title: 5Aza-dC and TSA treated MDA2b

status: Public on Jan 31 2011

type: RNA

city: Philadelphia

first: Ilsiya

last: Ibragimova

state: PA

address: 333 Cottman ave, w350

department: ICR

country: USA

institute: Fox Chase Cancer Center

hyb_protocol: Labelled cDNA hybridised according to the manufacturer’s instructions

scan_protocol: The hybridized slides were scanned using a GMS 428 Scanner (Affymetrix, Santa Clara, CA)

data_processing: Image analysis was performed using the ImaGene software (BioDiscovery, Inc, El Segundo, CA). The spots were identified using an optimized segmentation algorithm. Normalization and background correction were performed using LOWESS with a width of 0.7 and local background correction.

molecule: total RNA

organism: Homo sapiens

label_protocol: cDNA labelled with Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ) according to the manufacturer’s instructions

growth_protocol: Four prostate cancer cell lines were grown at 37C using RPMI medium (LNCaP), F12K medium (PC3 and MDA2b) and MEM medium (DU-145).

extract_protocol: Total RNA was isolated from drug-treated and mock cultured cells using TRIZOL reagent (Invitrogen, Carlsbad, CA)  and purified with the RNAeasy Mini kit (Qiagen, Valencia, CA) combined with DNase treatment.

treatment_protocol: Cells were exposed to 5Aza-dC to a final concentration of 5mM at 0, 24 and 72 hours, over two cell divisions by counting of the cells, and then, treated with TSA to a final concentration of 500nM during the 24 hours before DNA extraction. Mock (untreated) cells were cultured with the equivalent volume of PBS alone and, for the 24 hours before RNA extraction, with the equivalent volume of EtOH.

tag: cell line

tag: strain


title: 5Aza-dC and TSA treated DU-145 Flip


title: 5Aza-dC and TSA treated LNCaP Flip

value: LNCaP


title: 5Aza-dC and TSA treated MDA2b Flip


title: 5Aza-dC and TSA treated PC3


title: 5Aza-dC and TSA treated PC3 Flip


title: HealthyBlood_0Gy_rep1_Ex19

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

description: Gene expression in 0Gy-irradiated healthy human blood

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded.

source_name: Peripheral Blood, 0Gy, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Qucik Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using the PAXgene Blood RNA Kit (Qiagen/BD company, TX) according to manufacturer’s instructions, followed by removal of globin transcripts using the GLOBINclear kit (Ambion Inc., Austin, TX) to remove both a- and b-globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood was collected several hours before the initial fraction of total body irradiation (TBI), then at 4 hr after first 1.25-Gy fraction and at 1 day after the first fraction.  The 1 day samples included exposure to three 1.25-Gy fractions with approximately 4 hr between fractions and received a total exposure of 3.75-Gy. Blood was drawn into PAXgene blood RNA tubes (PreAnalytiX GmbH, USA) and kept at room temperature at least 6 hrs before RNA isolation.

tag: tissue

value: whole blood

tag: gender

value: male

tag: age

value: 41 years

tag: disease status

value: healthy control

tag: treatment group


title: HealthyBlood_0Gy_rep1_Ex8

value: female

value: 30 years


title: HealthyBlood_0Gy_rep1_Ex9

value: 33 years


title: HealthyBlood_0Gy_rep1_Ex16

value: 44 years


title: HealthyBlood_0Gy_rep1_Ex20

value: 34 years


title: 5Aza-dC and TSA treated LNCaP


title: HealthyBlood_0Gy_rep1_Ex14

value: 28 years


title: HealthyBlood_0Gy_rep1_Ex13

value: 26 years


title: HealthyBlood_0Gy_rep1_Ex5

value: 22 years


title: HealthyBlood_0Gy_rep1_Ex3


title: HealthyBlood_0Gy_rep1_Ex1


title: TBI Blood_20hr_3.75Gy_rep1_091

description: Gene expression after 20hr with 3.75Gy-TBI cancer patient blood

source_name: Peripheral Blood, 20hr, 3.75Gy, replicate 1

value: 53 years

value: TBI patient #091


title: HealthyBlood_0Gy_rep1_Ex6

value: 35 years


title: HealthyBlood_0Gy_rep1_Ex7


title: TBI Blood_4hr_1.25Gy_rep1_091

description: Gene expression after 4hr with 1.25Gy-TBI cancer patient blood

source_name: Peripheral Blood, 4hr, 1.25Gy, replicate 1


title: TBI Blood_4hr_1.25Gy_rep1_089

value: 19 years

value: TBI patient #089


title: Pre-TBI Blood_0Gy_rep1_091

description: Gene expression in 0Gy-irradiated cancer patient blood

value: whole blood


title: TBI Blood_20hr_3.75Gy_rep1_071

value: male

value: 50 years

value: TBI patient #071


title: HealthyBlood_0Gy_rep1_Ex4

value: female

value: healthy control


title: TBI Blood_4hr_1.25Gy_rep1_071


title: Pre-TBI Blood_0Gy_rep1_089


title: Pre-TBI Blood_0Gy_rep1_071


title: TBI Blood_4hr_1.25Gy_rep1_057

value: 54 years

value: TBI patient #057


title: transgenic myo-4::his-SUMO-1 JS63_3

city: Kuopio

first: Garry

last: Wong

department: Biosciences

country: Finland

institute: Eastern Finland University

description: transgenic myo-4::his-SUMO-1

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

scan_protocol: GeneChips were scanned using the Affymetrix scanner.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings.

label: biotin

organism: Caenorhabditis elegans

source_name: whole body L1 larvae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were grown on NGM agar plates with OP50 bacteria as food.

extract_protocol: Ambion RiboPure according to the manufactures instructions

treatment_protocol: Animals were synchronized by bleaching and grown to L1 stage

value: whole body

tag: developmental stage

value: L1 larvae

tag: genotype

value: transgenic myo-4::his-SUMO-1


title: TBI Blood_20hr_3.75Gy_rep1_057


title: TBI Blood_4hr_1.25Gy_rep1_055

value: 31 years

value: TBI patient #055


title: transgenic aex-3::his-SUMO-1 JS62_2

description: transgenic aex-3::his-SUMO-1

value: transgenic aex-3::his-SUMO-1


title: Pre-TBI Blood_0Gy_rep1_057


title: transgenic myo-4::his-SUMO-1 JS63_2

description: transgenic myo-4::his-SUMO-1


title: transgenic myo-4::his-SUMO-1 JS63_1

description: transgenic myo-4::his-SUMO-1


title: control wild type N2_3

description: control wild type

value: control wild type


title: Pre-TBI Blood_0Gy_rep1_055


title: TBI Blood_20hr_3.75Gy_rep1_055


title: TBI Blood_20hr_3.75Gy_rep1_051

value: 33 years

value: TBI patient #051


title: transgenic aex-3::his-SUMO-1 JS62_3

description: transgenic aex-3::his-SUMO-1


title: transgenic aex-3::his-SUMO-1 JS62_1

description: transgenic aex-3::his-SUMO-1


title: Pre-TBI Blood_0Gy_rep1_051

value: whole blood


title: TBI Blood_20hr_3.75Gy_rep1_049

value: male

value: 19 years

value: TBI patient #049


title: Pre-TBI Blood_0Gy_rep1_053

value: female

value: TBI patient #053


title: TBI Blood_4hr_1.25Gy_rep1_040

value: 57 years

value: TBI patient #040


title: control wild type N2_2

description: control wild type

value: whole body


title: Pre-TBI Blood_0Gy_rep1_049


title: TBI Blood_4hr_1.25Gy_rep1_053

value: 54 years


title: TBI Blood_20hr_3.75Gy_rep1_040


title: TBI Blood_4hr_1.25Gy_rep1_049


title: TBI Blood_20hr_3.75Gy_rep1_035

value: 53 years

value: TBI patient #035


title: Pre-TBI Blood_0Gy_rep1_040


title: control wild type N2_1

description: control wild type

value: L1 larvae


title: TBI Blood_4hr_1.25Gy_rep1_051


title: 8-cell rep3 dye-swap

city: Charlestown

first: Petr

last: Vodicka

state: Massachusetts

address: 114 16th Street

department: Department of Neurology

institute: Massachusetts General Hospital

description: 8-cell stage embryos in vivo/in vitro replicate 3

hyb_protocol: Labelled aRNA probes were mixed together and denatured for 5 min at 90 °C. Denatured probes were mixed with 45 µl of SlideHyb™ Glass Array Hybridization Buffer #1 (Ambion, Austin, TX) preheated to 68°C and incubated on the array for 18 hours at 50 °C in a humidified chamber. Slides were washed twice with 2x SSC-0.5% SDS for 15 min at 55 °C, twice with 0.5x SSC-0.5 % SDS for 15 min at 55 °C and dried by centrifugation at the room temperature for 5 min at 1200g.

scan_protocol: Arrays were scanned using GeneTAC UC4 microarray scanner (Genomic Solutions, Ann Arbor, MI).

data_processing: Images were analyzed using TIGR Spotfinder software 3.1.1 (TM4 software suit). After lowess and scale normalization of background corrected total intensity values in TIGR Midas 2.19, the data were sorted in Excel (Microsoft, Redmond, USA), and only the experimental features with signal present in all three within array replicates were selected. Total intensity values of within array replicates for each channel were averaged and used to calculate the log2 transformed in vivo/in vitro intensity ratios. Log2 transformed ratios were used for further analysis of differential expression in significant analysis for microarray (SAM) software (Stanford University; http://www-stat.stanford.edu/~tibs/SAM).

label: Alexa Fluor 555

molecule: polyA RNA

organism: Bos taurus

source_name: 8-cell stage in vivo embryos

label_protocol: aRNA was prepared with two round amplification protocol using Amino Allyl MessageAmp ™II aRNA Amplification kit (Ambion, Austin, TX). aRNA was labelled with either Alexa Fluor 555 or Alexa Fluor 647dyes (Invitrogen) as manufacturers instructions. Samples were purified using Pico Pure isolation Kit (Arcturus) before hybridization.

growth_protocol: In vitro cultured embryos: Bovine embryos were obtained after in vitro maturation of oocytes and their subsequent fertilization and culture in vitro. In brief, follicles from bovine ovaries obtained at local slaughterhouse were dissected with fine scissors and then punctured. The oocytes were transferred to a modified Parker medium (MPM) within 2 hr after arrival at the laboratory. The oocytes were evaluated and selected according to the morphology of cumulus and transferred into four-well Nunclon dishes (Nunc, Roskilde, Denmark) with 0.5 ml MPM and cultured in an atmosphere composed of 5% CO2 - 7% O2 - 88% N2 at 39 °C for 24 hr. For in vitro fertilization (IVF), cumulus oocyte complexes were washed four times in PBS and once in fertilization medium then transferred in groups of up to 40 into four-well dishes (Nunc) containing 250 μl of fertilization medium per well. Viable spermatozoa were washed in fertilization medium and pelleted by centrifugation at 100 x g for 5 min. Spermatozoa were counted in a haemocytometer and diluted in the appropriate volume of fertilization medium to give a concentration of 2 x 10^6 spermatozoa/ml. A 250 μl aliquot of this suspension was added to each fertilization well to obtain a final concentration of 1 x 10^6  spermatozoa/ml. Plates were incubated for approximately 20 hr at 39 ˚C under atmosphere composed of 5% CO2 - 7% O2 - 88% N2. At approximately 20 hr post fertilization (hpf) presumptive zygotes were denuded by gentle pipeting and transferred to Bovine Vitro Cleave medium (BVC, COOK, Eight Mile Plains, Australia) and cultured in an atmosphere of 5% CO2 - 7% O2 - 88% N2 at maximum humidity (25 zygotes in 25 μl of medium under mineral oil). The 4-cell stage embryos were collected at 44 hpf and the 8-cell stage embryos at 92 hpf.

extract_protocol: Poly (A)+ mRNA was extracted from pools of 20 in vivo or in vitro produced embryos, using a Dynabeads mRNA DIRECT Micro Kit (Dynal, Oslo, Norway)

treatment_protocol: In vivo derived embryos: A total of 24 heifers (crossbreed Czech Motley and Holstein) were pre-synchronized by administration of prostaglandin F2α analogue (cloprostenol 500 µg i.m., Oestrophan® 0.25 mg/ml Bioveta, Czech Rep.) twice within 11 days. Two days after each of the PGF2α treatments the animals received GnRH analogue (lecirelin 50 µg i.m., Supergestran® inj. ad us. vet., Nordic Pharma, Czech Rep.) Ultrasound-guided transvaginal aspirations of the dominant follicles were performed on day 9 after GnRH administration.  Forty two hours later the animals received the first of eight consecutive FSH-injections (in total 450 UI of FSH at 12 h intervals in decreasing doses, Pluset®, Calier S.A., Spain). Two PGF2α treatments were performed 60 and 72 h after the initial FSH-treatment. Finally, 48 hours after the first PGF2α treatment, ovulation was induced by giving hCG (2500 UI i.v., Pregnyl® 1500, Organon, Netherlands) simultaneously with the artificial insemination (AI) using one straw of cooled semen from a bull of proven fertility. Embryos at 4-cell and late 8-cell stage were recovered by oviductal flushing using a minimally invasive endoscopic approach 1-4 days after artificial insemination. The developmental stage as well as the morphological integrity of the recovered embryos was assessed according to IETS guidelines. Embryos of the same developmental stage assessed excellent and good were pooled in groups of ten embryos, washed in PBS, frozen in a minimum amount of medium in siliconized 0.6 mL cups and stored at −80 °C. Typically, the time period between flushing and freezing was less than 30 min.

value: 8-cell stage embryo

tag: source

value: in vivo derived

label: Alexa Fluor 647

source_name: 8-cell stage in vitro embryos

value: in vitro produced


title: 8-cell rep2

description: 8-cell stage embryos in vivo/in vitro replicate 2


title: 4-cell rep3

description: 4-cell stage embryos in vivo/in vitro replicate 3

source_name: 4-cell stage in vivo embryos

value: 4-cell stage embryo

source_name: 4-cell stage in vitro embryos


title: 8-cell rep1

description: 8-cell stage embryos in vivo/in vitro replicate 1


title: Pre-TBI Blood_0Gy_rep1_024

value: whole blood

value: 43 years

value: TBI patient #024


title: TBI Blood_20hr_3.75Gy_rep1_031

value: male

value: 47 years

value: TBI patient #031


title: TBI Blood_20hr_3.75Gy_rep1_024

value: female


title: Pre-TBI Blood_0Gy_rep1_031


title: TBI Blood_20hr_3.75Gy_rep1_022

value: 51 years

value: TBI patient #022


title: 4-cell rep2

description: 4-cell stage embryos in vivo/in vitro replicate 2


title: Pre-TBI Blood_0Gy_rep1_035


title: TBI Blood_4hr_1.25Gy_rep1_024


title: TBI Blood_4hr_1.25Gy_rep1_022


title: TBI Blood_20hr_3.75Gy_rep1_021

value: 44 years

value: TBI patient #021


title: 4-cell rep1 dye-swap

description: 4-cell stage embryos in vivo/in vitro replicate 1


title: Pre-TBI Blood_0Gy_rep1_022


title: Pre-TBI Blood_0Gy_rep1_021


title: TBI Blood_20hr_3.75Gy_rep1_020

value: 50 years

value: TBI patient #020


title: TBI Blood_4hr_1.25Gy_rep1_020


title: Pre-TBI Blood_0Gy_rep1_020


title: TBI Blood_20hr_3.75Gy_rep1_016

value: 36 years

value: TBI patient #016


title: TBI Blood_4hr_1.25Gy_rep1_016


title: TBI Blood_20hr_3.75Gy_rep1_002

value: 23 years

value: TBI patient #002


title: Aspergillus niger AreBKO, glycerol, biological rep2

city: Göteborg

first: Margarita

last: Salazar Peña

address: Kemigården 4

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Gene expression data from A. niger areB complete deletion strain grown in batch cultivations

hyb_protocol: Approximately 15 mg of fragmented cRNA was hybridized for 16 hr at 45 °C on the 3AspergDTU Affymetrix GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Agilent GeneArray Scanner 3000 7G. Scanned probe array images (.DAT files) were converted into .CEL files using the Affymetrix GeneChip Operating Software.

data_processing: Affymetrix CEL data files were preprocessed using the statistical language R version 2.9.2 and Bioconductor version 2.4. Normalization was performed using the qspline algorithm and gene expression indexes were calculated from the PM probes with the median polish summary method. All statistical preprocessing methods were implemented in affy package using R scripts and limma package.

organism: Aspergillus niger

source_name: AreBKO-Glycerol

label_protocol: Biotin-labeled cRNA was prepared from approximately 1 mg of total RNA according to the protocol described in the Affymetrix GeneChipÒ Expression Analysis Technical Manual (Affymetrix and GeneChip. (2007) P/N 702232, Affymetrix, Santa Clara, CA, Revision 2).

growth_protocol: Aspergillus niger strains were grown in 2.7 L batch cultivations with pH, agitation and temperature control.

extract_protocol: Approximately 1 g of fungal biomass was used for total RNA isolation using the Qiagen RNeasy Mini Kit according to the protocol for isolation of total RNA from plants and fungi.

treatment_protocol: Fungal biomass from each of the Aspergillus fermentation replicates was harvested in the mid exponential phase of growth, filtered, washed, dryed by squeezing, frozen in liquid nitrogen and stored at -80 °C until further processing.

value: ATCC 1015

tag: genotype/variation

value: areB complete deletion mutant

value: Fungal  biomass


title: TBI Blood_4hr_1.25Gy_rep1_002

value: whole blood

value: male


title: TBI Blood_20hr_3.75Gy_rep1_001

value: 30 years

value: TBI patient #001


title: HealthyBlood_0Gy_rep1_Ex15

value: female

value: 33 years

value: healthy control


title: Aspergillus niger ATCC 1015, glycerol, biological rep3

description: Gene expression data from A. niger ATCC 1015 strain grown in batch cultivations

value: wild type


title: Pre-TBI Blood_0Gy_rep1_016


title: Aspergillus niger AreBKO, glucose, biological rep2

source_name: AreBKO-Glucose


title: 5Aza-dC and TSA treated DU-145

source_name: DU-145 _Mock_Cy3


title: TBI Blood_4hr_1.25Gy_rep1_001


title: Aspergillus niger ATCC 1015, glycerol, biological rep2


title: MUT_5

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

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

organism: Mus musculus

source_name: Mutant group 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix).

growth_protocol: Mice were grown in the SPF facilty at the UF Cancer/Genetics Research Complex

extract_protocol: Total RNA was harvested using the RNeasy RNA Isolation kit  standard protocol (Qiagen, Valencia, CA)

treatment_protocol: Pregent moms were cevericaly dislocated and embryos dissected in PBS. Limbs were cut off of embryos for RNA processing.

tag: mutant


title: Pre-TBI Blood_0Gy_rep1_002


title: Aspergillus niger ATCC 1015, glucose, biological rep3


title: Aspergillus niger AreBKO, glucose, biological rep3


title: Aspergillus niger AreBKO, glycerol, biological rep3


title: WT_5

source_name: Wild type group 5

tag: wild type


title: MUT_4

source_name: Mutant group 4


title: Pre-TBI Blood_0Gy_rep1_001


title: Aspergillus niger ATCC 1015, glycerol, biological rep1


title: Aspergillus niger ATCC 1015, glucose, biological rep1


title: WT_3

source_name: Wild type group 3


title: WT_4

source_name: Wild type group 4


title: MUT_3

source_name: Mutant group 3


title: MUT_1

source_name: Mutant group 1


title: Aspergillus niger ATCC 1015, glucose, biological rep2


title: Aspergillus niger CreAKO, glucose, biological rep2

description:
Gene expression data from A. niger creA deletion strain grown in batch cultivations.

This sample was included in the CreA deletion mutant dataset.

hyb_protocol: Approximately 15 ug of fragmented cRNA was hybridized for 16 hr at 45 °C on the 3AspergDTU Affymetrix GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
Affymetrix CEL data files were preprocessed using the statistical language R version 2.9.2 and Bioconductor version 2.4. Normalization was performed using the qspline algorithm across subsets of samples (12 samples for each comparison), i.e., each gene deletion strain grown in triplicate on glucose or glycerol carbon sources was compared to the wild type strain ATCC 1015 grown in triplicate on the same carbon sources. The same six ATCC 1015 CEL files were used for each normalization. Gene expression indexes were calculated from the PM probes with the median polish summary method. All statistical preprocessing methods were implemented in affy package using R scripts and limma package.

The Sample data tables include the gene expression indexes calculated for the datasets used for each ANOVA comparison.

source_name: Fungal  biomass, CreAKO, glucose

label_protocol: Biotin-labeled cRNA was prepared from approximately 1 ug of total RNA according to the protocol described in the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix and GeneChip. (2007) P/N 702232, Affymetrix, Santa Clara, CA, Revision 2).

treatment_protocol: Fungal biomass from each of the Aspergillus fermentation replicates was harvested in the mid-exponential phase of growth, filtered, washed, dryed by squeezing, frozen in liquid nitrogen and stored at -80 °C until further processing.

value: creA deletion mutant on ATCC 1015 background

tag: carbon source

value: glucose


title: Aspergillus niger CreAKO, glucose, biological rep3


title: Aspergillus niger CreAKO, glycerol, biological rep3

source_name: Fungal  biomass, CreAKO, glycerol

value: glycerol


title: MUT_2

source_name: Mutant group 2


title: WT_2

source_name: Wild type group 2


title: Aspergillus niger CreAKO, glycerol, biological rep2


title: Aspergillus niger CreAKO, glycerol, biological rep1


title: Aspergillus niger ATCC 1015, glycerol, biological rep3c

description:
Gene expression data from A. niger ATCC 1015 strain grown in batch cultivations.

This sample was included in the CreA deletion mutant dataset.

source_name: Fungal  biomass, ATCC 1015, glycerol

value: ATCC 1015 wild type


title: TBI Blood_4hr_1.25Gy_rep1_035

source_name: Peripheral Blood, 4hr, 1.25Gy, replicate 1

value: 53 years

value: TBI patient #035


title: Aspergillus niger CreAKO, glucose, biological rep1


title: WT_1

source_name: Wild type group 1


title: TBI Blood_4hr_1.25Gy_rep1_031

value: 47 years

value: TBI patient #031


title: Aspergillus niger ATCC 1015, glucose, biological rep3c

source_name: Fungal  biomass, ATCC 1015, glucose


title: Aspergillus niger ATCC 1015, glucose, biological rep2c


title: Aspergillus niger ATCC 1015, glycerol, biological rep2c


title: C404A mutant, control, rep3

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description:
JC5
Gene expression from C404A mutant control rep3.

hyb_protocol: Following fragmentation, 15 ug of cRNA were processed through second-cycle single-stranded cDNA. Fragmented and labelled cDNA were then hybridized for 16 hr at 45C on an Affymetrix Yeast 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene array data is processd by Expression Console software in which mean probeset signals for all probesets are analysed. A receiver operating curve (ROC) is generated by thresholding the computed value for the probesets. PLIER signals that pass this QC control is used for subsequent analysis.

organism: Saccharomyces cerevisiae

source_name: C404A mutant control

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

growth_protocol: Cultures were grown in 200 ml of SC-Leu to OD600 of 0.4 at 30°C .

extract_protocol: Cultures were collected in tubes containing 40 g of –80°C crushed ice and cells pelleted by centrifugation (4000 g, 3 min), washed once in PBS before storage at –80°C. Frozen cell pellets were resuspended in 1 ml of Trizol® reagent (Invitrogen), lysed in a bead-beater with acid-washed glass beads and RNA was extracted as described by the manufacturer.

treatment_protocol: Equal aliquots for linoleic acid hydroperoxide (LoaOOH) treatment (30 μM) for 45 min.

value: Swi6 C404A mutation

tag: treatment


title: C404A mutant, LoaOOH, rep3

description:
JC6
Gene expression from C404A mutant LoaOOH rep3.

source_name: C404A mutant LoaOOH

value: LoaOOH


title: Aspergillus niger ATCC 1015, glycerol, biological rep1c


title: swi6 deletant, LoaOOH, rep3

description:
JC2
Gene expression from swi6 deletant LoaOOH rep3.

source_name: swi6 deletant LoaOOH

value: Swi6 deletion


title: SWI6 wild type, control, rep3

description:
JC3
Gene expression from SWI6 wild type control rep3.

source_name: SWI6 wild type control

value: Swi6 wild type


title: TBI Blood_4hr_1.25Gy_rep1_021

value: whole blood

value: 44 years

value: TBI patient #021


title: Aspergillus niger FacBKO, glycerol, biological rep3

description:
Gene expression data from A. niger facB deletion strain grown in batch cultivations.

This sample was included in the FacB deletion mutant dataset.

source_name: Fungal  biomass, FacBKO, glycerol

value: facB deletion mutant on ATCC 1015 background


title: SWI6 wild type, LoaOOH, rep3

description:
JC4
Gene expression from SWI6 wild type LoaOOH rep3.

source_name: SWI6 wild type LoaOOH


title: Aspergillus niger ATCC 1015, glucose, biological rep1c


title: Aspergillus niger FacBKO, glycerol, biological rep2


title: swi6 deletant, control, rep3

description:
JC1
Gene expression from swi6 deletant control rep3.

source_name: swi6 deletant control


title: Aspergillus niger FacBKO, glycerol, biological rep1


title: Aspergillus niger FacBKO, glucose, biological rep3

source_name: Fungal  biomass, FacBKO, glucose


title: NP knockout rep1

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

country: Switzerland

institute: University Hospital Bern

hyb_protocol: 1500 ng cRNA was hybridized on two Illumina MouseWG-6 v2 slides acording to the manufacturers protocol. Biological replicates were distributed among both slides.

scan_protocol: Fluorescent signals were imaged by laser scanning using the Illumina iScan system.

data_processing: The data was processed with Illumina genome studio software (gene expression module 1.0.6) with no background correction or normalization. VST (variance stabilization) transformation 'lumiT()', quantile normalization 'lumiN(, method = quantile)' and statistical analysis were performed with R (2.9.0) / Bioconductor using the package lumi (1.10.1) and libraries contained therein, in particular limma (2.16.4).

source_name: Neuronal precursor cells, TDG knock-out, day 4

label_protocol: Starting with 500 ng / sample of total RNA, total RNAs was transcribed and labeled with Illumina(r) TotalPrep RNA Amplification Kit (Ambion). cRNA was quantified with QuantIT (Invitrogen) against ribosomal RNA standard (Invitrogen).

growth_protocol: ES cells: grown in DMEM, 15 % heat inactivated FCS, LIF (1,000 U/ml), 1x nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine and 90 µM β-mercaptoethanol

extract_protocol: Total RNA was prepared using TRIZOL.

treatment_protocol: differentiation: embryoid body formation in absence of feeder cells and LIF, induction of differentiation with 5 µM all-trans retinoic acid and further growth in DMEM- F12 nutrient mixture (1:1) + 1x N2 supplement

tag: differentiation stage

value: neuronal precursor

tag: differentiation time days

value: Tdg-/-

tag: cell type

value: Neuronal precursor cells


title: NP knockout rep3


title: C404A mutant, control, rep2

description:
CT11
Gene expression from C404A mutant control rep2.


title: C404A mutant, LoaOOH, rep2

description:
CT12
Gene expression from C404A mutant LoaOOH rep2.


title: NP knockout rep2


title: Aspergillus niger FacBKO, glucose, biological rep2

tag: strain

value: glucose


title: SWI6 wild type, LoaOOH, rep2

description:
CT10
Gene expression from SWI6 wild type LoaOOH rep2.


title: Parental Fibroblast line HFF, passage 10

type: genomic

city: Toronto

first: Samer

last: Hussein

address: 25 Orde St.

country: Canada

institute: SLRI-Mount Sinai Hosp.

description: Hybridized to SNP 6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed and stained using GeneChip fluidics station 450, and scanned using the GeneChip Scanner 3000 with Autoloader.

data_processing:
CEL files were generated by Affymetrix GeneChip Command Console Software 1.1(AGCC), and were processed and analyzed using Affymetrix Genotyping Console 3.0.2 and Birdseed v2-algorithm. Samples were normalized against 40 International HapMap samples hybridized in-house, and which are listed in supplementary table of associated manuscript.
CHP files: Copy number analysis, probset coordinates, CN state, signal log2 ratio, LOH and allele difference calls. Segment files: Segment analysis, Copy number variation coordinates and size, CN state, cytoband location, start and end probe position, and CNV annotation

label: Biotin

molecule: genomic DNA

source_name: human foreskin fibroblast line HFF

label_protocol: As per manufacturer user guide (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions, and as described in associated manuscript

extract_protocol: Genomic DNA was extracted from hiPSCs, hESCs, and fibroblast cell culture plates using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Thermo  Multiscan Spectrum spectrophotometer, and agarose gel electrophoresis.

value: human neonatal foreskin fibroblast

tag: cell line/clone

value: HFF line

tag: cell passage

value: passage #10


title: Aspergillus niger FacBKO, glucose, biological rep1


title: NP heterozygotes rep3

source_name: Neuronal precursor cells, TDG heterozygotes, day 4

value: Tdg+/-


title: NP heterozygotes rep2


title: SWI6 wild type, control, rep2

description:
CT9
Gene expression from SWI6 wild type control rep2.


title: hiPSC line FiPS5-7, passage 26

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS5-7

value: human induced pluripotent stem cell line

value: clone FiPS5-7

value: passage #26

tag: cell origin

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #13


title: Parental Fibroblast line HFF, passage 11

description: Hybridized to SNP 6.0 array

value: passage #11


title: Parental Fibroblast line IMR90, passage 14

description: Hybridized to SNP 6.0 array

source_name: human embryonic lung fibroblast line IMR90

value: human embryonic lung fibroblast

value: line IMR90

value: passage #14


title: hiPSC line FiPS7-10, passage 22

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-10

value: clone FiPS7-10

value: passage #22

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: Parental Fibroblast line MRC5, passage 19

description: Hybridized to SNP 6.0 array

source_name: human embryonic lung fibroblast line MRC5

value: line MRC5

value: passage #19


title: NP heterozygotes rep1

value: neuronal precursor

value: Neuronal precursor cells


title: Aspergillus niger ATCC 1015, glycerol, biological rep3b

description:
Gene expression data from A. niger ATCC 1015 strain grown in batch cultivations.

This sample was included in the FacB deletion mutant dataset.

source_name: Fungal  biomass, ATCC 1015, glycerol

value: ATCC 1015 wild type

value: glycerol


title: swi6 deletant, LoaOOH, rep2

description:
CT8
Gene expression from swi6 deletant LoaOOH rep2.

value: Swi6 deletion

value: LoaOOH


title: Parental Fibroblast line XHEF, passage 6

description: Hybridized to SNP 6.0 array

source_name: human embryonic fibroblast line XHEF

value: human embryonic fibroblast

value: XHEF line

value: passage #6


title: Aspergillus niger ATCC 1015, glycerol, biological rep2b


title: swi6 deletant, control, rep2

description:
CT7
Gene expression from swi6 deletant control rep2.


title: ES knockout rep3

source_name: Embryonic stem cells, TDG knock-out

value: embryonal stem

value: Tdg-/-

value: Embryonic stem cells


title: C404A mutant, LoaOOH, rep1

description:
CT6
Gene expression from C404A mutant LoaOOH rep1.

source_name: C404A mutant LoaOOH

value: Swi6 C404A mutation


title: ES knockout rep2


title: Aspergillus niger ATCC 1015, glucose, biological rep3b

source_name: Fungal  biomass, ATCC 1015, glucose

value: glucose


title: Aspergillus niger ATCC 1015, glycerol, biological rep1b


title: C404A mutant, control, rep1

description:
CT5
Gene expression from C404A mutant control rep1.

source_name: C404A mutant control


title: hiPSC line FiPS2-13, passage 12

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS2-13

value: human induced pluripotent stem cell line

value: clone FiPS2-13

value: passage #12

value: cell line is derived from Human embryonic lung fibroblast IMR90 cell, passage #14


title: ES heterozygotes rep3

source_name: Embryonic stem cells, TDG heterozygotes

value: Tdg+/-


title: Aspergillus niger ATCC 1015, glucose, biological rep2b

value: ATCC 1015 wild type


title: SWI6 wild type, LoaOOH, rep1

description:
CT4
Gene expression from SWI6 wild type LoaOOH rep1.

source_name: SWI6 wild type LoaOOH

value: Swi6 wild type


title: hiPSC line FiPS8-3, passage 17

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS8-3

value: clone FiPS8-3

value: passage #17

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #10


title: SWI6 wild type, control, rep1

description:
CT3
Gene expression from SWI6 wild type control rep1.

source_name: SWI6 wild type control


title: Aspergillus niger ATCC 1015, glucose, biological rep1b


title: ES heterozygotes rep2


title: hiPSC line FiPS1-14, passage 13

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS1-14

value: clone FiPS1-14

value: passage #13


title: hiPSC line FiPS7-1, passage 17

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-1

value: clone FiPS7-1

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: hiPSC line PB110, passage 11

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB110

value: clone PB110

value: passage #11

value: cell line is derived from Human embryonic fibroblast XHEF cell, passage #6


title: Aspergillus niger AdrAKO, glycerol, biological rep3

description:
Gene expression data from A. niger adrA deletion strain grown in batch cultivations.

This sample was included in the Adr deletion mutant dataset.

source_name: Fungal  biomass, AdrAKO, glycerol

value: adrA deletion mutant on ATCC 1015 background

value: glycerol


title: swi6 deletant, LoaOOH, rep1

description:
CT2
Gene expression from swi6 deletant LoaOOH rep1.

source_name: swi6 deletant LoaOOH

value: Swi6 deletion

value: LoaOOH


title: hiPSC line FiPS2-10, passage 16

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS2-10

value: human induced pluripotent stem cell line

value: clone FiPS2-10

value: passage #16

value: cell line is derived from Human embryonic lung fibroblast IMR90 cell, passage #14


title: hiPSC line FiPS6-3, passage 14

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS6-3

value: clone FiPS6-3

value: passage #14


title: hiPSC line FiPS5-3, passage 12

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS5-3

value: clone FiPS5-3

value: passage #12


title: Aspergillus niger AdrAKO, glycerol, biological rep2


title: Aspergillus niger AdrAKO, glycerol, biological rep1


title: hiPSC line FiPS7-1, passage 10

description: Hybridized to SNP 6.0 array

value: clone FiPS7-1

value: passage #10


title: ES heterozygotes rep1

value: embryonal stem

value: Tdg+/-

value: Embryonic stem cells


title: D1D2KO-DIFF3

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

description: Gene expression data

hyb_protocol: Manufacturer's Spec.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Bioconductor v 2.6

source_name: D1D2KO MEFs Differentiated

label_protocol: Manufacturer's Spec.

growth_protocol: DMEM+10% FBS

extract_protocol: Trizol

treatment_protocol: E14 embryos were harvested for MEFs. The treatment is as follows: "Cells were grown to confluency. 2 Days post confluency, cells were treated with 1 microM dexamethasone, 500 microM isobutylmethylxanthine, 5 microgram/milliliter insulin and 15 microM troglitazone for 2-3 days. Cells were then changed to media containing 5 micrograms/milliliter insulin and 15 microM troglitazone for 2 days. After this, cells were maintained in normal media (DMEM+10% serum) until harvest."

tag: tissue

value: Adipocytes


title: hiPSC line FiPS6-12, passage 14

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS6-12

value: clone FiPS6-12

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: D1D2KO-DIFF2

description: Gene expression data


title: hiPSC line FiPS8-3, passage 11

description: Hybridized to SNP 6.0 array

value: clone FiPS8-3

value: passage #11

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #10


title: ES knockout rep1

source_name: Embryonic stem cells, TDG knock-out

value: Tdg-/-


title: D1D2KO-DIFF1

description: Gene expression data


title: Aspergillus niger AdrAKO, glucose, biological rep3

source_name: Fungal  biomass, AdrAKO, glucose

value: adrA deletion mutant on ATCC 1015 background

value: glucose


title: Aspergillus niger AdrAKO, glucose, biological rep2


title: D1D2KO-UNDIFF3

description: Gene expression data

source_name: D1D2KO MEFs Undifferentiated

treatment_protocol: E14 embryos were harvested for MEFs.

value: Fibroblast


title: hiPSC line FiPS7-5, passage 12

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-5

value: human induced pluripotent stem cell line

value: clone FiPS7-5


title: hiPSC line FiPS7-10, passage 19

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-10

value: clone FiPS7-10

value: passage #19


title: swi6 deletant, control, rep1

description:
CT1
Gene expression from swi6 deletant control rep1.

source_name: swi6 deletant control

value: Swi6 deletion


title: D1D2KO-UNDIFF2

description: Gene expression data


title: Aspergillus niger AdrAKO, glucose, biological rep1


title: Aspergillus niger ATCC 1015, glycerol, biological rep2a

description:
Gene expression data from A. niger ATCC 1015 strain grown in batch cultivations.

This sample was included in the Adr deletion mutant dataset.

source_name: Fungal  biomass, ATCC 1015, glycerol

value: ATCC 1015 wild type

value: glycerol


title: Aspergillus niger ATCC 1015, glycerol, biological rep3a


title: D1D2KO-UNDIFF1

description: Gene expression data


title: hiPSC line PB66, passage 9

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB66

value: clone PB66

value: passage #9

value: cell line is derived from Human embryonic fibroblast XHEF cell, passage #6


title: hiPSC line PB60, passage 9

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB60

value: clone PB60


title: WT-DIFF3

description: Gene expression data

source_name: WT MEFs Differentiated

value: Adipocytes


title: Aspergillus niger ATCC 1015, glycerol, biological rep1a


title: Aspergillus niger ATCC 1015, glucose, biological rep3a

source_name: Fungal  biomass, ATCC 1015, glucose


title: WT-DIFF2

description: Gene expression data


title: hiPSC line FiPS5-7, passage 10

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS5-7

value: clone FiPS5-7

value: passage #10

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #13


title: WT-DIFF1

description: Gene expression data


title: hiPSC line PB67, passage 9

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB67

value: clone PB67


title: WT-UNDIFF3

description: Gene expression data

source_name: WT MEFs Undifferentiated

value: Fibroblast


title: hiPSC line PB1-53, passage 8

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB1-53

value: human induced pluripotent stem cell line

value: clone PB1-53

value: passage #8

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #10


title: Aspergillus niger ATCC 1015, glucose, biological rep1a

value: glucose


title: hiPSC line PB1-56, passage 8

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB1-56

value: clone PB1-56


title: Lung Normal 167N

status: Public on Jan 30 2011

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

description: Gene expression data from 167N

hyb_protocol: The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA).  After 16 hours of hybridization at 45 °C, the arrays were washed by Fluidics Station 450

scan_protocol: Chips were scanned using the GeneChip Scanner 3000

data_processing: Background-adjusted signals were normalized by three steps: Robust Multichip Analysis (RMA), median polish method, and quantile normalization algorithm.

source_name: frozen tissue of adjacent normal

label_protocol: The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

extract_protocol: Total RNA from the tissue specimens were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen) according to the manufacturer's instructions.

value: paired normal adjacent

tag: gender

value: female

tag: age

tag: stage


title: Lung Normal 189N

description: Gene expression data from 189N


title: WT-UNDIFF1

description: Gene expression data


title: Lung Normal 159N

description: Gene expression data from 159N


title: Lung Normal 165N

description: Gene expression data from 165N


title: Lung Normal 177N

description: Gene expression data from 177N


title: hiPSC line FiPS7-5, passage 8

description: Hybridized to SNP 6.0 array

value: clone FiPS7-5

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: WT-UNDIFF2

description: Gene expression data


title: Aspergillus niger ATCC 1015, glucose, biological rep2a

value: ATCC 1015 wild type


title: Lung Normal 156N

description: Gene expression data from 156N


title: Lung Normal 157N

description: Gene expression data from 157N


title: hiPSC line FiPS8-5, passage 6

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS8-5

value: clone FiPS8-5

value: passage #6


title: Lung Normal 154N

description: Gene expression data from 154N


title: Lung Normal 144N

description: Gene expression data from 144N


title: Lung Normal 149N

description: Gene expression data from 149N


title: Lung Normal 142N

description: Gene expression data from 142N


title: Lung Normal 148N

description: Gene expression data from 148N


title: Lung Normal 145N

description: Gene expression data from 145N


title: hiPSC line FiPS8-2, passage 5

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS8-2

value: clone FiPS8-2

value: passage #5


title: Lung Normal 146N

description: Gene expression data from 146N


title: hiPSC line PB1-2, passage 8

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB1-2

value: clone PB1-2


title: Lung Normal 143N

description: Gene expression data from 143N


title: Lung Normal 137N

description: Gene expression data from 137N


title: Lung Normal 152N

description: Gene expression data from 152N


title: hiPSC line FiPS7-12, passage 5

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-12

value: clone FiPS7-12


title: Lung Normal 179N

description: Gene expression data from 179N


title: Lung Normal 134N

description: Gene expression data from 134N


title: hiPSC line PB110, passage 7

description: Hybridized to SNP 6.0 array

source_name: hiPSC line PB110

value: human induced pluripotent stem cell line

value: clone PB110

value: passage #7

value: cell line is derived from Human embryonic fibroblast XHEF cell, passage #6


title: Lung Normal 131N

description: Gene expression data from 131N


title: Lung Normal 136N

description: Gene expression data from 136N


title: Lung Normal 139N

description: Gene expression data from 139N


title: Lung Normal 133N

description: Gene expression data from 133N


title: Lung Normal 130N

description: Gene expression data from 130N


title: Lung Normal 135N

description: Gene expression data from 135N


title: Lung Normal 123N

description: Gene expression data from 123N


title: Lung Normal 127N

description: Gene expression data from 127N


title: Lung Normal 126N

description: Gene expression data from 126N


title: Lung Normal 125N

description: Gene expression data from 125N


title: Lung Normal 158N

description: Gene expression data from 158N


title: Lung Normal 132N

description: Gene expression data from 132N


title: Lung Normal 120N

description: Gene expression data from 120N


title: Lung Normal 122N

description: Gene expression data from 122N


title: Lung Normal 124N

description: Gene expression data from 124N


title: Lung Normal 121N

description: Gene expression data from 121N


title: Lung Normal 129N

description: Gene expression data from 129N


title: Lung Normal 119N

description: Gene expression data from 119N


title: hiPSC line FiPS7-5, passage 5

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-5


title: Lung Normal 118N

description: Gene expression data from 118N


title: hiPSC line FiPS7-1, passage 5

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-1

value: clone FiPS7-1


title: hiPSC line PB1-53, passage 4

description: Hybridized to SNP 6.0 array

value: clone PB1-53

value: passage #4

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #10


title: Lung Normal 114N

description: Gene expression data from 114N

value: paired normal adjacent

value: female


title: hiPSC line PB1-2, passage 4

description: Hybridized to SNP 6.0 array


title: Lung Normal 115N

description: Gene expression data from 115N


title: Lung Normal 102N

description: Gene expression data from 102N


title: Lung Normal 103N

description: Gene expression data from 103N


title: Lung Normal 116N

description: Gene expression data from 116N


title: Lung Normal 40N

description: Gene expression data from 40N


title: Lung Normal 109N

description: Gene expression data from 109N


title: Lung Normal 117N

description: Gene expression data from 117N


title: Lung Normal 79N

description: Gene expression data from 79N


title: Lung Normal 97N

description: Gene expression data from 97N


title: Lung Normal 37N

description: Gene expression data from 37N


title: Lung Normal 94N

description: Gene expression data from 94N


title: Lung Normal 33N

description: Gene expression data from 33N


title: Lung Normal 106N

description: Gene expression data from 106N


title: Lung Normal 43N

description: Gene expression data from 43N


title: hiPSC line FiPS7-10, passage 5

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-10

value: clone FiPS7-10

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: hESC line CA1, passage 20

description: Hybridized to SNP 6.0 array

source_name: hESC line CA1

value: human embryonic stem cell line

value: clone CA1

value: passage # 20


title: hiPSC line PB1-56, passage 4

description: Hybridized to SNP 6.0 array

value: clone PB1-56


title: hiPSC line FiPS8-3, passage 4

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS8-3

value: clone FiPS8-3


title: UPS-BP24

city: Durham

first: Jeffrey

last: Mito

state: NC

institute: Duke University Medical Center

description: Undifferentiated Pleomorphic Sarcoma initiated by Adeno-Cre injection into LSL-Kras; p53 Flox/Flox mice

hyb_protocol: Labeled targets were hybridized to arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 according to stantared affymetrix protocols (santa Clara, CA)

scan_protocol: Affymetrix GeneChip® Scanner 7G according to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)

data_processing: Data was normalized using affymetrix expression console version 1.1 using RMA

source_name: primary undifferentiated pleomorphic sarcoma generated by intramuscular adeno-cre injection

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA

extract_protocol: RNA was isolated using either the Qiagen RNeasy Fibrous Tissue Mini Kit or TRIzol reagent and puried using RNAeasy columns (Qiagen).  Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

value: mixed 129S4/SvJae and C57BL/6

value: Bulk Tumor


title: Lung Normal 92N

description: Gene expression data from 92N


title: UPS-131179


title: UPS-1628


title: nm8

description: bulk Normal Muscle Tissue

source_name: normal muscle

value: Normal Muscle

value: Wild Type mice


title: UPS-1944


title: UPS-1949


title: Lung Normal 2N

description: Gene expression data from 2N


title: Lung Normal 32N

description: Gene expression data from 32N


title: Lung Normal 17N

description: Gene expression data from 17N


title: Lung Cancer 159T

description: Gene expression data from 159T

source_name: frozen tissue of primary tumor

value: lung cancer


title: Lung Normal 3N

description: Gene expression data from 3N


title: Lung Cancer 177T

description: Gene expression data from 177T


title: nm7

description: bulk Normal Muscle Tissue


title: hiPSC line FiPS7-8, passage 5

description: Hybridized to SNP 6.0 array

source_name: hiPSC line FiPS7-8

value: human induced pluripotent stem cell line

value: clone FiPS7-8

value: passage #5


title: Lung Normal 91N

description: Gene expression data from 91N

value: paired normal adjacent


title: Lung Normal 6N

description: Gene expression data from 6N

value: female


title: Lung Cancer 189T

description: Gene expression data from 189T


title: RMS-180904

description: Rhabdomyosarcoma induced by tamoxifen injection in Pax7-CreER; LSL-Kras; p53 Flox/Flox mice

source_name: primary rhabdomyosarcoma generated by tamoxifen injection

value: Pax7-CreER; LSL-KrasG12D;Trp53Flox/Flox


title: Lung Cancer 167T

description: Gene expression data from 167T


title: skm4

description: bulk Normal Muscle Tissue


title: Lung Cancer 179T

description: Gene expression data from 179T


title: SMP4

description: Rhabdomyosarcoma induced by in vitro tamoxifen treatment of sorted myogenic progenitors in Rosa26-CreER; LSL-Kras; p53 Flox/Flox mice

source_name: transplanted rhabdomyosarcoma generated by tamoxifen treatment in vitro and cell injection into athymic nude mice


title: SMP5


title: Lung Cancer 165T

description: Gene expression data from 165T


title: Lung Cancer 154T

description: Gene expression data from 154T


title: SMP2


title: Lung Cancer 157T

description: Gene expression data from 157T


title: Lung Cancer 158T

description: Gene expression data from 158T


title: Lung Cancer 152T

description: Gene expression data from 152T


title: RMS-180343


title: RMS-180341


title: Lung Cancer 156T

description: Gene expression data from 156T


title: Lung Cancer 149T

description: Gene expression data from 149T


title: SMP3


title: RMS-180324

value: Pax7-CreER/+; LSL-KrasG12D;Trp53Flox/+


title: Lung Cancer 146T

description: Gene expression data from 146T


title: Lung Cancer 148T

description: Gene expression data from 148T


title: RMS-180357


title: RMS-180331


title: Lung Cancer 143T

description: Gene expression data from 143T


title: RMS-180332


title: Lung Cancer 145T

description: Gene expression data from 145T


title: Lung Cancer 142T

description: Gene expression data from 142T


title: Lung Cancer 139T

description: Gene expression data from 139T


title: RMS-539

value: Pax7-CreER; Trp53Flox/Flox


title: RMS-754


title: RMS-348


title: RMS-754L

source_name: lineage depleted primary rhabdomyosarcoma generated by tamoxifen injection

value: Lineage Depleted Tumor


title: Lung Cancer 136T

description: Gene expression data from 136T


title: Lung Cancer 135T

description: Gene expression data from 135T


title: RMS-590


title: RMS-751L


title: RMS-748L


title: Lung Cancer 144T

description: Gene expression data from 144T


title: Lung Cancer 132T

description: Gene expression data from 132T


title: UPS-1444


title: Lung Cancer 130T

description: Gene expression data from 130T


title: Lung Cancer 133T

description: Gene expression data from 133T


title: skm5

description: bulk Normal Muscle Tissue


title: Lung Cancer 127T

description: Gene expression data from 127T


title: Lung Cancer 126T

description: Gene expression data from 126T


title: Lung Cancer 129T

description: Gene expression data from 129T


title: MDS tumor cells patient 106

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description:
Agilent Feature Extraction file: sample_106.txt
MDS tumor cells

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and LOWESS normalization.

source_name: MDS tumor cells, patient 106

label_protocol: Protocol Version 5.0, June 2007, Agilent.Same gender reference/control DNA was purchased from Promega as pool.

growth_protocol: Bone marrow cells were cultured unstimulated 24, 48 or 72 hrs in RPMI or Marrow Max Medium and 10% FCS. Colcemid was used to arrest cell cycle in metaphases.

extract_protocol:
For samples marked Qiagen: DNA was extracted from methanol-acetic acid fixed cells with QIAamp DNA Blood Midi Kit (Qiagen).
For samples marked PC: DNA was extracted from methanol-acetic acid fixed cells with Proteinase K, SDS and Phenol-Chloroform.

treatment_protocol: Hypotonic treatment to eliminate red blood cells and fixation with methanol-acetic acid (3:1) of white blood cells.

value: F

tag: International Prognostic Scoring System (IPSS)

tag: extract protocol

value: Qiagen

source_name: control DNA

tag: reference

value: Pooled, same gender reference/control DNA (Promega)


title: Lung Cancer 125T

description: Gene expression data from 125T


title: Lung Cancer 137T

description: Gene expression data from 137T


title: MDS tumor cells patient 107

description:
Agilent Feature Extraction file: sample_107.txt
MDS tumor cells

hyb_protocol: Protocol Version 5.0, June 2007, Agilent.

source_name: MDS tumor cells, patient 107

value: M


title: MDS tumor cells patient 67

description:
Agilent Feature Extraction file: sample_67.txt
MDS tumor cells

source_name: MDS tumor cells, patient 67


title: Lung Cancer 124T

description: Gene expression data from 124T


title: Lung Cancer 134T

description: Gene expression data from 134T


title: Lung Cancer 122T

description: Gene expression data from 122T


title: hESC line CA2, passage 19

description: Hybridized to SNP 6.0 array

source_name: hESC line CA2

value: human embryonic stem cell line

value: clone CA2

value: passage # 19


title: Lung Cancer 121T

description: Gene expression data from 121T

value: lung cancer


title: MDS tumor cells patient 105

description:
Agilent Feature Extraction file: sample_105.txt
MDS tumor cells

source_name: MDS tumor cells, patient 105


title: MDS tumor cells patient 92

description:
Agilent Feature Extraction file: sample_92.txt
MDS tumor cells

source_name: MDS tumor cells, patient 92


title: MDS tumor cells patient 55

description:
Agilent Feature Extraction file: sample_55.txt
MDS tumor cells

source_name: MDS tumor cells, patient 55


title: Lung Cancer 120T

description: Gene expression data from 120T


title: Lung Cancer 118T

description: Gene expression data from 118T


title: MDS tumor cells patient 57

description:
Agilent Feature Extraction file: sample_57.txt
MDS tumor cells

source_name: MDS tumor cells, patient 57


title: MDS tumor cells patient 59

description:
Agilent Feature Extraction file: sample_59.txt
MDS tumor cells

source_name: MDS tumor cells, patient 59


title: Lung Cancer 119T

description: Gene expression data from 119T


title: Lung Cancer 123T

description: Gene expression data from 123T


title: MDS tumor cells patient 50

description:
Agilent Feature Extraction file: sample_50.txt
MDS tumor cells

source_name: MDS tumor cells, patient 50


title: Lung Cancer 117T

description: Gene expression data from 117T


title: Lung Cancer 116T

description: Gene expression data from 116T


title: MDS tumor cells patient 33

description:
Agilent Feature Extraction file: sample_33.txt
MDS tumor cells

source_name: MDS tumor cells, patient 33


title: MDS tumor cells patient 91

description:
Agilent Feature Extraction file: sample_91.txt
MDS tumor cells

source_name: MDS tumor cells, patient 91


title: Lung Cancer 115T

description: Gene expression data from 115T

source_name: frozen tissue of primary tumor


title: MDS tumor cells patient 53

description:
Agilent Feature Extraction file: sample_53.txt
MDS tumor cells

source_name: MDS tumor cells, patient 53


title: MDS tumor cells patient 29

description:
Agilent Feature Extraction file: sample_29.txt
MDS tumor cells

source_name: MDS tumor cells, patient 29


title: MDS tumor cells patient 46

description:
Agilent Feature Extraction file: sample_46.txt
MDS tumor cells

source_name: MDS tumor cells, patient 46


title: Lung Cancer 109T

description: Gene expression data from 109T


title: MDS tumor cells patient 26

description:
Agilent Feature Extraction file: sample_26.txt
MDS tumor cells

source_name: MDS tumor cells, patient 26


title: MDS tumor cells patient 31

description:
Agilent Feature Extraction file: sample_31.txt
MDS tumor cells

source_name: MDS tumor cells, patient 31

source_name: control DNA


title: Lung Cancer 114T

description: Gene expression data from 114T


title: MDS tumor cells patient 19

description:
Agilent Feature Extraction file: sample_19.txt
MDS tumor cells

source_name: MDS tumor cells, patient 19


title: MDS tumor cells patient 2

description:
Agilent Feature Extraction file: sample_2.txt
MDS tumor cells

source_name: MDS tumor cells, patient 2


title: Lung Cancer 106T

description: Gene expression data from 106T


title: Lung Cancer 102T

description: Gene expression data from 102T


title: MDS tumor cells patient 98

description:
Agilent Feature Extraction file: sample_98.txt
MDS tumor cells

source_name: MDS tumor cells, patient 98


title: Lung Cancer 97T

description: Gene expression data from 97T


title: Lung Cancer 91T

description: Gene expression data from 91T


title: Lung Cancer 92T

description: Gene expression data from 92T


title: Lung Cancer 94T

description: Gene expression data from 94T


title: Lung Cancer 79T

description: Gene expression data from 79T


title: Lung Cancer 43T

description: Gene expression data from 43T


title: MDS tumor cells patient 94

description:
Agilent Feature Extraction file: sample_94.txt
MDS tumor cells

source_name: MDS tumor cells, patient 94


title: MDS tumor cells patient 82

description:
Agilent Feature Extraction file: sample_82.txt
MDS tumor cells

source_name: MDS tumor cells, patient 82


title: Lung Cancer 32T

description: Gene expression data from 32T


title: Lung Cancer 40T

description: Gene expression data from 40T


title: Lung Cancer 33T

description: Gene expression data from 33T


title: MDS tumor cells patient 96

description:
Agilent Feature Extraction file: sample_96.txt
MDS tumor cells

source_name: MDS tumor cells, patient 96


title: Lung Cancer 37T

description: Gene expression data from 37T


title: Lung Cancer 131T

description: Gene expression data from 131T


title: MDS tumor cells patient 79

description:
Agilent Feature Extraction file: sample_79.txt
MDS tumor cells

source_name: MDS tumor cells, patient 79


title: MDS tumor cells patient 77

description:
Agilent Feature Extraction file: sample_77.txt
MDS tumor cells

source_name: MDS tumor cells, patient 77


title: Lung Cancer 6T

description: Gene expression data from 6T


title: MDS tumor cells patient 90

description:
Agilent Feature Extraction file: sample_90.txt
MDS tumor cells

source_name: MDS tumor cells, patient 90


title: MDS tumor cells patient 62

description:
Agilent Feature Extraction file: sample_62.txt
MDS tumor cells

source_name: MDS tumor cells, patient 62


title: MDS tumor cells patient 65

description:
Agilent Feature Extraction file: sample_65.txt
MDS tumor cells

source_name: MDS tumor cells, patient 65


title: MDS tumor cells patient 80

description:
Agilent Feature Extraction file: sample_80.txt
MDS tumor cells

source_name: MDS tumor cells, patient 80


title: MDS tumor cells patient 68

description:
Agilent Feature Extraction file: sample_68.txt
MDS tumor cells

source_name: MDS tumor cells, patient 68


title: MDS tumor cells patient 75

description:
Agilent Feature Extraction file: sample_75.txt
MDS tumor cells

source_name: MDS tumor cells, patient 75


title: MDS tumor cells patient 56

description:
Agilent Feature Extraction file: sample_56.txt
MDS tumor cells

source_name: MDS tumor cells, patient 56


title: MDS tumor cells patient 73

description:
Agilent Feature Extraction file: sample_73.txt
MDS tumor cells

source_name: MDS tumor cells, patient 73


title: MDS tumor cells patient 70

description:
Agilent Feature Extraction file: sample_70.txt
MDS tumor cells

source_name: MDS tumor cells, patient 70

source_name: control DNA


title: Lung Cancer 3T

description: Gene expression data from 3T

source_name: frozen tissue of primary tumor


title: Lung Cancer 17T

description: Gene expression data from 17T


title: MDS tumor cells patient 69

description:
Agilent Feature Extraction file: sample_69.txt
MDS tumor cells

source_name: MDS tumor cells, patient 69

value: unclear 1 or 2


title: MDS tumor cells patient 32

description:
Agilent Feature Extraction file: sample_32.txt
MDS tumor cells

source_name: MDS tumor cells, patient 32


title: MDS tumor cells patient 36

description:
Agilent Feature Extraction file: sample_36.txt
MDS tumor cells

source_name: MDS tumor cells, patient 36


title: Lung Cancer 2T

description: Gene expression data from 2T


title: MDS tumor cells patient 84

description:
Agilent Feature Extraction file: sample_84.txt
MDS tumor cells

source_name: MDS tumor cells, patient 84

value: PC


title: MDS tumor cells patient 52

description:
Agilent Feature Extraction file: sample_52.txt
MDS tumor cells

source_name: MDS tumor cells, patient 52


title: MDA-MB-231_variant_SCP3

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

description:
Weakly metastatic derivative of MDA-MB-231.
SCP3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133A Array Set HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Genespring GX 7.3 Expression Analysis using Per Chip (normalize to 50th percentile) and Per Gene (normalize to median) normalization methods.

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

growth_protocol: Cell lines were maintained in DMEM with 10% FBS and antibiotics.

extract_protocol: Total RNA extracted using Qiagen RNAeasy mini kit following manufacturer's instructions.

treatment_protocol: Cells were grown to sub-confluency before harvesting RNA.

tag: cell line

tag: cell derivative

value: breast cancer


title: MDS tumor cells patient 72

description:
Agilent Feature Extraction file: sample_72.txt
MDS tumor cells

source_name: MDS tumor cells, patient 72


title: MDS tumor cells patient 76

description:
Agilent Feature Extraction file: sample_76.txt
MDS tumor cells

source_name: MDS tumor cells, patient 76


title: MDS tumor cells patient 38

description:
Agilent Feature Extraction file: sample_38.txt
MDS tumor cells

source_name: MDS tumor cells, patient 38


title: MDA-MB-231_variant_SCP4

description:
Weakly metastatic derivative of MDA-MB-231.
SCP4


title: MDS tumor cells patient 49

description:
Agilent Feature Extraction file: sample_49.txt
MDS tumor cells

source_name: MDS tumor cells, patient 49


title: MDS tumor cells patient 104

description:
Agilent Feature Extraction file: sample_104.txt
MDS tumor cells

source_name: MDS tumor cells, patient 104


title: Post-dormancy_PD2R

description:
Mildly metastatic derivative of PD1.
PD2R

source_name: Mildly metastatic derivative of PD1


title: MDS tumor cells patient 28

description:
Agilent Feature Extraction file: sample_28.txt
MDS tumor cells

source_name: MDS tumor cells, patient 28


title: MDS tumor cells patient 81

description:
Agilent Feature Extraction file: sample_81.txt
MDS tumor cells

source_name: MDS tumor cells, patient 81


title: MDS tumor cells patient 71

description:
Agilent Feature Extraction file: sample_71.txt
MDS tumor cells

source_name: MDS tumor cells, patient 71


title: MDS tumor cells patient 54

description:
Agilent Feature Extraction file: sample_54.txt
MDS tumor cells

source_name: MDS tumor cells, patient 54


title: MDS tumor cells patient 40

description:
Agilent Feature Extraction file: sample_40.txt
MDS tumor cells

source_name: MDS tumor cells, patient 40

source_name: control DNA


title: MDS tumor cells patient 25

description:
Agilent Feature Extraction file: sample_25.txt
MDS tumor cells

source_name: MDS tumor cells, patient 25


title: MDS tumor cells patient 30

description:
Agilent Feature Extraction file: sample_30.txt
MDS tumor cells

source_name: MDS tumor cells, patient 30


title: MDS tumor cells patient 24

description:
Agilent Feature Extraction file: sample_24.txt
MDS tumor cells

source_name: MDS tumor cells, patient 24


title: MDA-MB-231_variant_SCP6

description:
Weakly metastatic derivative of MDA-MB-231.
SCP6


title: Post-dormancy_PD2D

description:
Highly metastatic derivative of PD1.
PD2D

source_name: Highly metastatic derivative of PD1


title: MDS tumor cells patient 22

description:
Agilent Feature Extraction file: sample_22.txt
MDS tumor cells

source_name: MDS tumor cells, patient 22


title: Post-dormancy_PD2E

description:
Highly metastatic derivative of PD1.
PD2E


title: Post-dormancy_PD2C

description:
Highly metastatic derivative of PD1.
PD2C


title: MDS tumor cells patient 74

description:
Agilent Feature Extraction file: sample_74.txt
MDS tumor cells

source_name: MDS tumor cells, patient 74


title: MDS tumor cells patient 45

description:
Agilent Feature Extraction file: sample_45.txt
MDS tumor cells

source_name: MDS tumor cells, patient 45


title: Lung Cancer 103T

description: Gene expression data from 103T

source_name: frozen tissue of primary tumor


title: MDS tumor cells patient 48

description:
Agilent Feature Extraction file: sample_48.txt
MDS tumor cells

source_name: MDS tumor cells, patient 48


title: MDS tumor cells patient 18

description:
Agilent Feature Extraction file: sample_18.txt
MDS tumor cells

source_name: MDS tumor cells, patient 18


title: Post-dormancy_PD2A

description:
Highly metastatic derivative of PD1.
PD2A


title: Post-dormancy_PD2B

description:
Highly metastatic derivative of PD1.
PD2B


title: MDS tumor cells patient 20

description:
Agilent Feature Extraction file: sample_20.txt
MDS tumor cells

source_name: MDS tumor cells, patient 20


title: MDS tumor cells patient 47

description:
Agilent Feature Extraction file: sample_47.txt
MDS tumor cells

source_name: MDS tumor cells, patient 47


title: Post-dormancy_PD1

description:
Highly metastatic derivative of SCP6.
PD1

source_name: Highly metastatic derivative of SCP6


title: MDS tumor cells patient 17

description:
Agilent Feature Extraction file: sample_17.txt
MDS tumor cells

source_name: MDS tumor cells, patient 17


title: MDS tumor cells patient 27

description:
Agilent Feature Extraction file: sample_27.txt
MDS tumor cells

source_name: MDS tumor cells, patient 27


title: MDS tumor cells patient 41

description:
Agilent Feature Extraction file: sample_41.txt
MDS tumor cells

source_name: MDS tumor cells, patient 41


title: MDS tumor cells patient 16

description:
Agilent Feature Extraction file: sample_16.txt
MDS tumor cells

source_name: MDS tumor cells, patient 16

source_name: control DNA


title: MDA-MB-231_parental_replicate_1

description:
Parental cell line of SCP6.
Parental-1

source_name: Parental cell line of SCP6


title: MDS tumor cells patient 14

description:
Agilent Feature Extraction file: sample_14.txt
MDS tumor cells

source_name: MDS tumor cells, patient 14


title: MDS tumor cells patient 21

description:
Agilent Feature Extraction file: sample_21.txt
MDS tumor cells

source_name: MDS tumor cells, patient 21


title: MDA-MB-231_parental_replicate_2

description:
Parental cell line of SCP6.
Parental-2


title: MDS tumor cells patient 35

description:
Agilent Feature Extraction file: sample_35.txt
MDS tumor cells

source_name: MDS tumor cells, patient 35


title: MDS tumor cells patient 7

description:
Agilent Feature Extraction file: sample_7.txt
MDS tumor cells

source_name: MDS tumor cells, patient 7


title: MDS tumor cells patient 6

description:
Agilent Feature Extraction file: sample_6.txt
MDS tumor cells

source_name: MDS tumor cells, patient 6


title: MDS tumor cells patient 58

description:
Agilent Feature Extraction file: sample_58.txt
MDS tumor cells

source_name: MDS tumor cells, patient 58


title: BNE_SCHIZ_Disease_39/02

status: Public on Jan 29 2011

city: London

first: Pascal

middle: Francis

last: Durrenberger

address: hammersmith hospital, Du cane road

department: Infectious disease and immunity

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The BeadChips were scanned using the Illumina BeadArray Reader according to standard Illumina scan protocol.

data_processing: The data was extracted using BeadStudio 3.2 (Illumina). Data normalisation and gene differential expression analyses were conducted using the Rosetta error models available in the Rosetta Resolver® system v7.0 (Rosetta Biosoftware, Seattle, Wa, USA).

source_name: Grey matter in Brodmann area 36

label_protocol: RNA samples were prepared for array analysis using the Illumina TotalPrep™-96 RNA Amplification Kit.

extract_protocol: Total RNA was extracted from dissected snap-frozen tissue by the individual laboratories according to a BNE optimised common protocol using the RNeasy® tissue lipid mini kit. Quality was assessed using Bioanalyzer.

tag: disease

value: Schizophrenia

tag: age at death (in years)

tag: illness duration (in years)

tag: post-mortem delay (in hours)


title: MDS tumor cells patient 1

description:
Agilent Feature Extraction file: sample_1.txt
MDS tumor cells

source_name: MDS tumor cells, patient 1


title: MDS tumor cells patient 11

description:
Agilent Feature Extraction file: sample_11.txt
MDS tumor cells

source_name: MDS tumor cells, patient 11


title: BNE_SCHIZ_Disease_43/03

source_name: Grey matter in Brodmann area 38


title: BNE_SCHIZ_Disease_1/00

source_name: Grey matter in Brodmann area 32


title: BNE_SCHIZ_Disease_13/00

source_name: Grey matter in Brodmann area 33


title: BNE_SCHIZ_Disease_36/02

source_name: Grey matter in Brodmann area 35


title: BNE_SCHIZ_Control_73/02

source_name: Grey matter in Brodmann area 28

tag: post-mortem delay


title: BNE_SCHIZ_Disease_83/01

source_name: Grey matter in Brodmann area 41


title: BNE_SCHIZ_Disease_46/00

source_name: Grey matter in Brodmann area 39


title: BNE_SCHIZ_Control_RZ77

source_name: Grey matter in Brodmann area 29


title: BNE_SCHIZ_Disease_39/03

source_name: Grey matter in Brodmann area 37


title: BNE_SCHIZ_Control_RZ84

source_name: Grey matter in Brodmann area 30


title: BNE_SCHIZ_Disease_35/00

source_name: Grey matter in Brodmann area 34


title: MDS tumor cells patient 3

description:
Agilent Feature Extraction file: sample_3.txt
MDS tumor cells

source_name: MDS tumor cells, patient 3

source_name: control DNA


title: BNE_SCHIZ_Control_61/01

source_name: Grey matter in Brodmann area 27


title: BNE_SCHIZ_Control_51/02

source_name: Grey matter in Brodmann area 24


title: BNE_SCHIZ_Control_RZ99

source_name: Grey matter in Brodmann area 31


title: BNE_SCHIZ_Control_57/02

source_name: Grey matter in Brodmann area 25


title: MDS tumor cells patient 8

description:
Agilent Feature Extraction file: sample_8.txt
MDS tumor cells

source_name: MDS tumor cells, patient 8


title: BNE_SCHIZ_Control_43/01

source_name: Grey matter in Brodmann area 23


title: BNE_PD_Disease_PD93

source_name: Substantia nigra

value: Parkinson's disease


title: BNE_SCHIZ_Control_59/02

source_name: Grey matter in Brodmann area 26


title: BNE_PD_Disease_PD99


title: BNE_SCHIZ_Control_02/02/2007

source_name: Grey matter in Brodmann area 22


title: BNE_PD_Disease_PD86


title: BNE_PD_Disease_PD84


title: BNE_PD_Disease_PD63


title: MDS tumor cells patient 42

description:
Agilent Feature Extraction file: sample_42.txt
MDS tumor cells

source_name: MDS tumor cells, patient 42


title: MDS tumor cells patient 60

description:
Agilent Feature Extraction file: sample_60.txt
MDS tumor cells

source_name: MDS tumor cells, patient 60


title: BNE_PD_Disease_PD51


title: BNE_PD_Disease_PD16


title: BNE_PD_Disease_PD09


title: BNE_SCHIZ_Disease_50/01

source_name: Grey matter in Brodmann area 40


title: BNE_PD_Disease_PD13


title: BNE_PD_Control_PDC07


title: BNE_PD_Control_224/01b


title: BNE_PD_Control_223/00


title: BNE_PD_Control_208/02


title: BNE_PD_Disease_PD41


title: BNE_PD_Control_224/01a


title: BNE_PD_Disease_PD22


title: BNE_PD_Control_PDC05


title: BNE_PD_Control_41/06


title: HsO4A-109_346186

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description:
EPC Early + Ado vs EPC Early + DMSO
Date: 2010/05/19

hyb_protocol: Agilent : 80 pmol at 60 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner Image intensity data were extracted with GenePix Pro 6.0 analysis software

data_processing: Lowess non linear normalization

source_name: EPC early m9 6h AE

label_protocol: Ambion

extract_protocol: Qiagen

value: EPC early m9 6h AE

value: Trizol

value: EPC Early

source_name: EPC early m9 6h DMSO

value: EPC early m9 6h DMSO


title: HsO4A-110_346183

description:
EPC Early + Ado vs EPC Early + DMSO
Date: 2010/05/26

source_name: EPC early m10 6h AE

value: EPC early m10 6h AE

source_name: EPC early m10 6h DMSO

value: EPC early m10 6h DMSO


title: HsO4A-104_346229

description:
EPC Late + Ado vs EPC Late + DMSO
Date: 2009/01/06

source_name: EPC M4 CD34 AE 10uM 6h

value: EPC M4 CD34 AE 10uM 6h

value: EPC Late

source_name: EPC M4 CD34 DMSO 10uM 6h

value: EPC M4 CD34 DMSO 10uM 6h


title: HsO4A-098_345939

description:
EPC Early + Ado vs EPC Early + DMSO
Date: 2008/06/09

source_name: EPC AE 10uM 6h

value: EPC AE 10uM 6h

source_name: EPC DMSO 6h

value: EPC DMSO 6h


title: HsO4A-113_346376


title: HsO4A-112_345898


title: HsO4A-108_346185


title: BNE_PD_Control_117/02

value: M


title: HsO4A-099_345936


title: HsO4A-106_346189


title: BNE_MS_Disease_MS289

source_name: Subpial grey matter lesions from the frontal gyri

value: Multiple sclerosis


title: HsO4A-101_346232


title: BNE_MS_Disease_MS88

value: F


title: HsO4A-100_345937


title: HsO4A-107_346190


title: HsO4A-105_346192


title: HsO4A-093_346237

description:
EPC Late + Ado vs EPC Late + DMSO
Date: 2010/06/08

source_name: EPC M15 CD34 6h AE

value: EPC M15 CD34 6h AE

source_name: EPC M15 CD34 6h DMSO

value: EPC M15 CD34 6h DMSO


title: BNE_MS_Disease_MS230


title: BNE_PD_Disease_PD45

source_name: Substantia nigra

value: Parkinson's disease


title: HsO4A-089_346366

description:
EPC Early + Ado vs EPC Early + DMSO
Date: 2010/05/31

source_name: EPC 6h M11 early AE

value: EPC 6h M11 early AE

source_name: EPC 6h M11 early DMSO

value: EPC 6h M11 early DMSO


title: BNE_MS_Disease_MS256


title: BNE_MS_Disease_MS255


title: HsO4A-088_346365

value: Trizol

value: EPC Early


title: HsO4A-092_346234


title: HsO4A-087_346364

description:
EPC Late + Ado vs EPC Late + DMSO
Date: 2010/06/10

source_name: EPC M16 CD34 6h AE

value: EPC M16 CD34 6h AE

source_name: EPC M16 CD34 6h DMSO

value: EPC M16 CD34 6h DMSO


title: BNE_MS_Disease_MS286


title: HsO4A-091_346235


title: BNE_MS_Disease_MS235


title: BNE_MS_Disease_MS229


title: HsO4A-085_346362


title: BNE_MS_Control_CMS-RZ99


title: BNE_MS_Disease_MS197


title: BNE_MS_Disease_MS203


title: HsO4A-067_346027


title: BNE_MS_Control_CMS-RZ90


title: HsO4A-086_346363


title: HsO4A-084_346361


title: HsO4A-066_346028


title: BNE_MS_Control_CMS-RZ77


title: BNE_MS_Control_CMS-RZ82


title: HsO4A-064_346030

description:
EPC Late + Ado vs EPC Late + DMSO
Date: 2010/06/16

source_name: EPClate 6h m17 AE

value: EPClate 6h m17 AE

source_name: EPClate 6h m17 DMSO

value: EPClate 6h m17 DMSO


title: HsO4A-083_346360

value: EPC Late


title: BNE_MS_Control_227SFG


title: BNE_MS_Control_CMS-RZ84


title: HsO4A-063_346032


title: HsO4A-111_346377

value: EPC early m10 6h AE

value: EPC early m10 6h DMSO


title: HsO4A-065_346029


title: HsO4A-062_346033

description:
EPC Early + Ado vs EPC Early + DMSO
Date: 2008/08/22

source_name: EPC M2 AE 10uM 6h

value: EPC M2 AE 10uM 6h

source_name: EPC M2 DMSO 6h

value: EPC M2 DMSO 6h


title: HsO4A-061_346034


title: HsO4A-059_346079


title: HsO4A-055_346039

description:
EPC Early + Ado vs EPC Early + DMSO
Date: 2008/08/26

source_name: EPC M3 AE 10uM 6h

value: EPC M3 AE 10uM 6h

source_name: EPC M3 DMSO 6h

value: EPC M3 DMSO 6h


title: BNE_MS_Control_216SFG

value: Multiple sclerosis

value: M


title: BNE_HD_Disease_WU35/02

source_name: Ventral head of the caudate nucleus

value: Huntington's disease

value: F


title: BNE_MS_Control_06-189


title: BNE_MS_Control_146SFG


title: BNE_MS_Control_01/06/1965


title: HsO4A-056_346038

value: Trizol


title: HsO4A-054_346040

value: EPC Early


title: BNE_HD_Disease_RZ448


title: BNE_HD_Disease_RZ93


title: HsO4A-052_346042


title: HsO4A-051_346043

source_name: EPC early m9 6h AE

value: EPC early m9 6h AE

source_name: EPC early m9 6h DMSO

value: EPC early m9 6h DMSO


title: HsO4A-068_346026

value: EPClate 6h m17 AE


title: BNE_HD_Disease_RZ364


title: BNE_HD_Disease_RZ349


title: BNE_HD_Disease_RZ157


title: BNE_HD_Control_RZ146h


title: BNE_HD_Control_WU138/00


title: BNE_HD_Control_RZ90h


title: HsO4A-048_346050

description:
EPC Late + Ado vs EPC Late + DMSO
Date: 2009/01/23

source_name: EPC M5 CD34 AE 10uM 6h

value: EPC M5 CD34 AE 10uM 6h

source_name: EPC M5 CD34 DMSO 10uM 6h

value: EPC M5 CD34 DMSO 10uM 6h


title: HsO4A-046_346048

value: EPC Late


title: BNE_HD_Disease_RZ428


title: HsO4A-049_346076


title: HsO4A-053_346041


title: HsO4A-044_346102

description:
EPC Late + Ado vs EPC Late + DMSO
Date: 2009/03/17

source_name: EPC M6 CD34 AE 10uM 6h

value: EPC M6 CD34 AE 10uM 6h

source_name: EPC M6 CD34 DMSO 10uM 6h

value: EPC M6 CD34 DMSO 10uM 6h


title: HsO4A-047_346049


title: HsO4A-045_346103


title: HsO4A-050_346077


title: BNE_HD_Control_RZ084h


title: BNE_HD_Control_RZ082h


title: BNE_HD_Control_RZ077h


title: HsO4A-043_346104


title: HsO4A-042_346105


title: BNE_HD_Disease_RZ431


title: BNE_HD_Control_CMS36


title: BNE_HD_Control_CMS28


title: BNE_HD_Control_CMS14


title: H1_p47_rep1

city: BRONX

first: Chan-Jung

last: Chang

address: 1300 MORRIS PARK AVE

department: Hematology/Cell biology

institute: Albert Einstein College of medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA express software

source_name: Human Embryonic Stem Cells

label_protocol: total RNA was labelled with a fluorophore using standard Affymetrix procedure (primer extension usig a polydT primer)

growth_protocol: Cells were grown in ES cell medium contain N2, B27, 100ug/mL BSA, and 100ng/mL basic FGF.

extract_protocol: total RNA were extracted  using the RNAeasy kit (Qiagen)

value: male

tag: cell type

value: embryonic stem cells


title: FLiPSC_p23_rep1

source_name: induced pluripotent stem cells

value: fetal liver mesenchymal cells


title: H1_KM_rep1


title: BNE_ALS_Disease_1746a

source_name: Cervical spinal cord

value: Amyotrophic lateral sclerosis


title: BNE_HD_Disease_RZ406

value: M


title: iPSC_p19_rep1

value: embryonic fibroblasts


title: FLiPSC_p12_rep1


title: BNE_ALS_Disease_1746b


title: BNE_HD_Control_RZ076h

value: Huntington's disease


title: iPSA_KM_rep1


title: BNE_ALS_Disease_1814


title: BNE_ALS_Disease_1822


title: iPSC_KM_rep1


title: Treatment, replicate 3

city: Frederick

first: Richard

middle: A

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

description: treatment

hyb_protocol: Labeled cRNA was hybridized to the Affymetrix Gene 1.0 ST microarray according to the manufacturer's recommended standard protocol.

scan_protocol: Hybridized Affymetrix Human Gene 1.0 ST microarrays were scanned according to the manufacturer's recommended standard protocol.

data_processing: Gene expression profiles of DNA-transfected cells were analyzed using Partek Genomic Sutie, as previously described (Blood 109:1841-1849).

source_name: HEK cells treated with Neo vector

label_protocol: cRNA was labelled according to the manufacturer's recommended standard protocol for the Affymetrix Gene 1.0 ST microarray .

growth_protocol: HEK293 cells were obtained from ATCC.

extract_protocol: Total cellular RNA was extracted from HEK293 cells using RNeasy isolate kit (Qiagen).

treatment_protocol: Treatment was done as previously described (Blood 109:1841-1849)

value: HEK cell

value: HEK293 cells


title: BNE_ALS_Disease_2353


title: Control, replicate 3

description: control

source_name: HEK cells treated with transient vector


title: iPSA_p24_rep1


title: iPSB_p23_rep1


title: BNE_ALS_Disease_1672

value: F


title: Treatment, replicate 1

description: treatment


title: Treatment, replicate 2

description: treatment


title: BNE_ALS_Disease_1693


title: iPSB_KM_rep1


title: BNE_ALS_Disease_2114


title: Control, replicate 2

description: control


title: BNE_ALS_Disease_1653


title: BNE_ALS_Disease_1731


title: BNE_ALS_Control_C039a


title: BNE_ALS_Control_C036


title: Control, replicate 1

description: control

value: HEK cells


title: BNE_HD_Disease_WU230/99


title: BNE_ALS_Control_C037a


title: BNE_ALS_Control_C011


title: BNE_ALS_Control_C037b


title: siControl, (+TGFbeta, 8 hours), biological replicate 3

first: John

middle: M

last: Di Guglielmo

state: ON

address: 1151 Richmond

department: Phys/Pharm

institute: University of Western Ontario

hyb_protocol: Following fragmentation, 5.5 ug of ss cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe level data was generated using Affymetrix Command Console v1.1. Probes were summarized to gene level data in Partek Genomics Suite using the RMA algorithm.

source_name: A549 cells transfected with control siRNA and treated with TGFbeta. RNA isolated 8 hours after TGFbeta treatment.

label_protocol: Biotinylated ds cDNA were prepared according to the Affymetrix Whole Transcript protocol from 200 ng total RNA (The Ambion WT Expression Kit 2009 and GeneChip WT Terminal Labeling and Hybridization User Manual, 2009-2010, Affymetrix).

growth_protocol: A549 Non small cell lung cancer cells were grown in F-12K media supplemented with 10% fetal bovine serum.

extract_protocol: Extraction of total RNA was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Control or aPKC silenced A549 cells were serum starved and then treated with 250 pM TGFbeta  for 1 hour. Cells were then washed 3x with phosphate buffered saline and further incubated for an additional 7 or 23 hours in serum deprived media (0.2% FBS) prior to total RNA extraction.

value: A549 human lung cancer cells from ATCC (ATCC number CCL-185)

tag: transfection

value: siControl

tag: treatment

value: +TGFbeta

tag: time

value: 8 hours


title: siControl, (+TGFbeta, 8 hours), biological replicate 2


title: siControl, (+TGFbeta, 24 hours), biological replicate 3

source_name: A549 cells transfected with control siRNA and treated with TGFbeta. RNA isolated 24 hours after TGFbeta treatment.

value: 24 hours


title: siPKCiz (+TGFbeta, 8 hours), biological replicate 3

source_name: A549 cells transfected with  siRNA directed at aPKC (PKCiota and PKCzeta) and treated with TGFbeta. RNA isolated 8 hours after TGFbeta treatment.

value: siPKCiz


title: siPKCiz (-TGFbeta) biological replicate 3

source_name: Untreated A549 cells transfected with siRNA directed at aPKC (PKCiota and PKCzeta).

value: -TGFbeta


title: BNE_ALS_Control_A0741

tag: gender


title: siPKCiz (+TGFbeta, 8 hours), biological replicate 2


title: siPKCiz (+TGFbeta, 24 hours) biological replicate 2

source_name: A549 cells transfected with  siRNA directed at aPKC (PKCiota and PKCzeta) and treated with TGFbeta. RNA isolated 24 hours after TGFbeta treatment.


title: siControl, (-TGFbeta) biological replicate 3

source_name: Untreated, A549 cells transfected with control siRNA.


title: BNE_ALS_Control_C039b


title: BNE_ALS_Control_A0744


title: siPKCiz (+TGFbeta, 24 hours) biological replicate 3


title: BNE_AD_Disease_A06-154

source_name: Entorhinal cortex

value: Alzheimer's disease


title: BNE_ALS_Control_A05149a


title: siPKCiz (+TGFbeta, 24 hours) biological replicate 1


title: siControl, (+TGFbeta, 24 hours), biological replicate 2


title: siControl, (-TGFbeta) biological replicate 2


title: siPKCiz (-TGFbeta) biological replicate 2


title: BNE_AD_Disease_A06-064


title: BNE_AD_Disease_A06-062


title: BNE_AD_Disease_A06-102


title: BNE_ALS_Control_A05149b


title: siControl, (+TGFbeta, 24 hours), biological replicate 1


title: siPKCiz (+TGFbeta, 8 hours), biological replicate 1


title: siPKCiz (-TGFbeta) biological replicate 1


title: BNE_AD_Disease_A05-084


title: siControl, (+TGFbeta, 8 hours), biological replicate 1


title: BNE_AD_Disease_A05-082


title: BNE_AD_Disease_A02-066


title: siControl, (-TGFbeta) biological replicate 1


title: BNE_AD_Disease_A05-172


title: FR-si222-3

city: Bloomington

first: Meng

last: Li

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

institute: Indiana University

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

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

source_name: MCF7 fulvestrant-resistant cell line transfected by antisense hsa-miR-222

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: MCF7-FR cells were growing in phenol red-free medium with 10% charcoal-stripped fetal bovine serum (FBS) and 10E-7 mol/L fulvestrant

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

treatment_protocol: For transfection assays, cells were plated in antibiotic-free media and transfected with Lipofectamine 2000 (Invitrogen, Carlasbad, CA) according to the manufacturer's instructions.  Antagomirs were transfected at 100nM concentrations.


title: BNE_AD_Disease_A02-054


title: BNE_AD_Disease_A02-021


title: Spleen Follicular B cells from B6 mouse #92769

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina MouseRef-8 BeadChips V2  at 58oC for 20 hrs

scan_protocol: Fluoresent array images were collected using Illumina BeadStation 500GX scanner and image intensity data were extracted using  Illumina BeadStudio v3.

data_processing: Illumina probe data were exported from BeadStudio as raw data and were screened for quality. Samples failing chip visual inspection and control examination were removed. The R software was used to quantile-normalized the probe intensities, and to minimun replace (surrogate-replacement policy) values below backround using the mean backround value of the built-in Illumina probe controls as an alternative to background substraction (which may introduce negative values) to reduce ‘over inflated’ expression ratios in subsequent steps.

source_name: B6 Spleen Follicular B cells

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol.

growth_protocol: Viable spleen follicular B cells and MZB cells were sorted based on C19, CD21 and CD23 expression (sytox_blue_neg, CD19_pos, CD21_int, CD23_pos and sytox_blue_neg, CD19_pos, CD21_high, CD23_neg respectively)

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: Cells were obtained from control B6 mice or mice transgenic for KLF3 (CD19:KLF3)

tag: animal id

value: Spleen Follicular B cells

tag: genetic background

tag: genotype

value: wild type


title: BNE_AD_Control_A06-189b


title: Spleen Follicular B cells from CD19:KLF3 mouse #92768

source_name: CD19:KLF3 Spleen Follicular B cells

value: CD19:KLF3 mouse #92768

value: CD19:KLF3 transgenic


title: Nonlesional Epithelium Nonatopic Control rep4a

city: Baltimore

first: Alan

middle: E.

last: Berger

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description: Nonatopic Control biological replicate 4 technical replicate a

hyb_protocol: cRNA was hybridized to Illumina Sentrix HumanRef-8 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.

scan_protocol: All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction.  Two types of processed data were used for analysis: 1. Data was Z-transformed based on probes which were Present for at least one sample (the Illumina Detection Pvalue was < 0.01).  Specifically, for each sample, define m to be the mean of the expression values for that sample taken over all probes present in at least 1 sample, and define s to be the corresponding standard deviation. Then for all  the probes on the array, for that sample the Z-transformed expression value corresponding to an expression value e is (e-m)/s. 2. For use in calculating correlations of gene expression levels with the values of clinical variables; the expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed. For the data matrices, the ID_REF is the Illumina probe identifier, and the Detection Pval is the Illumina call for whether the measured expression level is Present (above background).  Detection Pvalues near 0 indicate Present.  In our analysis we considered expression values with a Detection Pvalue below 0.01 to be Present. Z-transformed data (item 1) provided as a supplementary file on GSE26952. Data median scaled (to median = 256) and then log base 2 transformed (item 2) included in Sample table.

source_name: Full-thickness epidermis

label_protocol: Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).

extract_protocol:
Tissue samples were obtained and prepared as described in the Methods section of the paper cited in the overall design section of this GEO submission. Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany). The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany).
The quality of total RNA samples was assessed using
an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: disease group

value: Nonatopic Control

tag: Sex

value: m

tag: age

tag: race

value: African American

tag: easi/pasi

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:0

tag: ar or asthma

value: YES, subject has history of AR (allergic rhinitis), asthma or both:no

tag: eosinophil level (cells/ml)

tag: ige (kiu/l)

tag: rast (radioallergosorbent test)

value: detects IgE that reacts specifically with suspected or known allergens:negative

tag: s. aureus

value: Skin culture positive or negative for S. Aureus:neg


title: Nonlesional Epithelium Nonatopic Control rep5

description: Nonatopic Control biological replicate 5

value: Caucasian

value: detects IgE that reacts specifically with suspected or known allergens:positive


title: BNE_AD_Disease_A03-045

tag: disease

value: M

tag: age at death (in years)

tag: post-mortem delay (in hours)

tag: post-mortem delay


title: Spleen MZB cells from CD19:KLF3 mouse #92768

source_name: CD19:KLF3 Spleen MZB

tag: animal id

tag: cell type

value: Spleen MZB


title: FR-si222-1

tag: treatment

tag: cell line


title: Nonlesional Epithelium Nonatopic Control rep2a

description: Nonatopic Control biological replicate 2 technical replicate a

tag: disease group

tag: Sex

value: f

value: YES, subject has history of AR (allergic rhinitis), asthma or both:YES

value: normal (120-300 cells/ml):50


title: FR-si222-2


title: Nonlesional Epithelium Nonatopic Control rep3

description: Nonatopic Control biological replicate 3

tag: age

tag: race


title: Spleen MZB cells from B6 mouse #92769

description: Spleen MZB cells from B6 mouse #92769

source_name: B6 Spleen MZB

tag: genetic background

tag: genotype

value: wild type


title: BNE_AD_Control_A06-189a

value: Alzheimer's disease

tag: gender

value: F


title: Spleen Follicular B cells from CD19:KLF3 mouse #92751

value: CD19:KLF3 mouse #92751

value: Spleen Follicular B cells

value: CD19:KLF3 transgenic


title: BNE_AD_Control_A06-065


title: Nonlesional Epithelium Nonatopic Control rep4b

description: Nonatopic Control biological replicate 4 technical replicate b

value: Nonatopic Control

value: m

value: African American

tag: easi/pasi

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:0

tag: ar or asthma

tag: eosinophil level (cells/ml)

tag: ige (kiu/l)

tag: rast (radioallergosorbent test)