title: Human lymphatic endothelial cells TNFalpha_Rep 1

source_name: Primary lymphatic endothelial cells cultured in vitro for 72h +/- TNFalpha derived from skin samples obtained from healthy human donors during elective surgery.


title: CD4_T_cells_2

status: Public on Dec 01 2006

type: RNA

city: New York

first: Diana

last: Dudziak

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: Gene expression data from purified splenic DCs from 5-8 WT C57BL6 mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE-430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: The data were analyzed with GCOS (same algorithm as MAS5.0 and newer version) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Wildtype (WT) C57BL/6 mice

tag: Splenic CD4 T Cells from WT mice, enriched withThy1.2 beads (Milteny) and sorted for CD3/CD4 positive CD4 T cells (CD3/CD4/CD8 staining)

tag: C57BL/6 mice, Gender Female, Age 6-8 weeks


title: p63shRNA_B3, p63-depleted

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix HG-U133 plus 2.0 GeneChip, washed, and stained according to manufacturer’s instructions.

data_processing: Data were processed by Affymetrix GeneChip Operating Software (GCOS), followed by global median normalization.

organism: Homo sapiens

source_name: Cervical carcinoma

label_protocol: Total RNA was converted to cDNA using T7-oligo(dT) and in vitro transcribed to obtain biotin-labeled cRNA for hybridization.

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum.

extract_protocol: Trizol (Invitrogen), per manufacturer’s instructions.

treatment_protocol: Cells were transduced with lentiviral supernatant containing pLL p63shRNA or empty vector (control), and harvested ~65 hours later.

tag: Age

value: 66 yrs Gender:Female  Ethnicity:Caucasian


title: CD8_T_cells_1

tag: Splenic CD8 T Cells from WT mice, enriched withThy1.2 beads (Milteny) and sorted for CD3/CD8 positive CD8 T cells (CD3/CD4/CD8 staining)


title: CD4_T_cells_3


title: T98G_T3_R2, Spheroid Recovery

city: Blacksburg

first: Richard

middle: F.

last: Helm

state: VA

address: West Campus Drive

department: Biochemistry, Fralin Biotechnology Center

institute: Virginia Polytechnic Institute and State University

description:
60% confluent human T98G glioma cancer cells were split into suspension over agarose to form spheroids and grown for an additional 4 days in suspension over agarose prepared with 10% FBS and 5% non essential amino acids supplemented EMEM.
Following growth, media was removed and the spheroids were stored on the surface of the agarose in vacuum sealed flasks for a 2 week interval at room temperature in the dark.
The samples were compared against monolayer (at 60% confluence)samples. All samples were conducted intriplicate.
Samples from the two week arrest were removed from storage and supplemented with EMEM (Invitrogen) containing 15% FBS (spheroid recovery sample).  These cells were then allowed to grow out as adherent monolayers for 7 days (monolayer recovery sample).

source_name: Human T98G Glioma Cancer Cells


title: CD4_T_cells_1


title: CD8_T_cells_3


title: control_B2, empty vector


title: T98G_T4_R1, Monolayer Recovery


title: T98G_T2_R3, Spheroid


title: CD8_T_cells_2


title: T98G_T4_R3, Monolayer Recovery


title: T98G_T4_R2, Monolayer Recovery


title: T98G_T3_R3, Spheroid Recovery


title: T98G_T1_R3, Monolayer


title: control_B1, empty vector


title: B_cells_3

tag: Spleen B Cells from Wtmice, negatively enriched with CD43 beads (Milteny) and sorted for B220/CD19/IgM positive B cells


title: T98G_T2_R2, Spheroid


title: T98G_T2_R1, Spheroid


title: T98G_T1_R1, Monolayer


title: B_cells_1


title: T98G_T3_R1, Spheroid Recovery


title: T98G_T1_R2, Monolayer


title: B_cells_2


title: 33D1_WT_3

description: Gene expression data from purified splenic DCs from 40-80 WT C57BL6 mice

tag: Spleen Dendritic Cells from WT mice, negatively enriched with CD19, CD90.2 and DX5 beads (Milteny) and sorted for 33D1 positive DCs (33D1A647, DEC205bio/SAPECy7/CD11cPE (High)), (equivalent to CD11c(High),CD8neg spleen DCs)


title: DEC205_WT_3

tag: Spleen Dendritic Cells from WT mice, negatively enriched with CD19, CD90.2 and DX5 beads (Milteny) and sorted for DEC205/CD205 positive DCs (33D1A647, DEC205bio/SAPECy7/CD11cPE (High)), (equivalent to CD11c(High),CD8 Positive spleen DCs


title: HFF2_T3_R1, Spheroid Recovery

description:
60% confluent human foreskin fibroblast (HFF2) primary cells were split into suspension over agarose to form spheroids and grown for an additional 4 days in suspension over agarose prepared with 15% FBS supplemented DMEM.
Following growth, media was removed and the spheroids were stored on the surface of the agarose in vacuum sealed flasks for a 2 week interval at room temperature in the dark.
The samples were compared against monolayer (at 60% confluence). All samples were conducted in triplicate.
Samples from the two week arrest were removed from storage and supplemented with DMEM (Invitrogen) containing 15% FBS (spheroid recovery sample).  These cells were then allowed to grow out as adherent monolayers for 7 days (monolayer recovery sample).

source_name: Human Foreskin Fibroblast (HFF2) Primary Cells


title: HFF2_T3_R2, Spheroid Recovery


title: DEC205_Flt3L_2

description: Gene expression data from purified splenic DCs from 20 Flt3L Melanom injected C57BL6 mice

treatment_protocol: Flt3L Melanom injected, sacrified day 10-12

tag: Spleen Dendritic Cells from Flt3L Melanom injected mice (12days), negatively enriched with CD19, CD90.2 and DX5 beads (Milteny) and sorted for DEC205/CD205 positive DCs (33D1A647, DEC205bio/SAPECy7/CD11cPE (High)), (equivalent to CD11c(High),CD8 Positive spleen DCs


title: DEC205_WT_1


title: HFF2_T2_R3, Spheroid


title: HFF2_T4_R3, Monolayer Recovery


title: DEC205_Flt3L_1


title: 33D1_WT_1


title: HFF2_T3_R3, Spheroid Recovery


title: HFF2_T4_R2, Monolayer Recovery


title: DEC205_Flt3L_3


title: HFF2_T1_R2, Monolayer


title: HFF2_T4_R1, Monolayer Recovery


title: HFF2_T2_R1, Spheroid


title: HFF2_T2_R2, Spheroid


title: HFF2_T1_R3, Monolayer


title: 33D1_Flt3L_3

tag: Spleen Dendritic Cells from Flt3L Melanom injected mice (12days), negatively enriched with CD19, CD90.2 and DX5 beads (Milteny) and sorted for 33D1 positive DCs (33D1A647, DEC205bio/SAPECy7/CD11cPE (High)), (equivalent to CD11c(High),CD8neg spleen DCs)


title: 33D1_Flt3L_1


title: 33D1_Flt3L_2


title: HFF2_T1_R1, Monolayer


title: prostate cancer, metastatic

status: Public on Nov 27 2006

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Gene expression data from human prostate cancer of metastatic tissue

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

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

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

label: biotin

source_name: Human Prostate Cancer, Metastatic Tissue Sample

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

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

tag: prostate cancer

tag: metastatic


title: prostate cancer, non-metastatic

description: Gene expression data from human prostate cancer of non-metastatic tissue

source_name: Human Prostate Cancer, Non-metastatic Tissue Sample

tag: non-metastatic


title: chorion villus cells_normalkaryotype_rep4

city: Tuebingen

first: Oezge

last: Altug Teber

address: Calwerstr. 7

department: Medical Genetics

country: Germany

institute: University of Tuebingen

description: prenatal euploid sample

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Call detection and signal intensities were generated by Affymetrix GCOS software. Raw data were imorted into ArrayAssist version 4.1 software. For normalization, GC-RMA normalization algorithm implemented in ArrayAssist were applied.

source_name: chorion villus cells, normal karyotype

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Primary cell cultures of the amniocytes were performed using slide flasks (with NunclonTM surface, 9 cm2, NUNCTM). Amniocytes were grown in Amnio Max C100 Basal Medium and Amnio Max C100 Supplement (Invitrogen) at 37°C in 5% CO2. The second successive subculture was set up in culture flasks (with CELLSTAR® surface, 25 cm2, Greiner bio-one) using the same medium.

extract_protocol: Cells were harvested by centrifugation and media was removed by suction. The cells were then resuspended in RLT-buffer provided in RNeasy mini kit (QIAGEN) and total RNA was isolated from each cell culture using RNeasy mini kit according to manufacturer’s instructions (QIAGEN).

treatment_protocol: No treatment

tag: tissue

value: prenatal chorion villus cells

value: 12 gestational weeks

tag: gender

value: female

tag: karyotype

value: normal


title: 33D1_WT_2


title: small airways, COPD 021, MAS5

status: Public on Nov 21 2006

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: small airways, COPD 021, MAS5

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Sex

value: F

tag: Ethnic group

value: white

tag: Smoking Status

value: COPD, GOLD-0, 20 pack-years


title: small airways, early-COPD 064, MAS5

description: small airways, early-COPD 064, MAS5

value: M

value: hispanic

value: early-COPD, 90 pack-years


title: small airways, COPD 020, MAS5

description: small airways, COPD 020, MAS5

value: COPD, GOLD-I, 20 pack-years


title: small airways, COPD 015, MAS5

description: small airways, COPD 015, MAS5

value: COPD, GOLD-II, 18 pack-years


title: small airways, early-COPD 086, MAS5

description: small airways, early-COPD 086, MAS5

value: black

value: early-COPD, 20 pack-years


title: small airways, early-COPD 037, MAS5

description: small airways, early-COPD 037, MAS5

value: early-COPD, 43 pack-years


title: small airways, COPD 012, MAS5

description: small airways, COPD 012, MAS5

tag: age

tag: sex

tag: ethnic group

tag: smoking status

value: COPD, GOLD-II, 33 pack-years


title: small airways, smoker 023, RMA and MAS

description: small airways, smoker 023, RMA and MAS

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

data_processing: The CEL files were generated using Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

tag: Age

value: smoker, 20 pack-years


title: small airways, COPD 008, MAS5

description: small airways, COPD 008, MAS5

value: COPD, GOLD-I, 50 pack-years


title: small airways, early-COPD 009, MAS5

description: small airways, early-COPD 009, MAS5


title: small airways, smoker 041, RMA and MAS

description: small airways, smoker 041, RMA and MAS

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


title: small airways, smoker 049, RMA and MAS

description: small airways, smoker 049, RMA and MAS

value: smoker, 23 pack-years


title: small airways, early-COPD 045, MAS5

description: small airways, early-COPD 045, MAS5

value: early-COPD, 31 pack-years


title: small airways, smoker 044, RMA and MAS

description: small airways, smoker 044, RMA and MAS

value: smoker, 38 pack-years


title: small airways, COPD 002, MAS5

description: small airways, COPD 002, MAS5

value: COPD, GOLD-0, 13 pack-years


title: small airways, early-COPD 012, MAS5

description: small airways, early-COPD 012, MAS5

value: early-COPD, 12 pack-years


title: small airways, smoker 063, MAS5

description: small airways, smoker 063, MAS5

value: white

value: smoker, 60 pack-years


title: small airways, early-COPD 020, MAS5

description: small airways, early-COPD 020, MAS5

value: F

value: early-COPD, 30 pack-years


title: small airways, smoker 027, RMA and MAS

description: small airways, smoker 027, RMA and MAS

value: M

value: smoker, 45 pack-years


title: small airways, smoker 048, RMA and MAS

description: small airways, smoker 048, RMA and MAS

value: black

value: smoker, 28 pack-years


title: small airways, smoker 033, RMA and MAS

description: small airways, smoker 033, RMA and MAS

value: smoker, 15 pack-years


title: small airways, smoker 003, RMA and MAS

description: small airways, smoker 003, RMA and MAS

value: smoker, 25 pack-years


title: small airways, smoker 058, MAS5

description: small airways, smoker 058, MAS5

value: smoker, 80 pack-years


title: small airways, smoker 002, RMA and MAS

description: small airways, smoker 002, RMA and MAS

value: smoker, 21 pack-years


title: small airways, early-COPD 054, MAS5

description: small airways, early-COPD 054, MAS5

value: early-COPD, 50 pack-years


title: small airways, non-smoker 015, RMA and MAS

value: non-smoker


title: DEC205_WT_2

tag: Spleen Dendritic Cells from WT mice, negatively enriched with CD19, CD90.2 and DX5 beads (Milteny) and sorted for DEC205/CD205 positive DCs (33D1A647, DEC205bio/SAPECy7/CD11cPE (High)), (equivalent to CD11c(High),CD8 Positive spleen DCs

tag: C57BL/6 mice, Gender Female, Age 6-8 weeks


title: small airways, smoker 001, RMA and MAS

description: small airways, smoker 001, RMA and MAS

value: smoker, 23 pack-years


title: small airways, non-smoker 005, RMA and MAS


title: small airways, non-smoker 021, RMA and MAS

value: hispanic


title: small airways, non-smoker 019, RMA and MAS


title: small airways, non-smoker 013, RMA and MAS


title: small airways, non-smoker 008, RMA and MAS


title: larrydissectedbudsample3

status: Public on Nov 18 2006

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7113

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 5ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: ureteric bud

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: Approx 50 sections from 5 kidneys
Pooled sample: Yes
Dissection Method: Laser capture microdissection
CD-1 mice are time-mated.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses placed in OCT in a mold, frozen in liquid nitrogen and stored at -80°C. Blocks are sectioned, stained and used for laser capture micro-dissection.

tag: gene reported

value: wild-type

tag: strain

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: MetmescollagenaseE115Larry

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7109

source_name: metanephric mesenchyme


title: larrydissectmes5

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7108


title: small airways, non-smoker 014, RMA and MAS

value: white


title: LCM1151BMM10_7_04

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7105


title: Loosestroma_4_4_11_8_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7099

source_name: renal medullary interstitium


title: small airways, non-smoker 006, RMA and MAS


title: 4_2_8_05MMcollagenase

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7107


title: small airways, non-smoker 002, RMA and MAS


title: larrydissectedbudsample4

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7111


title: small airways, non-smoker 004, RMA and MAS


title: small airways, non-smoker 001, RMA and MAS


title: E115closemesLCM5B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7102


title: small airways, non-smoker 003, RMA and MAS

value: F


title: E115MM2B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7103


title: Loosestroma_5_4_11_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7100


title: 5_2_8_05UBcollagenase

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7112


title: larrydissectedmesenchymesample2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7106


title: E115MMLCM4B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7104


title: Sshaped_3_10_6_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7097

source_name: s-shaped body


title: larrydissectedbudsample1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7110


title: Sshaped_2_10_6_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7096


title: OuterUB_4_11_8_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7093

source_name: Ureteric Tip


title: Steve_2_1_6_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7101


title: Glom_1_11_21_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7082

source_name: capillary loop renal corpuscle & maturing renal corpuscle


title: OuterUB_1_1_6_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7091


title: Sshaped_1_10_06_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7094


title: Proxtubules_1_2_8_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7086

source_name: Early Proximal Tubule


title: Glom_4_10_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7085


title: Glom_2_9_30_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7084


title: WT_RV_2_7_12_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7080

source_name: Renal Vesicle


title: MedUB_2_11_8_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7089

source_name: Medullary Collecting Duct


title: MedUB_1_9_30_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7088


title: Loosestroma_3_11_8_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7098

treatment_protocol:
pool size: Approx 50 sections from 5 kidneys
Pooled sample: Yes
CD-1 mice are time-mated.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses placed in OCT in a mold, frozen in liquid nitrogen and stored at -80°C. Blocks are sectioned, stained and used for laser capture micro-dissection.


title: Glom_3_4_11_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7083


title: Proxtubules_1_11_8_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7087


title: 2_RV_6_6_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7077


title: OuterUB_3_11_21_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7092

treatment_protocol:
pool size: Approx 50 sections from 5 kidneys
Pooled sample: Yes
Dissection Method: Laser capture microdissection


title: JS_060301_1_Urethra

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6967

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10 ug

source_name: urethra

extract_protocol: Qiagen: RNeasy

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: The urethra region was microdissected based on the presence of SMGA/EGFP expression.
Female FVB/N mice were time-mated to SMGA/EGFP transgenic males.  Pregnant FVB/N mice were euthanized by standard carbon dioxide asphyxiation at 14 days post-coitus.  Embryonic samples were euthanized by decapitation and tissues were micro-dissected, rapidly frozen and stored at -80 °C until RNA was extracted for gene expression analysis.

value: SMGA/EGFP transgenic / PMID:14713859

value: FVB/N

value: Unknown

value: ND

value: Distal borders of anterior and posterior footplates indented; digit widths and locations discernable


title: 060301_RefRNA_

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6970

source_name: postnatal day 1/whole mouse

treatment_protocol:
pool size: whole mouse (4 male & 4 female)
Pooled sample: yes;
Dissection Method: none; whole animals used
This sample represents the universal standard for cross comparison of microarray data.

value: Both (male & female)

value: postnatal day 1


title: 3_RV_6_6_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7078


title: JS_RefRNA

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6972


title: JS_060301_2_Urethra

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6968


title: WT_RV_3_7_12_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7081


title: 060301_1UGS

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6963

source_name: urogenital sinus

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Urogenital sinus region microdissected based on an absence of SMGA/EGFP expression between the developing bladder and urethra regions.
Female FVB/N mice were time-mated to SMGA/EGFP transgenic males.  Pregnant FVB/N mice were euthanized by standard carbon dioxide asphyxiation at 14 days post-coitus.  Embryonic samples were euthanized by decapitation and tissues were micro-dissected, rapidly frozen and stored at -80 °C until RNA was extracted for gene expression analysis.


title: JS_5

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6971

treatment_protocol:
pool size: whole mouse (4male & 4 female)
Pooled sample: yes;
Dissection Method: none; whole animals used
This sample represents the universal standard for cross comparison of microarray data.


title: JS_060301_6_Urethra

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6969

value: Individual fingers visible in the anterior footplate with indentations between the toes which are not discernable


title: Tsu_genomic_hyb_2

type: genomic

city: St. Louis

first: Ivan

last: Baxter

state: MO

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

description: DNA sample for Bulk Segregant analysis

hyb_protocol: Affymetrix standard protocol

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: ~6 week-old leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

value: ~6 weeks

tag: tissue

value: Leaves


title: Tsu_genomic_hyb_1

description: DNA sample for Bulk Segregant analysis


title: Tsu_genomic_hyb_3

description: DNA sample for Bulk Segregant analysis


title: WT_RV_5_11

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7079

tag: Sex


title: Sshaped_1_11_8_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7095


title: Low_Na_seg_pool_tsu_col_F2

description: DNA sample for Bulk Segregant analysis


title: JS_7

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6966


title: col3DNA

description: DNA sample for Bulk Segregant analysis from http://naturalsystems.uchicago.edu/naturalvariation/methods/ColLerCEL.zip Borevitz J. Array Genotyping and Mapping, Arabidopsis Protocols


title: High_Na_seg_pool_tsu_col_F2

description: DNA sample for Bulk Segregant analysis


title: MedUB_4_11_21_05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7090


title: col2DNA


title: col1DNA


title: JS_8

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6962

source_name: bladder

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Bladder region microdissected based on SMGA/EGFP expression.
Female FVB/N mice were time-mated to SMGA/EGFP transgenic males.  Pregnant FVB/N mice were euthanized by standard carbon dioxide asphyxiation at 14 days post-coitus.  Embryonic samples were euthanized by decapitation and tissues were micro-dissected, rapidly frozen and stored at -80 °C until RNA was extracted for gene expression analysis.


title: Ts_genomic_hyb_3

description: DNA sample for Bulk Segregant analysis


title: Ts_genomic_hyb_1

description: DNA sample for Bulk Segregant analysis


title: Ts_genomic_hyb_2

description: DNA sample for Bulk Segregant analysis


title: 060301_6UGS

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6965


title: High_Na_seg_pool_ts_col_F2

description: DNA sample for Bulk Segregant analysis


title: Low_Na_seg_pool_ts_col_F2

description: DNA sample for Bulk Segregant analysis


title: 060301_6BLAD

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6961

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Bladder region microdissected based on SMGA/EGFP expression
Female FVB/N mice were time-mated to SMGA/EGFP transgenic males.  Pregnant FVB/N mice were euthanized by standard carbon dioxide asphyxiation at 14 days post coitus.  Embryonic samples were euthanized by decapitation and tissues were micro-dissected, rapidly frozen and stored at -80 °C until RNA was extracted for gene expression analysis.


title: Control_2_intestine_30days

city: Kansas City

first: Linheng

last: Li

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: The study examines the effect of conditional PTEN deletion in the small intestine. Deletion of the PTEN exon 5 (encoding the phosphatase motif) was accomplished using the interferon-inducible Mx1-Cre, induced by five injections of polyinosinic-polycytidylic acid. The experiment compared the gene expression profiles of polyp regions from three PTEN mutant animals with intestines from two control animals. Genes were considered up-regulated or down-regulated if all of the following conditions were met: 1) There was at least a two-fold change in the average values measured between controls and mutants; 2) There was no overlap between the range of mutant and control data; and 3) The control mean was outside the 95% confidence interval of the PTEN-mutant mean.

hyb_protocol: Hybridization to Affymetrix mouse Genome 430 2.0 arrays using GeneChipFluidics Station450. 20 micrograms of fragmented cRNA was used for each chip hybridization. Hyridization and wash protocols were as described in Affymetrix Technical Manual, "GENE EXPRESSION MONITORING, GeneChip® Expression Analysis" 701021 Rev. 5. Hybridization buffer was 100 mM MES(2-(N-Morpholino)ethanesulfonic acid sodium salt), 1M [Na+], 20 mM EDTA, 0.01% Tween-20. Hybridization was performed at 45 celsius for 16 hours.

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS GeneChip Operating software Version 1.2.0.037

data_processing: Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW_SIGNAL * 100/(97.194 + 4.2422*LN(RAW_SIGNAL))

label: Biotin, detected with Strepavidin R-phycoerythrin

source_name: Control 2 small intestine, 30 days

label_protocol: Biotin-labeled cRNA was prepared from 6 micrograms of total RNA using the Affymetrix One-cycle protocol. (Affymetrix Cat. #900493). Quantity and quality of unfragmented cRNA and fragmented cRNA was assessed using a Bioanalyzer (Agilent).

growth_protocol: Animals were maintained under specific pathogen free conditions in vivarium with a 12 hour light/12 hour dark cycle. Animals had food and water ad libitum.

extract_protocol: Total RNA was extracted by Trizol Reagent (Invitrogen) according to manufacturer's protocol. Quality and quantity of the total RNA was assessed using a Bioanalyzer (Agilent).

treatment_protocol: PTEN mutant and control animals were injected a total of five times with polyinosinic-polycytidylic acid (Poly I:C), with single injections of 250 micrograms/mouse/day given every other day. Injections were performed on days 21, 23, 25, 27, 29. Mice were analyzed 30 days after the final Poly I:C injection.

tag: Strain

value: mixed genetic background, predominantly (>87.5%) C57BL/6 with some CD1. Genotype:Mx1-Cre negative:PTENfx/+. Sex:Female. Age:

tag: Eight and a half weeks (at tissue isolation). Tissue

value: small intestine (jejunum/ileum).


title: 060301_2BLAD

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6960

source_name: primitive bladder

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Bladder region microdissected based on SMGA/EGFP expression.
Female FVB/N mice were time-mated to SMGA/EGFP transgenic males.  Pregnant FVB/N mice were euthanized by standard carbon dioxide asphyxiation at 14 days post-coitus.  Embryonic samples were euthanized by decapitation and tissues were micro-dissected, rapidly frozen and stored at -80 °C  until RNA was extracted for gene expression analysis.


title: 060301_2UGS

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:6964


title: PTEN_mutant_2_intestinal_polyp_30days

data_processing: Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW SIGNAL * 100/(2.5416*LN(RAW SIGNAL) + 77.834)

source_name: PTEN mutant 2 intestinal polyp, polyI:C, 30 days

value: mixed genetic background, predominantly (>87.5%) C57BL/6 with some CD1. Genotype:PTEN mutant = Mx1-Cre positive:PTENfx/fx. Sex:Female. Age:Eight and a half weeks (at tissue isolation). Tissue:Intestinal polyp from small intestine (jejunum/ileum region).


title: PTEN_mutant_3_intestinal_polyp_30_days

data_processing: Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE= RAW SIGNAL * 100/(105.83+ 4.6698*LN(RAW_SIGNAL))

source_name: PTEN mutant 3 intestinal polyp, polyI:C, 30 days


title: Control_1_intestine_30days

data_processing: Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW_SIGNAL* 100/(2.0635*LN(RAW_SIGNAL)+56.98)

source_name: Control small intestine 1, polyI:C, 30 days

value: Mixed genetic background, predominantly (>87.5%) C56BL/6 with some CD1. Genotype:Mx1-Cre negative:PTENfx/+. Sex:Female

value: eight and a half weeks (at tissue isolation). Tissue:Small Intestine (jejunum/ileum region).


title: PTEN_mutant_1_intestinal_polyp_30days

data_processing: Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW_SIGNAL * 100/(103.8 -4.3937*LN(RAW_SIGNAL))

source_name: PTEN mutant 1 intestinal polyp, 30 days post polyI:C

value: mixed genetic background, predominantly (>87.5%) C57BL/6 with some CD1. Genotype:PTEN mutant = Mx1-Cre positive:PTENfx/fx. Sex:Male. Age:Eight and a half weeks (at tissue isolation). Tissue:Intestinal Polyp (from jejunun/ileum).


title: brain, cerebellum: Lh-/-_Crb3_e1_le1

status: Public on Nov 14 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description:
Total RNA extracted from the cerebellum of a Lh-/- mutant mouse
Treatment, type=sacrifice

source_name: brain, cerebellum


title: brain, forebrain: Sample5_e1_le1

description:
Total RNA extracted from the forebrain of a Tg-/- mutant mouse
Treatment, type=sacrifice

source_name: brain, forebrain


title: brain, cerebellum: Lh-/-_Crb2_e1_le1


title: brain, cerebellum: Stg-/-_Crb2_e1_le1

description:
Total RNA extracted from the cerebellum of a stg-/- mutant mouse
Treatment, type=sacrifice


title: brain, cerebellum: Stg-/-_Crb3_e1_le1


title: brain, cerebellum: Tg-/-_Crb3_e1_le1

description:
Total RNA extracted from the cerebellum of a Tg-/- mutant mouse
Treatment, type=sacrifice


title: brain, forebrain: Sample7_e1_le1

description:
Total RNA extracted from the forebrain of a Lh-/- mutant mouse
Treatment, type=sacrifice


title: brain, cerebellum: Tg-/-_Crb2_e1_le1


title: brain, cerebellum: Tg-/-_Crb1_e1_le1


title: brain, forebrain: Total RNA_le1

description:
Total RNA extracted from the forebrain of a stg-/- mutant mouse
Treatment, type=sacrifice


title: brain, forebrain: Sample9_e1_le1


title: brain, forebrain: Sample3_e1_le1


title: brain, forebrain: Stg-/-_FB2_le1


title: kidney, Cell line: 1-3_le1

description:
hIMP1 Dmut
Treatment, type=transfect, description=hIMP Dmut

source_name: kidney, Cell line


title: brain, cerebellum: Lh-/-_Crb1_e1_le1


title: brain, forebrain: Sample4_e1_le1


title: kidney, Cell line: 2-3_le1

description:
hIMP1 Dmut
Treatment, type=transfect, description=hIMP1 Dmut


title: kidney, Cell line: 1-2_le1

description:
hIMP1 wt
Treatment, type=transfect, description=hIMP1 wt


title: kidney, Cell line: 2-1_le1

description:
mock
Treatment, type=transfect, description=Empty vector


title: brain, forebrain: Sample8_e1_le1


title: brain, cerebellum: Stg-/-_Crb1_e1_le1


title: kidney, Cell line: 2-2_le1


title: brain, forebrain: Sample6_e1_le1


status: Public on Nov 12 2006

city: South San Francisco

first: David

middle: S

last: Shames

state: CA

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

hyb_protocol: please see the Southwestern Medical Center Microarray Core Facility website for details

data_processing: Raw signal data without normalization

source_name: Immortalized human bronchial epithelial cells

label_protocol: Affymetrix

growth_protocol: See publication for details.

extract_protocol: Trizol

treatment_protocol: HBEC4-Rep2 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.

tag: See publication for details.


scan_protocol: please see the Southwestern Medical Center Microarray Core Facility website for details

treatment_protocol: HBEC2-Rep2 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.


source_name: Immortalzied human bronchial epithelial cells

treatment_protocol: HBEC3-Rep2 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.


treatment_protocol: HBEC2 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.


title: A549 Control treatment group (DMSO).

description: A549 Control treatment group (DMSO).

source_name: NSCLC cell line

treatment_protocol: A549 Control treatment group.  DMSO qod for 6 days.


treatment_protocol: H1299 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.


treatment_protocol: HBEC4 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.


treatment_protocol: HBEC3 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.


treatment_protocol: H460 High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.


title: HBEC3-Rep2 Control treatment group (DMSO)

treatment_protocol: HBEC3-Rep2 Control treatment group.  DMSO qod for 6 days.


title: A549 High dose treatment group (1000 nM).


title: HBEC4-Rep2 Control treatment group (DMSO)

treatment_protocol: HBEC4-Rep2 Control treatment group.  DMSO qod for 6 days.


title: Lmna H222P heterozygous male 1

status: Public on Dec 02 2006

first: antoine

last: Muchir

address: 630W 168th street

department: Medicine

institute: columbia university

description: 10 weeks

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GC-RMA

source_name: whole heart

label_protocol: standard Affymetrix procedures

extract_protocol: RNA was extracted using Rneasy kit (QIAGEN)


title: wt PGC-1, repeat 3

status: Public on Nov 10 2006

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description: HePG2 cells infected with adenovirus expressing wt PGC-1

hyb_protocol: As per standard Affymetrix protocol (performed at Expression Analysis Institute, Durham, NC)

source_name: HepG2 cells

growth_protocol: HePG2 cells were maintained in MEM supplemented with 8% FBS, non-essential aminoacids and sodium pyruvate on plastic coated with 0.1% gelatin.

extract_protocol: RNEASY (Qiagen)

treatment_protocol: 4,000,000 cells were plated per 10 cm plate coated with gelatin (0.1% gelatin for 10 min). Cells were infected on the next day with adenovirus expressing the construct identified in the title. MOI=10 to 30. Infected for 2 hrs at RT in 0.5 mL phenol-free charcoal filtered MEM (8% serum), after which the medium was repaced with 2 mL of phenol red-free MEM. Plates were incubated at 37 C 5% CO2 for 24 hrs, and cells were harvested for RNA isolation immediately following this incubation.

tag: Human hepatocellular carcinoma cell line


title: L2L3 mutant, repeat 3

description: HePG2 cells infected with adenovirus expressing the L2L3 mutant of PGC-1

scan_protocol: As per standard Affymetrix protocol (performed at Expression Analysis Institute, Durham, NC)


title: L2L3 mutant, repeat 2

label_protocol: As per standard Affymetrix protocol (performed at Expression Analysis Institute, Durham, NC)


title: 2x9 PGC-1 mutant, repeat 3

description: HePG2 cells infected with adenovirus expressing the 2x9 mutant of PGC-1

source_name: HePG2 cells

treatment_protocol: 4,000,000 cells were plated per 10 cm plate coated with gelatin (0.1% gelatin for 10 min). Cells were infected on the next day with adenovirus expressing the construct identified inthe title. MOI=10 to 30. Infected for 2 hrs at RT in 0.5 mL phenol-free charcoal filtered MEM (8% serum), after which the medium was repaced with 2 mL of phenol red-free MEM. Plates were incubated at 37 C 5% CO2 for 24 hrs, and cells were harvested for RNA isolation immediately following this incubation.


title: HBEC2 Control treatment group (DMSO)

description: HBEC2 Control treatment group (DMSO)

source_name: Immortalized bronchial epithelial cells

treatment_protocol: HBEC3 Control treatment group.  DMSO qod for 6 days.


title: HBEC4 Control treatment group (DMSO).

description: HBEC4 Control treatment group (DMSO).

treatment_protocol: HBEC4 Control treatment group.  DMSO qod for 6 days.


title: wt PGC-1, repeat 1


title: kidney, Cell line: 1-1_le1


title: HBEC2-Rep2 Control treatment group (DMSO).

treatment_protocol: HBEC2-Rep2 Control treatment group.  DMSO qod for 6 days.


title: L2L3 mutant, repeat 1


title: 2x9 PGC-1 mutant, repeat 1


title: 2x9 PGC-1 mutant, repeat 2


title: BGAL, repeat 3

description: HePG2 cells infected with adenovirus expressing the BGAL control


title: BGAL, repeat 1


title: H460 Control treatment group (DMSO)

description: H460 Control treatment group (DMSO)

treatment_protocol: H460 Control treatment group.  DMSO qod for 6 days.


title: BGAL, repeat 2


title: wt PGC-1, repeat 2


title: HUVEC S48h_2

status: Public on Nov 09 2006

city: Singapore

first: yulan

last: zhao

address: Level 1,  Service Block,  #B1-15

department: Paediatrics

country: Singapore

institute: National University of Singapore

description: Gene expression data from HUVEC of passage 4 without any stimulation.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: HUVEC S48h_2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: EGM-2MV medium, 5% CO2, 37ºC

extract_protocol: Qiagen Rneasy Mini kit

treatment_protocol: SAA 20ug/ml treatment for 48h

tag: HUVEC SAA 20ug/ml 48h_2


title: HUVEC S24h_2

source_name: HUVEC S24h_2

treatment_protocol: SAA 20ug/ml treatment for 24h

tag: HUVEC SAA 20ug/ml 24h_2


title: negative control transfection for 72 hours

status: Public on Nov 03 2006

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

data_processing: RMA from the BioConductor package

source_name: HepG2 cell line

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

extract_protocol: Total RNA was extracted from the cell lysate using Ambion's RNA isolation kit.

tag: Originated from human liver


title: miR-124 transfection for 120 hours

description: miR-124 transfection for 120 hours


title: negative control transfection for 32 hours


title: miR-124 transfection for 16 hours

description: miR-124 transfection for 16 hours


title: genes expression in ezrin- knockdown esophageal squamous carcinoma cells, biological rep1

city: shantou

first: Enmin

state: guangdong

address: 22 Xinling Road

country: China

institute: Shantou university, medical college

description: expression genes data from ec109 cells tranfected with blank vector

source_name: homo sapiens_esophageal squamous carcinoma cell line EC109

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

treatment_protocol: The mammalian expression vector, pSUPER.neo.circular (OligoEngine), was used for expression of siRNA in EC109 cells. Briefly, two primer pairs were synthesized, one pair encoding nucleotides 274?92 (TCCACTATGTGGATAATAA) followed by a 9 base ‘‘loop’’ (TTCAAGAGA) and the inverted repeat (PSE1), and the second encoding nucleotides 265?83 (ACTTTGGCCTCCACTATGT) again followed by the loop and inverted repeat (PSE2). And pSUPER.neo vector of nonspecific siRNA was taken as negative control (PSC). The primer pairs were annealed and inserted into the BglII and HindIII sites of pSUPER.neo and transformed into JM109 competent cells (Promega). Positive clones were verified and transfected into EC109 cells using FuGENE 6 transfection reagent (Roche) according to the manufacturer’s instructions. G418 (400 ?g/ml, Calbiochem) was added into the culture medium after 24 h. Stable G418-resistant clones were obtained in 7? days. The expanded cells were then used for studies.

tag: GENE EXPRESSION

value: Ezrin high-expressed


title: HUVEC S24h_1

source_name: HUVEC S24h_1

tag: HUVEC SAA 20ug/ml 24h_1


title: miR-124 transfection for 24 hours

description: miR-124 transfection for 24 hours


title: miR-124 transfection for 4 hours

description: miR-124 transfection for 4 hours


title: miR-124 transfection for 8 hours

description: miR-124 transfection for 8 hours


title: miR-124 transfection for 72 hours

description: miR-124 transfection for 72 hours


title: negative control transfection for 16 hours


title: HUVEC S4h_1

source_name: HUVEC S4h_1

treatment_protocol: SAA 20ug/ml treatment for 4h

tag: HUVEC SAA 20ug/ml 4h_1


title: negative control transfection for 4 hours


title: HUVEC control_1

source_name: HUVEC control_1

treatment_protocol: control

tag: HUVEC Control_1 without stimulation


title: HUVEC control_2

source_name: HUVEC control_2

tag: HUVEC Control_2 without stimulation


title: HUVEC S4h_2

source_name: HUVEC S4h_2

tag: HUVEC SAA 20ug/ml 4h_2


title: negative control transfection for 120 hours


title: HUVEC S48h_1

source_name: HUVEC S48h_1

tag: HUVEC SAA 20ug/ml 48h_1


title: miR-124 transfection for 32 hours

description: miR-124 transfection for 32 hours


title: negative control transfection for 8 hours


title: negative control transfection for 24 hours


title: genes expression in esophageal squamous carcinoma cells, biological rep1

treatment_protocol: The mammalian expression vector, pSUPER.neo.circular (OligoEngine), was used for expression of siRNA in EC109 cells. Briefly, two primer pairs were synthesized, one pair encoding nucleotides 274–292 (TCCACTATGTGGATAATAA) followed by a 9 base ‘‘loop’’ (TTCAAGAGA) and the inverted repeat (PSE1), and the second encoding nucleotides 265–283 (ACTTTGGCCTCCACTATGT) again followed by the loop and inverted repeat (PSE2). And pSUPER.neo vector of nonspecific siRNA was taken as negative control (PSC). The primer pairs were annealed and inserted into the BglII and HindIII sites of pSUPER.neo and transformed into JM109 competent cells (Promega). Positive clones were verified and transfected into EC109 cells using FuGENE 6 transfection reagent (Roche) according to the manufacturer’s instructions. G418 (400 ?g/ml, Calbiochem) was added into the culture medium after 24 h. Stable G418-resistant clones were obtained in 7–9 days. The expanded cells were then used for studies.


title: MV8

status: Public on Nov 02 2006

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

description: total RNA extracted from cells in the amnionic fluid - normal control

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite version 5.0

label: standard Affymetrix procedure

source_name: amniocentesis

label_protocol: standard Affymetrix procedure

extract_protocol: Qiagen Rneasy

value: amniotic fluid

tag: disease state

value: normal control


title: MV7

tag: tissue


title: mouse kidney sense 430 2.0

status: Public on Nov 07 2006

city: Newcastle

first: Andreas

last: Werner

address: Framlington Place

department: Cell and Molecular Biosciences

institute: Newcastle University

description: Sense transcriptome

hyb_protocol: Following fragmentation, 15 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 the GeneChip? Scanner 3000 (Affymetrix).

source_name: total mouse kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6.75 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Kidneys were dissected, rinsed in ice cold PBS and directly used for RNA extraction with TRIzol (Invitrogen).

tag: Strain C57B6

tag: Male, age 2 weeks


title: MV4

description: total RNA extracted from cells in the amnionic fluid - spina bifida

value: spina bifida


title: MV2


title: MV11


title: MV13


title: MV12


title: MV1


title: con_B043

status: Public on Nov 01 2006

city: Rotterdam

first: Lindy

last: Santegoets

department: Obstetrics & Gynecology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description: Gene expression data of normal vulvar tissue

hyb_protocol: Hybridization to Affymetrix U133plus2 GeneChips , staining and  washing were carried out as described (Affymetrix, Santa Clara).

scan_protocol: Scanning procedures were carried out as described  by Affymetrix, Santa Clara.

data_processing: The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T

source_name: vulva biopsy of normal tissue

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: not applicable

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)

treatment_protocol: Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).

tag: Gender

value: female, Age:54 years, Tissue:normal vulva,


title: VIN_B077

description: Gene expression data of vulvar intraepithelial neoplasia (VIN)

source_name: vulva biopsy of vulvar intraepithelial neoplasia (VIN)

value: female, Age:32 years, Tissue:VIN 3


title: con_B130

value: female, Age:37 years, Tissue:normal vulva,


title: MV6


title: con_B149

value: female, Age:41 years, Tissue:normal vulva,


title: VIN_B090

value: female, Age:48 years, Tissue:VIN 3


title: VIN_B060

value: female, Age:45 years, Tissue:VIN 3


title: con_B132


title: VIN_B109

value: female, Age:39 years, Tissue:VIN 3


title: VIN_B027

value: female, Age:33 years, Tissue:VIN 3


title: VIN_B116

value: female, Age:36 years, Tissue:VIN 3


title: con_B135

value: female, Age:43 years, Tissue:normal vulva,


title: con_B124

value: female, Age:16 years, Tissue:normal vulva,


title: con_B148


title: con_B084

value: female, Age:23 years, Tissue:normal vulva,


title: con_B131

value: female, Age:38 years, Tissue:normal vulva,


title: VIN_B017


title: VIN_B105

value: female, Age:44 years, Tissue:VIN 3


title: con_B004

value: female, Age:33 years, Tissue:normal vulva,


title: Liver_Chow_B6.C3H-6T_Female_8wks_Ped#41

status: Public on Oct 29 2006

city: Bar Harbor

first: Cheryl

middle: Lynne

last: Ackert-Bicknell

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: The images were quantified using GeneChip(TM) Operating Software (GCOS) v1.2.

hyb_protocol: Fifteen micrograms of biotin-labeled and fragmented cRNA was then hybridized onto MOE430v2.0* GeneChip™ arrays (Affymetrix) for 16 hours at 45°C.  Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: Finally, the arrays were scanned with a GeneChip™ Scanner 3000 laser confocal slide scanner.

data_processing: Expression values were summarized using the RMA (Robust MultiChip Average) function in the R/affy package.

source_name: Liver

label_protocol: Following reverse transcription with an oligo(dT)-T7 primer (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized with the Superscript double-stranded cDNA synthesis custom kit (Invitrogen). In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified and labeled with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY).

extract_protocol: The tissue was homogenized in TRIzol (Invitrogen, Carlsbad, CA). Total RNA was isolated by standard TRIzol methods according to the manufacturer's protocols, and quality was assessed using a 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Tissue samples were stored in RNAlater (Ambion, Austin, TX) following dissection.

tag: Sample is from the liver of a female C57BL/6J female. Mouse was 8 wks of age at raised on a chow diet (Cat. # 5K52, LabDiet, St. Louis, MO). Mouse was fasted for 5 hours prior to sample collection.

tag: Creation of the B6.C3H-6T mouse is described at

value: Bouxsein et.al. 2002. J Bone Miner. Res. 17(4):570-579


title: Liver_Chow_B6.C3H-6T_Female_8wks_Ped#39

tag: Sample is from the liver of a female B6.C3H-6T female. Mouse was 8 wks of age at raised on a chow diet (Cat. # 5K52, LabDiet, St. Louis, MO). Mouse was fasted for 5 hours prior to sample collection.

tag: Creation of the B6.C3H-6T mouse is found at

value: Bouxsein et al. 2002. J Bone Miner. Res. 17(4):570-579


title: Liver_Chow_B6.C3H-6T_Female_8wks_Ped#40


title: A2780_TRT_6h_rep2

status: Public on Oct 28 2006

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

description:
Human Ovarian cell line A2780 was obtained from ECACC (Cat no.93112519) and cells were untreated or exposed to 3 micromolar of a cell cycle inhibitor for 6hrs.  Three biological replicates were performed for each treatment. Only attached cells were harvested. RNA was purified using a Qiagen RNA purification kit. RNA was quantitated using a spectrophotometer and the quality of the RNA was assessed using a Bioanalyser.
Biological replicates were pooled to obtain a unique sample for each treatment, which was then divided to generate three aliquots for each condition (technical replicates).

hyb_protocol: 10 micrograms of fragmented cRNA was hybridised to a Human Genome U133 Plus 2.0 Array (900466). Hybridisations, washing and staining were performed according to Affymetrix protocols

scan_protocol: Hybridised arrays were scanned with the Genechip Scanner 3000

data_processing: Probe set intensities were calculated using the RMA algorithm and normalized by the quantiles method

source_name: A2780 ovarian carcinoma cell line

label_protocol: 5 micrograms of each RNA samples was used for the amplification/labelling reaction. 1st and 2nd strand cDNA synthesis was performed with the Invitrogen kit (11917-020) and the IVT reaction was done with Megascript T7 from Ambion (1334). All steps were done according to manufacturers instructions and cRNA was quantitated on a spectrophotometer. 15 micrograms of cRNA was fragmented and checked by denaturing gel electrophoresis. Bacterial transcripts at the cRNA level were spiked into each sample prior to hybridisation.

growth_protocol: A2780 was grown in RMPI 1640 + 10% FCS +2mM Glutamine and maintained at 37C in an atmosphere of 5% CO2 and 95% room air. Cells were plated at 2 x 106 cell/ml and after 24hrs were exposed to 3 micromolar of the inhibitor for 6hrs.

extract_protocol: Total RNA extraction was performed using Qiagen RNeasy Mini kit 74106 following manufacturers instructions.

treatment_protocol: Human Ovarian cell line A2780 was untreated or exposed to 3 micromolar of a cell cycle inhibitor for 6hrs

tag: A2780 ovarian carcinoma cell line


title: VIN_B040

value: female, Age:35 years, Tissue:VIN 3


title: Liver_Chow_C57BL/6J_Female_8wks_Ped#37


title: A2780_6h_rep3


title: Liver_Chow_C57BL/6J_Female_8wks_Ped#38


title: Total_plus

status: Public on Oct 24 2006

city: New York

first: Alina

last: Patke

address: 1230 York Avenue

institute: Rockefeller University

description: Total RNA was isolated from B cells, which had been stimulated with BAFF for 36 hours, as described (Patke et. al., 2006).

data_processing: Affymetrix GeneChip Operating Software v 1.4

source_name: total RNA

tag: Total RNA isolated from B cells which had been stimulated with BAFF for 36 hours


title: A2780_6h_rep2


title: Liver_Chow_C57BL/6J_Female_8wks_Ped#36

tag: Sample is from the liver of a female C57BL/6J female.  Mouse was 8 wks of age at raised on a chow diet (Cat. # 5K52, LabDiet, St. Louis, MO).  Mouse was fasted for 5 hours prior to sample collection.


title: Total_minus

description: Total RNA was isolated from unstimulated B cells as described (Patke et. al., 2006).

tag: total RNA isolated from unstimulated B cells


title: A2780_6h_rep1


title: A2780_TRT_6h_rep1


title: NRMRL control replicate05, uninfected batch093005

status: Public on Oct 21 2006

city: Cincinnati

first: Samuel

last: Hayes

state: OH

address: 26 W. Martin Luther King Dr.

institute: United States Environmental Protection Agency

hyb_protocol: MAS 5.0 software EukGE-WS1

scan_protocol: MAS 5.0 with model 4500 scanner

data_processing: GCOS software, target signal scaling 500; normalization 1; Alpha1 0.05; Alpha2 0.065; Tau 0.015; Gamma1L and 1H 0.0045; Gamma 2L and 2H 0.06; and Pertubation 1.1.

label: Streptavidin Phycoerythrin (SAPE)

source_name: neonatal mouse small intestinal tissue, 5 hours

label_protocol: Affymetrix SOP, EukGE-WS2

extract_protocol: TriZol procedure

tag: Swiss Webster neonate, 5 days old


title: NRMRL control replicate01, uninfected batch093005


title: NRMRL control replicate04, uninfected batch093005

source_name: neonatal mouse small intestinal tissue, 5 hourd


title: NRMRL test replicate04, EPA80 batch093005

source_name: neonatal mouse small intestinal tissue, 5 hour infection


title: NRMRL control replicate03, uninfected batch093005


title: NRMRL test replicate01, EPA82 batch093005


title: Polysome_minus

description: Polysomal RNA was isolated from unstimulated B cells as described (Patke et. al., 2006).

tag: sample isolated from polysomal RNA of unstimulated B cells


title: A2780_TRT_6h_rep3


title: NRMRL test replicate03, EPA82 batch093005


title: NRMRL test replicate02, EPA82 batch093005


title: Polysome_plus

description: Polysomal RNA was isolated from B cells, which had been stimulated with BAFF for 36 hours, as described (Patke et. al., 2006).

tag: polysomal RNA isolated from B cells which had been stimulated with BAFF for 36 hours


title: NRMRL test replicate05, EPA80 batch093005


title: NRMRL control replicate02, uninfected batch093005


title: NRMRL test replicate04, EPA82 batch093005


title: NRMRL test replicate05, EPA82 batch093005


title: NRMRL test replicate03, EPA80 batch093005


title: NRMRL test replicate05, EPA73 batch093005


title: NRMRL test replicate02, EPA73 batch093005

source_name: noenatal mouse small intestinal tissue, 5 hour infection


title: NRMRL test replicate03, EPA73 batch093005

source_name: neonatal small intestinal tissue, 5 hour infection


title: NRMRL test replicate01, EPA80 batch093005


title: NRMRL test replicate03, EPA52 batch093005


title: NRMRL test replicate02, EPA51 batch093005

source_name: neonatal mouse small intestinal tissue, 5 hoour infection


title: NRMRL test replicate01, EPA73 batch093005

source_name: neonatal mouse small intestinal tissue, 5 day infection


title: NRMRL test replicate04, EPA52 batch093005

tag: Swiss Webster noenate, 5 days old


title: NRMRL test replicate02, EPA52 batch093005


title: NRMRL test replicate05, EPA51 batch093005


title: NRMRL test replicate01, EPA52 batch093005


title: NRMRL test replicate04, EPA73 batch093005


title: NRMRL test replicate04, EPA72 batch051905


title: NRMRL test replicate05, EPA52 batch093005


title: NRMRL test replicate02, EPA80 batch093005


title: NRMRL test replicate02, EPA72 batch051905


title: NRMRL test replicate05, EPA 72 batch051905


title: NRMRL test replicate01, EPA72 batch051905


title: NRMRL test replicate01, EPA51 batch093005


title: NRMRL test replicate03, EPA10 batch051905


title: NRMRL test replicate02, EPA61 batch051905


title: NRMRL test replicate03, EPA51 batch093005


title: NRMRL test replicate04, EPA61 batch051905


title: NRMRL test replicate05, EPA61 batch051905


title: NRMRL test replicate04, EPA10 batch051905


title: NRMRL test replicate04, EPA51 batch093005

source_name: neonatal mouse small intestine tissue, 5 hour infection


title: NRMRL test replicate05, EPA10 batch051905


title: NRMRL test replicate03, EPA 72 batch 051905


title: NRMRL test replicate01, EPA61 batch051905


title: NRMRL test replicate03, EPA61 batch051905

source_name: neonatal mouse intestinal tissue, 5 hour infection


title: NRMRL test replicate02, EPA10 batch051905


title: NRMRL test replicate05, EPA9 batch051905


title: NRMRL test replicate03, EPA9 batch051905


title: NRMRL test replicate04, EPA9 batch051905


title: NRMRL test replicate01, EPA5 batch051905


title: NRMRL test replicate03, EPA5 batch051905


title: NRMRL test replicate01, EPA10 batch051905


title: NRMRL test replicate05, EPA5 batch051905


title: NRMRL test replicate02, EPA5 batch051905


title: NRMRL control replicate04, uninfected batch051905

source_name: neonatal mouse small intestinal tissue


title: NRMRL test replicate04, EPA2 batch051905


title: NRMRL control replicate02, uninfected batch051905

source_name: neonatal mouse small intestinal tissue, 5 hour


title: NRMRL test replicate02, EPA2 batch051905


title: NRMRL test replicate04, EPA5 batch051905


title: NRMRL test replicate02, EPA9 batch051905


title: NRMRL test replicate04, EPA71 batch032405

source_name: murine small intestinal cell culture, 5 hour infection

tag: MICcl2 cell line


title: NRMRL test replicate05, EPA2 batch051905


title: NRMRL test replicate01, EPA2 batch051905


title: NRMRL test replicate03, EPA2 batch051905


title: NRMRL control replicate01, uninfected, batch051905

tag: Swiss Webster, neonates, 5 days old


title: NRMRL test replicate02, EPA71 batch032405


title: NRMRL test replicate05, EPA71 batch032405


title: NRMRL test replicate04, EPA63 batch032405


title: NRMRL control replicate03, uninfected batch051905


title: NRMRL test replicate03, EPA71 batch032405


title: NRMRL test replicate03, EPA63 batch032405


title: NRMRL test replicate05, EPA63 batch032405

source_name: murine small intestinal cell culture


title: NRMRL control replicate05, uninfected batch051905


title: NRMRL test replicate01, EPA71 batch032405


title: NRMRL test replicate01, EPA9 batch051905


title: NRMRL test replicate02, EPA63 batch032405


title: NRMRL test replicate01, EPA63 batch032405


title: NRMRL test replicate02, EPA61 batch032405


title: NRMRL test replcate04, EPA61 batch032405


title: NRMRL test replicate05, EPA9 batch032405


title: NRMRL test replicate03, EPA1 batch032405

source_name: murine small intestine cell culture, 5 hour infection


title: NRMRL test replicate05, EPA61 batch032405


title: NRMRL test replicate03, EPA9 batch032405


title: NRMRL test replicate02, EPA1 batch032405

source_name: murine small intestinal tissue, 5 hour infection


title: NRMRL control replicate03, batch032405

source_name: murine cell mall intestinal cell culture, 5 hours, uninfected


title: NRMRL control replicate04, batch032405

source_name: murine small intestinal cell culture, uninfected, 5 hours

tag: MICcl2 cell  line


title: NRMRL test replicate05, EPA1 batch032405


title: NRMRL test replicate02, EPA5 batch032405


title: NRMRL test replicate04, EPA5 batch032405


title: NRMRL test replicate01, EPA9 batch032405


title: NRMRL test replicate01, EPA61 batch032405


title: NRMRL test replicate04, EPA1 batch032405


title: NRMRL test replicate03, EPA61 batch 032405


title: NRMRL replicate control02, batch032405

source_name: murine intestinal tissue, unifected, 5 hours


title: NRMRL test replicate01, EPA5 batch032405


title: NRMRL test replicate01, EPA1, batch032405

source_name: murine small intestinal tissue


title: NRMRL test replicate03, EPA5 batch032405


title: NRMRL test replicate05, EPA5 batch032405


title: NRMRL test replicate02, EPA9, batch032405


title: NRMRL test replicate04, EPA9 batch032405


title: NRMRL control replicate05, batch032405

source_name: murine small intestinal cell culture, 5 hours, unifnected


status: Public on Oct 20 2006

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

description: None.

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Standard Protocol

data_processing: dChip used.

molecule: nuclear RNA

source_name: Murine Pit Cells, Gastric from Laser Capture Microdissection

label_protocol: Affymetrix Standard Protocol

tag: C57BL/6, Pooled from Mixed Sex.

tag: Tissue

value: Pit Cells from Laser-Capture Microdissection. Murine Stomach.


title: HOK/Bmi-1 with E6

city: Los Angeles

first: Reuben

middle: Han-Kyu

last: Kim

address: 10083 Le Conte Ave.

department: Dentistry

institute: UCLA

description: Cells were harvested at the actively proliferating stage.

hyb_protocol: cRNA (15 ug) was fragmented and hybridized to Affymetrix HG-U133 Plus 2.0.

scan_protocol: The chip was stained with streptavidinphycoerythrin and analyzed using GCOS 1.2 software for pairwise comparison of gene expression.

data_processing: Original "signal" values from Affymetrix GCOS1.2 software.

source_name: HOK/Bmi-1 cells infected with E6

label_protocol: Biotin-labeled antisense cRNA was produced by in vitro transcription using the ENZO BioArray HighYield kit.

growth_protocol: Keratinocyte Growth Medium (KGM)

extract_protocol: tRNA was isolated from actively proliferating Bmi-1/E6 cells using Qiagen RNeasy total RNA isolation kit (Qiagen Inc.) according to their protocols.

treatment_protocol: Used retroviruses to express Bmi-1 and E6.

tag: Normal human oral keratinocytes (NHOK); Normal human oral keratinocytes (NHOK) explanted from normal human gingival tissue; infected with Bmi-1-expressing retrovirus; superinfected with E6 expressing retrovirus.


description: None.

source_name: Murine Zymogenic Cells, Gastric from Laser Capture Microdissection

value: Zymogenic Cells from Laser-Capture Microdissection. Murine Stomach.


title: HOK/Bmi-1 with E6(Delta)118-122.

source_name: HOK/Bmi-1 cells infected with E6(Delta)118-122.

extract_protocol: tRNA was isolated from actively proliferating Bmi-1/E6(Delta)118-122  cells using Qiagen RNeasy total RNA isolation kit (Qiagen Inc.) according to their protocols.

treatment_protocol: Used retroviruses to express Bmi-1 and E6(Delta)118-122 .

tag: Normal human oral keratinocytes (NHOK); Normal human oral keratinocytes (NHOK) explanted from normal human gingival tissue; infected with Bmi-1-expressing retrovirus; superinfected with E6(Delta)118-122 expressing retrovirus.


description: None.

source_name: Murine Parietal Cells, Gastric from Laser Capture Microdissection

value: Parietal Cells from Laser-Capture Microdissection.  Murine Stomach.


title: NRMRL control replicate01, batch032405

tag: mouse intestinal tissue, cell line MICcl2


title: HOK/Bmi-1 with LXSN

source_name: HOK/Bmi-1 cells infected with LXSN

extract_protocol: tRNA was isolated from actively proliferating Bmi-1/LXSN cells using Qiagen RNeasy total RNA isolation kit (Qiagen Inc.) according to their protocols.

treatment_protocol: Used retroviruses to express Bmi-1 and control vector (LXSN).

tag: Normal human oral keratinocytes (NHOK) explanted from normal human gingival tissue; infected with Bmi-1-expressing retrovirus; superinfected with LXSN-rexpressing retrovirus.


title: TTP_WT_120ActD_BioRep5

status: Public on Oct 17 2006

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using Mouse Genome 2.0 array (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

data_processing: quantile normalization of CEL file, PDNN (PerfectMatch) estimation, log2 transformation

source_name: RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 120 minutes

growth_protocol: The fibroblasts were maintained at 37oC (5% CO2) in Dulbecco Minimal Essential Medium supplemented with 10% FBS, 2 mM L-glutamine, 100U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol: The cell monolayer was rinsed twice in cold PBS, 5 ml each. Each plate of cells was then lysed in 0.6 ml of Buffer RLT (RNeasy Mini Kit, Qiagen) and total cellular RNA was prepared following the RNeasy protocol.

treatment_protocol: Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 120 minutes and were extracted for RNA.

tag: Cell line

value: Fibroblast TTP WT cell line prepared from littermate E14.5 mouse embryos, derived from parental TTP +/- male and TTP +/- female strain 129/B6;  Embryo age: E14.5, Tissue: Whole embryo excluding head and organs


title: TTP_WT_60ActD_BioRep4

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

source_name: RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 60 minutes

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.

treatment_protocol: Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 60 minutes and were extracted for RNA.


title: TTP_KO_60ActD_BioRep5

value: Fibroblast TTP KO cell line prepared from littermate E14.5 mouse embryos, derived from parental TTP +/- male and TTP +/- female strain 129/B6;  Embryo age: E14.5, Tissue: Whole embryo excluding head and organs


title: TTP_WT_30ActD_BioRep5

source_name: RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 30 minutes

treatment_protocol: Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 30 minutes and were extracted for RNA.


title: TTP_WT_60ActD_BioRep5


title: TTP_WT_30ActD_BioRep4


title: TTP_KO_90ActD_BioRep4

source_name: RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 90 minutes

treatment_protocol: Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 90 minutes and were extracted for RNA.


title: TTP_KO_30ActD_BioRep4


title: TTP_WT_0ActD_BioRep4

source_name: RNA prepared from fibroblast cell lines treated with 10% serum for 90 min

treatment_protocol: Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min and were extracted for RNA.


title: TTP_WT_90ActD_BioRep4


title: TTP_WT_30ActD_BioRep3


title: TTP_KO_90ActD_BioRep5


title: TTP_KO_0ActD_BioRep4


title: TTP_WT_120ActD_BioRep4


title: TTP_WT_60ActD_BioRep3


title: TTP_WT_120ActD_BioRep3


title: TTP_KO_120ActD_BioRep5


title: TTP_WT_0ActD_BioRep3


title: TTP_WT_90ActD_BioRep5


title: TTP_KO_30ActD_BioRep5


title: TTP_KO_120ActD_BioRep4


title: TTP_KO_90ActD_BioRep3


title: TTP_WT_120ActD_BioRep2


title: TTP_KO_120ActD_BioRep3


title: TTP_KO_60ActD_BioRep3


title: TTP_WT_0ActD_BioRep5


title: TTP_KO_0ActD_BioRep3


title: TTP_WT_90ActD_BioRep2


title: TTP_WT_60ActD_BioRep2


title: TTP_KO_30ActD_BioRep3


title: TTP_WT_30ActD_BioRep2


title: TTP_WT_0ActD_BioRep2


title: TTP_KO_30ActD_BioRep2


title: TTP_KO_60ActD_BioRep2


title: TTP_WT_90ActD_BioRep1


title: TTP_KO_90ActD_BioRep2


title: TTP_WT_120ActD_BioRep1


title: TTP_WT_0ActD_BioRep1


title: TTP_KO_30ActD_BioRep1


title: TTP_WT_30ActD_BioRep1


title: TTP_KO_0ActD_BioRep1


title: Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 2	U2AF

status: Public on Oct 14 2006

city: Lisboa

first: Margarida

last: Gama-Carvalho

address: Av. Prof. Egas Moniz

country: Portugal

institute: Institute of Molecular Medicine

hyb_protocol: hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays as described (Brodsky, Meyer et al. 2005), following standard Affymetrix hybridization protocols

scan_protocol: Gama-Carvalho et al, 2006

data_processing: The data were analyzed with dChip  using  default analysis settings. The model based expression index was calculated using the PM/MM model

molecule: polyA RNA

source_name: anti-U2AF65 immunoprecipitate from HeLa cell cytoplasmic extract

label_protocol: 15ug of PCR amplified cDNA from input and immunoprecipitated samples were fragmented, end labeled with biotin

growth_protocol: Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting.

extract_protocol: mRNAs were isolated by immunoprecipitation from 200ul of precleared HeLa cell extract, using the anti-U2AF65 MC3 mAb (Gama-Carvalho, Krauss et al. 1997) or the Bb7 anti-PTB mAb (ATCC) for 2h at 4C. Immune complexes were precipitated with a slurry with 50% of protein A/protein G agarose beads (Amersham), blocked with 100ug/ul of tRNA and RNAse free BSA (Ambion), by rotating for 1h at 4C and washed  with lysis buffer. Complexes bound to the beads were eluted with TES buffer (10mM Tris, 0.5M EDTA, 0.5% SDS, pH 8.0) by heating at 65C for 10 minutes and Trizol extracted. Polyadenilated RNA in the cell extract (input) and in the immunoprecipitation sample was reverse transcribed, end-tagged and PCR amplified using the Super SMART PCR cDNA synthesis kit from Clontech, following manufacturer instructions. 1ug of input or precipitated RNA was used per RT-PCR reaction to produce samples for microarray hybridization. For each set of samples (input and immunoprecipitated) a 100ul test PCR reaction was performed according to manufacturer instructions and analyzed by agarose gel electrophoresis to select ideal conditions for amplification in the linear range. PCR reactions were pooled to obtain enough material for microarray hybridization.

treatment_protocol: Gama-Carvalho et al, 2006

tag: HeLa cell line


title: Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 1	U2AF


title: TTP_KO_120ActD_BioRep1


title: TTP_KO_120ActD_BioRep2


title: TTP_KO_60ActD_BioRep1


title: TTP_WT_60ActD_BioRep1


title: Total cDNA from HeLa cell extract from Immunoprecipitation experiment 3 U2AF

source_name: HeLa cell cytoplasmic extract


title: TTP_KO_90ActD_BioRep1


title: Total cDNA from HeLa cell extract from Immunoprecipitation experiment 1 U2AF


title: Total cDNA from HeLa cell extract from Immunoprecipitation experiment 2 PTB


title: Total cDNA from HeLa cell extract from Immunoprecipitation experiment 2 U2AF


title: Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 3	U2AF


title: PC90: Thyroid cancer invasive area paired with PC89

status: Public on Oct 11 2006

city: Columbus

first: Sandya

last: Liyanarachchi

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

data_processing: Robust Multichip Averages

source_name: frozen surgical tissue

label_protocol: Approximately 8 micrograms of total RNA was processed to produce biotinylated cRNA targets

extract_protocol: standard Trizol reagent procedures

value: Thyroid cancer center area; Gender:female; Age; 42


title: PC73: Thyroid cancer invasive area paired with PC72

value: Thyroid cancer center area; Gender:female; Age; 45


title: PC80: Thyroid cancer invasive area paired with PC81 and PC79

value: Thyroid cancer center area; Gender:female; Age; 21


title: PC67: Thyroid cancer invasive area paired with PC66

value: Thyroid cancer center area; Gender:female; Age; 30


title: Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 2 PTB

source_name: anti-PTB immunoprecipitate from HeLa cell cytoplasmic extract


title: Total cDNA from HeLa cell extract from Immunoprecipitation experiment 1 PTB


title: TTP_KO_0ActD_BioRep2


title: Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 1 PTB


title: PC45: Thyroid cancer invasive area paired with PC47 and PC44

value: Thyroid cancer center area; Gender:female; Age; 29


title: PC89: Thyroid cancer center area paired with PC90


title: PC40: Thyroid cancer invasive area paired with PC41 and PC39

value: Thyroid cancer center area; Gender:female; Age; 34


title: PC6: Thyroid cancer invasive area paired with PC10 and PC5

value: Thyroid cancer center area; Gender:male; Age; 71


title: PC79: Thyroid cancer center area paired with PC81 and PC79


title: PC5: Thyroid cancer center area paired with PC10 and PC6


title: PC72: Thyroid cancer center area paired with PC73


title: Cervical Cancer Patient 10, Biopsy 5

status: Public on Oct 01 2006

city: Toronto

first: Paul

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: Gene expression data from cervical cancer patients

hyb_protocol: A total of 1.5 ug of purified total RNA template was reverse transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 ug of each generated cRNA preparation was fragmented and hybridized to an oligonucleotide array.

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

data_processing: The data were processed using GC-RMA as implemented in the gcrma package (v1.1.3) of BioConductor using default settings

source_name: Cervical Cancer Patient 10

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

growth_protocol: Immediately upon removal from the patient, the specimens were bisected; one-half was placed in a storage medium (optimal cutting temperature compound) for conventional histopathologic examination, then immediately flash-frozen in liquid nitrogen. The other half of each sample was flash-frozen without any storage medium. The specimens were subsequently evaluated by a pathologist (J. Schwock) based on the morphology of the frozen H&E-stained tissue sections cut from the optimal cutting temperature–embedded material.

extract_protocol: Total RNA was purified using the Absolutely RNA Microprep Kit (Stratagene, La Jolla, CA). Briefly, tumor tissue was lysed in guanidine thiocyanate, mixed with ethanol, and RNA was captured on a silica-based fiber matrix within a microspin cup. RNA was then washed with saline buffers, DNA contamination was removed with DNase, and RNA was then eluted in RNase-free water. The quality of the purified RNA was assessed by analyzing 200 pg of each sample using a Bioanalyzer 2100 (Agilent, Palo Alto, CA). Only samples with a 28S/18S ribosomal peak ratio of 1.8 to 2.0 were considered suitable for labeling.

treatment_protocol: Flash-frozen punch biopsies were obtained from patients with cervical cancer who were undergoing examination under general anesthesia as part of their pretreatment evaluation for cervical cancer.

tag: FIGO

tag: Histology

value: SCC

tag: Grade

value: MD

tag: HGB

tag: ifp

tag: age

tag: tumsizeMR

tag: ResponseToTherapy

value: CR


title: Cervical Cancer Patient 7, Biopsy 4

source_name: Cervical Cancer Patient 7

value: ASC

value: PR


title: PC10: Normal thyroid paired with PC5 and PC6

value: normal thyroid; Gender:male; Age; 71


title: PC66: Thyroid cancer center area paired with PC67


title: PC39: Thyroid cancer center area paired with PC41 and PC40


title: Cervical Cancer Patient 9, Biopsy 2

source_name: Cervical Cancer Patient 9


title: PC81: Normal thyroid paired with PC79 and PC80

value: normal thyroid; Gender:female; Age; 21


title: PC44: Thyroid cancer center area paired with PC47 and PC45


title: PC47: Normal thyroid paired with PC44 and PC45

value: normal thyroid; Gender:female; Age; 29


title: Cervical Cancer Patient 1, Biopsy 4

source_name: Cervical Cancer Patient 1


title: Cervical Cancer Patient 9, Biopsy 3


title: TTP_WT_90ActD_BioRep3

value: Fibroblast TTP WT cell line prepared from littermate E14.5 mouse embryos, derived from parental TTP +/- male and TTP +/- female strain 129/B6;  Embryo age: E14.5, Tissue: Whole embryo excluding head and organs


title: Cervical Cancer Patient 13, Biopsy 5

source_name: Cervical Cancer Patient 13


title: Cervical Cancer Patient 9, Biopsy 5


title: Cervical Cancer Patient 6, Biopsy 5

source_name: Cervical Cancer Patient 6

value: PD


title: PC41: Normal thyroid paired with PC39 and PC40

value: normal thyroid; Gender:female; Age; 34


title: Cervical Cancer Patient 6, Biopsy 3


title: Cervical Cancer Patient 13, Biopsy 3


title: Cervical Cancer Patient 11, Biopsy 7

source_name: Cervical Cancer Patient 11


title: Cervical Cancer Patient 15, Biopsy 3

source_name: Cervical Cancer Patient 15


title: Cervical Cancer Patient 15, Biopsy 4


title: Cervical Cancer Patient 11, Biopsy 6


title: Cervical Cancer Patient 10, Biopsy 7


title: Cervical Cancer Patient 16, Biopsy 2

source_name: Cervical Cancer Patient 16

value: WD

value: NR


title: Cervical Cancer Patient 7, Biopsy 1


title: Cervical Cancer Patient 15, Biopsy 2


title: Cervical Cancer Patient 1, Biopsy 3


title: Cervical Cancer Patient 12, Biopsy 1

source_name: Cervical Cancer Patient 12


title: Cervical Cancer Patient 16, Biopsy 1


title: Cervical Cancer Patient 12, Biopsy 5


title: Cervical Cancer Patient 12, Biopsy 4


title: Cervical Cancer Patient 10, Biopsy 2


title: Cervical Cancer Patient 10, Biopsy 3


title: Cervical Cancer Patient 4, Biopsy 2

source_name: Cervical Cancer Patient 4


title: Cervical Cancer Patient 6, Biopsy 4


title: Cervical Cancer Patient 1, Biopsy 6


title: Cervical Cancer Patient 4, Biopsy 1


title: Cervical Cancer Patient 6, Biopsy 1


title: Cervical Cancer Patient 4, Biopsy 3


title: Cervical Cancer Patient 6, Biopsy 2


title: Cervical Cancer Patient 10, Biopsy 6


title: Colon - 231866

status: Public on Sep 28 2006

city: Phoenix

first: Erin

last: Curley

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Nausea
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Mucinous Carcinoma

source_name: Colon


title: Kidney - 215952

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 1
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Colon - 231850

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 17
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma