpr

description: Cy5 =  Aburtoni18Fab(C1-f5)-030708brain01 Cy3 = Aburtoni27MaNT(C1-6)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=700_640 ScanPower=33_33


title: p1.04s39a03scpr031117.gpr

description: Cy5 =  Aburtoni34MaNT(C3-16)-030708brain01 Cy3 = Aburtoni19Fab(C3-f6)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=630_620 ScanPower=33_33


title: p1.04s39b03scpr031117.gpr

description: Cy5 =  Aburtoni16Fab(A3-f3)-030708brain01 Cy3 = Aburtoni40MaT(C2-24)-030708brain01 hybed by SCP Renn on 20031117


title: p1.04s40a03scpr031117.gpr

description: Cy5 =  Aburtoni35MaT(B1-18)-030708brain01 Cy3 = Aburtoni26MaNT(C1-5)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=650_580 ScanPower=33_33


title: p1.04s37a03scpr031117.gpr

description: Cy5 =  Aburtoni21Fab(A2-f8)-030708brain01 Cy3 = Aburtoni30MaNT(A2-9)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=670_630 ScanPower=33_33


title: p1.04s29b03scpr031117.gpr

description: Cy5 =  Aburtoni26MaNT(C1-5)-030708brain01 Cy3 = Aburtoni21Fab(A2-f8)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=660_670 ScanPower=33_33


title: p1.04s32b03scpr031117.gpr

description: Cy5 =  Aburtoni16Fab(A3-f3)-030708brain01 Cy3 = Aburtoni34MaNT(C3-16)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=650_650 ScanPower=33_33


title: p1.04s30b03scpr031117.gpr

description: Cy5 =  Aburtoni26MaNT(C1-5)-030708brain01 Cy3 = Aburtoni40MaT(C2-24)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=650_630 ScanPower=33_33


title: p1.04s33b03scpr031117.gpr

description: Cy5 =  Aburtoni27MaNT(C1-6)-030708brain01 Cy3 = Aburtoni35MaT(B1-18)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=670_670 ScanPower=33_33


title: p1.04s30a03scpr031117.gpr

description: Cy5 =  Aburtoni40MaT(C2-24)-030708brain01 Cy3 = Aburtoni19Fab(C3-f6)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=670_610_ ScanPower=33_33_


title: p1.04s33a03scpr031117.gpr

description: Cy5 =  Aburtoni35MaT(B1-18)-030708brain01 Cy3 = Aburtoni16Fab(A3-f3)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=640_660 ScanPower=33_33


title: p1.04s37b03scpr031117.gpr

description: Cy5 =  Aburtoni38MaT(C3-22)-030708brain01 Cy3 = Aburtoni21Fab(A2-f8)-030708brain01 hybed by SCP Renn on 20031117


title: p1.04s35b03scpr031119.gpr

description: Cy5 =  Aburtoni17Fab(B1-f4)-030708brain01 Cy3 = Aburtoni37MaNT (B1-21)-030708brain01 hybed by SCP Renn on 20031119

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=690_670 ScanPower=33_33


title: p1.04s32a03scpr031117.gpr

description: Cy5 =  Aburtoni34MaNT(C3-16)-030708brain01 Cy3 = Aburtoni33MaT(C3-15)-030708brain01 hybed by SCP Renn on 20031117

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=670_610 ScanPower=33_33


title: F344 rat 30d NMU Treatment, biological rep3

city: Seattle

first: Xuefeng

last: Ren

state: WA

institute: Fred Hutchinson Cancer Research Center

description: Mammary gland collected at 30 days post NMU treated  55 days old F344 rats

hyb_protocol: Following fragmentation, the cRNA were hybridized  on Affymetrix Genechips Rat Genome 230 2.0 arrays according to to the GeneChip Expression Analysis Manual

scan_protocol: GeneChips were scanned using GeneChip« Scanner 3000 with AutoLoader

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling.

organism: Rattus norvegicus

source_name: F344 rat 55 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Qiagen RNAEasy Maxi kit  with Modified Protocol

tag: Puberty Rat Mammary gland


title: Cop rat 30d Control, biological rep1

description: Mammary gland collected at 30 days post Saline vehical treated  55 days old Cop rats

source_name: Cop rat 55 days


title: Cop rat 30d Control, biological rep3

description: Mammary gland collected at 30 day post Saline vehical treated  55 days old Cop rats


title: Cop rat 30d NMU Treatment, biological rep2

description: Mammary gland collected at 30 day post NMU treated  55 days old Cop rats


title: Cop rat 30d NMU Treatment, biological rep1


title: F344 rat 30d NMU Treatment, biological rep1


title: Cop rat 30d NMU Treatment, biological rep3


title: Cop rat 30d Control, biological rep2

source_name: FCop rat 55 days


title: 03KM2187, 46,XX[10]

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62853.gif

source_name: aCR (Stratagene)


title: F344 rat 30d Control, biological rep2

description: Mammary gland collected at 30 days post Saline vehical treated  55 days old F344 rats


title: Cop rat 1d NMU Treatment, biological rep3

description: Mammary gland collected at 1 day post NMU treated  55 days old Cop rats


title: F344 rat 30d NMU Treatment, biological rep2


title: F344 rat 30d Control, biological rep3


title: F344 rat 1d NMU Treatment, biological rep2

description: Mammary gland collected at 1 day post NMU treated  55 days old F344 rats


title: F344 rat 1d NMU Treatment, biological rep1


title: F344 rat 1d NMU Treatment, biological rep3


title: Cop rat 1d Control, biological rep3

description: Mammary gland collected at 1 day post Saline vehical treated  55 days old Cop rats


title: Cop rat 1d NMU Treatment, biological rep1


title: Cop rat 1d Control, biological rep2


title: F344 rat 30d Control, biological rep1


title: F344 rat 1d Control, biological rep2

description: Mammary gland collected at 1day post Saline vehical treated  55 days old F344 rats


title: F344 rat 1d Control, biological rep3

description: Mammary gland collected at 1 day post Saline vehical treated  55 days old F344 rats


title: F344 rat 1d Control, biological rep1


title: Cop rat 1d Control, biological rep1


title: Cop rat 1d NMU Treatment, biological rep2


title: Cop rat 6h Control, biological rep1

description: Mammary gland collected at 6 hour post Saline vehical treated  55 days old Cop rats


title: Cop rat 6h Control, biological rep2


title: Cop rat 6h NMU Treatment, biological rep3

description: Mammary gland collected at 6 hour post NMU treated  55 days old Cop rats


title: Cop rat 6h NMU Treatment, biological rep2


title: Cop rat 6h NMU Treatment, biological rep1


title: 2.0 Biological 4 Technical 2

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

country: Canada

institute: National Research Council

description: pooled replicate for 2.0h dye swap

hyb_protocol: Arrays were prehybridized at 42 °C for 30 min–3 h with 5× sodium chloride–sodium citrate (SSC), 0.1% SDS and 1% BSA (Sigma-Aldrich, Canada) to block non-specific hybridizations. They were washed twice in sterile dH2O and once in filtered isopropanol and then dried in a plate centrifuge at 500 rpm for 5 min. The labelled cDNAs were resuspended in hybridization solution containing 20 μg poly(dA), 50% formamide and 25% hybridization buffer (GE Healthcare Life Sciences) and were incubated at 42 °C for 10 min. The warmed hybridization mixture was added to the prehybridized array under a glass coverslip, placed in a hybridization chamber (Die-Tech) and incubated at 42 °C in a water bath for 18 h. Arrays were washed once for 10 min at 42 °C in 1× SSC with 0.2% SDS, twice for 10 min each at 42 °C in 0.1× SSC with 0.2% SDS and once for 5 min at 25 °C in 0.1× SSC. Arrays were dried by centrifugation for 5 min at 500 rpm before scanning.

scan_protocol: Scanned on Perkin Elmer ScanArray 5000XL, ScanArray Express software v3.0.1

data_processing: Spot intensities were quantified using the QuantArray microarray analysis software from the same supplier, and normalization and data analysis were carried out using the GeneTraffic software (Iobion Informatics). Background fluorescence was subtracted from the spot intensities and spots were flagged and removed from the data set if the signal to background ratio was less than 1, the signal to average background ratio was less than 1, or the signal intensity was less than 250. Data were normalized on a global basis by the Lowess method [15]. Normalization values were generated from the ratio of the total (combined) intensity of valid Cy3 spots to the total intensity of valid Cy5 spots on each array subgrid.

organism: Salmo salar

label_protocol: Synthesis and amplification of cDNA was carried out as previously described [30] on pooled mRNA samples from infected (cohab) and from uninfected control fish, with the following modifications: 100 ng of salmon polyA+ RNA and 80 pg of Arabidopsis thaliana chlorophyll synthetase G4 mRNA (Accession U19382) were reverse-transcribed using the SuperSMARTTM PCR cDNA synthesis kit (Clontech) and the RNase Inhibitor used previously was excluded.  All of column-purified single-stranded cDNA (85 ul) was combined with 40 ul PCR mixture and 75 ul PCR-grade dH2O, mixed well and split to yield two 100 ul reaction mixtures.  Amplification was performed in a Model 9700 thermocycler (Perkin Elmer) using the following conditions:  95 degC for 1 minute; 15-24 cycles of 95 degC for 5 s, 65 degC for 5 s and 68 degC for 3 min.  After 15 cycles, 70 ul of the reaction were removed and stored on ice, while the remaining 30 ul were returned to the thermocycler for further cycles.  The optimal number of cycles was determined by the removal of 5 ul aliquots after 15, 18, 21 and 24 cycles and assessment by agarose gel electrophoresis.  The original 70 ul reaction mix was returned to the thermocycler for the required number of additional cycles. The amplified cDNA was purified using QIAquick columns (Qiagen) and labelled in two 60 ul reactions containing 1X Advantage 2 PCR buffer, 0.2 mM d(A/T/G)TPs, 0.04 mM dCTP, 120 pmol anchor dT primer and 3 nmol Cy3-dCTP or Cy5-dCTP.

growth_protocol: Saint John River stock Atlantic salmon (Salmo salar L.) were maintained in single-pass, heated, dechlorinated fresh water at 12 °C at the Aquatron at Dalhousie University, Halifax, NS, Canada. Immediately before sampling, fish (100 g) were transferred to a bucket containing an overdose of TMS-Aqua MS-222 (Syndel). Using sterile technique, head kidneys were removed and placed in ice-cold L-15 media (Sigma-Aldrich, Canada) containing 2% FBS, 10 U/ml sodium heparin (Sigma-Aldrich, Canada) and 100 U/ml penicillin–streptomycin (Sigma-Aldrich, Canada) that had been passed through a 0.22 μm filter unit.

extract_protocol: Medium was removed from the macrophages and replaced with 100 μl Trizol. Plates were placed at 4 °C. Cell lysates from macrophages from individual fish were pooled and stored at −80 °C until use. Since all fish were responders as judged by a respiratory burst assay, lysates from the three replicates were pooled for each time point and for each condition (infected versus control) and total RNA was isolated according to the manufacturer's recommendations. The mRNA was isolated using the Micro FastTrack 2.0 kit (Invitrogen) and stored at −80 °C until use.

treatment_protocol: A. salmonicida subsp. salmonicida strain A449 [11] was grown in broth (in vitro) and in implants (in vivo) for this study because differences in the growth and characteristics of the bacteria, e.g. capsule formation and changes in superoxide dismutase activity [2] and [7] have been shown to result from these different growth milieus. For broth-grown cultures, bacteria were cultured to mid-logarithmic growth in tryptic soy broth at 17 °C and were resuspended to approximately 1.5×107 colony forming units (cfu)/ml in sterile Hank's balanced salt solution (HBSS). For implant-grown cultures, the same strain was cultured to mid-logarithmic phase as above, and placed in 12 cm lengths of dialysis tubing (SpectraPor 2 MWC 12–14,000 Da) that had been presoaked in HBSS and autoclaved [3]. The dialysis tubing was closed at one end by tying with suture, filled with 2×108 cells of A. salmonicida and closed at the other end by twisting and tying with suture. Dialysis bags were washed 6 times in 200 ml of HBSS and kept on ice until implanted into the peritoneal cavities of six salmon. Three days post-surgery, the dialysis bags were removed and the bacterial cells were collected and quantified. The concentrations of bacteria used for infection of macrophages were estimated by absorbance at 600 nm and calculated exactly by plate counts on tryptic soy agar. Head kidney tissue was dissociated by repeated passage through a 3 ml syringe and centrifuged at 500g for 10 min at 4 °C. The cell pellet was resuspended in 10 ml of L-15/2% FBS, centrifuged as before and the cell pellet finally resuspended in 4 ml of L-15/2% FBS. The cell suspension was layered on a Percoll gradient consisting of 4 ml of 51% Percoll and 4 ml of 34% Percoll and centrifuged at 400g for 20 min at 4 °C [12]. The macrophage-enriched cell preparation was collected from the 34%/51% interphase, the volume adjusted to 10 ml with L-15/2% FBS and cells pelleted by centrifugation at 500g for 10 min at 4 °C. The cell pellet was resuspended again in L-15/2% FBS, centrifuged as above and resuspended in 5 ml L-15/2% FBS. Viable cells were enumerated using Trypan blue and then resuspended in L-15/0.1% FBS at a concentration of 1×107 cells/ml. Macrophage-enriched cells (100 μl; 1×106 cells) isolated from each of the 24 fish were plated in individual wells of 96-well flat-bottom polystyrene tissue culture plates (Costar) and incubated in L-15 medium for 40 h at 17 °C. Half of the plate was used for the control treatment and half for exposure to bacteria. Additional 96-well plates were seeded at the same density for respiratory burst assay using phorbol myristate (Sigma) and assayed as described above. The cells were allowed to rest for 1 day prior to treatment. Medium was removed, the adherent cells gently washed once in L-15 medium and incubated in L-15/5% FBS until the following day. A. salmonicida (10 μl) grown in broth (1×105 cells) or in implants (2×105 cells) were warmed to 17 °C, added to the macrophages and incubated for 0.5, 1.0 or 2.0 h. Control wells received 10 μl of HBSS.

tag: pooled mRNA from macrophages

tag: infected, 2.0h

tag: control, 2.0h


title: 2.0 Biological 3 Technical 2

description: pooled replicate for 2.0h


title: 2.0 Biological 4 Technical 1

description: pooled replicate for 2.0h dye swap


title: F344 rat 6h Control, biological rep2

description: Mammary gland collected at 6 hour post Saline vehical treated  55 days old F344 rats


title: F344 rat 6h NMU Treatment, biological rep3

description: Mammary gland collected at 6 hour post NMU treated  55 days old F344 rats


title: F344 rat 6h Control, biological rep3


title: 2.0 Biological 1 Technical 1

description: pooled replicate for 2.0h


title: F344 rat 6h NMU Treatment, biological rep2


title: F344 rat 6h Control, biological rep1


title: Cop rat 6h Control, biological rep3


title: 2.0 Biological 1 Technical 2

description: pooled replicate for 2.0h


title: 1.0 Biological 4 Technical 2

description: pooled replicate for 1.0h dye swap

tag: infected, 1.0h

tag: control, 1.0h


title: 2.0 Biological 2 Technical 1

description: pooled replicate for 2.0h dye swap


title: 2.0 Biological 2 Technical 2

description: pooled replicate for 2.0h dye swap


title: AML 110

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32905.gif

source_name: CRH

tag: universal reference RNA (pooled from 11 cell lines)

source_name: AML 110

tag: normal karyotype acute myeloid leukemia


title: 1.0 Biological 3 Technical 2

description: pooled replicate for 1.0h


title: 1.0 Biological 4 Technical 1

description: pooled replicate for 1.0h dye swap


title: F344 rat 6h NMU Treatment, biological rep1


title: Cj11168_CmeR_Rep6

city: Ames

first: Qijing

last: Zhang

state: IA

address: 1116 Veterinary Medicine Complex

department: Veterinary Microbiology and Preventive Medicine

institute: Iowa State University

description: Compare the transcriptomes of Cj NCTC11168 and its isogenic cmeR mutant.

scan_protocol: Hybridized slides were scanned at 650 nm for Cy5 and 550 nm for Cy3 using a General Scanning ScanArray 5000 ( Perkin Elmer, Boston, MA) at 10-um resolution. The collection of the fluorescent intensities was performed with ImaGene software ( BioDiscovery, El Segundo, CA).

data_processing: Background subtraction, Lowess( locally weighted polynomial regression) normalization, scale normalization and median centering were performed using the R statistical package ( Version 2.0.1, the R foundation for Statistical Computing).

organism: Campylobacter jejuni

source_name: Cj 11168 cmeR mutant

label_protocol: The cDNA synthesis and fluorescence labeling were performed using the SuperScript Indirect cDNA Labelling System (Invitrogen, Carlbad, CA) according to the manufacturer's instructions.

extract_protocol: Bacterial RNA was isolated using the RNeasy Mini Kit ( Qiagen) according to the manufacturer's instruction. Isolated RNA was treated with the on-column DNase Digestion Kit (Qiagen) followed by the removal of DNase using RNeasy Mini Kit.

tag: C. jejuni cmeR mutant 11168R, grown in MH broth to mid-log phase, OD600 0.13

source_name: Cj11168 wild type

tag: C. jejuni NCTC 11168, grown in MH broth to mid-log phase, OD600 0.13


title: 1.0 Biological 3 Technical 1

description: pooled replicate for 1.0h


title: 1.0 Biological 1 Technical 1

description: pooled replicate for 1.0h


title: p1.04s26a03scpr031211.gpr

description: Cy5 =  Aburtoni24MaT(C1-3)-030708brain01 Cy3 = Aburtoni27MaNT(C1-6)-030708brain01 hybed by SCP Renn on 20031211

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=630_580 ScanPower=100_100


title: 0.5 Biological 4 Technical 2

description: pooled replicate for 0.5h dye swap

tag: infected, 0.5h

tag: control, 0.5h


title: 0.5 Biological 3 Technical 1

description: pooled replicate for 0.5h


title: 2.0 Biological 3 Technical 1

description: pooled replicate for 2.0h


title: Cj11168_CmeR_Rep3


title: Cj11168_CmeR_Rep4


title: 0.5 Biological 4 Technical 1

description: pooled replicate for 0.5h dye swap


title: Cj11168_CmeR_Rep5


title: 0.5 Biological 2 Technical 1

description: pooled replicate for 0.5h dye swap


title: 1.0 Biological 1 Technical 2

description: pooled replicate for 1.0h


title: 0.5 Biological 2 Technical 2

description: pooled replicate for 0.5h dye swap


title: 1.0 Biological 2 Technical 1

description: pooled replicate for 1.0h dye swap


title: 0.5 Biological 1 Technical 2

description: pooled replicate for 0.5h

tag: pooled mRNA from macrophages derived from head kidney at 0.5h timepoint


title: Cj11168_CmeR_Rep2


title: 0.5 Biological 1 Technical 1

description: pooled replicate for 0.5h


title: 0.5 Biological 3 Technical 2

description: pooled replicate for 0.5h


title: 1.0 Biological 2 Technical 2

description: pooled replicate for 1.0h dye swap


title: Brassica napus seed_31 days after pollination_rep1

status: Public on Feb 26 2008

city: Shanghai

first: Hong-Wei

last: Xue

state: Shanghai

address: 300 Fenglin Road

department: molecular genetics

country: China

institute: Institute of Plant Physiology & Ecology

description: Siliques at different day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.

hyb_protocol: Prehybridization: 1、	Mix the hybridization solution I and II in 1.5ml EP tube(prehybridization solution); 2、	Denature the prehybridization solution at 95℃ for 2min, incubate the glass-based chip for 30sec at 95℃, immediately in ethanol for 30sec, air-dry at room temperature; 3、	Add the denatured prehybridization solution to spotting area of the chip, prehybridized 5-6h at 42℃; Hybridization: 1、	Resuspend the labeled probes in 6.5μl hybridization solution I, the Add another 6.5μl hybridization solution II; 2、	Wash the prehybridized chips with ddH2O; 3、	 Denature the probe at 95℃ for 2min, and rapidly cooling on ice-water, incubate chips for 30sec at 95 ℃, rapidly in ethanol for 30sec; 4、	Add the denature probe to the chips, hybrid for 16-18h at 42℃. Washing after hybridization: 1、	Rinse the chip with 0.5% washing buffer I; 2、	Wash 2×10 min in 0.5% washing buffer I; 2% washing buffer II; 5% washing buffer III at 60℃; 3、	Rinse the chip with 0.5% washing buffer I, air-dry.

scan_protocol: Automated process conducted using ScanArray4000 Standard Biochip Scanning System (Axon Instruments, California, USA)

data_processing: Mean fluorescence intensities for each cDNA clone were determined using GenePix Pro (Ver 3.0). Cy5 or Cy3 signal intensity of each gene was the feature intensity minus the background intensity. In order to avoid the weak signal interference of Cy5, signals less than 200 are replaced with 200. Genes that participate in normalization followed 2 principles, 1) both of Cy3 and Cy5 intensities were >200 or one of them >800; 2) Cy5/Cy3 value of gene was between 0.1-10. r=ln (Cy5/Cy3), “R” was the average of the “r” of all genes that participate in normalization. The normalization coefficient was the reciprocal of R(EXP(R)). Cy3* was Cy3 multiply the EXP (R), signal intensities of Cy3* was replace with 200 if it was <200.Value of each gene expression diversity (ratio) was Cy5/Cy3*. Gene expression of each developmental stage is compared to that at 3 DAP, and ratios were rescaled by setting that at 3 DAP as 1.

organism: Brassica napus

source_name: 31 days after pollination Brassica napus seeds

label_protocol:
1、	Add the following to a 1.5ml EP tube(all the solutions are RNase free):
Sterile, distilled water           23μl
Primers                              5μl
Total RNA                        30-50μg
Incubate at 70℃ for 5 min, rapidly chilling on ice ;
2、	Add the following reagents to the mixture:
RT buffer                   2μl
DTT                         5μl
dNTPs                      4μl
3、	Add the following reagents to the mixture in dark:
RT enzyme                 2μl
Cy5-dCTP                  3μl
4、	Mix well by pipetting gently up and down, centrifuge briefly, incubate at 42 ℃ for 2h;
5、	Add 4μl labeling buffer I in the mixture, 65℃ for 10 min, then add 4μl labeling buffer II, mix well, mix the control(Cy3-dCTP labeled) and sample(Cy5-dCTP labeled) tube, concentrate to about 50μl;
6、	Purify the DNA with a DNA purifying column;
7、	Add 8μl labeling buffer III, dry it on vacuum dryer.

growth_protocol: Brassica Napus plants (Huyou-15) were grown in field at the last ten-day of September of the first year. And the immature seeds were harvested at April-May of the second year. The average temperature of these months of Shanghai is as follow: September 23.4℃, October 18℃, November 12.3℃, December 6.2℃, January 3.5℃, February 4.6℃, March 8.3℃, April 14℃, May 18.8 ℃.

extract_protocol:
1、	Weigh appropriate Brassica Napus immature seeds, grind the tissue in liquid N2 using a mortar and pestle;
2、	Transfer the material into 15ml centrifuge tube, 12000g, 4℃, 10min;
3、	Transfer the top phase to a new 15ml centrifuge tube, incubate for 5min at 15-30℃;
4、	Add chloroform, vortex vigorously, incubate for 3min at 15-30℃;
5、	12000g, 4℃, 15min;
6、	Transfer the top phase to a new 15ml centrifuge tube, add isopropyl alcohol, invert several times, incubate for 10min at 15-30℃;
7、	12000g, 4℃, 10min;
8、	Remove the supernatant by pipet, add 5ml 75% ethanol, invert several times, remove the ethanol;
9、	Add 10ml 75% ethanol, vortex briefly, 8000g, 4℃, 10min;
10、	Remove the supernatant carefully, centrifuge briefly, remove all the supernatant by pipet, air-dry the pellet for 5min;
11、	Resuspend the RNA with RNase-free Milli-Q wate.

tag: Ecotype

tag: Tissue

value: Immature seeds

tag: Stage

value: 31 day after pollination (DAP)

tag: Siliques at 31 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.

source_name: 3 days after pollination Brassica napus seeds

label_protocol:
1、	Add the following to a 1.5ml EP tube(all the solutions are RNase free):
Sterile, distilled water           23μl
Primers                              5μl
Total RNA                        30-50μg
Incubate at 70℃ for 5 min, rapidly chilling on ice ;
2、	Add the following reagents to the mixture:
RT buffer                   2μl
DTT                         5μl
dNTPs                      4μl
3、	Add the following reagents to the mixture in dark:
RT enzyme                 2μl
Cy3-dCTP                  3μl
4、	Mix well by pipetting gently up and down, centrifuge briefly, incubate at 42 ℃ for 2h;
5、	Add 4μl labeling buffer I in the mixture, 65℃ for 10 min, then add 4μl labeling buffer II, mix well, mix the control(Cy3-dCTP labeled) and sample(Cy5-dCTP labeled) tube, concentrate to about 50μl;
6、	Purify the DNA with a DNA purifying column;
7、	Add 8μl labeling buffer III, dry it on vacuum dryer.

value: 3 day after pollination (DAP)

tag: Siliques at 3 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.


title: Brassica napus seed_25 days after pollination_rep1

source_name: 25 days after pollination Brassica napus seeds

value: 25 day after pollination (DAP)

tag: Siliques at 25 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.


title: Brassica napus seed_21 days after pollination_rep1

source_name: 21 days after pollination Brassica napus seeds

value: 21 day after pollination (DAP)

tag: Siliques at 21 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.


title: Brassica napus seed_17 days after pollination_rep2

source_name: 17 days after pollination Brassica napus seeds

value: 17 day after pollination (DAP)

tag: Siliques at 17 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.


title: Cj11168_CmeR-Rep1


title: IPC knockout, 14 day old female flies, 48h yeast feeding chip4 (dyeswap)

city: Karlsruhe

middle: J.

last: Pankratz

department: Institute of Genetics

country: Germany

institute: Forschungszentrum Karlsruhe

description:
dyeswap
control line: InsP3-Gal4 x UAS-LacZ
IPC knockout line: InsP3-Gal4 x UAS-RPR/HID

hyb_protocol: The concentrated probes were hybridized to the microarray in 1x dig easy hyb buffer (Hoffman-la Roche; Basel, Switzerland) overnight (minimum 16 h) at 42°C. For further details, see publication PMID: 16569777.

scan_protocol: Arrays were scanned using the dual-laser scanner Axon 4000B and the corresponding software Genepix 4 (Axon; Union City, CA). Each array was scanned three times (low, medium, and high scan) with different signal amplification factors (voltage settings of the photo multiplier tubes) but with the same laser power. For further details, see publication PMID: 16569777.

data_processing:
Data processing was carried out with the Karlsruhe Microarray Analysis Tool (KAMAAN), a program written in the R programming language.  For further details, see publication PMID: 16569777.
The VALUE column reports loess-normalized, log2 (test/control) ratios.

organism: Drosophila melanogaster

source_name: whole animal_control

label_protocol: CyScribe labelling kit (Amersham). Removal of incorporated dyes and concentration of the target were done with Microcon 30 spin columns (Millipore; Bedford, MA) according to the manufacturer's instructions.

extract_protocol: Phenol chloroform extraction (trizol)

tag: gender

value: female

tag: age

value: 14 days

tag: diet

value: 48h yeast paste

source_name: whole animal_IPC deficient flies


title: Brassica napus seed_12 days after pollination_rep2

source_name: 12 days after pollination Brassica napus seeds

label_protocol:
1、	Add the following to a 1.5ml EP tube(all the solutions are RNase free):
Sterile, distilled water           23μl
Primers                              5μl
Total RNA                         30-50μg
Incubate at 70℃ for 5 min, rapidly chilling on ice ;
2、	Add the following reagents to the mixture:
RT buffer                   2μl
DTT                          5μl
dNTPs                       4μl
3、	Add the following reagents to the mixture in dark:
RT enzyme                 2μl
Cy5-dCTP                  3μl
4、	Mix well by pipetting gently up and down, centrifuge briefly, incubate at 42 ℃ for 2h;
5、	Add 4μl labeling buffer I in the mixture, 65℃ for 10 min, then add 4μl labeling buffer II, mix well, mix the control(Cy3-dCTP labeled) and sample(Cy5-dCTP labeled) tube, concentrate to about 50μl;
6、	Purify the DNA with a DNA purifying column;
7、	Add 8μl labeling buffer III, dry it on vacuum dryer.

value: 12 day after pollination (DAP)

tag: Siliques at 12 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.

label_protocol:
1、	Add the following to a 1.5ml EP tube(all the solutions are RNase free):
Sterile, distilled water           23μl
Primers                              5μl
Total RNA                         30-50μg
Incubate at 70℃ for 5 min, rapidly chilling on ice ;
2、	Add the following reagents to the mixture:
RT buffer                   2μl
DTT                          5μl
dNTPs                       4μl
3、	Add the following reagents to the mixture in dark:
RT enzyme                 2μl
Cy3-dCTP                  3μl
4、	Mix well by pipetting gently up and down, centrifuge briefly, incubate at 42 ℃ for 2h;
5、	Add 4μl labeling buffer I in the mixture, 65℃ for 10 min, then add 4μl labeling buffer II, mix well, mix the control(Cy3-dCTP labeled) and sample(Cy5-dCTP labeled) tube, concentrate to about 50μl;
6、	Purify the DNA with a DNA purifying column;
7、	Add 8μl labeling buffer III, dry it on vacuum dryer.


title: Brassica napus seed_31 days after pollination_rep2


title: IPC knockout, 14 day old female flies, 48h yeast feeding chip3 (dyeswap)


title: IPC knockout, 14 day old female flies, 48h yeast feeding chip5 (dyeswap)


title: Brassica napus seed_21 days after pollination_rep2


title: Brassica napus seed_19 days after pollination_rep2

source_name: 19 days after pollination Brassica napus seeds

value: 19 day after pollination (DAP)

tag: Siliques at 19 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.


title: IPC knockout, 14 day old female flies, 48h yeast feeding chip2

description:
control line: InsP3-Gal4 x UAS-LacZ
IPC knockout line: InsP3-Gal4 x UAS-RPR/HID


title: Brassica napus seed_9 days after pollination_rep2

source_name: 9 days after pollination Brassica napus seeds

value: 9 day after pollination (DAP)

tag: Siliques at 9 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.


title: Brassica napus seed_25 days after pollination_rep2


title: IPC knockout, 14 day old female flies, 48h yeast feeding


title: Brassica napus seed_17 days after pollination_rep1


title: Brassica napus seed_7 days after pollination_rep1

source_name: 7 days after pollination Brassica napus seeds

value: 7 day after pollination (DAP)

tag: Siliques at 7 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.


title: Brassica napus seed_12 days after pollination_rep1


title: Brassica napus seed_19 days after pollination_rep1


title: Brassica napus seed_7 days after pollination_rep2


title: OH1ST vs. 4H1ST Cy3: 4H1ST Cy5: OH1ST

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.    For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.    Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v8.1).

data_processing: Agilent Feature Extraction protocol for 44K arrays, log2ratio Treated/Control.  VALUE column reports log10 (Treated/Control) ratios.

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 0.5µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.

extract_protocol: Total RNA was prepared from H460 cells treated for 4hrs with 250uM FOH or vehicle (DMSO) using TriReagent (Sigma) following the manufacturer's protocol.

treatment_protocol: Human lung carcinoma cell line H460 was obtained from American Type Culture Collection grown in RPMI1640 supplemented with 10% heat-inactivated FBS.  RNA was collected from cells treated for 4 hour with 250 uM FOH or vehicle (DMSO)

tag: control

tag: treated


title: Brassica napus seed_9 days after pollination_rep1

tag: Ecotype


title: OH2ST vs. 4H2ST Cy3: OH2ST Cy5: 4H2ST

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v8.1).


title: OH2ST vs. 4H2ST Cy3: 4H2ST Cy5: OH2ST


title: Mock3 MOE430A

status: Public on Feb 25 2008

city: Zurich

first: Gino

last: Miele

address: Schmelzbergstrasse 12

department: Institute for Neuropathology

country: Switzerland

institute: University Hospital Zurich

description: Mock infected murine neuroblastoma cells

hyb_protocol: Affymetrix hybridisation protocols

scan_protocol: Affymetrix 2500 scanner

label: Biotin

source_name: Murine Neuroblastoma N2a cells (PK1 subclone)

label_protocol: 15ug total RNA labelled according to Affymetrix 1 cycle labelling protocol

extract_protocol: Trizol isolated total RNA followed by Qiagen RNeasy clean up

tag: PK1 subclone


title: RML1 MOE430B

description: RML Prion infected murine neuroblastoma cells


title: OH1ST vs. 4H1ST Cy3: OH1ST Cy5: 4H1ST


title: endogenous small RNAs from Arabidopsis thaliana col-0, wild type, flower buds

city: Norwich

first: Frank

last: Schwach

address: University of East Anglia

department: School of Computing Sciences

country: United Kingdom

institute: University of East Anglia

description: Total endogenous small RNAs from Arabidopsis thaliana col-0 wild type

data_processing: Small RNA sequences that did not match tRNA or rRNA sequences (obtained from RFAM; www.sanger.ac.uk/Software/Rfam) were mapped to the Arabidopsis thaliana genome (TAIR6, www.arabidopsis.org). Only full-length complete matches were allowed. Only sequences that had at least one match to the genome are contained in the table.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana col-0 wild type flower buds

growth_protocol: Plants were grown under 16h light.

extract_protocol: Total RNA was extracted and further purifed on polyacrylamide gels.

tag: flower buds from plants grown under 16h light


title: RML1 MOE430A


title: endogenous small RNAs from Arabidopsis thaliana col-0, nrpd1a mutant, flower buds

description: Total endogenous small RNAs from Arabidopsis thaliana col-0 nrpd1a mutant

source_name: Arabidopsis thaliana col-0 nrpd1a mutant flower buds


title: Stressed leaves vs Control leaves_7d_rep1_A

city: jinan

first: juren

last: zhang

address: shanda nanlv 27

institute: shandong university

hyb_protocol: according to the protocols at the website of the Maize Oligonucleotide Array Project.

scan_protocol: Scanned on an GenePix 4000B scanner. Images were quantified using GENEPIX 6.0 software.

data_processing: Global normalized, background subtracted data. VALUE column represents normalized, log2(test/reference) ratios.

organism: Zea mays

source_name: maize DH4866 leaves

label_protocol: Using SuperScript™ Indirect cDNA Labeling System (L1014-02)

extract_protocol: Total RNA was isolated as McCarty (1986) described.

treatment_protocol: The plants were stressed for 168 h (7 days) by watering every day to maintain a similar water-dificency state by adjusting water supply, according to the osmotic potential of the fully expended leaf of the plants measured at 8:00 am each day.

tag: maize DH4866 leaves

tag: Age

value: at the heading stage

tag: Tissue

value: maize flag leaves

treatment_protocol: The control plants were fully watered.


title: RML3 MOE430A

hyb_protocol: Affymetrix protocols

source_name: Murine neuoroblastoma cells (PK1 subclone)

label_protocol: 15ug total RNA labelled according to Affymetrix 1 cycle protocols


title: endogenous small RNAs from Arabidopsis thaliana col-0, nrpd1b mutant, flower buds

description: Total endogenous small RNAs from Arabidopsis thaliana col-0 nrpd1b mutant

source_name: Arabidopsis thaliana col-0 nrpd1b mutant flower buds


title: Mock2 MOE430A


title: Mock2 MOE430B


title: RML2 MOE430B


title: Mock1 MOE430A


title: Control leaves vs Stressed leaves_1d_rep2_A

treatment_protocol: The plants were subjected to drought stress by withholding water for 24 h (1 day).


title: Mock3 MOE430B


title: Mock1 MOE430B


title: Stressed leaves vs Control leaves_1d_rep1_B


title: Control leaves vs Stressed leaves_7d_rep2_A


title: RML2 MOE430A


title: RML3 MOE430B


title: Control leaves vs Stressed leaves_1d_rep2_B


title: Stressed leaves vs Control leaves_7d_rep1_B


title: E15.5 minus liver rep3

status: Public on Feb 23 2008

city: Philadelphia

first: Joshua

last: Friedman

state: PA

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

hyb_protocol: The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: slides were scanned by a ScanArray 4000 XL scanner (Packard Biochip Technologies, USA) Image analysis was carried out using the ImaGene 6.1.0 software (BioDiscovery, Inc., USA)

data_processing: The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm

source_name: E15.5 embryo without liver

label_protocol: 5 mcg total RNA from sample and reference pool were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array labeling kit (Exiqon, Denmark)

extract_protocol: RNA was purified using the mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions

tag: F/VBN mice

source_name: Pool of all RNA samples


title: E15.5 minus liver rep2


title: P1 liver rep3

source_name: P1 liver


title: P1 liver rep1


title: P1 liver rep2


title: E18.5 liver rep2

source_name: E18.5 liver


title: E18.5 liver rep3


title: B37xB73 11-day seedling aerial tissue; bio rep 2

status: Public on Feb 22 2008

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: B37xB73 11-day seedling aerial tissue versus pooled reference; bio rep 2

hyb_protocol: The 70-mer arrays were hybridized on a Tecan 4800 HS Pro hybridization station (Tecan Services Inc., Durham, NC) which is capable of processing 12 arrays in a single hybridization run.

scan_protocol: The arrays were scanned on an Axon 4100 AL scanner (Molecular Devices Corporation, Sunnyvale, CA) immediately after being hybridized.

data_processing: Per chip and per gene normalizations using GeneSpring version 7.2; Cy3 normalized as a single channel; multiple normalizations based on different comparisons and analyses. Cy5 reference channel data was used for filtering out bad spots (ratio data was not generated).

source_name: Zea mays 11-day seedling aerial tissue genotype B37xB73

label_protocol: Hybridization target was prepared according to an RNA amplification protocol posted at http://www.maizearray.org/maize_protocols.shtml

growth_protocol: Seeds for maize inbreds and hybrids were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression analysis. Three biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 30ºC and night temperature of 22ºC) and sampled between 8:00 and 9:00 am. The plants were cut immediately above the highest brace root, thus all above-ground tissues and meristems were collected. Each biological replicate consisted of pooled tissue from eight different seedlings of the same genotype. The sampled tissues were flash frozen in liquid nitrogen and stored at -80 C prior to RNA isolation.

extract_protocol: Total RNA samples were isolated using TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy system (QIAGEN, Valencia, CA).

tag: Genotype

value: B37xB73; Stage:11-day old seedling, all aerial tissue


title: B37xB73 11-day seedling aerial tissue; bio rep 1

description: B37xB73 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: B37xB73 11-day seedling aerial tissue; bio rep 3

description: B37xB73 11-day seedling aerial tissue versus pooled reference; bio rep 3


title: E18.5 liver rep1


title: E15.5 liver rep3

source_name: E15.5 liver


title: Wf9 11-day seedling aerial tissue; bio rep 2

description: Wf9 11-day seedling aerial tissue versus pooled reference; bio rep 2

source_name: Zea mays 11-day seedling aerial tissue genotype Wf9

value: Wf9; Stage:11-day old seedling, all aerial tissue


title: E15.5 liver rep1


title: E15.5 liver rep2


title: Control leaves vs Stressed leaves_7d_rep2_B


title: Stressed leaves vs Control leaves_1d_rep1_A


title: EP4 agonist (Experiment5b; technical repeat)

status: Public on Feb 24 2008

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

institute: UCLA

description: Manufacturer's scanner and feature extraction - normalization software

hyb_protocol: Agilent 44K hybridization, 17 hrs

scan_protocol: Agilent scanner and Feature Extraction Software

data_processing: log2-transformed ratio of Cy3 (treated) over Cy5 (control)

source_name: Human ciliary smooth muscle cells (treated)

label_protocol: Low RNA Input Fluor Linear Amplification Kit (Agilent Technologies, USA)

extract_protocol: Ambion RNAqueous RNA isolation kit

tag: Primary culture from ciliary body of the eye

source_name: Human ciliary smooth muscle cells (control)


title: EP2 agonist (Experiment4; dye swap)

data_processing: log2-transformed ratio of Cy3 (treated) over Cy5 (control) (dye swap)

source_name: Primary culture from ciliary body of the eye (control)


title: Wf9 11-day seedling aerial tissue; bio rep 3

description: Wf9 11-day seedling aerial tissue versus pooled reference; bio rep 3


title: E15.5 minus liver rep1


title: EP2 agonist (Experiment3)

data_processing: log2-transformed ratio of Cy5 (treated) over Cy3 (control)


title: EP4 agonist (Experiment7a)


title: EP4 agonist (Experiment6; dye swap)


title: EP4 agonist (Experiment7b; technical repeat)


title: EP4 agonist (Experiment5a)


title: B37 11-day seedling aerial tissue; bio rep 2

description: B37 11-day seedling aerial tissue versus pooled reference; bio rep 2

source_name: Zea mays 11-day seedling aerial tissue genotype B37

value: B37; Stage:11-day old seedling, all aerial tissue


title: B37 11-day seedling aerial tissue; bio rep 3

description: B37 11-day seedling aerial tissue versus pooled reference; bio rep 3


title: B14a 11-day seedling aerial tissue; bio rep 2

description: B14a 11-day seedling aerial tissue versus pooled reference; bio rep 2

source_name: Zea mays 11-day seedling aerial tissue genotype B14a

value: B14a; Stage:11-day old seedling, all aerial tissue


title: B37 11-day seedling aerial tissue; bio rep 1

description: B37 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: B14a 11-day seedling aerial tissue; bio rep 3

description: B14a 11-day seedling aerial tissue versus pooled reference; bio rep 3


title: Oh43xMo17 11-day seedling aerial tissue; bio rep 1

description: Oh43xMo17 11-day seedling aerial tissue versus pooled reference; bio rep 1

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43xMo17

value: Oh43xMo17; Stage:11-day old seedling, all aerial tissue


title: Oh43xB73 11-day seedling aerial tissue; bio rep 3

description: Oh43xB73 11-day seedling aerial tissue versus pooled reference; bio rep 3

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43xB73

value: Oh43xB73; Stage:11-day old seedling, all aerial tissue


title: Oh43xB73 11-day seedling aerial tissue; bio rep 2

description: Oh43xB73 11-day seedling aerial tissue versus pooled reference; bio rep 2


title: Wf9 11-day seedling aerial tissue; bio rep 1

description: Wf9 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: EP2 agonist (Experiment2)


title: Oh43xMo17 11-day seedling aerial tissue; bio rep 3

description: Oh43xMo17 11-day seedling aerial tissue versus pooled reference; bio rep 3


title: B84xB73 11-day seedling aerial tissue; bio rep 3

description: B84xB73 11-day seedling aerial tissue versus pooled reference; bio rep 3

source_name: Zea mays 11-day seedling aerial tissue genotype B84xB73

value: B84xB73; Stage:11-day old seedling, all aerial tissue


title: Oh43xMo17 11-day seedling aerial tissue; bio rep 2

description: Oh43xMo17 11-day seedling aerial tissue versus pooled reference; bio rep 2


title: B84xB73 11-day seedling aerial tissue; bio rep 2

description: B84xB73 11-day seedling aerial tissue versus pooled reference; bio rep 2


title: Oh43xB73 11-day seedling aerial tissue; bio rep 1

description: Oh43xB73 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: W22 11-day seedling aerial tissue; bio rep 3

description: W22 11-day seedling aerial tissue versus pooled reference; bio rep 3

source_name: Zea mays 11-day seedling aerial tissue genotype W22

value: W22; Stage:11-day old seedling, all aerial tissue


title: Oh43 11-day seedling aerial tissue; bio rep 3

description: Oh43 11-day seedling aerial tissue versus pooled reference; bio rep 3

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43

value: Oh43; Stage:11-day old seedling, all aerial tissue


title: Oh43 11-day seedling aerial tissue; bio rep 1

description: Oh43 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: W22 11-day seedling aerial tissue; bio rep 2

description: W22 11-day seedling aerial tissue versus pooled reference; bio rep 2


title: W22 11-day seedling aerial tissue; bio rep 1

description: W22 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: Mo17 11-day seedling aerial tissue; bio rep 3

description: Mo17 11-day seedling aerial tissue versus pooled reference; bio rep 3

source_name: Zea mays 11-day seedling aerial tissue genotype Mo17

value: Mo17; Stage:11-day old seedling, all aerial tissue


title: Oh43 11-day seedling aerial tissue; bio rep 2

description: Oh43 11-day seedling aerial tissue versus pooled reference; bio rep 2


title: B14a 11-day seedling aerial tissue; bio rep 1

description: B14a 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: Mo17 11-day seedling aerial tissue; bio rep 2

description: Mo17 11-day seedling aerial tissue versus pooled reference; bio rep 2


title: B84xB73 11-day seedling aerial tissue; bio rep 1

description: B84xB73 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: Mo17 11-day seedling aerial tissue; bio rep 1

description: Mo17 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: B84 11-day seedling aerial tissue; bio rep 2

description: B84 11-day seedling aerial tissue versus pooled reference; bio rep 2

source_name: Zea mays 11-day seedling aerial tissue genotype B84

value: B84; Stage:11-day old seedling, all aerial tissue


title: B84 11-day seedling aerial tissue; bio rep 3

description: B84 11-day seedling aerial tissue versus pooled reference; bio rep 3


title: B73 11-day seedling aerial tissue; bio rep 3

description: B73 11-day seedling aerial tissue versus pooled reference; bio rep 3

source_name: Zea mays 11-day seedling aerial tissue genotype B73

value: B73; Stage:11-day old seedling, all aerial tissue


title: B73 11-day seedling aerial tissue; bio rep 2

description: B73 11-day seedling aerial tissue versus pooled reference; bio rep 2


title: B73 11-day seedling aerial tissue; bio rep 1

description: B73 11-day seedling aerial tissue versus pooled reference; bio rep 1


title: B84 11-day seedling aerial tissue; bio rep 1

description: B84 11-day seedling aerial tissue versus pooled reference; bio rep 1