title: adult GBM tumor sample (ABGM_xB00012)

description:
adult GBM tumor sample
GBM_xB00012_1.CEL


title: PP242 12h treatment, replicate 4 cytosolic RNA

status: Public on May 21 2012

type: RNA

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: MCF7 treated with PP242 for 12h follwed by extraction of cytosolic RNA.

hyb_protocol: The resulting labelled samples were hybridized to the Human Genome U133 Plus 2.0 gene arrays from Affymetrix according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data was extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: 500 µg cytoplasmic or polysome-associated RNA was used as starting material for the 3’ IVT Express Kit (Affymetrix).

growth_protocol: MCF7 cells were obtained from ATCC and grown in RPMI (Invitrogen), supplemented with 10% fetal bovine serum (FBS; Invitrogen), 2 mM L-glutamine, and 100 units/ml penicillin/streptomycin (all from Invitrogen) at 37oC and 5% CO2.

extract_protocol: Polysome profile analysis was carried out as previously described (Dowling RJ, Zakikhani M, Fantus IG, Pollak M, & Sonenberg N (2007) Cancer Res 67, 10804-10812). A parallel sample was collected from post-nuclear lysates that are loaded onto the sucrose gradient and RNA was isolated using Trizol (Invitrogen) (“cytoplasmic mRNA”). Polysome fractions with mRNA associated with >3 ribosomes were pooled (“polysome-associated” mRNA) and RNA was isolated using Trizol.

treatment_protocol: Cells were treated with vehicle, rapamycin (100nM), PP242 (1M) and metformin (10mM) for 12h

tag: cell line

tag: tumor type

value: Breast cancer

tag: rna source

value: cytosolic

tag: treatment

tag: experiment


title: adult GBM tumor sample (ABGM_xB00017)

city: Aurora

first: Diane

middle: K

last: Birks

state: CO

department: Neurosurgery

country: USA

institute: University of Colorado, Denver - Anschutz Medical Campus

description:
adult GBM tumor sample
GBM_xB00017_1.CEL

hyb_protocol: For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to  the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).

scan_protocol: All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.

source_name: patient tumor sample

label_protocol: For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer.  For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions

treatment_protocol: all samples were collected at time of surgery

tag: gender

value: M

tag: age at diagnosis (years)

tag: disease state

value: adult GBM tumor


title: metformin 12h treatment, replicate 4 cytosolic RNA

description: MCF7 treated with metformin for 12h follwed by extraction of cytosolic RNA.

value: metformin


title: PP242 12h treatment, replicate 4 polysome-associated RNA

description: MCF7 treated with PP242 for 12h follwed by extraction of polysome-associated RNA.

value: polysome-associated


title: 24hr PBS rep1

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description: Gene expression data from lung tissue of mouse treated with PBS at 24-hour time point.

hyb_protocol: Samples were hybridized with Affymetrix Mouse Genome 430 2.0 Arrays per manufacturer’s instructions.

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

data_processing: The expression level was summarized by gcrma package in Bioconductor with GC robust multichip average (GCRMA) normalization.

organism: Mus musculus

source_name: 24hr PBS

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

extract_protocol: Total mouse lung RNA was isolated by directly solubilizing lung tissue in Trizol LS (Life Technologies) using a Brinkman Polytron tissue disruptor.

treatment_protocol: Seven-week-old female C57BL/6J mice (Jackson Laboratories, Wilmington, MA) were inoculated via the intranasal route with phosphate-buffered saline (PBS).

tag: strain

value: female

tag: tissue

value: lung


title: rapamycin 12h treatment, replicate 3 cytosolic RNA

description: MCF7 treated with rapamycin for 12h follwed by extraction of cytosolic RNA.

value: rapamycin


title: adult GBM tumor sample (ABGM_xB00057)

description:
adult GBM tumor sample
GBM_xB00057_1.CEL

value: F


title: adult GBM tumor sample (ABGM_xB00011)

description:
adult GBM tumor sample
GBM_xB00011_1.CEL


title: rapamycin 12h treatment, replicate 4 polysome-associated RNA

description: MCF7 treated with rapamycin for 12h follwed by extraction of polysome-associated RNA.


title: WT2 GMP

city: Saint Louis

first: Ansuman

last: Satpathy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: Hybed onto Mouse 430 2.0 (Affymetrix)

scan_protocol: Standard Affymetrix procedures

data_processing: Data was analyzed using dCHIP software.

source_name: WT GMP

label_protocol: 3' IVT Express Kit (Affymetrix)

growth_protocol: Cells from bone marrow were harvested by crushing bones with a mortal and pestel and isolating cells with Histopaque 1119 gradient.  Cells were Ack lysed, filtered through a 70um strainer and stained with the appropriate antibodies.

extract_protocol:
BM progenitor sorts: CMPs were sorted as PI- Lin- IL7R- MHCII- CD16/32- CD11c- Cd117hi CD135+, CDPs were sorted as PI-Lin-IL7R-MHCII- CD16/32- CD11c- CD117int CD135+, pre-cDCs were sorted as PI- Lin-IL7R-. BM G MHCII- CD16/32- CD117lo CD135+ CD11c+, GMPs were sorted as PI-IL7R-IL7R-MHCII-CD11c-CD117hiCD16/32+ CD135-.
BM GM-CSF and M-CSF cultures:  whole BM was harvested as described and cultured in either 20ng/ml of GM-CSF or M-CSF for 7 days.  Non-adherent CD11c+ cells from GM-CSF were purified and analyzed.  Adherent cells from GM-CSF and M-CSF were isolated following PBS washes to remove non-adherent cells and analyzed.
BM monocytes were purified by negative selection using antibodies for Ly6G, B220, CD4, CD8a, DX5, CD11c, Ter119, and CD117, resulting in a fraction of cells that were greater than 90% pure for expression of  CD11b and Ly6C.  Cells were cultured with 20 ng/ml of GM-CSF for the indicated number of hours (Hr), harvested and microarray analysis performed.

treatment_protocol: Mice were analyzed at steady-state.

tag: background strain

tag: cell type

value: bone marrow progenitor


title: WT CD4+ DC

hyb_protocol: Hybed onto Mouse Gene 1.0 (Affymetrix)

data_processing: Data was analyzed using Arraystar software (DNASTAR) with Quantile RMA normalization

source_name: Zbtb46+/+ mice

label_protocol: Ambion/Affymetrix WT Expression Kit

extract_protocol: Pre MegE cells were sorted as Lin- CD117+ CD150+ CD105-CD41-CD16/32-. Pre CFU-E cells were sorted as Lin- CD117+ CD150+ CD105lo CD41- CD16/32-.  CFU-E cells were sorted as Lin- CD117+ CD150- CD105+ Cd41- CD16/32-.  Splenic CD4+ DCs were sorted as B220- CD11c+ MHCII+ CD8- CD172+ CD11b+ CD4+.

tag: genotype/variation

value: CD4+ DC


title: adult GBM tumor sample (ABGM_xB00010)

description:
adult GBM tumor sample
GBM_xB00010_1.CEL


title: PP242 12h treatment, replicate 3 cytosolic RNA


title: rapamycin 12h treatment, replicate 3 polysome-associated RNA


title: PP242 12h treatment, replicate 3 polysome-associated RNA


title: vehicle 12h treatment, replicate 3 cytosolic RNA

description: MCF7 treated with vehicle for 12h follwed by extraction of cytosolic RNA.

value: vehicle


title: metformin 12h treatment, replicate 3 cytosolic RNA


title: WT1 PrecDC BM

source_name: WT PrecDC BM


title: pediatric GBM tumor sample (PBGM_ID00678)

description:
pediatric GBM tumor sample
GBM_ID00678_1.CEL

value: pediatric GBM tumor


title: metformin 12h treatment, replicate 3 polysome-associated RNA

description: MCF7 treated with metformin for 12h follwed by extraction of polysome-associated RNA.


title: vehicle 12h treatment, replicate 3 polysome-associated RNA

description: MCF7 treated with vehicle for 12h follwed by extraction of polysome-associated RNA.


title: metformin 12h treatment, replicate 2 cytosolic RNA


title: WT1 PrecDC Spl

source_name: WT PrecDC Spl


title: metformin 12h treatment, replicate 2 polysome-associated RNA


title: WT1 CDP

source_name: WT CDP


title: PP242 12h treatment, replicate 2 cytosolic RNA


title: vehicle 12h treatment, replicate 2 cytosolic RNA


title: WT2 CMP

source_name: WT CMP


title: pediatric GBM tumor sample (PBGM_ID00309)

description:
pediatric GBM tumor sample
GBM_ID00309_1.CEL


title: pediatric GBM tumor sample (PBGM_ID00668)

description:
pediatric GBM tumor sample
GBM_ID00668_1.CEL


title: pediatric GBM tumor sample (PBGM_ID00637)

description:
pediatric GBM tumor sample
GBM_ID00637_1.CEL


title: PP242 12h treatment, replicate 2 polysome-associated RNA


title: pediatric GBM tumor sample (PBGM_ID00434)

description:
pediatric GBM tumor sample
GBM_ID00434_1.CEL


title: WT1 CMP


title: WT1 GMP


title: pediatric GBM tumor sample (PBGM_ID00391)

description:
pediatric GBM tumor sample
GBM_ID00391_1.CEL


title: WT Pre MegE

value: Pre MegE


title: vehicle 12h treatment, replicate 1 cytosolic RNA


title: PP242 12h treatment, replicate 1 polysome-associated RNA


title: rapamycin 12h treatment, replicate 2 cytosolic RNA


title: Mono GMCSF 0hr

source_name: Mono GMCSF 0hr

value: bone marrow monocyte


title: vehicle 12h treatment, replicate 2 polysome-associated RNA


title: Mono GMCSF 24hr

source_name: Mono GMCSF 24hr


title: pediatric GBM tumor sample (PBGM_ID00281)

description:
pediatric GBM tumor sample
GBM_ID00281_1.CEL


title: rapamycin 12h treatment, replicate 1 polysome-associated RNA


title: vehicle 12h treatment, replicate 1 polysome-associated RNA


title: rapamycin 12h treatment, replicate 1 cytosolic RNA


title: Mono GMCSF 48hr

source_name: Mono GMCSF 48hr


title: PP242 12h treatment, replicate 1 cytosolic RNA

description: MCF7 treated with PP242 for 12h follwed by extraction of cytosolic RNA.


title: pediatric GBM tumor sample (PBGM_ID00098)

description:
pediatric GBM tumor sample
GBM_ID00098_1.CEL


title: rapamycin 12h treatment, replicate 2 polysome-associated RNA


title: pediatric GBM tumor sample (PBGM_ID00271)

description:
pediatric GBM tumor sample
GBM_ID00271_1.CEL


title: NZ131

city: Chicago

first: Michael

middle: J

last: Federle

state: IL

address: 900 S Ashland Ave. MC870

department: Microbiology & Imm. / Cntr Pharm Biotech

institute: University of Illinois at Chicago

description: This sample is of wild-type Streptococcus pyogenes NZ131 and consists of total RNA isolated from three separate cultures and pooled in equimloar amounts prior to cDNA synthesis

hyb_protocol: Hybridization to S. pyogenes whole genome microarrays (Nimbelgen) was performed by the W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, in accordance with the Nimbelgen Hyrbidization protocol (www.nimblegen.com)

scan_protocol: Scanning was performed by the W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, using the Nimlescan software according to manufacturer's instructinos (Nimblegen)

data_processing: The raw data was subjected to RMA normalization by the W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, using Partek software. See www.partek.com.

organism: Streptococcus pyogenes NZ131

source_name: Streptococcus pyogenes NZ131 wild type

label_protocol: Standard NimbleGen label protocol

growth_protocol: Streptococcus pyogenes NZ131 and NZ131 serR- was grown to mid-log phase (OD 600nm 0.4) statically at 37°C in C-medium

extract_protocol: Total RNA was extracted using the RiboPure-Bacteria Kit (Ambion) according to manufacturer's instreuctions. RNA quality was determined by agarose gel electrophoresis and concentration was measured using a NanoDrop 1000 spectrophotometer (Thermo Scientifiic)

tag: genotype

value: Wild-type


title: vehicle 12h treatment, replicate 4 cytosolic RNA

value: Breast cancer


title: GM-CSF Adh

source_name: GM-CSF Adh

value: adherent bone marrow


title: MCSF Adh

source_name: MCSF Adh


title: BNL100

description: This sample is of Streptococcus pyogenes NZ131 serR-, a mutant in which the serR gene was deleted entirely,  and consists of total RNA isolated from three separate cultures and pooled in equimloar amounts prior to cDNA synthesis

source_name: Streptococcus pyogenes NZ131 serR- (spy49_0126c)

value: Mutant serR-


title: pediatric GBM tumor sample (PBGM_ID00089)

description:
pediatric GBM tumor sample
GBM_ID00089_1.CEL

value: M


title: pediatric GBM tumor sample (PBGM_ID00057)

description:
pediatric GBM tumor sample
GBM_ID00057_1.CEL


title: metformin 12h treatment, replicate 1 cytosolic RNA

description: MCF7 treated with metformin for 12h follwed by extraction of cytosolic RNA.

value: cytosolic

value: metformin


title: End exposure 45C for 30 min, replicate 2

status: Public on May 20 2012

city: Norwich

first: Carmen

last: Pin

address: Colney lane

country: United Kingdom

institute: institute of Food Research

description:
Temp2_1
Biological replicate 2 of 3. Control culture vs. culture exposed to 45C for 30 min.

hyb_protocol: The labeled cDNA from the two cultures were mixed together and competitively hybridized on an 8x15K Agilent microarray slide constructed for Salmonella Typhimurium strain SL1344 at 65°C for 17 h and washed.

scan_protocol: Scanned according to the “Two-Color Microarray-Based Prokaryote Analysis Protocol” (Agilent Technologies). The scanning was done using an Axon GenePix 4200A Microarray scanner (Axon, Foster City, CA)).

data_processing: Feature intensities were quantified using GenePix Pro 6.1 software (Axon, Foster City, CA). Data normalization was carried out as described in Pin and Reuter (2007, BMC Bioinformatics, 8:455 (PMID 18021437)). Microarray data analysis was carried out using the program ArrayLeaRNA (http://www.ifr.ac.uk/safety/ArrayLeaRNA/). Blank values in the Sample data table represent features with very low intensity values for both channels.

source_name: Control culture, 25C, 30 min

label_protocol: cDNA from the untreated cultures was labeled with Cy5 and cDNA from the stressed culture was labeled with Cy3.

growth_protocol: Salmonella enterica subsp. enterica serovar Typhimurium strain 4/74 was subcultured twice in tryptone soy broth (TSB, Oxoid, Basingstoke, UK) and incubated at 25°C for 24 hr before being inoculated in 200 ml of TSB and incubated at 25°C for 16 h to early stationary phase. This culture was divided in two parts; one untreated control culture kept at 25°C and pH 7 while the other part of the culture underwent stressing conditions either at pH 5 or at 45°C.

extract_protocol: Total RNA was purified from the RNAlater solution using the RNeasy Mini Kit (Qiagen, Copenhagen, Denmark) according to the manufacturer’s instructions (“RNeasy Mini Protocol for Isolation of Total RNA from Bacteria”) with minor adjustments; for lysis, a 15 mg/ml lysozyme solution with proteinase K was used and on-column DNase digestion was performed. The quality of the RNA was checked using the NanoDrop (Fisher Scientific, Slangerup, Denmark). Labeled cDNA was synthesized from total RNA using the FairPlay III Microarray Labeling Kit (Agilent Technologies, Hoersholm, Denmark) according to manufacturer’s instructions without the Spike-in step.

treatment_protocol: The temperature shift was carried out by moving the culture from a 25°C water bath to one at 45°C. Once the culture reached 45°C, it was left there for 30 min before being moved back to 25°C. The change of temperature with time was measured by a thermocouple applied to a replicate bottle of uninoculated medium. For the pH stress condition, the pH was lowered to pH 5 with hydrochloride acid and after 30 min changed back with sodium hydroxide to the original pH. At each sampling time, 10 ml culture was harvested by adding 10 ml Ambion RNAlater Tissue Collection solution (Life Technologies, Taastrup, Denmark) and placed at 4°C overnight and stored at -20°C until RNA extraction.

tag: treatment time

value: 30 min

source_name: Stressed culture, 45C, 30 min


title: End exposure 45C for 30 min, replicate 3

description:
Temp3_1
Biological replicate 3 of 3. Control culture vs. culture exposed to 45C for 30 min.

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: Shocked cells (45C 30 min) 30 min after temp set back to 25, replicate 3

description:
Temp3_3
Biological replicate 3 of 3. Control culture vs. culture exposed to 45C for 30 min and 30 min after temp is set back to 25.

source_name: Control culture, 25C, 60 min

value: 60 min

source_name: Stressed culture, 45C, 30 min and 30 min after temp back to 25C

value: 45C, back to 25C

value: 30 min and 30 min after end of shock


title: metformin 12h treatment, replicate 1 polysome-associated RNA

description: MCF7 treated with metformin for 12h follwed by extraction of polysome-associated RNA.

value: polysome-associated


title: Shocked cells (45C 30 min) immediately after temp set back to 25, replicate 3

description:
Temp3_4
Biological replicate 3 of 3. Control culture vs. culture exposed to 45C for 30 min immediately after temp is set back to 25.

source_name: Stressed culture, 45C, 30 min and immediately after temp back to 25C

value: 30 min and immediately after end of shock


title: Before temp 45C exposure, replicate 3

description:
Temp3_2
Biological replicate 3 of 3. Control culture vs. control culture (time 0 before stress application).

source_name: Control culture, 25C, 0 min

value: 0 min

source_name: Stressed culture, 45C, 0 min


title: GM-CSF CD11c

source_name: GM-CSF CD11c

value: non-adherent bone marrow


title: End exposure pH 5 for 30 min, replicate 3

description:
pH3_1
Biological replicate 3 of 3. Control culture vs. culture exposed to pH 5 for 30 min.

source_name: Control culture, pH 7, 30 min

source_name: Stressed culture, pH 5, 30 min

value: pH 5


title: congenital GBM tumor sample (CBGM_ID00280)

description:
congenital GBM tumor sample
GBMI_ID00280_1.CEL

source_name: patient tumor sample

value: congenital GBM tumor


title: Shocked cells (45C 30 min) 30 min after temp set back to 25, replicate 2

description:
Temp2_3
Biological replicate 2 of 3. Control culture vs. culture exposed to 45C for 30 min and 30 min after temp is set back to 25.


title: Shocked cells (45C 30 min) immediately after temp set back to 25, replicate 2

description:
Temp2_4
Biological replicate 2 of 3. Control culture vs. culture exposed to 45C for 30 min immediately after temp is set back to 25.


title: pediatric GBM tumor sample (PBGM_ID00000)

description:
pediatric GBM tumor sample
GBM_ID00000_1.CEL

value: pediatric GBM tumor


title: Shocked cells (pH 5 30 min) 30 min after pH set back to 7, replicate 2

description:
pH2_3
Biological replicate 2 of 3. Control culture vs. culture exposed to pH 5 for 30 min and 30 min after pH is set back to 7.

source_name: Control culture, pH 7, 60 min

source_name: Stressed culture, pH 5, 30 min and 30 min after pH back to 7

value: pH 5, back to pH 7


title: WT CFU-E

source_name: Zbtb46+/+ mice

value: CFU-E


title: Shocked cells (45C 30 min) immediately after temp set back to 25, replicate 1

description:
Temp1_4
Biological replicate 1 of 3. Control culture vs. culture exposed to 45C for 30 min immediately after temp is set back to 25.


title: Shocked cells (pH 5 30 min) 30 min after pH set back to 7, replicate 1

description:
pH1_3
Biological replicate 1 of 3. Control culture vs. culture exposed to pH 5 for 30 min and 30 min after pH is set back to 7.


title: Shocked cells (45C 30 min) 30 min after temp set back to 25, replicate 1

description:
Temp1_3
Biological replicate 1 of 3. Control culture vs. culture exposed to 45C for 30 min and 30 min after temp is set back to 25.


title: Before temp 45C exposure, replicate 2

description:
Temp2_2
Biological replicate 2 of 3. Control culture vs. control culture (time 0 before stress application).


title: Shocked cells (pH 5 30 min) immediately after pH set back to 7, replicate 3

description:
pH3_4
Biological replicate 3 of 3. Control culture vs. culture exposed to pH 5 for 30 min immediately after pH is set back to 7.

source_name: Stressed culture, pH 5, 30 min and immediately after pH back to 7


title: Shocked cells (pH 5 30 min) immediately after pH set back to 7, replicate 1

description:
pH1_4
Biological replicate 1 of 3. Control culture vs. culture exposed to pH 5 for 30 min immediately after pH is set back to 7.


title: End exposure 45C for 30 min, replicate 1

description:
Temp1_1
Biological replicate 1 of 3. Control culture vs. culture exposed to 45C for 30 min.


title: End exposure pH 5 for 30 min, replicate 1

description:
pH1_1
Biological replicate 1 of 3. Control culture vs. culture exposed to pH 5 for 30 min.


title: End exposure pH 5 for 30 min, replicate 2

description:
pH2_1
Biological replicate 2 of 3. Control culture vs. culture exposed to pH 5 for 30 min.


title: Before pH 5 exposure, replicate 2

description:
pH2_2
Biological replicate 2 of 3. Control culture vs. control culture (time 0 before stress application).

source_name: Control culture, pH 7, 0 min

source_name: Stressed culture, pH 5, 0 min


title: Shocked cells (pH 5 30 min) 30 min after pH set back to 7, replicate 3

description:
pH3_3
Biological replicate 3 of 3. Control culture vs. culture exposed to pH 5 for 30 min and 30 min after pH is set back to 7.


title: Before pH 5 exposure, replicate 3

description:
pH3_2
Biological replicate 3 of 3. Control culture vs. control culture (time 0 before stress application).


title: Shocked cells (pH 5 30 min) immediately after pH set back to 7, replicate 2

description:
pH2_4
Biological replicate 2 of 3. Control culture vs. culture exposed to pH 5 for 30 min immediately after pH is set back to 7.


title: Before temp 45C exposure, replicate 1

description:
Temp1_2
Biological replicate 1 of 3. Control culture vs. control culture (time 0 before stress application).


title: Before pH 5 exposure, replicate 1

description:
pH1_2
Biological replicate 1 of 3. Control culture vs. control culture (time 0 before stress application).


title: Gene expression profile of U373MG exposed to anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids (V)

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

country: Japan

institute: Meiji Pharmaceutical University

hyb_protocol: Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).

source_name: U373MG cells treated with DMSO as a control for RM

label_protocol: Three hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).

growth_protocol: The cells were maintained in Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (feeding medium).

extract_protocol: Total RNA was isolated from the cells by using the TRIZOL Plus RNA Purification kit (Invitrogen).

treatment_protocol: The cells were exposed to dimethyl sulfoxide (DMSO) for 24 hours at a concentration equivalent to RM.

value: glioblastoma


title: 03_CpGB stimulation 4h

city: Meguro-ku, Tokyo

first: hideo

last: negishi

address: Komaba 4-6-1

department: Molecular Immunology

institute: University of Tokyo

hyb_protocol: Following fragmentation, aRNA were hybridized for 16hrs at 45˚C on GeneChip Mouse Genome 430 2.0 Array. Arrays were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Array(RMA) using Affymetrix default analysis settings.

source_name: CpG-B stimulated macrophege

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

growth_protocol: Mice were maintaind under specific pathogen-free condition in the animal facility of the University of Tokyo.

extract_protocol: Total RNA was extruced by using Rneasy Mini kit (QIAGEN Cat.No.74104)  according to the manufacturer's instructions.

treatment_protocol: Mice were injected I.p. with 2ml of 4% thioglycolate (Difco), and peritoneal macrophages were harvested from the peritoneal cavity 3 days after by lavage with cold PBS. Cell were then cultured for 2 hours and stimulated with B-DNA (10μg/ml) or CpG-B(3μM) for 4 hours, and then subjected to microarray analysis.

value: CpG-B(3uM) for 4 hr


title: EA0910_04

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: VSV infected IRF3-/- macrophege

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions.  Biotinylated cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Mice were injected I.p. with 2ml of 4% thioglycolate (Difco), and peritoneal macrophages were harvested from the peritoneal cavity 3 days after by lavage with cold PBS. Cell were then cultured for 2 hours and infected with VSV (1 M.O.I.) for 6 hours, and then subjected to microarray analysis.

value: peritoneal macrophage

value: VSV (1 M.O.I.) for 6 hr


title: 02_B-DNA stimulation 4h

source_name: B-DNA stimulated macrophege

value: B-DNA (10ug/ml) for 4 hr


title: 01_-

source_name: unstimlated macrophage


title: Gene expression profile of U373MG exposed to anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids (III)

source_name: U373MG cells treated with DMSO as a control for ET-770-DR

treatment_protocol: The cells were exposed to dimethyl sulfoxide (DMSO) for 24 hours at a concentration equivalent to ET-770-DR.


title: Gene expression profile of U373MG exposed to anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids (VI)

source_name: U373MG cells treated with RM

treatment_protocol: The cells were exposed to RM for 24 hours at a concentration of IC50 (3.10 nM).


title: EA0910_02

source_name: VSV infected WT macrophege

value: wild type


title: EA0907_07

source_name: unstimlated WT macrophage


title: Gene expression profile of U373MG exposed to anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids (I)

source_name: U373MG cells treated with DMSO as a control for ET-770

treatment_protocol: The cells were exposed to dimethyl sulfoxide (DMSO) for 24 hours at a concentration equivalent to ET-770.


title: HR_30-9 HR_SAL_Lsal_30ppt_Cop

status: Public on May 19 2012

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

hyb_protocol: Sample loading was performed as per manufacturers’ instructions using a 4x44k array and SureHyb chambers (Agilent). Arrays were hybridized at 65ºC for 17 hr at 10 rpm in a hybridization oven (Agilent). Washing was performed as per manufacturers’ instructions, using the optional protocol to prevent ozone degradation. All slides were transferred to a dark box and kept at low ozone until scanned.

scan_protocol: Arrays were scanned on a Perkin Elmer ScanArray Express at 5 μM resolution using PMT settings optimized to have the median signal of ~1-2% of array spots saturated (Cy5: 70; Cy3: 70).

data_processing: Images were quantified in Imagene 8.1 (Biodiscovery) using a custom eArray GAL file (Agilent). Poor spots and control spots were flagged by the software for downstream filtering. A block-specific background correction was performed by subtracting the average median signal for negative control spots from each signal median. Each experiment was normalized and filtered separately, using the following: raw values thresholded to 1; intensity-dependent Lowess normalization; and baseline transformation to the median of all samples. Control spots, and any entities not passing the following filter were removed from the analysis: raw values ≥ 500 in at least 65% of samples in any one condition; no flags in at least 65% of samples in any one condition.

organism: Lepeophtheirus salmonis

source_name: Pool of whole copepodids

label_protocol: Purified total RNA (200ng) was reverse-transcribed to cDNA using Low Input Quick Amp Labeling kits (Agilent), as per manufacturer’s instructions for hybridization to a 4x44K oligo gene expression microarray. Labelled cRNA was then purified through RNeasy columns as per manufacturer’s instructions (QIAGEN) and quantified using spectrophotometry (NanoDrop-1000). For quality control, the specific activity of all samples was greater than 6 pmol dye per μg cRNA (Agilent). Samples were kept at -80ºC until hybridization.

growth_protocol: L. salmonis obtained from seawater netpen-reared Atlantic salmon Salmo salar in coastal British Columbia, were maintained in cold aerated seawater during transport to the Pacific Biological Station, Nanaimo, BC. Intact and pigmented egg strings were removed and incubated in flasks containing 400ml of filtered and aerated seawater. The resulting nauplii were maintained at 30 ppt salinity until a majority moulted to copepodids.

extract_protocol: Frozen filters containing lice were homogenized, and extracted using TRIzol® (Invitrogen), as per manufacturers’ instructions. Total RNA was purified through RNeasy spin columns with an on-column DNase I treatment (QIAGEN) to degrade genomic DNA. Total RNA was then quantified by spectrophotometry (NanoDrop-1000), and quality checked by electrophoresis on a 1% agarose gel. Samples were then randomized for all downstream nucleic acid manipulations.

treatment_protocol: Copepodids were pooled into groups of ~500 lice per beaker. Triplicate flasks were incubated for 24 hr at 4, 10, or 16ºC with salinity held constant at 30 ppt.  In another experiment, triplicate flasks containing seawater diluted to 30, 25, 20, or 10 ppt were incubated at 10ºC. Both of these low resolution experiments were repeated once.  A single trial of a high resolution salinity experiment was conducted as above, but with 6 beakers per condition and a salinity range of 30, 29, 28, 27, 26 and 25 ppt, and a constant temperature of 10ºC. The lice were recovered onto 47 mm cellulose acetate/cellulose nitrate filter membranes with a pore size of 8.0 μm.  The membranes were flash frozen in liquid nitrogen and stored at -80ºC.

tag: salinity

value: 30 ppt

tag: temperature

source_name: Pool of samples from current experiment (from all HR_SAL conditions)

tag: sample type

value: reference


title: HR_30-7 HR_SAL_Lsal_30ppt_Cop


title: Gene expression profile of U373MG exposed to anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids (IV)

source_name: U373MG cells treated with ET-770-DR

treatment_protocol: The cells were exposed to ET-770-DR for 24 hours at a concentration of IC50 (1.70 nM).

tag: cell line


title: HR_30-12 HR_SAL_Lsal_30ppt_Cop


title: HR_29-8 HR_SAL_Lsal_29ppt_Cop

value: 29 ppt


title: Gene expression profile of U373MG exposed to anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids (II)

source_name: U373MG cells treated with ET-770

treatment_protocol: The cells were exposed to ET-770 for 24 hours at a concentration of IC50 (4.83 nM).


title: HR_29-11 HR_SAL_Lsal_29ppt_Cop


title: HR_29-9 HR_SAL_Lsal_29ppt_Cop


title: HR_30-11 HR_SAL_Lsal_30ppt_Cop


title: HR_28-9 HR_SAL_Lsal_28ppt_Cop

value: 28 ppt


title: HR_28-7 HR_SAL_Lsal_28ppt_Cop


title: HR_29-12 HR_SAL_Lsal_29ppt_Cop


title: HR_30-10 HR_SAL_Lsal_30ppt_Cop


title: HR_29-7 HR_SAL_Lsal_29ppt_Cop


title: HR_28-12 HR_SAL_Lsal_28ppt_Cop


title: HR_29-10 HR_SAL_Lsal_29ppt_Cop


title: HR_30-8 HR_SAL_Lsal_30ppt_Cop


title: HR_28-10 HR_SAL_Lsal_28ppt_Cop


title: HR_28-11 HR_SAL_Lsal_28ppt_Cop


title: HR_28-8 HR_SAL_Lsal_28ppt_Cop


title: HR_27-8 HR_SAL_Lsal_27ppt_Cop

value: 27 ppt


title: HR_27-9 HR_SAL_Lsal_27ppt_Cop


title: HR_27-11 HR_SAL_Lsal_27ppt_Cop


title: HR_27-10 HR_SAL_Lsal_27ppt_Cop


title: HR_26-7 HR_SAL_Lsal_26ppt_Cop

value: 26 ppt


title: HR_26-8 HR_SAL_Lsal_26ppt_Cop


title: HR_26-11 HR_SAL_Lsal_26ppt_Cop


title: HR_26-12 HR_SAL_Lsal_26ppt_Cop


title: HR_27-7 HR_SAL_Lsal_27ppt_Cop


title: HR_26-10 HR_SAL_Lsal_26ppt_Cop


title: HR_27-12 HR_SAL_Lsal_27ppt_Cop


title: HR_26-9 HR_SAL_Lsal_26ppt_Cop


title: HR_25-11 HR_SAL_Lsal_25ppt_Cop

value: 25 ppt


title: HR_25-12 HR_SAL_Lsal_25ppt_Cop


title: LR_T4-8 LR_TEMP_Lsal_T4degreeC_Cop_Trial1

source_name: Pool of samples from current experiment (from all temp conditions)


title: monocytes of Donor # D3 at time point (hour)48 cultured in presence of GMCSF

city: Bethesda

first: Luciano

last: Castiello

state: Maryland

address: 10 Center Drive

department: DTM

institute: NIH/CC

hyb_protocol: Samples were hybridized according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used with dafault settings for processed signals

label_protocol: Test RNA and Universal Reference RNA () were amplified and labeled according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

growth_protocol: Elutriated monocytes were cultured in RPMI-1640 media with 10% heat inactivated human AB plasma, gentamycin and one among GM-CSF, IL-4, 15 kDa Granulysin

extract_protocol: Total RNA extracted using miRNeasy kit from Qiagen

value: monocytes

tag: donor

tag: hour

tag: cytokine

value: GMCSF

source_name: Universal Human Reference RNA

tag: origin

value: Stratagene Catalog #740000


title: HR_25-8 HR_SAL_Lsal_25ppt_Cop


title: HR_25-9 HR_SAL_Lsal_25ppt_Cop


title: monocytes of Donor # D3 at time point (hour)4 cultured in presence of GRANULYSIN

value: GRANULYSIN


title: HR_25-10 HR_SAL_Lsal_25ppt_Cop


title: HR_25-7 HR_SAL_Lsal_25ppt_Cop


title: LR_T4-9 LR_TEMP_Lsal_T4degreeC_Cop_Trial1


title: monocytes of Donor # D3 at time point (hour)4 cultured in presence of IL4


title: LR_T4-7 LR_TEMP_Lsal_T4degreeC_Cop_Trial1


title: monocytes of Donor # D3 at time point (hour)48 cultured in presence of GRANULYSIN


title: monocytes of Donor # D3 at time point (hour)4 cultured in presence of GMCSF


title: LR_T4-11 LR_TEMP_Lsal_T4degreeC_NII&Cop_Trial2


title: monocytes of Donor # D3 at time point (hour)48 cultured in presence of IL4


title: monocytes of Donor # D3 at time point (hour)24 cultured in presence of GRANULYSIN


title: monocytes of Donor # D3 at time point (hour)24 cultured in presence of IL4-2


title: LR_T4-12 LR_TEMP_Lsal_T4degreeC_NII&Cop_Trial2


title: LR_T16-8 LR_TEMP_Lsal_T16degreeC_Cop_Trial1


title: monocytes of Donor # D3 at time point (hour)24 cultured in presence of GMCSF


title: monocytes of Donor # D3 at time point (hour)12 cultured in presence of IL4


title: LR_T16-9 LR_TEMP_Lsal_T16degreeC_Cop_Trial1


title: LR_T16-10 LR_TEMP_Lsal_T16degreeC_NII&Cop_Trial2


title: monocytes of Donor # D3 at time point (hour)24 cultured in presence of IL4


title: LR_T10-9 LR_TEMP_Lsal_T10degreeC_Cop_Trial1


title: LR_T4-10 LR_TEMP_Lsal_T4degreeC_NII&Cop_Trial2


title: monocytes of Donor # D1 at time point (hour)48 cultured in presence of IL4


title: LR_T10-8 LR_TEMP_Lsal_T10degreeC_Cop_Trial1


title: LR_T16-11 LR_TEMP_Lsal_T16degreeC_NII&Cop_Trial2


title: monocytes of Donor # D1 at time point (hour)24 cultured in presence of GMCSF


title: monocytes of Donor # D3 at time point (hour)12 cultured in presence of GRANULYSIN


title: monocytes of Donor # D3 at time point (hour)12 cultured in presence of GMCSF


title: monocytes of Donor # D3 at time point (hour)0 cultured in presence of


title: LR_T16-7 LR_TEMP_Lsal_T16degreeC_Cop_Trial1


title: LR_T10-11 LR_TEMP_Lsal_T10degreeC_NII&Cop_Trial2


title: LR_T10-10 LR_TEMP_Lsal_T10degreeC_NII&Cop_Trial2


title: monocytes of Donor # D2 at time point (hour)0 cultured in presence of


title: monocytes of Donor # D1 at time point (hour)48 cultured in presence of GRANULYSIN


title: monocytes of Donor # D1 at time point (hour)48 cultured in presence of GMCSF


title: monocytes of Donor # D2 at time point (hour)24 cultured in presence of GRANULYSIN


title: LR_T10-7 LR_TEMP_Lsal_T10degreeC_Cop_Trial1


title: monocytes of Donor # D1 at time point (hour)0 cultured in presence of


title: LR_T10-12 LR_TEMP_Lsal_T10degreeC_NII&Cop_Trial2


title: monocytes of Donor # D2 at time point (hour)24 cultured in presence of IL4


title: LR_S30-8 LR_SAL_Lsal_S30ppt_Cop_Trial1

source_name: Pool of samples from current experiment (from all LR_SAL conditions except 25 ppt)


title: monocytes of Donor # D2 at time point (hour)12 cultured in presence of IL4


title: LR_S30-9 LR_SAL_Lsal_S30ppt_Cop_Trial1


title: monocytes of Donor # D2 at time point (hour)12 cultured in presence of GRANULYSIN


title: LR_S30-7 LR_SAL_Lsal_S30ppt_Cop_Trial1


title: monocytes of Donor # D2 at time point (hour)4 cultured in presence of GMCSF


title: monocytes of Donor # D2 at time point (hour)12 cultured in presence of GMCSF


title: LR_S30-14 LR_SAL_Lsal_S30ppt_Cop_Trial2


title: LR_S30-13 LR_SAL_Lsal_S30ppt_Cop_Trial2


title: LR_S20-8 LR_SAL_Lsal_S20ppt_Cop_Trial1

value: 20 ppt


title: monocytes of Donor # D2 at time point (hour)48 cultured in presence of IL4


title: monocytes of Donor # D2 at time point (hour)4 cultured in presence of IL4


title: monocytes of Donor # D2 at time point (hour)4 cultured in presence of GRANULYSIN


title: LR_S25-9 LR_SAL_Lsal_S25ppt_Cop_Trial1


title: monocytes of Donor # D2 at time point (hour)48 cultured in presence of GMCSF


title: LR_S25-14 LR_SAL_Lsal_S25ppt_Cop_Trial2


title: LR_S25-7 LR_SAL_Lsal_S25ppt_Cop_Trial1


title: LR_T16-12 LR_TEMP_Lsal_T16degreeC_NII&Cop_Trial2


title: LR_S25-15 LR_SAL_Lsal_S25ppt_Cop_Trial2


title: monocytes of Donor # D2 at time point (hour)24 cultured in presence of GMCSF


title: monocytes of Donor # D1 at time point (hour)12 cultured in presence of GRANULYSIN


title: LR_S20-9 LR_SAL_Lsal_S20ppt_Cop_Trial1


title: monocytes of Donor # D1 at time point (hour)4 cultured in presence of GMCSF


title: LR_S30-15 LR_SAL_Lsal_S30ppt_Cop_Trial2


title: LR_S20-7 LR_SAL_Lsal_S20ppt_Cop_Trial1


title: LR_S25-8 LR_SAL_Lsal_S25ppt_Cop_Trial1


title: monocytes of Donor # D1 at time point (hour)4 cultured in presence of GRANULYSIN


title: monocytes of Donor # D1 at time point (hour)4 cultured in presence of IL4


title: LR_S20-15 LR_SAL_Lsal_S20ppt_Cop_Trial2


title: LR_S25-13 LR_SAL_Lsal_S25ppt_Cop_Trial2


title: monocytes of Donor # D1 at time point (hour)24 cultured in presence of IL4


title: LR_S20-13 LR_SAL_Lsal_S20ppt_Cop_Trial2


title: monocytes of Donor # D1 at time point (hour)12 cultured in presence of IL4


title: LR_S20-14 LR_SAL_Lsal_S20ppt_Cop_Trial2


title: LR_S10-9 LR_SAL_Lsal_S10ppt_Cop_Trial1

value: 10 ppt


title: monocytes of Donor # D1 at time point (hour)12 cultured in presence of GMCSF


title: monocytes of Donor # D1 at time point (hour)24 cultured in presence of GRANULYSIN


title: LR_S10-8 LR_SAL_Lsal_S10ppt_Cop_Trial1


title: LR_S10-13 LR_SAL_Lsal_S10ppt_Cop_Trial2


title: monocytes of Donor # D2 at time point (hour)48 cultured in presence of GRANULYSIN


title: LR_S10-15 LR_SAL_Lsal_S10ppt_Cop_Trial2


title: 6334167042_F.AVG_Signal

city: Boston

first: David

middle: A

last: Sullivan

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and then normalized using Cubic Spline normalisation

source_name: Differentiation

label_protocol: Biotinylated cRNA were prepared using a MessageAmp II-based protocol (Ambion Inc., Austin, TX) and one round of amplification.

growth_protocol: Cells were grown in proliferation (KSFM + 5 ng/ml EGF + 50 ug/ml bovine pituitary extract) and differentiation (DMEM/F12 + 10 ng/ml EGF + 10% FBS) media

extract_protocol: Total RNA was extracted wth Rneasy Mini Kit(Qiagen) per manufacturer's recommendations. Quality control and quantification were performed with Agilent Bioanalyser. Quality and quantity were checked again before subjected to microarray by Asuragen.

treatment_protocol: Cells were treated with or without 2 uM retinoic acid in the above media for 4 days at 37 C in 5% CO2

value: meibomian gland epithelial cells

tag: treatment

value: DMEM/F12 + 10 ng/ml EGF + 10% FBS media without retinoic acid


title: 6334167042_D.AVG_Signal

source_name: Proliferation RA

value: KSFM + 5 ng/ml EGF + 50 ug/ml bovine pituitary extract media with 2 uM retinoic acid


title: 6334167042_L.AVG_Signal

source_name: Differentiation RA

value: DMEM/F12 + 10 ng/ml EGF + 10% FBS media with 2 uM retinoic acid


title: LR_S10-7 LR_SAL_Lsal_S10ppt_Cop_Trial1


title: 6334167042_K.AVG_Signal


title: 6334167042_E.AVG_Signal


title: 6334167042_G.AVG_Signal


title: Mt DNA 16

status: Public on May 18 2012

type: genomic

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

description:
Total DNA (nuclear and mitochondrial)
Sample contained at least one stretch of N calls.

hyb_protocol: Following fragmentation, fragmented mtDNA were hybridized  for 16 hours at 49°C with 60 rpm rotation in a hybridization mix solution. MitoChip v2.0 was then washed and stained using the Affymetrix fluidics station 450 (Mini_DNAArray_WS5_450).

scan_protocol: Data was acquired on a 7G GeneChip Scanner 3000 and data extraction performed in GCOS version 1.4 Nucleotide calls made using GSEQ v 4.1.

data_processing:
The Affymetrix algorithm parameter settings recommended to achieve optimal performance were used to analyze the mitochondrial sequences, with ‘diploid’ selected as the genome model to enable the detection of heteroplasmy. A Quality Score Threshold (QST) of 3 provided the highest performance in terms of overall base calling accuracy and call rates by the GSEQ software. All other parameters used by the algorithm were also fixed for all samples: No Signal Threshold= 2, Weak Signal Fold Threshold= 20, Large SNR Threshold= 20, Min Fraction of Calls of Samples = 0.5, Trace Threshold = 1, Sequence Profile Threshold = -0.175.
additional results files (available on the Series Record): GSEQ results.txt, sPROFILER results.txt
GSEQ results.txt = Summary data from GSEQ using settings described in "data processing".
sPROFILER.txt = Summary data where data from GSEQ base calls was further analysed using sPROFILER (strand-specific PRObe cell intensity comparison for FILtERing- PMID20146813). This is a novel and free algorithm developed by Kothiyal et al 2010 for improving array call rates using MATLAB over GSEQ call rates, based on intensity signature.

molecule: genomic DNA

label_protocol: The entire mitochondrial genome (mtDNA) was amplified using three overlapping long PCR fragments using TaKaRa LA Taq (TaKaRa Biomedicals), with each reaction containing 25ng of genomic DNA. The three primers sets are described in the Affymetrix MitoChip v2.0 supporting documentation (GeneChip Human Mitochondrial Resequencing Array 2.0  Supporting Documentation). After target amplification, PCR products were purified using a High Pure PCR Product Purification Kit (Roche, Germany). PCRs were pooled, fragmented and end labelled according to Affymetrix GeneChip CustomSeq Resequenciong protocol  (fragmentation and labeling enzymes and reagents were part of the Affymetrix GeneChip Resequencing Reagent Kit).

growth_protocol: Eight fibroblasts cells recruited from patients with suspected metabolic diseases stored in liquid nitrogen at cell banks, Mater Adult Hospital (MHS), were recovered and cultured. Confluent fibroblast cell lines were received from the cell bank in 25cm2 NUNC vented flasks (Invitrogen). All fibroblast cell lines were genotyped for ITPA two common mutations (94C>A and IVS2+21 A>C), for analysis independent of this project. Ethics approval for the study was gained from the Matar Hospital. To maintain fibroblast cell cultures a complete media was used which contained: RPMI- 1640, without L-glutamine (Gibco BRL, Invitrogen, Australia), 10% foetal calf/bovine serum (FCS) (Gibco BRL, Australia), 100U/ml Penicillin, 100µg/ml Streptomycin, and 0.3g/ml L- glutamine (Invitrogen).  Blood and bone marrow samples were extracted fresh and no growth conditions applied.

extract_protocol: Total DNA was extracted using a QIAamp DNA blood mini kit (Qiagen, Valencia, CA), the extractions performed according to the manufacturer's instructions.

treatment_protocol: Only three cells lines (Mt DNA 2, Mt DNA 4 and MtDNA 6) were manipulated, beyond described growth conditions. Cell lines were incubated with ITPA siRNA, to block metabolism of rogue nucleotides such as dITP and dXTP. Cellular DNA then was extracted after a 96h incubation period to give time for rogue nucleotides to accumulate. DNA was analysed alongside the other 13 samples.

value: Peripheral blood


title: LR_S10-14 LR_SAL_Lsal_S10ppt_Cop_Trial2

value: reference


title: 6334167042_J.AVG_Signal


title: 6334167042_B.AVG_Signal

source_name: Proliferation

value: KSFM + 5 ng/ml EGF + 50 ug/ml bovine pituitary extract media without retinoic acid


title: 6334167042_C.AVG_Signal


title: 6334167042_H.AVG_Signal


title: 6334167042_I.AVG_Signal


title: Mt DNA 13


title: HEK293T Shigella infected rep2

city: Toronto

first: Stephen

last: Girardin

address: 1, King's College Circle

institute: University of Toronto

data_processing:
CEL data was processed with Affymetrix Power Tools (as part of AltAnalyze workflow)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
RMA normalized probe set expression using APT/AltAnalyze

label_protocol: Protocols were done as per The Ambion WT Expression Kit manual and WT Terminal Labeling Kit (Affymetrix) and were performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.

growth_protocol: HEK293T cells were grown in standard tissue culture (DMEM + 5% FBS, pen/strep)

extract_protocol: Cells were scraped in cold PBS and were extracted in Trizol.

treatment_protocol: Shigella infection was done with S. flexneri M90T and a 20 minute room temperature incubation followed by 4 hours of gentamicin medium. Rapamycin treatment was done with similar media and wash steps, but used 50 ug/mL final concentration

value: Shigella infected


title: Mt DNA 15


title: JF_A2_THP-1_PAM

first: Antonina

last: Risitano

address: 700 Albany St.

department: Whitaker Cardiovascular Institute

institute: Boston University School of Medicine

description: THP-1 gene expression analysis in activated conditions

hyb_protocol: After fragmentation 10 ug of aRNA was hybridized to Affymetrix GeneChip Human Genome U133 2.0 Array for 16 h at 45C in GeneChip Hybridization oven 640. The hybridized samples were washed and stained using Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin and the signal was amplified using a biotinilated goat anti-streptavidin antibody followed by another SAPE staining (Affymetrix).

scan_protocol: Microarrays were immediately scanned using Affimetrix GeneArray Scanner 3000 7G Plus.

data_processing: Expression estimates were derived from resulting CEL files using RMA algorithm as implemented in the affy package (version 1.28.1) for Bioconductor (version 2.7) in the R language for statistical computing (version 2.12.0).

source_name: THP-1_Pam activated

label_protocol: Biotin-labeled amplified RNA (aRNA) was purified using RNA binding beads according to Affymetrix directions .

extract_protocol: Total RNA was isolated using QIAGEN RNeasy kit according to the manufacturer protocol.

value: acute monocytic leukemia


title: Mt DNA 10


title: KRAS-mutant case 7 (non tumor)

city: Kiel

first: Christoph

last: Röcken

address: Arnold-Heller-Str. 3/14

department: Pathology

country: Germany

institute: Christian-Albrechts-University Kiel

description: KRAS-mutant colon cancer case # 7 (non tumor)

hyb_protocol: according to the manufacturer`s recommendations

data_processing: Data Mining Tool 3.0 (Affymetrix) and GeneSpring software package 7.2 (Silicon Genetics, Redwood City, CA)

source_name: nonneoplastic colon mucosa

growth_protocol: not applicable

extract_protocol: Total RNA of normal and CRC tissue was isolated using the mirVana miRNA Isolation Kit (Ambion/ Applied Biosystems, Darmstadt, Germany) according to the manufacturer’s instruction. To digest DNA, the samples were treated with DNAse of the Turbo DNA-free kit (Ambion). RNA quality was assessed in a 1.5% agarose gel and concentrations of the samples were measured in a NanoDrop 2000 (Thermo Fisher Scientific, Waltham, USA). RNAs were stored at -80°C.

treatment_protocol: fresh frozen

value: KRAS-mutant


title: JF_A3_THP-1_+MP_13

description: THP-1 gene expression analysis after co-cultured for 12 hours with platelet-like particles.

source_name: THP-1+PLPs_12 h


title: KRAS-mutant case 8 (tumor)

description: KRAS-mutant colon cancer case # 8 (tumor)

scan_protocol: according to the manufacturer`s recommendations

source_name: colon cancer


title: HEK293T Shigella infected rep1

hyb_protocol: performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.


title: JF_A4_THP-1_+MP_25

description: THP-1 gene expression analysis after co-cultured for 24 hours with platelet-like particles.

source_name: THP-1+PLPs_24 h


title: Mt DNA 9


title: KRAS-mutant case 8 (non tumor)

description: KRAS-mutant colon cancer case # 8 (non tumor)

label_protocol: according to the manufacturer`s recommendations


title: HEK293T Shigella infected rep3

scan_protocol: performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.


title: HEK293T control rep1

value: control


title: JF_A1_THP-1_CTR

description: THP-1 gene expression analysis in resting conditions


title: 6334167042_A.AVG_Signal


title: Mt DNA 14

value: Bone marrow


title: Mt DNA 12


title: HEK293T Rapamycin treated rep2

value: rapamycin treated


title: KRAS-mutant case 7 (tumor)

description: KRAS-mutant colon cancer case # 7 (tumor)


title: KRAS-mutant case 6 (tumor)

description: KRAS-mutant colon cancer case # 6 (tumor)


title: HEK293T Rapamycin treated rep1


title: KRAS-mutant case 6 (non tumor)

description: KRAS-mutant colon cancer case # 6 (non tumor)


title: Mt DNA 6

description:
Total DNA (nuclear and mitochondrial)
Cells were incubated with ITPA siRNA for 96hrs. Treatment with ITPA siRNA was for an unrelated biological question that was outside the scope of analysis of stretches of N calls. Sample contained at least one stretch of N calls.

value: Fibroblast cells


title: Mt DNA 5


title: KRAS-mutant case 4 (non tumor)

description: KRAS-mutant colon cancer case # 4 (non tumor)


title: KRAS-mutant case 5 (non tumor)

description: KRAS-mutant colon cancer case # 5 (non tumor)


title: KRAS-mutant case 5 (tumor)

description: KRAS-mutant colon cancer case # 5 (tumor)


title: HEK293T Rapamycin treated rep3


title: Mt DNA 3


title: Mt DNA 7


title: KRAS-mutant case 3 (tumor)

description: KRAS-mutant colon cancer case # 3 (tumor)


title: Mt DNA 2

value: Cells were incubated with ITPA siRNA for 96hrs. Treatment with ITPA siRNA was for an unrelated biological question that was outside the scope of analysis of stretches of N calls.


title: HEK293T control rep2


title: KRAS-mutant case 4 (tumor)

description: KRAS-mutant colon cancer case # 4 (tumor)


title: Mt DNA 1

description:
Total DNA (nuclear and mitochondrial)
Sample contained at least one stretch of N calls.


title: KRAS-mutant case 2 (non tumor)

description: KRAS-mutant colon cancer case # 2 (non tumor)


title: KRAS-mutant case 3 (non tumor)

description: KRAS-mutant colon cancer case # 3 (non tumor)


title: KRAS-mutant case 1 (non tumor)

description: KRAS-mutant colon cancer case # 1 (non tumor)


title: KRAS-mutant case 2 (tumor)

description: KRAS-mutant colon cancer case # 2 (tumor)


title: KRAS-mutant case 1 (tumor)

description: KRAS-mutant colon cancer case # 1 (tumor)


title: KRAS-wildtype case 8 (non tumor)

description: KRAS-wildtype colon cancer case # 8 (non tumor)

value: KRAS-wildtype


title: KRAS-wildtype case 7 (non tumor)

description: KRAS-wildtype colon cancer case # 7 (non tumor)


title: GAS_DIS_GC_jnu 24

city: Busan

first: Chae Hwa

last: Kwon

address: 1-10 Ami-Dong, Seo-Gu

country: South Korea

institute: Cancer Research Institue, Pusan National University

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 4 of the Illumina HT-12 expression beadChip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47323 probes on the HumanHT-12 beadChip ver. 4 were used.

label: Biotin

source_name: Primary gastric cancer

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol.

tag: gender

value: Male

tag: age (yrs)

tag: diagnosis

value: gastric cancer

tag: tissue type

value: primary gastric adenocarcinoma


title: KRAS-wildtype case 7 (tumor)

description: KRAS-wildtype colon cancer case # 7 (tumor)


title: GAS_DIS_GC_jnu 29

value: Female


title: GAS_DIS_GC_jnu 16


title: KRAS-wildtype case 8 (tumor)

description: KRAS-wildtype colon cancer case # 8 (tumor)


title: liver_1.0% phloridzin diet_rep6

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from liver after 14 day feeding of 1.0% phloridzin diet

hyb_protocol: Fragmented biotin-labeled cRNA was synthesized from the total RNA of each mouse using One-Cycle Target Labeling and Control Reagents (Affymetrix Japan KK, Tokyo, Japan) and then hybridized to an array (Mouse Genome 430 2.0 array; Affymetrix) at 45°C for 16 hours.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method..

source_name: liver, fed 1% phloridzin diet for 14 days

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

growth_protocol: Six-week-old male BALB/c mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

extract_protocol: After 14 days, the mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: We decided the dose levels of phloridzin as 0.1, 0.5 and 1% of diet. The mice were then divided into 4 groups of 6 mice each, housed in groups of 3 per cage, and fed a standard purified AIN-93G diet (Oriental Yeast Co.) containing 0%, 0.1%, 0.5%, or 1% phloridzin (purity > 97%, Funakoshi Ltd., Tokyo, Japan) for 2 weeks. All mice had access to food and water ad libitum during the experimental period.

value: male

tag: strain

value: BALB/c

tag: tissue

value: liver

tag: age

value: six-week-old


title: GAS_DIS_GC_jnu 23


title: liver_1.0% phloridzin diet_rep4


title: GAS_DIS_GC_jnu 6


title: KRAS-wildtype case 6 (non tumor)

description: KRAS-wildtype colon cancer case # 6 (non tumor)

tag: genotype/variation


title: GAS_DIS_GC_jnu 25


title: GAS_DIS_GC_jnu 14


title: GAS_DIS_GC_jnu 19


title: GAS_DIS_GC_jnu 4


title: liver_1.0% phloridzin diet_rep5


title: GAS_DIS_GC_jnu 3


title: KRAS-wildtype case 6 (tumor)

description: KRAS-wildtype colon cancer case # 6 (tumor)


title: KRAS-wildtype case 5 (non tumor)

description: KRAS-wildtype colon cancer case # 5 (non tumor)


title: liver_1.0% phloridzin diet_rep3


title: GAS_DIS_GC_pnu 35


title: GAS_DIS_GC_jnu 5


title: liver_1.0% phloridzin diet_rep2


title: GAS_DIS_GC_jnu 2


title: GAS_DIS_GC_jnu 1


title: GAS_DIS_GC_pnu 31


title: GAS_DIS_GC_pnu 26


title: GAS_DIS_GC_pnu 22


title: KRAS-wildtype case 5 (tumor)

description: KRAS-wildtype colon cancer case # 5 (tumor)


title: KRAS-wildtype case 4 (tumor)

description: KRAS-wildtype colon cancer case # 4 (tumor)


title: KRAS-wildtype case 3 (non tumor)

description: KRAS-wildtype colon cancer case # 3 (non tumor)


title: GAS_DIS_GC_pnu 23


title: liver_0.5% phloridzin diet_rep5

description: Gene expression data from liver after 14 day feeding of 0.5% phloridzin diet

source_name: liver, fed 0.5% phloridzin diet for 14 days


title: liver_0.5% phloridzin diet_rep6


title: GAS_DIS_GC_pnu 20


title: GAS_DIS_GC_pnu 32


title: KRAS-wildtype case 4 (non tumor)

description: KRAS-wildtype colon cancer case # 4 (non tumor)


title: Mt DNA 11

description:
Total DNA (nuclear and mitochondrial)
Sample contained at least one stretch of N calls.

value: Peripheral blood


title: GAS_DIS_GC_pnu 18


title: KRAS-wildtype case 2 (tumor)

description: KRAS-wildtype colon cancer case # 2 (tumor)


title: GAS_DIS_GC_jnu 28


title: liver_0.5% phloridzin diet_rep4


title: GAS_DIS_GC_pnu 1


title: GAS_DIS_GC_jnu 37


title: KRAS-wildtype case 2 (non tumor)

description: KRAS-wildtype colon cancer case # 2 (non tumor)


title: liver_0.5% phloridzin diet_rep3


title: Mt DNA 8


title: KRAS-wildtype case 1 (non tumor)

description: KRAS-wildtype colon cancer case # 1 (non tumor)


title: GAS_DIS_GC_pnu 14


title: GAS_DIS_GC_jnu 27


title: GAS_DIS_GC_pnu 29


title: liver_0.5% phloridzin diet_rep2


title: liver_0.1% phloridzin diet_rep6

description: Gene expression data from liver after 14 day feeding of 0.1% phloridzin diet

source_name: liver, fed 0.1% phloridzin diet for 14 days


title: GAS_DIS_GC_pnu 17


title: GAS_DIS_GC_jnu 22


title: Monocyte_obese_rep9

city: Leuven

first: Paul

last: Holvoet

address: Herestraat 49, PB 705

department: Department of Cardiovascular Diseases

country: Belgium

hyb_protocol: The hybridization was performed according to the miRCURY LNA array manual using a Tecan HS4800 hybridization station.

scan_protocol: The microarray slides were scanned using the Agilent G2565BA Microarray Scanner System and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery).

data_processing: The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global LOWESS (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Human, CD14+ monocytes, obese

label_protocol: 600 ng total RNA from sample and reference pool was labelled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labelling kit (Exiqon).

growth_protocol: Blood samples were collected and after removal of the plasma fraction, peripheral blood mononuclear cells (PBMCs) were isolated using gradient separation on Histopaque-1077. CD14+ monocytes were isolated from the PBMC fraction using CD14 immunomagnetic beads (Miltenyi).

extract_protocol: Total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Qiagen miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: female

tag: cell type

value: CD14+ monocytes

tag: disease state

value: obese

value: lean-obese

source_name: Human, CD14+ monocytes, lean-obese reference pool


title: KRAS-wildtype case 3 (tumor)

description: KRAS-wildtype colon cancer case # 3 (tumor)


title: GAS_DIS_GC_jnu 31


title: liver_0.5% phloridzin diet_rep1


title: Mt DNA 4

description:
Total DNA (nuclear and mitochondrial)
Cells were incubated with ITPA siRNA for 96hrs. Treatment with ITPA siRNA was for an unrelated biological question that was outside the scope of analysis of stretches of N calls. Sample contained at least one stretch of N calls.


title: liver_0.1% phloridzin diet_rep5


title: KRAS-wildtype case 1 (tumor)

description: KRAS-wildtype colon cancer case # 1 (tumor)


title: Monocyte_obese_rep8


title: Monocyte_obese_rep7


title: liver_0.1% phloridzin diet_rep3


title: GAS_DIS_GC_jnu 21


title: GAS_DIS_GC_jnu 17


title: Monocyte_obese_rep5


title: ZNF overexpression - SCp2_4

city: San Francisco

first: Laurie

last: Littlepage

state: CA

address: 513 Parnassus Avenue, Box 0452

department: Anatomy

institute: University of California, San Francisco

hyb_protocol: Hybridize at 65°C for 14 to 18 hours.

scan_protocol: Axon Instruments (V1.00) AxImageIO, GenePix 4000B

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

source_name: Vector

label_protocol: Ambion MessageAmp II Amino Allyl kit

extract_protocol: Qiagen RNeasy kit

tag: expression

value: vector control

value: ZNF217 overexpression


title: liver_0.1% phloridzin diet_rep1


title: GAS_DIS_GC_pnu 41


title: GAS_DIS_GC_pnu 40


title: liver_0.1% phloridzin diet_rep4


title: ZNF overexpression - SCp2_5

tag: cell line


title: liver_0.1% phloridzin diet_rep2


title: liver_1.0% phloridzin diet_rep1

description: Gene expression data from liver after 14 day feeding of 1.0% phloridzin diet


title: Monocyte_obese_rep4


title: ZNF overexpression - SCp2_1


title: GAS_DIS_GC_pnu 37


title: Monocyte_obese_rep3


title: liver_control diet_rep6

description: Gene expression data from liver after 14 day feeding of control AIN93G diet

source_name: liver, fed control AIN93G diet for 14 days


title: liver_control diet_rep5


title: Monocyte_obese_rep6


title: Monocyte_obese_rep2


title: Monocyte_obese_rep1


title: GAS_DIS_GC_jnu 15


title: Monocyte_lean_rep6

source_name: Human, CD14+ monocytes, lean

value: lean


title: GAS_DIS_GC_pnu 36


title: liver_control diet_rep4


title: liver_control diet_rep3


title: GAS_DIS_GC_pnu 27


title: Monocyte_lean_rep5


title: ZNF overexpression - Primary_2

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

value: primary mammary epithelial cells


title: ZNF overexpression - SCp2_2


title: liver_control diet_rep1


title: ZNF overexpression - Primary_3


title: GAS_DIS_GC_pnu 34


title: 131I_spleen_0kBq_24h

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

institute: University of Gothenburg

data_processing: The data were normalized using quantile normalization with BASE

source_name: Mouse spleen, 0kBq, 24h

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: Balb/c

value: spleen

tag: injected activity


title: 131I_spleen_260kBq_24h

source_name: Mouse spleen, 260kBq, 24h


title: Monocyte_lean_rep4


title: GAS_DIS_GC_pnu 21

value: gastric cancer

value: primary gastric adenocarcinoma


title: Monocyte_lean_rep3


title: GAS_DIS_GC_pnu 3

value: Male


title: ZNF overexpression - Primary_1


title: Liver_Keap1 KD_rep3.

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

description:
Agilent Feature Extraction file: Liver_Keap1 KD_rep3.txt
Gene expression in the liver of  Keap1 KD mice_rep3.

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Agilent Feature Extraction Software

source_name: liver, Keap1 knockdown, Keap1(Kd/-)

label_protocol: 500 ng of total RNA was amplified and labeled using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from liver tissues using Isogen (Nippon Gene).

value: Mixed

value: Keap1 KD

value: Female

value: Liver


title: Liver_Keap1 KD_rep2.

description:
Agilent Feature Extraction file: Liver_Keap1 KD_rep2.txt
Gene expression in the liver of  Keap1 KD mice_rep2.


title: 131I_spleen_13kBq_24h

source_name: Mouse spleen, 13kBq, 24h


title: 131I_lung_0kBq_24h

source_name: Mouse lung, 0kBq, 24h

value: lung


title: Monocyte_lean_rep2

value: female

value: CD14+ monocytes


title: GAS_DIS_GC_jnu 32


title: GAS_DIS_GC_jnu 30


title: Liver_Keap1 Control_rep2.

description:
Agilent Feature Extraction file: Liver_Keap1 Control_rep2.txt
Gene expression in the liver of  Keap1 Control mice_rep2.

source_name: liver, genetic control, Keap1(Kd/+)

value: Keap1 Control


title: liver_control diet_rep2

value: male

value: BALB/c

value: liver

value: six-week-old


title: GAS_DIS_GC_pnu 25


title: GAS_DIS_GC_pnu 28


title: 131I_lung_130kBq_24h

source_name: Mouse lung, 130kBq, 24h

value: Balb/c


title: Monocyte_lean_rep1

value: lean

value: lean-obese


title: GAS_DIS_GC_pnu 11

value: gastric cancer

value: primary gastric adenocarcinoma


title: SA3502 (ΔsgmT mutant) experiment 3

city: Marburg

first: Anke

middle: U

last: Treuner-Lange

state: Hessen

address: Karl von Frisch-Str. 10

department: Ecophysiology

institute: Max-Planck Institute for terrestrial Microbiology

description: standard protocol

hyb_protocol: protocol see: Mueller, F.-D., and J.S. Jakobsen. 2008. Myxococcus xanthus: Expression analysis, p.479-489. In Whitworth, D.E. (ed.), Myxobacteria: Multicellularity and Differentiation, ASM Press, Washington, DC

scan_protocol: GenePix 6.0

data_processing: spot finding algorithm GenePix 6.0; ratio-normalized (mean ratio of medians =1); Signal to noise ratio in ch1 or ch2 at least >2; F532median-B532>=400 or F635Median-B635>=400; Fail=1, Flags>=0

organism: Myxococcus xanthus

source_name: vegetative cells of SA3502 (ΔsgmT mutant)

growth_protocol: Standard protocol

treatment_protocol: Standard protocol

value: vegetative steady-state cells

value: SA3502 (ΔsgmT mutant)

source_name: vegetative cells DK1622 (wt)


title: SA3502 (ΔsgmT mutant) experiment 2

description: standard protocol

label_protocol: protocol see: Mueller, F.-D., and J.S. Jakobsen. 2008. Myxococcus xanthus: Expression analysis, p.479-489. In Whitworth, D.E. (ed.), Myxobacteria: Multicellularity and Differentiation, ASM Press, Washington, DC


title: Liver_Keap1 Control_rep1.

description:
Agilent Feature Extraction file: Liver_Keap1 Control_rep1.txt
Gene expression in the liver of  Keap1 Control mice_rep1.

value: Mixed

value: Female


title: Liver_Nrf2 KO_rep2.

description:
Agilent Feature Extraction file: Liver_Nrf2 KO_rep2.txt
Gene expression in the liver of  Nrf2 KO mice_rep2.

source_name: liver, Nrf2 knockout, Nrf2(-/-)

value: Nrf2 KO

value: Liver


title: SA3502 (ΔsgmT mutant) experiment 1

description: standard protocol

extract_protocol: protocol see: Mueller, F.-D., and J.S. Jakobsen. 2008. Myxococcus xanthus: Expression analysis, p.479-489. In Whitworth, D.E. (ed.), Myxobacteria: Multicellularity and Differentiation, ASM Press, Washington, DC

value: SA3502 (delta-sgmT mutant)


title: GAS_DIS_GC_jnu 36

source_name: Primary gastric cancer

value: Male


title: SA1804 (ΔdigR mutant) experiment 3

description: standard protocol

source_name: vegetative cells of SA1804 (ΔdigR mutant)

value: SA1804 (ΔdigR mutant)


title: Liver_Nrf2 KO_rep3.

description:
Agilent Feature Extraction file: Liver_Nrf2 KO_rep3.txt
Gene expression in the liver of  Nrf2 KO mice_rep3.


title: Liver_Keap1 Control_rep3.

description:
Agilent Feature Extraction file: Liver_Keap1 Control_rep3.txt
Gene expression in the liver of  Keap1 Control mice_rep3.

value: Keap1 Control


title: 131I_lung_260kBq_24h

source_name: Mouse lung, 260kBq, 24h

value: lung


title: 131I_lung_13kBq_24h

source_name: Mouse lung, 13kBq, 24h


title: 131I_liver_260kBq_24h

source_name: Mouse liver, 260kBq, 24h

value: liver


title: GAS_DIS_GC_pnu 5


title: 131I_liver_130kBq_24h

source_name: Mouse liver, 130kBq, 24h

value: Balb/c


title: 131I_liver_13kBq_24h

source_name: Mouse liver, 13kBq, 24h


title: Liver_Nrf2 KO_rep1.

description:
Agilent Feature Extraction file: Liver_Nrf2 KO_rep1.txt
Gene expression in the liver of  Nrf2 KO mice_rep1.


title: 131I_liver_0kBq_24h

source_name: Mouse liver, 0kBq, 24h


title: Liver_Nrf2 Control_rep3.

description:
Agilent Feature Extraction file: Liver_Nrf2 Control_rep3.txt
Gene expression in the liver of  Nrf2 Control mice_rep3.

source_name: liver, genetic control, Nrf2(+/+)

value: Nrf2 Control


title: Liver_Keap1 KD_rep1.

description:
Agilent Feature Extraction file: Liver_Keap1 KD_rep1.txt
Gene expression in the liver of  Keap1 KD mice_rep1.

source_name: liver, Keap1 knockdown, Keap1(Kd/-)

value: Keap1 KD


title: KIN_DMSO_20h_Sendai_3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
Description of analysis: For the creation of the normalized data, the limma package was used. Background correction was performed (method="normexp", offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Total RNA isolation and mRNA amplification were performed on equal masses of total RNA from MRC5 cells treated with either DMSO (negative control; n=3), or 10μM of the isoflavone agonist KIN 101 (n=3) at 20 hours post treatment. As a positive control for response to an RNA virus, total RNA isolation and mRNA amplification was performed on equal masses of total RNA from MRC5 cells infected with Sendai virus (n=3) at 20 hours post infection.

extract_protocol: Total RNA was isolated from the aqueous phase of the trizol homogenates using Qiagen microRNAsy kits according to the manufacturer's instructions.

treatment_protocol: Samples from individual replicates were prepared as TRIZol homogenates and stored at -80degrees C prior to RNA extraction.

value: Sendai virus

tag: replicate number

tag: sample collection time


title: SA1804 (ΔdigR mutant) experiment 1

description: standard protocol


title: SA1804 (ΔdigR mutant) experiment 2

description: standard protocol


title: KIN_DMSO_20h_Sendai_2


title: KIN_DMSO_20h_Sendai_1


title: Liver_Nrf1 CKO_rep3.

description:
Agilent Feature Extraction file: Liver_Nrf1 CKO_rep3.txt
Gene expression in the liver of  Nrf1 CKO mice_rep3.

source_name: liver, conditional Nrf1 knockout, Nrf1(dN/-)::Alb-Cre

value: Nrf1 CKO


title: Liver_Nrf2 Control_rep2.

description:
Agilent Feature Extraction file: Liver_Nrf2 Control_rep2.txt
Gene expression in the liver of  Nrf2 Control mice_rep2.


title: 131I_cortex_130kBq_24h

source_name: Mouse kidney cortex, 130kBq, 24h

value: kidney cortex


title: KIN_DMSO_20h_Mock_3

value: DMSO


title: Liver_Nrf2 Control_rep1.

description:
Agilent Feature Extraction file: Liver_Nrf2 Control_rep1.txt
Gene expression in the liver of  Nrf2 Control mice_rep1.


title: Liver_Nrf1 CKO_rep2.

description:
Agilent Feature Extraction file: Liver_Nrf1 CKO_rep2.txt
Gene expression in the liver of  Nrf1 CKO mice_rep2.

value: Mixed


title: Liver_Nrf1 Control_rep3.

description:
Agilent Feature Extraction file: Liver_Nrf1 Control_rep3.txt
Gene expression in the liver of  Nrf1 Control mice_rep3.

source_name: liver, genetic control, Nrf1(dN/+)

value: Nrf1 Control

value: Female


title: Liver_Nrf1 CKO_rep1.

description:
Agilent Feature Extraction file: Liver_Nrf1 CKO_rep1.txt
Gene expression in the liver of  Nrf1 CKO mice_rep1.

value: Liver


title: KIN_DMSO_20h_Mock_1


title: DK4398 (asgB mutant), Exp.1

first: Lotte

last: Sogaard-Andersen

address: Karl-von-Frisch-Str.

institute: Max Planck Institute for Terrestrial Microbiology

description: standard protocol

hyb_protocol: protocol see Mueller, F-D., and J.S. Jakobsen. 2008. Myxococcus xanthus: Expression Analysis, p. 479-489. In Whitworth, D.E. (ed.), Myxobacteria: Multicellularity and Differentiation, ASM Press, Washington, DC

data_processing: spot finding algorithm GenePix 6.0; ratio-normalized (mean ratio of medians = 1); Signal to noise ratio in ch1 or ch2 at least >2; F532median-B532>=400 or F635Median-B635>=400; Fail=1; Flags>= 0

source_name: vegetative cells DK4398 (asgB mutant)

value: vegetative

value: DK4398 (asgB mutant)


title: Chr8-1

city: Taipei

first: Jun-Yi

last: Leu

address: 128 Academia Road, Section 2, Nankang

department: Insititute of Molecular Biolody

country: Taiwan

institute: Academia Sinica

description: Analysing of Chromosome VIII of EC-C1 strains (S. cerevisiae)

hyb_protocol: The hybridization protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

scan_protocol: Scanned on an Molecular Device AXON 4000B (version GenePix 6.0) and got .gpr files

data_processing: Subtracted background  (no normalization) . Dividing by ch2 (control) was used to transform data (Agilent GeneSpring 7.3.1 software).

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae haploid evolved cells

label_protocol: The label protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

growth_protocol: Yeast cells were grown in YPD medium, at 30 degree.

extract_protocol: After PFGE, The ChrVIII DNA was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit.

tag: assayed molecule

value: ChrVIII genomic DNA

value: W303 diploid strain (JYL1127 X JYL1128)

value: total genomic DNA


title: 131I_cortex_260kBq_24h

source_name: Mouse kidney cortex, 260kBq, 24h


title: DK4398 (asgB mutant), Exp.3

description: standard protocol

label_protocol: protocol see Mueller, F-D., and J.S. Jakobsen. 2008. Myxococcus xanthus: Expression Analysis, p. 479-489. In Whitworth, D.E. (ed.), Myxobacteria: Multicellularity and Differentiation, ASM Press, Washington, DC

source_name: vegetative cells DK1622 (wt)


title: 131I_cortex_0kBq_24h

source_name: Mouse kidney cortex, 0kBq, 24h


title: DK4398 (asgB mutant), Exp.2

description: standard protocol

extract_protocol: protocol see Mueller, F-D., and J.S. Jakobsen. 2008. Myxococcus xanthus: Expression Analysis, p. 479-489. In Whitworth, D.E. (ed.), Myxobacteria: Multicellularity and Differentiation, ASM Press, Washington, DC


title: KIN_101_20h_Mock_3

tag: treatment

value: kin 101


title: DK5057 (asgA mutant), Exp.3

description: standard protocol

source_name: vegetative cells DK5057 (asgA mutant)

value: DK5057 (asgA mutant)


title: ZNF overexpression - SCp2_3

source_name: Vector

value: vector control

value: ZNF217 overexpression


title: 131I_cortex_13kBq_24h

source_name: Mouse kidney cortex, 13kBq, 24h

value: Balb/c


title: 131I_medulla_0kBq_24h

source_name: Mouse kidney medulla, 0kBq, 24h

value: kidney medulla


title: DK5057 (asgA mutant), Exp.2

description: standard protocol


title: 131I_medulla_130kBq_24h

source_name: Mouse kidney medulla, 130kBq, 24h


title: Liver_Nrf1 Control_rep1.

description:
Agilent Feature Extraction file: Liver_Nrf1 Control_rep1.txt
Gene expression in the liver of  Nrf1 Control mice_rep1.

tag: gender


title: KIN_101_20h_Mock_1


title: KIN_DMSO_20h_Mock_2


title: Liver_Nrf1 Control_rep2.

description:
Agilent Feature Extraction file: Liver_Nrf1 Control_rep2.txt
Gene expression in the liver of  Nrf1 Control mice_rep2.


title: 131I_medulla_260kBq_24h

source_name: Mouse kidney medulla, 260kBq, 24h


title: KIN_101_20h_Mock_2


title: DK5057 (asgA mutant), Exp.1

description: standard protocol


title: T2-FP_spleen_KO_rep3

status: Public on May 17 2012

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

country: Italy

institute: San Raffaele Scientific Institute

hyb_protocol: Hybridization on Mouse WG 6 v2 expression arrays (Illumina) was carried out according to the manufacturer’s instructions

scan_protocol: Scanning was carried out according to the manufacturer’s instructions

data_processing:
Data were normalized and analyzed using Illumina Beadstudio 3.1.3 (background correction and quantile normalization)
Expression profiles of each sample were imported into GeneSpringGX 7.3.1 (Agilent Technologies, USA).
In addition to expression values, Illumina BeadStudio software computes a detection p-value. Based on this, each probe was assigned a detection flag (P (present): p < 0.045; M (Marginal): p between 0.050 and 0.045, A (Absent): p>0.05). Expression values below a defined threshold (i.e. 20) are set to the threshold in order to remove negative values after background correction. To identify dysregulated genes in KO mice, t-test and/or ANOVA and additional steps of filtering were carried out.

source_name: spleen

label_protocol: 100 ng of RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion)

extract_protocol: 8-12 weeks old mouse splenocytes from 3 KO and 3 littermate control C57/bl6-129sv mice were sorted by flow cytometry on the basis of IgM, IgD, CD21 and CD23 expression: T2-FP= IgMhiIgDhiCD21intCD23pos; FO=IgMlowIgDhiCD21intCD23pos. T2-FP and FO cell RNA was extracted by MirVana kit (Ambion) and treated with DNAse (Turbo DNA free kit, Ambion), following manufacturer instructions. Quality control for RNA integrity was performed by capillary electrophoresis on Agilent 2100 Bioanalyzer,

value: Transcriptional 2 Follicular Progenitor (T2-FP) B cells

value: 8-12 weeks

value: KAP1 KO


title: T2-FP_spleen_KO_rep1


title: 131I_medulla_13kBq_24h

source_name: Mouse kidney medulla, 13kBq, 24h


title: FO_spleen_KO_rep1

value: Follicular (FO) B cells


title: FO_spleen_KO_rep3


title: FO_spleen_wt_rep1

value: WT


title: T2-FP_spleen_wt_rep1


title: FO_spleen_KO_rep2


title: T2-FP_spleen_KO_rep2


title: FO_spleen_wt_rep3


title: FO_spleen_wt_rep2


title: T2-FP_spleen_wt_rep3


title: T2-FP_spleen_wt_rep2


title: 131I_spleen_130kBq_24h

source_name: Mouse spleen, 130kBq, 24h

value: spleen


title: tumor  46

city: Chapel Hill

first: Matthew

middle: D

last: Wilkerson

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

hyb_protocol: Followed Affymetrix instructions.

scan_protocol: Arrays were scanned using the Affmetrix Gene Chip Scanner.

data_processing: For SNP6 and 250K_Sty platforms separately, probe intensities were processed using CRMAv2 (Bengtsson, et al. PMID: 19535535), converted to log2 values, sample-wise median centered, and divided by the mean of normal samples to make CN values.  CN values were smoothed by circular binary segmentation, sample-wise median centered using autosomes. Finally, CN values were standardized by dividing each sample by its standard deviation. Sex chromosomes were not used in final analysis, so these probesets have NULL for all samples.  SNP6 data were subjected to a within-sample outlier removal process (TCGA Research Network, PMID: 21720365), and struck probesets have 'NULL' values.

source_name: lung adenocarcinoma

label_protocol: Followed Affymetrix instructions.

extract_protocol: DNA was extracted using Qiagen’s QIAamp DNA minikit.

value: lung

value: adenocarcinoma


title: tumor  49


title: tumor  45


title: tumor  11


title: normal 4 [MSNP]

data_processing:
The DNA specimens in this dataset were additionally digested by HpaII restriction enzyme, which is methylation sensitive. These samples were concurrently analyzed with their StyI-only digested counterpart, which are contained in GSE36363 identified with the same Sample Name [see 'Affiliated with' link below]. All CEL files were processed by CRMAv2 (Bengtsson, et al. PMID: 19535535) and sample-wise median centered using control probes (those in a fragment without a HpaII binding site). For probes in fragments having a HpaII binding site, methylation values were calculated using the StyI-only digestion and the StyI+HpaII digestion arrays for each sample. The methylation normalized values were calculated as (StyI - StyI+HpaII)/StyI to give a relative estimate of methylation percentage. These values are given in the data table below.
Note that methylation values are given only for 'methylation sensitive' probesets that measure DNA fragments with a HpaII binding site - those that are methylation sensitive. Methylation sensitive probesets were identified by searching for the HpaII binding site in the StyI digested DNA. For more information on probeset classification, see Yuan et al. (PMID: 16585166). Control site probes have null values in the data table below.

source_name: normal lung

extract_protocol: DNA was extracted using Qiagen’s QIAamp DNA minikit and Affymetrix DNA prep instructions using the StyI restriction enzyme digestion. These samples were then additionally digested by HpaII, a methylation sensitive restriction enzyme, following the MSNP protocol (Yuan et al, PMID: 16585166).

value: normal


title: tumor  31


title: normal 5 [MSNP]


title: tumor 110 [MSNP]


title: tumor 109 [MSNP]


title: normal 6 [MSNP]


title: normal 1 [MSNP]


title: normal 8 [MSNP]


title: normal 20 [MSNP]


title: tumor 112 [MSNP]


title: tumor 114 [MSNP]


title: normal 19 [MSNP]


title: tumor  48


title: tumor  26


title: tumor 106 [MSNP]


title: tumor 99 [MSNP]


title: tumor  14


title: tumor  44


title: tumor 107 [MSNP]


title: tumor 113 [MSNP]


title: tumor 115 [MSNP]


title: tumor  42


title: normal 3 [MSNP]


title: normal 2 [MSNP]


title: normal 7 [MSNP]


title: tumor  47


title: tumor 85 [MSNP]


title: tumor 91 [MSNP]


title: SHPKO_WestD_Lv3

city: Rootstown

first: Yoonkwang

last: Lee

address: 4209 State Route 44

department: Integrative Medical Sciences

institute: Northeast Ohio Medical University

data_processing: The data were normalised using quantile normalisation using Illumina's BeadStudio software.

source_name: mouse liver

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep kit.

growth_protocol: Mouse were fed chow and a western diet for 6 months. The diet regimen started when they were at 4 month old.

extract_protocol: RNA was extracted with  QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed using a 1% agarose gel.

treatment_protocol: Liver samples were collected after overnight fasting.

value: male

value: SHP-/-

tag: diet

value: western

value: 10 months

value: liver


title: tumor 67 [MSNP]


title: tumor 79 [MSNP]


title: WT_WestD_Lv4

value: wild type


title: SHPKO_WestD_Lv2


title: SHPKO_WestD_Lv1


title: SHPKO_WestD_Lv4


title: tumor 87 [MSNP]


title: tumor 66 [MSNP]


title: tumor 78 [MSNP]


title: tumor 63 [MSNP]


title: tumor 98 [MSNP]


title: tumor 64 [MSNP]


title: tumor 84 [MSNP]


title: tumor 56 [MSNP]


title: tumor 80 [MSNP]


title: tumor 96 [MSNP]


title: tumor 65 [MSNP]


title: tumor 74 [MSNP]


title: tumor 62 [MSNP]


title: tumor 71 [MSNP]


title: tumor 88 [MSNP]


title: tumor 54 [MSNP]


title: WT_WestD_Lv3


title: WT_WestD_Lv2


title: tumor 55 [MSNP]


title: SHPKO_Chow_Lv4

value: chow


title: tumor 53 [MSNP]


title: tumor 69 [MSNP]


title: tumor 60 [MSNP]


title: tumor  111 [EXPID7363]

description: tumor  111

hyb_protocol: Microarrays were hybridized in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.

scan_protocol: Microarrays were scanned with Agilent Scanner and intensity was recorded using Agilent Feature Extraction Software.

data_processing: Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma.

source_name: lung adenocarcinoma tumor RNA

label_protocol: The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003 ), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all regents volumes were reduced by one half.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.

treatment_protocol: Not applicable

tag: subtype

value: bronchioid

tag: age (90=greater than or equal to 90)

tag: Sex

value: M

value: Smoker

tag: Stage

value: IA

tag: grade

tag: adenosquamous_content (0='no', 1='yes')

tag: kras (0='wt',1='mutated')

source_name: Stratagene Human Universal Reference

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  114 [EXPID7367]

description: tumor  114

value: F


title: tumor  112 [EXPID7364]

description: tumor  112

value: squamoid


title: tumor  116 [EXPID7373]

description: tumor  116

tag: sex

value: NeverSmoker

tag: stage

value: IB

tag: egfr (0='wt',1='mutated')


title: tumor  110 [EXPID7360]

description: tumor  110

value: IIIA


title: tumor  113 [EXPID7365]

description: tumor  113

value: magnoid


title: normal  20

tag: tissue type

value: lung

tag: cell type

value: normal


title: SHPKO_Chow_Lv2

hyb_protocol: Standard Illumina hybridization protocol

value: male

tag: strain

tag: genotype/variation

value: SHP-/-

tag: age

value: 10 months

tag: tissue


title: WT_WestD_Lv1

tag: gender

value: wild type

tag: diet

value: western

value: liver


title: SHPKO_Chow_Lv3

value: chow


title: normal  19


title: tumor  109 [EXPID7359]

description: tumor  109

tag: subtype

tag: age (90=greater than or equal to 90)

tag: Sex

value: Smoker

value: IIB


title: tumor  107 [EXPID7356]

description: tumor  107

value: F

tag: Stage

tag: grade

tag: adenosquamous_content (0='no', 1='yes')

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  108 [EXPID7358]

description: tumor  108

value: bronchioid

tag: kras (0='wt',1='mutated')

tag: reference


title: tumor  106 [EXPID7354]

description: tumor  106

value: squamoid

value: M

value: IA

tag: egfr (0='wt',1='mutated')


title: tumor  105 [EXPID7348]

description: tumor  105


title: normal  16

tag: tissue type

value: lung


title: normal  17

tag: cell type

value: normal


title: WT_Chow_Lv1

value: male

tag: strain


title: normal  15


title: WT_Chow_Lv3

tag: genotype/variation


title: tumor  100 [EXPID7336]

description: tumor  100

tag: sex

tag: stage


title: tumor  104 [EXPID7345]

description: tumor  104


title: tumor  99 [EXPID7333]

description: tumor  99


title: tumor  103 [EXPID7344]

description: tumor  103


title: tumor  101 [EXPID7339]

description: tumor  101


title: tumor  102 [EXPID7342]

description: tumor  102

value: magnoid


title: tumor  98 [EXPID7328]

description: tumor  98

value: IB


title: WT_Chow_Lv4

tag: gender

value: wild type

tag: age

value: 10 months

tag: tissue


title: tumor  96 [EXPID7326]

description: tumor  96

tag: subtype

tag: age (90=greater than or equal to 90)

value: NeverSmoker


title: tumor  97 [EXPID7327]

description: tumor  97

tag: Sex


title: tumor  94 [EXPID7313]

description: tumor  94

value: IIIA

tag: grade


title: tumor  92 [EXPID7297]

description: tumor  92

value: Smoker

tag: Stage

value: IIA

tag: adenosquamous_content (0='no', 1='yes')


title: normal  12


title: tumor  91 [EXPID7296]

description: tumor  91

value: IIB

tag: kras (0='wt',1='mutated')

tag: reference


title: tumor  90 [EXPID7295]

description: tumor  90

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: normal  9

tag: tissue type


title: tumor  93 [EXPID7303]

description: tumor  93

value: bronchioid

value: F


title: tumor  89 [EXPID7288]

description: tumor  89

value: squamoid


title: normal  11

tag: cell type


title: tumor  88 [EXPID7287]

description: tumor  88


title: normal  13


title: tumor  87 [EXPID7280]

description: tumor  87

tag: egfr (0='wt',1='mutated')


title: tumor  115 [EXPID7368]

description: tumor  115

value: M


title: normal  8

value: lung


title: tumor  86 [EXPID7275]

description: tumor  86


title: normal  7

value: normal


title: tumor  95 [EXPID7316]

description: tumor  95

value: IV


title: normal  14


title: normal  18


title: normal  6


title: tumor  84 [EXPID7269]

description: tumor  84

value: magnoid


title: tumor  83 [EXPID7267]

description: tumor  83

value: IA


title: normal  5


title: normal  4


title: tumor  85 [EXPID7271]

description: tumor  85


title: tumor  81 [EXPID7262]

description: tumor  81

value: IB


title: tumor  78 [EXPID7256]

description: tumor  78


title: tumor  82 [EXPID7264]

description: tumor  82


title: tumor  79 [EXPID7257]

description: tumor  79


title: tumor  80 [EXPID7261]

description: tumor  80


title: WT_Chow_Lv2

value: male

tag: strain

tag: genotype/variation

value: wild type

tag: diet

value: chow

value: 10 months

value: liver


title: SHPKO_Chow_Lv1

tag: gender

value: SHP-/-


title: tumor  76 [EXPID7254]

description: tumor  76

value: Smoker

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  77 [EXPID7255]

description: tumor  77

value: bronchioid


title: tumor  75 [EXPID7253]

description: tumor  75

value: F

value: IIB


title: tumor  72 [EXPID7242]

description: tumor  72

value: M


title: tumor  74 [EXPID7252]

description: tumor  74


title: tumor  73 [EXPID7246]

description: tumor  73

tag: sex

value: NeverSmoker

tag: stage

value: IIIA


title: normal  2

value: lung

value: normal


title: normal  1


title: tumor  115

value: adenocarcinoma


title: tumor  116


title: tumor  71 [EXPID7240]

description: tumor  71

tag: subtype

value: magnoid


title: tumor  70 [EXPID7231]

description: tumor  70

value: squamoid

tag: age (90=greater than or equal to 90)


title: tumor  68 [EXPID7222]

description: tumor  68

tag: Sex

value: IA


title: tumor  69 [EXPID7230]

description: tumor  69

tag: grade


title: tumor  67 [EXPID7220]

description: tumor  67

tag: Stage


title: normal  10


title: tumor  66 [EXPID7217]

description: tumor  66

value: IB

tag: adenosquamous_content (0='no', 1='yes')


title: tumor  114


title: normal  3


title: tumor  64 [EXPID7207]

description: tumor  64

tag: kras (0='wt',1='mutated')


title: tumor  63 [EXPID7201]

description: tumor  63

tag: reference


title: normal  30

tag: tissue type


title: tumor  112

tag: cell type


title: normal  28


title: tumor  113


title: tumor  110


title: tumor  62 [EXPID7199]

description: tumor  62

tag: egfr (0='wt',1='mutated')


title: tumor  109


title: normal  26


title: normal  29


title: tumor  107


title: tumor  58 [EXPID7188]

description: tumor  58


title: normal  25


title: tumor  65 [EXPID7209]

description: tumor  65


title: tumor  60 [EXPID7193]

description: tumor  60


title: tumor  106


title: normal  27


title: tumor  57 [EXPID7184]

description: tumor  57


title: tumor  59 [EXPID7192]

description: tumor  59


title: tumor  56 [EXPID7181]

description: tumor  56


title: tumor  61 [EXPID7194]

description: tumor  61


title: tumor  55 [EXPID7180]

description: tumor  55


title: tumor  54 [EXPID7179]

description: tumor  54


title: tumor  53 [EXPID7178]

description: tumor  53


title: tumor  51 [EXPID20264]

description: tumor  51


title: normal  22


title: tumor  99


title: normal  24


title: tumor  98


title: tumor  108


title: tumor  50 [EXPID18956]

description: tumor  50


title: tumor  111


title: normal  23


title: tumor  101


title: normal  21


title: tumor  49 [EXPID18954]

description: tumor  49


title: tumor  48 [EXPID18953]

description: tumor  48


title: tumor  92


title: tumor  46 [EXPID18950]

description: tumor  46


title: tumor  91


title: tumor  45 [EXPID18949]

description: tumor  45


title: tumor  97


title: tumor  47 [EXPID18952]

description: tumor  47


title: tumor  44 [EXPID18948]

description: tumor  44


title: tumor  100


title: tumor  43 [EXPID10591]

description: tumor  43

value: IIA


title: tumor  96


title: tumor  52 [EXPID7176]

description: tumor  52


title: tumor  42 [EXPID10590]

description: tumor  42


title: tumor  41 [EXPID10589]

description: tumor  41


title: tumor  40 [EXPID10588]

description: tumor  40


title: tumor  95


title: tumor  88


title: tumor  87


title: tumor  38 [EXPID10585]

description: tumor  38


title: tumor  86


title: tumor  37 [EXPID10584]

description: tumor  37


title: tumor  83


title: tumor  36 [EXPID10583]

description: tumor  36


title: tumor  94


title: tumor  85


title: tumor  34 [EXPID10580]

description: tumor  34


title: tumor  39 [EXPID10587]

description: tumor  39


title: tumor  35 [EXPID10581]

description: tumor  35


title: tumor  84


title: tumor  33 [EXPID10576]

description: tumor  33


title: tumor  32 [EXPID10574]

description: tumor  32


title: tumor  89


title: tumor  82


title: tumor  30 [EXPID10569]

description: tumor  30


title: tumor  80


title: tumor  29 [EXPID10567]

description: tumor  29


title: tumor  28 [EXPID10566]

description: tumor  28