title: Cloned Rhesus Embryonic Stem cells 3 (CRES-3), biological repA

description: Gene expression profile of CRES-3A is rhesus cloned ES in biological replicate A.

source_name: SCNT (cloned) rhesus embryo at blastocyst stage.

value: embryo, Blastocyst

value: cloned embryonic stem cell


title: Rhesus induced Pluripotent Stem cells 1 (RiPS1), biological repB

status: Public on Aug 31 2012

type: RNA

city: Beaverton

first: Shoukhrat

last: Mitalipov

address: 505 N.W. 185th Avenue

country: USA

institute: Oregon National Primate Research Center

description: Gene expression profile of RiPS1 B is  rhesus fetal iPS in biological replicate B.

hyb_protocol: Labeled target is fragmented at 95o C in the presence of high magnesium concentration.  The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Ten mg of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.CEL files). Image inspection was performed manually immediately following each scan.

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.

label: Biotin

molecule: total RNA

organism: Macaca mulatta

source_name: Fetal rhesus skin fibroblast.

label_protocol: Microarray assays were performed in the Affymetrix Microarray Core of the OHSU Gene Microarray Shared Resource. Messenger RNA is amplified and labeled from 2mg of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix).  In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

growth_protocol: All monkey pluripotent stem cells were grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mEF feeder cells in Dulbecco’s Modified Eagle’s Medium/F12 (DMEM/F12) (Invitrogen) supplemented with 15% defined fetal bovine serum (FBS) (Hyclone), 0.1mM b-mercaptoethanol (Sigma), 1% nonessential amino acids (Invitrogen), 2mM L-glutamine (Invitrogen) and a pH of 7.2 (altered with 4N NaOH). Pluripotent colonies were manually passaged every 4-5 days.  Somatic fibroblasts were also grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mEF feeder cells in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and a pH of 7.2 (altered with 4N NaOH).  Stem cells with an undifferentiated morphology were manually removed from culture and Fibroblasts were trypsinized for total RNA purification.

extract_protocol: Total RNA was extracted using Trizol® reagent (Invitrogen) followed by additional purification on RNeasy spin columns (Qiagen) following manufacturer recommendations.

treatment_protocol: All stem and somatic cell lines were generated by us at the Oregon National Primate Research Center. ORMES23, CRES, and RiPS were established from rhesus monkey IVF blastocyst, cloned (SCNT) blastocyst and adult rhesus skin fibroblast rhesus monkey by retroviral transduction with vectors carrying 4 factors (OCT4, SOX2, Klf4 and cMYC), respectively. RNA were isolated from only nice undifferentiated colonies. Somatic fibroblasts were derived from a skin biopsy from an eight year old adult female rhesus monkey.

tag: gender

value: male

tag: developmental stage

value: somatic cells, skin fibroblasts

tag: cell type

value: iPS


title: Cloned Rhesus Embryonic Stem cells 3 (CRES-3), biological repC

description: Gene expression profile of CRES-3C is  rhesus cloned ES in biological replicate C.

value: female


title: Rhesus induced Pluripotent Stem cells 2 (RiPS2), biological repA

description: Gene expression profile of RiPS2 A is  rhesus adult iPS in biological replicate A.

source_name: Adult rhesus skin fibroblast (10 years old)


title: Cloned Rhesus Embryonic Stem cells 3 (CRES-3), biological repB

description: Gene expression profile of CRES-3B is  rhesus cloned ES in biological replicate B.


title: PC3 T1 R3

type: genomic

city: Chapel Hill

first: Joel

last: Parker

state: NC

address: 5109 B Bioinformatics Building

department: Genetics

institute: UNC - CH

hyb_protocol: A hybridization mix containing 1.5 ug of Cy3‐labeled LNCaP or PC3 DNA, 1.5 ug Cy5‐labeled reference DNA, herring sperm DNA (Promega, San Luis Obispo, CA), and array comparative genomic hybridization blocking agent (Agilent Technologies, Santa Clara, CA) was incubated at 95oC for 3 min and then hybridized onto 8‐plex custom Agilent arrays as described.

scan_protocol: Agilent Feature Extractor software was used to scan microarray images

data_processing: Agilent Feature Extractor software

molecule: genomic DNA

organism: Homo sapiens

source_name: experimental plasmid DNA

label_protocol: Purified DNA fragments (1.5 ug) from LNCaP or PC3 cells were labeled with Cy3 and fragments from the library plasmid DNA were labeled with Cy5 by incubation with Cy3‐dCTP or Cy5‐dCTP (GE Healthcare, Piscataway, NJ), Klenow Fragment (New England Biolabs, Beverly, MA), and a random nanotamer (Sigma‐Aldrich) in labeling reaction buffer (100 mM Tris, pH 7.5, 50 mM MgCl2, 75 mM DTT, 2 mM dATP/dGTP/dTTP, 50 uM dCTP) for 4 h at 37oC. Reactions were stopped by the addition of 0.5 M EDTA, pH 8.0. Unincorporated nucleotides were removed using Microcon YM30 cutoff columns (Millipore).

growth_protocol: LNCaP and PC3 cells were infected with the 6K shRNA pooled library virus (MOI < 0.5) in triplicate to generate a total of 6 million infected cells per replicate, per cell line. Infection of target cells at MOI < 0.5 was confirmed by fluorescence microscopy and fluorescence activated cell sorting (FACS) 48 h after infection. LNCaP and PC3 cells were selected with 3 ug/ml puromycin until non‐infected cells were dead, 4 days or 6 days respectively, and then the selection media was removed. Forty‐eight hours after the selection media was removed, the cells were counted and plated in growth media containing 0.4 uM bicalutamide, 1.0 uM bicalutamide, or vehicle (DMSO) and cultured for 21 days. Cells were passaged, and bicalutamide and vehiclereplenished, every 4 days without allowing confluence. Cells were counted every 4 days to monitor growth in response to vehicle and bicalutamide.

extract_protocol:
LNCaP and PC3 cells from each replicate were harvested by trypsinization and centrifugation, and cell pellets were flash frozen and stored at ‐80oC at multiple time‐points during the screen. Cells were harvested 48 h after infection (T=0), and after 8 days (T=1) and 21 days (T=2) of exposure to vehicle or bicalutamide.
Genomic DNA was extracted from cells at the indicated time‐points by resuspending cells in lysis buffer (50 mM Tris, pH 8.0, 100 mM EDTA, 100 mM NaCl, 1% SDS) and incubating the lysates with Proteinase K solution (Ambion, Austin, TX) overnight at 55oC. Lysates were then treated with RNase A for 3 h at 37oC, phenol:chloroform extracted two times, and DNA was precipitated using isopropyl alcohol and resuspended in DNA resuspension buffer (10 mM Tris‐HCl, pH8.0, 1 mM EDTA). Barcodes and half‐hairpins from the library plasmid DNA (originally used to make the virus) and LNCaP and PC3 cell genomic DNA isolated above were PCR amplified using the following primers: 5’‐ TAGTGAAGCCACAGATGTA‐3’ and  5’‐AAAGCGCATGCTCCAGACTGCC‐3’. The PCR products were subject to gel electrophoresis and the resulting 350 bp bands were gel purified using the QIAEX II gel extraction kit (QIAGEN, Valencia, CA).

tag: cell line

tag: replicate

tag: time point

tag: dose

value: untx

tag: time

value: 8 d

source_name: control library plasmid DNA

tag: sample type

value: control library plasmid DNA


title: Cloned Rhesus Embryonic Stem cells 1 (CRES-1), biological repC

description: Gene expression profile of CRES-1C is  rhesus cloned ES in biological replicate C.

value: embryonic stem cell


title: Normal 1

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

country: Japan

institute: Sapporo medical university

hyb_protocol: Hybridization was performed using an aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.

source_name: Human Colon Tissue

label_protocol: Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and reference DNA was labeled with Cy3.

growth_protocol: A total of 86 colorectal tumor specimens were obtained from endoscopic biopsy.

extract_protocol: Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.

treatment_protocol: No treatment was carried out.

tag: tissue type

value: Human Colon

tag: pathology

value: Normal colon

tag: age

value: M

source_name: Human Genomic DNA from Normal Colon


title: Godfrey_MS340__GenomeWideSNP_6

city: Boston

first: Steven

middle: E

last: Schumacher

state: MA

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Esophageal adenocarcinoma-Tumor-EMPTY-SNP_6.0

hyb_protocol: Each sample was genotyped using the Sty I chip of the 500K Human Mapping Array wet (Affymetrix), containing probes to 238,270 SNP loci, according to manufacturer’s instructions. In brief, 250 ng of genomic DNA was digested with the StyI restriction enzyme (New England Biolabs), ligated to an adaptor with T4 ligase (New England Biolabs), and PCR-amplified using a 9700 Thermal Cycler I (Applied Biosystems) and Titanium Taq (Clontech) to achieve fragments ranging from 200-1100 bp. These fragments were pooled, concentrated, processed through a clean-up step, and further fragmented with DNaseI (Affymetrix) before being labeled, denatured, and hybridized to arrays

scan_protocol: Arrays were washed and scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Probe-level signal intensities were normalized to a common reference array using quantile normalization and combined to form SNP-level signal intensities using the dChip model-based expression (PM/MM) method . Genome-wide copy number estimates were obtained using five closest normal method, in which tumor signal intensities are divided by the geometric mean of the five normal samples closest to the tumor in Euclidean log2 ratio space (as described in Weir et al, Nature 2007).  Cancer samples were normalized against the plate normals included in this submission and also normals used in the TCGA ovarian cancer study (TCGA network, Nature, 2011). GEO Sample tables (VALUE) contain the resulting normalized copy-number values.

source_name: esophageal adenocarcinoma

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA was obtained from cell line pellets or tumors frozen at the time of surgical dissection and maintained at -80C until use.

tag: cancer type

value: esophageal adenocarcinoma

tag: batch


title: Cloned Rhesus Embryonic Stem cells 1 (CRES-1), biological repA

description: Gene expression profile of CRES-1A is rhesus cloned ES in biological replicate A.


title: Cloned Rhesus Embryonic Stem cells 1 (CRES-1), biological repB

description: Gene expression profile of CRES-1B is  rhesus cloned ES in biological replicate B.


title: LNCaP T0 R1 (pre select)

value: LNCaP

value: 0 - pre-selection

value: 48 h - pre-selection


title: Godfrey_MS342__GenomeWideSNP_6


title: PC3 T2 0.4 uM Casodex R3

value: low

tag: treatment

value: 0.4 uM Casodex


title: Rhesus induced Pluripotent Stem cells 1 (RiPS1), biological repA

description: Gene expression profile of RiPS1 A is  rhesus fetal iPS in biological replicate A.

value: male


title: Oregon Rhesus Macaque Embryonic Stem23 (ORMES23),biological rep C

description: Gene expression profile of ORMES23C is biparental controls profile in biological replicate C.

source_name: IVF rhesus embryo at blastocyst stage.

value: embryo, Blastocyst


title: PC3 T1 0 uM Casodex R1

value: vehicle

value: 0 uM Casodex


title: Godfrey_MS337__GenomeWideSNP_6


title: PC3 T2 1.0 uM Casodex R3

value: high

value: 1.0 uM Casodex


title: PC3 T0 R3 (pre select)

value: untx

value: control library plasmid DNA


title: Godfrey_MS327_2__GenomeWideSNP_6


title: Oregon Rhesus Macaque Embryonic Stem23 (ORMES23),biological rep B

description: Gene expression profile of ORMES23B is biparental controls profile in biological replicate B

value: embryonic stem cell


title: sp_903_deltaMMI1_b

city: La Tronche

first: andre

last: VERDEL

address: Rond point de la chantourne

department: Department of Cell Differentiation and Transformation

country: France

institute: INSERM/UJF U823

hyb_protocol: Hybridization was performed following instructions of the Affymetrix WT Double-Stranded Target Assay manual.

scan_protocol: Arrays were read with a confocal laser (Genechip scanner 3000, Affymetrix).

data_processing:
CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0.
Raw data were normalized with Partek Genomic Suite software 6.5 (Partek Inc., St. Louis, MO, US) using Robust Multiarray Average (RMA) statistical algorithm, which includes RMA background correction, quantile normalization, log2 transformation.

label: biotin

organism: Schizosaccharomyces pombe

source_name: yeast, spv903

label_protocol: Labelling was performed following instructions of the Affymetrix WT Double-Stranded Target Assay manual.

growth_protocol: S. pombe cells were grown in 100 ml yeast extract (YE) supplemented with Adenine at 32℃ and 220 rpm up to OD595=0.5.

extract_protocol: Total RNA was purified using a classic acid phenol/chloroform extraction and classical alcohol precipitation.100µg of total RNA were purified by Qiagen RNA easy kit (silica column tubes) and further digested by Dnase I Rnase-free.

treatment_protocol: No treatment

tag: genotype

value: MEI4∆, MMI1∆

tag: strain


title: PC3 T0 R2 (pre select)


title: sp_903_deltaMMI1_a


title: Godfrey_MS341__GenomeWideSNP_6


title: sp_481_deltaMEI4_b

source_name: yeast, spv481


title: PC3 T0 R1 (pre select)


title: LNCaP T2 0.4 uM Casodex R3 DUP


title: Godfrey_MS325__GenomeWideSNP_6


title: Godfrey_MS324__GenomeWideSNP_6


title: sp_481_deltaMEI4_a


title: Oregon Rhesus Macaque Embryonic Stem23 (ORMES23),biological rep A

description: Gene expression profile of ORMES23A is biparental controls profile in biological replicate A.

tag: gender


title: sp_8_WT_b

source_name: yeast, spv8

value: wild type


title: LNCaP T1 0 uM Casodex R2

value: 8 d


title: sp_8_WT_a


title: PC3 T2 1.0 uM Casodex R3 DUP


title: Godfrey_MS314_2__GenomeWideSNP_6

value: esophageal adenocarcinoma


title: Godfrey_MS318__GenomeWideSNP_6


title: Godfrey_MS322__GenomeWideSNP_6


title: Godfrey_MS334__GenomeWideSNP_6


title: PC3 T2 1.0 uM Casodex R1


title: Godfrey_MS315__GenomeWideSNP_6


title: UC_0312_1

city: Lund

first: Mattias

last: Aine

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

hyb_protocol: According to manufacturers specifications

data_processing:
Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly.  Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly.  Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly.  Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly.  Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly.
Normalized Average Beta with replicate samples UC_0556_1.B1, B2 and B3 as well as hybridization controls removed.
Unmethylated and methylated signal intensities in 'signals' matrix which is linked as supplementary file on the Series record.

source_name: Bladder tumor UC_0312_1

extract_protocol: Genomic DNA was extracted using DNeasy spin columns (QIAGEN) acording to manufacturers specifications

treatment_protocol: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resection at hospitals within the southern healthcare region of Sweden.

tag: bisulfite batch

value: Bladder tumor

tag: tumor stage

tag: tumor grade

tag: Sex

value: F


title: PC3 T2 0.4 uM Casodex R3 DUP

tag: cell line

tag: replicate

tag: time point

value: low


title: UC_0615_1

scan_protocol: According to manufacturers specifications

source_name: Bladder tumor UC_0615_1

value: M


title: PC3 T2 0.4 uM Casodex R2

tag: dose

tag: time

value: 0.4 uM Casodex

tag: sample type


title: PC3 T2 0.4 uM Casodex R1


title: Godfrey_MS305__GenomeWideSNP_6


title: Godfrey_MS329__GenomeWideSNP_6


title: Godfrey_MS330__GenomeWideSNP_6


title: PC3 T2 0 uM Casodex R3


title: UC_0545_1

source_name: Bladder tumor UC_0545_1

label_protocol: According to manufacturers specifications

tag: tissue type

tag: age


title: Godfrey_MS313_2__GenomeWideSNP_6

tag: cancer type

tag: batch


title: Godfrey_MS316__GenomeWideSNP_6


title: UC_0557_1

source_name: Bladder tumor UC_0557_1

value: Ta


title: Godfrey_MS1104_2__GenomeWideSNP_6


title: PC3 T2 0 uM Casodex R2

value: vehicle

tag: treatment


title: Godfrey_MS1105__GenomeWideSNP_6


title: UC_0536_1

source_name: Bladder tumor UC_0536_1


title: UC_0213_1

source_name: Bladder tumor UC_0213_1


title: PC3 T2 1.0 uM Casodex R2


title: PC3 T2 0 uM Casodex R1

value: 0 uM Casodex


title: UC_0576_1

source_name: Bladder tumor UC_0576_1


title: UC_0410_1a

source_name: Bladder tumor UC_0410_1a


title: Godfrey_MS1102__GenomeWideSNP_6


title: PC3 T1 1.0 uM Casodex R3

source_name: experimental plasmid DNA

value: high


title: UC_0322_2

source_name: Bladder tumor UC_0322_2


title: Godfrey_MS1099__GenomeWideSNP_6


title: Godfrey_MS1100__GenomeWideSNP_6


title: PC3 T1 1.0 uM Casodex R1

value: 1.0 uM Casodex

source_name: control library plasmid DNA


title: UC_0572_1

source_name: Bladder tumor UC_0572_1


title: Godfrey_MS326__GenomeWideSNP_6

source_name: esophageal adenocarcinoma


title: PC3 T1 1.0 uM Casodex R2


title: UC_0400_1b

source_name: Bladder tumor UC_0400_1b


title: Godfrey_MS1098_2__GenomeWideSNP_6


title: Godfrey_MS544_2__GenomeWideSNP_6


title: UC_0208_1

source_name: Bladder tumor UC_0208_1


title: Godfrey_MS1103__GenomeWideSNP_6


title: PC3 T1 0.4 uM Casodex R1


title: UC_0475_1

source_name: Bladder tumor UC_0475_1

value: Gx


title: PC3 T1 0.4 uM Casodex R3

value: control library plasmid DNA


title: Godfrey_MS1101A__GenomeWideSNP_6


title: PC3 T1 0 uM Casodex R3


title: PC3 T1 0 uM Casodex R2


title: PC3 T1 0.4 uM Casodex R2


title: UC_0579_1

source_name: Bladder tumor UC_0579_1


title: Godfrey_MS1096_2__GenomeWideSNP_6


title: Godfrey_MS1092__GenomeWideSNP_6__Rep2


title: Godfrey_MS310_2__GenomeWideSNP_6


title: UC_0626_1

source_name: Bladder tumor UC_0626_1


title: PC3 T0 R1

value: 0 - post-selection

value: untx

value: 48 h - post-selection


title: UC_0519_1

source_name: Bladder tumor UC_0519_1


title: PC3 T0 R2


title: PC3 T1 0 uM Casodex R1 DUP

value: 8 d


title: UC_0710_1

source_name: Bladder tumor UC_0710_1


title: UC_0616_1

source_name: Bladder tumor UC_0616_1


title: Godfrey_MS1094_2__GenomeWideSNP_6

value: esophageal adenocarcinoma


title: Godfrey_MS1089_2__GenomeWideSNP_6


title: PC3 T0 R2 (pre select) DUP

value: 0 - pre-selection

value: 48 h - pre-selection


title: UC_0414_1

source_name: Bladder tumor UC_0414_1

value: Bladder tumor


title: PC3 T0 R1 (pre select) DUP


title: Godfrey_MS1097_2__GenomeWideSNP_6


title: UC_0551_1

source_name: Bladder tumor UC_0551_1

value: M


title: LNCaP T2 1.0 uM Casodex R3

value: LNCaP


title: PC3 T0 R3 (pre select) DUP


title: Godfrey_MS1088_2__GenomeWideSNP_6


title: UC_0203_1

source_name: Bladder tumor UC_0203_1


title: UC_0372_1

source_name: Bladder tumor UC_0372_1


title: Godfrey_MS1087_2__GenomeWideSNP_6


title: LNCaP T2 1.0 uM Casodex R2

source_name: experimental plasmid DNA


title: Godfrey_MS1082B_2__GenomeWideSNP_6


title: UC_0495_1

source_name: Bladder tumor UC_0495_1

value: Ta


title: Godfrey_MS1084_2__GenomeWideSNP_6


title: LNCaP T2 0.4 uM Casodex R3

value: low

value: 0.4 uM Casodex

source_name: control library plasmid DNA


title: Godfrey_MS1091_2__GenomeWideSNP_6


title: LNCaP T2 1.0 uM Casodex R1

value: high


title: UC_0207_1

source_name: Bladder tumor UC_0207_1


title: UC_0089_1

source_name: Bladder tumor UC_0089_1


title: WHELK_p_Sty27_Mapping250K_Sty_H06_96920

data_processing: Probe-level signal intensities were normalized to a common reference array using quantile normalization and combined to form SNP-level signal intensities using the dChip model-based expression (PM/MM) method . Genome-wide copy number estimates were obtained using tangent normalization, in which tumor signal intensities are divided by signal intensities from the linear combination of all normal samples that is most similar to the tumor (as described in Beroukhim et al, In Press; and Getz et al., In Preparation).  Cancer samples were normalized against a pool of 1,480 reference samples derived from multiple studies; the code and reference data necessary to replicate this analysis are available for download in GEO (accession GSE19399, see GSE19399_tangent_norm_files.tar.gz). GEO Sample tables (VALUE) contain the normalized copy-number values produced by that algorithm.

source_name: gastric

value: gastric

value: WHELK


title: LNCaP T2 0.4 uM Casodex R2

value: control library plasmid DNA


title: UC_0340_1

source_name: Bladder tumor UC_0340_1

value: F


title: Godfrey_MS1090_2__GenomeWideSNP_6

source_name: esophageal adenocarcinoma


title: LNCaP T2 0.4 uM Casodex R1


title: UC_0248_2

source_name: Bladder tumor UC_0248_2


title: WHELK_p_Sty27_Mapping250K_Sty_H02_96856


title: WHELK_p_Sty27_Mapping250K_Sty_E01_96834


title: LNCaP T2 0 uM Casodex R3

value: vehicle

value: 0 uM Casodex


title: UC_0582_1

source_name: Bladder tumor UC_0582_1


title: WHELK_p_Sty27_Mapping250K_Sty_B07_96924


title: LNCaP T2 0 uM Casodex R2


title: Godfrey_MS1079_2__GenomeWideSNP_6


title: Godfrey_MS1077__GenomeWideSNP_6


title: Godfrey_MS1081_2__GenomeWideSNP_6


title: LNCaP T2 0 uM Casodex R1


title: UC_0234_1

source_name: Bladder tumor UC_0234_1


title: Godfrey_4935__GenomeWideSNP_6


title: Godfrey_82__GenomeWideSNP_6


title: LNCaP T1 1.0 uM Casodex R3

value: 8 d

value: 1.0 uM Casodex


title: UC_0335_1

source_name: Bladder tumor UC_0335_1


title: Godfrey_4933__GenomeWideSNP_6

value: esophageal adenocarcinoma


title: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_F11_121674

value: SPICA


title: Godfrey_4930__GenomeWideSNP_6


title: UC_0218_2

source_name: Bladder tumor UC_0218_2

value: Bladder tumor


title: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_F04_121562


title: LNCaP T1 1.0 uM Casodex R2


title: Godfrey_74_2__GenomeWideSNP_6


title: Godfrey_4932__GenomeWideSNP_6


title: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_F09_104702

value: KNACK


title: LNCaP T1 1.0 uM Casodex R1

value: LNCaP


title: UC_0139_1

source_name: Bladder tumor UC_0139_1

value: M


title: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_C04_121556


title: UC_0235_3

source_name: Bladder tumor UC_0235_3


title: N_031_Urothel

source_name: Normal Urothelium Sample

value: Normal Urothelium Sample


title: Godfrey_4929__GenomeWideSNP_6


title: LNCaP T1 0.4 uM Casodex R2

value: low

value: 0.4 uM Casodex


title: LNCaP T1 0.4 uM Casodex R3


title: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_D04_104618

value: gastric


title: Godfrey_4934__GenomeWideSNP_6


title: Godfrey_4928__GenomeWideSNP_6


title: UC_0438_1

source_name: Bladder tumor UC_0438_1

value: Ta


title: Godfrey_4927__GenomeWideSNP_6


title: CYMAR_p_STY38_Mapping250K_Sty_E02_183336

value: CYMAR


title: Godfrey_4925__GenomeWideSNP_6


title: CYMAR_p_STY38_Mapping250K_Sty_D06_187050


title: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_H12_104754


title: UC_0257_1

source_name: Bladder tumor UC_0257_1


title: UC_0024_1

source_name: Bladder tumor UC_0024_1


title: LNCaP T1 0 uM Casodex R3

source_name: experimental plasmid DNA

source_name: control library plasmid DNA

value: control library plasmid DNA


title: UC_0724_1

source_name: Bladder tumor UC_0724_1


title: LNCaP T1 0.4 uM Casodex R1


title: LNCaP T1 0 uM Casodex R1

value: vehicle


title: CYMAR_p_STY38_Mapping250K_Sty_A05_187042

source_name: gastric


title: UC_0692_1

source_name: Bladder tumor UC_0692_1


title: LNCaP T1 0 uM Casodex R2 DUP

value: 0 uM Casodex


title: LNCaP T0 R3

value: 0 - post-selection

value: untx

value: 48 h - post-selection


title: PAVIN_p_STY33_Mapping250K_Sty_H08_128926

description: Esophageal adenocarcinoma-Tumor-UMBEER_46_T-250K_Sty

source_name: esophageal adenocarcinoma

value: esophageal adenocarcinoma

value: PAVIN


title: PAVIN_p_STY33_Mapping250K_Sty_H09_128942

description: Esophageal adenocarcinoma-Tumor-UMBEER_50_T-250K_Sty


title: UC_0628_1

source_name: Bladder tumor UC_0628_1

value: Bladder tumor


title: Godfrey_4923__GenomeWideSNP_6


title: LNCaP T0 R2

value: LNCaP


title: PAVIN_p_STY33_Mapping250K_Sty_H11_128974

description: Esophageal adenocarcinoma-Tumor-UMBEER_48_T-250K_Sty


title: Godfrey_4924__GenomeWideSNP_6


title: LNCaP T0 R1


title: PAVIN_p_STY33_Mapping250K_Sty_H03_128846

description: Esophageal adenocarcinoma-Tumor-UMBEER_44_T-250K_Sty


title: Godfrey_4926__GenomeWideSNP_6


title: UC_0376_1

source_name: Bladder tumor UC_0376_1

value: M


title: Godfrey_4921__GenomeWideSNP_6


title: UC_0386_1

source_name: Bladder tumor UC_0386_1

value: F


title: Godfrey_4920__GenomeWideSNP_6


title: Godfrey_4919__GenomeWideSNP_6


title: PAVIN_p_STY33_Mapping250K_Sty_G09_128940

description: Esophageal adenocarcinoma-Tumor-UMBEER_42_T-250K_Sty


title: UC_0025_1

source_name: Bladder tumor UC_0025_1


title: UC_0398_1

source_name: Bladder tumor UC_0398_1


title: UC_0395_1a

source_name: Bladder tumor UC_0395_1a


title: LNCaP T0 R3 (pre select)

value: 0 - pre-selection

value: 48 h - pre-selection


title: Godfrey_4917__GenomeWideSNP_6


title: UC_0267_3

source_name: Bladder tumor UC_0267_3


title: PAVIN_p_STY33_Mapping250K_Sty_F11_128970

description: Esophageal adenocarcinoma-Tumor-UMBEER_38_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_G07_128908

description: Esophageal adenocarcinoma-Tumor-UMBEER_60_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_F04_128858

description: Esophageal adenocarcinoma-Tumor-UMBEER_34_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_G06_128892

description: Esophageal adenocarcinoma-Tumor-UMBEER_40_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_G01_128812

description: Esophageal adenocarcinoma-Tumor-UMBEER_26_T-250K_Sty


title: UC_0566_1

source_name: Bladder tumor UC_0566_1


title: Godfrey_4915__GenomeWideSNP_6

description: Esophageal adenocarcinoma-Tumor-EMPTY-SNP_6.0


title: PAVIN_p_STY33_Mapping250K_Sty_F08_128922

description: Esophageal adenocarcinoma-Tumor-UMBEER_36_T-250K_Sty


title: LNCaP T0 R2 (pre select)


title: N_007_ureter

source_name: Normal Ureter Sample

value: Normal Ureter Sample


title: Godfrey_4914__GenomeWideSNP_6


title: UC_0375_1

source_name: Bladder tumor UC_0375_1

value: Ta


title: UC_0040_1

source_name: Bladder tumor UC_0040_1


title: Godfrey_4911__GenomeWideSNP_6


title: PAVIN_p_STY33_Mapping250K_Sty_E11_128968

description: Esophageal adenocarcinoma-Tumor-UMBEER_32_T-250K_Sty


title: Godfrey_4909__GenomeWideSNP_6


title: UC_0103_1

source_name: Bladder tumor UC_0103_1


title: Godfrey_4913__GenomeWideSNP_6


title: Godfrey_4895_2__GenomeWideSNP_6


title: PAVIN_p_STY33_Mapping250K_Sty_E07_128904

description: Esophageal adenocarcinoma-Tumor-UMBEER_30_T-250K_Sty


title: Godfrey_4897__GenomeWideSNP_6


title: PAVIN_p_STY33_Mapping250K_Sty_F01_128810

description: Esophageal adenocarcinoma-Tumor-UMBEER_52_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_E04_128856

description: Esophageal adenocarcinoma-Tumor-UMBEER_28_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_E02_128824

description: Esophageal adenocarcinoma-Tumor-UMBEER_62_T-250K_Sty


title: Wild type control liver liver6w Wt 1 (nCounter)

city: Columbus

first: Madhu

last: Ouseph

state: Ohio

address: 460w 12th Ave

institute: The Ohio State University

description:
NanoString’s gene expression CodeSets are pairs of approximately 50-bases called capture and reporter probes (Capture and Reporter, synthesized in 96-well plates using semi-automated process) that hybridize to the RNA sample and are used to detect and count mRNA transcripts.
The reporter probe carries the signal and the capture probe is used to immobilize the complex for data collection.

hyb_protocol: standard NanoString protocol

scan_protocol: After hybridization, samples are transferred to the nCounter Prep Station where excess probes are removed and probe/target complexes are aligned and immobilized in the nCounter Cartridge. Cartridges are then placed in the nCounter Digital Analyzer for data collection.

data_processing:
The nCounter data is first normalized to the geometric mean of positive control spike counts in each lane of the cartridge, followed by subtracting the minimum negative control spike counts in each lane to remove the background.
Finally, expression of each gene in the codeset is normalized with respect to the geometric mean of the house keeping genes.

label: Alexa 488, Alexa 594, Alexa 647, Cy3

organism: Mus musculus

source_name: liver 6 weeks

label_protocol: Color-coded probe pairs (representing capture and reporter probes; reporter probe carries the fluorescent tags) are mixed together with total RNA in a single hybridization reaction that proceeds in solution.

extract_protocol: trizol method and Arcturus PicoPure RNA Isolation Kit

tag: tissue

value: liver

value: 6 weeks

tag: genotype

value: Wild type

tag: genetic background

value: FVB


title: Wild type control liver liver3wx Wt 1 (nCounter)

source_name: liver 3 weeks, 1 day post weaning

value: 3 weeks, 1 day post weaning


title: Wild type control liver liver3wx Wt 3 (nCounter)


title: UC_0701_1

source_name: Bladder tumor UC_0701_1

tag: bisulfite batch

tag: tumor stage


title: Godfrey_4918__GenomeWideSNP_6


title: Godfrey_MS1086A_2__GenomeWideSNP_6


title: UC_0580_1

source_name: Bladder tumor UC_0580_1

tag: tumor grade

tag: Sex


title: Godfrey_MS1085A_2__GenomeWideSNP_6

source_name: esophageal adenocarcinoma


title: N_039_Urothel

source_name: Normal Urothelium Sample

value: Normal Urothelium Sample


title: Godfrey_4891__GenomeWideSNP_6


title: Godfrey_4893_2__GenomeWideSNP_6


title: PAVIN_p_STY33_Mapping250K_Sty_D05_128870

description: Esophageal adenocarcinoma-Tumor-UMBEER_22_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_D01_128806

description: Esophageal adenocarcinoma-Tumor-UMBEER_20_T-250K_Sty


title: Godfrey_4894_2__GenomeWideSNP_6


title: UC_0231_1

source_name: Bladder tumor UC_0231_1


title: UC_0215_1

source_name: Bladder tumor UC_0215_1


title: Wild type control liver liver6w Wt 2 (nCounter)


title: Godfrey_4890__GenomeWideSNP_6


title: Wild type control liver liver3wx Wt 2 (nCounter)


title: Godfrey_4892_2__GenomeWideSNP_6


title: Wild type control liver liver2w Wt 2 (nCounter)

source_name: liver 2 weeks

value: 2 weeks


title: PAVIN_p_STY33_Mapping250K_Sty_D09_128934

description: Esophageal adenocarcinoma-Tumor-UMBEER_24_T-250K_Sty

value: esophageal adenocarcinoma


title: Wild type control liver liver3w Wt 5 (nCounter)

source_name: liver 3 weeks

value: 3 weeks


title: Wild type control liver liver3w Wt 6 (nCounter)


title: Godfrey_4887_2__GenomeWideSNP_6


title: Godfrey_4886_2__GenomeWideSNP_6


title: Wild type control liver liver2w Wt 1 (nCounter)


title: PAVIN_p_STY33_Mapping250K_Sty_C11_128964

description: Esophageal adenocarcinoma-Tumor-UMBEER_18_T-250K_Sty

value: PAVIN


title: UC_0552_1

source_name: Bladder tumor UC_0552_1

value: Bladder tumor


title: UC_0437_1

source_name: Bladder tumor UC_0437_1


title: Godfrey_4884__GenomeWideSNP_6


title: Wild type control liver liver1w Wt 2 (nCounter)

source_name: liver 1 week

value: 1 week


title: Wild type control liver liver1w Wt 1 (nCounter)


title: Wild type control liver liver13.5 Wt 3 (nCounter)

source_name: liver E13.5 embryo

value: E13.5 embryo


title: PAVIN_p_STY33_Mapping250K_Sty_C07_128900

description: Esophageal adenocarcinoma-Tumor-UMBEER_16_T-250K_Sty


title: Wild type control liver liverP0 Wt 2 (nCounter)

source_name: liver P0


title: UC_0694_1

source_name: Bladder tumor UC_0694_1

value: F


title: Godfrey_4885_2__GenomeWideSNP_6


title: UC_0610_1

source_name: Bladder tumor UC_0610_1

value: M


title: Godfrey_4883_2__GenomeWideSNP_6


title: Godfrey_4880_2__GenomeWideSNP_6


title: Godfrey_4881_2__GenomeWideSNP_6


title: PAVIN_p_STY33_Mapping250K_Sty_C09_128932

description: Esophageal adenocarcinoma-Tumor-UMBEER_54_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_B05_128866

description: Esophageal adenocarcinoma-Tumor-UMBEER_10_T-250K_Sty


title: UC_0706_1

source_name: Bladder tumor UC_0706_1


title: UC_0713_1

source_name: Bladder tumor UC_0713_1


title: UC_0521_1

source_name: Bladder tumor UC_0521_1


title: Wild type control liver liverP0 Wt 1 (nCounter)


title: Wild type control liver liver13.5 Wt 2 (nCounter)


title: PAVIN_p_STY33_Mapping250K_Sty_C04_128852

description: Esophageal adenocarcinoma-Tumor-UMBEER_14_T-250K_Sty


title: PAVIN_p_STY33_Mapping250K_Sty_A04_128848

description: Esophageal adenocarcinoma-Tumor-UMBEER_2_T-250K_Sty


title: UC_0573_1

source_name: Bladder tumor UC_0573_1


title: Godfrey_4888_2__GenomeWideSNP_6

description: Esophageal adenocarcinoma-Tumor-EMPTY-SNP_6.0

source_name: esophageal adenocarcinoma


title: Wild type control liver liver13.5 Wt 1 (nCounter)


title: UC_0009_1

source_name: Bladder tumor UC_0009_1


title: PAVIN_p_STY33_Mapping250K_Sty_B02_128818

description: Esophageal adenocarcinoma-Tumor-UMBEER_8_T-250K_Sty


title: Wild type control trophoblast giant cells GC17.5 Wt1 (nCounter)

source_name: trophoblast giant cells E17.5 placenta

value: E17.5 placenta

tag: cell type

value: trophoblast giant cells


title: LINED_p_STY36_Mapping250K_Sty_C12_147862

description: Esophageal adenocarcinoma-Tumor-UMBEER_148_T-250K_Sty

value: LINED


title: LINED_p_STY36_Mapping250K_Sty_A05_147746

description: Esophageal adenocarcinoma-Tumor-UMBEER_146_T-250K_Sty


title: Godfrey_4882_2__GenomeWideSNP_6


title: Godfrey_4879_2__GenomeWideSNP_6


title: Wild type control trophoblast giant cells GC17.5 Wt2 (nCounter)


title: LINED_p_STY36_Mapping250K_Sty_G02_147710

description: Esophageal adenocarcinoma-Tumor-UMBEER_144_T-250K_Sty


title: UC_0299_1

source_name: Bladder tumor UC_0299_1


title: HAREM_p_STY35_Redo_Mapping250K_Sty_G07_151070

description: Esophageal adenocarcinoma-Tumor-UMBEER_158_T-250K_Sty

value: HAREM


title: UC_0095_1

source_name: Bladder tumor UC_0095_1


title: HAREM_p_STY35_Redo_Mapping250K_Sty_F07_151068

description: Esophageal adenocarcinoma-Tumor-UMBEER_152_T-250K_Sty


title: Godfrey_4876_2__GenomeWideSNP_6


title: Wild type control trophoblast giant cells GC13.5 Wt 2 (nCounter)

description:
NanoString’s gene expression CodeSets are pairs of approximately 50-bases called capture and reporter probes (Capture and Reporter, synthesized in 96-well plates using semi-automated process) that hybridize to the RNA sample and are used to detect and count mRNA transcripts.
The reporter probe carries the signal and the capture probe is used to immobilize the complex for data collection.

source_name: trophoblast giant cells E13.5 placenta

value: E13.5 placenta

value: Wild type


title: UC_0230_1

source_name: Bladder tumor UC_0230_1


title: Wild type control trophoblast giant cells GC13.5 Wt 1 (nCounter)

value: FVB


title: HAREM_p_STY35_Redo_Mapping250K_Sty_C09_151094

description: Esophageal adenocarcinoma-Tumor-UMBEER_154_T-250K_Sty


title: UC_0415_1

source_name: Bladder tumor UC_0415_1

value: Ta


title: Wild type control trophoblast giant cells GC15.5 Wt 2 (nCounter)

source_name: trophoblast giant cells E15.5 placenta

value: E15.5 placenta


title: Godfrey_4877_2__GenomeWideSNP_6

value: esophageal adenocarcinoma


title: HAREM_p_STY35_Redo_Mapping250K_Sty_A07_151058

description: Esophageal adenocarcinoma-Tumor-UMBEER_156_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_H11_131218

description: Esophageal adenocarcinoma-Tumor-UMBEER_119_T-250K_Sty

value: DECAY


title: UC_0544_1

source_name: Bladder tumor UC_0544_1


title: Wild type control trophoblast giant cells GC15.5 Wt 1 (nCounter)


title: Wild type control trophoblast giant cells GC10.5 Wt 2 (nCounter)

source_name: trophoblast giant cells E10.5 placenta

value: E10.5 placenta


title: Wild type control trophoblast giant cells GC10.5 Wt 1 (nCounter)


title: Godfrey_4878_2__GenomeWideSNP_6


title: Godfrey_4875_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_H05_131122

description: Esophageal adenocarcinoma-Tumor-UMBEER_117_T-250K_Sty


title: UC_0725_1

source_name: Bladder tumor UC_0725_1

value: Bladder tumor


title: UC_0111_1

source_name: Bladder tumor UC_0111_1


title: DECAY_p_STY34_Mapping250K_Sty_H01_131058

description: Esophageal adenocarcinoma-Tumor-UMBEER_116_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_H10_131202

description: Esophageal adenocarcinoma-Tumor-UMBEER_118_T-250K_Sty


title: Wild type control trophoblast giant cells GC8.5 Wt 1 (nCounter)

source_name: trophoblast giant cells E8.5 placenta

value: E8.5 placenta


title: DECAY_p_STY34_Mapping250K_Sty_G07_131152

description: Esophageal adenocarcinoma-Tumor-UMBEER_114_T-250K_Sty


title: Godfrey_4874_2__GenomeWideSNP_6


title: UC_0611_1

source_name: Bladder tumor UC_0611_1


title: Godfrey_4873_2__GenomeWideSNP_6


title: UC_0193_1

source_name: Bladder tumor UC_0193_1


title: Wild type control trophoblast giant cells GC8.5 Wt 2 (nCounter)


title: UC_0522_1

source_name: Bladder tumor UC_0522_1


title: DECAY_p_STY34_Mapping250K_Sty_G11_131216

description: Esophageal adenocarcinoma-Tumor-UMBEER_115_T-250K_Sty

source_name: esophageal adenocarcinoma


title: DECAY_p_STY34_Mapping250K_Sty_G03_131088

description: Esophageal adenocarcinoma-Tumor-UMBEER_113_T-250K_Sty


title: Godfrey_3024_2__GenomeWideSNP_6

description: Esophageal adenocarcinoma-Tumor-EMPTY-SNP_6.0


title: DECAY_p_STY34_Mapping250K_Sty_G01_131056

description: Esophageal adenocarcinoma-Tumor-UMBEER_121_T-250K_Sty


title: E2f8-/- GC 8KO 2 (nCounter)


title: Godfrey_328_2__GenomeWideSNP_6


title: UC_0456_2

source_name: Bladder tumor UC_0456_2


title: UC_0302_1

source_name: Bladder tumor UC_0302_1


title: N_036_Urothel

source_name: Normal Urothelium Sample

value: Normal Urothelium Sample


title: Wild type control trophoblast giant cells GC6.5 Wt 1 (nCounter)

source_name: trophoblast giant cells E6.5 placenta

value: E6.5 placenta


title: E2f8-/- GC 8KO 1 (nCounter)


title: Godfrey_3027_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_F10_131198

description: Esophageal adenocarcinoma-Tumor-UMBEER_112_T-250K_Sty


title: Godfrey_324__GenomeWideSNP_6__Rep2


title: Godfrey_2019__GenomeWideSNP_6


title: Wild type control trophoblast giant cells GC6.5 Wt 2 (nCounter)


title: UC_0055_1

source_name: Bladder tumor UC_0055_1

value: F


title: Godfrey_3028__GenomeWideSNP_6


title: Godfrey_2814_2__GenomeWideSNP_6


title: E2f7-/- GC 7KO 1 (nCounter)


title: UC_0115_1

source_name: Bladder tumor UC_0115_1

value: M


title: E2f7-/- E2f8-/- GC 78KO 2 (nCounter)

value: trophoblast giant cells


title: Godfrey_2154_2__GenomeWideSNP_6


title: UC_0152_1

source_name: Bladder tumor UC_0152_1


title: UC_0345_1

source_name: Bladder tumor UC_0345_1


title: E2f7-/- E2f8-/- GC 78KO 1 (nCounter)


title: Godfrey_327B_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_F01_131054

description: Esophageal adenocarcinoma-Tumor-UMBEER_108_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_E09_131180

description: Esophageal adenocarcinoma-Tumor-UMBEER_122_T-250K_Sty


title: N_035_Urothel


title: DECAY_p_STY34_Mapping250K_Sty_E12_131228

description: Esophageal adenocarcinoma-Tumor-UMBEER_106_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_E07_131148

description: Esophageal adenocarcinoma-Tumor-UMBEER_104_T-250K_Sty


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver2m 78KO 4 (nCounter)

description:
NanoString’s gene expression CodeSets are pairs of approximately 50-bases called capture and reporter probes (Capture and Reporter, synthesized in 96-well plates using semi-automated process) that hybridize to the RNA sample and are used to detect and count mRNA transcripts.
The reporter probe carries the signal and the capture probe is used to immobilize the complex for data collection.

source_name: liver 2 months

value: liver

value: 2 months

value: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp


title: Godfrey_1741_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_E04_131100

description: Esophageal adenocarcinoma-Tumor-UMBEER_102_T-250K_Sty


title: UC_0348_1

source_name: Bladder tumor UC_0348_1


title: Godfrey_1450A__GenomeWideSNP_6


title: UC_0117_1

source_name: Bladder tumor UC_0117_1


title: Godfrey_1448A_2__GenomeWideSNP_6


title: Albumin-Cre E2f8loxp/loxp liver2m 8KO 4 (nCounter)

value: Albumin-Cre E2f8loxp/loxp


title: Godfrey_4872_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_D10_131194

description: Esophageal adenocarcinoma-Tumor-UMBEER_86_T-250K_Sty


title: UC_0066_3

source_name: Bladder tumor UC_0066_3


title: DECAY_p_STY34_Mapping250K_Sty_F05_131118

description: Esophageal adenocarcinoma-Tumor-UMBEER_110_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_D05_131114

description: Esophageal adenocarcinoma-Tumor-UMBEER_84_T-250K_Sty


title: UC_0361_1

source_name: Bladder tumor UC_0361_1


title: Albumin-Cre E2f8loxp/loxp liver3w 8KO 4 (nCounter)

source_name: liver 3 weeks

value: 3 weeks

value: FVB


title: E2f7-/-  GC 7KO 2 (nCounter)

source_name: trophoblast giant cells E10.5 placenta


title: Godfrey_1011TE_2__GenomeWideSNP_6


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver3w 78KO 4 (nCounter)


title: Wild type control liver liver2m WT 4 (nCounter)

value: Wild type


title: Godfrey_1442A_2__GenomeWideSNP_6

value: esophageal adenocarcinoma


title: Albumin-Cre E2f7loxp/loxp liver2m 7KO 4 (nCounter)

value: Albumin-Cre E2f7loxp/loxp


title: Godfrey_1443A_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_D02_131066

description: Esophageal adenocarcinoma-Tumor-UMBEER_82_T-250K_Sty

value: DECAY


title: Albumin-Cre E2f7loxp/loxp liver3w 7KO 4 (nCounter)


title: UC_0287_1

source_name: Bladder tumor UC_0287_1

value: Bladder tumor


title: DECAY_p_STY34_Mapping250K_Sty_C07_131144

description: Esophageal adenocarcinoma-Tumor-UMBEER_78_T-250K_Sty

source_name: esophageal adenocarcinoma


title: DECAY_p_STY34_Mapping250K_Sty_C09_131176

description: Esophageal adenocarcinoma-Tumor-UMBEER_124_T-250K_Sty


title: UC_0530_1

source_name: Bladder tumor UC_0530_1


title: UC_0537_1

source_name: Bladder tumor UC_0537_1

value: Ta


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver2m 78KO 3 (nCounter)


title: Wild type control liver liver3w WT 4 (nCounter)


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver2m 78KO 2 (nCounter)


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_H11_455378

source_name: colorectal

value: colorectal

value: PONCE


title: UC_0226_1

source_name: Bladder tumor UC_0226_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_H12_455380


title: Godfrey_1010TE_2__GenomeWideSNP_6


title: UC_0461_1

source_name: Bladder tumor UC_0461_1


title: UC_0260_1

source_name: Bladder tumor UC_0260_1

value: F


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver2m 78KO 1 (nCounter)


title: Godfrey_1013A_2__GenomeWideSNP_6


title: Albumin-Cre E2f8loxp/loxp liver2m 8KO 3 (nCounter)


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_G02_455454


title: Godfrey_1444_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_B05_131110

description: Esophageal adenocarcinoma-Tumor-UMBEER_72_T-250K_Sty


title: UC_0405_1

source_name: Bladder tumor UC_0405_1

value: M


title: Godfrey_1446A_2__GenomeWideSNP_6


title: DECAY_p_STY34_Mapping250K_Sty_C01_131048

description: Esophageal adenocarcinoma-Tumor-UMBEER_126_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_C11_131208

description: Esophageal adenocarcinoma-Tumor-UMBEER_80_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_B09_131174

description: Esophageal adenocarcinoma-Tumor-UMBEER_74_T-250K_Sty


title: DECAY_p_STY34_Mapping250K_Sty_B03_131078

description: Esophageal adenocarcinoma-Tumor-UMBEER_130_T-250K_Sty


title: Albumin-Cre E2f8loxp/loxp liver2m 8KO 2 (nCounter)


title: DECAY_p_STY34_Mapping250K_Sty_B01_131046

description: Esophageal adenocarcinoma-Tumor-UMBEER_70_T-250K_Sty


title: Albumin-Cre E2f7loxp/loxp liver2m 7KO 3 (nCounter)


title: Albumin-Cre E2f8loxp/loxp liver2m 8KO 1 (nCounter)


title: UC_0518_1

source_name: Bladder tumor UC_0518_1


title: UC_0577_1

source_name: Bladder tumor UC_0577_1


title: UC_0394_1

source_name: Bladder tumor UC_0394_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_G01_455456


title: DECAY_p_STY34_Mapping250K_Sty_C03_131080

description: Esophageal adenocarcinoma-Tumor-UMBEER_76_T-250K_Sty


title: UC_0445_1

source_name: Bladder tumor UC_0445_1


title: Albumin-Cre E2f7loxp/loxp liver2m 7KO 2 (nCounter)

source_name: liver 2 months


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_G03_455452


title: UC_0695_1

source_name: Bladder tumor UC_0695_1


title: DECAY_p_STY34_Mapping250K_Sty_A07_131140

description: Esophageal adenocarcinoma-Tumor-UMBEER_66_T-250K_Sty


title: Albumin-Cre E2f7loxp/loxp liver2m 7KO 1 (nCounter)


title: Wild type control liver liver2m Wt 3 (nCounter)


title: UC_0265_1

source_name: Bladder tumor UC_0265_1


title: DECAY_p_STY34_Mapping250K_Sty_A09_131172

description: Esophageal adenocarcinoma-Tumor-UMBEER_132_T-250K_Sty


title: UC_0561_1a

source_name: Bladder tumor UC_0561_1a


title: DECAY_p_STY34_Mapping250K_Sty_A03_131076

description: Esophageal adenocarcinoma-Tumor-UMBEER_64_T-250K_Sty


title: UC_0605_1

source_name: Bladder tumor UC_0605_1


title: CYMAR_p_STY38_Mapping250K_Sty_H06_187088

description: Esophageal adenocarcinoma-Tumor-UMBEER_6_T-250K_Sty

source_name: esophageal adenocarcinoma

value: CYMAR


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F12_455458


title: Wild type control liver liver2m Wt 1 (nCounter)

description:
NanoString’s gene expression CodeSets are pairs of approximately 50-bases called capture and reporter probes (Capture and Reporter, synthesized in 96-well plates using semi-automated process) that hybridize to the RNA sample and are used to detect and count mRNA transcripts.
The reporter probe carries the signal and the capture probe is used to immobilize the complex for data collection.

value: liver


title: Wild type control liver liver2m Wt 2 (nCounter)

value: 2 months


title: UC_0516_1

source_name: Bladder tumor UC_0516_1


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver3w 78KO 3 (nCounter)

source_name: liver 3 weeks

value: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp


title: Godfrey_1437_2__GenomeWideSNP_6

description: Esophageal adenocarcinoma-Tumor-EMPTY-SNP_6.0


title: DECAY_p_STY34_Mapping250K_Sty_A11_131204

description: Esophageal adenocarcinoma-Tumor-UMBEER_68_T-250K_Sty


title: UC_0329_1

source_name: Bladder tumor UC_0329_1


title: CYMAR_p_STY38_Mapping250K_Sty_C02_183332

description: Esophageal adenocarcinoma-Tumor-UMBEER_58_T-250K_Sty


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver3w 78KO 2 (nCounter)


title: UC_0244_1

source_name: Bladder tumor UC_0244_1


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver3w 78KO 1 (nCounter)


title: UC_0333_1

source_name: Bladder tumor UC_0333_1


title: UC_0499_1

source_name: Bladder tumor UC_0499_1


title: Albumin-Cre E2f8loxp/loxp liver3w 8KO 3 (nCounter)

value: Albumin-Cre E2f8loxp/loxp


title: CYMAR_p_STY38_Mapping250K_Sty_F03_187110

description: Esophageal adenocarcinoma-Tumor-UMBEER_4_T-250K_Sty


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F08_455466

source_name: colorectal


title: CYMAR_p_STY38_Mapping250K_Sty_A10_187100

description: Esophageal adenocarcinoma-Tumor-UMBEER_12_T-250K_Sty


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F06_455470


title: UC_0613_1

source_name: Bladder tumor UC_0613_1


title: Albumin-Cre E2f8loxp/loxp liver3w 8KO 2 (nCounter)

value: 3 weeks


title: BRISK_p_STY37_Mapping250K_Sty_F07_147596

description: Esophageal adenocarcinoma-Tumor-UMBEER_150_T-250K_Sty

value: BRISK


title: BRISK_p_STY37_Mapping250K_Sty_E08_147610

description: Esophageal adenocarcinoma-Tumor-UMBEER_140_T-250K_Sty


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F09_455464


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F07_455468


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F05_455472


title: UC_0343_1

source_name: Bladder tumor UC_0343_1


title: UC_0595_1

source_name: Bladder tumor UC_0595_1


title: Albumin-Cre E2f7loxp/loxp liver3w 7KO 3 (nCounter)

value: FVB


title: Albumin-Cre E2f8loxp/loxp liver3w 8KO 1 (nCounter)


title: BRISK_p_STY37_Mapping250K_Sty_D02_147512

description: Esophageal adenocarcinoma-Tumor-UMBEER_138_T-250K_Sty

value: esophageal adenocarcinoma


title: BRISK_p_STY37_Mapping250K_Sty_B12_147668

description: Esophageal adenocarcinoma-Tumor-UMBEER_136_T-250K_Sty


title: UC_0041_2

source_name: Bladder tumor UC_0041_2


title: Albumin-Cre E2f7loxp/loxp liver3w 7KO 2 (nCounter)

value: Albumin-Cre E2f7loxp/loxp


title: MUS_4C.2

city: Seattle

first: Christopher

middle: L

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: Muscle (quadriceps) at 4 degrees celsius for 4 hours replicate 1

hyb_protocol: Samples were hybridized to Illumina BeadChips using standard protocols (The Southern California Genotyping Consortium at UCLA). In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.

data_processing: The data were normalized using quantile normalization through the beadarray R package.

source_name: Muscle 4C

label_protocol: Samples were then labeled using standard Illumina protocols (The Southern California Genotyping Consortium at UCLA). Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: Total RNA was isolated from mouse tissues by extraction with TRIzol (Invitrogen).

treatment_protocol: Animal studies were performed under approved UCLA animal research protocols and according to guidelines established in the Guide for Care and Use of Laboratory Animals.  Mice were maintained in 12-h light/dark conditions and fed a laboratory chow diet that consisted of 4.5% fat, 50% carbohydrate by weight (Lab Diet, Purina 50010).  Prior to cold exposure, C57BL/6J mice were provided with food and water ad libitum overnight.  On the next morning, the mice were housed without food or bedding and then were placed at 4°C for 4 h. After euthanasia, tissues were collected and frozen until use.

tag: strain

value: skeletal muscle (quadriceps)

value: 4 degrees celsius for 4 hours

tag: replicate


title: BRISK_p_STY37_Mapping250K_Sty_G10_147646

description: Esophageal adenocarcinoma-Tumor-UMBEER_142_T-250K_Sty


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F02_455478


title: BRISK_p_STY37_Mapping250K_Sty_A09_147618

description: Esophageal adenocarcinoma-Tumor-UMBEER_134_T-250K_Sty


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F04_455474


title: Wild type control liver liver3w Wt 3 (nCounter)

value: Wild type


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F11_455460

value: colorectal


title: UC_0704_1

source_name: Bladder tumor UC_0704_1

value: Bladder tumor


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E12_455420

value: PONCE


title: UC_0624_1

source_name: Bladder tumor UC_0624_1

value: Ta

value: M


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F03_455476


title: Wild type control liver liver3w Wt 2 (nCounter)

value: liver


title: MUS_4C.1

description: Muscle (quadriceps) at 4 degrees celsius for 4 hours replicate 2


title: MUS_RT.2

description: Muscle (quadriceps) control at room temperature replicate 2

source_name: Muscle RT

value: room temperature (control)


title: UC_0195_1

source_name: Bladder tumor UC_0195_1

value: F


title: MUS_RT.1

description: Muscle (quadriceps) control at room temperature replicate 1


title: BAT_4C.2

description: Brown adipose tissue at 4 degrees celsius for 4 hours replicate 2

source_name: Brown Adipose Tissue 4C

value: brown adipose tissue


title: Wild type control liver liver3w Wt 1 (nCounter)

description:
NanoString’s gene expression CodeSets are pairs of approximately 50-bases called capture and reporter probes (Capture and Reporter, synthesized in 96-well plates using semi-automated process) that hybridize to the RNA sample and are used to detect and count mRNA transcripts.
The reporter probe carries the signal and the capture probe is used to immobilize the complex for data collection.

value: 3 weeks


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E09_455422


title: Albumin-Cre E2f7loxp/loxp liver3w 7KO 1 (nCounter)


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E06_455432


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E11_455418


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E07_455426


title: UC_0589_1

source_name: Bladder tumor UC_0589_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E08_455428


title: UC_0429_1a

source_name: Bladder tumor UC_0429_1a


title: UC_0722_1

source_name: Bladder tumor UC_0722_1


title: BAT_RT.1

description: Brown adipose tissue control at room temperature replicate 1

source_name: Brown Adipose Tissue RT


title: UC_0546_1

source_name: Bladder tumor UC_0546_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F01_455480


title: BAT_RT.2

description: Brown adipose tissue control at room temperature replicate 2


title: UC_0507_1

source_name: Bladder tumor UC_0507_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E10_455424

source_name: colorectal


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E05_455430


title: UC_0384_1

source_name: Bladder tumor UC_0384_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E04_455436


title: BAT_4C.1

description: Brown adipose tissue at 4 degrees celsius for 4 hours replicate 1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_F10_455462


title: UC_0539_1

source_name: Bladder tumor UC_0539_1


title: UC_0284_1

source_name: Bladder tumor UC_0284_1


title: UC_0209_1

source_name: Bladder tumor UC_0209_1


title: SC, cKO, biological rep1

city: Dallas

first: Qing

middle: Richard

last: Lu

address: 5323 Harry Hines Boulevard

institute: UT southwestern medical center

hyb_protocol: Processed as UCLA DNA microarray facility's instructions.

data_processing: Data were processed by RMA using GeneSpring software.

source_name: P14 spinal cord, Sip1 cKO

growth_protocol: All animal use and studies were approved by the Institutional Animal Care and Use Committee of the University of Texas Southwestern Medical Center at Dallas.

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

value: c57.129 mixed background

value: spinal cord


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E02_455440


title: SC, Ctrl, biological rep1

scan_protocol: Processed as UCLA DNA microarray facility's instructions.

source_name: P14 spinal cord, control


title: SC, cKO, biological rep2

label_protocol: Processed as UCLA DNA microarray facility's instructions.


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E03_455434


title: UC_0274_1

source_name: Bladder tumor UC_0274_1


title: mucinous tumor_3

city: Cincinnati

first: Yutaka

last: Maeda

state: OH

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital

description: Gene expression data from mouse lungs

hyb_protocol: We created a hybridization cocktail for a single probe array that contains 2.5 micrograms of fragmented cRNA. Incubate at 45C for 17 hours in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. The probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

scan_protocol: The Genechip 1.0 ST arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G. The Scanning software was Affymetrix Genechip Command Console version 3.2.

data_processing: RMA was used to normalize all samples. The means of replicate samples were averaged to create interpretations to compare the different groups, and the raw data was filtered to remove entities not being expressed. We performed fold change analysis to create a list of genes with a fold change 2.0 or higher and used a T-Test unpaired with a p-value cutoff of 0.05 and multiple testing correction (FDR) to create a list of genes with statistical significance.

source_name: left lobe lungs from the mice at 3 months of age

label_protocol: The Ambion® WT Expression Kit (Life Technologies) combined with the GeneChip® WT Terminal Labeling Kit (Affymetrix), was used to create biotin – labeled sense -strand cDNA targets from 300 ng of total RNA

growth_protocol: Mice were housed in a pathogen-free barrier facility in humidity and temperature-controlled rooms on a 12:12 h light/dark cycle and were allowed food and water ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  The RNA was further purified using Qiagen Rneasy MinElute Cleanup Kit according to the manufacturer's instructions.

treatment_protocol: Doxycycline was administered to the control and transgenic mice (Scgb1a1-rtTA/[tetO]-KRAS.G12D/Nkx2-1+/-) for 2 months and sacrificed at 3 months of age according to the protocols approved by the Institutional Animal Care and Use Committee at the Cincinnati Children’s Hospital Medical Center.

value: C57BL/6-129/Sv-FVB/N mixed

value: left lobe lung

value: mucinous tumor


title: UC_0263_1

source_name: Bladder tumor UC_0263_1


title: SC, Ctrl, biological rep2


title: mucinous tumor_2

description: Gene expression data from mouse lungs


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_E01_455438


title: UC_0100_1

source_name: Bladder tumor UC_0100_1


title: UC_0176_2

source_name: Bladder tumor UC_0176_2


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D12_455444


title: Control_3

description: Gene expression data from mouse lungs

value: wild type

value: control


title: UC_0002_1

source_name: Bladder tumor UC_0002_1


title: mucinous tumor_1

description: Gene expression data from mouse lungs


title: UC_0567_1

source_name: Bladder tumor UC_0567_1


title: UC_0488_2

source_name: Bladder tumor UC_0488_2


title: N_037_Urothel

source_name: Normal Urothelium Sample

value: Normal Urothelium Sample


title: UC_0367_1

source_name: Bladder tumor UC_0367_1

value: Bladder tumor


title: Control_1

description: Gene expression data from mouse lungs


title: Control_2

description: Gene expression data from mouse lungs


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D08_455518

source_name: colorectal

value: colorectal

value: PONCE


title: UC_0726_1

source_name: Bladder tumor UC_0726_1

value: Ta


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D09_455446


title: UC_0614_1

source_name: Bladder tumor UC_0614_1

value: M


title: UC_0008_1

source_name: Bladder tumor UC_0008_1


title: UC_0696_1

source_name: Bladder tumor UC_0696_1


title: UC_0533_1

source_name: Bladder tumor UC_0533_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D11_455442


title: UC_0374_2a

source_name: Bladder tumor UC_0374_2a


title: UC_0393_1

source_name: Bladder tumor UC_0393_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D02_455522


title: UC_0162_1

source_name: Bladder tumor UC_0162_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D06_455514


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D07_455520


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D10_455448


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D01_455524


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_C12_455534


title: PARN KD C2C12_actinomycinD_230_min_rep_2

city: Newark

first: Ju Youn

last: Lee

state: NJ

address: 185 South Orange Ave. MSB-E501

department: Biochemistry

institute: UMDNJ-New Jersey Medical School

description:
This is sample was collected at 230 min after actinomycin D treatment
PARNKD.230.B.CEL

hyb_protocol: 300ng of total RNA for half life arrays were used to generate labeled cDNA fragments for hybridization to Mouse Affymetrix Gene 1.0 ST Arrays following the manufacturer’s protocol (GeneChipTM WT cDNA Synthesis Kit #900652 and #900720).

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000G

data_processing: All the probe sets were applied median normalization by Affymetrix Power Tools (APT) with ‘no adjustment’ option and were normalized to the 5th percentile value of all probe sets on the same array.

source_name: PARN KD C2C12 with actinomycin D, time 230 min, rep 2

label_protocol: Biotinylated DNA probes were prepared according to Whole Transcript Sense Target Labeling Manual (Affymetrix)

growth_protocol: The mouse C2C12 myoblast cell line was obtained from the American Type Culture Collection (CRL1772).  Two derivatives of the C2C12 cell line, CTRL and PARN KD,  were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% Fetal Bovine Serum (FBS), 1µg/ml puromycin,  10U/ml penicillin and 10µg/ml streptomycin in 5% CO2 at 37°C. Transfections were performed using Lipofectamine 2000 and transfection efficiency was routinely in the 50-70% range. The CTRL cell line stably transfected with LKO1 vector was described previously (GSE21236).  The PARN KD clonal cell line was generated by puromycin selection following transduction with an shRNA-encoding lentivirus derived from the LKO1 vector.

extract_protocol: Cells were collected in Trizol™ (Invitrogen) at the indicated time points following the incubation and total RNA was prepared according to the manufacturers instructions. RNA concentration, purity, and quality were determined via Bioanalyzer (Agilent).

treatment_protocol: To inhibit transcription, cells were treated with actinomycin D  (8µg/ml) for 30 min prior to the start of the time course.

tag: cell line

value: C2C12 myoblast cell line

tag: genotype/variation

value: PARN Knock Down

tag: agent

value: actinomycin D

tag: time after actinomycin d treatment

value: 230 min


title: UC_0399_1

source_name: Bladder tumor UC_0399_1

tag: tissue type

value: F

tag: age


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D05_455516

tag: cancer type

tag: batch


title: PARN KD C2C12_actinomycinD_230_min_rep_3

description:
This is sample was collected at 230 min after actinomycin D treatment
PARNKD.230.C.CEL

source_name: PARN KD C2C12 with actinomycin D, time 230 min, rep 3


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D04_455526


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_D03_455528


title: UC_0497_1

source_name: Bladder tumor UC_0497_1


title: PARN KD C2C12_actinomycinD_230_min_rep_1

description:
This is sample was collected at 230 min after actinomycin D treatment
PARNKD.230.A.CEL

source_name: PARN KD C2C12 with actinomycin D, time 230 min, rep 1


title: UC_0707_1

source_name: Bladder tumor UC_0707_1


title: UC_0154_2

source_name: Bladder tumor UC_0154_2


title: PARN KD C2C12_actinomycinD_110_min_rep_2

description:
This is sample was collected at 110 min after actinomycin D treatment
PARNKD.110.B.CEL

source_name: PARN KD C2C12 with actinomycin D, time 110 min, rep 2

value: 110 min


title: PARN KD C2C12_actinomycinD_110_min_rep_1

description:
This is sample was collected at 110 min after actinomycin D treatment
PARNKD.110.A.CEL

source_name: PARN KD C2C12 with actinomycin D, time 110 min, rep 1


title: PARN KD C2C12_actinomycinD_50_min_rep_3

description:
This is sample was collected at 50 min after actinomycin D treatment
PARNKD.50.C.CEL

source_name: PARN KD C2C12 with actinomycin D, time 50 min, rep 3

value: 50 min


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_F02_465866

source_name: colorectal

value: COOKY


title: PARN KD C2C12_actinomycinD_110_min_rep_3

description:
This is sample was collected at 110 min after actinomycin D treatment
PARNKD.110.C.CEL

source_name: PARN KD C2C12 with actinomycin D, time 110 min, rep 3


title: UC_0166_1

source_name: Bladder tumor UC_0166_1


title: PONCE_p_ICP_SNParray_P1_GenomeWideSNP_6_C11_455536


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_H01_160100

value: GHATS


title: UC_0354_2c

source_name: Bladder tumor UC_0354_2c


title: PARN KD C2C12_actinomycinD_50_min_rep_2

description:
This is sample was collected at 50 min after actinomycin D treatment
PARNKD.50.B.CEL

source_name: PARN KD C2C12 with actinomycin D, time 50 min, rep 2


title: UC_0528_1

source_name: Bladder tumor UC_0528_1


title: PARN KD C2C12_actinomycinD_50_min_rep_1

description:
This is sample was collected at 50 min after actinomycin D treatment
PARNKD.50.A.CEL

source_name: PARN KD C2C12 with actinomycin D, time 50 min, rep 1


title: PARN KD C2C12_actinomycinD_10_min_rep_3

description:
This is sample was collected at 10 min after actinomycin D treatment
PARNKD.10.C.CEL

source_name: PARN KD C2C12 with actinomycin D, time 10 min, rep 3

value: 10 min


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_F03_465872


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G11_160258


title: PARN KD C2C12_actinomycinD_10_min_rep_2

description:
This is sample was collected at 10 min after actinomycin D treatment
PARNKD.10.B.CEL

source_name: PARN KD C2C12 with actinomycin D, time 10 min, rep 2


title: UC_0196_1

source_name: Bladder tumor UC_0196_1


title: PARN KD C2C12_actinomycinD_10_min_rep_1

description:
This is sample was collected at 10 min after actinomycin D treatment
PARNKD.10.A.CEL

source_name: PARN KD C2C12 with actinomycin D, time 10 min, rep 1


title: UC_0339_1

source_name: Bladder tumor UC_0339_1


title: UC_0491_1

source_name: Bladder tumor UC_0491_1


title: UC_0712_1

source_name: Bladder tumor UC_0712_1


title: PARN KD C2C12_actinomycinD_0_min_rep_3

description:
This is sample was collected at 0 min after actinomycin D treatment
PARNKD.0.C.CEL

source_name: PARN KD C2C12 with actinomycin D, time 0 min, rep 3

value: 0 min


title: UC_0506_1

source_name: Bladder tumor UC_0506_1


title: PARN KD C2C12_actinomycinD_0_min_rep_2

description:
This is sample was collected at 0 min after actinomycin D treatment
PARNKD.0.B.CEL

source_name: PARN KD C2C12 with actinomycin D, time 0 min, rep 2


title: UC_0598_1

source_name: Bladder tumor UC_0598_1


title: UC_0556_1_rep4

source_name: Bladder tumor UC_0556_1


title: UC_0199_1

source_name: Bladder tumor UC_0199_1


title: N_034_Urothel

source_name: Normal Urothelium Sample

value: Normal Urothelium Sample


title: 29E4 vs. Sakai Replicate 1

status: Public on Aug 30 2012

first: Deborah

middle: R.

last: Yoder-Himes

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

hyb_protocol: Samples were paired based on dye specific activity and equal amounts of each sample were hybridized to the arrays as described in Abu-Ali GS, Lacher DW, Wick LM, Qi WH, Whittam TS (2009) Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex (Bmc Genomics 10) and washed according to the manufacturer's instructions for hybridization using coverslips.

scan_protocol: The Genepix 4000B array scanner (Axon Instruments, Union City, Calif.) was used to scan the arrays were scanned and probe intensities were retrieved using the associated Genepix 6.0 software.

data_processing: To obtain the signal threshold for calling a gene present based on microarray signal, the following approach was used. The probe sequence identity against available genome sequences was used to determine (in-silico) gene presence/absence, using a minimum cut-off of a BLAST-based 83% sequence identity (BINF_score, 1 = presence or 0 = absence). Gene presence/absence based on hybridization data was determined using the average log hybridization ratio (signal), or LHR, that corresponded to probes with exactly 83% sequence identity (LHR83%). Our previous studies demonstrated that i) the LHR83% outperformed other frequently used metrics in calling gene presence/absence from hybridization data and ii) the result of the subtraction of LHR83% from LHR100% remained constant for tester strains varying in their genetic divergence to the reference strain (i.e., LHR100% - LHR83% = 0.45±0.15). For strains whose genome sequences were not available (and thus did not have probes available to calculate LHR83%), we estimated the LHR83% indirectly, using a normalization factor that was determined based on the analysis of strains from which both genome sequences and hybridization data were available. More specifically, the LHR83% for the former strains was calculated using the equation LHR83% = LHR100% - 0.45; where LHR100% was estimated using the five house keeping gene sequences available for each strain and their corresponding hybridization data. The LHR value obtained from each probe signal was converted into experimental binary scores (EXPL_score, 1 = presence or 0 = absence) using LHR83% BSR as the cut-off signal for presence. The experimentally determined gene callings (EXPL_scores) were compared with the bioinformatically determined gene callings (BINF_scores). Genes were classified into three clases based on the combination of the EXPL_score and the BINF_score: good probes (GP, BINF_score = EXPL_score), false negatives (FN, BINF_score = 1 and EXPL_score = 0), and false positives (FP, BINF_score = 1 and EXPL_score = 0). The performance of different microarray platforms was compared based on the fraction of the three classes of probes: GP, FN, and FP.

label: Cy 5

organism: Escherichia coli

label_protocol: Ten micrograms of DNA was sheared using a Heat Systems Ultrasonics W-225 20-kHz, 200-W cup sonicator (Misonix, Farmingdale, NY) to generate sheared genomic DNA from 0.5 to 3 7 kb long. For each sample, 300 ng of sheared DNA was labeled with either Cy3 or Cy5 dye using the methods described by Wick LM, Qi W, Lacher DW, Whittam TS (2005) Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7.

growth_protocol: Bacteria grown overnight in Luria Broth (Lennox formulation) at 37 degrees C with 300 rpm shaking

extract_protocol: Genomic DNA was prepared with Promega Wizard Genomic DNA Preparation kit according to manufacturer's instructions

label: Cy 3

organism: Escherichia coli O157:H7 str. Sakai

source_name: Sakai

value: Sakai


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_F01_465868

source_name: colorectal

value: colorectal


title: Z205 vs. Sakai Replicate 2

organism: Escherichia sp. Z205


title: 29E4 vs. Sakai Replicate 2


title: RL325/96 vs. Sakai Replicate 2

organism: Escherichia sp. RL325/96


title: RL325/96 vs. Sakai Replicate 1


title: Z205 vs. Sakai Replicate 1


title: TW 14267 vs. Sakai Replicate 2

organism: Escherichia sp. TW14267


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E08_465888


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E11_465878


title: TW 14265 vs. Sakai Replicate 2

organism: Escherichia sp. TW14265


title: TW 14265 vs. Sakai Replicate 1


title: TW 14266 vs. Sakai Replicate 1

organism: Escherichia sp. TW14266


title: TW 14266 vs. Sakai Replicate 2


title: TW 14264 vs. Sakai Replicate 2

organism: Escherichia sp. TW14264


title: TW 14263 vs. Sakai Replicate 2

organism: Escherichia sp. TW14263


title: TW 14264 vs. Sakai Replicate 1


title: TW 14182 vs. Sakai Replicate 1

organism: Escherichia sp. TW14182


title: TW 12018 vs. Sakai Replicate 2


title: TW 14263 vs. Sakai Replicate 1


title: TW 12018 vs. Sakai Replicate 1


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E09_465874


title: TW 11966 vs. Sakai Replicate 2

organism: Escherichia sp. TW11966


title: PARN KD C2C12_actinomycinD_0_min_rep_1

description:
This is sample was collected at 0 min after actinomycin D treatment
PARNKD.0.A.CEL

source_name: PARN KD C2C12 with actinomycin D, time 0 min, rep 1


title: TW 11966 vs. Sakai Replicate 1


title: TW 11930 vs. Sakai Replicate 1

organism: Escherichia sp. TW11930


title: TW 11588 vs. Sakai Replicate 2

organism: Escherichia sp. TW11588


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E10_465876


title: TW 11930 vs. Sakai Replicate 2


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E07_465886


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E05_465882


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E02_465892


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E06_465884


title: TW 09308 vs. Sakai Replicate 1

organism: Escherichia sp. TW09308


title: TW 09308 vs. Sakai Replicate 2


title: TW 11588 vs. Sakai Replicate 1


title: TW 09276 vs. Sakai Replicate 2

organism: Escherichia sp. TW09276


title: TW 09266 vs. Sakai Replicate 1

organism: Escherichia sp. TW09266


title: TW 09254 vs. Sakai Replicate 2

organism: Escherichia sp. TW09254


title: TW 09254 vs. Sakai Replicate 1


title: TW 09231 vs. Sakai Replicate 2

organism: Escherichia sp. TW09231


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_D12_465904

organism: Homo sapiens


title: TW 09231 vs. Sakai Replicate 1

organism: Escherichia coli O157:H7 str. Sakai


title: CFT073 vs. Sakai Replicate 1

organism: Escherichia coli CFT073


title: CFT073 vs. Sakai Replicate 2


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E03_465894


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E12_465880


title: MG1655 vs. Sakai Replicate 2

organism: Escherichia coli str. K-12 substr. MG1655


title: MG1655 vs. Sakai Replicate 1


title: 19982 vs. Sakai Replicate 2

organism: Escherichia albertii TW07627


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E01_465890


title: e2348/69 vs. Sakai Replicate 2

organism: Escherichia coli O127:H6 str. E2348/69


title: 19982 vs. Sakai Replicate 1


title: 2457T vs. Sakai Replicate 1

organism: Shigella flexneri 2a str. 2457T


title: e2348/69 vs. Sakai Replicate 1


title: TW 14267 vs. Sakai Replicate 1

organism: Escherichia sp. TW14267


title: 9194 vs. Sakai Replicate 2

organism: Escherichia albertii


title: 042 vs. Sakai Replicate 1

organism: Escherichia coli 042


title: 2457T vs. Sakai Replicate 2


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_D11_465902


title: 042 vs. Sakai Replicate 2


title: 9194 vs. Sakai Replicate 1


title: RIP_IgG_TGFb_16A

city: Charleston

first: Philip

middle: H

last: Howe

state: SC

address: howelab

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description: Gene expression data from RNA IP post TGFbeta treatment with IgG antibody

hyb_protocol: Fragmented cRNA samples were hybridized overnight at 45°C to Affymetrix Mouse Genome 430 2.0 GeneChips®.

scan_protocol: Post hybridization washing, phycoerythrin-streptavidin staining and fluorescence scanning were performed using Affymetrix instrumentation in accordance with manufacturer protocols.

data_processing: Hybridization data (CEL files) were normalized by RMA algorithm using Affymetrix Expression Console software; detection calls were obtained by Affymetrix MAS5 algorithm. Expression data were compared using dChip software.

organism: Mus musculus

source_name: RNA-immunoprecipitated RNA from TGF-beta-treated NMuMG cells using IgG antibody; biological rep1

label_protocol: Synthesis of double stranded cDNA, in vitro transcription of biotin-labeled cRNA targets and fragmentation of target cRNAs were performed following established Affymetrix procedures.

growth_protocol: NMuMGs and the E1KD (hnRNP E1 knockdown) derivative were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 10 mg/ml insulin, and antibiotics/antimycotics (100 units/ml penicillin G, 100 mg/ml streptomycin, and 0.25 mg/ml amphotericin B).

extract_protocol: Polysome analysis was performed from cell lysates layered onto a 10%-50% sucrose gradient and centrifuged at 100,000 x g at 40C for 4 h. Gradient fractions were collected using a fraction collector with continuous monitoring of absorbance at 254 nm. RNA was extracted with Trizol and purified with RNeasy minikit according to the manufacturers instructions. RNA immunoprecipitation was performed from cytosolic extract incubated with 10 μg of mouse hnRNP E1 antibody or mouse IgG at 4°C overnight, and precipitated with Protein A-Sepharose. The beads were washed three times with IP Wash Solution (150 mM NaCl, 50 mM Tris pH 7.5, 0.5% NP40), and immunoprecipitated RNAs isolated by Trizol and treated with RNase-free DNase I. Total RNA was isolated by Trizol extraction.

treatment_protocol: TGF-beta2 was used at a final concentration of 5 ng/ml. Where indicated, cells were treated with 10 micromolar of LY294002 30 min before TGF-beta treatment.

tag: antibody

value: IgG

value: Normal murine mammary gland (NMuMG) cell

value: wild type

tag: molecule/fraction

value: cytosolic RNA


title: RIP_IgG_TGFb_16B

source_name: RNA-immunoprecipitated RNA from TGF-beta-treated NMuMG cells using IgG antibody; biological rep2


title: EDL933 vs. Sakai Replicate 1

organism: Escherichia coli O157:H7 str. EDL933


title: COOKY_p_TCGAb15_ICPp3_061909_GenomeWideSNP_6_E04_465896


title: RIP_hnRNPE1_TGFb_14A

description: Gene expression data from RNA IP post TGFbeta treatment with hnRNP E1 antibody

source_name: RNA-immunoprecipitated RNA from TGF-beta-treated NMuMG cells using hnRNP E1 antibody; biological rep1

value: hnRNP E1


title: RIP_IgG_con_15A

description: Gene expression data from RNA IP with IgG antibody

source_name: RNA-immunoprecipitated RNA from non-treated NMuMG cells using IgG antibody; biological rep1


title: TW 14182 vs. Sakai Replicate 2

organism: Escherichia sp. TW14182


title: RIP_hnRNPE1_con_13A

description: Gene expression data from RNA IP with hnRNP E1 antibody

source_name: RNA-immunoprecipitated RNA from non-treated NMuMG cells using hnRNP E1 antibody; biological rep1


title: E1KD_tot_TGFb_12B

description: Gene expression data from total RNA post TGFbeta treatment

source_name: Total RNA from TGF-beta-treated (24h), E1KD cells; biological rep2

value: hnRNP E1 knockdown (E1KD)

value: total RNA


title: TW 09276 vs. Sakai Replicate 1

organism: Escherichia sp. TW09276


title: RIP_hnRNPE1_TGFb_13B

source_name: RNA-immunoprecipitated RNA from TGF-beta-treated NMuMG cells using hnRNP E1 antibody; biological rep2


title: RIP_hnRNPE1_con_14B

source_name: RNA-immunoprecipitated RNA from non-treated NMuMG cells using hnRNP E1 antibody; biological rep2


title: NMuMG_tot_TGFb_10B

source_name: Total RNA from TGF-beta-treated (24h), NMuMG cells; biological rep2


title: E1KD_tot_con_11B

description: Gene expression data from total RNA

source_name: Total RNA from non-treated, E1KD cells; biological rep2


title: NMuMG_tot_con_9B

description: Gene expression data from total RNA

source_name: Total RNA from non-treated, control NMuMG cells; biological rep2


title: E1KD_tot_con_11A

description: Gene expression data from total RNA

source_name: Total RNA from non-treated, E1KD cells; biological rep1


title: RIP_IgG_con_15B

source_name: RNA-immunoprecipitated RNA from non-treated NMuMG cells using IgG antibody; biological rep2


title: NMuMG_tot_TGFb_10A

source_name: Total RNA from TGF-beta-treated (24h), NMuMG cells; biological rep1


title: E1KD_poly_con_6A

description: Gene expression data from actively translating polysomal mRNA

source_name: Polysomal pool of RNA from non-treated, E1KD cells; biological rep1

value: polysomal RNA


title: E1KD_poly_TGFb_8A

description: Gene expression data from actively translating polysomal mRNA  post TGFbeta treatment

source_name: Polysomal pool of RNA from TGF-beta-treated (24hr), E1KD cells; biological rep1


title: NMuMG_tot_con_9A

description: Gene expression data from total RNA

source_name: Total RNA from non-treated, control NMuMG cells; biological rep1


title: E1KD_poly_TGFb_8B

source_name: Polysomal pool of RNA from TGF-beta-treated (24hr), E1KD cells; biological rep2


title: E1KD_poly_con_6B

source_name: Polysomal pool of RNA from non-treated,  E1KD cells; biological rep2


title: E1KD_tot_TGFb_12A

source_name: Total RNA from TGF-beta-treated (24h), E1KD cells; biological rep1


title: E1KD_mono_con_5A

description: Gene expression data from non-translating monosomal mRNA

source_name: Monosomal pool of RNA from non-treated, E1KD cells; biological rep1

value: monosomal RNA


title: NMuMG_poly_TGFb_4B

source_name: Polysomal pool of RNA from TGF-beta-treated (24hr), NMuMG cells; biological rep2


title: E1KD_mono_TGFb_7A

description: Gene expression data from non-translating monosomal mRNA post TGFbeta treatment

source_name: Monosomal pool of RNA from TGF-beta-treated (24hr), E1KD cells; biological rep1


title: E1KD_mono_TGFb_7B

description: Gene expression data from non-translating monosomal mRNA  post TGFbeta treatment

source_name: Monosomal pool of RNA from TGF-beta-treated (24hr), E1KD cells; biological rep2


title: NMuMG_poly_TGFb_4A

source_name: Polysomal pool of RNA from TGF-beta-treated (24hr), NMuMG cells; biological rep1


title: 157B

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

description:
157B_P_P
KO+/+_20 dpp_replicate6

hyb_protocol: Hybridization, staining and detection of cRNAs on Illumina Mouse WG-6 v2 Expression BeadChips were performed according to the manufacturer’s protocol.

scan_protocol: The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations.

data_processing: GenomeStudio 2011.1 software (Illumina Inc., San Diego, USA) and its Gene Expression Analysis Module (version 1.9.0) were used for signal extraction and quantile normalization.

source_name: Prebuperal mouse testis

label_protocol: The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

extract_protocol: Total RNA was extracted using Trizol reagent. 0.5-1 μg RNA was reverse transcribed with the SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA). Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA). A RNA integrity number (RIN) greater or equal to 7.00 was achieved for all samples.

tag: genotype (brdt)

tag: age (in days post-partum)

value: 20 dpp

tag: testis weight (g)

tag: siblings

value: sib 1

tag: sample groups


title: 157A

description:
157A_P_P
KO+/+_20 dpp_replicate5

tag: strain


title: 149A

description:
149A_P_P
KO+/+_20 dpp_replicate3


title: 149B

description:
149B_P_P
KO+/+_20 dpp_replicate4


title: E1KD_mono_con_5B

source_name: Monosomal pool of RNA from non-treated, E1KD cells; biological rep2

tag: cell type


title: NMuMG_mono_TGFb_3B

source_name: Monosomal pool of RNA from TGF-beta-treated (24hr), NMuMG cells; biological rep2


title: 152A

description:
152A_N_N
KO-/-_20 dpp_replicate5


title: NMuMG_poly_con_2A

source_name: Polysomal pool of RNA from non-treated, control NMuMG cells; biological rep1


title: NMuMG_mono_con_1A

source_name: Monosomal pool of RNA from non-treated, control NMuMG cells; biological rep1


title: NMuMG_mono_TGFb_3A

source_name: Monosomal pool of RNA from TGF-beta-treated (24hr), NMuMG cells; biological rep1


title: 140

description:
140_N_N
KO-/-_20 dpp_replicate2

value: sib 2


title: 148B

description:
148B_N_N
KO-/-_20 dpp_replicate4


title: 146A

description:
146A_P_P
KO+/+_20 dpp_replicate1


title: 146B

description:
146B_P_P
KO+/+_20 dpp_replicate2


title: 152B

description:
152B_N_N
KO-/-_20 dpp_replicate6


title: NMuMG_mono_con_1B

source_name: Monosomal pool of RNA from non-treated, control NMuMG cells; biological rep2


title: 196A

description:
196A_P_P
BD1+/+_20 dpp_replicate5

value: sib 5


title: 139

description:
139_N_N
KO-/-_20 dpp_replicate1


title: 196B

description:
196B_P_P
BD1+/+_20 dpp_replicate6


title: TBmc iTreg Rep2

city: New York

first: Jonathan

last: Weiss

address: 550 First Ave

institute: NYU Medical Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: Tbmc CD4+ Foxp3+ Treg Cells After 1 week Oral Ova

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

value: Balb/c TBmc Foxp3 GFP

value: Mesenteric LN CD4+ Foxp3+ Nrp-

value: 4-6 Weeks


title: TBmc iTreg Rep3


title: Wild Type Total Treg Rep1

source_name: Wild Type CD4+ Foxp3+ Treg Cells

value: Balb/c Wild Type Foxp3 GFP


title: Wild Type Total Treg Rep3

value: Mesenteric LN CD4+ Foxp3+


title: 148A

description:
148A_N_N
KO-/-_20 dpp_replicate3


title: 195A

description:
195A_P_P
BD1+/+_20 dpp_replicate3


title: Wild Type Total Treg Rep2


title: NMuMG_poly_con_2B

source_name: Polysomal pool of RNA from non-treated, control NMuMG cells; biological rep2

value: Normal murine mammary gland (NMuMG) cell


title: TBmc iTreg Rep1

value: Balb/c


title: Spleen CD4+ Foxp3+ Nrp+ Rep 1

source_name: Spleen CD4+ Foxp3+ Nrp+ Cells

value: Balb/c Foxp3 GFP

value: Spleen CD4+ Foxp3+ Nrp+


title: Spleen CD4+ Foxp3+ Nrp- Rep1

source_name: Spleen CD4+ Foxp3+ Nrp+ Treg Cells

value: Spleen CD4+ Foxp3+ Nrp+ cells

value: 4-8 weeks


title: 219

description:
219_P_N
BD1+/-_20 dpp_replicate1

value: sib 6


title: Spleen CD4+ Foxp3+ Nrp+ Rep2

source_name: Spleen CD4+ Foxp3+ Nrp+ cells


title: 222B

description:
222B_N_N
BD1-/-_20 dpp_replicate6


title: Spleen CD4+ Foxp3+ Nrp- Rep2

source_name: Spleen CD4+ Foxp3+ Nrp- Cells

value: Spleen CD4+ Foxp3+ Nrp-


title: 195B

description:
195B_P_P
BD1+/+_20 dpp_replicate4

value: 20 dpp


title: 222A

description:
222A_N_N
BD1-/-_20 dpp_replicate5


title: 191B

description:
191B_P_N
BD1+/-_20 dpp_replicate2

value: sib 4


title: 197B

description:
197B_N_N
BD1-/-_20 dpp_replicate4


title: round sperm, biological rep3

city: Beijing

first: Wei

last: Li

address: Beichen West Road

department: State key lab of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Gene expression data from round sperm

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

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

data_processing:
Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: round sperm

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: ahES cells and ES cells were cultured in N2B27 medium plus 2i and LIF. MEF cells were cultured in DMEM plus 10% FBS. Round sperm were freshly isolated from testis.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: ahES cells and round sperm cells were G0/G1 phase haploid cells purified by FACS sorting

tag: genetic background

value: round sperm


title: 197A

description:
197A_N_N
BD1-/-_20 dpp_replicate3

value: sib 5


title: 131

description:
131_P_N
KO+/-_17 dpp_replicate6

value: 17 dpp

value: sib 8


title: MEF, biological rep1

description: Gene expression data from MEF cells

source_name: mouse embryonic fibroblast cells

value: mouse embryonic fibroblast cells


title: R1, biological rep2

description: Gene expression data from R1

source_name: diploid ES cell line R1

value: diploid ES cell

tag: cell line

value: diploid ES cell line R1


title: 193A

description:
193A_N_N
BD1-/-_20 dpp_replicate1

source_name: Prebuperal mouse testis


title: 193B

description:
193B_N_N
BD1-/-_20 dpp_replicate2


title: round sperm, biological rep1

description: Gene expression data from round sperm


title: MEF, biological rep2

description: Gene expression data from MEF cells


title: MEF, biological rep3

description: Gene expression data from MEF cells


title: round sperm, biological rep2

description: Gene expression data from round sperm


title: 75

description:
75_P_N
KO+/-_17 dpp_replicate1

value: sib 7


title: CS1-1, biological rep2

description: Gene expression data from CS1-1

source_name: diploid ES cell line CS1-1

value: diploid ES cell line CS1-1


title: R1, biological rep1

description: Gene expression data from R1


title: 127

description:
127_P_N
KO+/-_17 dpp_replicate5


title: 116

description:
116_P_N
KO+/-_17 dpp_replicate2

value: sib 9


title: 129B

description:
129_N_N_b
KO-/-_17 dpp_replicate6


title: R1, biological rep3

description: Gene expression data from R1


title: 126

description:
126_P_N
KO+/-_17 dpp_replicate4


title: 129A

description:
129_N_N
KO-/-_17 dpp_replicate5


title: AH129-NC1, biological rep2

description: Gene expression data from AH-NC1

source_name: ahES cell line AH129-NC1

value: G0/G1 stage androgenetic haploid embryonic stem cell

value: ahES cell line AH129-NC1


title: 122B

description:
122_N_N_b
KO-/-_17 dpp_replicate4


title: 122A

description:
122_N_N
KO-/-_17 dpp_replicate3


title: CS1-1, biological rep3

description: Gene expression data from CS1-1


title: 73

description:
73_N_N
KO-/-_17 dpp_replicate2


title: AH129-N1,biological rep3

description: Gene expression data from AH-N1

source_name: ahES cell line AH129-N1

value: ahES cell line AH129-N1


title: AH129-NC1, biological rep1

description: Gene expression data from AH-NC1


title: 121

description:
121_P_N
KO+/-_17 dpp_replicate3


title: CS1-1, biological rep1

description: Gene expression data from CS1-1


title: AH129-NC1, biological rep3

description: Gene expression data from AH-NC1


title: 5 pooled F2 SED male gastrocnemius RNA 8 wks age 2

city: College Park

first: Stephen

last: Roth

state: MD

address: 2309 SPH Building

department: Kinesiology

institute: University of Maryland

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Maryland School of Medicine Biopolymer-Genomics Core Facility

scan_protocol: Array scanning was performed with the GeneChip Scanner 3000 according to Affymetrix standard protocol

data_processing: The microarray gene expression data were imported from the probe cell intensity CEL files and the Affymetrix Expression Console software was used to calculate the summary measure of the probe level data.

source_name: gastrocnemius muscle

label_protocol: Sense-strand cDNA was generated from total RNA using the Ambion WT Expression Kit and then was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit

growth_protocol: F0 C57BL/6 mice were exposed to voluntary exercise or sedentary lifestyle and bred with like-exposed mates to produce an F1 generation. F1 mice of both ancestries were sedentary and sacrificed at 8 wk or bred with littermates to produce an F2 generation, which was also sedentary and sacrificed at 8 wk.

extract_protocol: Total RNA was extracted from powdered gastrocnemius muscle using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD). All samples were diluted to 98 ng/µl and pooled by generation and condition (5 pooled samples per array).

treatment_protocol: animals were either directly (F0) or indirectly through ancestry (F1, F2) exposed to exercise (EX) or sedentary (SED) lifestyle

tag: generation

tag: ancestry

value: SED

tag: Sex

value: male


title: AH129-N1,biological rep2

description: Gene expression data from AH-N1


title: 72

description:
72_N_N
KO-/-_17 dpp_replicate1


title: AH129-5, biological rep2

description: Gene expression data from AH129-5

source_name: ahES cell line AH129-5

value: ahES cell line AH129-5


title: 5 pooled F1 EX male gastrocnemius RNA 8 wks age 1

value: EX


title: 5 pooled F2 EX male gastrocnemius RNA 8 wks age 1


title: AH129-5, biological rep3

description: Gene expression data from AH129-5


title: 5 pooled F0 SED male gastrocnemius RNA 28 wks age


title: 5 pooled F2 SED male gastrocnemius RNA 8 wks age 1


title: 5 pooled F0 EX male gastrocnemius RNA 28 wks age