title: AML1-ETO expressing cord blood cell, clone 11.40.2 grown serum-free, CD34 purified, replicate 3


title: siRNA Control Duplicate 2

status: Public on Dec 26 2007

type: RNA

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

country: Canada

institute: Université de Montréal

description: Human HeLa cells were transiently transfected with in vitro-synthesized nonspecific control siRNA.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HeLa cells transiently transfected with a control siRNA

label_protocol: Standard Affymetrix procedures

growth_protocol: Human HeLa cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HeLa cells were transiently transfected with in vitro-synthesized nonspecific control siRNA.

extract_protocol: TriZol reagent

tag: HeLa cells transiently transfected with a nonspecific control siRNA


title: AML1-ETO expressing cord blood cell, clone 11.40.2 grown serum-free, CD34 purified, replicate 2

status: Public on Dec 20 2007

city: Cincinnati

first: James

last: Mulloy

state: OH

address: 3333 Burnet Ave

department: Experimental Hematology

country: USA

institute: Cincinnati Children's Hospital Research Foundation

description: Gene expression data from long-term serum-free cultures of AML1-ETO-transduced cord blood cells, CD34 selected

hyb_protocol: All hybridization, staining and washing steps were carried out as specified by the Affymetrix technical manual. (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf)

scan_protocol: Affymetrix GeneChip Scanner 3000 7G with GeneChip Operating Software Version 1.4.0.036 (Affymetrix)

data_processing: Data were pre-processed with Microarray Suite version 5.0 function of Bioconductor package (R) using default settings

label: biotin

source_name: Human CD34+ cord blood cells

label_protocol: For cDNA generation, and cRNA labeling we used the ëOne-cycle target labelingí protocol as described by the respective Affymetrix technical manual. (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf)

extract_protocol: total RNA from cells was extracted using the Rneasy Mini Kit (Qiagen)

tag: normal donors


title: AML1-ETO expressing cord blood cell, clone 9 grown serum-free, CD34 purified, replicate 1


title: AML1-ETO expressing cord blood cell, clone 11.40.2 grown serum-free, CD34 purified, replicate 1


title: Mouse eye, biological replicate 3

city: Leuven-Heverlee

first: Léon-Charles

last: Tranchevent

address: Kasteelpark Arenberg 10

department: Departement of Electrical Engineering

country: Belgium

institute: Katholieke Universiteit Leuven

description: Mouse eye

hyb_protocol: Fragmented cRNA was hybridised to mouse 430 2.0 arrays (Affymetrix) during 16h at 45??C.

scan_protocol: The arrays were washed and stained in a fluidics station (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All image files were analysed using the affy library of the BioConductor project (no background adjustment, probe-level quantile normalization, and average difference summarization)

organism: Mus musculus

source_name: Mouse eye

label_protocol: Cellular mRNA was reverse transcribed into cDNA (SuperScript Choice System Invitrogen, Carlsbad, CA using oligo-dT primers and a T7 RNA polymerase promoter site). Two ??g of total RNA was used to prepare biotinylated cRNA with IVT labeling kit (Affymetrix, Santa Clara, CA) according to the Genechip expression analysis technical manual 701025 Rev.5. The concentration of labelled cRNA was measured using the NanoDrop ND-1000 spectrophotometer. Labeled cRNA was fragmented in a fragmentation buffer during 35 min at 94??C. The quality of labelled and fragmented cRNA was analysed using the Agilent bioanalyzer 2100.

extract_protocol: Total RNA was extracted using TRIzol Reagent according to the manufacturerÆs protocol (Gibco BRL, Carlsbad, CA), followed by a cleanup procedure with RNeasy columns (Qiagen, Cologne, Germany).The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

tag: C57Bl6 male mice (10-12 weeks old)


title: Mouse ES cells, biological replicate 3

description: Mouse ES cells

source_name: Mouse ES cells

extract_protocol: Total RNA was extracted using the Absolutely RNA microprep from Stratagene (CA). The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

tag: C57Bl6 male mice


title: Mouse fetus, biological replicate 3

description: Mouse fetus

source_name: Mouse fetus

tag: C57Bl6 mice


title: Mouse placenta, biological replicate 1

description: Mouse placenta

source_name: Mouse placenta

tag: C57Bl6 female mice (10-12 weeks old)


title: Mouse fetus, biological replicate 2

description: Mouse fetus


title: Mouse eye, biological replicate 2

description: Mouse eye


title: Mouse ovary, biological replicate 2

description: Mouse ovary

source_name: Mouse ovary


title: Mouse fetus, biological replicate 1

description: Mouse fetus


title: Mouse heart, biological replicate 2

description: Mouse heart

source_name: Mouse heart


title: Mouse ES cells, biological replicate 1

description: Mouse ES cells


title: Mouse ovary, biological replicate 3

description: Mouse ovary


title: Mouse ovary, biological replicate 1

description: Mouse ovary


title: Mouse eye, biological replicate 1

description: Mouse eye


title: Mouse small intestine, biological replicate 3

description: Mouse small intestine

source_name: Mouse small intestine


title: Mouse heart, biological replicate 3

description: Mouse heart


title: Mouse small intestine, biological replicate 2

description: Mouse small intestine


title: Mouse ES cells, biological replicate 2

description: Mouse ES cells


title: Mouse placenta, biological replicate 3

description: Mouse placenta


title: Mouse thymus, biological replicate 2

description: Mouse thymus

source_name: Mouse thymus


title: Mouse thymus, biological replicate 3

description: Mouse thymus


title: Mouse heart, biological replicate 1

description: Mouse heart


title: Mouse testis, biological replicate 3

description: Mouse testis

source_name: Mouse testis


title: Mouse small intestine, biological replicate 1

description: Mouse small intestine


title: Mouse testis, biological replicate 2

description: Mouse testis


title: Mouse seminal vesicle, biological replicate 2

description: Mouse seminal vesicle

source_name: Mouse seminal vesicle


title: Mouse seminal vesicle, biological replicate 1

description: Mouse seminal vesicle


title: Mouse thymus, biological replicate 1

description: Mouse thymus


title: Mouse salivary gland, biological replicate 3

description: Mouse salivary gland

source_name: Mouse salivary gland


title: Mouse seminal vesicle, biological replicate 3

description: Mouse seminal vesicle


title: Mouse salivary gland, biological replicate 1

description: Mouse salivary gland


title: Mouse pituitary gland, biological replicate 5

description: Mouse pituitary gland

source_name: Mouse pituitary gland

label_protocol: Cellular mRNA was reverse transcribed into cDNA (SuperScript Choice System Invitrogen, Carlsbad, CA using oligo-dT primers and a T7 RNA polymerase promoter site). One ??g of total RNA was used to prepare biotinylated cRNA with IVT labeling kit (Affymetrix, Santa Clara, CA) according to the Genechip expression analysis technical manual 701025 Rev.5. The concentration of labelled cRNA was measured using the NanoDrop ND-1000 spectrophotometer. Labeled cRNA was fragmented in a fragmentation buffer during 35 min at 94??C. The quality of labelled and fragmented cRNA was analysed using the Agilent bioanalyzer 2100.


title: Mouse adipose tissue, biological replicate 2

description: Mouse adipose tissue

source_name: Mouse adipose tissue


title: Mouse pituitary gland, biological replicate 3

description: Mouse pituitary gland


title: Mouse bone marrow, biological replicate 2

description: Mouse bone marrow

source_name: Mouse bone marrow


title: Mouse pituitary gland, biological replicate 1

description: Mouse pituitary gland


title: Mouse placenta, biological replicate 2

description: Mouse placenta


title: Mouse bone marrow, biological replicate 3

description: Mouse bone marrow


title: Mouse pituitary gland, biological replicate 2

description: Mouse pituitary gland


title: Mouse adrenal gland, biological replicate 2

description: Mouse adrenal gland

source_name: Mouse adrenal gland


title: Mouse bone marrow, biological replicate 1

description: Mouse bone marrow


title: Mouse salivary gland, biological replicate 2

description: Mouse salivary gland


title: Mouse testis, biological replicate 1

description: Mouse testis


title: Mouse adipose tissue, biological replicate 3

description: Mouse adipose tissue


title: Mouse adipose tissue, biological replicate 1

description: Mouse adipose tissue


title: Mouse bone marrow, biological replicate 4

description: Mouse bone marrow


title: Mouse kidney, biological replicate 3

description: Mouse kidney

source_name: Mouse kidney


title: Mouse kidney, biological replicate 1

description: Mouse kidney


title: Mouse pituitary gland, biological replicate 4

description: Mouse pituitary gland


title: Mouse kidney, biological replicate 2

description: Mouse kidney


title: Mouse adrenal gland, biological replicate 1

description: Mouse adrenal gland


title: Mouse lung, biological replicate 2

description: Mouse lung

source_name: Mouse lung


title: Mouse lung, biological replicate 3

description: Mouse lung


title: Mouse adrenal gland, biological replicate 3

description: Mouse adrenal gland


title: Mouse lung, biological replicate 1

description: Mouse lung


title: Mouse brain, biological replicate 1

description: Mouse brain

source_name: Mouse brain


title: Mouse brain, biological replicate 2

description: Mouse brain


title: Mouse liver, biological replicate 1

description: Mouse liver

source_name: Mouse liver


title: Mouse muscle, biological replicate 3

description: Mouse muscle

source_name: Mouse muscle


title: Mouse diaphragm, biological replicate 3

description: Mouse diaphragm

source_name: Mouse diaphragm


title: Mouse liver, biological replicate 2

description: Mouse liver


title: Mouse muscle, biological replicate 1

description: Mouse muscle


title: Mouse brain, biological replicate 3

description: Mouse brain


title: Mouse liver, biological replicate 3

description: Mouse liver


title: Mouse diaphragm, biological replicate 1

description: Mouse diaphragm


title: Mouse diaphragm, biological replicate 2

description: Mouse diaphragm


title: Whole roots 3.5hr KNO3 treated then frozen, biological rep1

status: Public on Dec 19 2007

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array in the Affymetrix Hybridization oven 640 following standard Affymetrix protocol. GeneChips were washed and stained using the 'EukGE-WS2v4_450' protocol in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to standard Affymetrix protocols.

data_processing: The data were analyzed with dChip using dChip default analysis settings and 'Average' as the normalization model, PM match only. Note that samples were normalized in two batches according to the sample type: Cell type specific samples (columns B-BC), and protoplasts and whole roots (columns BD-CG), all using the procedure described above. Non nuclear-encoded or ambiguous probe-gene matches were not used (according to latest annotation file from Affymetrix (April 2007).  If the signal was log2 less than 6 in both treat and control experiments probes were removed from analysis; the value of 6 based on expression values of previously documented cell-specific genes. Probes determined to be affected by protoplast generation procedure were not analysed.

organism: Arabidopsis thaliana

source_name: 12 day old Arabidopsis roots, 3.5hr KNO3 treated then frozen

label_protocol: Biotinylated cRNA from all isolated cell samples (LRC, EpiC, EndoP, Peri, Stele) were prepared according to the standard two-cycle Affymetrix protocol from 50 ng total RNA, or from all whole root samples and protoplast samples according to the standard one-cycle Affymetrix protocol from 1 ug total RNA.

growth_protocol: Plants were grown for 12 days in long day (16hr light/8hr dark) 22 oC conditions in a Percival (Percival Scientific).  Plants were grown hydroponically in basal MS containing no nitrogen except 0.5mM ammonium succinate and 3mM sucrose.  All plant lines are in the Col-0 background.

extract_protocol: Total RNA was either extracted using the Plant RNAeasy kit (Qiagen, Hilden, Germany) for cell samples (LRC, EpiC, EndoP, Peri, Stele, Protoplasts), or for whole root samples using TRIzol reagent (Invitrogen, Carlsbad, CA).  Protocols were followed according to manufacturer's instructions.

treatment_protocol: At dawn on 12th day plants were either transitory/continuous nitrogen-treated (KNO3 to 5mM added) or KCl treated (KCl to 5mM added) as a control treatment for 2 hrs.  To isolate single cell types (LRC, EpiC, EndoP, Peri, Stele) cells were incubated in a solution containing cell-wall digesting enzymes and then Fluorescence Activated Cell Sorting (FACS) sorted as Birnbaum et al (2005) Nature Methods 2: 615-619.  To isolate mock FACS-sorted protoplasts the same proceedure was followed but the cells were not FACS-sorted, instead the protoplasts were incubated on ice for the time it takes to FACS-sort (1 hour).  After FACS or mock-FACS cell sorting cells were frozen using liquid nitrogen.  5mM KNO3 was either maintained in the protoplast-generating solution (continuous treat) or not (transitory treat) to test how to best preserve the cellular nitrogen-response during the 1 hr protoplast generating procedure.  As well as the 'protoplasts' controls we harvested whole roots that were either frozen using liquid nitrogen directly after the 2hr treatment or 3.5hr treatment, or whole roots incubated in protoplast-generating solultion (minus enzymes; transitory or continuous treated) and then frozen.  1mM MSX in combination with 5mM KNO3 (or with 5mM KCl as a control), or also with 5mM glutamine (Gln) for 2 hrs was used to block and then release the block of the assimilation of KNO3 in order to seperate KNO3 effects from assimilated-nitrogen effects in FACS-sorted pericycle cells.

tag: Genotype

tag: All root cells


title: Mouse spleen, biological replicate 3

description: Mouse spleen

source_name: Mouse spleen


title: Mouse muscle, biological replicate 4

description: Mouse muscle


title: Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep2

description: KNO3 and MSX and Gln were maintained in the protoplast-generating solution at 5mM and 1mM and 5mM respectively

source_name: FACS-sorted 12 day old Arabidopsis Pericycle root cells, 2 hr KNO3&MSX&Gln continuous treated

tag: Cell type

value: pericycle root cells


title: Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep3


title: Mouse spleen, biological replicate 2

description: Mouse spleen


title: Whole roots 3.5hr KNO3 treated then frozen, biological rep2


title: Mouse spleen, biological replicate 1

description: Mouse spleen


title: Protoplasted root cells 2hr transitory KNO3 treated, biological rep1

description: KNO3 was not maintained in the protoplast-generating solution

source_name: Mock FACS-sorted 12 day old Arabidopsis root cell protoplasts, 2 hr KNO3 transitory treated

tag: All protoplasts from root cells


title: Whole roots 3.5hr KCl control treated then frozen, biological rep1

source_name: 12 day old Arabidopsis roots, 3.5hr KCl control treated then frozen


title: Protoplasted root cells 2hr transitory KNO3 treated, biological rep3


title: Whole roots 3.5hr KCl control treated then frozen, biological rep2


title: Whole roots 3.5hr KNO3 treated then frozen, biological rep3


title: Whole roots 3.5hr KCl control treated then frozen, biological rep3


title: Mouse muscle, biological replicate 2

description: Mouse muscle


title: Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep1


title: Protoplasted root cells 2hr transitory KNO3 treated, biological rep2


title: Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes with KNO3, biological rep3

description: KNO3 was maintained in the protoplast-generating solution (minus enzymes) at 5mM

source_name: 12 day old Arabidopsis roots, 2hr KNO3 continuous treated then incubated in protoplast-generating solution minus enzymes


title: Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes with KNO3, biological rep2


title: Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep3

source_name: 12 day old Arabidopsis roots, 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes


title: Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2


title: Whole roots 2hr KCl control treated then frozen, biological rep3

source_name: 12 day old Arabidopsis roots, 2hr KCl control treated then frozen


title: Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1


title: Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep1

description: KNO3 was not maintained in the protoplast-generating solution (minus enzymes)

source_name: 12 day old Arabidopsis roots, 2hr KNO3 transitory treated then incubated in protoplast-generating solution minus enzymes


title: Whole roots 2hr KCl control treated then frozen, biological rep2


title: Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2


title: Whole roots 2hr KNO3 treated then frozen, biological rep1

source_name: 12 day old Arabidopsis roots, 2hr KNO3 treated then frozen


title: Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep3


title: Whole roots 2hr KNO3 treated then frozen, biological rep2


title: Whole roots 2hr KCl control treated then frozen, biological rep1


title: Whole roots 2hr KNO3 treated then frozen, biological rep3


title: Protoplasted root cells 2hr continuous KNO3 treated, biological rep2

description: KNO3 was maintained in the protoplast-generating solution at 5mM

source_name: Mock FACS-sorted 12 day old Arabidopsis root cell protoplasts, 2 hr KNO3 continuous treated


title: Stele root cells 2hr transitory KNO3 treated, biological rep3

source_name: FACS-sorted 12 day old Arabidopsis Stele root cells, 2 hr KNO3 transitory treated

value: stele root cells


title: Protoplasted root cells 2hr KCl control treated, biological rep1

source_name: Mock FACS-sorted 12 day old Arabidopsis root cell protoplasts, 2 hr control treated


title: Protoplasted root cells 2hr continuous KNO3 treated, biological rep3


title: Protoplasted root cells 2hr KCl control treated, biological rep3


title: Stele root cells 2hr continuous KNO3 treated, biological rep1

source_name: FACS-sorted 12 day old Arabidopsis Stele root cells, 2 hr KNO3 continuous treated


title: Stele root cells 2hr continuous KNO3 treated, biological rep3


title: Stele root cells 2hr KCl control treated, biological rep3

source_name: FACS-sorted 12 day old Arabidopsis Stele root cells, 2 hr KCl control treated


title: Protoplasted root cells 2hr KCl control treated, biological rep2


title: Stele root cells 2hr transitory KNO3 treated, biological rep2


title: Stele root cells 2hr transitory KNO3 treated, biological rep1


title: Stele root cells 2hr KCl control treated, biological rep1


title: Stele root cells 2hr KCl control treated, biological rep2


title: Protoplasted root cells 2hr continuous KNO3 treated, biological rep1


title: Stele root cells 2hr continuous KNO3 treated, biological rep2


title: Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep3

description: KNO3 and MSX were maintained in the protoplast-generating solution at 5mM and 1mM respectively

source_name: FACS-sorted 12 day old Arabidopsis Pericycle root cells, 2 hr KNO3&MSX continuous treated


title: Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep2


title: Pericycle root cells 2hr KCl control treated, biological rep2

source_name: FACS-sorted 12 day old Arabidopsis Pericycle root cells, 2 hr KCl control treated


title: Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes with KNO3, biological rep1


title: Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep3

description: KCl and MSX were maintained in the protoplast-generating solution at 5mM and 1mM respectively

source_name: FACS-sorted 12 day old Arabidopsis Pericycle root cells, 2 hr KCl&MSX continuous control treated


title: Pericycle root cells 2hr KCl control treated, biological rep3


title: Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep2

source_name: FACS-sorted 12 day old Arabidopsis Endodermis&Pericycle root cells, 2 hr KNO3 transitory treated

value: endodermal and pericycle root cells


title: Pericycle root cells 2hr continuous KNO3 treated, biological rep2

source_name: FACS-sorted 12 day old Arabidopsis Pericycle root cells, 2 hr KNO3 continuous treated


title: Endodermis&Pericycle root cells 2hr KCl control treated, biological rep3

source_name: FACS-sorted 12 day old Arabidopsis Endodermis&Pericycle root cells, 2 hr KCl control treated


title: Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep2


title: Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep1


title: Pericycle root cells 2hr KCl control treated, biological rep1


title: Endodermis&Pericycle root cells 2hr continuous KNO3 treated, biological rep1

source_name: FACS-sorted 12 day old Arabidopsis Endodermis&Pericycle root cells, 2 hr KNO3 continuous treated


title: Endodermis&Pericycle root cells 2hr continuous KNO3 treated, biological rep3


title: Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep1


title: Pericycle root cells 2hr continuous KNO3 treated, biological rep1


title: Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1


title: Pericycle root cells 2hr transitory KNO3 treated, biological rep2

source_name: FACS-sorted 12 day old Arabidopsis Pericycle root cells, 2 hr KNO3 transitory treated


title: Pericycle root cells 2hr transitory KNO3 treated, biological rep1


title: Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep3


title: Endodermis&Pericycle root cells 2hr continuous KNO3 treated, biological rep2


title: Pericycle root cells 2hr transitory KNO3 treated, biological rep3


title: Epidermis&Cortex root cells 2hr continuous KNO3 treated, biological rep3

source_name: FACS-sorted 12 day old Arabidopsis Epidermis&Cortex root cells, 2 hr KNO3 continuous treated

value: epidermal and cortical root cells


title: Epidermis&Cortex root cells 2hr continuous KNO3 treated, biological rep1


title: Endodermis&Pericycle root cells 2hr KCl control treated, biological rep2


title: Endodermis&Pericycle root cells 2hr KCl control treated, biological rep1


title: Pericycle root cells 2hr continuous KNO3 treated, biological rep3


title: Epidermis&Cortex root cells 2hr continuous KNO3 treated, biological rep2


title: Epidermis&Cortex root cells 2hr transitory KNO3 treated, biological rep3


title: Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep3

source_name: FACS-sorted 12 day old Arabidopsis Lateral Root Cap root cells, 2 hr KNO3 continuous treated

value: lateral root cap root cells


title: Epidermis&Cortex root cells 2hr KCl control treated, biological rep3


title: Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2


title: Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep1


title: Epidermis&Cortex root cells 2hr transitory KNO3 treated, biological rep2


title: Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep1

source_name: FACS-sorted 12 day old Arabidopsis Lateral Root Cap root cells, 2 hr KNO3 transitory treated


title: Epidermis&Cortex root cells 2hr KCl control treated, biological rep1


title: Lateral Root Cap root cells 2hr KCl control treated, biological rep1

source_name: FACS-sorted 12 day old Arabidopsis Lateral Root Cap root cells, 2 hr KCl control treated


title: Lateral Root Cap root cells 2hr KCl control treated, biological rep2


title: Epidermis&Cortex root cells 2hr KCl control treated, biological rep2


title: Lateral Root Cap root cells 2hr KCl control treated, biological rep3


title: Epidermis&Cortex root cells 2hr transitory KNO3 treated, biological rep1


title: Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2


title: Sca7cerebellum-wild type-biological rep3

status: Public on Dec 18 2007

city: Houston

first: Chad

middle: A

last: Shaw

state: TX

address: One Baylor Plaza

department: Department of Neuroscience

institute: Baylor College of Medicine

description:
Sca7cerebellum-wild type--biological rep3
gene expression data

hyb_protocol: Following fragmentation of 15.0 mg of the labeled cRNA, a hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip array.  The array was hybridized 16 hours at 45 degrees C with rotation at 60 rpm, then washed with a strepavidin, R-phycoerythrin conjugate stain.  Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The array was stained using the EukGEws2v5 protocol on the Fluidics Station 400.  The stained array was scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1.

source_name: cerebellum, Sca7 wild type

label_protocol: Total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the in vitro transcription reaction, producing biotin-labeled cRNA.  The labeled cRNA was quantified using the NanoDrop ND-1000 machine.  15.0 mg of the labeled cRNA was fragmented and re-checked on NanoDrop for concentration.

extract_protocol: Trizol extraction of total cerebellar RNA was performed, followed by Qiagen RNeasy clean-up, both according to manufacturers' instructions.

tag: genotype

value: wild type

tag: gender

value: female

tag: age

value: 5 weeks

tag: strain

value: C57BL/6J, 10 generations backcrossed


title: Sca7cerebellum-knock-in-biological rep4

description:
Sca7cerebellum-knock-in-biological rep4
gene expression data

source_name: cerebellum, Sca7 knock-in

value: knock-in


title: Sca7cerebellum-wild type-biological rep5

description:
Sca7cerebellum-wild type--biological rep5
gene expression data


title: Sca7cerebellum-wild type-biological rep4

description:
Sca7cerebellum-wild type--biological rep4
gene expression data


title: Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3


title: Sca7cerebellum-wild type-biological rep1

description:
Sca7cerebellum-wild type--biological rep1
gene expression data


title: Sca7cerebellum-knock-in-biological rep3

description:
Sca7cerebellum-knock-in-biological rep3
gene expression data


title: I,F9 ko cells

first: Dan

last: Su

address: 1300 york Ave

department: Pharmacology

institute: Weill Cornell Medical College

description: comparison between F9 wild type and F9 RAR gamma knock out cells treated with retinoic acid or ethanol in mouse to look at differentially expressed genes

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45 C on gene chip MG-430.2

scan_protocol: Gene chips were scanned using the hewlett-packard Gene Array Scanner G2500A

data_processing: Microarray Suite version 5.0 (MAS5.0) using default analysis settings and global scaling as normalized method.

source_name: F9 RAR gamma knock out cells

label_protocol: Biotinylated cRNA was prepared according to the standard protocol from 15 ug total RNA  (Expression technical manual 2005)

growth_protocol: 5% FCS +5%CS in DMEM medium at 10% CO2, 37°C

extract_protocol: Trizol extraction of total RNA according to the protocol

treatment_protocol: Retinoic Acid 1uM at dim light or vehicle control ethanol

tag: Retinoic acid receptor (RAR) gamma F9 cells from mouse


title: D,F9 wt cells + RA

source_name: F9 wild type cells after RA treatment

tag: F9 wild type cells from mouse


title: Sca7cerebellum-wild type-biological rep2

description:
Sca7cerebellum-wild type--biological rep2
gene expression data


title: LPS_3

first: Hector

middle: R

last: Wong

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

description: LPS treatment 3

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 microgram/microliter fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 microliter of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 microliter of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

source_name: Cultured THP-1 mononuclear cells treated with LPS

label_protocol: 120 ng of total RNA from 2 wild type [WT] and 4 beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen).
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the maufacturer's directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Cells were treated with either LPS (1 microgram/ml) for 4 hours, or heat shock (43°C for 1 hour) followed by a 4 hour recovery period at 37°C. Control cells were treated in basal growth media at 37°C.

tag: lipopolysaccharide treated cells


title: Sca7cerebellum-knock-in-biological rep1

description:
Sca7cerebellum-knock-in-biological rep1
gene expression data


title: C,F9 wt cells

source_name: F9 wild type cells


title: LPS_2

description: LPS treatment 2


title: Sca7cerebellum-knock-in-biological rep2

description:
Sca7cerebellum-knock-in-biological rep2
gene expression data


title: Sca7cerebellum-knock-in-biological rep5

description:
Sca7cerebellum-knock-in-biological rep5
gene expression data


title: HS+LPS_1

description: HS+LPS treatment 1

source_name: Cultured THP-1 mononuclear cells with heat shock and LPS

tag: heat shock/lipopolysaccharide treated cells


title: 8,F9 ko cells + RA

source_name: F9 RAR gamma knock out cells after RA treatment


title: J,F9 ko + RA


title: HS_2

description: Heat shock treatment 2

source_name: Cultured THP-1 mononuclear cells treated with heat shock

tag: heat shock treated cells


title: HS_3

description: Heat shock treatment 3


title: 3,F9 wt cells


title: 2,F9 wt cells + RA

tag: F9 wild type cells


title: LPS_1

description: LPS treatment 1


title: 7,F9 ko cells


title: 6,F9 ko cells + RA


title: HS+LPS_3

description: HS+LPS treatment 3


title: 4,F9 wt cells + RA


title: Ctrl_2

description: Control 2

source_name: Cultured THP-1 mononuclear cells

tag: control cells


title: 5,F9 ko cells


title: HS_1

description: Heat shock treatment 1


title: Ctrl_1

description: Control 1


title: Ctrl_3

description: Control 3


title: 1,F9 wt cells


title: HS+LPS_2

description: HS+LPS treatment 2


title: striatum_R62_95

status: Public on Dec 17 2007

city: Bethesda

first: Alexandre

last: Kuhn

state: MD

address: 35 Convent Dr

department: NIA

institute: NIH

description: Striatal sample from a 12-week-old R6/2 mouse.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: Striatum (brain) from R6/2 transgenic mice

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers’ protocols

tag: Strain

value: C57Bl/6 / CBA; Gender:female; Age:83 days; Tissue:striatum (brain); Mouse model:R6/2 transgenic mice (Mangiarini et al, Cell 87:493-506,1996)


title: low DC strenght 2

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: This sample is also known as IOSI06R-106

hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400

scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000

data_processing: Affymetrix GCOS 1.4

source_name: FACS-purified CFSE^lo CCR7+ IL-7R^ hi cells

label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 2ug of total RNA

growth_protocol: co-cultured with TSST-pulsed DC in 200 microl /well complete medium in 96-round bottom wells. After 7 days CFSElo cells were purified on a FACSAria (Becton Dickinson) according to CCR7 and IL-7Ra expression (IL-7Ra mAbs, Beckmann coulter and R&D system).

extract_protocol: cells were lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).

treatment_protocol: 104 CFSE-labeled naïve T cells were co-cultured with TSST-pulsed 10^2 DCs

tag: Total CD4+ T cells were isolated from the CD14- fraction by negative selection with a CD4+ T cell isolation kit on an Automacs (Miltenyi). CD4+ T cells were stained with anti-CCR7 mAb (R&D systems) followed by a biotin-labeled anti-g2a antibody and labeled streptavidin, FITC-labeled anti-CD45RA and PC5-labeled anti-CD8, anti-CD16 (Beckmann Coulter) and anti-CD19 (Becton Dickinson) and naïve CD4+ T cells (CD45RA+CCR7+) were purified by cell sorting to >99%. Then, T cells were DC stimulated, as desribed below


title: striatum_R62_109


title: high DC strenght 2

description: This sample is also known as IOSI06R-105

treatment_protocol: 104 CFSE-labeled naïve T cells were co-cultured with TSST-pulsed 10^4 DCs


title: striatum_R62_105


title: high DC strenght 1

description: This sample is also known as IOSI06R-102


title: striatum_R62_107


title: striatum_wildtype_49

description: Striatal sample from a 12-week-old wild-type mouse.

source_name: Striatum (brain) from wild-type mouse

value: C57Bl/6 / CBA; Gender:female; Age:85 days; Tissue:striatum (brain); Mouse model:wild-type


title: low DC strenght 1

description: This sample is also known as IOSI06R-101


title: striatum_wildtype_66


title: striatum_wildtype_46


title: striatum_R62_86

value: C57Bl/6 / CBA; Gender:female; Age:85 days; Tissue:striatum (brain); Mouse model:R6/2 transgenic mice (Mangiarini et al, Cell 87:493-506,1996)


title: striatum_wildtype_47


title: striatum_R62_78


title: striatum_R62_70


title: striatum_R62_65


title: striatum_R62_64


title: striatum_wildtype_63

source_name: Striatum (brain) from wild-type mice


title: striatum_wildtype_54


title: striatum_wildtype_42


title: striatum_wildtype_45


title: MCF7_TFAP2AsiRNA_noEstrogen

city: Iowa City

first: Ronald

last: Weigel

state: IA

address: 200 Hawkins Drive, Room 1509 JCP

department: Surgery

institute: University of Iowa

description: Total RNA was isolated and was subjected to analysis on the Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA) in conjunction with the DNA Core Facility at the University of Iowa following the GeneChip Expression Analysis Technical Manual.

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol on the fluidics station. Mix the following for each target:Fragmented cRNA, Control Oligonucleotide B2, 20xEukaryotic Hybridization Controls, Herring Sperm DNA, BSA, 2xHybridization Buffer, DMSO and water. Equilibrate probe array to room temperature immediately before use. Heat the hybridization cocktail to 99C for 5 min in a heat block. Meanwhile, wet the array bu filling it through one of the septa with appropriate volume of 1xHybridization Buffer using a micropipettor and appropriate tips. Incubate the probe array filled with 1xHybridization Buffer at 45C for 10 min with rotation. Transfer the hybridization cocktail that has been heated at 99C, to a 45C heat block for 5 min. Spin hybridization cocktail at maximum speed in a microcentrifuge for 5 min to remove any insoluble material from the hybridization mixture. Remove the buffer solution from the probe array cartridge and fill with appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. Place probe array into the Hybridization Oven, set to 45C. Hybridize for 16 hours.

scan_protocol: The arrays were washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner using the manufacturer's recommended protocols by the University of Iowa DNA Core Facility. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol on the fluidics station. Once the probe array has been hybridized, washed, and stained, it is scanned. Each workstation running Affymetrix Microarray Suite can control one scanner. The software defines the probe cells and computes an intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension. The arrays were washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner using the manufacturer's recommended protocols by the University of Iowa DNA Core Facility. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol on the fluidics station. Once the probe array has been hybridized, washed, and stained, it is scanned. Each workstation running Affymetrix Microarray Suite can control one scanner. The software defines the probe cells and computes an intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.

data_processing:
Initial expression values were generated using the microarray suite (MAS) v5.0 software (Affymetrix, Inc.).
CEL files were imported into ArrayAssist (Stratagene, Ja Jolla, CA) implementing the RMA (Robust Microarray Analysis) algorithm to generate gene expression values.

source_name: MCF7 cells, TFAP2A siRNA, no estrogen added

label_protocol:
An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization.
One-Cycle cDNA synthesis Kit  is used for this step. (Affymetrix, P\N 900493)
Mix RNA sample, diluted poly-A RNA controls, and T7-Oligo(dT) primer.
In a separate tube, assemble the First-Strand Master Mix.
Incubate for 1 hour at 42C, then cool the sample for at least 2 min at 4C.
After incubation at 4C, centrifuge the tube briefly to collect the reaction at the bottom of the tube and immediately proceed to Second-Strand cDNA Synthesis.
In a separate tube, assemble Second-Strand Master Mix.
Add 130 ul of Second-Strand Master Mix to each first-strand synthesis sample from First-Strand cDNA Synthesis for a total volume of 150 ul.
Incubate for 2 hours at 16C.
Add 2 ul of T4 DNA Polymerase to each sample and incubate for 5 minutes at 16C.
After incubation with T4 DNA Polymerase add 10 ul of EDTA, 0,5M and proceed to Cleanup of Double-Strand cDNA.
Synthesis of Biotin-Labeled cRNA
GeneChip IVT Labeling Kit is used for this step.
Determine the amount of cDNA used for each IVT reaction following the cDNA cleanup step.
Transfer the needed amount of template cDNA to RNase-free microfuge tubes and add the following reaction components:10xIVT Labeling Buffer, IVT Labeling NTP Mix, IVT Labeling Enzyme Mix, RNase-free Water.
Carefully mix the reagents and collect the mixture at the bottom of the tube by brief microcentrifugation.
Incubate at 37C for 16 hours. Proceed to Cleanup and Quantification of Biotin-Labeled cRNA.
Add 60 ul of RNase-free water to the IVT reaction and mix by vortexing for 3 seconds.
Add 350 ul IVT cRNA Binding Buffer to the sample and mix by vortexing for 3 seconds.
Add 250 ul ethanol (100%) to the lysate, and mix well by pipetting.
Apply sample (700 ul) to the IVT cRNA Cleanup Spin Column sitting in a 2ml Collection Tube. Centrifuge for 15 seconds at 10,000 rpm. Discard flow-through and collection tube.
Transfer the spin column into a new 2 ml collection tube. Pipet 500 ul IVT cRNA Wash Buffer onto the spin column. Centrifuge for 15 seconds  at full speed to wash. Discard flow-through.
Pipet 50 ul 80% ethanol onto the spin column and centrifuge for 15 seconds at full speed.
Centrifuge for 5 minutes at maximum speed.
Transfer spin column into a new 1.5 ml Collection Tube, and pipet 11 ul of RNase-free Water directly onto the spin column membrane. Centrifuge 1 min at full speed to elute.
Pipet 10 ul of RNase-free water directly onto the spin column membrane.
Centrifuge 1 minute at full speed.
Proceed to Quantification of the cRNA.

extract_protocol:
High-quality total RNA has been successfully isolated from MCF7 cells using the RNeasy Mini Kit from QIAGEN (P\N 74104)
Briefly, disrupt cells by using Buffer RLT.
Pipet the lysate directly onto a QIAshredder spin column placed in a 2ml collection tube, and centrifuge for 2 min at maximum speed.
Add 1 volume of 70% ethanol to the homogenized lysate, and mix well by pipetting.
Apply up to 700 ul of the sample, including any precipitate that may have formed, to an RNeasy mini column placed in a 2ml collection tube. Close the tube gently, and centrifuge for 15s at maximum speed. Discard the flow through.
Add 700ul Buffer RW1 to the RNeasy column. Close the tube gently, and centrifuge for 15s at maximum speed to wash the column. Discard the flow-through and collection tube.
Transfer the RNeasy column into a new 2ml collection tube. Pipet 500 ul Buffer RPE onto the RNeasy column. Close the tube gently, and centrifuge for 15s at maximum speed to wash the column. Discard the flow-through.
Add another 500 ul buffer RPE to the RNeasy column. Centrifuge for 2 min at maximum speed to dry the RNeasy silica-gel membrane.
Place the RNeasy column in a new collection tube. Centrifuge at full speed for 1 min.
Transfer the RNeasy column to a new collection tube. Pipet 50 ul RNase-free water directly onto the RNeasy silica-gel membrane. Close the tube gently, and centrifuge for 1 min at full speed to elute.

tag: Organ

value: mammary gland; breast.

value: epithelial.

tag: adenocarcinoma.

tag: Derived from metastatic site

value: pleural effusion


title: MCF7_nosiRNA_Estrogen

source_name: MCF7 cells, no siRNA, estrogen added

tag: Cell type

tag: Adenocarcinoma.


title: striatum_wildtype_48


title: MCF7_TFAP2AsiRNA_Estrogen

source_name: MCF7 cells, TFAP2A siRNA, estrogen added


title: MCF7_TFAP2CsiRNA_noEstrogen

hyb_protocol: Briefly, a hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol on the fluidics station. Mix the following for each target:Fragmented cRNA, Control Oligonucleotide B2, 20xEukaryotic Hybridization Controls, Herring Sperm DNA, BSA, 2xHybridization Buffer, DMSO and water. Equilibrate probe array to room temperature immediately before use. Heat the hybridization cocktail to 99C for 5 min in a heat block. Meanwhile, wet the array bu filling it through one of the septa with appropriate volume of 1xHybridization Buffer using a micropipettor and appropriate tips. Incubate the probe array filled with 1xHybridization Buffer at 45C for 10 min with rotation. Transfer the hybridization cocktail that has been heated at 99C, to a 45C heat block for 5 min. Spin hybridization cocktail at maximum speed in a microcentrifuge for 5 min to remove any insoluble material from the hybridization mixture. Remove the buffer solution from the probe array cartridge and fill with appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. Place probe array into the Hybridization Oven, set to 45C. Hybridize for 16 hours.

scan_protocol: The arrays were washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner using the manufacturer's recommended protocols by the University of Iowa DNA Core Facility. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol on the fluidics station. Once the probe array has been hybridized, washed, and stained, it is scanned. Each workstation running Affymetrix Microarray Suite can control one scanner. The software defines the probe cells and computes an intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.

source_name: MCF7 cells, TFAP2C siRNA, no estrogen added

tag: organ


title: MCF7_TFAP2CsiRNA_Estrogen

source_name: MCF7 cells, TFAP2C siRNA, estrogen added


title: Pax5-/- pro-B cells transduced with control (MigR1) retrovirus repl2

status: Public on Dec 15 2007

city: Chicago

first: Jian

last: Zhou

state: IL

address: 5841 S Maryland Ave

department: functional Genomics Facility

institute: University of Chicago

description: Gene expression data from Pax5-/- proB cells transduced with control virus.

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

scan_protocol: GeneChips were scanned using Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500. Cel files were further imported into dChip Analyzer 2006 for comparison analysis with d=120 and r=1.2.

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

growth_protocol: Pax5-/- pro-B cells were cultured on ST2 cells in the presence of IL-7 (5ng/ml).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and further purified on RNeasy columns (Qiagen). RNA concentration and purity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies). Integrity of RNA was analyzed with the Agilent 2100 Biolanalyzer (Agilent Technologies).

treatment_protocol: Pax5-/- pro-B cells were infected by spin-infection using control retroviral supernatant. Following infection, cells were cultured on ST2 cells in the presence of IL-7 (5ng/ml). After two days, transduced cells were FACS sorted based on GFP expression and total RNA was isolated.

tag: Pax5-/- proB cell lines were derived from Pax5-/- deficient mice.


title: MCF7_nosiRNA_noEstrogen

source_name: MCF7 cells, no siRNA, no estrogen added


title: Pax5-/- pro-B cells transduced with control (MigR1) retrovirus repl1


title: Pax5-/- pro-B cells transduced with control (MigR1) retrovirus repl3


title: Pax5-/- pro-B cells transduced with EBF (Mig-EBF) retrovirus repl1

description: Gene expression data from Pax5-/- proB cells transduced with EBF.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and further purified on RNeasy columns (Qiagen).  RNA concentration and purity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies).  Integrity of RNA was analyzed with the Agilent 2100 Biolanalyzer (Agilent Technologies).

treatment_protocol: Pax5-/- pro-B cells were infected by spin-infection using EBF retroviral supernatant.  Following infection, cells were cultured on ST2 cells in the presence of IL-7 (5ng/ml).  After two days, transduced cells were FACS sorted based on GFP expression and total RNA was isolated.


title: Pax5-/- pro-B cells transduced with EBF (Mig-EBF) retrovirus repl2


title: Pax5-/- pro-B cells transduced with EBF (Mig-EBF) retrovirus repl3

treatment_protocol: Pax5-/- pro-B cells were infected by spin-infection using EBF retroviral supernatant. Following infection, cells were cultured on ST2 cells in the presence of IL-7 (5ng/ml). After two days, transduced cells were FACS sorted based on GFP expression and total RNA was isolated.


title: striatum_wildtype_2

city: Boston

first: Bradley

last: Molyneaux

state: MA

department: MGH-HMS Center For Nervous System Repair

institute: Harvard Medical School

description: medium spiny neuron, striatum, brain, mutant mouse, Ctip2, Bcl11b, affymetrix

hyb_protocol: Per Affymetrix instructions for Mouse 430 2.0 arrays

data_processing: Microarray data were normalized using the RMA function within Bioconductor (Irizarry et al., 2003).

source_name: Wild type mouse striatum, postnatal day 0

label_protocol: Affymetrix small smple protocol

extract_protocol: RNA was extracted using the StrataPrep Total RNA Mini Kit (Stratagene, La Jolla, CA), and RNA quality was assayed using a bioanalyzer (Agilent Technologies, Paola Alto, CA)

value: BALB/c

tag: Age

value: postnatal day 0

tag: Genotype

value: Wild type


title: CD11b+ sorted rep 3

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

country: Germany

institute: Charité

description: gene expression data of human bone marrow myeloid cells (granulomonocytic series )

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de).

source_name: CD11b+ cells sorted from bone marrow aspirates of normal donor 3

label_protocol: 2µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

growth_protocol: Human BM cells obtained from iliac crest aspirates were amplified by cultivation in alpha-MEM with 10 % fetal calf serum (FCS), 1 ng/mL fibroblast growth factor 2 (FGF2), 20 µmol/L L-glutamine and 100 units/mL penicillin G

extract_protocol: RNA was collected using the RNeasy mini kit (Qiagen)

treatment_protocol: CD235a+, CD45+ and CD11b+ hematopoietic fractions were isolated from BM samples using MACS (Miltenyi).

tag: cell type

value: granulopoietic cells sorted by CD11b labeling of BM cells immediately after BM aspiration


title: striatum_ctip2_KO_1

scan_protocol: Per Affymetrix instructions for Mouse 430 2.0 arrays

source_name: Ctip2 knockout mouse striatum, postnatal day 0

value: Ctip2 null mutant


title: striatum_ctip2_KO_4


title: striatum_het_1

source_name: Ctip2 heterozygous mouse striatum, postnatal day 0

value: Ctip2 heterozygote


title: striatum_wildtype_1


title: striatum_wildtype_3


title: striatum_ctip2_KO_2


title: CD45+ sorted rep 3

description: gene expression data of human bone marrow hematopoietic cells (mostly granulomonocytic series and lymphocytes)

source_name: CD45+ cells sorted from bone marrow aspirates of normal donor 3

value: hematopoietic cells sorted by CD45 labeling of BM cells immediately after BM aspiration


title: CD45+ sorted rep 2

source_name: CD45+ cells sorted from bone marrow aspirates of normal donor 2


title: striatum_ctip2_KO_3


title: CD45+ sorted rep 1

source_name: CD45+ cells sorted from bone marrow aspirates of normal donor 1


title: CD11b+ sorted rep 2

source_name: CD11b+ cells sorted from bone marrow aspirates of normal donor 2


title: CD235a+ sorted rep 2

description: gene expression data of human bone marrow erythroblasts

source_name: CD235a+ cells sorted from bone marrow aspirates of normal donor 2

value: erythropoietic cells sorted by CD235a labeling of BM cells immediately after BM aspiration


title: CD11b+ sorted rep 1

source_name: CD11b+ cells sorted from bone marrow aspirates of normal donor 1


title: CD235a+ sorted rep 3

source_name: CD235a+ cells sorted from bone marrow aspirates of normal donor 3


title: mammary tumor F433T4P1, transplanted, sorted

status: Public on Dec 14 2007

first: Zhe

last: Li

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

description: Gene expression data from sorted mammary tumor

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to MOE 430.2 chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The raw CEL files were imported into dChip and normalized with dChip.

source_name: mammary tumor isolated from a RAG2-/- recipient transplanted with primary tumor #4 from mouse F433, passage 1, sorted

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA followed by cleaning up using columns from the Promega SV total RNA isolation kit.


title: mammary tumor F433T3, sorted

source_name: mammary tumor #3 isolated from mouse F433, sorted


title: mammary tumor D396TP3, transplanted, sorted

source_name: mammary tumor isolated from a RAG2-/- recipient transplanted with primary tumor from mouse D396, passage 3, sorted


title: CD235a+ sorted rep 1

source_name: CD235a+ cells sorted from bone marrow aspirates of normal donor 1


title: hyperplastic MECs H464H, sorted

description: Gene expression data from sorted hyperplastic mammary epithelial cells

source_name: hyperplastic mammary epithelial cells from mouse H464, sorted


title: mammary tumor D279T1P4, transplanted, sorted

source_name: mammary tumor isolated from a RAG2-/- recipient transplanted with primary tumor #1 from mouse D279, passage 4, sorted


title: mammary tumor F433T1, sorted

source_name: mammary tumor #1 isolated from mouse F433, sorted


title: mammary tumor F433T4, sorted

source_name: mammary tumor #4 isolated from mouse F433, sorted


title: WT mammary gland G337, unsorted

description: Gene expression data from unfractionated WT mammary glands

source_name: Wild type mammary glands from mouse G337, unsorted


title: WT mammary gland H235, unsorted

source_name: Wild type mammary glands from mouse H235, unsorted


title: mammary tumor F464T, sorted

source_name: mammary tumor isolated from mouse F464, sorted


title: mammary tumor F402TP2, transplanted, sorted

source_name: mammary tumor isolated from a RAG2-/- recipient transplanted with primary tumor from mouse F402, passage 2, sorted


title: WT mammary gland G360, unsorted

source_name: Wild type mammary glands from mouse G360, unsorted


title: mammary tumor F405T, sorted

source_name: mammary tumor isolated from mouse F405, sorted


title: hyperplastic MECs G376H, sorted

source_name: hyperplastic mammary epithelial cells from mouse G376, sorted


title: mammary tumor E344T2P1, transplanted, sorted

source_name: mammary tumor isolated from a RAG2-/- recipient transplanted with primary tumor #2 from mouse E344, passage 1, sorted


title: mammary tumor D254T2, unsorted

description: Gene expression data from unfractionated mammary tumor

source_name: mammary tumor #2 isolated from mouse D254, unsorted

tag: Wap-Cre;Etv6-NTRK3 nulliparous female


title: mammary tumor D203T1, unsorted

source_name: mammary tumor #1 isolated from mouse D203, unsorted


title: WT mammary gland G340, unsorted

source_name: Wild type mammary glands from mouse G340, unsorted


title: mammary tumor D279T2P2, transplanted, sorted

source_name: mammary tumor isolated from a RAG2-/- recipient transplanted with primary tumor #2 from mouse D279, passage 2, sorted


title: mammary tumor G421T1, sorted

source_name: mammary tumor #1 isolated from mouse G421, sorted


title: WT mammary gland G397, unsorted

source_name: Wild type mammary glands from mouse G397, unsorted


title: mammary tumor D9, unsorted

source_name: mammary tumor isolated from mouse D9, unsorted


title: mammary tumor E344T, sorted

source_name: mammary tumor #1 isolated from mouse E344, sorted


title: mammary tumor G294T, sorted

source_name: mammary tumor isolated from mouse G294, sorted


title: mammary tumor D279T1P2, transplanted, sorted

source_name: mammary tumor isolated from a RAG2-/- recipient transplanted with primary tumor #1 from mouse D279, passage 2, sorted


title: hyperplastic MECs F493H, sorted

source_name: hyperplastic mammary epithelial cells from mouse F493, sorted


title: mammary tumor E93T1, unsorted

source_name: mammary tumor #1 isolated from mouse E93, unsorted


title: mammary tumor D254T1, unsorted

source_name: mammary tumor #1 isolated from mouse D254, unsorted


title: mammary tumor C395T5, unsorted

source_name: mammary tumor #5 isolated from mouse C395, unsorted


title: mammary tumor D14T2, unsorted

source_name: mammary tumor #2 isolated from mouse D14, unsorted

tag: Wap-Cre;Etv6-NTRK3 parous female


title: mammary tumor D206T1, unsorted

source_name: mammary tumor #1 isolated from mouse D206, unsorted


title: mammary tumor C117T6, unsorted

source_name: mammary tumor #6 isolated from mouse C117, unsorted


title: mammary tumor C231T1, unsorted

source_name: mammary tumor #1 isolated from mouse C231, unsorted


title: mammary tumor C393T1, unsorted

source_name: mammary tumor #1 isolated from mouse C393, unsorted


title: mammary tumor D14T1, unsorted

source_name: mammary tumor #1 isolated from mouse D14, unsorted


title: mammary tumor C395T2, unsorted

source_name: mammary tumor #2 isolated from mouse C395, unsorted


title: mammary tumor CR115-4, transplanted, unsorted

source_name: mammary tumor isolated from a RAG2-/- recipient #4 transplanted with primary tumor from mouse CR115, unsorted


title: mammary tumor D481, unsorted

source_name: mammary tumor isolated from mouse D481, unsorted


title: mammary tumor CR90-2, transplanted, unsorted

source_name: mammary tumor isolated from a RAG2-/- recipient #2 transplanted with primary tumor from mouse CR90, unsorted


title: mammary tumor CR115, unsorted, replicate 2

source_name: mammary tumor isolated from mouse CR115, unsorted


title: mammary tumor D206T2, unsorted

source_name: mammary tumor #2 isolated from mouse D206, unsorted


title: mammary tumor CR115, unsorted, replicate 1


title: mammary tumor CR90-1, transplanted, unsorted

source_name: mammary tumor isolated from a RAG2-/- recipient #1 transplanted with primary tumor from mouse CR90, unsorted


title: mammary tumor B459U, unsorted

source_name: mammary tumor U isolated from mouse B459, unsorted


title: mammary tumor D279T1, unsorted

source_name: mammary tumor #1 isolated from mouse D279, unsorted


title: mammary tumor C117T5, unsorted

source_name: mammary tumor #5 isolated from mouse C117, unsorted


title: mammary tumor C117T3, unsorted

source_name: mammary tumor #3 isolated from mouse C117, unsorted


title: mammary tumor CR115-3, transplanted, unsorted

source_name: mammary tumor isolated from a RAG2-/- recipient #3 transplanted with primary tumor from mouse CR115, unsorted


title: mammary tumor C117T1, unsorted

source_name: mammary tumor #1 isolated from mouse C117, unsorted


title: mammary tumor B459L, unsorted

source_name: mammary tumor L isolated from mouse B459, unsorted


title: PARVB/3D/40% Matrigel

city: East Melbourne

first: Cameron

middle: N

last: Johnstone

state: Vic

address: 2 St. Andrew's Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

description: The MAS5 algorithm was used to determine gene expression ratios [Flagged as I (increased), D (decreased), MI (marginally increased), MD (marginally decreased), or NC (no change)], and p values for the change.  Ratios of mRNA expression level between 231_VC and 231_PARVb cells were calculated by determining the inverse log2 of the signal log ratio (S.L.R.) for each differentially-expressed gene.  Array results from 2D and 3D experiments were compared, and Venn diagrams generated using Genespring GX software (Agilent Technologies, Palo Alto, CA).

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix U133_Plus_2 gene chip microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All signal values from one microarray were then multiplied by the appropriate scaling factor.

label: biotinylated CTP and UTP

source_name: MDA-MB-231_PARVB cells (PARVB long isoform)

label_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. 8ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase (Invitrogen) primed by a poly(T) oligomer that incorporated the T7 promoter.  Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript.  The resulting cRNA was used as template for random-primed cDNA synthesis and a second round of in vitro transcription, which incorporated biotinylated CTP and UTP.

growth_protocol: For embedded growth in Matrigel, 6-well plates were coated with 1 ml/well of 80% growth-factor reduced MatrigelTM (BD Biosciences, Bedford, MA) diluted in serum-free DME medium and allowed to set at 37oC.  Cells (3 x 105) were mixed with 1 ml of 40% growth-factor reduced MatrigelTM (also diluted in serum-free DME medium), spread on top of the solidified 80% MatrigelTM layer, and allowed to set prior to addition of 10% FBS-supplemented DME medium. Cells were cultured for 7 days with a change of medium every 2 days.

extract_protocol: 10ml of Trizol reagent (Invitrogen) was added to the well containing MDA-MB-231_PARVB cells embedded in Matrigel. The cells and Matrigel (approximately 2ml volume) were digested in Trizol by drawing the mixture through a 21G needle (at least 10 times) times followed by incubation at room temperature for 10-15min in a 15ml sterile plastic tube. 2.5ml of chloroform was then added and the mixture shaken vigorously. The sample was then centrifuged at 11,000rpm (at 4oC) for 30min and the clear upper (aqueous) layer transferred to a sterile 15ml glass tube. 5ml of isopropanol was then added and the mixture cooled at -20oC for at least 20min. The mixture was then centrifuged at 11,000rpm (4oC) for 30min and the RNA pellet washed thoroughly with 75% ethanol in DEPC-treated sterile water. RNA was then resuspended in DEPC-treated sterile water.

treatment_protocol: MDA-MB-231 cells were cultured in DMEM containing 10% fetal bovine serum (FBS) at 37oC in a 5% carbon-dioxide containing incubator without antibiotics or anti-fungal agents.

tag: MDA-MB-231 human metastatic breast ductal carcinoma cell line derived from pleural effusion transfected with human Parvin-beta (long isoform) cDNA cloned into the pcDNA3.1/Myc-His (clone B) plasmid and selected for stable integration using G418.


title: vector/3D/bovine type I collagen

source_name: MDA-MB-231 vector control cells (pcDNA3.1)

growth_protocol:
For embedded growth in type I collagen, cells (3 x 105) were mixed with 1.5mg/ml bovine epidermal type I collagen (Inamed Biomaterials, Fremont, CA) to a total volume of 2ml, and then added to 6 well plates.  The collagen was allowed to set at 37oC prior to addition of 10% FBS-containing DMEM culture medium.  Cells were cultured for 7 days with a change of medium every 2 days.
 and allowed to set prior to addition of 10% FBS-supplemented DME medium. Cells were cultured for 7 days with a change of medium every 2 days.

extract_protocol: 10ml of Trizol reagent (Invitrogen) was added to the well containing MDA-MB-231_vector control cells embedded in bovine type I collagen. The cells and collagen (approximately 2ml volume) were digested in Trizol by drawing the mixture through a 21G needle (at least 10 times) times followed by incubation at room temperature for 10-15min in a 15ml sterile plastic tube. 2.5ml of chloroform was then added and the mixture shaken vigorously. The sample was then centrifuged at 11,000rpm (at 4oC) for 30min and the clear upper (aqueous) layer transferred to a sterile 15ml glass tube. 5ml of isopropanol was then added and the mixture cooled at -20oC for at least 20min. The mixture was then centrifuged at 11,000rpm (4oC) for 30min and the RNA pellet washed thoroughly with 75% ethanol in DEPC-treated sterile water. RNA was then resuspended in DEPC-treated sterile water.

treatment_protocol: MDA-MB-231 cells were cultured in DMEM containing 10% fetal bovine serum (FBS) at 37oC in a 5% carbon dioxide-containing incubator without antibiotics or anti-fungal agents.

tag: MDA-MB-231 human metastatic breast ductal carcinoma cell line derived from pleural effusion transfected with pcDNA3.1 Myc-His (clone B) plasmid and selected for stable integration using G418.


title: Eph_EN_DN tumor 2

description: Gene expression data from mammary epithelial cell line generated tumor

source_name: mammary tumor #2 isolated from a nude mouse transplanted with ETV6-NTRK3 transduced Eph4 cells co-expressing the dominant negative (DN) version of c-Jun (TAM67)

tag: EN/DN-Eph4 cells transplanted into nude mice


title: PARVB/3D/bovine type I collagen

growth_protocol:
For embedded growth in type I collagen, cells (3 x 105) were mixed with 1.5mg/ml bovine epidermal type I collagen (PureCol, Inamed Biomaterials, Fremont, CA) to a total volume of 2ml, and then added to 6 well plates.  The collagen was allowed to set at 37oC prior to addition of 10% FBS-containing DMEM culture medium.  Cells were cultured for 7 days with a change of medium every 2 days.
 and allowed to set prior to addition of 10% FBS-supplemented DME medium. Cells were cultured for 7 days with a change of medium every 2 days.

extract_protocol: 10ml of Trizol reagent (Invitrogen) was added to the well containing MDA-MB-231_PARVB3 cells embedded in bovine type I collagen. The cells and collagen (approximately 2ml volume) were digested in Trizol by drawing the mixture through a 21G needle (at least 10 times) times followed by incubation at room temperature for 10-15min in a 15ml sterile plastic tube. 2.5ml of chloroform was then added and the mixture shaken vigorously. The sample was then centrifuged at 11,000rpm (at 4oC) for 30min and the clear upper (aqueous) layer transferred to a sterile 15ml glass tube. 5ml of isopropanol was then added and the mixture cooled at -20oC for at least 20min. The mixture was then centrifuged at 11,000rpm (4oC) for 30min and the RNA pellet washed thoroughly with 75% ethanol in DEPC-treated sterile water. RNA was then resuspended in DEPC-treated sterile water.

tag: MDA-MB-231 human metastatic breast ductal carcinoma cell line derived from pleural effusion transfected with human Parvin-beta (long isoform) cloned into the pcDNA3.1 Myc-His (clone B) plasmid and selected for stable integration using G418.


title: Eph_EN_DN tumor 1

source_name: mammary tumor #1 isolated from a nude mouse transplanted with ETV6-NTRK3 transduced Eph4 cells co-expressing the dominant negative (DN) version of c-Jun (TAM67)


title: Eph_EN tumor 1

source_name: mammary tumor #1 isolated from a nude mouse transplanted with ETV6-NTRK3 transduced Eph4 cells

tag: EN-Eph4 cells transplanted into nude mice


title: Lip-O-treated sham OBX C57 mouse, biol rep1

city: Lexington

first: Marilyn

middle: L.

last: Getchell

state: KY

address: 800 South Limestone St.

department: Anatomy and Neurobiology

institute: University of Kentucky

description: Gene expression data from olfactory epithelium of Lip-O-treated sham OBX C57 mice

hyb_protocol: Following fragmentation, 13.33 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner

data_processing: The data were analyzed with Affymetrix MicroArray Suite 5.0 using Affymetrix default analysis settings.  A threshold value of 1,500 was used to normalize the data across all the microarrays.

source_name: microdissected olfactory epithelium

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: The mice were purchased from Jackson Laboratories (Bar Harbor, ME) at 5 weeks of age and were maintained in an animal facility at the University of Kentucky Department of Laboratory Animal Research (DLAR) until they reached 6 weeks of age.  At the DLAR, they were kept on a 12 hr light:dark cycle in Bioclean units with sterile-filtered air and provided food and water ad libitum.

extract_protocol: Snap-frozen microdissected olfactory epithelium was pulverized in TRI Reagent (Sigma-Aldrich, St. Louis, MO) and processed through a QIAshredder column (Qiagen, Valencia, CA).  The total RNA was further purified using the Qiagen RNeasy Mini-Kit according to the manufacturer’s protocol.  Total RNA yield and purity was assessed with a spectrophotometer and with the model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA); all samples had A260/A280 ratios of 1.9–2.2 and showed two sharp peaks corresponding to 18S and 28S RNA on the Bioanalyzer electropherograms.

treatment_protocol: For controls, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of empty liposomes (Lip-O) once per day at 4 PM for three consecutive days and injected intravenously (i.v.) with 200 µl Lip-O in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral sham olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following sham OBX. Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.

value: w/t; strain C57BL/6J; male, 6 weeks old, olfactory epithelium


title: Eph_EN tumor 2

source_name: mammary tumor #2 isolated from a nude mouse transplanted with ETV6-NTRK3 transduced Eph4 cells


title: Lip-O-treated 48 hr OBX C57 mouse, biol rep2

description: Gene expression data from olfactory epithelium of Lip-O-treated 48 hr OBX C57 mice

treatment_protocol: For controls, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of empty liposomes (Lip-O) once per day at 4 PM for three consecutive days and injected intravenously (i.v.) with 200 µl Lip-O in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following OBX. Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.


title: vector/3D/40% Matrigel

source_name: MDA-MB-231_vector control cells (pcDNA3.1)

extract_protocol: 10ml of Trizol reagent (Invitrogen) was added to the well containing MDA-MB-231_vector control cells embedded in Matrigel. The cells and Matrigel (approximately 2ml volume) were digested in Trizol by drawing the mixture through a 21G needle (at least 10 times) times followed by incubation at room temperature for 10-15min in a 15ml sterile plastic tube. 2.5ml of chloroform was then added and the mixture shaken vigorously. The sample was then centrifuged at 11,000rpm (at 4oC) for 30min and the clear upper (aqueous) layer transferred to a sterile 15ml glass tube. 5ml of isopropanol was then added and the mixture cooled at -20oC for at least 20min. The mixture was then centrifuged at 11,000rpm (4oC) for 30min and the RNA pellet washed thoroughly with 75% ethanol in DEPC-treated sterile water. RNA was then resuspended in DEPC-treated sterile water.

tag: MDA-MB-231 human metastatic breast ductal carcinoma cell line derived from pleural effusion transfected with pcDNA3.1/Myc-His (clone B) plasmid and selected for stable integration using G418.


title: Lip-C-treated 48 hr OBX C57 mouse, biol rep2

description: Gene expression data from olfactory epithelium of Lip-C-treated 48 hr OBX C57 mice

treatment_protocol: To deplete OE macrophages, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of liposomes containing clodronate (Lip-C) once per day at 4 PM for three consecutive days.  To deplete a subpopulation of blood monocytes, the mice were injected intravenously (i.v.) with 200 µl Lip-C in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following OBX. Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.


title: Neuron_CTL_IBN_Rep2

status: Public on Dec 13 2007

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

description: The control for hybridization and labeling were from Affymetrix.

hyb_protocol: Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Human Genome HG-U133_Plus_2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.

scan_protocol: Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software

data_processing: Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition

label: phycoerythrin

source_name: Human Clonal Cord blood stem cells transdifferentiated into Human Neuronal cells that were initially derived from Human CD34+ & CD133+ Cord Blood stem cell population.

label_protocol: One ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)

extract_protocol: Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer

value: Adult, Human Cord Blood derived stem cells

tag: They were maintained in the undifferentiated state in Celprogen’s Human Neuronal Cell Complete Growth undifferentiating Medium and subcultured every 24 to 48 hours on Human Neuronal Extracellular matrix.

tag: Untreated


title: Lip-O-treated sham OBX C57 mouse, biol rep2

treatment_protocol: For controls, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of empty liposomes (Lip-O) once per day at 4 PM for three consecutive days and injected intravenously (i.v.) with 200 µl Lip-O in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral sham olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following sham OBX.  Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.


title: Lip-O-treated 48 hr OBX C57 mouse, biol rep1

treatment_protocol: For controls, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of empty liposomes (Lip-O) once per day at 4 PM for three consecutive days and injected intravenously (i.v.) with 200 µl Lip-O in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following OBX.  Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.


title: NHA_BV_IBN_Rep3

source_name: Normal Human Astrocytes from Lonza infected at MOI 100 with Baculovirus expressing luciferase

tag: Cell strain

value: Normal Human Astrocytes (NHA)

tag: Passage

tag: Growth Medium

value: Astrocyte Basal Medium (ABM™) and the following growth supplements:rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.

tag: Grown at 37C in 5%CO2, seeded at 5000 cells/cm2

tag: Infected overnight with Baculovirus expressing luciferase gene under control of CMV promoter, extraction was done 48h after infection


title: PARVB/2D/bovine type I collagen

growth_protocol: Plastic tissue culture plates were coated with bovine type I collagen (60ug/ml) (PureCol, Inamed Biomaterials, Fremont, CA) and allowed to air-dry before addition of medium. MDAMB231 cells were cultured for 5-7 days and harvested while still pre-confluent.

extract_protocol: Trizol reagent (Invitrogen) was added to a 10cm plate containing pre-confluent MDA-MB-231 vector control cells. The lyzed cells were drawn through a 21G needle several times and allowed to stand at room temperature for 5min in a 15ml sterile plastic tube. 1.3ml of chloroform was then added and the mixture shaken vigorously. The sample was then centrifuged at 11,000rpm (at 4oC) for 30min and the upper (aqueous) layer transferred to a sterile 15ml glass tube. 2.5ml of isopropanol was then added and the mixture cooled at -20oC for at least 20min. The mixture was then centrifuged at 11,000rpm (4oC) for 30min and the RNA pellet washed thoroughly with 75% ethanol in DEPC-treated sterile water. RNA was then resuspended in DEPC-treated sterile water.

tag: MDA-MB-231 human metastatic breast ductal carcinoma cell line derived from pleural effusion transfected with Parvin-beta (long isoform) cloned into the pcDNA3.1 Myc-His (clone B) plasmid and selected for stable integration using G418.


title: Lip-C-treated 48 hr OBX C57 mouse, biol rep3

treatment_protocol: To deplete OE macrophages, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of liposomes containing clodronate (Lip-C) once per day at 4 PM for three consecutive days.  To deplete a subpopulation of blood monocytes, the mice were injected intravenously (i.v.) with 200 µl Lip-C in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following OBX.  Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.

tag: Genotype


title: vector/2D/bovine type I collagen


title: Lip-C-treated sham OBX C57 mouse, biol rep2

description: Gene expression data from olfactory epithelium of Lip-C-treated sham OBX C57 mice

treatment_protocol: To deplete OE macrophages, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of liposomes containing clodronate (Lip-C) once per day at 4 PM for three consecutive days.  To deplete a subpopulation of blood monocytes, the mice were injected intravenously (i.v.) with 200 µl Lip-C in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral sham olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following sham OBX.  Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.


title: Neuron_CTL_IBN_Rep1

tag: Human Clonal Cord blood stem cells transdifferentiated into Human Neuronal cells that were initially derived from Human CD34+ & CD133+ Cord Blood stem cell population.

tag: Age


title: Neuron_CTL_IBN_Rep3


title: Lip-O-treated 48 hr OBX C57 mouse, biol rep3


title: Neuron_BV_IBN_Rep1

source_name: Human Clonal Cord blood stem cells transdifferentiated into Human Neuronal cells that were initially derived from Human CD34+ & CD133+ Cord Blood stem cell population infected with baculovirus (MOI 100).

tag: Infected 48hrs with Baculovirus expressing GFP at MOI 100


title: Lip-C-treated sham OBX C57 mouse, biol rep1

treatment_protocol: To deplete OE macrophages, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of liposomes containing clodronate (Lip-C) once per day at 4 PM for three consecutive days.  To deplete a subpopulation of blood monocytes, the mice were injected intravenously (i.v.) with 200 µl Lip-C in the lateral tail vein on the first and third days of i.n. injections at the same time of day.  Mice underwent bilateral sham olfactory bulbectomy on the second day of i.n. injections.  Mice were euthanized at 48 h following sham OBX. Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.


title: Neuron_BV_IBN_Rep3


title: TERT-ON skin at 24hr, biological rep2

city: Stanford

first: Jinkuk

last: Choi

state: CA

address: 269 Campus Dr. CCSR Rm. 1150

department: Medicine

institute: Stanford University

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 24 hr timepoint, biological replicate 2

hyb_protocol: 10 mcg of biotinylated aRNA were hybridized for 16 hr at 45C on Genechip (Affymetrix Mouse Genome 430 2.0 Array) at the Stanford University Protein and Nucleic Acid Facility.

scan_protocol: Array was scanned at the Stanford University Protein and Nucleic Acid Facility. Pixel Size 1.56, Filter 570, Scanner ID 50102080, Number of Scans 1, Scanner Type M10

data_processing: Probe intensity was calculated by Affymetrix MAS software, and the resulting CEL files were analyzed by dChip software; arrays were normalized based on invariant sets, and gene expression levels were calculated using the PM/MM difference model.

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 24-hr timepoint, no doxycycline injection

label_protocol: mRNA from purified total RNA (1 mcg) was amplified, labeled and fragmented using MessageAmp II-Biotin Enhanced Kit (Ambion).

growth_protocol: Doxycycline (5 mcg/ml) was administered in drinking water throughout development until post-natal day 10-21 to continually suppress transgenic TERT expression during development and allow TERT upregulation to occur postnatally.

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen), and subsequently purified by RNeasy column (Qiagen).

treatment_protocol: Dorsal skin biopsies (3 cm^2) were immediately soaked in 10 volume of RNAlater (Ambion) overnight at 4 ¨¬C. The subcutaneous fat layer was surgically removed later, prior to RNA extraction.

value: iK5-TERT (K5tTA-tetop-TERT), Hair follicle status:Anagen, Age:day 60

tag: Doxycycline injection

value: No (TERT is continually over-expressed), Time-point:24 hr, Biological replicate 2


title: Lip-C-treated sham OBX C57 mouse, biol rep3


title: Lip-O-treated sham OBX C57 mouse, biol rep3


title: Lip-C-treated 48 hr OBX C57 mouse, biol rep1


title: Neuron_BV_IBN_Rep2


title: TERT-ON skin at 6hr, biological rep2

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 6 hr timepoint, biological replicate 2

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 6-hr timepoint, no doxycycline injection

value: No (TERT is continually over-expressed), Time-point:6 hr, Biological replicate 2


title: NHA_BV_IBN_Rep2


title: NHA_CTL_IBN_Rep1

source_name: Normal Human Astrocytes from Lonza


title: NHA_CTL_IBN_Rep2


title: NHA_CTL_IBN_Rep3


title: TERT-ON skin at 12hr, biological rep2

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 12 hr timepoint, biological replicate 2

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 12-hr timepoint, no doxycycline injection

value: No (TERT is continually over-expressed), Time-point:12 hr, Biological replicate 2


title: TERT-ON skin at 24hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 24 hr timepoint, biological replicate 1

value: No (TERT is continually over-expressed), Time-point:24 hr, Biological replicate 1


title: TERT-ON skin at 6hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 6 hr timepoint, biological replicate 1

data_processing: Probe intensity was calculated by Affymetrix MAS software, and the resulting CEL files were analyzed by dChip software; arrays were normalized based on invariant sets, and gene expression levels were calculated using the  PM/MM difference model.

value: No (TERT is continually over-expressed), Time-point:6 hr, Biological replicate 1


title: HepG2/C3A cells control medium for 42 h  (Long +Cys) #6

city: Ithaca

first: Wei

last: Wang

address: T2-003 Vet Res Tower

institute: Cornell University

description: Affymetrix standard

hyb_protocol: Affymetrix standarad

scan_protocol: Affymetrix standarad

source_name: Human cell line; C3A cells derived from HepG2 cells

label_protocol: Affymetrix standarad

extract_protocol: Qiagen RNeasy

tag: C3A cells derived from HepG2 cells; human hepatoma cell line; study of cysteine deprivation


title: NHA_BV_IBN_Rep1


title: TERT-ON skin at 0hr, biological rep2

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 0 hr timepoint, biological replicate 2

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 0-hr timepoint, no doxycycline injection

value: No (TERT is continually over-expressed), Time-point:0 hr, Biological replicate 2


title: TERT-OFF skin at 24hr, biological rep2

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 24 hr timepoint, biological replicate 2

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 24-hr timepoint, doxycycline (8 mcg/g body weight) injected

value: Yes (TERT is acutely withdrawed), Time-point:24 hr, Biological replicate 2


title: hyperplastic MECs G420H, sorted

description: Gene expression data from sorted hyperplastic mammary epithelial cells

source_name: hyperplastic mammary epithelial cells from mouse G420, sorted


title: HepG2/C3A cells complete medium followed by 6 h of cysteine deprivation (Short -Cys) #3

description: Affymetrix standard

source_name: Human cell line  C3A cells derived from HepG2 cells


title: TERT-OFF skin at 24hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 24 hr timepoint, biological replicate 1

value: Yes (TERT is acutely withdrawed), Time-point:24 hr, Biological replicate 1


title: HepG2/C3A cells control medium for 42 h  (Long +Cys) #5

description: Affymetrix standard

source_name: Human cell line; C3A/HepG2 cells


title: HepG2/C3A cells control medium for 42 h (Long +Cys) #4

description: Affymetrix standard

source_name: Human cell line ; C3A/HepG2 cells


title: TERT-ON skin at 12hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 12 hr timepoint, biological replicate 1

value: No (TERT is continually over-expressed), Time-point:12 hr, Biological replicate 1


title: TERT-OFF skin at 6hr, biological rep2

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 6 hr timepoint, biological replicate 2

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 6-hr timepoint, doxycycline (8 mcg/g body weight) injected

value: Yes (TERT is acutely withdrawed), Time-point:6 hr, Biological replicate 2


title: TERT-OFF skin at 12hr, biological rep2

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 12 hr timepoint, biological replicate 2

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 12-hr timepoint, doxycycline (8 mcg/g body weight) injected

value: Yes (TERT is acutely withdrawed), Time-point:12 hr, Biological replicate 2


title: HepG2/C3A cells complete medium followed by 6 h of cysteine deprivation (Short -Cys) #1

description: Affymetrix standard


title: TERT-OFF skin at 6hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 6 hr timepoint, biological replicate 1

value: Yes (TERT is acutely withdrawed), Time-point:6 hr, Biological replicate 1


title: TERT-OFF skin at 0hr, biological rep2

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 0 hr timepoint, biological replicate 2

source_name: iK5-TERT mouse dorsal skin biopsy at postnatal day 60, 0-hr timepoint, doxycycline (8 mcg/g body weight) injected

value: Yes (TERT is acutely withdrawed), Time-point:0 hr, Biological replicate 2


title: HepG2/C3A cells complete medium followed by 6 h of cysteine deprivation (Short -Cys) #2

description: Affymetrix standard

source_name: Human cell line C3A cells derived from HepG2 cells


title: TERT-ON skin at 0hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-ON cohort at 0 hr timepoint, biological replicate 1

value: No (TERT is continually over-expressed), Time-point:0 hr, Biological replicate 1


title: HepG2/C3A cells cys depletion followed by 6 h +Cys (Short +Cys) #6

description: Affymetrix standard

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

source_name: human cell line

label_protocol: Affymetrix 1 cycle


title: HepG2/C3A cells control medium for 42 h  (Long +Cys)#8

description: Affymetrix standard


title: HepG2/C3A cells control medium for 42 h  (Long +Cys)#9

description: Affymetrix standard


title: TERT-OFF skin at 12hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 12 hr timepoint, biological replicate 1

value: Yes (TERT is acutely withdrawed), Time-point:12 hr, Biological replicate 1


title: TERT-OFF skin at 0hr, biological rep1

description: Gene expression data from mouse skin in TERT-induced anagen, TERT-OFF cohort at 0 hr timepoint, biological replicate 1

value: Yes (TERT is acutely withdrawed), Time-point:0 hr, Biological replicate 1


title: HepG2/C3A cells cys depletion followed by 6 h +Cys (Short +Cys) #4

description: Affymetrix standard


title: HepG2/C3A cells cys depletion followed by 6 h +Cys (Short +Cys)  #5

description: Affymetrix standard