title: self3-self3


title: 933M

status: Public on Jul 30 2015

type: genomic

city: Gdansk

first: Arkadiusz

last: Piotrowski

address: Hallera 107

department: Biology and Pharmaceutical Botany

country: Poland

institute: Medical University of Gdansk

description: Comparative Genomic Hybridization of tissues from breast cancer patients

hyb_protocol: Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).

data_processing: Microarray data were extracted with DEVA software v1.2 CGH, including spatial correction (LOESS) and qspline fit normalization, in order to compensate for differences in signal between the two dyes (Workman et al., 2002, Genome Biol 3(9):research0048, PMID: 12225587).

molecule: genomic DNA

organism: Homo sapiens

source_name: lymph node metastasis

extract_protocol: DNA from solid tissues was isolated using standard phenol – chloroform extraction method (Sambrook, J., Russell, D.W., 2001, Molecular Cloning: A Laboratory Manual, Volume 1st of 3, 6.4-6.12, Cold Spring Harbor Laboratory Press, ISBN 9780879695774) with modifications. DNA from blood samples was isolated by QIAamp DNA Blood Kit according to manufacturer’s protocol (QIAamp DNA Blood Midi Kit, QIAGEN, Hilden, Germany, #5118).

tag: gender

value: female

source_name: peripheral blood leukocytes


title: shSOX17 D4 rep2

type: RNA

city: London

first: Michael

middle: D.

last: Schneider

address: Du Cane Road

department: Imperial Centre for Translational and Experimental Medicine

country: United Kingdom

institute: Imperial College London

description: Gene expression data from mouse ES cells containing shRNA against Sox17 at day 4 of differentiation.

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol by the Baylor College of Medicine Microarray Facility, using Affymetrix Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GeneArray 2500 Scanner.

data_processing: The data were analysed with the R/Bioconductor platform (version 3.0.2). The expression signal values were generated using the Frozen-RMA (fRMA) pre-processing algorithm [PMID:20097884].

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mESCs, Sox17-shRNA, day 4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by the Baylor College of Medicine Microarray Facility (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse embryonic stem cells (AB2.2) were differentiated in vitro by embryoid body formation with hanging droplet technique [PMID:8155574]

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and RNeasy reagents (Qiagen) according to the manufacturers' instructions.

treatment_protocol: ESCs were transduced with lentiviral vectors coexpressing enhanced green fluorescent protein (eGFP) with shRNA against Sox17, or against firefly luciferase. Transduced cells were flow-sorted based on GFP fluorescence, grown as embryoid bodies, and transferred to tissue culture plates after 4.5 days [PMID:17360443]. Expression profiling was performed after further culture for up to 10 days.

tag: cell line

tag: transduction

value: Sox17 shRNA

tag: differentiation

value: day 4


title: 1436H

scan_protocol: Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).

source_name: uninvolved glandular tissue

source_name: genomic DNA from a pool of female individuals (Promega)


title: shSOX17 D4 rep1


title: 951H

label_protocol: Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).


title: 949M


title: 915T

source_name: primary tumor


title: 960H


title: 933T


title: 949H


title: shSOX17 D2 rep1

description: Gene expression data from mouse ES cells containing shRNA against Sox17 at day 2 of differentiation.

source_name: mESCs, Sox17-shRNA, day 2

value: day 2


title: shSOX17 D2 rep2


title: 956T


title: 643M


title: 902M


title: 910T


title: 631M


title: 600H


title: shSOX17 D0 rep1

description: Gene expression data from mouse ES cells containing shRNA against Sox17 at day 0 of differentiation. Single replicate, 2nd biological replicate failed.

source_name: mESCs, Sox17-shRNA, day 0

value: day 0


title: 974T


title: 915H


title: shLUC D10 rep2

description: Gene expression data from mouse ES cells containing shRNA against Luciferase at day 10 of differentiation.

source_name: mESCs, Luciferase-shRNA, day 10

value: Luciferase shRNA

value: day 10


title: shLUC D10 rep1


title: 904T


title: 642H


title: 631H


title: 906T


title: 961M


title: shLUC D8 rep2

description: Gene expression data from mouse ES cells containing shRNA against Luciferase at day 8 of differentiation.

source_name: mESCs, Luciferase-shRNA, day 8

value: day 8


title: 983M


title: 963T


title: 643T


title: 633H


title: 946H


title: 906M


title: shLUC D8 rep1


title: 961T


title: 900T


title: 980H


title: 980T


title: shLUC D6 rep2

description: Gene expression data from mouse ES cells containing shRNA against Luciferase at day 6 of differentiation.

source_name: mESCs, Luciferase-shRNA, day 6

value: day 6


title: 913M


title: 604M


title: shLUC D6 rep1


title: shLUC D5 rep2

description: Gene expression data from mouse ES cells containing shRNA against Luciferase at day 5 of differentiation.

source_name: mESCs, Luciferase-shRNA, day 5

value: day 5


title: 999M


title: 915M


title: 956H


title: 962H


title: 946M


title: 917M


title: 961H


title: 905M


title: shLUC D4 rep2

description: Gene expression data from mouse ES cells containing shRNA against Luciferase at day 4 of differentiation.

source_name: mESCs, Luciferase-shRNA, day 4


title: 608H


title: 001H


title: shLUC D5 rep1


title: 600T


title: 913T


title: 956M


title: 983T


title: 904H


title: 604T


title: shLUC D2 rep2

description: Gene expression data from mouse ES cells containing shRNA against Luciferase at day 2 of differentiation.

source_name: mESCs, Luciferase-shRNA, day 2


title: shLUC D2 rep1


title: 951M


title: shLUC D0 rep2

description: Gene expression data from mouse ES cells containing shRNA against Luciferase at day 0 of differentiation.

source_name: mESCs, Luciferase-shRNA, day 0


title: shLUC D0 rep1


title: shLUC D4 rep1


title: 631T


title: 608T


title: 642T


title: 909T


title: 641H


title: 2512T


title: 962T


title: 974H


title: 902T


title: 962M


title: 001T


title: 633M


title: 907T


title: 642M


title: 909H


title: 2720_UAB-58_individuals

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis; Enzymatic Labeling for Blood, Cells or Tissues (with a High Throughput option); Protocol Version 6.0, November 2008

scan_protocol: The arrays were scanned at 5 micrometer resolution using Axon 4000B microarray scanner.

data_processing: Data extraction background subtraction and LOWESS normalization were carried out using Feature Extraction software v.9.5.

source_name: unrelated individual blood DNA

extract_protocol: DNA extraction was carried out with QuickGene-610L  instrument  (AUTOGEN; http://www.autogen.com/assets/pdf/QG-610L%20Brochure.pdf) using QuickGene DNA whole blood kit L (catalog number : DB-L, version 2.0) according to manufacturer's protocol.

treatment_protocol: Peripheral blood was collected into anticoagulant containing tubes and stored at ambient temperature until DNA extraction.

tag: sample type

value: reference

tag: tissue

value: peripheral blood leukocytes

source_name: Patient DNA samples with non-overlapping CNCs

tag: disease


title: NSC_hypoxia_replicate4

city: Barcelona

first: Nuria

last: de la Iglesia

address: Rossello 153

country: Spain

institute: IDIBAPS

description: Gene expression in NSC after long term culture in hypoxia

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (Agilent-028005) for 17 hours at 65°C in a rotating 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), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color (Cy3) scan setting for expression array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Neural Stem Cells, cultured at 5% oxygen, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: NSC freshly isolated from E13.5 mouse embryos were cultured in parallel from DIV 0 at either 21% (atmospheric) or 5% oxygen during a minimum of 10 days in serum-free medium.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality control was monitored in a 2100 Bioanalyzer (Agilent Technologies). In all cases, the RNA integrity number was >7.

treatment_protocol: NSC were cultured at either 21% (atmospheric) or 5% oxygen (normoxia and hypoxia, respectively).

tag: cell type

value: embryonic Neural Stem Cells

tag: developmental stage


title: NSC_hypoxia_replicate3

source_name: Neural Stem Cells, cultured at 5% oxygen, replicate 3


title: NSC_normoxia_replicate4

description: Gene expression in NSC after long term culture in normoxia

source_name: Neural Stem Cells, cultured at 21% oxygen, replicate 4


title: UAB-5_1365_individuals

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis; Enzymatic Labeling for Blood, Cells or Tissues (with a High Throughput option); Protocol Version 6.0, November 2008


title: 604H

source_name: uninvolved glandular tissue


title: 971M

source_name: lymph node metastasis


title: UAB-53_UAB-3_individuals


title: NSC_normoxia_replicate3

source_name: Neural Stem Cells, cultured at 21% oxygen, replicate 3


title: 943M

source_name: peripheral blood leukocytes


title: 2652H


title: NSC_hypoxia_replicate2

source_name: Neural Stem Cells, cultured at 5% oxygen, replicate 2


title: self1-self1


title: 943T

source_name: primary tumor


title: 641M


title: NSC_normoxia_replicate2

source_name: Neural Stem Cells, cultured at 21% oxygen, replicate 2


title: 1255T


title: 900M


title: 907M


title: 633T


title: 916H

source_name: genomic DNA from a pool of female individuals (Promega)


title: NSC_hypoxia_replicate1

source_name: Neural Stem Cells, cultured at 5% oxygen, replicate 1


title: 903T


title: 652T


title: 947H


title: 903M


title: NSC_normoxia_replicate1

source_name: Neural Stem Cells, cultured at 21% oxygen, replicate 1


title: 954H


title: 959T


title: IL10+/+ Treg replicate 2

city: Adelaide

first: John

middle: E

last: Schjenken

state: South Australia

address: The Robinson Research Institute and School of Paediatrics and Reproductive Health. Level 6. Medical School North. Frome Road

country: Australia

institute: The University of Adelaide

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

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

data_processing: RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. Cel files for each chip were generated using Affymetrix GeneChip Command Console (Affymetrix).  Quality control was assessed using the Affymetrix Expression Console software.  The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to Partek Genomic Suite. A threshold of either <1.5 fold change (low stringency) or <2.0 fold change (high stringency) was used to identify differentially expressed genes with a p<0.05.  Bioinformatics was performed using Ingenuity Pathway Analysis (IPA) version 18488943 Build 308606M.

label: Biotin

source_name: mouse Treg cells from uterine draining lymph nodes, d9.5pc

label_protocol: Standard Affymetrix Protocol

growth_protocol: All animal experiments were performed in accordance with the Guiding Principles for the Care and Use of Research Animals endorsed by the Society for the Study of Reproduction, with approval from the University of Adelaide Animal Ethics Committee. Mice were housed in a specific pathogen-free facility at the University of Adelaide with controlled temperature and lighting (12L:12D). Food and water were supplied ad libitum. C57BL/6 (B6, Il10+/+) and Il10-/- mutant mice back-crossed through the same B6 colony were bred in-house and Balb/c male mice were purchased from the University of Adelaide Central Animal Facility. Females were stored at a maximum of 7 females per cage while males were stored separately. All mice were kept in individually ventilated cages (Techniplast).-Il10−/− mice received broad-spectrum antibiotics (Oxymav 100: 100 g/kg oxytetracycline hydrochloride; Mavlab, Logan, QLD, Australia) in autoclaved drinking water twice weekly at a concentration of 2 mg/ml to prevent colitis.

extract_protocol: Total RNA was amplified using the Ovation PicoSL WTA System V2 (Nugen Inc., San Carlos, CA, USA) and MinElute Reaction Cleanup Kit (Qiagen Inc., Valencia, CA, USA), according to the manufacturer’s instructions, to provide 5 μg of cRNA for each microarray.

treatment_protocol: PALN were excised from pregnant female mice on d9.5 post-coitus and CD4+CD25+ lymphocytes were purified using flow cytometry.

value: Tregs

tag: genotype/variation

tag: source

value: uterine draining lymph node

tag: age

value: d9.5 pc


title: IL10+/+ Treg replicate 3


title: IL10+/+ Treg replicate 4


title: 960M


title: IL10+/+ Treg replicate 1


title: 1431T


title: 640T


title: 912M


title: 907H


title: 901H


title: 924M


title: HUSK_28926

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

country: USA

institute: NHGRI

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

organism: Canis lupus familiaris

source_name: whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: origin

value: North America

tag: breed

value: Siberian Husky (HUSK)


title: 912T

value: female


title: IL10-/- Treg replicate 3


title: IL10-/- Treg replicate 2


title: 901T


title: HUSK_29464


title: 640M


title: HUSK_15872


title: IL10-/- Treg replicate 1


title: IL10-/- Treg replicate 4


title: HUSK_28487


title: 903H


title: Heart__Lamb_Replicate 8

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >9.7 pmol Cy3/µg cRNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) design 019921 by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least four arrays.

organism: Ovis aries

source_name: Heart septum_lamb

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent, Newcastle DE) 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 from heart septa with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen RNeasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer.

treatment_protocol: No treatment was given to either ewe or fetus.

tag: developmental age

value: 14 days of age

value: Heart septum


title: 916M


title: HUSK_28925


title: 947T


title: 989M


title: 1255H


title: 905H


title: 914T


title: Heart__Lamb_Replicate 7


title: HUSK_15873


title: Heart__Lamb_Replicate 5


title: 1251T


title: Heart__Lamb_Replicate 6


title: 951T


title: 943H


title: 968M


title: AMAL_29547

value: Alaskan Malamute (AMAL)


title: 999T


title: Heart__Lamb_Replicate 4


title: Heart__Lamb_Replicate 3


title: HUSK_11480


title: 971T


title: HUSK_11487


title: Heart__Lamb_Replicate 2


title: 947M


title: 924H


title: HUSK_14529


title: HUSK_11490


title: 957H


title: Heart__Term_Replicate 8

source_name: Heart septum_term

value: Term (around 145 days of fetal age)


title: 901M


title: 960T


title: 959H


title: Heart__Term_Replicate 7


title: Heart__Term_Replicate 4


title: Heart__Term_Replicate 5


title: Heart__Term_Replicate 3


title: 906H


title: Heart__Term_Replicate 2


title: Heart_130 days of gestational life_Replicate 5

source_name: Heart septum_130 days of gestational life

value: 130 days of fetal age


title: 974M


title: Heart__Term_Replicate 6


title: AMAL_29544


title: Heart_130 days of gestational life_Replicate 6


title: Heart__Lamb_Replicate 1


title: 912H


title: AMAL_29542


title: 924T


title: AMAL_29540


title: Heart_130 days of gestational life_Replicate 4


title: 914M


title: AMAL_27127


title: Heart_130 days of gestational life_Replicate 3


title: 1255M


title: 914H


title: 905T


title: Heart_130 days of gestational life_Replicate 2


title: AMAL_29541


title: 968H


title: 911H


title: 1409H


title: AMAL_14509


title: Heart_130 days of gestational life_Replicate 1


title: Heart__Term_Replicate 1


title: 2512M


title: 904M


title: Endometrium

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

department: Pathology

institute: Wayne State University School of Medicine

hyb_protocol: Hybridization was performed overnight on a µparaflo microfluidic chip using a micro-circulation pump.

scan_protocol: hybridization images were collected using a laser scaner and digitized using Array-Pro image analysis software (Media Cybemetics).

data_processing: data were analyzed by first substracting the backgound and then normaling the signals using a LOWESS filter 10.

source_name: Endometrium tissue

label_protocol: 5 ug total RNA was size frationated using a YM-100 Micocon centrifugal filter and small RNA (,300nt) isolated were 3'-extended with a polyA tail using polyA polymerase. An oligonucleotide tag specific-Cy3 was then ligated to the polyA tail

growth_protocol: Retrospective archival paired ovarian cancer patient tissues and endometrium tissues were obtained

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using miRNeasy FFPE kit from Qiagen

treatment_protocol: These patients underwent surgical removal

tag: subject status

value: ovarian cancer patient

value: Endometrium tissue

value: FFPE tissue


title: Tumor Ovarian

source_name: ovarian cancer tissue

value: ovarian cancer tissue


title: AMAL_29543


title: SZ_white_dn1140

status: Public on Jul 29 2015

city: Toronto

first: Arturas

last: Petronis

address: 250 College Street

country: Canada

institute: Centre for Addiction and Mental Health

description:
SNP genotyping CEL file: GW6_090309T_AP187_APdn1140.CEL
hypomethylation CEL file: GW6_090309T_AP205_APdn1140_hypo.CEL

hyb_protocol: For each sample, DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to one SNP 6.0 array according to the manufacturer's instructions. A second array was also run for each sample, using the enriched unmethylated fraction of the genome instead of the usual library created with the SNP 6.0 protocol.

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: We used R (v2.12.1) and the R package crlmm (v1.8.11), to background correct, normalize, and summarize (RMA) the SNP probes, and to make genotype calls. Datasets were normalized separately as were the two arrays.

label: Proprietary biotin-labeled reagent for end-labeling fragmented PCR amplicons

source_name: Brain

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from frozen post-mortem prefrontal cortex followed by an ethanol precipitation. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: study

value: Harvard Brain Tissue Resource Center

tag: Sex

value: M

tag: self-reported race

value: white

tag: cohort

value: case

value: Schizophrenia


title: BD_white_1142

description:
SNP genotyping CEL file: GW6_081909W_AP109_1142.CEL
hypomethylation CEL file: GW6_081909W_AP118_1142_hypo.CEL

value: F

value: Bipolar


title: 911M

source_name: lymph node metastasis

tag: gender

value: female

source_name: uninvolved glandular tissue


title: 1409T


title: Ler_rep2

city: Potsdam

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

hyb_protocol: Performed by NASC Affymetrix service, Nottingham, UK.

data_processing: Data were gcrma normalized using R/Bioconductor.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Growth conditions were as described in Disch et al., 2006 (PMID: 16461280).

extract_protocol: RNA was extracted from inflorescences with young flower buds from individual tink/ibr5-6 mutant or Ler plants with three replicates using the RNEasy kit (Qiagen)

treatment_protocol: The tink/ibr5-6 mutant was isolated from an EMS-mutagenesized population in the klu-2 background and backcrossed three times to Ler plants to isolate tink/ibr5-6 single mutants. klu-2 mutants are described in Anastisou et al., 2007 (PMID: 18061566).

tag: genotype

value: Ler

tag: cultivar

value: inflorescence


title: CTRL_white_1137

description:
SNP genotyping CEL file: GW6_011309H_AP93_1137.CEL
hypomethylation CEL file: GW6_011309H_AP106_1137-hypo.CEL

value: control

tag: disease


title: tink/ibr5-6_rep3

scan_protocol: Performed by NASC Affymetrix service, Nottingham, UK.

tag: tissue


title: BD_white_1136

description:
SNP genotyping CEL file: GW6_081909Wf_AP107_1136.CEL
hypomethylation CEL file: GW6_081909W_AP116_1136_hypo.CEL


title: Ler_rep3

label_protocol: Performed by NASC Affymetrix service, Nottingham, UK.


title: tink/ibr5-6_rep2


title: 1251M

description: Comparative Genomic Hybridization of tissues from breast cancer patients

source_name: peripheral blood leukocytes


title: tink/ibr5-6_rep1


title: 971H


title: 980M


title: CTRL_white_1141

description:
SNP genotyping CEL file: GW6_121808H_AP31_1141.CEL
hypomethylation CEL file: GW6_121808H_AP36_1141-hypo.CEL


title: 1436M


title: SZ_white_1140

description:
SNP genotyping CEL file: GW6_081909W_AP108_1140.CEL
hypomethylation CEL file: GW6_081909W_AP117_1140_hypo.CEL


title: 983H


title: CTRL_white_1135

description:
SNP genotyping CEL file: GW6_011309H_AP92_1135.CEL
hypomethylation CEL file: GW6_011309H_AP105_1135-hypo.CEL


title: CTRL_white_1139

description:
SNP genotyping CEL file: GW6_121808H_AP30_1139.CEL
hypomethylation CEL file: GW6_121808H_AP35_1139-hypo.CEL


title: 913H


title: 1251H


title: 957M


title: BD_white_1131

description:
SNP genotyping CEL file: GW6_081909W_AP105_1131.CEL
hypomethylation CEL file: GW6_081909W_AP114_1131_hypo.CEL


title: BD_white_1134

description:
SNP genotyping CEL file: GW6_081909W_AP106_1134.CEL
hypomethylation CEL file: GW6_081909W_AP115_1134_hypo.CEL


title: CTRL_white_1132

description:
SNP genotyping CEL file: GW6_011309H_AP91_1132.CEL
hypomethylation CEL file: GW6_011309H_AP104_1132-hypo.CEL


title: BD_white_dn1130

description:
SNP genotyping CEL file: GW6_090309T_AP186_APdn1130.CEL
hypomethylation CEL file: GW6_090309T_AP204_APdn1130_hypo.CEL


title: AMAL_29545

value: North America

value: Alaskan Malamute (AMAL)


title: CTRL_white_1128

description:
SNP genotyping CEL file: GW6_011309H_AP89_1128.CEL
hypomethylation CEL file: GW6_011309H_AP102_1128-hypo.CEL


title: CTRL_unknown_dn1128

description:
SNP genotyping CEL file: GW6_090309T_AP177_APdn1128.CEL
hypomethylation CEL file: GW6_090309T_AP195_APdn1128_hypo.CEL

value: unknown


title: CTRL_white_1127

description:
SNP genotyping CEL file: GW6_011309H_AP88_1127.CEL
hypomethylation CEL file: GW6_011309H_AP101_1127-hypo.CEL


title: SZ_white_1126

description:
SNP genotyping CEL file: GW6_081909W_AP103_1126.CEL
hypomethylation CEL file: GW6_081909W_AP112_1126_hypo.CEL


title: CTRL_white_1124

description:
SNP genotyping CEL file: GW6_011309H_AP86_1124.CEL
hypomethylation CEL file: GW6_011309H_AP99_1124-hypo.CEL


title: CTRL_white_1123

description:
SNP genotyping CEL file: GW6_011309H_AP85_1123.CEL
hypomethylation CEL file: GW6_011309H_AP98_1123-hypo.CEL


title: BD_white_1121

description:
SNP genotyping CEL file: GW6_081909W_AP101_1121.CEL
hypomethylation CEL file: GW6_081909W_AP110_1121_hypo.CEL


title: BD_white_1122

description:
SNP genotyping CEL file: GW6_081909W_AP102_1122.CEL
hypomethylation CEL file: GW6_081909W_AP111_1122_hypo.CEL


title: BD_white_1130

description:
SNP genotyping CEL file: GW6_081909W_AP104_1130.CEL
hypomethylation CEL file: GW6_081909W_AP113_1130_hypo.CEL


title: BD_white_1119

description:
SNP genotyping CEL file: GW6_082509W_AP167_1119.CEL
hypomethylation CEL file: GW6_082509W_AP176_1119_hypo.CEL


title: SZ_white_1120

description:
SNP genotyping CEL file: GW6_081309W_AP72_1120.CEL
hypomethylation CEL file: GW6_081309W_AP74_1120_hypo.CEL


title: BD_white_dn1121

description:
SNP genotyping CEL file: GW6_090309T_AP185_APdn1121.CEL
hypomethylation CEL file: GW6_090309T_AP203_APdn1121_hypo.CEL


title: CTRL_white_1117

description:
SNP genotyping CEL file: GW6_011309H_AP83_1117.CEL
hypomethylation CEL file: GW6_011309H_AP96_1117-hypo.CEL


title: BD_white_1116

description:
SNP genotyping CEL file: GW6_082509W_AP166_1116.CEL
hypomethylation CEL file: GW6_082509W_AP175_1116_hypo.CEL


title: CTRL_unknown_1129

description:
SNP genotyping CEL file: GW6_011309H_AP90_1129.CEL
hypomethylation CEL file: GW6_011309H_AP103_1129-hypo.CEL


title: SZ_white_1115

description:
SNP genotyping CEL file: GW6_082509W_AP165_1115.CEL
hypomethylation CEL file: GW6_082509W_AP174_1115_hypo.CEL


title: SZ_white_dn1115

description:
SNP genotyping CEL file: GW6_090309T_AP184_APdn1115.CEL
hypomethylation CEL file: GW6_090309T_AP202_APdn1115_hypo.CEL


title: BD_white_1114

description:
SNP genotyping CEL file: GW6_082509W_AP164_1114.CEL
hypomethylation CEL file: GW6_082509W_AP173_1114_hypo.CEL


title: SZ_white_1113

description:
SNP genotyping CEL file: GW6_082509W_AP163_1113.CEL
hypomethylation CEL file: GW6_082509W_AP172_1113_hypo.CEL


title: Ler_rep1


title: CTRL_white_1111

description:
SNP genotyping CEL file: GW6_011309H_AP82_1111.CEL
hypomethylation CEL file: GW6_011309H_AP95_1111-hypo.CEL


title: CTRL_white_1110

description:
SNP genotyping CEL file: GW6_011309H_AP81_1110.CEL
hypomethylation CEL file: GW6_011309H_AP94_1110-hypo.CEL


title: CTRL_white_1107

description:
SNP genotyping CEL file: GW6_010809Hb_AP64_1107.CEL
hypomethylation CEL file: GW6_010809H_AP80_1107-hypo.CEL


title: BD_unknown_dn1105

description:
SNP genotyping CEL file: GW6_090309T_AP183_APdn1105.CEL
hypomethylation CEL file: GW6_090309T_AP201_APdn1105_hypo.CEL


title: BD_white_1109

description:
SNP genotyping CEL file: GW6_082509W_AP161_1109.CEL
hypomethylation CEL file: GW6_082509W_AP170_1109_hypo.CEL


title: BD_white_1105

description:
SNP genotyping CEL file: GW6_082509W_AP159_1105.CEL
hypomethylation CEL file: GW6_082509W_AP168_1105_hypo.CEL


title: SZ_white_1104

description:
SNP genotyping CEL file: GW6_081309W_AP71_1104.CEL
hypomethylation CEL file: GW6_081309W_AP73_1104_hypo.CEL


title: AMAL_29546


title: CTRL_white_1118

description:
SNP genotyping CEL file: GW6_011309H_AP84_1118.CEL
hypomethylation CEL file: GW6_011309H_AP97_1118-hypo.CEL


title: BD_white_1101

description:
SNP genotyping CEL file: GW6_082009W_AP148_1101.CEL
hypomethylation CEL file: GW6_082009W_AP157_1101_hypo.CEL


title: SZ_white_1100

description:
SNP genotyping CEL file: GW6_082009W_AP147_1100.CEL
hypomethylation CEL file: GW6_082009W_AP156_1100_hypo.CEL


title: CTRL_unknown_dn1099

description:
SNP genotyping CEL file: GW6_090909T2h_AP176_APdn1099.CEL
hypomethylation CEL file: GW6_090309T_AP194_APdn1099_hypo.CEL


title: SZ_white_1097

description:
SNP genotyping CEL file: GW6_082009W_AP145_1097.CEL
hypomethylation CEL file: GW6_082009W_AP154_1097_hypo.CEL


title: CTRL_white_1099

description:
SNP genotyping CEL file: GW6_010809H_AP63_1099.CEL
hypomethylation CEL file: GW6_010809H_AP79_1099-hypo.CEL


title: SZ_white_1098

description:
SNP genotyping CEL file: GW6_082009W_AP146_1098.CEL
hypomethylation CEL file: GW6_082009W_AP155_1098_hypo.CEL


title: SZ_white_1094

description:
SNP genotyping CEL file: GW6_082009W_AP142_1094.CEL
hypomethylation CEL file: GW6_082009W_AP151_1094_hypo.CEL


title: CTRL_white_1093

description:
SNP genotyping CEL file: GW6_010809H_AP62_1093.CEL
hypomethylation CEL file: GW6_010809H_AP78_1093-hypo.CEL


title: BD_white_1092

description:
SNP genotyping CEL file: GW6_082009W_AP141_1092.CEL
hypomethylation CEL file: GW6_082009W_AP150_1092_hypo.CEL


title: BD_white_1090

description:
SNP genotyping CEL file: GW6_081309W_AP67_1090.CEL
hypomethylation CEL file: GW6_081309W_AP69_1090_hypo.CEL


title: SZ_white_1089

description:
SNP genotyping CEL file: GW6_080709W_AP18_1089.CEL
hypomethylation CEL file: GW6_080709W_AP20_1089_hypo.CEL


title: SZ_white_1095

description:
SNP genotyping CEL file: GW6_082009W_AP143_1095.CEL
hypomethylation CEL file: GW6_082009W_AP152_1095_hypo.CEL


title: BD_white_1112

description:
SNP genotyping CEL file: GW6_082509W_AP162_1112.CEL
hypomethylation CEL file: GW6_082509W_AP171_1112_hypo.CEL


title: CTRL_white_1086

description:
SNP genotyping CEL file: GW6_010809H_AP59_1086.CEL
hypomethylation CEL file: GW6_010809H_AP75_1086-hypo.CEL


title: CTRL_white_1088

description:
SNP genotyping CEL file: GW6_010809H_AP61_1088.CEL
hypomethylation CEL file: GW6_010809H_AP77_1088-hypo.CEL


title: BD_white_1085

description:
SNP genotyping CEL file: GW6_081109W_AP39_1085.CEL
hypomethylation CEL file: GW6_081109W_AP48_1085_hypo.CEL


title: BD_white_1083

description:
SNP genotyping CEL file: GW6_082709W2h_AP37_1083.CEL
hypomethylation CEL file: GW6_081109W_AP46_1083_hypo.CEL


title: BD_white_1103

description:
SNP genotyping CEL file: GW6_081309W_AP68_1103.CEL
hypomethylation CEL file: GW6_081309W_AP70_1103_hypo.CEL


title: BD_white_1084

description:
SNP genotyping CEL file: GW6_081109W_AP38_1084.CEL
hypomethylation CEL file: GW6_081109W_AP47_1084_hypo.CEL


title: SZ_white_1081

description:
SNP genotyping CEL file: GW6_081109W_AP36_1081.CEL
hypomethylation CEL file: GW6_081109W_AP45_1081_hypo.CEL


title: CTRL_white_1080

description:
SNP genotyping CEL file: GW6_010809H_AP58_1080.CEL
hypomethylation CEL file: GW6_010809H_AP74_1080-hypo.CEL


title: CTRL_white_1087

description:
SNP genotyping CEL file: GW6_010809H_AP60_1087.CEL
hypomethylation CEL file: GW6_010809H_AP76_1087-hypo.CEL


title: CTRL_white_1079

description:
SNP genotyping CEL file: GW6_010809H_AP57_1079.CEL
hypomethylation CEL file: GW6_010809H_AP73_1079-hypo.CEL


title: SZ_white_1102

description:
SNP genotyping CEL file: GW6_082009W_AP149_1102.CEL
hypomethylation CEL file: GW6_082009W_AP158_1102_hypo.CEL


title: CTRL_white_1078

description:
SNP genotyping CEL file: GW6_010809H_AP56_1078.CEL
hypomethylation CEL file: GW6_010809H_AP72_1078-hypo.CEL


title: SZ_white_1077

description:
SNP genotyping CEL file: GW6_081109W_AP35_1077.CEL
hypomethylation CEL file: GW6_081109W_AP44_1077_hypo.CEL


title: SZ_white_1096

description:
SNP genotyping CEL file: GW6_082009W_AP144_1096.CEL
hypomethylation CEL file: GW6_082009W_AP153_1096_hypo.CEL


title: SZ_white_1076

description:
SNP genotyping CEL file: GW6_081109W_AP34_1076.CEL
hypomethylation CEL file: GW6_081109W_AP43_1076_hypo.CEL


title: CTRL_white_1075

description:
SNP genotyping CEL file: GW6_010809H_AP55_1075.CEL
hypomethylation CEL file: GW6_010809H_AP71_1075-hypo.CEL


title: SZ_white_1073

description:
SNP genotyping CEL file: GW6_081109W_AP33_1073.CEL
hypomethylation CEL file: GW6_081109W_AP42_1073_hypo.CEL


title: CTRL_white_1074

description:
SNP genotyping CEL file: GW6_010809H_AP54_1074.CEL
hypomethylation CEL file: GW6_010809H_AP70_1074-hypo.CEL


title: CTRL_white_1071

description:
SNP genotyping CEL file: GW6_010809H_AP52_1071.CEL
hypomethylation CEL file: GW6_010809H_AP68_1071-hypo.CEL


title: CTRL_white_1070

description:
SNP genotyping CEL file: GW6_010809H_AP51_1070.CEL
hypomethylation CEL file: GW6_010809H_AP67_1070-hypo.CEL


title: SZ_white_1061

description:
SNP genotyping CEL file: GW6_090109T_AP122_AP1061.CEL
hypomethylation CEL file: GW6_090109T_AP168_AP1061_hypo.CEL


title: SZ_white_1069

description:
SNP genotyping CEL file: GW6_081109W_AP32_1069.CEL
hypomethylation CEL file: GW6_081109W_AP41_1069_hypo.CEL


title: SZ_white_1060

description:
SNP genotyping CEL file: GW6_090109T_AP121_AP1060.CEL
hypomethylation CEL file: GW6_090109T_AP167_AP1060_hypo.CEL


title: BD_white_1064

description:
SNP genotyping CEL file: GW6_090109T_AP123_AP1064.CEL
hypomethylation CEL file: GW6_090109T_AP169_AP1064_hypo.CEL


title: 1436T

description: Comparative Genomic Hybridization of tissues from breast cancer patients

source_name: primary tumor


title: BD_white_dn1083

description:
SNP genotyping CEL file: GW6_090309T_AP182_APdn1083.CEL
hypomethylation CEL file: GW6_090309T_AP200_APdn1083_hypo.CEL


title: BD_white_1059

description:
SNP genotyping CEL file: GW6_081809T_AP120_AP1059.CEL
hypomethylation CEL file: GW6_081809T_AP166_AP1059_hypo.CEL


title: BD_white_1056

description:
SNP genotyping CEL file: GW6_081809T_AP119_AP1056.CEL
hypomethylation CEL file: GW6_081809T_AP165_AP1056_hypo.CEL


title: CTRL_unknown_1055

description:
SNP genotyping CEL file: GW6_010809H_AP50_1055.CEL
hypomethylation CEL file: none


title: SZ_white_1052

description:
SNP genotyping CEL file: GW6_081809T_AP116_AP1052.CEL
hypomethylation CEL file: GW6_081809T_AP162_AP1052_hypo.CEL


title: BD_white_1053

description:
SNP genotyping CEL file: GW6_081809T_AP117_AP1053.CEL
hypomethylation CEL file: GW6_081809T_AP163_AP1053_hypo.CEL


title: SZ_white_1054

description:
SNP genotyping CEL file: GW6_081809T_AP118_AP1054.CEL
hypomethylation CEL file: GW6_081809T_AP164_AP1054_hypo.CEL


title: CTRL_unknown_dn1055

description:
SNP genotyping CEL file: GW6_090209T_AP175_APdn1055.CEL
hypomethylation CEL file: GW6_090209T_AP193_APdn1055_hypo.CEL


title: SZ_white_dn1052

description:
SNP genotyping CEL file: GW6_081209T_AP181_APdn1052.CEL
hypomethylation CEL file: GW6_081209T_AP199_APdn1052_hypo.CEL


title: BD_white_1051

description:
SNP genotyping CEL file: GW6_081809T_AP115_AP1051.CEL
hypomethylation CEL file: GW6_081809T_AP161_AP1051_hypo.CEL


title: CTRL_white_1049

description:
SNP genotyping CEL file: GW6_010809H_AP49_1049.CEL
hypomethylation CEL file: GW6_010809H_AP65_1049-hypo.CEL


title: BD_white_1048

description:
SNP genotyping CEL file: GW6_073009T2s_AP114_AP1048.CEL
hypomethylation CEL file: GW6_073009T2s_AP160_AP1048_hypo.CEL


title: CTRL_white_1046

description:
SNP genotyping CEL file: GW6_010709H_AP41_1046.CEL
hypomethylation CEL file: GW6_010709H_AP47_1046-hypo.CEL


title: CTRL_white_1072

description:
SNP genotyping CEL file: GW6_010809H_AP53_1072.CEL
hypomethylation CEL file: GW6_010809H_AP69_1072-hypo.CEL


title: BD_white_dn1045

description:
SNP genotyping CEL file: GW6_090309T_AP180_APdn1045.CEL
hypomethylation CEL file: GW6_090309T_AP198_APdn1045_hypo.CEL


title: CTRL_white_dn1046

description:
SNP genotyping CEL file: GW6_090209T_AP174_APdn1046.CEL
hypomethylation CEL file: GW6_090209T_AP192_APdn1046_hypo.CEL


title: CTRL_white_1047

description:
SNP genotyping CEL file: GW6_010709H_AP42_1047.CEL
hypomethylation CEL file: GW6_010709H_AP48_1047-hypo.CEL


title: BD_white_1045

description:
SNP genotyping CEL file: GW6_073009T_AP113_AP1045.CEL
hypomethylation CEL file: GW6_073009T_AP159_AP1045_hypo.CEL


title: SZ_white_1065

description:
SNP genotyping CEL file: GW6_081109W_AP31_1065.CEL
hypomethylation CEL file: GW6_081109W_AP40_1065_hypo.CEL


title: SZ_white_1038

description:
SNP genotyping CEL file: GW6_073109T_AP109_AP1038.CEL
hypomethylation CEL file: GW6_073109T_AP155_AP1038_hypo.CEL


title: SZ_white_1039

description:
SNP genotyping CEL file: GW6_073109T_AP110_AP1039.CEL
hypomethylation CEL file: GW6_073109T_AP156_AP1039_hypo.CEL


title: SZ_white_1036

description:
SNP genotyping CEL file: GW6_073109T_AP107_AP1036.CEL
hypomethylation CEL file: GW6_073109T_AP153_AP1036_hypo.CEL


title: CTRL_white_1034

description:
SNP genotyping CEL file: GW6_010709H_AP40_1034.CEL
hypomethylation CEL file: GW6_010709H_AP46_1034-hypo.CEL


title: CTRL_unknown_dn1032

description:
SNP genotyping CEL file: GW6_090209T_AP173_APdn1032.CEL
hypomethylation CEL file: GW6_090209T_AP191_APdn1032_hypo.CEL


title: CTRL_white_1032

description:
SNP genotyping CEL file: GW6_010709Hb_AP39_1032.CEL
hypomethylation CEL file: GW6_010709H_AP45_1032-hypo.CEL


title: BD_white_1031

description:
SNP genotyping CEL file: GW6_073109T_AP106_AP1031.CEL
hypomethylation CEL file: GW6_073109T_AP152_AP1031_hypo.CEL


title: CTRL_white_1030

description:
SNP genotyping CEL file: GW6_010709H_AP38_1030.CEL
hypomethylation CEL file: GW6_010709H_AP44_1030-hypo.CEL


title: CTRL_white_1029

description:
SNP genotyping CEL file: GW6_010709H_AP37_1029.CEL
hypomethylation CEL file: GW6_010709H_AP43_1029-hypo.CEL


title: CTRL_white_1028

description:
SNP genotyping CEL file: GW6_010609T_AP36_AP1028.CEL
hypomethylation CEL file: GW6_010609T_AP77_AP1028-hypo.CEL


title: CTRL_white_1024

description:
SNP genotyping CEL file: GW6_010609T_AP33_AP1024.CEL
hypomethylation CEL file: GW6_010609T_AP74_AP1024-hypo.CEL


title: CTRL_white_1025

description:
SNP genotyping CEL file: GW6_122308T_AP34_AP1025.CEL
hypomethylation CEL file: GW6_122308T_AP75_AP1025-hypo.CEL


title: SZ_white_1043

description:
SNP genotyping CEL file: GW6_081809T_AP112_AP1043.CEL
hypomethylation CEL file: GW6_081809T_AP158_AP1043_hypo.CEL


title: BD_white_1041

description:
SNP genotyping CEL file: GW6_081809T2s_AP111_AP1041.CEL
hypomethylation CEL file: GW6_081809T_AP157_AP1041_hypo.CEL


title: CTRL_white_1022

description:
SNP genotyping CEL file: GW6_122308T_AP32_AP1022.CEL
hypomethylation CEL file: GW6_122308T_AP73_AP1022-hypo.CEL


title: CTRL_white_dn1022

description:
SNP genotyping CEL file: GW6_081209T_AP170_APdn1022.CEL
hypomethylation CEL file: GW6_081209T_AP188_APdn1022_hypo.CEL


title: CTRL_white_1021

description:
SNP genotyping CEL file: GW6_010609T_AP31_AP1021.CEL
hypomethylation CEL file: GW6_010609T_AP72_AP1021-hypo.CEL


title: BD_white_1027

description:
SNP genotyping CEL file: GW6_073109T_AP105_AP1027.CEL
hypomethylation CEL file: GW6_073109T_AP151_AP1027_hypo.CEL


title: CTRL_unknown_dn1026

description:
SNP genotyping CEL file: GW6_090209T_AP171_APdn1026.CEL
hypomethylation CEL file: GW6_090209T_AP189_APdn1026_hypo.CEL


title: BD_white_1018

description:
SNP genotyping CEL file: GW6_073009T_AP103_AP1018.CEL
hypomethylation CEL file: GW6_073009T_AP149_AP1018_hypo.CEL


title: CTRL_white_1020

description:
SNP genotyping CEL file: GW6_010609T_AP30_AP1020.CEL
hypomethylation CEL file: GW6_010609T_AP71_AP1020-hypo.CEL


title: SZ_white_dn1039

description:
SNP genotyping CEL file: GW6_090309T_AP179_APdn1039.CEL
hypomethylation CEL file: GW6_090309T_AP197_APdn1039_hypo.CEL


title: SZ_white_1017

description:
SNP genotyping CEL file: GW6_073009T_AP102_AP1017.CEL
hypomethylation CEL file: GW6_073009T_AP148_AP1017_hypo.CEL


title: BD_white_1019

description:
SNP genotyping CEL file: GW6_073109T_AP104_AP1019.CEL
hypomethylation CEL file: GW6_073109T_AP150_AP1019_hypo.CEL


title: SZ_white_1016

description:
SNP genotyping CEL file: GW6_073109T_AP101_AP1016.CEL
hypomethylation CEL file: GW6_073109T_AP147_AP1016_hypo.CEL


title: BD_white_1015

description:
SNP genotyping CEL file: GW6_081209T_AP100_AP1015.CEL
hypomethylation CEL file: GW6_081209T_AP146_AP1015_hypo.CEL


title: SZ_white_1037

description:
SNP genotyping CEL file: GW6_073109T_AP108_AP1037.CEL
hypomethylation CEL file: GW6_073109T_AP154_AP1037_hypo.CEL


title: SZ_white_dn1016

description:
SNP genotyping CEL file: GW6_090309T_AP178_APdn1016.CEL
hypomethylation CEL file: GW6_090309T_AP196_APdn1016_hypo.CEL


title: CTRL_white_1013

description:
SNP genotyping CEL file: GW6_123008T_AP28_AP1013.CEL
hypomethylation CEL file: GW6_123008T_AP69_AP1013-hypo.CEL


title: CTRL_white_1014

description:
SNP genotyping CEL file: GW6_010609T_AP29_AP1014.CEL
hypomethylation CEL file: GW6_010609T_AP70_AP1014-hypo.CEL


title: CTRL_unknown_dn1030

description:
SNP genotyping CEL file: GW6_090209T_AP172_APdn1030.CEL
hypomethylation CEL file: GW6_090209T_AP190_APdn1030_hypo.CEL


title: BD_white_1012

description:
SNP genotyping CEL file: GW6_090209T_AP99_AP1012.CEL
hypomethylation CEL file: GW6_090209T_AP145_AP1012_hypo.CEL


title: CTRL_unknown_1026

description:
SNP genotyping CEL file: GW6_122308T_AP35_AP1026.CEL
hypomethylation CEL file: GW6_122308T_AP76_AP1026-hypo.CEL


title: CTRL_white_1011

description:
SNP genotyping CEL file: GW6_123008T_AP27_AP1011.CEL
hypomethylation CEL file: GW6_123008T_AP68_AP1011-hypo.CEL


title: BD_white_1010

description:
SNP genotyping CEL file: GW6_090209T_AP98_AP1010.CEL
hypomethylation CEL file: GW6_090209T_AP144_AP1010_hypo.CEL


title: SZ_white_1009

description:
SNP genotyping CEL file: GW6_090209T_AP97_AP1009.CEL
hypomethylation CEL file: GW6_090209T_AP143_AP1009_hypo.CEL


title: CTRL_white_1005

description:
SNP genotyping CEL file: GW6_123008T_AP25_AP1005.CEL
hypomethylation CEL file: GW6_123008T_AP66_AP1005-hypo.CEL


title: SZ_white_1004

description:
SNP genotyping CEL file: GW6_090209T_AP96_AP1004.CEL
hypomethylation CEL file: GW6_090209T_AP142_AP1004_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD51_rep1

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with beadarray (version 1.16) in R/BioConductor. This algorithm includes a log transformation. Probes were reassigned to Entrez GeneIDs by aligning the probe sequence to the mm9 genome using the BLAT algorithm. Replicate expression data for the same GeneID were then merged by calculating the mean. Illumina probe IDs and sequences used for each merged probeset are given as comma-delimited lists in the columns ‘Probes’ and ‘Probe_Sequences’ in the normalised data matrix.

source_name: hippocampal precursor cell culture

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: Cells were cultured on poly-D-lysine/laminin-coated plates in Neurobasal media supplemented with 2 % B27, GlutaMAX,  20 ng/ml bFGF and 20 ng/ml EGF

extract_protocol: RNA was extracted using the Quiagen RNEasy Mini kit, including the on-column DNase step, following the manufacturer’s protocol.

tag: strain

tag: passage number


title: hippocampal_precursor_cell_culture_BXD31_rep3


title: CTRL_white_A-105

description:
SNP genotyping CEL file: GW6_010609T_AP23_AP105.CEL
hypomethylation CEL file: GW6_010609T_AP64_AP105-hypo.CEL

value: Stanley Medical Research Institute


title: hippocampal_precursor_cell_culture_BXD73_rep1


title: hippocampal_precursor_cell_culture_BXD2_rep3


title: hippocampal_precursor_cell_culture_BXD87_rep2


title: hippocampal_precursor_cell_culture_BXD2_rep2


title: CTRL_white_1008

description:
SNP genotyping CEL file: GW6_123008T_AP26_AP1008.CEL
hypomethylation CEL file: GW6_123008T_AP67_AP1008-hypo.CEL


title: BD_white_A-104

description:
SNP genotyping CEL file: GW6_090209T_AP95_AP104.CEL
hypomethylation CEL file: GW6_090209T_AP141_AP104_hypo.CEL


title: hippocampal_precursor_cell_culture_C57BL/6J_rep1


title: BD_white_A-102

description:
SNP genotyping CEL file: GW6_090209T_AP94_AP102.CEL
hypomethylation CEL file: GW6_090209T_AP140_AP102_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD65_rep1


title: SZ_white_A-101

description:
SNP genotyping CEL file: GW6_090209T_AP93_AP101.CEL
hypomethylation CEL file: GW6_090209T_AP139_AP101_hypo.CEL


title: CTRL_unknown_1003

description:
SNP genotyping CEL file: GW6_081809W_AP75_dn1003.CEL
hypomethylation CEL file: GW6_081809W_AP77_dn1003_hypo.CEL


title: CTRL_unknown_1005

description:
SNP genotyping CEL file: GW6_081809W_AP76_dn1005.CEL
hypomethylation CEL file: GW6_081809W_AP78_dn1005_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD96_rep1


title: hippocampal_precursor_cell_culture_BXD96_rep2


title: CTRL_white_A-103

description:
SNP genotyping CEL file: GW6_010609Tb_AP22_AP103.CEL
hypomethylation CEL file: GW6_010609T_AP63_AP103-hypo.CEL


title: SZ_white_A-100

description:
SNP genotyping CEL file: GW6_090209Tb_AP92_AP100.CEL
hypomethylation CEL file: GW6_090209T_AP138_AP100_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD96_rep3


title: CTRL_white_A-99

description:
SNP genotyping CEL file: GW6_010609T_AP21_AP99.CEL
hypomethylation CEL file: GW6_010609T_AP62_AP99-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD43_rep3


title: hippocampal_precursor_cell_culture_BXD61_rep1


title: CTRL_white_1003

description:
SNP genotyping CEL file: GW6_123008T_AP24_AP1003.CEL
hypomethylation CEL file: GW6_123008T_AP65_AP1003-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD86_rep3


title: CTRL_white_A-95

description:
SNP genotyping CEL file: GW6_010609T_AP20_AP95.CEL
hypomethylation CEL file: GW6_010609T_AP61_AP95-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD65_rep3


title: SZ_white_A-94

description:
SNP genotyping CEL file: GW6_090209T_AP89_AP94.CEL
hypomethylation CEL file: GW6_090209T_AP135_AP94_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD62_rep2


title: SZ_white_A-93

description:
SNP genotyping CEL file: GW6_090109T_AP88_AP93.CEL
hypomethylation CEL file: GW6_090109T_AP134_AP93_hypo.CEL


title: CTRL_white_A-90

description:
SNP genotyping CEL file: GW6_010609T_AP19_AP90.CEL
hypomethylation CEL file: GW6_010609T_AP60_AP90-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD43_rep1


title: BD_white_A-89

description:
SNP genotyping CEL file: GW6_090109T_AP87_AP89.CEL
hypomethylation CEL file: GW6_090109T_AP133_AP89_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD61_rep2


title: hippocampal_precursor_cell_culture_BXD24_rep1


title: CTRL_white_A-86

description:
SNP genotyping CEL file: GW6_010609T_AP18_AP86.CEL
hypomethylation CEL file: GW6_010609T_AP59_AP86-hypo.CEL


title: SZ_white_A-88

description:
SNP genotyping CEL file: GW6_090109T_AP86_AP88.CEL
hypomethylation CEL file: GW6_090109T_AP132_AP88_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD1_rep2


title: SZ_hispanic_A-85

description:
SNP genotyping CEL file: GW6_090109T_AP84_AP85.CEL
hypomethylation CEL file: GW6_090109T_AP130_AP85_hypo.CEL

value: hispanic


title: hippocampal_precursor_cell_culture_BXD24_rep2


title: BD_white_A-98

description:
SNP genotyping CEL file: GW6_090209T_AP91_AP98.CEL
hypomethylation CEL file: GW6_090209T_AP137_AP98_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD32_rep3


title: CTRL_white_A-83

description:
SNP genotyping CEL file: GW6_010609T_AP17_AP83.CEL
hypomethylation CEL file: GW6_010609T_AP58_AP83-hypo.CEL


title: SZ_white_A-82

description:
SNP genotyping CEL file: GW6_090109T_AP83_AP82.CEL
hypomethylation CEL file: GW6_090109T_AP129_AP82_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD61_rep3


title: SZ_white_A-81

description:
SNP genotyping CEL file: GW6_090109T_AP82_AP81.CEL
hypomethylation CEL file: GW6_090109T_AP128_AP81_hypo.CEL


title: SZ_white_A-97

description:
SNP genotyping CEL file: GW6_090209Tb_AP90_AP97.CEL
hypomethylation CEL file: GW6_090209T_AP136_AP97_hypo.CEL


title: CTRL_white_A-80

description:
SNP genotyping CEL file: GW6_010609T_AP16_AP80.CEL
hypomethylation CEL file: GW6_010609T_AP57_AP80-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD65_rep2


title: hippocampal_precursor_cell_culture_BXD11_rep1


title: hippocampal_precursor_cell_culture_BXD11_rep2


title: CTRL_white_A-79

description:
SNP genotyping CEL file: GW6_010609Tb_AP15_AP79.CEL
hypomethylation CEL file: GW6_010609T_AP56_AP79-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD32_rep1


title: SZ_white_A-78

description:
SNP genotyping CEL file: GW6_090109T_AP81_AP78.CEL
hypomethylation CEL file: GW6_090109T_AP127_AP78_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD40_rep2


title: SZ_white_A-87

description:
SNP genotyping CEL file: GW6_090109Tb_AP85_AP87.CEL
hypomethylation CEL file: GW6_090109T_AP131_AP87_hypo.CEL


title: BD_white_A-76

description:
SNP genotyping CEL file: GW6_090109T_AP80_AP76.CEL
hypomethylation CEL file: GW6_090109T_AP126_AP76_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD11_rep3


title: SZ_white_A-75

description:
SNP genotyping CEL file: GW6_081209T_AP79_AP75.CEL
hypomethylation CEL file: GW6_081209T_AP125_AP75_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD69_rep2


title: hippocampal_precursor_cell_culture_BXD33_rep3


title: BD_white_A-74

description:
SNP genotyping CEL file: GW6_090109T_AP78_AP74.CEL
hypomethylation CEL file: GW6_090109T_AP124_AP74_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD87_rep1


title: hippocampal_precursor_cell_culture_DBA/2J_rep2


title: SZ_white_1106

description:
SNP genotyping CEL file: GW6_082509W_AP160_1106.CEL
hypomethylation CEL file: GW6_082509W_AP169_1106_hypo.CEL


title: SZ_white_A-73

description:
SNP genotyping CEL file: GW6_082009W_AP129_73.CEL
hypomethylation CEL file: GW6_082009W_AP140_73_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD69_rep3


title: BD_white_A-72

description:
SNP genotyping CEL file: GW6_082009Wb_AP128_72.CEL
hypomethylation CEL file: GW6_082009W_AP139_72_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD33_rep1


title: CTRL_white_A-70

description:
SNP genotyping CEL file: GW6_011409Tb_AP12_AP70.CEL
hypomethylation CEL file: GW6_011409T_AP53_AP70-hypo.CEL


title: BD_white_A-69

description:
SNP genotyping CEL file: GW6_082009W_AP127_69.CEL
hypomethylation CEL file: GW6_082009W_AP138_69_hypo.CEL


title: CTRL_white_A-71

description:
SNP genotyping CEL file: GW6_011409T_AP13_AP71.CEL
hypomethylation CEL file: GW6_011409T_AP54_AP71-hypo.CEL


title: hippocampal_precursor_cell_culture_C57BL/6J_rep2


title: hippocampal_precursor_cell_culture_BXD73_rep3


title: CTRL_white_A-67

description:
SNP genotyping CEL file: GW6_011409T_AP11_AP67.CEL
hypomethylation CEL file: GW6_011409T_AP52_AP67-hypo.CEL


title: hippocampal_precursor_cell_culture_C57BL/6J_rep3


title: CTRL_white_1125

description:
SNP genotyping CEL file: GW6_011309H_AP87_1125.CEL
hypomethylation CEL file: GW6_011309H_AP100_1125-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD86_rep1


title: SZ_white_A-66

description:
SNP genotyping CEL file: GW6_082009W_AP126_66.CEL
hypomethylation CEL file: GW6_082009W_AP137_66_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD43_rep2


title: CTRL_white_A-77

description:
SNP genotyping CEL file: GW6_011409Tb_AP14_AP77.CEL
hypomethylation CEL file: GW6_011409T_AP55_AP77-hypo.CEL


title: CTRL_white_A-65

description:
SNP genotyping CEL file: GW6_011409T_AP10_AP65.CEL
hypomethylation CEL file: GW6_011409T_AP51_AP65-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD62_rep1


title: hippocampal_precursor_cell_culture_BXD32_rep2


title: BD_white_A-64

description:
SNP genotyping CEL file: GW6_082009W_AP125_64.CEL
hypomethylation CEL file: GW6_082009W_AP136_64_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD24_rep3


title: hippocampal_precursor_cell_culture_DBA/2J_rep3


title: BD_white_A-62

description:
SNP genotyping CEL file: GW6_082009W_AP123_62.CEL
hypomethylation CEL file: GW6_082009W_AP134_62_hypo.CEL


title: BD_white_A-61

description:
SNP genotyping CEL file: GW6_082009W_AP122_61.CEL
hypomethylation CEL file: GW6_082009W_AP133_61_hypo.CEL


title: BD_white_A-63

description:
SNP genotyping CEL file: GW6_082009W_AP124_63.CEL
hypomethylation CEL file: GW6_082009W_AP135_63_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD62_rep3


title: hippocampal_precursor_cell_culture_BXD51_rep2


title: CTRL_white_A-56

description:
SNP genotyping CEL file: GW6_011409Tb_AP9_AP56.CEL
hypomethylation CEL file: GW6_011409T_AP50_AP56-hypo.CEL


title: SZ_white_A-55

description:
SNP genotyping CEL file: GW6_082009W_AP120_55.CEL
hypomethylation CEL file: GW6_082009W_AP131_55_hypo.CEL


title: CTRL_white_A-59

description:
SNP genotyping CEL file: GW6_111507H_AP4_P17A4_59.CEL
hypomethylation CEL file: GW6_011409T_AP41_AP59-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD2_rep1


title: hippocampal_precursor_cell_culture_BXD1_rep3


title: BD_white_A-58

description:
SNP genotyping CEL file: GW6_082009W_AP121_58.CEL
hypomethylation CEL file: GW6_082009W_AP132_58_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD73_rep2


title: CTRL_white_A-53

description:
SNP genotyping CEL file: GW6_111507H_AP2_P17A2_53.CEL
hypomethylation CEL file: GW6_011409T_AP39_AP53-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD40_rep3


title: CTRL_white_A-54

description:
SNP genotyping CEL file: GW6_111507H_AP3_P17A3_54.CEL
hypomethylation CEL file: GW6_011409T_AP40_AP54-hypo.CEL


title: CTRL_white_A-52

description:
SNP genotyping CEL file: GW6_111507H_AP1_P17A1_52.CEL
hypomethylation CEL file: GW6_011409T_AP38_AP52-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD31_rep2


title: hippocampal_precursor_cell_culture_BXD33_rep2


title: CTRL_white_A-51

description:
SNP genotyping CEL file: GW6_011409T_AP8_AP51.CEL
hypomethylation CEL file: GW6_011409T_AP49_AP51-hypo.CEL


title: hippocampal_precursor_cell_culture_BXD51_rep3


title: BD_white_A-50

description:
SNP genotyping CEL file: GW6_082009W_AP119_50.CEL
hypomethylation CEL file: GW6_082009W_AP130_50_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD69_rep1


title: CTRL_white_A-49

description:
SNP genotyping CEL file: GW6_011409Tb_AP7_AP49.CEL
hypomethylation CEL file: GW6_011409T_AP48_AP49-hypo.CEL


title: BD_white_A-48

description:
SNP genotyping CEL file: GW6_072909W_AP03_48.CEL
hypomethylation CEL file: GW6_072909W_AP06_48_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD87_rep3


title: SZ_white_A-47

description:
SNP genotyping CEL file: GW6_072909W_AP02_47.CEL
hypomethylation CEL file: GW6_072909W_AP05_47_hypo.CEL


title: hippocampal_precursor_cell_culture_DBA/2J_rep1


title: hippocampal_precursor_cell_culture_BXD31_rep1


title: hippocampal_precursor_cell_culture_BXD40_rep1


title: BD_white_A-46

description:
SNP genotyping CEL file: GW6_081109W_AP25_46.CEL
hypomethylation CEL file: GW6_081109W_AP30_46_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD1_rep1


title: SZ_white_A-45

description:
SNP genotyping CEL file: GW6_081109W_AP24_45.CEL
hypomethylation CEL file: GW6_081109W_AP29_45_hypo.CEL


title: hippocampal_precursor_cell_culture_BXD86_rep2


title: CTRL_white_A-43

description:
SNP genotyping CEL file: GW6_011409T_AP6_AP43.CEL
hypomethylation CEL file: GW6_011409T_AP47_AP43-hypo.CEL


title: SZ_white_A-44

description:
SNP genotyping CEL file: GW6_081109W_AP23_44.CEL
hypomethylation CEL file: GW6_081109W_AP28_44_hypo.CEL


title: BD_white_A-42

description:
SNP genotyping CEL file: GW6_072909W_AP01_42.CEL
hypomethylation CEL file: GW6_072909W_AP04_42_hypo.CEL


title: SZ_white_A-41

description:
SNP genotyping CEL file: GW6_081109W_AP22_41.CEL
hypomethylation CEL file: GW6_081109W_AP27_41_hypo.CEL


title: SZ_white_A-40

description:
SNP genotyping CEL file: GW6_081109W_AP21_40.CEL
hypomethylation CEL file: GW6_081109W_AP26_40_hypo.CEL


title: SZ_white_A-39

description:
SNP genotyping CEL file: GW6_080709Wb_AP09_39.CEL
hypomethylation CEL file: GW6_080709W_AP12_39_hypo.CEL


title: CTRL_white_A-38

description:
SNP genotyping CEL file: none
hypomethylation CEL file: GW6_011409T_AP37_AP38-hypo.CEL


title: SZ_white_A-37

description:
SNP genotyping CEL file: GW6_080709W_AP08_37.CEL
hypomethylation CEL file: GW6_080709W_AP11_37_hypo.CEL


title: BD_white_A-36

description:
SNP genotyping CEL file: GW6_080709W_AP07_36.CEL
hypomethylation CEL file: GW6_080709W_AP10_36_hypo.CEL


title: CTRL_white_A-33

description:
SNP genotyping CEL file: GW6_010609T_AP5_AP33.CEL
hypomethylation CEL file: GW6_010609T_AP46_AP33-hypo.CEL


title: BD_white_A-32

description:
SNP genotyping CEL file: GW6_081909W_AP89_32.CEL
hypomethylation CEL file: GW6_081909W_AP100_32_hypo.CEL


title: SZ_white_A-31

description:
SNP genotyping CEL file: GW6_081909W_AP88_31.CEL
hypomethylation CEL file: GW6_081909W_AP99_31_hypo.CEL


title: C.thermocellumDSM1313_MethylViologen_420min_1

city: Oak Ridge

first: Kyle

last: Sander

state: TN

address: 1 Bethel Valley Road, MS 6038

department: Biosciences

institute: University of Tennessee/Oak Ridge National Laboratory

description: C. thermocellum DSM 1313, 420 min exposure to methyl viologen

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 6.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus DSM 1313

growth_protocol: C. thermocellum DSM 1313 was grown at 55oC in duplicate 1L (total vessel capacity 1.3L) chemostat cultures using water-jacketed BioFlo110 bioreactors (New Brunswick Scientific, Edison, NJ) with 1.1 g/L cellobiose as the carbon source in MTC medium, which was fed at a dilution rate of 0.1 hr-1. Temperature, pH and agitation speed were monitored and controlled during fermentation. Culture pH was monitored using pH electrodes (Mettler-Toledo, Columbus, OH) and the pH control set point was maintained at 7.0 by automatic titration with 3 N KOH. Fermenter redox potential was measured using DPAS K8S 325 combination redox probes (Mettler-Toledo) attached to an independent signal transducer and readout (Sartorious Stedim Biotech, model # 8890354). Redox probes were checked for accuracy using new redox probe calibration solutions (Ricca Chemical Company catalog #4330-16, Ricca Chemical Company catalog #9880-16, Orion Application Solution # 967901). Agitation was supplied by a central impeller with two paddled rotors maintained at 200 rpm and no additional baffles.  Fermenters were inoculated using 100 mL of overnight cultures into 900 mL of neutral MTC previously sparged overnight with N2 gas. After inoculation, N2 sparging was stopped and for the duration of chemostat growth N2 was flushed into the fermenter headspace. Chemostat steady state growth was defined as being at least 50 hours of continuous growth during which the culture OD600 fluctuated less than 5%.

extract_protocol: 50 mL aliquots from chemostat cultures were harvested by centrifugation (8,000 rpm, 4oC, 4 min using a Sorvall RC5C plus centrifuge), the supernatant decanted and removed and the remaining pellets were quickly frozen in liquid nitrogen and stored at -80°C. Frozen cell pellets were resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA), lysed by adding 1.5 mL of cell pellet/TRIzol mixture to 2 mL screw top tubes containing 0.25 g of glass beads (MoBio Laboratories, CA) followed by bead beating for three 20 second cycles at 6,500 rpm using a Precellys-24 (Bertin Technologies, Montigny-le-Bretonneux, France). Total cellular RNA was purified using a QIAGEN RNeasy Mini kit according to the manufacturer's instructions, which included an on column RNase-free DNase treatment to digest residual chromosomal DNA. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE) and a BioAnalyzer (Agilent Technologies Inc., CA).

treatment_protocol: Individual chemical stressors were added to media feed carboys at final concentrations of 10 mg/L H202 or 150 mg/L methyl viologen and fed into the reactors with media feed over 60 hours (6 retention times).  Upon completion of each chemostat stress treatment, a 500 mL volume was withdrawn from each vessel and then reactors were re-filled in fed-batch mode to 1L with only MTC media and then chemostat operation was resumed. Remaining stressor was allowed to wash out for an additional 50 hours (5 retention times) and a re-equilibration period of 50 hours followed before the next stress application. Methyl viologen and hydrogen peroxide concentrations or chemical stability were not measured or assayed directly in the fermenters or feed carboys.

tag: redox stress chemical

value: MV

tag: exposure time

tag: replicate


title: C.thermocellumDSM1313_MethylViologen_35min_1

description: C. thermocellum DSM 1313, 35 min exposure to methyl viologen

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: C.thermocellumDSM1313_MethylViologen_840min_1

description: C. thermocellum DSM 1313, 840 min exposure to methyl viologen

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: BD_black_A-28

description:
SNP genotyping CEL file: GW6_081909W_AP87_28.CEL
hypomethylation CEL file: GW6_081909W_AP98_28_hypo.CEL

tag: age

value: black


title: C.thermocellumDSM1313_MethylViologen_3min_2

description: C. thermocellum DSM 1313, 3 min exposure to methyl viologen


title: C.thermocellumDSM1313_HydrogenPeroxide_840min_2

description: C. thermocellum DSM 1313, 840 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_HydrogenPeroxide_35min_2

description: C. thermocellum DSM 1313, 35 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_MethylViologen_35min_2

source_name: C. thermocellum DSM 1313, 35 min exposure to methyl viologen


title: C.thermocellumDSM1313_HydrogenPeroxide_3600min_1

description: C. thermocellum DSM 1313, 3600 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_Untreated1_2

description: C. thermocellum DSM 1313, untreated sample, prior to methyl viologen exposure


title: CTRL_white_A-27

description:
SNP genotyping CEL file: GW6_010609T_AP4_AP27.CEL
hypomethylation CEL file: GW6_010609T_AP45_AP27-hypo.CEL

value: M


title: C.thermocellumDSM1313_HydrogenPeroxide_35min_1

source_name: C. thermocellum DSM 1313, 35 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_MethylViologen_420min_2

source_name: C. thermocellum DSM 1313, 420 min exposure to methyl viologen


title: C.thermocellumDSM1313_HydrogenPeroxide_3min_2

description: C. thermocellum DSM 1313, 3 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_HydrogenPeroxide_15min_1

description: C. thermocellum DSM 1313, 15 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_MethylViologen_3min_1

source_name: C. thermocellum DSM 1313, 3 min exposure to methyl viologen


title: C.thermocellumDSM1313_HydrogenPeroxide_840min_1

source_name: C. thermocellum DSM 1313, 840 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_HydrogenPeroxide_420min_1

description: C. thermocellum DSM 1313, 420 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_Untreated1_1

source_name: C. thermocellum DSM 1313, untreated sample, prior to methyl viologen exposure


title: C.thermocellumDSM1313_HydrogenPeroxide_3000min_2

description: C. thermocellum DSM 1313, 3000 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_HydrogenPeroxide_15min_2

source_name: C. thermocellum DSM 1313, 15 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_HydrogenPeroxide_3600min_2

source_name: C. thermocellum DSM 1313, 3600 min exposure to hydrogen peroxide


title: C.thermocellumDSM1313_Untreated2_2

description: C. thermocellum DSM 1313, untreated sample, prior to hydrogen peroxide exposure


title: C.thermocellumDSM1313_Untreated2_1

source_name: C. thermocellum DSM 1313, untreated sample, prior to hydrogen peroxide exposure


title: C.thermocellumDSM1313_HydrogenPeroxide_420min_2

source_name: C. thermocellum DSM 1313, 420 min exposure to hydrogen peroxide


title: SZ_white_A-26

description:
SNP genotyping CEL file: GW6_081909W_AP86_26.CEL
hypomethylation CEL file: GW6_081909W_AP97_26_hypo.CEL

source_name: Brain

value: white


title: C.thermocellumDSM1313_HydrogenPeroxide_3min_1

source_name: C. thermocellum DSM 1313, 3 min exposure to hydrogen peroxide


title: CTRL_white_A-24

description:
SNP genotyping CEL file: GW6_123008T_AP3_AP24.CEL
hypomethylation CEL file: GW6_123008T_AP44_AP24-hypo.CEL


title: BD_white_A-23

description:
SNP genotyping CEL file: GW6_081909W_AP85_23.CEL
hypomethylation CEL file: GW6_081909W_AP96_23_hypo.CEL

value: case


title: C.thermocellumDSM1313_MethylViologen_840min_2

source_name: C. thermocellum DSM 1313, 840 min exposure to methyl viologen


title: SZ_white_A-22

description:
SNP genotyping CEL file: GW6_081909W_AP84_22.CEL
hypomethylation CEL file: GW6_081909W_AP95_22_hypo.CEL

value: Schizophrenia


title: BD_white_A-21

description:
SNP genotyping CEL file: GW6_081909W_AP83_21.CEL
hypomethylation CEL file: GW6_081909W_AP94_21_hypo.CEL


title: BD_white_A-20

description:
SNP genotyping CEL file: GW6_081909W_AP82_20.CEL
hypomethylation CEL file: GW6_081909W_AP93_20_hypo.CEL

value: F


title: C.thermocellumDSM1313_MethylViologen_3600min_1

description: C. thermocellum DSM 1313, 3600 min exposure to methyl viologen


title: CTRL_white_A-19

description:
SNP genotyping CEL file: GW6_123008T_AP2_AP19.CEL
hypomethylation CEL file: GW6_123008T_AP43_AP19-hypo.CEL


title: C.thermocellumDSM1313_MethylViologen_3600min_2

source_name: C. thermocellum DSM 1313, 3600 min exposure to methyl viologen


title: C.thermocellumDSM1313_MethylViologen_15min_2

description: C. thermocellum DSM 1313, 15 min exposure to methyl viologen


title: C.thermocellumDSM1313_MethylViologen_3000min_2

description: C. thermocellum DSM 1313, 3000 min exposure to methyl viologen


title: Rat cerebellum, PCA+NH3+LPS, sample 1

first: Teresa

last: García-Lezana

address: Paseo de la Vall d'hebron 119-129

institute: Vall d'Hebron Research Institute

hyb_protocol: Approximately 5μg of fragmented and labeled ssDNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 17 hours at 45° at Gene Titan platform

scan_protocol: Arrays were scanned on an Affymetrix Gene Titan platform

data_processing: RMA algorithm was used to normalize the arrays and summarized the probes.

organism: Rattus norvegicus

source_name: Rat cerebellum after 6 months of PCA and 10 combined infusions (NH3+LPS)

label_protocol: 5.5µg of ssDNA were fragmented and labeled using the WT Plus kit (Affymetrix) following protocol guides.

extract_protocol: not provided

value: Sprague-Dawley

value: Cerebellum

tag: treatment

value: PCA  (6 months)+ Lipopolisaccharide (10 infusions)+ Ammonium acetate (10 infusions)


title: BD_white_A-18

description:
SNP genotyping CEL file: GW6_081909W_AP81_18.CEL
hypomethylation CEL file: GW6_081909W_AP92_18_hypo.CEL

value: Bipolar


title: Rat cerebellum, PCA+LPS, sample 5

source_name: Rat cerebellum after 6 months of PCA and 10 LPS infusions

value: PCA  (6 months)+ Lipopolisaccharide (10 infusions)


title: SZ_white_A-17

description:
SNP genotyping CEL file: GW6_080709Wb_AP17_17.CEL
hypomethylation CEL file: GW6_080709W_AP19_17_hypo.CEL


title: BD_white_A-16

description:
SNP genotyping CEL file: GW6_081909W_AP80_16.CEL
hypomethylation CEL file: GW6_081909W_AP91_16_hypo.CEL


title: CTRL_white_A-15

description:
SNP genotyping CEL file: GW6_123008T_AP1_AP15.CEL
hypomethylation CEL file: GW6_123008T_AP42_AP15-hypo.CEL

value: control


title: Rat cerebellum, PCA+NH3+LPS, sample 4


title: Rat cerebellum, PCA+NH3+LPS, sample 2


title: C.thermocellumDSM1313_MethylViologen_3000min_1

source_name: C. thermocellum DSM 1313, 3000 min exposure to methyl viologen


title: Rat cerebellum, PCA+LPS, sample 4


title: BD_white_A-14

description:
SNP genotyping CEL file: GW6_081909W_AP79_14.CEL
hypomethylation CEL file: GW6_081909W_AP90_14_hypo.CEL


title: C.thermocellumDSM1313_MethylViologen_15min_1

source_name: C. thermocellum DSM 1313, 15 min exposure to methyl viologen


title: 2000mg/kg for DAM study, biological rep2

city: Osaka

first: Masayuki

last: Kanki

address: 2-1-6, Yodogawa-ku

country: Japan

institute: Astellas Pharma Inc.

description: DAM_2000 mg_02

hyb_protocol: Hybridization and following washing by fluidics were performed with hybridization, wash and stain kit(Affymetrix Inc.), in accordance with the manufacturer's instruction.

scan_protocol: Gene chip  was scanned using GeneChip scanner GCS3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings (ExpressionStat 5.0). 1st normalization was performed for the median of all probe sets (31099 probe sets) per chip and 2nd normalization was performed for the 1st normalized value per gene by Gene Spring 7.3 (Agilent technology). Statistical anlalysis were performed by Gene Spring 7.3 (Agilent technology).

source_name: Fischer344_diet containing 5% (equivalent to 2000mg/kg) DAM for 28days

label_protocol: In vitro transcription with IVT labeling kit(Affymetrix Inc.) generated multiple copies of biotin-labelled aRNA from the double-stranded cDNA templates.

growth_protocol: Animals were maintained under standard conditions(room temperture, 23±1°C; relative humidity, 44±1°C; and light/dark cycle, 12h)

extract_protocol: The livers treated by PBO were removed and transfered in RNAlater solution, stocked in -80°C. The livers treated by DAM were removed and frozen immediately in liquid nitrogen, then stocled in -80°C. The collected livers were lysed by the buffer RLT in the collection tube supplied in RNeasy Kit(QIAGEN), then extracted total RNA using RNeasy Kit in accordance with the manufacturer's instruction.

treatment_protocol: In PBO repeated study, rats were treated by 0.5% methyl cellulose, 500, 1000 and 1500mg/kg via p.o. for 7days. In DAM repeated study, rats were trated by basal diet, diet containing 2% and 5% (equivalent to 800mg/kg and 2000mg/kg, respectively) for 28days.

value: male

tag: treated with

value: liver


title: Rat cerebellum, PCA+NH3, sample 1

source_name: Rat cerebellum after 6 months of PCA and 10 ammonia infusions

value: PCA  (6 months)+ Ammonium acetate (10 infusions)


title: 800mg/kg for DAM study, biological rep2

description: DAM_800 mg_02

source_name: Fischer344_diet containing 2% DAM for 28days

value: diet containing 2% (equivalent to 800mg/kg) DAM for 28days


title: Rat cerebellum, PCA+NH3, sample 2


title: Rat cerebellum, PCA+NH3, sample 3


title: Rat cerebellum, PCA, sample 5

source_name: Rat cerebellum 6 months after PCA surgery

value: Portocaval anatomosis surgery (PCA) 6 months


title: BD_white_A-13

description:
SNP genotyping CEL file: GW6_080709Wb_AP14_13.CEL
hypomethylation CEL file: GW6_080709W_AP16_13_hypo.CEL

tag: study

value: Stanley Medical Research Institute


title: Rat cerebellum, PCA+LPS, sample 3


title: Rat cerebellum, PCA+LPS, sample 1


title: C.thermocellumDSM1313_HydrogenPeroxide_3000min_1

description: C. thermocellum DSM 1313, 3000 min exposure to hydrogen peroxide


title: 2000mg/kg for DAM study, biological rep1

description: DAM_2000 mg_01

value: diet containing 5% (equivalent to 2000mg/kg) DAM for 28days


title: 1500mg/kg for PBO study, biological rep2

description: PBO_1500 mg_02

source_name: Sprague-Dawley_1500mg/kg PBO via p.o. for 7days

value: Sprague‐Dawley

value: 1500mg/kg PBO via p.o. for 7days


title: Rat cerebellum, PCA+NH3+LPS, sample 3


title: Rat cerebellum, PCA+NH3, sample 4


title: Rat cerebellum, PCA+LPS, sample 2


title: 800mg/kg for DAM study, biological rep1

description: DAM_800 mg_01


title: Rat cerebellum, PCA, sample 3


title: Rat cerebellum, PCA, sample 4


title: SZ_white_A-12

description:
SNP genotyping CEL file: GW6_081309Wb_AP57_12.CEL
hypomethylation CEL file: GW6_081309W_AP66_12_hypo.CEL

tag: Sex

value: M

value: white

value: case

value: Schizophrenia


title: SZ_white_A-11

description:
SNP genotyping CEL file: GW6_081309W_AP56_11.CEL
hypomethylation CEL file: GW6_081309W_AP65_11_hypo.CEL

tag: self-reported race


title: Rat cerebellum, PCA, sample 2

value: Sprague-Dawley

value: Cerebellum


title: Rat cerebellum, PCA+NH3, sample 5


title: 2000mg/kg for DAM study, biological rep3

description: DAM_2000 mg_03


title: Rat cerebellum, PCA, sample 1


title: 0 mg/kg for DAM study, biological rep2

description: DAM_0 mg_02

source_name: Fischer344_basal diet for 28days

value: basal diet for 28days


title: SZ_white_A-10

description:
SNP genotyping CEL file: GW6_081309W_AP55_10.CEL
hypomethylation CEL file: GW6_081309W_AP64_10_hypo.CEL

tag: cohort


title: BD_white_A-8

description:
SNP genotyping CEL file: GW6_081309W_AP53_8.CEL
hypomethylation CEL file: GW6_081309W_AP62_8_hypo.CEL

value: Bipolar


title: SZ_white_A-9

description:
SNP genotyping CEL file: GW6_081309W_AP54_9.CEL
hypomethylation CEL file: GW6_081309W_AP63_9_hypo.CEL

value: F


title: BD_white_A-6

description:
SNP genotyping CEL file: GW6_081309W_AP52_6.CEL
hypomethylation CEL file: GW6_081309W_AP61_6_hypo.CEL


title: 800mg/kg for DAM study, biological rep3

description: DAM_800 mg_03

tag: gender

value: male

value: liver


title: 1500mg/kg for PBO study, biological rep1

description: PBO_1500 mg_01


title: BD_native american_A-5

description:
SNP genotyping CEL file: GW6_081309W_AP51_5.CEL
hypomethylation CEL file: GW6_081309W_AP60_5_hypo.CEL

value: native american


title: 0 mg/kg for DAM study, biological rep1

description: DAM_0 mg_01


title: 1500mg/kg for PBO study, biological rep3

description: PBO_1500 mg_03


title: 1000mg/kg for PBO study, biological rep3

description: PBO_1000 mg_03

source_name: Sprague-Dawley_1000mg/kg PBO via p.o. for 7days

value: 1000mg/kg PBO via p.o. for 7days


title: 0 mg/kg for DAM study, biological rep3

description: DAM_0 mg_03


title: Rat cerebellum, Sham, sample 3

source_name: Rat cerebellum sham surgery control

value: Sham


title: Rat cerebellum, Sham, sample 4


title: BD_white_A-4

description:
SNP genotyping CEL file: GW6_081309W_AP50_4.CEL
hypomethylation CEL file: GW6_081309W_AP59_4_hypo.CEL

value: Stanley Medical Research Institute


title: Early Blight Resistant Treated-3

city: VARANASI

first: PRITI

last: UPADHYAY

address: VARANASI

department: GENETICS AND PLANT BREEDING

country: India

institute: BANARAS HINDU UNIVERSITY

description: Gene expression data from Tomato Early Blight Resistant treated plants

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

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

organism: Solanum habrochaites

source_name: Resistant plant leaf at vegetative stage chalenged with fungal spore

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: Plants were sown in plastic pots at optimal conditions for tomato plants.

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

treatment_protocol: Sample 1,2,3,7,8,9 were grown in normal growth conditions without any stress in green house. While sample 4,5,6, and 10,11,12 were challenged with 10 days old culture  A. solani  in optimal conditions for disease development in chamber . The sample was collected after 24hrs of inoculation at which fungal mycelia start to penetrate the host tissue (Dita et al. 2007)

tag: genotype

value: Early Blight Tolerant Genotype

value: leaf

value: fungal spore challenge


title: Rat cerebellum, Sham, sample 5


title: SZ_white_A-3

description:
SNP genotyping CEL file: GW6_081309W_AP49_3.CEL
hypomethylation CEL file: GW6_081309W_AP58_3_hypo.CEL

source_name: Brain

value: M

value: white


title: Early Blight Resistant Treated-2


title: BD_white_A-2

description:
SNP genotyping CEL file: GW6_080709W_AP13_2.CEL
hypomethylation CEL file: GW6_080709W_AP15_2_hypo.CEL

value: case


title: Rat cerebellum, Sham, sample 2

value: Sprague-Dawley


title: 500mg/kg for PBO study, biological rep3

description: PBO_500 mg_03

source_name: Sprague-Dawley_500mg/kg PBO via p.o. for 7days

value: Sprague‐Dawley

value: 500mg/kg PBO via p.o. for 7days


title: 1000mg/kg for PBO study, biological rep2

description: PBO_1000 mg_02


title: Early Blight Resistant Control-3

description: Gene expression data from Tomato Early Blight Resistant untreated plants

source_name: Resistant plant leaf vegetative stage in normal growth condition

value: control


title: 500mg/kg for PBO study, biological rep2

description: PBO_500 mg_02


title: 500mg/kg for PBO study, biological rep1

description: PBO_500 mg_01


title: 0 mg/kg for PBO study, biological rep3

description: PBO_0 mg_03

source_name: Sprague-Dawley_0.5% methyl cellulose via p.o. for 7days


title: Early Blight Resistant Control-2

source_name: Resistant plant leaf at vegetative stage in normal growth condition


title: 0 mg/kg for PBO study, biological rep1

description: PBO_0 mg_01

value: 0.5% methyl cellulose via p.o. for 7days


title: Early Blight Resistant Control-1


title: Early Blight Susceptible Treated-2

description: Gene expression data from Tomato Early Blight Susceptible treated plants

organism: Solanum lycopersicum

source_name: Sensitive plant leaf at vegetative stage chalenged with fungal spore

value: Early Blight Susceptible Genotype


title: Early Blight Susceptible Treated-3


title: Early Blight Susceptible Treated-1


title: Escherichia coli O157:H7 EDL933, control

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

description: Gene expression data of E. coli O157:H7 incubated for 8 hrs at 37oC with 250 rpm shaking

hyb_protocol: Following affymetrix protocol.   Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA.  After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours.    After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol.   After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: The data were analyzed with Robust Multi-array Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.5 (Agilent technologies, CA). Fold change filters included the requirement that the genes be present in at least 150% of controls for up-regulated genes and lower than 66% of controls for down-regulated genes. Hierarchical clustering data were clustered groups that behave similarly across experiments using GeneSpring GX 12.5 (Agilent technologies, CA). Clustering algorithm was Euclidean distance, average linkage.

organism: Escherichia coli O157:H7 str. EDL933

source_name: Escherichia coli O157:H7 EDL933

label_protocol: Following affymetrix protocol.  cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

growth_protocol: E. coli was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 8 h with shaking at 250 rpm with and without ginkgolic acid (0.005 mg/ml)

extract_protocol: DNA microarray analysis with one biological replicate was performed with an Affymetrix system. E. coli was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 8 h with shaking at 250 rpm with and without 0.005 mg/ml of ginkgolic acid. Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA) with Qiagen RNase-free DNase I (Cat# 79254).

treatment_protocol: Sample 2 was incubated with 0.005 mg/ml of Ginkgolic acid at 37oC for 8 hrs with 250 rpm shaking


title: Early Blight Resistant Treated-1


title: Early Blight Susceptible Control-3

description: Gene expression data from Tomato Early Blight Susceptible untreated plants

source_name: Sensitive plant leaf at vegetative stage in normal growth condition


title: Escherichia coli O157:H7 EDL933, 0.005 mg/ml of Ginkgolic acid

description: Gene expression data of E. coli O157:H7 incubated with 0.005 mg/ml of Ginkgolic acid for 8 hrs at 37oC with 250 rpm shaking

value: 0.005 mg/ml Ginkgolic acid


title: Early Blight Susceptible Control-2


title: Early Blight Susceptible Control-1


title: TmTNF-α+ cells sorted from primary AML sample, biological rep2

city: Wuhan

first: Shiqiu

last: Zhou

address: Liberation Road

country: China

institute: Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: AMLTNFα+ 2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

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

growth_protocol: SKM-1 cells were cultured in IMDM supplemented with 10% FBS in a humidified atmosphere of 5 % CO2 at 37℃. RNA of human CD45+ leukemia cells from mice and cells sorted from primary AML sample, were extracted as soon as the cells were obtained.

tag: cell type


title: TmTNF-α+ cells sorted from primary AML sample, biological rep1

description: AMLTNFα+ 1


title: 0 mg/kg for PBO study, biological rep2

description: PBO_0 mg_02

value: male

value: liver


title: TmTNF-α- cells sorted from primary AML sample, biological rep2

description: AMLTNFα- 2


title: TmTNF-α- cells sorted from primary AML sample, biological rep1

description: AMLTNFα- 1


title: Human CD45+ leukemia cells from mice, treated with IgG1 after first transplantation, biological rep2

source_name: Human CD45+ leukemia cells from mice_treated with IgG1 after first transplantation

value: Human CD45+ leukemia cells from mice

value: IgG1 after first transplantation


title: Human CD45+ leukemia cells from mice, treated with C1 after first transplantation, biological rep2

source_name: Human CD45+ leukemia cells from mice_treated with C1 after first transplantation

value: C1 after first transplantation


title: Human CD45+ leukemia cells from mice, treated with C1 after first transplantation, biological rep1


title: Human CD45+ leukemia cells from mice, treated with IgG1 after first transplantation, biological rep1


title: 6929742060_R05C02 CP 8

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

institute: Princess Margaret Cancer Centre

description:
Diseased oral cavity
CP 8

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software 2011.1

label: Cy5 and Cy3

source_name: oral cavity

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from oral samples using Qiagen DNeasy Kit according to standard instructions

tag: sample type

value: genomic

tag: disease state

value: Inflammation


title: 6929742060_R02C01 CP 3

description:
Diseased oral cavity
CP 3


title: 6929742060_R06C02 CP 9

description:
Diseased oral cavity
CP 9


title: SKM-1 cell line, stably transfected with tmTNF-α shRNA, biological rep2

description: SKM-1 89 2

source_name: SKM-1 cell line_stably transfected with tmTNF-α shRNA

tag: cell line

value: SKM-1 cell line

tag: genotype/variation

value: stably transfected with tmTNF-α shRNA


title: 6929742056_R05C02 Normal 9

description:
normal oral cavity
Normal 9

value: Normal


title: 1000mg/kg for PBO study, biological rep1

description: PBO_1000 mg_01

tag: strain

value: 1000mg/kg PBO via p.o. for 7days

tag: tissue


title: 6929742060_R04C01 CP 6

description:
Diseased oral cavity
CP 6


title: 6929742056_R06C02 Normal 11

description:
normal oral cavity
Normal 11


title: 6929742060_R03C02 CP 5

description:
Diseased oral cavity
CP 5


title: 6929742060_R01C02 CP 2

description:
Diseased oral cavity
CP 2


title: 6929742060_R01C01 CP 1

description:
Diseased oral cavity
CP 1


title: 6929742060_R04C02 CP 7

description:
Diseased oral cavity
CP 7


title: SKM-1 cell line, stably transfected with control shRNA, biological rep2

description: SKM-1 NC 2

source_name: SKM-1 cell line_stably transfected with control shRNA

value: stably transfected with control shRNA


title: 6929742056_R04C02 Normal 7

description:
normal oral cavity
Normal 7


title: 6929742060_R02C02 CP 4

description:
Diseased oral cavity
CP 4


title: SKM-1 cell line, stably transfected with tmTNF-α shRNA, biological rep1

description: SKM-1 89 1


title: NCI-H1299 miR-34a transfectant

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

institute: Tokyo Medical University

description: Gene expression data from lung cancer cell lne at miR-34a transfection.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C with GeneChip 3'IVT PLUS Reagent Kit and GeneChip Hybridization, Wash, and Stain Kit.

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

source_name: NCI-H1299 miR-34a transfectant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: NCI-H1299 lung cancer cell lines were grown in RPMI-1640 with 10% FBS.

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

treatment_protocol: miR-34a and ghR-34a were transfected into cells using Lipofectamin RNAiMAX transfection reagent (Life Technologies) at 25 nM for 48 hours.

value: Lung cancer


title: NCI-H1299 Mock

description: Gene expression data from lung cancer cell lne.

source_name: NCI-H1299 Mock


title: Rat cerebellum, Sham, sample 1

source_name: Rat cerebellum sham surgery control

value: Sprague-Dawley

value: Cerebellum

value: Sham


title: 6929742056_R06C01 Normal 10

description:
normal oral cavity
Normal 10


title: SKM-1 cell line, stably transfected with control shRNA, biological rep1

description: SKM-1 NC 1


title: OAT_Obese non-diabetic [Lot  OM031808A]

first: Ayo

middle: P

last: Doumatey

address: 12 South Drive

department: NHGRI

institute: NIH

description: gene expression data from omental adipose tissue of obese and non- diabetic African American

hyb_protocol: Labeled cRNAs was hybridized to the Affymetrix Human Genome U133 2.0 Gene Chip according to manufacturer's protocol.

scan_protocol: Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays

data_processing: Probe cell intensity data (Affymetrix CEL files) were generated using Affymetrix GeneChip Command Console (AGCC) software. Affymetrix microarray CEL files with probe cell information were further processed in Partek Genomics Suite 6.0 (St Louis, MO) and were summarized into probe-set level data with robust multi-array average (RMA) algorithm

source_name: Omental adipose tissue

label_protocol: Per RNA labeling, 500 ng of total RNA was used in conjunction with the Illumina® TotalPrep RNA Amplification Protocol and labelled biotin.

extract_protocol: Omental adipose tissue samples were disrupted and homogenized in QIAzol lysis reagent using a tissuelyser (Qiagen Inc., Valencia, CA)  and followed by chloroform extraction. The upper aqueous phase containing the RNA was processed with EZ1 RNA universal tissue kit on the EZ1 workstation following manufacturer's instructions.

value: Female


title: 6929742056_R03C01 Normal 5

description:
normal oral cavity
Normal 5


title: 6929742056_R05C01 Normal 8

description:
normal oral cavity
Normal 8


title: OAT_Obese non-diabetic [Lot  OM042208B]


title: 6929742056_R04C01 Normal 6

description:
normal oral cavity
Normal 6


title: OAT_Obese non-diabetic [Lot OM032608B]

description: gene expression data from omental adipose tissue of obese and non-diabetic African American

value: Male


title: OAT_Obese non-diabetic [Lot OM042208A]


title: 6929742056_R02C02 Normal 4

description:
normal oral cavity
Normal 4


title: 9343114114_R06C02 CP 10

description: Diseased oral cavity


title: 9343114114_R05C02 CP 9

description: Diseased oral cavity


title: OAT_Obese non-diabetic [Lot  OM101707]


title: OAT_Obese non-diabetic [Lot  OMM020808]


title: OAT_Obese and diabetic [DOM111307B]

description: gene expression data from omental adipose tissue of obese and diabetic African American


title: 6929742056_R01C02 Normal 2

description:
normal oral cavity
Normal 2


title: 6929742056_R02C01 Normal 3

description:
normal oral cavity
Normal 3


title: OAT_Obese and diabetic [DOM120507]


title: OAT_Obese and diabetic [DOM101105A]


title: 6929742056_R01C01 Normal 1

description:
normal oral cavity
Normal 1


title: OAT_Obese and diabetic [DOM091907]


title: 9343114114_R05C01 CP 8

description: Diseased oral cavity


title: B_CLL404

city: Brisbane

first: Nicholas

last: Saunders

address: 37 Kent Street

institute: University of Queensland Diamantina Institute

description: MDCs Resistant CLL

hyb_protocol: Standard Illumina hybridisation protocol

data_processing: Data have been background corrected and quantile normalized using control probe with the neqc function of the limma R package (v3.24.4)

source_name: resistant CLL patient_MDCs_Day 7

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina Arrays

growth_protocol: CLL PBMCs were isolated from patient blood. CD14 positive monocytes were selected from PBMCs on day 0 using MACS microbeads. CLL PBMCs were maintained in RPMI 10% FCS for seven days and MDCs isolated after removal on non-adherent cells

extract_protocol: RNA was extracted with Bioline Isolate II RNA Micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Untreated

tag: subject status

value: Chronic lymphocytic leukemia patient

tag: antibody response

value: Resistant

value: Monocyte derived cells (MDCs)


title: 9343114114_R04C02 CP 7

description: Diseased oral cavity


title: OAT_Obese and diabetic [OMM041007]


title: B_CLL409

description: MDCs Resistant CLL


title: 9343114114_R02C02 CP 4

description: Diseased oral cavity


title: B_CLL395

description: MDCs Sensitive CLL

source_name: sensitive CLL patient_MDCs_Day 7

value: Sensitive


title: OAT_Obese and diabetic [DOM032707A]


title: 9343114114_R01C02 CP 2

description: Diseased oral cavity

value: genomic


title: B_CLL398

description: MDCs Sensitive CLL


title: 9343114114_R03C02 CP 5

description: Diseased oral cavity

value: Inflammation


title: 9343114114_R04C01 CP 6

description: Diseased oral cavity


title: B_CLL414

description: MDCs Sensitive CLL


title: OAT_Obese and diabetic [DOM051906]


title: B_CLL315

description: MDCs Sensitive CLL


title: 9343114114_R01C01 CP 1

description: Diseased oral cavity


title: 9343114114_R02C01 CP 3

description: Diseased oral cavity


title: OAT_Obese and diabetic [DOM091107]


title: 9374342135_R06C02 Normal 12

description: normal oral cavity


title: 9374342135_R06C01 Normal 11

description: normal oral cavity


title: B_CLL399

description: MDCs Resistant CLL


title: NCI-H1299 ghR-34a transfectant

description: Gene expression data from lung cancer cell lne at ghR-34a transfection.

source_name: NCI-H1299 ghR-34a transfectant


title: OAT_Obese and diabetic [DOM073107]


title: 9374342135_R04C02 Normal 8

description: normal oral cavity


title: OAT_Obese and diabetic [DOM050708A]


title: OAT_Obese and diabetic [DOM040108C]


title: D0_CLL338

description: Monocytes Sensitive CLL

source_name: sensitive CLL patient_CD14 monocytes_Day 0

value: CD14 monocytes


title: OAT_Obese and diabetic [DOMM041007]


title: OAT_Obese and diabetic [DOM040407]


title: 9374342135_R03C02 Normal 6

description: normal oral cavity


title: Treated with Aphidicolin and AZD7762 for 96h in differentiation medium rep3 [9479628135_L_Grn.idat]

status: Public on Jul 28 2015

city: Singapore

first: Kevin Andrew

last: Gonzales

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: replicate 3

data_processing: Data were rank invariant normalized using BeadStudio

source_name: H1 hESCs

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by Dnase I treatment and clean-up with PureLink RNA Mini kit in accordance with the prescribed protocol provided with the kit.

tag: passage number

tag: treatment type

value: Aphidicolin and AZD7762

tag: treatment length

value: 96 hours

tag: incubation medium

value: mTeSR1 without select factors


title: 9374342135_R05C02 Normal 10

description: normal oral cavity

value: Normal


title: D0_CLL261

description: Monocytes Resistant CLL

source_name: resistant CLL patient_CD14 monocytes_Day 0


title: OAT_Obese and diabetic [OM032007]

tag: Sex


title: D0_CLL292

description: Monocytes Resistant CLL


title: Treated with Aphidicolin and AZD7762 for 96h in differentiation medium rep1 [9479628135_J_Grn.idat]

description: replicate 1