title: Nasal Epithelium Inhalation Formaldehyde 6ppm 8d ID301

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 8 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

tag: Sacrifice Method


title: Mouse ileum Germ-free_A_5553

status: Public on Apr 23 2007

type: RNA

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

country: USA

institute: Washington University

hyb_protocol: Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

scan_protocol: Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

data_processing: MAS5; scaling = 500

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- Germ-free_A_5553

label_protocol: In vitro transcription (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) was performed on cRNA derived from 40ug total RNA followed by standard fragmentation.  For detailed protocol see http://pathimm.wustl.edu/~mgacore/protocols.htm

extract_protocol: RNA was purified from ileum of each mouse [Midi RNeasy kit (Qiagen) with on-column DNase digestion]. Equivalent amounts of RNA from mice in each treatment group (n=4/experiment) were pooled and two biotinylated cRNA targets (40 ug/replicate) were independently prepared from each sample.

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_Germ-free_A_5553


title: alp13D_vs_WT_2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, alp13 null versus wild type expression replicate 2

hyb_protocol: 500 ng of Cy3 labeled cDNA was mixed with 500 ng of Cy5 labeled cDNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted with Agilent Feature Extraction software version 8.1.1.1 and analyzed with the Genespring software.

data_processing: Log ratios of alp13 null over wild type were obtained by dividing median Cy5 value over its corrresponding normalized Cy3 value

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe wild type RNA

label_protocol: 26 ug total RNA were reverse-transcribed by Invitrogen Superscript Indirect cDNA Labeling System incorporating amino-allyl dUTP. Purified cDNA was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled cDNA was purified by Invitrogen SNAP column.

growth_protocol: Asynchronous growing fission yeast cells at 30 C

extract_protocol: total RNA isolated from asynchronous growing fission yeast cells at 30 C by Epicentre MasterPure Yeast RNA Purification Kit.

tag: cDNA reverse transcribed from total RNA isolated from wild type Schizosaccharomyces pombe cells

source_name: Schizosaccharomyces pombe alp13 null RNA

label_protocol: 26 ug total RNA were reverse-transcribed by Invitrogen Superscript Indirect cDNA Labeling System incorporating amino-allyl dUTP. Purified cDNA was covalently coupled with Cy5 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled cDNA was purified by Invitrogen SNAP column.

tag: cDNA reverse transcribed from total RNA isolated from alp13 null Schizosaccharomyces pombe cells


title: K9me2_1_control wt

type: genomic

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, control wt replicate 1

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

molecule: genomic DNA

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked at 18C with paraformaldehyde for 30 minutes

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformaldehyde at 18C for 30 minutes

tag: Chromatin DNA isolated from paraformaldehyde cross-linked control wt Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: K9me2_2_rrp6D

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, rrp6 null replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked rrp6 null Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: Mouse ileum with B.thetaiotaomicron_A_5559

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with B.thetaiotaomicron_A_5559

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with B.thetaiotaomicron_A_5559


title: K9me2_1_rrp6D

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, rrp6 null replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked rrp6 null Schizosaccharomyces pombe cells


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 8d ID300

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

organism: Rattus norvegicus

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Qiagen Micro RNA kit

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: ul

tag: Ratio

tag: Dilution

tag: Bioanalyzer Results

value: Good

tag: Sample Preservation

value: Cells resuspended in RNAlater and stored at 4 degrees Centigrade

tag: Strain or Line

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

value: Adult

value: Deep pentobarbital anesthesia followed by exsanguination

tag: Sex

value: Male

tag: Units of Age

value: weeks


title: K9me2_1_wt control

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: K9me2_2_wt control

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells


title: Mouse ileum with L.monocytogenes_D_5550

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes_D_5550

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes_D_5550


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 6h ID287

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hour time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

tag: RNA Integrity Number

tag: Sacrifice Method


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 8d ID298

tag: Array Type

tag: Amount to Core


title: K9me2_1_clr6-1

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, clr6-1 mutant replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr6-1 mutant Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 8d ID299

tag: Units of Amount

tag: Ratio

tag: Dilution


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID127

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hour time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line


title: Mouse ileum with L.monocytogenes(delta-inlAB)_A_5551

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes(delta-inlAB)_A_5551

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-inlAB)_A_5551


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID129

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

tag: Sex


title: Mouse ileum with L.monocytogenes_B_5544

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes_B_5544

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes_B_5544


title: Mouse ileum with L.monocytogenes(delta-inlAB)_B_5552

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes(delta-inlAB)_B_5552

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-inlAB)_B_5552


title: Mouse ileum with L.innocua_B_5548

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.innocua_B_5548

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.innocua_B_5548


title: K9ac_1_pst1-1

description: Schizosaccharomyces pombe pst1-1 mutant cells, K9ac ChIP(chromatin immunoprecipitation)-on-chip, replicate 1

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked at 18 C with paraformaldehyde for 30 minutes

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication. After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformaldehyde at 18 C for 30 minutes

tag: Chromatin DNA isolated from paraformaldehyde cross-linked pst1-1 mutant Schizosaccharomyces pombe cells and enriched for K9ac chromatin with anti-acetyl H3K9 (07-352, Upstate) antibody.


title: Mouse ileum with L.monocytogenes_C_5549

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes_C_5549

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes_C_5549


title: K9ac_2_alp13D

description: Schizosaccharomyces pombe alp13 null cells, K9ac ChIP(chromatin immunoprecipitation)-on-chip, replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked alp13 null Schizosaccharomyces pombe cells and enriched for K9ac chromatin with anti-acetyl H3K9 (07-352, Upstate) antibody.


title: Mouse ileum with L.monocytogenes(delta-hly)_B_5542

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes(delta-hly)_A_5542

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-hly)_B_5542


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 5d ID140

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 5 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

tag: Array Type

tag: Amount to Core

tag: Units of Amount

tag: Ratio

tag: RNA Integrity Number

tag: Sacrifice Method

tag: Units of Age


title: K9ac_2_pst1-1

description: Schizosaccharomyces pombe pst1-1 mutant cells, K9ac ChIP(chromatin immunoprecipitation)-on-chip, replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked pst1-1 mutant Schizosaccharomyces pombe cells


title: K9me2_2_clr6-1

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, clr6-1 mutant replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr6-1 mutant Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: K9me2_1_alp13D

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, alp13 null replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked alp13 null Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 5d ID139

tag: Dilution

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

tag: Sex


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 5d ID138

tag: Array Type

tag: Amount to Core


title: Mouse ileum with L.monocytogenes_A_5543

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes_A_5543

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes_A_5543


title: K9ac_1_alp13D

description: Schizosaccharomyces pombe cells, H3K9ac ChIP(chromatin immunoprecipitation)-on-chip, alp13 null replicate 1

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformaldehyde

tag: Chromatin DNA isolated from paraformaldehyde cross-linked alp13 null Schizosaccharomyces pombe cells and enriched for K9ac chromatin with anti-acetyl H3K9 (07-352, Upstate) antibody.


title: K9me2_2_alp13D

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, alp13 null replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked alp13 null Schizosaccharomyces pombe cells


title: Mouse ileum with L.monocytogenes(delta-hly)_A_5541

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes(delta-hly)_A_5541

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-hly)_A_5541


title: K9ac_2_WT

description: Schizosaccharomyces pombe WT cells, K9ac ChIP (chromatin immunoprecipitation)-on-chip, replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for K9ac chromatin with anti-acetyl H3K9 (07-352, Upstate) antibody.


title: 168T

status: Public on Apr 21 2007

city: Pennington

first: Mark

middle: David

last: Ayers

state: NJ

address: 311 Pennington-Rocky Hill Rd.

department: Clinical Discovery Technologies

institute: Bristol-Myers Squibb

description: Gene expression data from human colon tumor tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained using the Affymetrix Fluidics Station 400 according to Affymetrix standard procedures

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 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 1500.

organism: Homo sapiens

source_name: 168T Human colon tumor tissue sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA isolated from cell culture using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: tissue


title: 167T

source_name: 167T Human colon tumor tissue sample


title: K9ac_1_WT

description: Schizosaccharomyces pombe WT cells, K9ac ChIP (chromatin immunoprecipitation)-on-chip, replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells


title: 165T

source_name: 165T Human colon tumor tissue sample


title: 159T

source_name: 159T Human colon tumor tissue sample


title: 153T

source_name: 153T Human colon tumor tissue sample


title: 155T

source_name: 155T Human colon tumor tissue sample


title: 150T

source_name: 150T Human colon tumor tissue sample


title: 161T

source_name: 161T Human colon tumor tissue sample


title: 151T

source_name: 151T Human colon tumor tissue sample


title: 162T

source_name: 162T Human colon tumor tissue sample


title: 142T

source_name: 142T Human colon tumor tissue sample


title: 156T

source_name: 156T Human colon tumor tissue sample


title: 149T

source_name: 149T Human colon tumor tissue sample


title: 147T

source_name: 147T Human colon tumor tissue sample


title: 152T

source_name: 152T Human colon tumor tissue sample


title: 160T

source_name: 160T Human colon tumor tissue sample


title: 139T

source_name: 139T Human colon tumor tissue sample


title: 143T

source_name: 143T Human colon tumor tissue sample


title: 144T

source_name: 144T Human colon tumor tissue sample


title: 141T

source_name: 141T Human colon tumor tissue sample


title: 145T

source_name: 145T Human colon tumor tissue sample


title: 140T

source_name: 140T Human colon tumor tissue sample


title: 136T

source_name: 136T Human colon tumor tissue sample


title: 135T

source_name: 135T Human colon tumor tissue sample


title: 138T

source_name: 138T Human colon tumor tissue sample


title: 132T

source_name: 132T Human colon tumor tissue sample


title: 131T

source_name: 131T Human colon tumor tissue sample


title: 129T

source_name: 129T Human colon tumor tissue sample


title: Polysomal 15

type: mixed

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: Samples from cell culture

hyb_protocol: for details, see the hybridization section in the direct labeling protocol (2004.10.22) at the UHN Microarray Centre (University Health Network, Princess Margaret Hospital, Ontario Cancer Institute) website

scan_protocol: Slides were digitalized using Axon GenePix 4000B scanner and software using default settings.

data_processing: The data from the final analysis was normalized using the bioconductor (Gentleman et al. 2004) library limma (Wettenhall and Smyth 2004) and the non-print tip lowess approach without background subtraction (Yang et al. 2002) as this increases the accuracy of the obtained measurements (Irizarry et al. 2005). Replicate spots on each array were separated and treated as independent

molecule: other

source_name: 3T3-parental induced 5hrs- POLY RNA-Cy5

label_protocol: direct labeling protocol (2004.10.22) as described at the UHN Microarray Centre (University Health Network, Princess Margaret Hospital, Ontario Cancer Institute) website

extract_protocol: Trizol

tag: NIH3T3/parental cells induced polysomal fraction

source_name: 3T3-parental induced 5hrs- TOTAL RNA-Cy3

tag: NIH3T3/parental cells uninduced


title: 134T

source_name: 134T Human colon tumor tissue sample


title: 133T

source_name: 133T Human colon tumor tissue sample


title: Polysomal 16

description: Samples from cell culture


title: 126T

source_name: 126T Human colon tumor tissue sample


title: Polysomal 12

description: Samples from cell culture

source_name: 3T3-parental induced 5hrs- POLY RNA-Cy3

source_name: 3T3-parental induced 5hrs- TOTAL RNA-Cy5


title: 127T

source_name: 127T Human colon tumor tissue sample


title: 137T

source_name: 137T Human colon tumor tissue sample


title: 125T

source_name: 125T Human colon tumor tissue sample


title: 128T

source_name: 128T Human colon tumor tissue sample


title: Polysomal 10

description: Samples from cell culture


title: Polysomal 11

description: Samples from cell culture


title: Polysomal 14

description: Samples from cell culture


title: Polysomal 13

description: Samples from cell culture


title: Polysomal 7

description: Samples from cell culture

source_name: 3T3-eIF4E-induced 5hrs POLYSOMAL RNA-Cy3

tag: NIH3T3/eIF4E cells induced polysomal fraction

source_name: 3T3-eIF4E-uninduced TOTAL RNA-Cy5

tag: NIH3T3/eIF4E cells uninduced


title: 122T

source_name: 122T Human colon tumor tissue sample


title: 121T

source_name: 121T Human colon tumor tissue sample


title: Polysomal 9

description: Samples from cell culture


title: Polysomal 5

description: Samples from cell culture


title: 123T

source_name: 123T Human colon tumor tissue sample


title: Polysomal 6

description: Samples from cell culture


title: Polysomal 4

description: Samples from cell culture

source_name: 3T3-eIF4E-induced 5hrs POLYSOMAL RNA-Cy5

source_name: 3T3-eIF4E-uninduced TOTAL RNA-Cy3


title: 119T

source_name: 119T Human colon tumor tissue sample


title: Polysomal 3

description: Samples from cell culture


title: 124T

source_name: 124T Human colon tumor tissue sample


title: 118T

source_name: 118T Human colon tumor tissue sample


title: Polysomal 2

description: Samples from cell culture


title: Polysomal 8

description: Samples from cell culture


title: Total RNA 16

description: Samples from cell culture

source_name: 3T3-eIF4E-induced 5hrs TOTAL RNA-Cy5

tag: NIH3T3/eIF4E cells induced


title: Polysomal 1

description: Samples from cell culture


title: 120T

source_name: 120T Human colon tumor tissue sample


title: 116T

source_name: 116T Human colon tumor tissue sample


title: 114T

source_name: 114T Human colon tumor tissue sample


title: 115T

source_name: 115T Human colon tumor tissue sample


title: Total RNA 14

description: Samples from cell culture

source_name: 3T3-eIF4E-induced 5hrs TOTAL RNA-Cy3


title: Total RNA 15

description: Samples from cell culture


title: 113T

source_name: 113T Human colon tumor tissue sample


title: Total RNA 12

description: Samples from cell culture


title: Total RNA 13

description: Samples from cell culture


title: 111T

source_name: 111T Human colon tumor tissue sample


title: 110T

source_name: 110T Human colon tumor tissue sample


title: Total RNA 10

description: Samples from cell culture


title: 108T

source_name: 108T Human colon tumor tissue sample


title: Total RNA 7

description: Samples from cell culture

source_name: 3T3-parental induced 5hrs- TOTAL RNA-Cy3

tag: NIH3T3/parental cells induced

source_name: 3T3-parental uninduced- TOTAL RNA-Cy5


title: Total RNA 9

description: Samples from cell culture


title: 107T

source_name: 107T Human colon tumor tissue sample


title: Total RNA 8

description: Samples from cell culture


title: 106T

source_name: 106T Human colon tumor tissue sample


title: 105T

source_name: 105T Human colon tumor tissue sample


title: Total RNA 4

description: Samples from cell culture

source_name: 3T3-parental induced 5hrs- TOTAL RNA-Cy5

source_name: 3T3-parental uninduced- TOTAL RNA-Cy3


title: Total RNA 5

description: Samples from cell culture


title: treatedtumor_4

description: Gene expression data from xenograft L2987 lung tumor tissue samples

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3012

source_name: Xenograft L2987 lung tumor tissue sample treatedtumor_4


title: 104T

source_name: 104T Human colon tumor tissue sample


title: treatedtumor_2

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3010

source_name: Xenograft L2987 lung tumor tissue sample treatedtumor_2


title: Total RNA 6

description: Samples from cell culture


title: Total RNA 3

description: Samples from cell culture


title: treatedtumor_1

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3008

source_name: Xenograft L2987 lung tumor tissue sample treatedtumor_1


title: 103T

source_name: 103T Human colon tumor tissue sample


title: treatedtumor_5

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3014

source_name: Xenograft L2987 lung tumor tissue sample treatedtumor_5


title: controltumor_8

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3006

source_name: Xenograft L2987 lung tumor tissue sample controltumor_8


title: 102T

source_name: 102T Human colon tumor tissue sample


title: controltumor_6

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3002

source_name: Xenograft L2987 lung tumor tissue sample controltumor_6


title: controltumor_7

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3004

source_name: Xenograft L2987 lung tumor tissue sample controltumor_7


title: Total RNA 2

description: Samples from cell culture

source_name: 3T3-parental induced 5hrs- TOTAL RNA-Cy3


title: 101T

source_name: 101T Human colon tumor tissue sample


title: controltumor_1

source_name: Xenograft L2987 lung tumor tissue sample controltumor_1


title: Reovirus MyRV2-CpC18 infection (sample B, dye-swab)

status: Public on Apr 20 2007

city: Rockville

first: Donald

middle: Lee

last: Nuss

address: 9600 Gudelsky Drive

department: Center for Biosystems Research

institute: University of Maryland Biotechnology Institute

hyb_protocol: Printed slides were prepared for hybridization by the addition of 30 μl of prehybridization solution, which contained 50% formamide, 6X SSPE (1X SSPE is 0.15 M NaCl, 0.001 M NaH2PO4 and 0.001 M EDTA), 0.5% SDS, 5X Denhardt’s solution, and 100 μg of salmon sperm DNA/ml, to the arrayed surface of a glass slike (covered with a coverslip to evenly distribute the prehybridization solution). The slide was incubated for 30 min at 42 C in a hybridization chamber. Fluorescence-labeled probes were dried and resuspended in 20 μl of hybridization solution, which contained 50% formamide, 6x SSPE, 0.5% SDS, 5x Denhardt's solution, blocking solution [2 µg of poly(dA), 4 µg of yeast tRNA, 10 µg of salmon sperm DNA)], 14 µl of master mix solution (70% formamide, 3x Denhardt's solution, 0.7% SDS), and 6 µl of 20x SSPE. The resuspended probes were heated to 100°C for 2 min, vortexed, and collected by a brief spin in a microcentrifuge. The probes were applied to the arrayed surface, covered with a coverslip, and placed in a hybridization chamber overnight at 42°C.

scan_protocol: Hybridized slides were washed in each of three solutions (solution 1 is 1x SSC- 0.1% SDS, solution 2 is 2x SSC- 0.1% SDS, and solution 3 is 2x SSC) for 10 min, spun dry, scanned in both Cy3 and Cy5 channels with an Affymetrix 418 Scanner at a 10-µm resolution and a 70% photomultiplier tube value, and exported as 16-bit TIFF images for analysis.

data_processing: Integrated pixel intensity values for each spot were calculated using TIGR Spotfinder software (TIGR, Rockville, MD; http://www.tigr.org/software) and saved in tab-delimited format for analysis in Mathematica 5.1 (Wolfram Research Inc., Champaign, IL; http://www.wolfram.com). All hybridization data among two sets of dye-swap experiments (representing a total of 4 datasets) were processed according to the following pipeline: (Step 1) Each hybridization dataset was individually processed using a locally weighted linear regression (Lowess) algorithm (smoothing factor = 0.15) to remove systemic dye bias present in each group of spots within a single metarow, metacolumn block of the microarray chip. (Step 2) Following the intra-slide normalization routine described above, all lowess-normalized datasets were loaded simultaneously to rescale each spot through the use of a Z-transformation. Specifically, the global log2 (cy3/cy5) mean and standard deviations were calculated across all four datasets simultaneously and then used to rescale each spot in all four normalized datasets using Equation 1: the rescaled log2 (cy3/cy5) value of an individual spot = [the spot’s own log2 (cy3/cy5) value – global mean of all log2 (cy3/cy5) values] / by the global standard deviation of all log2 (cy3/cy5) values.

organism: Cryphonectria parasitica

source_name: Wild type strains EP155

label_protocol: Fluorescence-labeled cDNA probes were prepared from total RNA (25 μg per probe) by the direct incorporation of Cy3-UTP using a CyScribe first-strand cDNA labeling kit (Amersham pharmacia) primed with oligo (dT) according to the manufacturer’s instructions. Unincorporated nucleotides were removed with a Microcon-30 spin column.

growth_protocol: Grow at 22-24 C with a 12-h light-dark cycle at 1300-1600 lx.

extract_protocol: Cultures used for RNA isolation were grown on PDA-cellophane for 6 days and harvested by freezing the mycelia in liquid nitrogen and then immediately grinding the mycelia into a fine powder by using a mortar and pestle. The powder was resuspended in RNA extraction buffer (200 mM NaCl, 100 mM Tris-Cl [pH 8.0], 4 mM EDTA [pH 8.0], 2% sodium dodecyl sulfate [SDS], 2 mM dithiothreitol) at a ratio of 4 ml of buffer per g of mycelia. This step was followed sequentially by extraction with equal volumes of water-saturated phenol, acid phenol-chloroform-isoamyl alcohol (25:24:1) (pH 4.5), and chloroform. Single-stranded RNA was precipitated on ice for 2 h by the addition of LiCl to a final concentration of 2 M. The single-stranded RNA precipitate was collected by centrifugation, resuspended in 2 ml of double-distilled H2O, reprecipitated by the addition of 2.5 volumes of ice-cold ethanol and 0.1 volume of 3 M sodium acetate (pH 5.2), and incubated for 30 min at -20°C. The RNA was collected by centrifugation, washed with 2 ml of ice-cold 75% ethanol, dried, and treated with 2 U of RQ1 DNase (Promega) in 0.5 ml of 20 mM Tris (pH 8.0)-20 mM MgCl2 in the presence of 40 U of RNasin (Promega) for 1 h at 37°C. Following phenol-chloroform and chloroform extractions, the RNA was precipitated with ethanol and resuspended in 100 µl of double-distilled H2O.

treatment_protocol: No treatment

tag: Strain EP155 grown on PDA with cellophane overlay (sample B).

source_name: Wild type strain EP155 infected with reovirus MyRV2-CpC18

label_protocol: Fluorescence-labeled cDNA probes were prepared from total RNA (25 μg per probe) by the direct incorporation of Cy5-UTP using a CyScribe first-strand cDNA labeling kit (Amersham pharmacia) primed with oligo (dT) according to the manufacturer’s instructions. Unincorporated nucleotides were removed with a Microcon-30 spin column.

treatment_protocol: Reovirus MyRV2-CpC18 infection

tag: Reovirus MyRV2-CpC18 infected strain EP155 grown on PDA with cellophane overlay (sample B).


title: 100T

source_name: 100T Human colon tumor tissue sample


title: Total RNA 1

description: Samples from cell culture

source_name: 3T3-parental uninduced- TOTAL RNA-Cy5


title: Reovirus MyRV2-CpC18 infection (sample A, dye-swab)

tag: Strain EP155 grown on PDA with cellophane overlay (sample A).

tag: Reovirus MyRV2-CpC18 infected strain EP155 grown on PDA with cellophane overlay(sample A).


title: Whole Seed at the heart stage, biological replicate 1

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole seeds containing heart-stage embryos were ground in liquid nitrogen using a mortar and pestle.

hyb_protocol: Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45°C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G System.

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.

organism: Glycine max

source_name: Soybean heart stage seed

label_protocol: Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22°C.

extract_protocol: Total RNA was extracted using Plant RNA Isolation Reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: From pods with lengths between 1.3 and 2.0 cm, seeds with heart-stage embryos were collected, freezed in liquid nitrogen, and ground into powder with liquid nitrogen using a mortar and pestle.

tag: Soybean cv. Asgrow A3237


title: Laser capture microdissected (LCM) outer integument at the heart stage, biological replicate 2

description: Outer integument regions from heart stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage outer integument captured by LCM

extract_protocol: Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Pods with lengths between 1.3 and 2.0 cm containing seeds with heart-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from eight-micron sections using a Leica AS LMD System.


title: Whole Seed at the heart stage, biological replicate 2


title: Laser capture microdissected (LCM) inner integument at the heart stage, biological replicate 1

description: Inner integument regions from heart stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage inner integument captured by LCM


title: Reovirus MyRV2-CpC18 infection (Sample B)

source_name: Reovirus MyRV2-CpC18 infected strain EP155

treatment_protocol: Rovirus MyRV2-CpC18 infection

tag: Rovirus MyRV2-CpC18 infected strain EP155 grown on PDA with cellophane overlay (sample B).

source_name: Wild type strain EP155

tag: Wild type strain EP155 grown on PDA with cellophane overlay (sample B).


title: Laser capture microdissected (LCM) outer integument at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) epidermis at the heart stage, biological replicate 2

description: Epidermis regions from heart stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage epidermis captured by LCM


title: Reovirus MyRV2-CpC18 infection (sample A)

tag: Rovirus MyRV2-CpC18 infected strain EP155 grown on PDA with cellophane overlay (sample A).

tag: Wild type strain EP155 grown on PDA with cellophane overlay (sample A).


title: Laser capture microdissected (LCM) inner integument at the heart stage, biological replicate 2


title: Laser capture microdissected (LCM) endothelium at the heart stage, biological replicate 2

description: Endothelium regions from heart stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage endothelium captured by LCM


title: Laser capture microdissected (LCM) hilum at the heart stage, biological replicate 2

description: Hilum regions from heart stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage hilum captured by LCM


title: Laser capture microdissected (LCM) epidermis at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) hilum at the heart stage, biological replicate 1


title: Reovirus MyRV1-Cp9B21 infection (sample A, dye-swab)

source_name: Wild type strain EP155 infected with reovirus MyRV1-Cp9B21

treatment_protocol: Reovirus  MyRV1-Cp9B21 infection

tag: Reovirus MyRV1-Cp9B21 infected strain EP155 grown on PDA with cellophane overlay(sample A).


title: Reovirus MyRV1-Cp9B21 infection (sample B)

source_name: Reovirus MyRV1-Cp9B21 infectied strain EP155

treatment_protocol: Reovirus MyRV1-Cp9B21 infection

tag: Reovirus MyRV1-Cp9B21 infected strain EP155 grown on PDA with cellophane overlay(sample B).

source_name: Wild type strain EEP155

tag: Wild type strain EEP155 grown on PDA with cellophane overlay(sample B).


title: Reovirus MyRV1-Cp9B21 infection (sample B, dye-swab)

treatment_protocol: Wild type strain EP155

tag: Reovirus MyRV1-Cp9B21 infected strain EP155 grown on PDA with cellophane overlay (sample B).


title: Reovirus MyRV1-Cp9B21 infection (sample A)

treatment_protocol: Rovirus MyRV1-Cp9B21 infection

tag: Rovirus MyRV1-Cp9B21 infected strain EP155 grown on PDA with cellophane overlay (sample A).


title: Laser capture microdissected (LCM) suspensor at the heart stage, biological replicate 2

description: Suspensor regions from heart embryos were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage suspensor captured by LCM


title: Laser capture microdissected (LCM) endosperm at the heart stage, biological replicate 2

description: Endosperm regions from heart stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage endosperm captured by LCM


title: Laser capture microdissected (LCM) endosperm at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) embryo proper at the heart stage, biological replicate 2

description: Embryo proper regions from heart embryos were microdissected using the LEICA AS LMD system.

source_name: Soybean heart stage embryo proper captured by LCM


title: Laser capture microdissected (LCM) embryo proper at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) suspensor at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) suspensor at the heart stage, biological replicate 3


title: Laser capture microdissected (LCM) endothelium at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) embryo proper at the heart stage, biological replicate 3


title: OAF3 IP O vs OAF3 WCE O 04050F1

status: Public on Apr 19 2007

city: Seattle

first: Jennifer

middle: Joy

last: Smith

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

description: OAF3_WCE_vs_OAF3_IP; 0.15% oleate; slide 04050F; SR8190

scan_protocol: Fluorescent array images were collected at two PMT settings for both Cy3 and Cy5 with a PerkinElmer ScanArray 5000 fluorescent scanner, to yield high and low intensity images per each fluorophore. Image intensity data were extracted and analyzed with MolecularWare AnalyzerDG analysis software.

data_processing: Raw spot intensities were integrated between high and low intensity scans, followed by background subtraction and median normalization between the Cy3 and Cy5 channels.

organism: Saccharomyces cerevisiae

label_protocol: Sheared genomic DNA was labelled by PCR amplification as described (Ren et al., Genome-wide location and function of DNA binding proteins. Science. 2000 Dec 22; 290(5500):2306-9; Lee et al., Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25; 298(5594):799-804).

growth_protocol: An overnight YPD culture from a single colony was diluted to ~5x10E3 cells/mL in 150 mL of SCIM medium without oleate (1.7g yeast nitrogen base without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g complete supplement mixture/L, 5 g ammonium sulfate/L and 0.1% glucose (but not oleate or Tween40)) in a 500 mL bevelled flask and grown at 30 deg C with 180 rpm rotation for 16 h to a density of ~5x10E6 cells/mL.  Cells were pelleted and transferred to fresh SCIM medium without glucose and with oleate and Tween 40 (oleate and Tween 40 were premixed and added to final concentrations of 0.15% and 0.5% (w/v) after autoclaving, respectively) and grown for an additional 5 h under the same conditions to a density of ~1.5x10E7 cells/mL.

extract_protocol: sheared genomic DNA isolation and IP were done as previously described (Ren et al., Genome-wide location and function of DNA binding proteins. Science. 2000 Dec 22; 290(5500):2306-9; Lee et al., Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25; 298(5594):799-804). Fixing was for 20 min at RT and then for 16 h at 4 deg C in 1% formaldehyde.

tag: Total genomic DNA of strain with DNA encoding myc-tag genomically integrated in frame and downstream of OAF3(YKR064W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H50 clone 3.

tag: Genomic DNA immunoprecipitated with antibodies to myc-tag from strain with DNA encoding myc-tag genomically integrated in frame and downstream of OAF3(YKR064W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H50 clone 3.


title: OAF3 IP O vs OAF3 WCE O 04038F1

description: OAF3_WCE_vs_OAF3_IP; 0.15% oleate; slide 04038F; SR8103

growth_protocol: An overnight YPD culture from a single colony was diluted to ~5x10E3 cells/mL in 150 mL of SCIM medium without oleate (1.7g yeast nitrogen base without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g complete supplement mixture/L, 5 g ammonium sulfate/L and 0.1% glucose (but not oleate or Tween40)) in a 500 mL bevelled flask and grown at 30 deg C with 180 rpm rotation for 16 h to a density of ~5x10E6 cells/mL.  Cells were pelleted and transferred to fresh SCIM medium without glucose and with oleate and Tween 40 (oleate and Tween 40 were premixed and added to final concentrations of 0.15% and 0.5% (w/v) after autoclaving, respectively) and grown for an additional 5 h under the same conditions to a density of ~1.5x10E7 cells/mL


title: Developmentally regulated piRNA clusters implicate MILI in transposon control

type: MPSS

city: Cold spring Harbor

first: ravi

last: Sachidanandam

state: NY

address: 1 bungtown road

institute: Cold Spring Harbor Laboratory

description: piRNAs from testes  of 10-day old mice obtained by immunoprecipitation of Mili RNP complexes

data_processing:
adaptor sequences were stripped off by using exact matches to 10 bp
ends of the 5' and 3' adaptors. These were also used to identify the
orientation of the smallRNAs.

source_name: testes from 10-day old CD-1 mice

extract_protocol: Mili RNP complexes were immunoprecipitated from testes extract of 10 day old CD-1 mice using polyclonal antibodies against two MILI peptides (MILI-N, amino acids 2-18 and MILI-N2, amino acids 107-122).   Immunoprecipitation of MILI RNP complexes and RNA isolation was performed as described in A. Aravin et al., Nature 442, 203 (2006). Two cDNA libraries were created and sequenced separately.  After preliminary analysis, sequences were pooled. Small RNA cloning and 454 sequencing of small cDNA libraries were performed as described in J. Brennecke et al., Cell 128, 1089 (2007).

tag: Strain:CD-1,tissue:testes,Age:10 days


title: OAF1 IP O vs OAF1 WCE O 04020F1

description: OAF1_WCE_vs_OAF1_IP; 0.15% oleate; slide 04020F; SR8099

tag: Total genomic DNA of strain with DNA encoding myc-tag genomically integrated in frame and downstream of OAF1(YAL051W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H55B clone 9.

tag: Genomic DNA immunoprecipitated with antibodies to myc-tag from strain with DNA encoding myc-tag genomically integrated in frame and downstream of OAF1(YAL051W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H55B clone 9.


title: ADR1 IP O vs ADR1 WCE O 04021F1

description: ADR1_WCE_vs_ADR1_IP; 0.15% oleate; slide 04021F; SR8102

tag: Total genomic DNA of strain with DNA encoding myc-tag genomically integrated in frame and downstream of ADR1(YDR216W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H52 clone 4.

tag: Genomic DNA immunoprecipitated with antibodies to myc-tag from strain with DNA encoding myc-tag genomically integrated in frame and downstream of ADR1(YDR216W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H52 clone 4.


title: 117T

description: Gene expression data from human colon tumor tissue

source_name: 117T Human colon tumor tissue sample

tag: tissue


title: ADR1 IP D vs ADR1 WCE D 04984F1

description: ADR1_WCE_vs_ADR1_IP; 0.1% glucose; slide 04984F; SR8957

growth_protocol: An overnight YPD culture from a single colony was diluted to ~5x10E3 cells/mL in 150 mL of SCIM medium without oleate (1.7g yeast nitrogen base without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g complete supplement mixture/L, 5 g ammonium sulfate/L and 0.1% glucose (but not oleate or Tween40)) in a 500 mL bevelled flask and grown at 30 deg C with 180 rpm rotation for 16 h to a density of ~5x10E6 cells/mL.  Cells were pelleted and transferred to fresh SCIM medium (without oleate or Tween 40) and grown for an additional 5 h under the same conditions to a density of ~1.5x10E7 cells/mL.


title: tao1-D168A-DN_pole-cell_1G

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

description: Germ-line transcriptome of tao-1(D168A;dominant-negative form) expressing flies.

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/5-screw Hyb Chamber). See manufacturer's manual (#G4140-90010).

scan_protocol: Scanned using Agilent microarray scanner (G2565BA).

data_processing: Data were extracted with Agilent Feature Extraction 7.1 Software.

organism: Drosophila melanogaster

source_name: Tao1D168A-Drive: tao-1 dominant negative form (drived by nos-GAL4), pole cells from fly embryos (stage 8-14)

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol. 100ng of total RNA was used.

extract_protocol: We used FACS to isolate pole cells from transgenic Drosophila embryos harboring the germ-line marker EGFP-Vas.

tag: A RNA sample "Tao1D168A-Drive" was prepared from pole cells isolated from stage 8-14 fly embryos, which were derived from nosGal4:VP16/nosGal4:VP16 females mated with UAS-tao-1(D168A);EGFP-Vas males. In this line, the expression of the dominant-negative form of tao-1 is induced in a germline-specific manner.

source_name: Tao1D168A-Ctrl: tao-1 dominant negative form (non-drived), pole cells from fly embryos (stage 8-14)

tag: A RNA sample "Tao1D168A-Ctrl" was prepared from pole cells isolated from stage 8-14 fly embryos, which were derived from yw females mated with UAS-tao-1(D168A);EGFP-Vas male.


title: 109T

source_name: 109T Human colon tumor tissue sample


title: ADR1 IP O vs ADR1 WCE O 04806F1

description: ADR1_WCE_vs_ADR1_IP; 0.15% oleate; slide 04806F; SR8652


title: ADR1 IP D vs ADR1 WCE D 04983F1

description: ADR1_WCE_vs_ADR1_IP; 0.1% glucose; slide 04983F; SR8956


title: ADR1 IP D vs ADR1 WCE D 04985F1

description: ADR1_WCE_vs_ADR1_IP; 0.1% glucose; slide 04985F; SR8958


title: tao1-gof_pole-cell_1G

description: Germ-line transcriptome of tao-1 overexpressing flies.

source_name: Tao1D168D-Drive: tao-1 (drived by nos-GAL4), pole cells from fly embryos (stage 8-14)

tag: A RNA sample "Tao1D168D-Drive" was prepared from pole cells isolated from stage 8-14 fly embryos, which were derived from nosGal4:VP16/nosGal4:VP16 females mated with UAS-tao-1(D168D);EGFP-Vas males. In this line,  wild-type of tao-1 is overexpressed in a germline-specific manner.

source_name: Tao1D168D-Ctrl: tao-1 (non-drived), pole cells from fly embryos (stage 8-14)

tag: A RNA sample "Tao1D168D-Ctrl" was prepared from pole cells isolated from stage 8-14 fly embryos, which were derived from yw females mated with UAS-tao-1(D168D);EGFP-Vas males.


title: OAF1 IP D vs OAF1 WCE D 04482F1

description: OAF1_WCE_vs_OAF1_IP; 0.1% glucose; slide 04482F; SR8370


title: OAF1 IP O vs OAF1 WCE O 04017F1

description: OAF1_WCE_vs_OAF1_IP; 0.15% oleate; slide 04017F; SR7984


title: OAF1 IP D vs OAF1 WCE D 04483F1

description: OAF1_WCE_vs_OAF1_IP; 0.1% glucose; slide 04483F; SR8371


title: OAF3 IP D vs OAF3 WCE D 04493F1

description: OAF3_WCE_vs_OAF3_IP; 0.1% glucose; slide 04493F; SR8467


title: OAF1 IP D vs OAF1 WCE D 04496F1

description: OAF1_WCE_vs_OAF1_IP; 0.1% glucose; slide 04496F; SR8465


title: OAF3 IP D vs OAF3 WCE D 04492F1

description: OAF3_WCE_vs_OAF3_IP; 0.1% glucose; slide 04492F; SR8466


title: ADR1 IP O vs ADR1 WCE O 04805F1

description: ADR1_WCE_vs_ADR1_IP; 0.15% oleate; slide 04805F; SR8651


title: delta PIP2 vs WT 04148R 1

description: delta_ADR1_5h_oleate_vs_WT_5h_oleate_(slide_04148R; SR8430)

molecule: polyA RNA

label_protocol: 4 micrograms of Poly A+ RNA were added to 1 microgram Oligo dT(12-18), 6 micrograms of random 6-9-mers in 20 microlitres of DEPC water and heated at 70 deg C for 10 min, chilled on ice 1 min, pelleted and placed at room temperature.  mRNA was reverse-transcribed into cDNA with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) for 2-3 h at 42 deg C in the presence of 0.5 mM dGTP, 0.5 mM dTTP 0.5 mM dATP, 0.05 mM dCTP, and 0.1 mM Cy3 or Cy5-dCTP according to manufacturers instructions. EDTA was added to 20 mM and RNA was subsequently hydrolyzed by the addition of 0.25 M NaOH (10 min at 70 degrees C) and the solution was quenched with 0.25 M HCl. 10 microlitres of 0.5 M tris pH 7.0 was added and labelled cDNA was purified using QIAquick PCR purification kit (Qiagen, Valencia, CA). Incorporated fluorescence was quantified by spectrophotometry and 40 pmol of each dye were hybridized to each array in DIG easy hyb (Roche, Alamedia, CA) at 37 deg C for 16 h.

growth_protocol: An overnight YPD culture from a single colony was diluted to ~5x10E3 cells/mL in 150 mL of SCIM medium without oleate (1.7g yeast nitrogen base without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g complete supplement mixture/L, 5 g ammonium sulfate/L and 0.1% glucose (but not oleate or Tween40)) in a 500 mL bevelled flask and grown at 30 deg C with 180 rpm rotation to a density of ~5x10E6 cells/mL.  Oleate and Tween 40 were premixed and added to final concentrations of 0.15% and 0.5% (w/v), respectively, and the culture was grown for an additional 5 h under the same conditions to a density of ~1.5x10E7 cells/mL.  Cells were pelleted and frozen in liquid nitrogen and stored at -80 deg C.

extract_protocol: Total RNA was isolated by hot acid phenol extraction.  Poly A+ RNA was isolated from total RNA using poly (A) Pure mRNA Purification Kit (Ambion (Austin, TX); Catalogue number 1915) and resuspended in Rnase free water.

tag: delta_PIP2(YOR363C) in BY4742 background Invitrogen (Carlsbad, CA); plate location 107C1; record number 11660; Lab id jjs_H39

source_name: WT

tag: Wild-type_BY4742; Lab id jjs_H75


title: WT vs WT 05705F1

description: WT_5h_oleate_vs_WT_5h_oleate_(slide_05705F; SR7132)


title: tao1-D168A-DN_pole-cell_1R


title: tao1-gof_pole-cell_1R

tag: A RNA sample "Tao1D168D-Drive" was prepared from pole cells isolated from stage 8-14 fly embryos, which were derived from nosGal4:VP16/nosGal4:VP16 females mated with UAS-tao-1(D168D);EGFP-Vas males. In this line, wild-type of tao-1 is overexpressed in a germline-specific manner.


title: PIP2 IP O vs PIP2 WCE O 03705F1

description: PIP2_WCE_vs_PIP2_IP; 0.15% oleate; slide 03705F; SR7874

tag: Total genomic DNA of strain with DNA encoding myc-tag genomically integrated in frame and downstream of PIP2(YOR363C) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H47 clone 6c.

tag: Genomic DNA immunoprecipitated with antibodies to myc-tag from strain with DNA encoding myc-tag genomically integrated in frame and downstream of PIP2(YOR363C) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H47 clone 6c.


title: OAF3 IP O vs OAF3 WCE O 03715F1

description: OAF3_WCE_vs_OAF3_IP; 0.15% oleate; slide 03715F; SR7922

tag: Total genomic DNA of strain with DNA encoding myc-tag genomically integrated in frame and downstream of OAF3(YKR064W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H50 clone 3.


title: PIP2 IP O vs PIP2 WCE O 03708F1

description: PIP2_WCE_vs_PIP2_IP; 0.15% oleate; slide 03708F; SR7899


title: PIP2 IP D vs PIP2 WCE D 03706F1

description: PIP2_WCE_vs_PIP2_IP; 0.1% glucose; slide 03706F; SR7875


title: oleate vs low glucose 5h 05693R 1

description: WT_low_glucose_vs_WT_oleate_5h(slide_05693R; SR10038)

tag: wild-type BY4742 background; Lab id jjs_H75

growth_protocol: An overnight YPD culture from a single colony was diluted to ~5x10E3 cells/mL in 150 mL of SCIM medium without oleate (1.7g yeast nitrogen base without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g complete supplement mixture/L, 5 g ammonium sulfate/L and 0.1% glucose (but not oleate or Tween40)) in a 500 mL bevelled flask and grown at 30 deg C with 180 rpm rotation to a density of ~5x10E6 cells/mL.  Cells were pelleted and frozen in liquid nitrogen and stored at -80 deg C.


title: OAF1 IP O vs OAF1 WCE O 04485F1

description: OAF1_WCE_vs_OAF1_IP; 0.15% oleate; slide 04485F; SR8373


title: delta ADR1 vs WT 03586R 1

description: WT_5h_oleate_vs_delta_ADR1_5h_oleate_(slide_03586R; SR8428)

tag: delta_ADR1(YDR216W) in BY4742 background Invitrogen (Carlsbad, CA); plate location 121B4; record number 13575; Lab id jjs_H33


title: oleate vs low glucose 5h 03399R 1

description: WT_low_glucose_vs_WT_oleate_5h(slide_03399R; SR7813)


title: PIP2 IP D vs PIP2 WCE D 03700F1

description: PIP2_WCE_vs_PIP2_IP; 0.1% glucose; slide 03700F; SR7842


title: PIP2 IP O vs PIP2 WCE O 03704F1

description: PIP2_WCE_vs_PIP2_IP; 0.15% oleate; slide 03704F; SR7873


title: WT vs WT 02805R 1

description: WT_5h_oleate_vs_WT_5h_oleate_(slide_02805R; SR7356)


title: deltaADR1 vs WT 03584F1

description: WT_5h_oleate_vs_delta_ADR1_5h_oleate_(slide_03584F; SR8429)


title: deltaPIP2 vs WT 04146F1

description: delta_PIP2_5h_oleate_vs_WT_5h_oleate_(slide_04146F; SR8431)


title: OAF3 IP D vs OAF3 WCE D 03718F1

description: OAF3_WCE_vs_OAF3_IP; 0.1% glucose; slide 03718F; SR7929

tag: Genomic DNA immunoprecipitated with antibodies to myc-tag from strain with DNA encoding myc-tag genomically integrated in frame and downstream of OAF3(YKR064W) in BY4742 background; myc tag encodes 13 copies of the c-myc epitope from pFA6-13MYC (Longtine et al., 1998); Lab id jjs_H50 clone 3.


title: PIP2 IP D vs PIP2 WCE D 03709F1

description: PIP2_WCE_vs_PIP2_IP; 0.1% glucose; slide 03709F; SR7900


title: deltaOAF1 vs WT 04886F1

description: delta_OAF1_5h_oleate_vs_WT_5h_oleate_(slide_04886F; SR8997)

tag: Wild-type_BY4742_METminus; Lab id jjs_H36

tag: delta_OAF1(YAL051W) in BY4742_METminus background; Lab id jjs_H37


title: deltaYKR064W vs WT 03576F1

description: delta_YKR064W_5h_oleate_vs_WT_5h_oleate_(slide_03576F; SR7955)

tag: delta_YKR064W in BY4742 background Invitrogen (Carlsbad, CA); plate location 128B3 record number 15135; Lab id jjs_H35


title: delta OAF1  vs WT 03316R 1

description: delta_OAF1_5h_oleate_vs_WT_5h_oleate_(slide_03316R; SR7641)

tag: Wild Wild-type_BY4742_METminus; Lab id jjs_H36


title: deltaPIP2 vs WT 02663F1

description: delta_PIP2_5h_oleate_vs_WT_5h_oleate_(slide_02663F; SR7129)


title: delta ADR1 vs WT 02659R 1

description: WT_5h_oleate_vs_delta_ADR1_5h_oleate_(slide_02659R; SR7132)


title: deltaYKR064W vs WT 05118F1

description: delta_YKR064W_5h_oleate_vs_WT_5h_oleate_(slide_05118F; SR8940)


title: oleate 5h vs low glucose 03398F1

description: WT_low_glucose_vs_WT_oleate_5h(slide_03398F; SR7812)


title: WT vs WT 02804F1

description: WT_5h_oleate_vs_WT_5h_oleate_(slide_02804F; SR7355)


title: delta OAF1  vs WT 05698R 1

description: delta_OAF1_5h_oleate_vs_WT_5h_oleate_(slide_05698R; SR10035)


title: oleate 5h vs low glucose 05699F1

description: WT_low_glucose_vs_WT_oleate_5h(slide_05699F; SR10037)


title: deltaADR1 vs WT 03556F1

description: WT_5h_oleate_vs_delta_ADR1_5h_(slide_03556F; SR7825)


title: delta YKR064W vs WT 05117R 1

description: delta_YKR064W_5h_oleate_vs_WT_5h_oleate_(slide_05117R; SR8939)

tag: delta_YKR064W in BY4742 background; Invitrogen (Carlsbad, CA); plate location 128B3 record number 15135; Lab id jjs_H35


title: delta PIP2  vs WT 02658R 1

description: delta_PIP2_5h_oleate_vs_WT_5h_oleate_(slide_02658R; SR7131)


title: delta YKR064W vs WT 03577R 1

description: delta_YKR064W_5h_oleate_vs_WT_5h_oleate_(slide_03577R; SR7954)


title: Blood_Control4_3_5_R1

status: Public on Apr 18 2007

city: San Francisco

first: Sergio

last: Baranzini

address: 513 Parnassus Ave

department: Neurology

institute: University of California San Francisco

description: Control4 time 3_5 replicate 1

data_processing: Lowess normalized ratios as calculated by BRB array Tools Software (NIH)

source_name: Individual Control4, Time 3_5, Replicate 1.

tag: Gender

value: Male; IFN injected:

source_name: Common reference RNA pool

tag: RNA from brain and PBMC (equal amounts)


title: deltaOAF1 vs WT 03322F1

description: delta_OAF1_5h_oleate_vs_WT_5h_oleate_(slide_03322F; SR7638)


title: Blood_Control4_6_25_R3

description: Control4 time 6_25 replicate 3

source_name: Individual Control4, Time 6_25, Replicate 3.


title: Blood_Control4_9_5_R3

description: Control4 time 9_5 replicate 3

source_name: Individual Control4, Time 9_5, Replicate 3.


title: Blood_Control4_49_R3

description: Control4 time 49 replicate 3

source_name: Control. Individual Control4, Time 49, Replicate 3.

value: Male; IFN injected:NO


title: WT vs WT 04878R 1

description: WT_5h_oleate_vs_WT_5h_oleate_(slide_04878R)


title: Blood_Control4_9_5_R2

description: Control4 time 9_5 replicate 2

source_name: Individual Control4, Time 9_5, Replicate 2.


title: Blood_Control4_49_R2

description: Control4 time 49 replicate 2

source_name: Control. Individual Control4, Time 49, Replicate 2.


title: Blood_Control4_6_25_R1

description: Control4 time 6_25 replicate 1

source_name: Individual Control4, Time 6_25, Replicate 1.


title: Blood_Control4_3_5_R2

description: Control4 time 3_5 replicate 2

source_name: Individual Control4, Time 3_5, Replicate 2.


title: Blood_Control4_25_R3

description: Control4 time 25 replicate 3

source_name: Control. Individual Control4, Time 25, Replicate 3.


title: Blood_Control4_25_R2

description: Control4 time 25 replicate 2

source_name: Control. Individual Control4, Time 25, Replicate 2.


title: Blood_Control4_9_5_R1

description: Control4 time 9_5 replicate 1

source_name: Individual Control4, Time 9_5, Replicate 1.


title: Blood_Control4_25_R1

description: Control4 time 25 replicate 1

source_name: Control. Individual Control4, Time 25, Replicate 1.


title: Blood_Control4_6_25_R2

description: Control4 time 6_25 replicate 2

source_name: Individual Control4, Time 6_25, Replicate 2.


title: Blood_Control4_49_R1

description: Control4 time 49 replicate 1

source_name: Control. Individual Control4, Time 49, Replicate 1.


title: Blood_Control4_156_R3

description: Control4 time 156 replicate 3

source_name: Control. Individual Control4, Time 156, Replicate 3.


title: Blood_Control4_16_5_R3

description: Control4 time 16_5 replicate 3

source_name: Individual Control4, Time 16_5, Replicate 3.


title: Blood_Control4_16_5_R2

description: Control4 time 16_5 replicate 2

source_name: Individual Control4, Time 16_5, Replicate 2.


title: Blood_Control4_3_5_R3

description: Control4 time 3_5 replicate 3

source_name: Individual Control4, Time 3_5, Replicate 3.

source_name: Common reference RNA pool


title: Blood_Control4_156_R2

description: Control4 time 156 replicate 2

source_name: Control. Individual Control4, Time 156, Replicate 2.


title: Blood_Control4_156_R1

description: Control4 time 156 replicate 1

source_name: Control. Individual Control4, Time 156, Replicate 1.


title: Blood_Control4_11_5_R3

description: Control4 time 11_5 replicate 3

source_name: Individual Control4, Time 11_5, Replicate 3.


title: Blood_Control4_0_R3

description: Control4 time 0 replicate 3

source_name: Control. Individual Control4, Time 0, Replicate 3.


title: Blood_Control4_11_5_R1

description: Control4 time 11_5 replicate 1

source_name: Individual Control4, Time 11_5, Replicate 1.


title: Blood_Control4_0_R2

description: Control4 time 0 replicate 2

source_name: Control. Individual Control4, Time 0, Replicate 2.


title: Blood_Patient2_7_25_R3

description: Patient2 time 7_25 replicate 3

source_name: Individual Patient2, Time 7_25, Replicate 3.


title: Blood_Patient2_33_R2

description: Patient2 time 33 replicate 2

source_name: IFN injected. Individual Patient2, Time 33, Replicate 2.

value: Male; IFN injected:YES


title: Blood_Patient2_7_25_R1

description: Patient2 time 7_25 replicate 1

source_name: Individual Patient2, Time 7_25, Replicate 1.


title: Blood_Patient2_156_R2

description: Patient2 time 156 replicate 2

source_name: IFN injected. Individual Patient2, Time 156, Replicate 2.


title: Blood_Patient2_156_R3

description: Patient2 time 156 replicate 3

source_name: IFN injected. Individual Patient2, Time 156, Replicate 3.


title: Blood_Patient2_33_R1

description: Patient2 time 33 replicate 1

source_name: IFN injected. Individual Patient2, Time 33, Replicate 1.


title: Blood_Patient2_7_25_R2

description: Patient2 time 7_25 replicate 2

source_name: Individual Patient2, Time 7_25, Replicate 2.


title: Blood_Patient2_15_5_R1

description: Patient2 time 15_5 replicate 1

source_name: Individual Patient2, Time 15_5, Replicate 1.


title: Blood_Patient2_15_5_R2

description: Patient2 time 15_5 replicate 2

source_name: Individual Patient2, Time 15_5, Replicate 2.


title: Blood_Patient2_33_R3

description: Patient2 time 33 replicate 3

source_name: IFN injected. Individual Patient2, Time 33, Replicate 3.


title: Blood_Patient2_10_25_R3

description: Patient2 time 10_25 replicate 3

source_name: Individual Patient2, Time 10_25, Replicate 3.

source_name: Common reference RNA pool


title: Blood_Patient2_13_R2

description: Patient2 time 13 replicate 2

source_name: IFN injected. Individual Patient2, Time 13, Replicate 2.


title: Blood_Patient2_10_25_R2

description: Patient2 time 10_25 replicate 2

source_name: Individual Patient2, Time 10_25, Replicate 2.


title: Blood_Patient2_15_5_R3

description: Patient2 time 15_5 replicate 3

source_name: Individual Patient2, Time 15_5, Replicate 3.


title: Blood_Patient2_156_R1

description: Patient2 time 156 replicate 1

source_name: IFN injected. Individual Patient2, Time 156, Replicate 1.


title: Blood_Patient2_13_R3

description: Patient2 time 13 replicate 3

source_name: IFN injected. Individual Patient2, Time 13, Replicate 3.


title: Blood_Control4_16_5_R1

description: Control4 time 16_5 replicate 1

source_name: Individual Control4, Time 16_5, Replicate 1.


title: Blood_Patient2_13_R1

description: Patient2 time 13 replicate 1

source_name: IFN injected. Individual Patient2, Time 13, Replicate 1.


title: Blood_Control4_11_5_R2

description: Control4 time 11_5 replicate 2

source_name: Individual Control4, Time 11_5, Replicate 2.


title: Blood_Patient2_10_25_R1

description: Patient2 time 10_25 replicate 1

source_name: Individual Patient2, Time 10_25, Replicate 1.


title: Blood_Control3_7_25_R3

description: Control3 time 7_25 replicate 3

source_name: Individual Control3, Time 7_25, Replicate 3.


title: Blood_Control3_7_25_R2

description: Control3 time 7_25 replicate 2

source_name: Individual Control3, Time 7_25, Replicate 2.


title: Blood_Control4_0_R1

description: Control4 time 0 replicate 1

source_name: Control. Individual Control4, Time 0, Replicate 1.


title: Blood_Control3_33_R3

description: Control3 time 33 replicate 3

source_name: Control. Individual Control3, Time 33, Replicate 3.


title: Blood_Control3_33_R2

description: Control3 time 33 replicate 2

source_name: Control. Individual Control3, Time 33, Replicate 2.


title: Blood_Control3_33_R1

description: Control3 time 33 replicate 1

source_name: Control. Individual Control3, Time 33, Replicate 1.


title: Blood_Control3_7_25_R1

description: Control3 time 7_25 replicate 1

source_name: Individual Control3, Time 7_25, Replicate 1.


title: Blood_Control3_15_5_R1

description: Control3 time 15_5 replicate 1

source_name: Individual Control3, Time 15_5, Replicate 1.

source_name: Common reference RNA pool


title: Blood_Control3_156_R2

description: Control3 time 156 replicate 2

source_name: Control. Individual Control3, Time 156, Replicate 2.


title: Blood_Control3_156_R3

description: Control3 time 156 replicate 3

source_name: Control. Individual Control3, Time 156, Replicate 3.


title: Blood_Control3_15_5_R3

description: Control3 time 15_5 replicate 3

source_name: Individual Control3, Time 15_5, Replicate 3.


title: Blood_Control3_13_R1

description: Control3 time 13 replicate 1

source_name: Control. Individual Control3, Time 13, Replicate 1.


title: Blood_Control3_10_25_R3

description: Control3 time 10_25 replicate 3

source_name: Individual Control3, Time 10_25, Replicate 3.


title: Blood_Control2_156_R2

description: Control2 time 156 replicate 2

source_name: Control. Individual Control2, Time 156, Replicate 2.


title: Blood_Control3_156_R1

description: Control3 time 156 replicate 1

source_name: Control. Individual Control3, Time 156, Replicate 1.


title: Blood_Control2_7_25_R3

description: Control2 time 7_25 replicate 3

source_name: Individual Control2, Time 7_25, Replicate 3.


title: Blood_Control3_15_5_R2

description: Control3 time 15_5 replicate 2

source_name: Individual Control3, Time 15_5, Replicate 2.


title: Blood_Control3_10_25_R1

description: Control3 time 10_25 replicate 1

source_name: Individual Control3, Time 10_25, Replicate 1.


title: Blood_Control2_33_R1

description: Control2 time 33 replicate 1

source_name: Control. Individual Control2, Time 33, Replicate 1.


title: Blood_Control3_10_25_R2

description: Control3 time 10_25 replicate 2

source_name: Individual Control3, Time 10_25, Replicate 2.


title: Blood_Control2_7_25_R2

description: Control2 time 7_25 replicate 2

source_name: Individual Control2, Time 7_25, Replicate 2.


title: Blood_Control2_156_R3

description: Control2 time 156 replicate 3

source_name: Control. Individual Control2, Time 156, Replicate 3.


title: Blood_Control2_33_R2

description: Control2 time 33 replicate 2

source_name: Control. Individual Control2, Time 33, Replicate 2.


title: Blood_Control2_15_5_R1

description: Control2 time 15_5 replicate 1

source_name: Individual Control2, Time 15_5, Replicate 1.


title: Blood_Control2_33_R3

description: Control2 time 33 replicate 3

source_name: Control. Individual Control2, Time 33, Replicate 3.

source_name: Common reference RNA pool


title: Blood_Control2_15_5_R3

description: Control2 time 15_5 replicate 3

source_name: Individual Control2, Time 15_5, Replicate 3.


title: Blood_Control2_15_5_R2

description: Control2 time 15_5 replicate 2

source_name: Individual Control2, Time 15_5, Replicate 2.


title: Blood_Control2_13_R2

description: Control2 time 13 replicate 2

source_name: Control. Individual Control2, Time 13, Replicate 2.


title: Blood_Control2_156_R1

description: Control2 time 156 replicate 1

source_name: Control. Individual Control2, Time 156, Replicate 1.


title: Blood_Control2_13_R1

description: Control2 time 13 replicate 1

source_name: Control. Individual Control2, Time 13, Replicate 1.


title: Blood_Control2_10_25_R3

description: Control2 time 10_25 replicate 3

source_name: Individual Control2, Time 10_25, Replicate 3.


title: Blood_Control2_7_25_R1

description: Control2 time 7_25 replicate 1

source_name: Individual Control2, Time 7_25, Replicate 1.


title: Blood_Control2_10_25_R1

description: Control2 time 10_25 replicate 1

source_name: Individual Control2, Time 10_25, Replicate 1.


title: Blood_Control2_13_R3

description: Control2 time 13 replicate 3

source_name: Control. Individual Control2, Time 13, Replicate 3.


title: Blood_Control2_10_25_R2

description: Control2 time 10_25 replicate 2

source_name: Individual Control2, Time 10_25, Replicate 2.


title: Blood_Control1_9_5_R2

description: Control1 time 9_5 replicate 2

source_name: Individual Control1, Time 9_5, Replicate 2.


title: Blood_Control1_6_25_R2

description: Control1 time 6_25 replicate 2

source_name: Individual Control1, Time 6_25, Replicate 2.


title: Blood_Control1_6_25_R1

description: Control1 time 6_25 replicate 1

source_name: Individual Control1, Time 6_25, Replicate 1.


title: Blood_Control1_6_25_R3

description: Control1 time 6_25 replicate 3

source_name: Individual Control1, Time 6_25, Replicate 3.


title: Blood_Control1_49_R3

description: Control1 time 49 replicate 3

source_name: Control. Individual Control1, Time 49, Replicate 3.


title: Blood_Control1_49_R1

description: Control1 time 49 replicate 1

source_name: Control. Individual Control1, Time 49, Replicate 1.


title: Blood_Control1_3_5_R3

description: Control1 time 3_5 replicate 3

source_name: Individual Control1, Time 3_5, Replicate 3.

source_name: Common reference RNA pool


title: Blood_Control1_25_R2

description: Control1 time 25 replicate 2

source_name: Control. Individual Control1, Time 25, Replicate 2.


title: Blood_Control1_49_R2

description: Control1 time 49 replicate 2

source_name: Control. Individual Control1, Time 49, Replicate 2.


title: Blood_Control1_9_5_R3

description: Control1 time 9_5 replicate 3

source_name: Individual Control1, Time 9_5, Replicate 3.


title: Blood_Control1_9_5_R1

description: Control1 time 9_5 replicate 1

source_name: Individual Control1, Time 9_5, Replicate 1.


title: Blood_Control1_3_5_R2

description: Control1 time 3_5 replicate 2

source_name: Individual Control1, Time 3_5, Replicate 2.


title: Blood_Control1_16_5_R2

description: Control1 time 16_5 replicate 2

source_name: Individual Control1, Time 16_5, Replicate 2.


title: Blood_Control1_25_R3

description: Control1 time 25 replicate 3

source_name: Control. Individual Control1, Time 25, Replicate 3.


title: Blood_Control1_3_5_R1

description: Control1 time 3_5 replicate 1

source_name: Individual Control1, Time 3_5, Replicate 1.


title: Blood_Control1_16_5_R3

description: Control1 time 16_5 replicate 3

source_name: Individual Control1, Time 16_5, Replicate 3.


title: Blood_Control1_11_5_R3

description: Control1 time 11_5 replicate 3

source_name: Individual Control1, Time 11_5, Replicate 3.


title: Oct4 knockdown R1 ES cells 1 of 2

city: Toronto

first: Emily

last: Walker

state: ON

address: 164 College Street Room 407

department: Institute for Biomaterials and Biomedical Engineering

country: Canada

institute: University of Toronto

description: ES cells were cultured under normal ES cell culture condition and density.

hyb_protocol: Mixed labeled cDNAs were added to hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate (MES), pH 6.5, 33% formamide and 40 μg herring sperm DNA (Invitrogen, Carlsbad, USA). Hybridizations were carried out in a final volume of 0.5 ml injecting into an Agilent hybridization chamber at 42°C on a rotating platform in a hybridization oven (Robbins Scientific Corporation, Sunnyvale, USA) for 16–24 h. Slides were then washed (rocking for approximately 30 seconds in 6 × SSPE, 0.005% sarcosine, then rocking for approximately 30 seconds in 0.06 × SSPE)

scan_protocol: Slides were scanned with a 4000A microarray scanner (Axon Instruments, Union City, USA).

data_processing: TIFF images were quantitated with GenePix (Axon Instruments). Individual channels were spatially detrended (that is, overall correlations between spot intensity and position on the slide were removed) by high-pass filtering (using 10% outliers. We applied variance stabilizing normalization (VSN) using 25% of the genes to normalize all single channels to each other. Measurements were transformed to arcsinh values (which are similar to natural log values, but are defined for negative numbers which emerge from the VSN). Missing values were set to zero

source_name: Oct4 knockdown R1 cells

label_protocol: The mRNA (1–2 μg) was reverse-transcribed with random nonamer primers (1 μg per reaction) and T18VN (0.25 μg per reaction) to synthesize cDNA. The reaction contained a 1:1 mixture of 5-(3-aminoallyl) thymidine 5'-triphosphate (Sigma, St. Louis, USA) and thymidine triphosphate (TTP) in place of TTP alone. The cDNA products were bound to QIAquick PCR Purification columns (Qiagen, Hilden, Germany) following the manufacturer's instructions, washed three times with 80% ethanol, and eluted with water.

extract_protocol: RNA was extracted using homogenization and Trizol reagent (Invitrogen, Carlsbad, USA) following the instructions from the manufacturer, and mRNA was purified using polyT beads

tag: Using shRNA, Oct4 expression is knockdown in R1 mouse ES cells, which were established from (129/Svj x 129/Sv-CP) F1 male blastocyst.

source_name: empty vector control

label_protocol: The mRNA (1–2 μg) was reverse-transcribed with T18VN (1 μg per reaction) to synthesize cDNA. The reaction contained a 1:1 mixture of 5-(3-aminoallyl) thymidine 5'-triphosphate (Sigma, St. Louis, USA) and thymidine triphosphate (TTP) in place of TTP alone. The cDNA products were bound to QIAquick PCR Purification columns (Qiagen, Hilden, Germany) following the manufacturer's instructions, washed three times with 80% ethanol, and eluted with water.

tag: R1 ES cells were transfected with empty shRNA vector


title: Sox2 knockdown R1 ES cells 1 of 2

source_name: Sox2 knockdown R1 cells

tag: Using shRNA, Sox2 expression is knockdown in R1 mouse ES cells, which were established from (129/Svj x 129/Sv-CP) F1 male blastocyst.

source_name: Empty vector control

tag: R1 ES cells were transfected with shRNA empty vectors


title: Blood_Control1_16_5_R1

description: Control1 time 16_5 replicate 1

source_name: Individual Control1, Time 16_5, Replicate 1.


title: Blood_Control1_156_R3

description: Control1 time 156 replicate 3

source_name: Control. Individual Control1, Time 156, Replicate 3.


title: Blood_Control1_156_R1

description: Control1 time 156 replicate 1

source_name: Control. Individual Control1, Time 156, Replicate 1.

source_name: Common reference RNA pool


title: Blood_Control1_156_R2

description: Control1 time 156 replicate 2

source_name: Control. Individual Control1, Time 156, Replicate 2.


title: Blood_Control1_11_5_R2

description: Control1 time 11_5 replicate 2

source_name: Individual Control1, Time 11_5, Replicate 2.


title: Blood_Control1_0_R3

description: Control1 time 0 replicate 3

source_name: Control. Individual Control1, Time 0, Replicate 3.


title: RIIIS-J_male_hypothalamus

city: San Diego

first: John

middle: R

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: standard Affymetrix procedures using the GeneChip Fluidics Station 450

scan_protocol: standard Affymetrix procedures using the GeneChip 3000 scanner

label_protocol: cDNA synthesis and amplification employed the Affymetrix 3' IVT protocol.

extract_protocol: Hypothalamus tissue was harvested from 32 strains of mice from the Mouse Diversity Panel.  Total RNA was isolated from frozen tissue using Trizol, and cleaned up using an RNeasy kit (Qiagen).  For the male samples, 1 ug total RNA from three separate samples was pooled and 3 ug used for cDNA synthesis and amplification.  For the female samples, 1 ug total RNA from the hypothalamus of an individual mouse was used for cDNA synthesis and amplification.


title: Blood_Control1_25_R1

description: Control1 time 25 replicate 1

source_name: Control. Individual Control1, Time 25, Replicate 1.


title: NZB-BlNJ_male_hypothalamus


title: Blood_Control1_0_R1

description: Control1 time 0 replicate 1

source_name: Control. Individual Control1, Time 0, Replicate 1.


title: SM-J_male_hypothalamus


title: Blood_Control1_0_R2

description: Control1 time 0 replicate 2

source_name: Control. Individual Control1, Time 0, Replicate 2.


title: DBA-2J_male_hypothalamus


title: NZW-LacJ_male_hypothalamus


title: Blood_Patient1_6_25_R3

description: Patient1 time 6_25 replicate 3

source_name: Individual Patient1, Time 6_25, Replicate 3.


title: C57BL-6J_male_hypothalamus


title: Blood_Patient1_9_5_R3

description: Patient1 time 9_5 replicate 3

source_name: Individual Patient1, Time 9_5, Replicate 3.


title: Blood_Control1_11_5_R1

description: Control1 time 11_5 replicate 1

source_name: Individual Control1, Time 11_5, Replicate 1.


title: Blood_Patient1_9_5_R2

description: Patient1 time 9_5 replicate 2

source_name: Individual Patient1, Time 9_5, Replicate 2.


title: Blood_Patient1_9_5_R1

description: Patient1 time 9_5 replicate 1

source_name: Individual Patient1, Time 9_5, Replicate 1.


title: Blood_Patient1_6_25_R2

description: Patient1 time 6_25 replicate 2

source_name: Individual Patient1, Time 6_25, Replicate 2.


title: BUB-BnJ_male_hypothalamus


title: Blood_Patient1_6_25_R1

description: Patient1 time 6_25 replicate 1

source_name: Individual Patient1, Time 6_25, Replicate 1.


title: BTBR T+ tf-tf_male_hypothalamus

description: BTBR T+ tf-tf_male_hypothalamus

source_name: BTBR T+ tf-tf_male_hypothalamus

tag: BTBR T+ tf-tf_male_hypothalamus


title: BALB-cByJ_male_hypothalamus


title: AKR-J_male_hypothalamus


title: Blood_Patient1_49_R3

description: Patient1 time 49 replicate 3

source_name: IFN injected. Individual Patient1, Time 49, Replicate 3.


title: Blood_Patient1_49_R1

description: Patient1 time 49 replicate 1

source_name: IFN injected. Individual Patient1, Time 49, Replicate 1.


title: 129S1-SvImJ_male_hypothalamus


title: Blood_Patient1_49_R2

description: Patient1 time 49 replicate 2

source_name: IFN injected. Individual Patient1, Time 49, Replicate 2.

source_name: Common reference RNA pool


title: NZW/LacJ_female_hypothalamus


title: Blood_Patient1_3_5_R1

description: Patient1 time 3_5 replicate 1

source_name: Individual Patient1, Time 3_5, Replicate 1.


title: SM/J_female_hypothalamus


title: A-J_male_hypothalamus


title: RIIIS/J_female_hypothalamus


title: NZB/BlNJ_female_hypothalamus


title: Blood_Patient1_3_5_R3

description: Patient1 time 3_5 replicate 3

source_name: Individual Patient1, Time 3_5, Replicate 3.


title: Blood_Patient1_3_5_R2

description: Patient1 time 3_5 replicate 2

source_name: Individual Patient1, Time 3_5, Replicate 2.


title: DBA/2J_female_hypothalamus


title: Blood_Patient1_25_R1

description: Patient1 time 25 replicate 1

source_name: IFN injected. Individual Patient1, Time 25, Replicate 1.


title: BUB/BnJ_female_hypothalamus


title: Blood_Patient1_25_R3

description: Patient1 time 25 replicate 3

source_name: IFN injected. Individual Patient1, Time 25, Replicate 3.


title: Blood_Patient1_16_5_R3

description: Patient1 time 16_5 replicate 3

source_name: Individual Patient1, Time 16_5, Replicate 3.


title: Blood_Patient1_25_R2

description: Patient1 time 25 replicate 2

source_name: IFN injected. Individual Patient1, Time 25, Replicate 2.


title: Blood_Patient1_11_5_R3

description: Patient1 time 11_5 replicate 3

source_name: Individual Patient1, Time 11_5, Replicate 3.


title: BTBR T+ tf/J_female_hypothalamus

description: BTBR T+ tf/J_female_hypothalamus

source_name: BTBR T+ tf/J_female_hypothalamus

tag: BTBR T+ tf/J_female_hypothalamus


title: BALB/cByJ_female_hypothalamus


title: C57BL/6J_female_hypothalamus


title: AKR/J_female_hypothalamus


title: Blood_Patient1_11_5_R1

description: Patient1 time 11_5 replicate 1

source_name: Individual Patient1, Time 11_5, Replicate 1.


title: Blood_Patient1_11_5_R2

description: Patient1 time 11_5 replicate 2

source_name: Individual Patient1, Time 11_5, Replicate 2.


title: Sox2 knockdown R1 ES cells 2 of 2

source_name: Sox2 knockdown ES cells

tag: Using shRNA,Sox2 expression is knockdown in R1 mouse ES cells, which were established from (129/Svj x 129/Sv-CP) F1 male blastocyst.

source_name: Empty vector control


title: Blood_Patient1_16_5_R1

description: Patient1 time 16_5 replicate 1

source_name: Individual Patient1, Time 16_5, Replicate 1.


title: Blood_Patient1_16_5_R2

description: Patient1 time 16_5 replicate 2

source_name: Individual Patient1, Time 16_5, Replicate 2.


title: Hen's egg allergic Patient 2

city: Toyoake

first: Nakajima

last: Yoichi

address: 1-98 Dengakugakubo Kutsukake

department: Pediatrics

institute: Fujita Health University

description: Hen's egg allergic Patient 2

hyb_protocol: Hybridizations on the microarray slide of Human Whole Genome were carried out for 17 hours in a rotating hybridization oven using an in situ hybridization kit plus.

scan_protocol: The slide was washed as indicated in protocol and were then scanned with an Agilent G2565BA microarray scanner.

data_processing: Microarray expression data were obtained using the Feature Extraction software.

source_name: un-stimulated CD4 positive cells

label_protocol: Total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit.

extract_protocol: Total RNA was extracted from these CD4 positive cells with an RNeasy mini-kit according to the manufacturer’s instruction.

tag: PBMCs from a  hen's egg allergic child wascultured in RPMI 1640 supplemented with 10% autologous plasma for 16 hours without hen’s egg white allergen. Cells bearing CD4 antigen were isolated from cultured PBMCs using a Magnetic cell sorter after CD14 positive cell depletion.

source_name: allergen-stimulated CD4 positive cells

tag: PBMCs from a  hen's egg allergic child wascultured in RPMI 1640 supplemented with 10% autologous plasma for 16 hours with hen’s egg white allergen. Cells bearing CD4 antigen were isolated from cultured PBMCs using a Magnetic cell sorter after CD14 positive cell depletion.


title: Hen's egg non-allergic individual 2

description: Hen's egg non-allergic individual 2

growth_protocol: PBMCs from a  hen's egg allergic child wascultured in RPMI 1640 supplemented with 10% autologous plasma for 16 hours without hen’s egg white allergen.

treatment_protocol: Cells bearing CD4 antigen were isolated from cultured PBMCs using a Magnetic cell sorter after CD14 positive cell depletion.


title: FB1 yap1 mutant exposed to 5 mM H2O2 during 1 hour try 1

status: Public on Apr 17 2007

city: Marburg

first: Lazaro

last: Molina

address: Karl-von-Frish

department: Organismic interactions

country: Germany

institute: Max Planck Institute

description: all the required information was supplied

hyb_protocol: Hybridization was performed with fragmented copy RNA according to the Affymetrix protocol for eukaryotic targets on the Affymetrix custom array MPIUstilagoA. Subsequently, a three-stain procedure was performed according to the protocol EukGE-WS2 on a GeneChip Fluidics Station 400, which included signal amplification as well as washing steps (Affymetrix).

scan_protocol: Arrays were scanned twice using a GeneArray Scanner (Agilent/Affymetrix).

data_processing: The resulting image data were analyzed using the GeneChip Expression Analysis software (GCOS) Microarray Suite 5.0 (Affymetrix), using standard settings: Smooth factor, 100; Epsilon, 0.5; alpha1, 0.0575; alpha2, 0.0971; tau, 0.015; Gamma1H, 0.000423; Gamma1L, 0.000423; Gamma2H, 0.000627; Gamma2L, 0.000627; Perturbation, 1.1; TGT, 300.

organism: Mycosarcoma maydis

source_name: Ustilago maydis strain FB1 yap1 mutant exposed to 5mM H2O2 during 1 hour

label_protocol: transcribed in vitro with the ENZO BioArray High Yields RNA transcript 21 labeling kit (ENZO Diagnostics) using biotinylated ribonucleotides. Copy RNA was purified using the GeneChip sample cleanup module (Qiagen) and subsequently fragmented according to standard protocols (Affymetrix). The quality of RNA, cDNA, and copy RNA fragments was analyzed with an Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChips or DNA 7500 LabChips, respectively (Agilent Technologies).

growth_protocol: Cultures in CM glucose

extract_protocol: Briefly, total RNA (isolated with trizol standar protocol) was purified applying the RNeasy Mini kit (Qiagen). Purified RNA (10 µg) was reverse-transcribed using the Superscript Choice system (Invitrogen). The cDNA generated was purified using the GeneChip sample cleanup module (Qiagen)

treatment_protocol: Cultures in CM-glucose with addition of 5 mM H2O2 during 1 hour

tag: FB1 strain yap1 mutant exposed to H2O2 during 1 hour


title: FB1yap1 mutant exposed to 5 mM of H2O2 during 1 hour try 2

source_name: Ustilago maydis FB1yap1 mutant exposed to 5 mM H2O2 during 1 hour

tag: Ustilago maydis FB1yap1 mutant


title: Ustilago maydis strain FB1 after treatment with 5 mM H2O2 during 1 hour try 2

source_name: Ustilago maydis strain FB1 treated with 5 mM H2O2 during 1 hour

tag: Ustilago maydis strain FB1


title: FB1 exposed to 5 mM H2O2 during 1 hour try 1

description: all the required information is provided

source_name: Ustilago maydis strain FB! exposed during 1 hour to 5 mM H2O2

label_protocol: The cDNA generated was purified using the GeneChip sample cleanup module (Qiagen) and transcribed in vitro with the ENZO BioArray High Yields RNA transcript 21 labeling kit (ENZO Diagnostics) using biotinylated ribonucleotides. Copy RNA was purified using the GeneChip sample cleanup module (Qiagen) and subsequently fragmented according to standard protocols (Affymetrix). The quality of RNA, cDNA, and copy RNA fragments was analyzed with an Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChips or DNA 7500 LabChips, respectively (Agilent Technologies).

growth_protocol: Cultures in CM-glucose medium

extract_protocol: Standar trizol extraction, total RNA was purified applying the RNeasy Mini kit (Qiagen). Purified RNA (10 µg) was reverse-transcribed using the Superscript Choice system (Invitrogen). The cDNA generated was purified using the GeneChip sample cleanup module (Qiagen)

treatment_protocol: Cultures in CM-glucose medium, 5 mM H2O2 during 1 hour


title: FB1 without H2O2 treatment try 2

source_name: Ustilago maydis strain FB1

treatment_protocol: Cultures in CM-glucose medium


title: Blood_Patient1_0_R2

description: Patient1 time 0 replicate 2

source_name: IFN injected. Individual Patient1, Time 0, Replicate 2.

source_name: Common reference RNA pool


title: A/J_female_hypothalamus


title: Oct4 knockdown R1 ES cells 2 of 2

source_name: Oct4 knockdown R1 ES cells

tag: R1 ES cell transfected with shRNA empty vectors


title: Hen's egg non-allergic individual 1

description: Hen's egg non-allergic individual 1


title: Ustilago maydis strain FB1 without H2O2 try 1

source_name: Ustilago maydis RNA


title: Whole neuroblastoma tumor_2216

city: genoa

first: Domenico

last: Albino

address: L.go R. Benzi, 10

country: Italy

institute: National Institute for Cancer Research (IST)

description: Gene expression data from whole tumor

hyb_protocol: In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed  with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.

scan_protocol: GeneChips were scanned using the laser confocal fluorescence scanner.

data_processing: Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.

source_name: Frozen neuroblastoma tumor

label_protocol: We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).

extract_protocol: Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA). Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA)., total RNA

tag: Phenotype

value: Neuroblastoma (Schwannian stroma-poor)


title: Whole neuroblastoma tumor_2237

description: Gene expression data from whole tumor

extract_protocol: Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).


title: 129S1/SvImJ_female_hypothalamus


title: Whole neuroblastoma tumor_2259

description: Gene expression data from whole tumor


title: Hen's egg allergic Patient 3

description: Hen's egg allergic Patient 3


title: Hen's egg allergic Patient 1

description: Hen's egg allergic Patient 1


title: Blood_Patient1_0_R3

description: Patient1 time 0 replicate 3

source_name: IFN injected. Individual Patient1, Time 0, Replicate 3.


title: Blood_Patient1_0_R1

description: Patient1 time 0 replicate 1

source_name: IFN injected. Individual Patient1, Time 0, Replicate 1.


title: Whole ganglioneuroma tumor_2782

description: Gene expression data from whole tumor

source_name: Frozen ganglioneuroma tumor

value: Ganglioneuroma


title: Whole neuroblastoma tumor_2215

description: Gene expression data from whole tumor


title: Microdissected area # 3 of 2182 tumor

description: Gene expression data from microdissected area # 3 of 2182 tumor

value: Neuroblastoma (Schwannian stroma-poor) with areas of large neuroblastic round cells


title: Whole neuroblastoma tumor_2182

description: Gene expression data from whole tumor