title: CHD Patient 1720

tag: DNA isolated from blood of a patient with congenital heart disease (Ventricular septal defect). Gender


title: CHD Patient 1693

status: Public on May 12 2008

type: genomic

city: Berlin

first: Fikret

last: Erdogan

address: Ihnestr. 73

country: Germany

institute: Max-Planck-Institute

description: Array CGH analysis of a patient with congenital heart disease

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner .

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA isolated from blood

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from peripheral blood by a salting out procedure (Grimberg et al.,1989).

tag: DNA isolated from blood of a patient with congenital heart disease (Pulmonary stenosis). Gender

value: male

extract_protocol: DNA was extracted from peripheral blood by a salting out procedure (Blin and Stafford,1976).

tag: DNA isolated from blood of a healthy male donor


title: CHD Patient 1775

tag: DNA isolated from blood of a patient with congenital heart disease (Atrioventricular septum defect). Gender


title: CHD Patient 1690

value: female

tag: DNA isolated from blood of a healthy female donor


title: CHD Patient 1688


title: Mo9 #06141 Bmo

type: RNA

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Mo9 #06141 Bmo

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

molecule: total RNA

source_name: CD14+ cells, Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy extraction kit

tag: tissue

value: Blood


title: CHD Patient 1684


title: CHD Patient 1713


title: CHD Patient 1678

tag: DNA isolated from blood of a patient with congenital heart disease (Atrial Septal Defect). Gender


title: Mo7 #06124 Dmo

description: Mo7 #06124 Dmo

source_name: CD14+ cells, Decidual

value: Decidual


title: Mo8 #06128 Dmo

description: Mo8 #06128 Dmo


title: Mo8 #06128 Bmo

description: Mo8 #06128 Bmo


title: Mo6 #06055 Dmo

description: Mo6 #06055 Dmo


title: Mo7 #06124 Bmo

description: Mo7 #06124 Bmo


title: CHD Patient 1682


title: CHD Patient 1665

tag: DNA isolated from blood of a patient with congenital heart disease (Double outlet right ventricle (DORV), PS). Gender


title: CHD Patient 1669

tag: DNA isolated from blood of a patient with congenital heart disease (TGA, VSD). Gender


title: CHD Patient 1826


title: CHD Patient 1653

tag: DNA isolated from blood of a patient with congenital heart disease (Pulmonary atresia). Gender


title: CHD Patient 1657


title: Mo6 #06055 Bmo

description: Mo6 #06055 Bmo


title: Mo5 #06043 Bmo

description: Mo5 #06043 Bmo


title: Mo5 #06043 Dmo

description: Mo5 #06043 Dmo


title: CHD Patient 1647

tag: DNA isolated from blood of a patient with congenital heart disease (Tetralogy of Fallot). Gender


title: CHD Patient 1644

tag: DNA isolated from blood of a patient with congenital heart disease (DORV, PS). Gender


title: LID #6445 Bmo

description: LID #6445 Bmo


title: CHD Patient 1624


title: LID #6445 Dmo

description: LID #6445 Dmo


title: 3111 mother and 3112 father of the CHD patient 3110

hyb_protocol: Hybridization was done overnight at 42?C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

extract_protocol: DNA was extracted from peripheral blood by  a salting out procedure  (Grimberg et al.,1989).

tag: DNA isolated from blood of the mother.

extract_protocol: DNA was extracted from peripheral blood by  a salting out procedure (Blin and Stafford,1976).

tag: DNA isolated from the blood of the father.


title: LID #6444 Dmo

description: LID #6444 Dmo


title: LID #6444 Bmo

description: LID #6444 Bmo


title: CHD Patient 1607


title: 4778 mother and 4779 father of the CHD patient 4770


title: 1499 mother and 1500 father of the CHD patient 2930


title: CHD Patient 1597


title: CHD Patient 1602

tag: DNA isolated from blood of a patient with congenital heart disease (Aortic coarctation). Gender


title: CHD Patient 1616

tag: DNA isolated from blood of a patient with congenital heart disease (Transposition of the great arteria). Gender


title: YCU_patient1_CGH1

status: Public on May 11 2008

city: Yokahama

first: Takeshi

last: Mizuguchi

address: Fukuura 3-9, Kanazawa-ku

department: Department of Human Genetics

country: Japan

institute: Yokohama City University

description: Investigation of submicroscopic chromosomal imbalances in patients with MR using YCU Human 4.2k BAC microarray

hyb_protocol: Differentially labeled DNA (Cy3:control, Cy5:Patient with MR) was mixed with 67.5 ug Cot I DNA (Invitrogen, Tokyo, Japan) and co-precipitated. The DNA pellet was resuspended with 126 ul hybridization buffer (50% formamide/10% dextran sulfate/0.1% Tween 20/2X SSC/10 mM Tris-HCl, pH 7.4) with 60 ug yeast tRNA. Probe DNA was denatured for 10 min at 70 C° and incubated for 1hr at 37 C° before hybridization. Microarray slide was prehybridized for 1 hr at 37 C° with 180ul hybridization buffer containing the 400ug herring sperm DNA and 67.5 ug human Cot I DNA. After prehybridization using in situ frame (Eppendorf, Hamburg, Germany) on a slide in a hybrid-chamber (Genetix, New Milton, UK), Prehybridization mixture was removed carefully and labeled probe mixture was applied to microarray slide. Slide was incubated at 37 C° for 72 hrs with gentle shaking, and then washed twice with solution A (0.05 % Tween 20/1X PBS) for 10 min at room temperature, and twice with solution B (50% formamide/2X SSC) at 43 C° for 15 min, and with again solution A at room temperature for 10 min. Slide was dried by centrifuge at 800 rpm for 5 min.

scan_protocol: The arrays were scanned by GenePix 4000B (Axon Instruments, Union City, CA) and analyzed using GenePix Pro 6.0 (Axon Instruments).

data_processing:
Global normalization method was applied so that the ratio of medians from every feature selected on the array was equal to 1 according to the manufactures instruction (GenePix Pro 6.0). Clones located at the autosome were included in normalization.
The base two logarithm (Log2) of the ratio of medians were extracted by GenePix Pro 6.0. We took the average of duplicate features and calculated the standard deviation of all clones with Excel. We regarded the signal ratio as “abnormal” if it ranged out of ±3SD.

source_name: Female control DNA

label_protocol: After complete digestion using DpnII, Female control DNA (1ug) was labeled with Cy-3 dCTP (Amersham Biosciences) using Bioprime CGH labeling Kit (Invitrogen, Carlsbad, CA) and purified by use of Microcon YM-30.

extract_protocol: Genomic DNA from peripheral blood lymphocytes was isolated using an automatic DNA isolation systems NA-3000 (Kurabo, Osaka, Japan).

tag: Subject:a healthy female donor.

tag: DNA extracted from peripheral blood lymphocytes.

label_protocol: After complete digestion using DpnII, patien't DNA (1ug) was labeled with Cy-5 dCTP (Amersham Biosciences) using Bioprime CGH labeling Kit (Invitrogen, Carlsbad, CA) and purified by use of Microcon YM-30.

tag: Subject:Patient with Mental retardation.


title: 1790 mother and 1791 father of the CHD patient 1789


title: CHD Patient 1553

tag: DNA isolated from blood of a patient with congenital heart disease (Ventricular septal defect). Gender

tag: DNA isolated from blood of a healthy male donor


title: YCU_patient1_CGH2

hyb_protocol: Differentially labeled DNA (Cy3:Patient with MR, Cy5:control) was mixed with 67.5 ug Cot I DNA (Invitrogen, Tokyo, Japan) and co-precipitated. The DNA pellet was resuspended with 126 ul hybridization buffer (50% formamide/10% dextran sulfate/0.1% Tween 20/2X SSC/10 mM Tris-HCl, pH 7.4) with 60 ug yeast tRNA. Probe DNA was denatured for 10 min at 70 C° and incubated for 1hr at 37 C° before hybridization. Microarray slide was prehybridized for 1 hr at 37 C° with 180ul hybridization buffer containing the 400ug herring sperm DNA and 67.5 ug human Cot I DNA. After prehybridization using in situ frame (Eppendorf, Hamburg, Germany) on a slide in a hybrid-chamber (Genetix, New Milton, UK), Prehybridization mixture was removed carefully and labeled probe mixture was applied to microarray slide. Slide was incubated at 37 C° for 72 hrs with gentle shaking, and then washed twice with solution A (0.05 % Tween 20/1X PBS) for 10 min at room temperature, and twice with solution B (50% formamide/2X SSC) at 43 C° for 15 min, and with again solution A at room temperature for 10 min. Slide was dried by centrifuge at 800 rpm for 5 min.

label_protocol: After complete digestion using DpnII, Patient's DNA (1ug) was labeled with Cy-3 dCTP (Amersham Biosciences) using Bioprime CGH labeling Kit (Invitrogen, Carlsbad, CA) and purified by use of Microcon YM-30.

tag: Subject:Patient with Mental retardation (MR).

label_protocol: After complete digestion using DpnII, Female control DNA (1ug) was labeled with Cy-5 dCTP (Amersham Biosciences) using Bioprime CGH labeling Kit (Invitrogen, Carlsbad, CA) and purified by use of Microcon YM-30.


title: CHD Patient 1559

tag: DNA isolated from blood of a patient with congenital heart disease (Aortic stenosis). Gender

tag: DNA isolated from blood of a healthy female donor


title: CHD Patient 1610


title: CHD Patient 1562


title: CHD Patient 1988

tag: DNA isolated from blood of a patient with congenital heart disease (ventricular septal defect). Gender


title: Normal Peripheral Blood_F_Sty1 + HpaII_rep1

status: Public on May 10 2008

city: New York

first: Le

last: Jiang

state: NY

address: 1130 St. Nicholas Ave

country: USA

institute: Columbia University

description: Each sample was subjected to 5 runs of genotyping on the 250K SNP StyI chips, including 2 styI alone, 2 HpaII pre-digestion plus StyI and 1 MspI pre-digestion plus styI.

hyb_protocol: Hybridization was performed for 16 hr at 49C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner G3000A.

data_processing: Data from .cel files were processed by normalization and model-based expression (PM-only model) in dChip, assigning a numerical ploidy of 2 to the StyI-alone samples

source_name: Normal Peripheral Blood_Sty1 + HpaII

label_protocol: Ninety ug of amplified genomic DNA was biotinylated according to standard Affymetrix protocol (Genechip Mapping 500K Assy Manual, Rev. 3)

extract_protocol: Genomic DNA was extracted using conventional phenol/chloroform method or the QIAGEN DNeasy blood and tissue kit.

tag: Normal Peripheral Blood with StyI + HpaII pre-digestion


title: Normal Peripheral Blood_F_Sty1 + HpaII_rep2


title: Normal Peripheral Blood_F_Sty1 alone_rep2

source_name: Normal Peripheral Blood_Sty1

tag: Normal Peripheral Blood with StyI alone


title: Normal Peripheral Blood_F_Sty1 alone_rep1


title: Normal Peripheral Blood_E_Sty1 + HpaII_rep2


title: Normal Peripheral Blood_E_Sty1 + MspI

source_name: Normal Peripheral Blood_Sty1 + MspI

tag: Normal Peripheral Blood with StyI + MspI pre-digestion


title: Normal Peripheral Blood_F_Sty1 + MspI


title: 1669 mother and 1774 father of the CHD patient 1745

tag: DNA isolated from blood of the mother.  Gender


title: Normal Peripheral Blood_E_Sty1 alone_rep1


title: Normal Peripheral Blood_E_Sty1 alone_rep2


title: Placenta_B_StyI alone_rep2

tag: Placenta with StyI alone


title: Normal Peripheral Blood_E_Sty1 + HpaII_rep1


title: Placenta_B_StyI alone_rep1


title: Placenta_C_StyI + HpaII_rep2

source_name: Placenta_StyI + HpaII

tag: Placenta with StyI + HpaII pre-digestion


title: Placenta_C_StyI + MspI

source_name: Placenta_StyI + MspI

tag: Placenta with StyI + MspI pre-digestion


title: Placenta_C_StyI + HpaII_rep1


title: Placenta_B_StyI + MspI


title: Placenta_C_StyI alone_rep1


title: Placenta_B_StyI + HpaII_rep2

tag: Placenta  with StyI + HpaII pre-digestion


title: normal bone marrow_B_StyI + MspI

source_name: normal bone marrow_StyI + MspI

tag: normal bone marrow with StyI + MspI pre-digestion


title: Placenta_B_StyI + HpaII_rep1


title: normal bone marrow_B_StyI alone_rep2

source_name: normal bone marrow_StyI

tag: normal bone marrow with StyI alone


title: Placenta_C_StyI alone_rep2


title: normal bone marrow_A_StyI + MspI


title: normal bone marrow_A_StyI + HpaII_rep2

source_name: normal bone marrow_StyI + HpaII

tag: normal bone marrow with StyI + HpaII pre-digestion


title: normal bone marrow_A_StyI + HpaII_rep1


title: normal bone marrow_B_StyI + HpaII_rep2


title: CHD Patient 1812

tag: DNA isolated from blood of a patient with congenital heart disease (Ventricular septal defect). Gender


title: normal bone marrow_B_StyI alone_rep1


title: Placenta_A_StyI alone_rep2


title: normal bone marrow_B_StyI + HpaII_rep1


title: Placenta_A_StyI + MspI


title: Placenta_A_StyI alone_rep1


title: normal bone marrow_A_StyI alone_rep2


title: Placenta_A_StyI + HpaII_rep1


title: normal bone marrow_A_StyI alone_rep1


title: Placenta_A_StyI + HpaII_rep2


title: Normal Peripheral Blood_D_Sty1 alone_rep2


title: Normal Peripheral Blood_C_Sty1 + HpaII_rep2


title: Normal Peripheral Blood_D_Sty1 + MspI


title: Normal Peripheral Blood_C_Sty1 + MspI


title: Normal Peripheral Blood_C_Sty1 alone_rep2


title: Normal Peripheral Blood_D_Sty1 alone_rep1


title: Normal Peripheral Blood_C_Sty1 + HpaII_rep1


title: Normal Peripheral Blood_C_Sty1 alone_rep1


title: Differentiated Luminal Biological Rep2

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

description: Gene expression data from differentiated luminal subpopulation of mammary epithelial cells

hyb_protocol: cDNA probes were hybridized to Affymetrix human X3P GeneChip arrays according to the manufacturer’s protocol (Tietjen et al., 2003)

scan_protocol: GeneChip® Scanner 3000 7G, Affymetrix

data_processing: The data were analyzed with ArrayAssist software (http://Stratagene.com/software solutions) using Affymetrix default analysis settings.

source_name: Differentiated luminal Cells

label_protocol: 50 pg aliquotsof RNA were PCR amplified (Iscove et al., 2002) from each sample yielding 2-3 µg of amplified product.  The amplified cDNA preparations were then purified using the High Pure PCR Product purification kit (Roche Applied Science), end-labelled with Biotin-N6 ddATP (StemCore Laboratories, OHRI, Ottawa, Ont., Canada)

growth_protocol: Primary cells extracted from reduction mammoplasty samples were cultured in EpiCult-B medium (StemCell Technologies) with 5% fetal Calf Serum supplementation.

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

treatment_protocol: Epithelial-enriched fraction of reduction mammoplasty samples were made into single cell suspenssions and co-culutred with irratdiated mouse fibroblasts for 3 days

tag: Human reduction mammoplasty sample, 26 year old patient


title: Normal Peripheral Blood_D_Sty1 + HpaII_rep1


title: Normal Peripheral Blood_B_Sty1 + MspI


title: Differentiated Luminal Biological Rep1

tag: Human reduction mammoplasty sample, 25 year old patient


title: Differentiated Luminal Biological Rep3

tag: Human reduction mammoplasty sample, 55 year old patient


title: Normal Peripheral Blood_B_Sty1 + HpaII_rep2


title: Differentiated basal Biological Rep2

description: Gene expression data from differentiated basal subpopulation of mammary epithelial cells

source_name: Differentiated basal Cells


title: Differentiated Basal Biological Rep1


title: Normal Peripheral Blood_B_Sty1 alone_rep2


title: Normal Peripheral Blood_B_Sty1 alone_rep1


title: Normal Peripheral Blood_D_Sty1 + HpaII_rep2


title: Normal Peripheral Blood_B_Sty1 + HpaII_rep1


title: Differentiated basal Biological Rep3


title: Committed Luminal progentiors Biological Rep3

description: Gene expression data from committed luminal progenitor-enriched subpopulation of mammary epithelial cells

source_name: Committed luminal progenitor-enriched subpopulation


title: Committed Luminal progentiorsBiological Rep2


title: Normal Peripheral Blood_A_Sty1 + HpaII_rep2


title: Normal Peripheral Blood_A_Sty1 + MspI


title: Mouse Segmental Duplication and Copy-Number Variation sample 10

city: Seattle

first: Ze

last: Cheng

state: WA

address: 1905 NE Pacific St.

department: Genome Sciences

institute: University of Washington

description: Custom Nimblegen chip, all steps per Nimblegen protocol.

hyb_protocol: per NimbleGen protocol

scan_protocol: Scanned on Axon scanner with GenePix, per NimbleGen

data_processing: NimbleScan software, per protocol; normalization strategy: qspline

organism: Mus musculus

label_protocol: Labeled using random 9mer primers per Nimblegen protocol

extract_protocol: standard genomic DNA extraction protocol


title: Normal Peripheral Blood_A_Sty1 + HpaII_rep1


title: Committed Luminal progentiors Biological Rep1


title: Mouse Segmental Duplication and Copy-Number Variation sample 11

source_name: DDY/JclSidSeyFrkJ

tag: DDY/JclSidSeyFrkJ


title: Normal Peripheral Blood_A_Sty1 alone_rep2


title: Mouse Segmental Duplication and Copy-Number Variation sample 14

source_name: NZO/HiLtJ

tag: NZO/HiLtJ


title: Mouse Segmental Duplication and Copy-Number Variation sample 1

tag: DNA sample from mouse inbreed strain C57BL/6J

tag: DNA sample from mouse inbreed stain DBA/2J


title: normal bone marrow CD 34+ cells_StyI + HpaII_rep2

tag: normal bone marrow CD 34+ cells with StyI + HpaII pre-digestion


title: Bipotent-enriched Biological Rep3

description: Gene expression data from bipotent progenitor-enriched subpopulation of mammary epithelial cells

source_name: Bipotent progenitor Enriched subpopulation


title: normal bone marrow CD34+ cells_StyI alone_rep2

source_name: normal bone marrow CD34+ cells_StyI

tag: normal bone marrow CD34+ cells with StyI alone


title: Generation of pluripotent stem cells from adult human testis_hGS2

status: Public on May 09 2008

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

description: hGS cells from testis, cultivated with KO Medium+GDNF

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol with the GeneChip scanner 3000

data_processing: GC-RMA normalisation with ArrayAssist 5.1 software

label: Affymetrix standard protocol

label_protocol: Affymetrix standard protocol

growth_protocol: Spermatogonial cells (hGS) from 3 different normal patients (patient 59, 73 and 81, passage 0) were cultured for 4 days in Knockout medium, 20% Knockout-FBS, 1% L-glutamine and 4ng/ml GDNF. After enrichment with CD49f and matrix selection with collagen and laminin the cells were washed with phosphate buffered saline (PBS) and pelleted at 1000rpm/10min./4°C, lysed with RLT buffer + ß-Mercaptoethanol and stored at -80°C.

extract_protocol: standard Qiagen Mini protocol


title: Generation of pluripotent stem cells from adult human testis_haGSC4

description: haGSC cells from testis, cultivated with KO Medium+GDNF

growth_protocol: human adult germ stem cells (haGSCs) were derived from hGS cells from 3 different normal patients after the enrichment and further cultivation in LIF supplemented medium. haGSC from patient 52, 54 and 35 (from lower and higher passages) were cultured for 10 days in basic medium (DMEM high glucose, 15% FCS (Biochrom), 1% non-essential amino acids (NEAA), 1% L-glutamine and 0.05 mM ß-mercaptoethanol (Gibco) with 103 units/ml leukemia inhibitory factor (LIF, human, Chemicon) on 0,1% gelatine coated dishes. After  the clusters were manually cut, the isolated clusters were  washed with phosphate buffered saline (PBS) and pelleted at 1000rpm/10min./4°C and lysed with RLT buffer + ß-Mercaptoethanol and stored at -80°C.


title: Generation of pluripotent stem cells from adult human testis_haGSC5

source_name: haGSC cells from testis, cultivated with KO Medium+GDNF


title: Generation of pluripotent stem cells from adult human testis_haGSC6

tag: haGSC cells from testis, cultivated with KO Medium+GDNF


title: Mouse Segmental Duplication and Copy-Number Variation sample 6


title: Generation of pluripotent stem cells from adult human testis_hGS3

source_name: hGS cells from testis, cultivated with KO Medium+GDNF


title: Mouse Segmental Duplication and Copy-Number Variation sample 13


title: normal bone marrow CD34+ cells_StyI + HpaII_rep1

tag: normal bone marrow CD34+ cells with StyI + HpaII pre-digestion


title: Mouse Segmental Duplication and Copy-Number Variation sample 4

source_name: CZECHI/EiJ

tag: CZECHI/EiJ


title: normal bone marrow CD 34+ cells_StyI + MspI

tag: normal bone marrow CD 34+ cells with StyI + MspI pre-digestion


title: N2A cells treated with shRNA for PTB, biological rep 3

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Mouse Exon 1.0 ST Arrays (exon arrays) according to manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility.

scan_protocol: Hybridized Affymetrix Mouse Exon 1.0 ST Arrays (exon arrays) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility.

data_processing: Raw image files were processed using Affymetrix GCOS 1.3 software to generate CEL data files. Exon array expression indexes were calculated using the GeneBASE program (Kapur et al., 2007, Genome Biol 8:R82). Briefly, the program employs a sequence-specific background model to correct background intensities of exon-array probes (Kapur et al., 2007, Genome Biol 8:R82), followed by an iterative probe selection procedure (Xing et al., 2006, PLoS ONE 1:e88) that selects a subset of highly correlated probes of a gene for expression index computation. Differential splicing events were detected using the MADS algorithm (Xing et al., 2008).

source_name: N2A cells treated with shRNA for PTB

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

growth_protocol: N2A cells were grown on DMEM suplemented with 10%FBS, glutamine, penicilin and streptomycin.

extract_protocol: Total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA samples were then treated with DNase I to remove residual DNA contamination and extracted with chloroform. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: Short hairpin knockdown of PTB in mouse N2A neuroblastoma cells was performed as described before (Boutz et al., 2007, Genes Dev 21:1636-1652). The efficiency of the PTB knockdown was monitored by western blot using PTB-NT primary antibody and Cy5 labeled secondary antibody (GE Life Sciences). The blots were imaged using Typhoon 9410 (GE Life Sciences). The band intensities were measured using ImageQuant and normalized to GAPDH. The GAPDH levels were monitored on the same western blot using mouse anti-GAPDH and Cy3 coupled secondary anti-mouse antibodys. In all cases the efficiency of the knockdown was close to 80% (data not shown).

tag: mouse N2A neuroblastoma cell line


title: Mouse Segmental Duplication and Copy-Number Variation sample 8


title: Generation of pluripotent stem cells from adult human testis_ES2

description: H1 cells from testis, cultivated in ES Medium+FGF2

growth_protocol: hES(H1) cells (hES) were cultured for 10 days (passage 48, 57 and 67) in Knockout medium, 20% Knockout-Serum-Replacer, 1% L-glutamine, 1% NEAA, 1% penicillin/streptomycin and 4ng/ml FGF-2, on CF1 inactivated feeder on 0,1% gelatine coated dishes. After the clusters were manually cut, the isolated clusters were washed with phosphate buffered saline (PBS) and pelleted at 1000rpm/10min./4°C and lysed with RLT buffer + ß-Mercaptoethanol and stored at -80°C.

tag: H1 cells from testis, cultivated with ES Medium+FGF2


title: Bipotent-enriched Biological Rep1


title: Mouse Segmental Duplication and Copy-Number Variation sample 15

source_name: NOD/LtJ

tag: NOD/LtJ


title: Mouse Segmental Duplication and Copy-Number Variation sample 12


title: Mouse Segmental Duplication and Copy-Number Variation sample 2

source_name: A/J

tag: A/J


title: N2A cells treated with shRNA for PTB, biological rep 2


title: Normal Peripheral Blood_A_Sty1 alone_rep1

source_name: Normal Peripheral Blood_Sty1

tag: Normal Peripheral Blood with StyI alone


title: Mouse Segmental Duplication and Copy-Number Variation sample 7

source_name: BALB/cByJ

tag: BALB/cByJ


title: Mouse Segmental Duplication and Copy-Number Variation Sample 3


title: N2A cells treated with empty vector, biological rep 1

source_name: N2A cells treated with empty vector


title: Bipotent-enriched Biological Rep2

tag: Human reduction mammoplasty sample, 26 year old patient


title: N2A cells treated with shRNA for PTB, biological rep 1


title: Mouse Segmental Duplication and Copy-Number Variation sample 9


title: N2A cells treated with empty vector, biological rep 3


title: normal bone marrow CD 34+ cells_StyI alone_rep1

source_name: normal bone marrow CD 34+ cells_StyI

tag: normal bone marrow CD 34+ cells with StyI alone


title: GM9016, affected brother

status: Public on May 08 2008

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: GM9016, affected brother, 38yrs, family 2112

hyb_protocol: Standard Codelink protocol

scan_protocol: Standard Codelink protocol on Axon genePix 4000B

data_processing: Codelink Expression Analysis Softwarev4.2

label_protocol: Standard Codelink protocol

growth_protocol: B-Cells from Corielle were incubated at 37oC and 5% CO2 overnight, the day after cells are counted. Cells were expanded in RPMI 1640 with 2mM L-glutamine and 15% FBS following Corielle's lymphoblast line maintenance protocols. 1x10^7 cells were spun down and resuspended in 2 ml Tri-Reagent and frozen overnight at -80oC prior to RNA extraction

extract_protocol: Std Tri-Reagent protocol followed by cleanup on RNEasy columns using an on-column DNase step. RNA quality is checked using a Nanodrop and an Agilent Bioanalyzer

tag: affected brother


title: GM8922A, affected sister

description: GM8922A, affected sister, 43yrs, family 2108

tag: affected sister


title: Generation of pluripotent stem cells from adult human testis_ES3

source_name: H1 cells from testis, cultivated in ES Medium+FGF2

tag: H1 cells from testis. cultivated with ES Medium+FGF2


title: GM9017, unaffectd brother

description: GM9017, unaffected brother, 45yrs, family 2112

tag: unaffectd brother


title: GM9013, proband-MS

description: GM9013, proband male, 35yrs, family 2112

tag: proband-MS


title: GM9023, unaffected brother

description: GM9023, unaffected brother, 47yrs, family 2112

tag: unaffected brother


title: GM8923, proband-MS

description: GM8923, proband male, 38yrs, family 2108


title: GM8921A, unaffected brother

description: GM8921A, unaffected brother, 46yrs, family 2108


title: GM8839, affected sister

description: GM8839, affected sister, 39yrs, family 2102

tag: affected sister,


title: GM9018, unaffected brother

description: GM9018, unaffected brother, 42yrs, family 2112


title: US-1078955 vs. 178

first: eric

middle: e

last: schadt

address: 401 Terry Ave N

department: Genetics

institute: Merck

description: Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.

hyb_protocol: Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed

scan_protocol: slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced

data_processing: Rosetta Resolver Ratio Experiment using Rosetta Resolver Agilent Error Model

source_name: Liver

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

treatment_protocol: No treatment

tag: pool


title: US-1078955 vs. HH-F220


title: US-1078955 vs. HH-F186


title: US-1078955 vs. HH-F174


title: US-1078955 vs. HH-F212


title: US-1078955 vs. HH-F240


title: US-1078955 vs. HH-F157


title: US-1078955 vs. HH-F189


title: US-1078955 vs. HH-F176


title: US-1078955 vs. HH-F177


title: US-1078955 vs. HH-F218


title: US-1078955 vs. HH-F206


title: US-1078955 vs. HH-F222


title: US-1078955 vs. HH-F175


title: US-1078955 vs. HH-F191


title: US-1078955 vs. HH-F170


title: US-1078955 vs. HH-F168


title: US-1078955 vs. HH-F171


title: US-1078955 vs. 644


title: GM8830, MS-proband

description: GM8830, proband female, 47yrs, family 2102

tag: MS-proband


title: US-1078955 vs. HH-F166


title: Mouse Segmental Duplication and Copy-Number Variation sample 5

source_name: CAST/EiJ

tag: CAST/EiJ


title: US-1078955 vs. HH-F164


title: US-1078955 vs. HH-D278


title: N2A cells treated with empty vector, biological rep 2

tag: mouse N2A neuroblastoma cell line


title: US-1078955 vs. HH-D287


title: US-1078955 vs. HH-F151


title: US-1078955 vs. HH-D272


title: US-1078955 vs. HH-D264


title: US-1078955 vs. HH-F163


title: US-1078955 vs. HH-D335


title: US-1078955 vs. HH-D260


title: US-1078955 vs. HH-D162


title: US-1078955 vs. HH-D175


title: US-1078955 vs. HH-871


title: US-1078955 vs. HH-666


title: US-1078955 vs. 872-1017


title: US-1078955 vs. HH-873


title: US-1078955 vs. HH-D371


title: US-1078955 vs. HH-863


title: US-1078955 vs. HH-646-1


title: US-1078955 vs. HH-646-2


title: US-1078955 vs. HH-861


title: US-1078955 vs. HH-D173


title: US-1078955 vs. HH-604


title: US-1078955 vs. HH-654


title: US-1078955 vs. HH-F152


title: US-1078955 vs. HH-667


title: US-1078955 vs. HH-858


title: US-1078955 vs. HH-1246


title: US-1078955 vs. HH-1249


title: US-1078955 vs. HH-1223


title: US-1078955 vs. HH-1233


title: US-1078955 vs. HH-1240


title: US-1078955 vs. HH-1226


title: US-1078955 vs. HH-1194


title: US-1078955 vs. HH-1213


title: US-1078955 vs. HH-1234


title: US-1078955 vs. HH-1227


title: US-1078955 vs. HH-1186


title: US-1078955 vs. HH-1112


title: US-1078955 vs. HH-1180


title: US-1078955 vs. HH-1201


title: US-1078955 vs. HH-1121


title: US-1078955 vs. HH-1210


title: US-1078955 vs. HH-1220


title: US-1078955 vs. HH-1187


title: US-1078955 vs. HH-1095


title: US-1078955 vs. HH-1183


title: US-1078955 vs. HH-1117


title: US-1078955 vs. HH-1125


title: US-1078955 vs. HH-1179


title: US-1078955 vs. HH-1115


title: US-1078955 vs. HH-1111


title: US-1078955 vs. HH-1174


title: US-1078955 vs. HH-1209


title: US-1078955 vs. HH-1105


title: US-1078955 vs. HH-1248


title: US-1078955 vs. HH-1182


title: US-1078955 vs. HH-1090


title: US-1078955 vs. HH-1091


title: US-1078955 vs. HH-1084


title: US-1078955 vs. HH-1083


title: US-1078955 vs. HH-1069


title: US-1078955 vs. HH-1066


title: US-1078955 vs. HH-1050


title: US-1078955 vs. HH-1077


title: US-1078955 vs. HH-1170


title: US-1078955 vs. HH-1058


title: US-1078955 vs. HH-1068


title: US-1078955 vs. HH-1089


title: US-1078955 vs. HH-1044


title: US-1078955 vs. HH-1040


title: US-1078955 vs. HH-994


title: US-1078955 vs. HH-916


title: US-1078955 vs. HH-914


title: US-1078955 vs. HH-919


title: US-1078955 vs. HH-915


title: US-1078955 vs. HH-1031


title: US-1078955 vs. HH-1024


title: US-1078955 vs. HH-1051


title: US-1078955 vs. HH-946


title: US-1078955 vs. HH-1000


title: US-1078955 vs. HH-1020


title: US-1078955 vs. HH-911


title: US-1078955 vs. HH-1029


title: US-1078955 vs. HH-913


title: US-1078955 vs. HH-906


title: US-1078955 vs. HH-896


title: US-1078955 vs. HH-902


title: US-1078955 vs. HH-903


title: US-1078955 vs. HH-905


title: US-1078955 vs. HH-899


title: US-1078955 vs. HH-870


title: US-1078955 vs. HH-895


title: US-1078955 vs. HH-1156


title: US-1078955 vs. HH-862


title: US-1078955 vs. HH-1100


title: US-1078955 vs. HH-889


title: US-1078955 vs. HH-1076


title: US-1078955 vs. HH-890


title: US-1078955 vs. HH-864


title: US-1078955 vs. HH-881-2


title: US-1078955 vs. HH-1072


title: US-1078955 vs. HH-1087


title: US-1078955 vs. HH-883


title: US-1078955 vs. HH-1073


title: US-1078955 vs. HH-952-2


title: US-1078955 vs. HH-1165


title: US-1078955 vs. HH-1070


title: US-1078955 vs. HH-927-2


title: US-1078955 vs. HH-1079


title: US-1078955 vs. HH-1097


title: US-1078955 vs. HH-1039


title: US-1078955 vs. HH-1059


title: US-1078955 vs. HH-1042


title: US-1078955 vs. HH-1012


title: US-1078955 vs. HH-1033


title: US-1078955 vs. HH-1014


title: US-1078955 vs. HH-1001


title: US-1078955 vs. HH-989


title: US-1078955 vs. HH-1032


title: US-1078955 vs. HH-998


title: US-1078955 vs. HH-1002


title: US-1078955 vs. HH-1009


title: US-1078955 vs. HH-999


title: US-1078955 vs. HH-996


title: US-1078955 vs. HH-984


title: US-1078955 vs. HH-988


title: US-1078955 vs. HH-977


title: US-1078955 vs. HH-976


title: US-1078955 vs. HH-1008


title: US-1078955 vs. HH-973


title: US-1078955 vs. HH-967


title: US-1078955 vs. HH-995


title: US-1078955 vs. HH-940


title: US-1078955 vs. HH-961


title: US-1078955 vs. HH-982


title: US-1078955 vs. HH-965


title: US-1078955 vs. HH-970


title: US-1078955 vs. HH-972


title: US-1078955 vs. HH-941


title: US-1078955 vs. HH-929


title: US-1078955 vs. HH-928


title: US-1078955 vs. HH-881-1


title: US-1078955 vs. 9010c298# 506


title: US-1078955 vs. HH-841


title: US-1078955 vs. HH-945


title: US-1078955 vs. HH-930


title: US-1078955 vs. HH-926


title: US-1078955 vs. HH-922


title: US-1078955 vs. HH-932


title: US-1078955 vs. 1051099B 4# 484


title: US-1078955 vs. NDRI 5-26-95 SWFR# 501


title: US-1078955 vs. HH-819


title: US-1078955 vs. 14901 N# NORI#759, 1 hr # 505


title: US-1078955 vs. FH 76 second bonus# 504


title: US-1078955 vs. 13457 (C)# 490


title: US-1078955 vs. 90-06-A153 (8/17/90)# 499


title: US-1078955 vs. 1050692D 1# 476


title: US-1078955 vs. 4007448B 3# 457


title: US-1078955 vs. 1050441 B 4# 461


title: US-1078955 vs. 4007114B 6# 479


title: US-1078955 vs. 1050404 B 5# 460


title: US-1078955 vs. D-12597# 465


title: US-1078955 vs. 4050204B4# 480


title: US-1078955 vs. 1050507 A 1# 463


title: US-1078955 vs. 1050254B 4# 450


title: US-1078955 vs. 1050670B 3# 475


title: US-1078955 vs. 4007243B 4# 455


title: US-1078955 vs. 1050458 B 3# 462


title: US-1078955 vs. 4006452D 3# 453


title: US-1078955 vs. 1050253B 7# 449


title: US-1078955 vs. 1041613B# 440


title: US-1078955 vs. 4007246B 5# 456


title: US-1078955 vs. 35035 A3D# 445


title: US-1078955 vs. 4006401A 35# 452


title: US-1078955 vs. 4006531A 15# 478


title: US-1078955 vs. 3040630A# 435


title: US-1078955 vs. 104 1156B 10# 439


title: US-1078955 vs. 1050122B# 443


title: US-1078955 vs. 4040578B# 442


title: US-1078955 vs. 1050399 B 6# 459


title: US-1078955 vs. 1041699B# 441


title: US-1078955 vs. 104 1101A 8# 438


title: US-1078955 vs. 1050291B 5# 451


title: US-1078955 vs. HH-978


title: US-1078955 vs. 28771 A1J# 429


title: US-1078955 vs. 03-04-A129a# 407


title: US-1078955 vs. 0102c 104c# 182


title: US-1078955 vs. 29658 A1B# 415


title: US-1078955 vs. 02-11-A257c# 405


title: US-1078955 vs. 16223  A2C# 191


title: US-1078955 vs. 29547 A2E# 430


title: US-1078955 vs. 03-11-A026b# 423


title: US-1078955 vs. 33519 A1 A# 432


title: US-1078955 vs. 0010c 139j# 183


title: US-1078955 vs. FH 51# 148


title: US-1078955 vs. FH 55# 147


title: US-1078955 vs. 030-05-A396l# 413


title: US-1078955 vs. 103 0918A 1# 420


title: US-1078955 vs. 03-01-A020b# 406


title: US-1078955 vs. 03-08-A487e# 422


title: US-1078955 vs. 0303C 271# 408


title: US-1078955 vs. 9803  C203c# 187


title: US-1078955 vs. 9807  C23a# 186


title: US-1078955 vs. 16462 a/a# 190


title: US-1078955 vs. FH 39# 150


title: US-1078955 vs. S.P. 23# 167


title: US-1078955 vs. S.P. 16# 165


title: US-1078955 vs. S.P. 17# 166


title: US-1078955 vs. 29379 A2F# 414


title: US-1078955 vs. FH 38# 151


title: US-1078955 vs. 34683# 270


title: US-1078955 vs. 5803 A# 274


title: US-1078955 vs. 29173_(NDRI S94-7185)# 296


title: US-1078955 vs. 8528 C# 294


title: US-1078955 vs. 6059 E_(CHTN S93-6504)# 276


title: US-1078955 vs. 23128# 322


title: US-1078955 vs. 93-02-C009_(2/1/93# 281


title: US-1078955 vs. 8160 G_Very large piece# 295


title: US-1078955 vs. 7249 C# 302


title: US-1078955 vs. 9705C 197A# 266


title: US-1078955 vs. 90-080A 109_(8/17/90)_CHTN/Birmingham# 321


title: US-1078955 vs. 90-5-c-34_(5/2/90)# 312


title: US-1078955 vs. 34425# 269


title: US-1078955 vs. 34953 (S97-8910)# 265


title: US-1078955 vs. 5948 L_(102 99 394)# 275


title: US-1078955 vs. 8544 C# 293


title: US-1078955 vs. 27234 A2 G# 400


title: US-1078955 vs. 9708C 223A# 264


title: US-1078955 vs. 9704C 269C# 267


title: US-1078955 vs. 01-07-A290g# 398


title: US-1078955 vs. 01-11-A089i# 399


title: US-1078955 vs. 93 04 C327# 277


title: US-1078955 vs. 7283 C# 301


title: US-1078955 vs. 32471 A2 B# 431


title: US-1078955 vs. 0045976-02# 391


title: US-1078955 vs. 00-05-A256f# 397


title: US-1078955 vs. 9708C 015b# 263


title: US-1078955 vs. 22928# 323


title: US-1078955 vs. 0041327-01# 369


title: US-1078955 vs. 00-06-A289c# 375


title: US-1078955 vs. 0040667-03# 363


title: US-1078955 vs. 28235 A2 H# 402


title: US-1078955 vs. 22760 A3D# 379


title: US-1078955 vs. 4946 F_8/31/1992_(9569120)# 353


title: US-1078955 vs. 0206C 144F# 395


title: US-1078955 vs. 23769 A1 A# 387


title: US-1078955 vs. 0041842-05# 370


title: US-1078955 vs. 22988 A4I# 380


title: US-1078955 vs. 00-05-A256g# 374


title: US-1078955 vs. 4945 F_(9/3/92)_(10137818)# 352


title: US-1078955 vs. CHTN 13035D# 359


title: US-1078955 vs. 0041183-02# 368


title: US-1078955 vs. 92-02-W066# 347


title: US-1078955 vs. 0040642-01# 362


title: US-1078955 vs. 4931 A & B# 351


title: US-1078955 vs. 0040929-01# 365


title: US-1078955 vs. CHTN 12742E# 358


title: US-1078955 vs. 92-10-C201_(10/21/92)_diseased liver# 355


title: US-1078955 vs. 92 02 C221_(2/21/92)# 341


title: US-1078955 vs. 92-07-W081# 346


title: US-1078955 vs. 91-11-W012# 337


title: US-1078955 vs. 22883# 324


title: US-1078955 vs. 13672A# 244


title: US-1078955 vs. 3987_(1/30/92)_(9623091)# 343


title: US-1078955 vs. 9708C 055a# 259


title: US-1078955 vs. 32570 ((S96-3157)# 257


title: US-1078955 vs. 9706C 287g# 260


title: US-1078955 vs. 91-10-W168# 338


title: US-1078955 vs. 9706C 035ge# 261


title: US-1078955 vs. 3718_(NDRI 9644543)_(11/14/91)# 339


title: US-1078955 vs. 9707C 292e# 262


title: US-1078955 vs. 24870_(3/24/92)# 342


title: US-1078955 vs. 32753 (S96-5494)# 248


title: US-1078955 vs. 33414# 239


title: US-1078955 vs. 30383# 238


title: US-1078955 vs. 9710C 204b# 258


title: US-1078955 vs. 8233C (S94-8642)# 254


title: US-1078955 vs. 9605C103# 245


title: US-1078955 vs. 9607C079# 241


title: US-1078955 vs. 9512 C034G# 253


title: US-1078955 vs. 13457 (E)# 247


title: US-1078955 vs. 4003345D# 240


title: US-1078955 vs. 24493_(1/8/92)# 340


title: US-1078955 vs. 30531 (S95-180)# 236


title: US-1078955 vs. 95-6-C002G# 232


title: US-1078955 vs. 95-10-C056# 223


title: US-1078955 vs. 95-07-C096# 229


title: US-1078955 vs. 95-07-C006G# 224


title: US-1078955 vs. 95-02-C022G# 230


title: US-1078955 vs. 95-10-C220# 214


title: US-1078955 vs. 32224# 220


title: US-1078955 vs. 95-10-C159# 219


title: US-1078955 vs. 38400_NDRI (S99-5975)# 204


title: US-1078955 vs. 8914J (S94-164 39)# 221


title: US-1078955 vs. 95-11-C174# 217


title: US-1078955 vs. 38374# 206


title: US-1078955 vs. 17063  A2C# 212


title: US-1078955 vs. 36093_NDRI (S98-2046)# 202


title: US-1078955 vs. 95-09-C0209G# 222


title: US-1078955 vs. 37695_(S99-8)_(1/27/99)# 210


title: US-1078955 vs. 9812 C 016a# 208


title: US-1078955 vs. 95-06-C303# 231


title: US-1078955 vs. 95-09-C211# 225


title: US-1078955 vs. 24039 A4A# 388


title: US-1078955 vs. 38419_(S99-6078)_(4/5/99)# 203


title: US-1078955 vs. 38434# 205


title: US-1078955 vs. 95-11-C055G# 216


title: US-1078955 vs. 25071 A1 B# 396


title: US-1078955 vs. 16045 A1A# 197


title: US-1078955 vs. 16044 A2C# 194


title: US-1078955 vs. FH 56# 146


title: US-1078955 vs. 16046 A1C# 195


title: US-1078955 vs. HL 100# 132


title: US-1078955 vs. FH 60# 144


title: US-1078955 vs. FH 77# 138


title: US-1078955 vs. 9803 C008a# 199


title: US-1078955 vs. 16043 A2A# 193


title: US-1078955 vs. FH 76# 139


title: US-1078955 vs. HL 104# 129


title: US-1078955 vs. 36241_NDRI (S98-3829)_(3/4/98)# 198


title: US-1078955 vs. FH 84# 136


title: US-1078955 vs. FH 86# 134


title: US-1078955 vs. FH 73# 140


title: US-1078955 vs. HL 102# 131


title: US-1078955 vs. 16048 A1D# 196


title: US-1078955 vs. HL 109# 126


title: US-1078955 vs. HL 108# 127


title: US-1078955 vs. FH 88# 133


title: US-1078955 vs. FH 69# 141


title: US-1078955 vs. HL 103# 130


title: US-1078955 vs. HL 112# 124


title: US-1078955 vs. HL 124# 114


title: US-1078955 vs. HL 114# 122


title: US-1078955 vs. HL 130# 108


title: US-1078955 vs. HL 128# 111


title: US-1078955 vs. HL 126# 113


title: US-1078955 vs. HL 131# 107


title: US-1078955 vs. HL 11l# 118


title: US-1078955 vs. HL 127# 112


title: US-1078955 vs. HL 116# 120


title: US-1078955 vs. HL 129# 110


title: US-1078955 vs. HL 140# 98


title: US-1078955 vs. HL 16# 96


title: US-1078955 vs. HL 28# 88


title: US-1078955 vs. HL 132# 106


title: US-1078955 vs. HL 135# 103


title: US-1078955 vs. HL 17# 95


title: US-1078955 vs. HL 139# 100


title: US-1078955 vs. HL 26# 89


title: US-1078955 vs. HL 23# 91


title: US-1078955 vs. HL 123# 115


title: US-1078955 vs. HL 134# 104


title: US-1078955 vs. 9810 C 025a# 207


title: US-1078955 vs. FH 58# 145


title: US-1078955 vs. HL 141# 97


title: US-1078955 vs. HL 30# 86


title: US-1078955 vs. HL 98# 71


title: US-1078955 vs. HL 97# 72


title: US-1078955 vs. HL 92# 76


title: US-1078955 vs. HL-M-5# 67


title: US-1078955 vs. HL 29# 87


title: US-1078955 vs. HL 34# 83


title: US-1078955 vs. HL 40# 77


title: US-1078955 vs. HL 35# 82


title: US-1078955 vs. HL 33# 84


title: US-1078955 vs. HL 95# 73


title: US-1078955 vs. HL 39# 78


title: US-1078955 vs. 32923 (S96-7753)# 243


title: US-1078955 vs. 88-05-216# 33


title: US-1078955 vs. 89-7-147# 8


title: US-1078955 vs. 89-5-55# 9


title: US-1078955 vs. 88-03-250# 35


title: US-1078955 vs. HL-M-8# 64


title: US-1078955 vs. 95-05-C011G# 234


title: US-1078955 vs. 5331  (10/11/88)# 23


title: US-1078955 vs. 11264 N# 44


title: US-1078955 vs. 89-5-47# 6


title: US-1078955 vs. HL 113# 123


title: US-1078955 vs. 89-6-174# 11


title: US-1078955 vs. 89-6-77# 5


title: US-1078955 vs. Human Liver 131


title: US-1078955 vs. Human Liver 143


title: US-1078955 vs. Human Liver 130


title: US-1078955 vs. 93-84# 45


title: US-1078955 vs. Human Liver 127


title: US-1078955 vs. Human Liver 121


title: WTvsSig54_A control

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

description: WTvsSig54_A control mid exp wild type 1

hyb_protocol: Two individual differentially labeled cDNAs were incubated at 95° C for 3' cooled down to 68° C and mixed (final-volume 20 µl). To these mixed cDNAs 180 µl of pre-heated (68° C) Slidehyb#1 hybridization buffer (Ambion Austin USA) was added and the resulting solution was applied on a pre-heated slide (68° C). Slides were then hybridized at 44° C for 16 hours. Subsequently slides were washed at 42°C once in 1 x SSC/0.2% SDS and twice in 1 x SSC and dried by centrifugation (1 x SSC is 0.15 M NaCl and 0.15 M Sodium Citrate).

scan_protocol: Using the Scan Array Express microarray scanner. 1.Turn on the scanner and the computer (in this order) 2.Login: scanner 3.Double click the 'ScanArray Express' icon 4.Switch on lasers 1 and 3 at least 15 minutes prior to scanning arrays 5.Click the 'File' button This is to prevent you from accidentally turning off the laser after the 15 minutes warming-up phase 6.Insert the slide with the array-side up and the label towards the outside. On Agilent slides the array side is the side with the label that has the word Agilent"" on it 7.Press 'Scan | Prescan' 8.Put resolution at 50 m select both labels used and set PMT values for both channels 9.Press 'Start' 10.Press 'Palette ' 'Green' as soon as projection of the image has started (first dye) select the red colour as soon as scanning of the second layer (second dye) has started 11.Adjust PMT values to balance signals obtained for both channels. If necessary do a few low-resolution scans to obtain a optimal balance 12.Click the 'Scan' button again 13.Select frame for high resolution scan adjust resolution (to 10 m) and scan the array for both dyes 14.Press 'File | Save' to save the files 'Save all' saves both dye layers ," Create a new folder for each array 'Save all' saves the signals from both layers in individual files 15.Switch off the lasers

data_processing: 1.-Used script to split 10-array imagene file of cy3 intensity into 10 separate cy3 files. 2.-Used script to split 10-array imagene file of cy5 intensity into 10 separate cy5 files. 3.-For each indidivual array a merge file was produced consisting of merging the cy3 and cy5 intensity files created in step 1 and 2. The merged file is provided as supplementary file for each array. 4.-Background correction (Mean values)

organism: Lactiplantibacillus plantarum

label_protocol: Annealing Mix x µl RNA preparation (=5µg) y µl nuclease-free water 1 µl Random Nonamers 11 µl TOTAL 1. mix Annealing Mix in a 200 µl PCR tube gently by pipetting up and down 2. incubate for 5’ 70°C 3. cool at room temperature for 10’ (annealing) 4. spin down the mixture to the bottom of the tube 5. place on ice Reverse transcription Reverse Transcription Mix 4 µl 5x buffer 2 µl 0.1 M DTT 1 µl dNTP-mix 1 µl AA-dUTP 1 µl TMIII (keep only briefly outside 20°C) 20 µl TOTAL 1. Mix by very gently by pipetting up and down (vigorous pipetting will denature the enzyme!) 2. Incubate for 3 hrs at 42°C (in PCR-machine) 3. Cool on ice for immediate purification or place at 20°C for storage Degradation of mRNA 1. Add 2 µl 2.5 M NaOH 2. Mix (vortex) and spin down 3. Incubate for 15 min. at 37°C 4. Add 10 µl 2 M HEPES free acid 5. Mix (vortex) and spin down 6. Ready for purification or store at 20°C Labelling and purification of cDNA with cyanine dyes Followed Ge Healthcare kit "Amersham CyDye (Cy3/Cy5)Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA" code RPN5661 Labelling of amino allyl-modified cDNA with CyDye 1. Add the amino allyl modified cDNA (in 0.1 M sodium bicarbonate) directly into one aliquot of CyDye NHS Ester. Resuspend the ester completely by pipetting several times and transfer the solution to an amber 1.5 ml tube 2. Incubate at room temperature, in the dark for 60 to 90 minutes 3. Add 15 µl 4 M Hydroxylamine to each coupling reaction 4. Mix by stirring and incubate at room temperature, in the dark, for 15 minutes 5. Proceed directly to purification of CyDye-labelled cDNA Purification of CyDye labelled cDNA Followed Ge Healthcare kit "Amersham CyDye (Cy3/Cy5)Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA

extract_protocol: Collecting cells Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µll phenol/Chloroform -30 µl10% SDS -30 µl3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µlTE buffer 1.For each sample prepare a tube with Extraction Mixture 2.Harvest cells and quench them immediately in Quenching Buffer. Add 4 volumes of Quenching Buffer ( 40°C) to 1 volume of cell culture 3.Mix and store the sample at -40°C 4.Centrifuge cells at -20 C at 9000 rpm for 10 minutes (Centrifuge RC5B) 5.Discard the supernatant; keep the cell pellet cooled and work quickly to prevent condensation of water. Transfer the pellet with a pre-cooled spatula to a screw-crap tube with Extraction Mixture 6.Mix the cell pellet thoroughly with Extraction Mixture by shaking by hand 7.Freeze the tube immediately in liquid nitrogen 8.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary) 9.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm 10.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C) 11.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C) 5.Continue with the "High Pure RNA Isolation Kit" from Roche (order # 1 828 665) 6.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer 7.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.


title: US-1078955 vs. Human Liver 124


title: US-1078955 vs. Human Liver 89


title: WTvsSig54_B control

description: WTvsSig54_B control mid exp wild type 1


title: US-1078955 vs. Human Liver 108


title: US-1078955 vs. Human Liver 125


title: PSC, vector control, biological rep1

city: shantou

first: Enmin

last: Li

state: guangdong

address: 22 Xinling Road

country: China

institute: Shantou university, medical college

description: expression genes data from PSC (blank vector control)

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: blank vector control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cell lines were maintained in 199 medium(Invitrogen) containing 10% fetal calf serum (FCS)at 5% CO2 at 37℃

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

tag: esophageal squamous cell carcinoma

tag: Fascin high expression


title: H2O2_WTvsWT_A control

description: H2O2_WTvsWT_A control mid exp wild type 1


description: WT_normal_AvsWT_normal_B_(sig54) control mid exp wild type 1


title: H2O2_WTvsWT_B treatment

description: H2O2_WTvsWT_B treatment mid exp wild type 1 30 min, 3.5 mM H2O2


title: US-1078955 vs. Human Liver 71


title: US-1078955 vs. Human Liver 67


title: H2O2_WTvsSig54_A treatment

description: H2O2_WTvsSig54_A treatment mid exp wild type 1 H2O2, 3.5 mM, 30 min


title: Sig54_H2O2_AvsSig54_H2O2_B treatment

description: Sig54_H2O2_AvsSig54_H2O2_B treatment mid exp Sigma54 KO 1 30 min, 3.5 mM H2O2


title: H2O2_WTvsSig54_B treatment

description: H2O2_WTvsSig54_B treatment mid exp Sigma54 KO 1 30 min, 3.5 mM H2O2


title: Siomi Lab fruit fly S2 AGO2 Cloned Sequences v1.0

city: Koto-ku

first: Toutai

last: MITUYAMA

state: Tokyo

department: Artificial Intelligence Research Team

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description:
Cloning of small RNAs associated with AGO2 in S2 cells was carried out as described in (Nishida K.M. et al. RNA 13:1911-1922, 2007).
The deep sequencing of the libraries was performed on a GS20 system (Roche).

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
The raw data file (linked below as a supplementary file) was parsed by our custom perl script.
Raw sequences containing ambiguous Ns are discarded.
Small letters contained in the raw sequences are transformed to capitals letters.
The cloning frequency for each sequence is computed as counting the number of observation of a unique sequence shown in the raw data file.

organism: Drosophila melanogaster

source_name: Siomi laboratory, Institute for Genome Research, University of Tokushima

label_protocol: RNAs were dephosphorylated with CIP (NEB) and labeled with 32P-gamma-ATP with T4 polynucleotide kinase (TaKaRa) for visualization.

growth_protocol: S2 cells were grown under normal air conditions in a Schneider's Drosophila medium (Invitrogen) supplemented with 10% fetal calf serum.

extract_protocol:
Assay: immunoprecipitation
Antibody: monoclonal antibody against Drosophila AGO2
Antibody supplier: Siomi laboratory
Cell lysis buffer: 1XPBS supplemented with 1mM EDTA, 0.1mM DTT, 1% Empigen (Calbiochem), 2ug/ml Pepstatin, 2ug/ml Leupeptin and 0.5% Aprotinin.
AGO2 was immunopurified from S2 cells using anti-AGO2 antibody (9D6) immobilized on GammaBind beads (GE Healthcare).
GammaBind beads in a bound form with the immunoprecipitates were washed five times with cell lysis buffer.
Total RNAs were isolated from the immunoprecipitates with phenol:chloroform and precipitated with ethanol.

tag: Cell line

value: S2 cell


title: US-1078955 vs. Human Liver 119


title: US-1078955 vs. Human Liver 64


title: US-1078955 vs. Human Liver 65


title: US-1078955 vs. Human Liver 114


title: US-1078955 vs. Human Liver 79


title: US-1078955 vs. Human Liver 63


title: US-1078955 vs. Human Liver 93


title: US-1078955 vs. Human Liver 75


title: US-1078955 vs. Human Liver 59


title: US-1078955 vs. Human Liver 57


title: US-1078955 vs. Human Liver 53


title: H2O2_Sig54vsSig54_A treatment

description: H2O2_Sig54vsSig54_A treatment mid exp Sigma54 KO 1 peroxide, 3.5 mM, 30 minutes


title: DCM_Boxer_4

description: DCM Heart Tissue, Boxer

hyb_protocol: Std Affymetrix 1 cycle

scan_protocol: Std Affymetrix 1 cycle

organism: Canis lupus familiaris

source_name: DCM Heart Tissue

label_protocol: Std Affymetrix 1 cycle

extract_protocol: Trizol followed by RNEasy cleanup

tag: DCM Heart Tissue, Boxer


title: H2O2_Sig54vsSig54_B treatment

description: H2O2_Sig54vsSig54_B treatment mid exp Sigma54 KO 1 30 min, 3.5 mM H2O2


title: DCM_Boxer_3

description: DCM Heart Tissue, Boxer


title: ILL6002 96HPI

city: melbourne

first: barkat

middle: murtaja

last: mustafa

state: victoria

address: Corner of Royal Parade & Tin Alley

department: School of agriculture

country: Australia

institute: University of melbourne

description: data table contains condensed/normalized data from three biological replicates

hyb_protocol: Microarray slides were pre-hybridised by blocking in 5X SSC, 0.1% SDS, 25% Formamide, 1% BSA for 45 min at 42ºC, rinsed in distilled water and air dried. ).  A complete description of the microarray features can be found in the supplementary table. Purified combined Cy3 and Cy5 probes were resuspended in 2× hybridisation buffer (5× SSC, 0.2% SDS, 50% formamide (Sigma), 25 μg Cot1 DNA (Invitrogen), 0.4 mg polyA (Sigma), 0.5 mg salmon sperm DNA (Sigma), made up to 60.0 μL with sterile water) and was denaturated at 100 °C for 2 min before applied for hybridization to the array under a 60×25 mm Lifter slip (Grale Scientific). The slides were then incubated in a 42°C water bath for 16–20 h in a waterproof and humidified hybridisation chamber (Corning) in the dark.  Hybridized slides were slides were washed for 5 min in each of 1× SSC/0.2% SDS and 0.1× SSC/0.2% SDS, and twice for 2 min in 0.1× SSC followed by a gentle rinse in distill water and drying in air flow.  For each time point after inoculation, hybridisations were performed with six technical replicates (corresponding to the six complete grids on each microarray slide) and three biological replicates and included a dye-swapping (i.e. reciprocal labeling of Cy3 and Cy5) to eliminate any dye bias. In total 180 images were analysed from 30 slides, resulting in 18 data points for each time-point of each genotype.

scan_protocol: An Affymetrix® 428™ array scanner (Santa Clara, CA) was used to scan hybridized microarray slides at 660 nm for Cy5 (red laser) and 532 nm for Cy3 (green laser) at 10 µm resolution and the image was captured with Affymetrix® Jaguar™ software (v. 2.0, Santa Clara, CA). Scanned image was analysed and quantified using Imagene™ 5 (BioDiscovery, Marina Del Rey, CA) software, Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Transformation of quantified spot data with GeneSight™ 3 (BioDiscovery, Marina Del Rey, CA) consisted of a local background correction (subtracting mean background intensity from mean signal intensity for each spot), omitting flagged spots (i.e. empty spots, negative spots (signal mean<background mean), poor spots and spots with mean signal intensity less than two times the local background), LOWESS normalisation of the entire population, creating a test/reference mean signal ratio, taking a shifted log (base 2), and combination of duplicated spot data. For identifying differentially expressed (DE) genes, expression ratios were filtered to eliminate genes whose  mean fold change (FC) was less than 1.83-fold up or down at 95% confidence interval followed by Students t test and  False Discovery Rate (FDR) multiple testing correction to retain only genes in which expression ratio changes were significant at P < 0.05. Datasets for ILL7537 and ILL6002  was built from mean expression ratios of a non-redundant list of genes differentially expressed at any time-point for any  genotype at This dataset was then used to perform Figure of Merit (FOM) and k-means clustering using euclidean distance metrics with the MeV software.

label: Cy3, Cy5

organism: Lens culinaris subsp. culinaris

source_name: leaf and stem tissue of five plants of ILL6002, 96 hour after inoculted with Ascochyta lentis

label_protocol: Fifty μg of total RNA from each sample was reverse transcribed using Superscript II (Invitrogen) with incorporation of amino-allyl dUTP (Sigma) into the cDNA for post labeling  with Cy3- or Cy5-NHS esters (Amersham). Briefly, the dried down RNA and 5 μg of oligo(dT) 18mer primer was heated at 70 °C for 10 min and chilled on ice before adding first strand buffer to a final concentration of 1×, aa-dUTP/dNTPs mix (final concentrations of 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.2 mM dTTP, 0.3 mM aa-dUTP), DTT to a final concentration of 10 mM, and 150 units Superscript II in a total reaction volume of 30 μL. Reverse transcription was performed at 42 °C for 2 h before hydrolysis of RNA template with NaOH for 15 min at 65 °C  followed by neutralisation with HEPES (pH 7.0). cDNA samples were purified and labeled by applying  them to QIAquick™ PCR purification columns (QIAGEN™) and washed/dried according to manufacturers instructions, before adding the appropriate volume of Cy3/Cy5 dye (resuspended in 0.1 M Na2CO3 ,pH 9.0) to the column membrane and incubating for 1 h at room temperature in the dark. After incubation, Cy3/Cy5 labeled samples were eluted, appropriate (control and treatment) Cy3 and Cy5 probes were combined, and purification was repeated.

growth_protocol: Seeds were sown in 8cm diameter pots (five seeds pot-1) in sterile soil.  All plants were grown in a climate controlled growth cabinet (20 ± 2ºC) for 14 days before inoculation with A. lentis.

extract_protocol: Total RNA was extracted from pooled stem and leaf samples for each genotype at each time-point (including control samples) using the RNeasy® Plant Mini Kit (Qiagen, Valencia, CA). The quantity, quality and integrity of the total RNA samples were assessed by OD260/OD280 ratios and by gel electrophoresis.

treatment_protocol: Plants were inoculated by spraying approximately 5 mL Ascochyta lentis (strain: AL4) spore suspension (1 x 106 spores mL-1 ) per plant with a plastic sprayer until run-off.

tag: Age

value: 14 day old

tag: Tissue

value: stem and leaves

tag: Variety

source_name: leaf and stem tissue of five plants of ILL6002, 96 hour after mock inoculated wit water


title: Library 1:  Inflorescence, dT primed, pool-amplified

city: University Park

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

description: Sequences are 20 or 21 nt tags representing the 5' ends of uncapped, polyA+ RNAs.  Library #1 derived from 454 pyrosequencing.  Details described in Addo-Quaye et al. (2008)

data_processing:
Adapter sequences were computationally removed, and unique tags of 20 or 21nt length were counted.  Counts are the raw number of times each sequence was isolated.  For simplicity, tags are given in DNA form (i.e. T instead of U).

Raw fasta file prior to signature extraction from adapter regions, linked below as supplementary file.

label: not applicable

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Wild-type inflorescence

label_protocol: not applicable

extract_protocol: Total RNA isolated using Trizol per manufacturer's instructions.  Subsequent polyA purification was performed using oligo dT agarose beads (Qiagen) per manufacturer's protocol.

tag: Col-0 wild-type Arabidopsis thaliana grown at 22C, 16hr/8hr light/dark for ~60 days.  Inflorescence tissue was harvested and immediately frozen.


title: DCM_Boxer_2

description: DCM Heart Tissue, Boxer


title: US-1078955 vs. Human Liver 56


title: ILL6002 72HPI

source_name: leaf and stem tissue of five plants of ILL6002, 72 hour after inoculted with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL6002, 72 hour after mock inoculated wit water


title: Pacing_Mongrel_LV04

description: Pacing Heart Tissue, Mongrel

source_name: Pacing Heart Tissue

tag: Pacing Heart Tissue, Mongrel


title: DCM_Boxer_1

description: DCM Heart Tissue, Boxer


title: SV493_1

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54644.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5680; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.63; Parameter Scan Time = 08:00:35; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 180489; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.63; Parameter Scan Time = 08:00:35; Parameter PMT Volts = 660; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 545292; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.06; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson

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

source_name: CRG

label_protocol: not provided

extract_protocol: not provided

tag: CRG

tag: Disease State

value: seminal vesicle

tag: Individual


title: SV335_1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53850.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.45; Parameter Scan Time = 10:22:32; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 173382; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.45; Parameter Scan Time = 10:22:32; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 538186; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: PN471_5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54652.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.69; Parameter Scan Time = 09:42:42; Parameter PMT Volts = 660; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 179870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.69; Parameter Scan Time = 09:42:42; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 544674; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.92; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson

value: normal prostate


title: US-1078955 vs. Human Liver 55

description: Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.


title: ILL6002 48HPI

source_name: leaf and stem tissue of five plants of ILL6002, 48 hour after inoculted with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL6002, 48 hour after mock inoculated wit water


title: SV369_1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54643.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5920; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 08:21:31; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 180509; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 08:21:31; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 545313; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: PN340_5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53857.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5760; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.14; Parameter Scan Time = 08:10:26; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 175130; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.14; Parameter Scan Time = 08:10:26; Parameter PMT Volts = 680; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 539934; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: PN340_3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53856.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.97; Parameter Scan Time = 07:47:11; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 175105; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.97; Parameter Scan Time = 07:47:11; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 539909; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: ILL6002 24HPI

source_name: leaf and stem tissue of five plants of ILL6002, 24 hour after inoculted with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL6002, 24 hour after mock inoculated wit water


title: SV155_5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53858.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.43; Parameter Scan Time = 08:35:03; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 175155; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.43; Parameter Scan Time = 08:35:03; Parameter PMT Volts = 710; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 539959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: PN471_4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54650.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5760; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.58; Parameter Scan Time = 09:30:09; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 179858; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.58; Parameter Scan Time = 09:30:09; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 544661; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.83; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: PN340_2v

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53420.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 560, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.25; Parameter Scan Time = 10:07:03; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-24; Parameter Pixel Size = 10; Parameter Laser on time = 171755; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.25; Parameter Scan Time = 10:07:03; Parameter PMT Volts = 690; Parameter Scan Date = 2004-06-24; Parameter Pixel Size = 10; Parameter Laser on time = 536559; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: Pacing_Mongrel_LV02

description: Pacing Heart Tissue, Mongrel


title: ILL6002 6HPI

source_name: leaf and stem tissue of five plants of ILL6002, 6 hour after inoculted with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL6002, 6 hour after mock inoculated wit water


title: Pacing_Mongrel_LV01

description: Pacing Heart Tissue, Mongrel


title: US-1078955 vs. Human Liver 74

source_name: Liver


title: ILL7537 96HPI

source_name: leaf and stem tissue of five plants of ILL7537, 96 hour after inoculated with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL7537, 96 hour after mock inoculated wit water


title: DCM_Doberman_R

description: DCM Heart Tissue, Doberman

source_name: DCM Heart Tissue

tag: DCM Heart Tissue, Doberman


title: SV471_1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54649.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.38; Parameter Scan Time = 09:14:46; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 179842; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.38; Parameter Scan Time = 09:14:46; Parameter PMT Volts = 660; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 544646; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.84; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: SV340_1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53855.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.94; Parameter Scan Time = 09:17:23; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173755; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.94; Parameter Scan Time = 09:17:23; Parameter PMT Volts = 790; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538559; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: DCM_Doberman_L

description: DCM Heart Tissue, Doberman


title: ILL7537 48HPI

source_name: leaf and stem tissue of five plants of ILL7537, 48 hour after inoculated with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL7537, 48 hour after mock inoculated wit water


title: DCM_Doberman_K

description: DCM Heart Tissue, Doberman


title: Library 4:  Seedlings, random primed, primer extension

description: Sequences are 20 or 21 nt tags representing the 5' ends of uncapped, polyA+ RNAs.  Library #4 derived from Solexa/Illumina Genome Analyzer sequencing.  Details described in Addo-Quaye et al. (2008)

data_processing:
Adapter sequences were computationally removed, and unique tags of 20 or 21nt length were counted.  Counts are the raw number of times each sequence was isolated.  For simplicity, tags are given in DNA form (i.e. T instead of U).

Tab-delimited raw files with raw sequence [tab] count, prior to signature extraction from adapter regions, linked below as supplementary files.

source_name: Arabidopsis degradome library 4

tag: Col-0 wild-type Arabidopsis thaliana grown at 22C, 16hr/8hr light/dark for 10 days on MS-Agar plates.  Seedlings harvested and immediately frozen


title: Control_Mongrel_P9

description: Control Heart Tissue, Mongrel

source_name: Control Heart Tissue

tag: Control Heart Tissue, Mongrel


title: ILL7537 72HPI

source_name: leaf and stem tissue of five plants of ILL7537, 72 hour after inoculated with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL7537, 72 hour after mock inoculated wit water


title: PN341_7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53854.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5600; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.80; Parameter Scan Time = 09:02:04; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173738; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.80; Parameter Scan Time = 09:02:04; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538542; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson

source_name: CRG


title: PN341_3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53853.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5600; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 08:48:29; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173725; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 08:48:29; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538529; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: ILL7537 6HPI

description: data table contains condensed/normalized data from three biological replicates

source_name: leaf and stem tissue of five plants of ILL7537, 6 hour after inoculated with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL7537, 6 hour after mock inoculated wit water


title: ILL7537 24HPI

source_name: leaf and stem tissue of five plants of ILL7537, 24 hour after inoculated with Ascochyta lentis

source_name: leaf and stem tissue of five plants of ILL7537, 24 hour after mock inoculated wit water


title: Library 3:  Inflorescence, random primed, primer extension

description: Sequences are 20 or 21 nt tags representing the 5' ends of uncapped, polyA+ RNAs.  Library #3 derived from Solexa/Illumina Genome Analyzer sequencing.  Details described in Addo-Quaye et al. (2008)

source_name: Arabidopsis degradome library 3


title: PN493_5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54647.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 5840; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 07:31:58; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 180461; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 07:31:58; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 545264; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: Control_Mongrel_P4

description: Control Heart Tissue, Mongrel


title: Control_Mongrel_P1

description: Control Heart Tissue, Mongrel


title: PN155_7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53859.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.50; Parameter Scan Time = 08:50:25; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 175169; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.50; Parameter Scan Time = 08:50:25; Parameter PMT Volts = 690; Parameter Scan Date = 2004-07-13; Parameter Pixel Size = 10; Parameter Laser on time = 539973; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: SV341_1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53852.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 5640; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.06; Parameter Scan Time = 11:08:59; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 173430; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.06; Parameter Scan Time = 11:08:59; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 538234; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson


title: Cells grown with benzoate #2

status: Public on May 07 2008

first: Yasuhiro

last: Oda

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

description: A high-density oligonucleotide microarray (Affymetrix GeneChip) was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions. cDNA synthesis, fragmentation, labeling, hybridization, and processing of custom designed Rhodopseudomonas palustris GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix Microarray Suite was used for initial data acquisition and processing.

label: Biotinylated GeneChip reagent

organism: Rhodopseudomonas palustris

source_name: Rhodopseudomonas palustris strain CGA010 with benzoate #2

extract_protocol: Rhodopseudomonas palustris cells were disrupted by treatment with by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.

tag: Rhodopseudomonas palustris cells grown with benzoate #2


title: Cells grown with benzoate #1

scan_protocol: As recommended by the manufacturer (Affymetrix)

source_name: Rhodopseudomonas palustris strain CGA010 with benzoate #1

tag: Rhodopseudomonas palustris cells grown with benzoate #1


title: Library 2:  Inflorescence, dT primed, pool-amplified

description: Sequences are 20 or 21 nt tags representing the 5' ends of uncapped, polyA+ RNAs.  Library #2 derived from Solexa/Illumina Genome Analyzer sequencing.  Details described in Addo-Quaye et al. (2008)

scan_protocol: not applicable

source_name: Arabidopsis degradome library 2


title: PN493_4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54645.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5920; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 07:44:40; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 180473; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 07:44:40; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 545277; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson