title: Chironomus riparius_solvent control_replicate 9

description: Chironomus riparius solvent control treated sample replicate 9


title: genomic DNA from liver sample 66

status: Public on Aug 08 2013

type: genomic

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

description: control

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 iScan Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio V2011.1; methylation module 1.9.0

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: liver tissue 66

label_protocol: Standard Illumina Protocol

extract_protocol: For homogenisation of five to ten milligram frozen tissue and subsequent nucleic acid isolation, tubes with 1.4 mm ceramic beads (Precellys, Villeurbanne, France) and the AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) were used.

tag: group

value: NORMAL

tag: age

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue

value: liver


title: genomic DNA from liver sample 67

description: unknown

source_name: liver tissue 67

value: unknown


title: genomic DNA from liver sample 68

description: NASH

source_name: liver tissue 68

value: NASH


title: Chironomus riparius_solvent control_replicate 8

type: RNA

city: Amsterdam

first: Floyd

last: Wittink

address: Kruislaan 318

department: MAD

country: Netherlands

institute: Universiteit van Amsterdam

description: Chironomus riparius solvent control treated sample replicate 8

hyb_protocol: Hybridization samples, containing 1.1 µg test (Cy3) and 1.1 µg common reference (Cy5) sample, were made according to the manufacturer's instructions (NimbleGen Arrays User's Guide for Gene Expression Arrays Version 5.0, Roche/NimbleGen). Hybridization of the samples to the custom made 12*135K C. riparius microarrays (Marinković et al., 2012) was carried out for 18 hours at 42°C using NimbleGen Hybridization System 4 (Roche/Nimblegen).

scan_protocol: Microarrays were scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies).

data_processing: Feature extraction was performed with NimbleScan v2.5 (Roche/Nimblegen). The data was normalized using the vsn algorithm that performs intensity-based variance stabilization (Huber et al., 2002) and the duplicate probes per transcript were collapsed.

molecule: total RNA

organism: Chironomus riparius

source_name: solvent control

label_protocol: Per sample, 500 ng total RNA was amplified according to the Agilent QuickAmp kit manual (Agilent technologies).  Amino-allyl modified nucleotides were incorporated during the aRNA synthesis (2.5 mM rGAU (GE Healthcare), 0.75 mM  rCTP (GE Healthcare), 0.75 mM AA-rCTP (TriLink Biotechnologies).  Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek). Test samples were labeled with Cy3 and a Common Reference sample (made by pooling equimolar amounts of RNA from Test samples) was labeled with Cy5.  5 µg of aRNA was dried down and dissolved in 50 mM carbonate buffer pH 8.5. Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). The labeled aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit. The yields of aRNA and CyDye incorporation were measured on the NanoDrop ND-1000.

growth_protocol: The experiments were conducted with the University of Amsterdam’s Chironomus riparius culture that was maintained in aquaria containing quartz sand overlaid with Dutch Standard Water at 20 ± 1 ˚C, 65% humidity and a 16: 8 h light: dark photoperiod (Marinković et al., 2011). The culture was fed a mixture of Trouvit® (Trouw, Fontaine-les-Vervins, France) and Tetraphyll® (Tetrawerke, Melle, Germany) in a weight ratio of 20:1. This mixture was also used as food for all subsequent experiments.

extract_protocol: RNA was isolated from individual flash frozen C. riparius larvae using Qiazol (Qiagen) for RNA extraction and RNeasy MinElute columns (Qiagen) for RNA purification. RNA yield was determined on a NanoDrop ND-1000 UV-VIS spectrophotometer (Thermo Fisher Scientific), while RNA integrity was examined using a RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The 14-day Chironomus riparius sediment toxicity tests were conducted based on OECD guideline 218 (OECD, 2004) with slight modifications. OECD. Chironomid toxicity test using spiked sediment; Guideline for Testing of Chemicals No. 218; Organisation for Economic Co-operation and Development: Paris, 2004.

value: larvae


title: bone macrophages, LPS-stimulated rep1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: Quantile normalized the data using custom code originally provided by Kerby Shedden at the University of Michigan. The actual code used (in C++) is provided as a Series supplementary file [normalize2.Cpp.txt]. Please note that 'ProbeID' column in raw data files contains 'Array_Address_Id' identifiers.

label: biotin

organism: Mus musculus

label_protocol: According to Illumina protocol

growth_protocol: C57BL/6 mice were purchased from Jackson Laboratory (Bar Harbor, MA).  All mice were bred and maintained in a specific pathogen free environment in Baylor College of Medicine. C57BL/6 bone marrow derived macrophages were generated as previously described (PMID: 19016445). Briefly, marrow from femurs and tibias of 6-8 week old female mice were flushed and cultured at 37 deg in Dulbecco modified Eagle's minimal essential medium (DMEM) supplemented with 20% fetal calf serum (Invitrogen) and L929 fibroblast cell line secreting macrophage colony stimulating factor. After 5 days in culture, mature macrophages were harvested for further study.

extract_protocol: According to Illumina protocol. Total RNA was extracted with combination of RNA TRIzol reagent (Invitrogen) and the RNeasy Mini kit (QIAGEN).

treatment_protocol: Bone marrow derived macrophages from three animals were harvested and treated. C57BL/6 macrophages were stimulated at 37 deg for 24 hours with recombinant mouse/human IFN (20ng/mL; Applied Biosystems, Carlsbad,CA), lipopolysaccharide (LPS; 10ug/mL; SIGMA), PAO (10ug/mL) in CDMEM (DMEM, 10% FCS, 1% penicillin/streptomycin), or serum deficient media prior to phenotypic and functional characterization.  Murine experiments each involved three mice to generate biological replicates.

tag: strain

tag: genotype/variation

value: wild type

value: 6-8 week old

tag: gender

value: female

value: marrow from femurs and tibias

tag: cell type

value: bone marrow-derived macrophages (BMDMs)

tag: activated by

value: lipopolysaccharide (LPS; 10ug/mL)


title: bone macrophages, LPS-stimulated rep2


title: liver, S, A1359-63

city: Regensburg

first: Timo

last: Itzel

address: Franz-Josef-Strauß-Allee 11

institute: Universitätsklinikum Regensburg

hyb_protocol: according to the manufacturers protocols

data_processing: RMA normalization with Bioconductor package oligo

source_name: Steatosis

growth_protocol: liver biopsy

extract_protocol: For homogenisation of five to ten milligram frozen tissue and subsequent nucleic acid isolation, tubes with 1,4 mm ceramic beads (Precellys, Villeurbanne, France) and the AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) were used.

treatment_protocol: not applicable

tag: tissue type

value: liver biopsy

value: Steatosis

tag: fat

tag: inflammation

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: liver, N, A1359-62

scan_protocol: according to the manufacturers protocols

source_name: Nash

tag: group

value: Nash

value: male

tag: age

tag: bmi


title: genomic DNA from liver sample 64

description: Healthy Obese

source_name: liver tissue 64

value: Healthy Obese

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: tissue


title: genomic DNA from liver sample 65

description: NAFLD

source_name: liver tissue 65

value: NAFLD


title: bone macrophages, IFN-gamma-stimulated rep3

tag: strain

tag: genotype/variation

tag: gender

tag: cell type

tag: activated by

value: recombinant mouse/human IFN (20ng/mL)


title: liver, S, A1359-60

source_name: Steatosis, after surgery

label_protocol: according to the manufacturers protocols

tag: tissue type

tag: fat

tag: inflammation

tag: bariatric surgery

value: after surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: liver, N, A1359-61

tag: group

tag: age

tag: bmi

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: liver, N, A1359-59


title: Chironomus riparius_solvent control_replicate 7

description: Chironomus riparius solvent control treated sample replicate 7

tag: tissue


title: Chironomus riparius_solvent control_replicate 6

description: Chironomus riparius solvent control treated sample replicate 6


title: Chironomus riparius_solvent control_replicate 4

description: Chironomus riparius solvent control treated sample replicate 4


title: Chironomus riparius_solvent control_replicate 5

description: Chironomus riparius solvent control treated sample replicate 5


title: Chironomus riparius_low conc_cadmium_replicate 1

description: Chironomus riparius low  conc. cadmium treated sample replicate 1

source_name: low conc. cadmium


title: genomic DNA from liver sample 61

description: Healthy Obese

source_name: liver tissue 61

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

value: liver


title: bone macrophages, IFN-gamma-stimulated rep1

tag: strain

tag: genotype/variation

tag: gender

tag: cell type

tag: activated by


title: liver, H, A1359-58

source_name: Healthy obese, after surgery

tag: tissue type

value: Healthy obese

tag: fat

tag: inflammation

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: genomic DNA from liver sample 63

description: unknown

source_name: liver tissue 63

tag: group

value: unknown

tag: age

tag: bmi


title: liver, C, A1649-10

source_name: Control, after surgery

value: Control

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: bone macrophages (untreated) rep2

tag: strain

tag: genotype/variation

value: wild type

value: 6-8 week old

tag: gender

tag: tissue

tag: cell type

tag: activated by

value: none (Naïve)


title: Chironomus riparius_solvent control_replicate 2

description: Chironomus riparius solvent control treated sample replicate 2

value: larvae


title: genomic DNA from liver sample 60

description: NAFLD

source_name: liver tissue 60

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)


title: bone macrophages (untreated) rep3

value: female

value: marrow from femurs and tibias

value: bone marrow-derived macrophages (BMDMs)


title: liver, H, A1359-57

source_name: Healthy obese

tag: tissue type

value: liver biopsy

tag: fat

tag: inflammation

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: Chironomus riparius_solvent control_replicate 3

description: Chironomus riparius solvent control treated sample replicate 3


title: genomic DNA from liver sample 59

description: control

source_name: liver tissue 59

tag: group

value: NORMAL

tag: age

tag: bmi


title: bone macrophages, IFN-gamma-stimulated rep2

tag: strain

tag: genotype/variation

tag: gender


title: bone macrophages (untreated) rep1

tag: tissue

tag: cell type

tag: activated by


title: genomic DNA from liver sample 62

description: Healthy Obese

source_name: liver tissue 62

value: Healthy Obese

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)


title: Chironomus riparius_solvent control_replicate 1

description: Chironomus riparius solvent control treated sample replicate 1


title: genomic DNA from liver sample 58

description: control

source_name: liver tissue 58


title: Chironomus riparius_control_replicate 10

description: Chironomus riparius control treated sample replicate 10

source_name: control


title: genomic DNA from liver sample 57

description: Healthy Obese

source_name: liver tissue 57


title: genomic DNA from liver sample 56

description: NASH

source_name: liver tissue 56

value: NASH


title: liver, S, A1649-06

source_name: Steatosis, before surgery

tag: tissue type

value: Steatosis

tag: fat

tag: inflammation

value: before surgery

value: male

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: genomic DNA from liver sample 55

description: Healthy Obese

source_name: liver tissue 55

tag: group

tag: age

tag: bmi

value: liver


title: ESCs-overexp-5

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: Prdm4-EGFP overexpressor replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Rank invariant normalization with background subtraction using Gene Expression Module V1.9.0 of Illumina Studio

source_name: Embryonic stem cells

label_protocol: Total RNA was labeled according to the standard Illumina protocol

growth_protocol: Embryonic stem cells were cultured according to standard protocols

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: strain

value: Embryonic stem cells

tag: genotype


title: liver, S, A1649-12

source_name: Steatosis, after surgery

tag: bariatric surgery

value: after surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: liver, N, A1359-55

source_name: Nash

tag: tissue type

value: Nash

tag: fat


title: liver, S, A1359-56

tag: inflammation

tag: delta lar


title: liver, S, A1649-08

tag: delta leptin

tag: leptin


title: liver, H, A1649-09

value: Healthy obese

tag: adiponectin

tag: delta adipo


title: liver, C, A1359-54

source_name: Control

tag: group

value: Control

tag: age


title: genomic DNA from liver sample 54

description: NASH

source_name: liver tissue 54

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: ESCs-overexp-3

description: Prdm4-EGFP overexpressor replicate 3

tag: strain

tag: cell type

tag: genotype


title: ESCs-overexp-6

description: Prdm4-EGFP overexpressor replicate 6


title: Chironomus riparius_control_replicate 6

description: Chironomus riparius control treated sample replicate 6

value: larvae


title: ESCs-overexp-4

description: Prdm4-EGFP overexpressor replicate 4


title: ESCs-overexp-2

description: Prdm4-EGFP overexpressor replicate 2


title: Chironomus riparius_control_replicate 5

description: Chironomus riparius control treated sample replicate 5


title: Chironomus riparius_control_replicate 7

description: Chironomus riparius control treated sample replicate 7


title: Chironomus riparius_control_replicate 9

description: Chironomus riparius control treated sample replicate 9


title: Chironomus riparius_control_replicate 8

description: Chironomus riparius control treated sample replicate 8


title: genomic DNA from liver sample 53

description: Healthy Obese

source_name: liver tissue 53


title: Chironomus riparius_control_replicate 4

description: Chironomus riparius control treated sample replicate 4


title: Chironomus riparius_control_replicate 3

description: Chironomus riparius control treated sample replicate 3


title: liver, H, A1359-50

source_name: Healthy obese, after surgery

tag: tissue type

tag: bariatric surgery

tag: Sex

value: female

tag: nas

tag: fibrosis

tag: lar


title: genomic DNA from liver sample 51

description: Healthy Obese

source_name: liver tissue 51


title: liver, H, A1359-52

tag: fat

tag: inflammation

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin


title: ESCs-null-2

description: Prdm4 null ESC replicate 2


title: tAML patient sample SJTAML083

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array.  GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis.

source_name: RNA extracted from tumor cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from t-MN cases

extract_protocol: Trizol

tag: disease state

value: therapy-related myeloid neoplasm (t-MN)

tag: chromosome 5q status

value: Chromosome 5q wild type

value: mononuclear cell


title: liver, C, A1359-49

value: liver biopsy

tag: group

tag: age

tag: bmi

tag: delta adipo


title: Chironomus riparius_control_replicate 2

description: Chironomus riparius control treated sample replicate 2

tag: tissue


title: liver, S, A1649-05

tag: tissue type

tag: bariatric surgery

tag: Sex


title: liver, S, A1359-53

tag: nas

tag: fibrosis

tag: lar


title: ESCs-null-3

description: Prdm4 null ESC replicate 3

tag: strain

tag: cell type

tag: genotype


title: genomic DNA from liver sample 52

description: Healthy Obese

source_name: liver tissue 52

value: Healthy Obese

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)


title: genomic DNA from liver sample 48

description: unknown

source_name: liver tissue 48

value: unknown


title: ESCs-cont-6

description: Control ESC replicate 6


title: ESCs-null-4

description: Prdm4 null ESC replicate 4


title: ESCs-null-1

description: Prdm4 null ESC replicate 1


title: genomic DNA from liver sample 50

description: Healthy Obese

source_name: liver tissue 50


title: ESCs-overexp-1

description: Prdm4-EGFP overexpressor replicate 1


title: tAML patient sample SJTAML082

tag: disease state

tag: chromosome 5q status


title: Chironomus riparius_control_replicate 1

description: Chironomus riparius control treated sample replicate 1

source_name: control


title: genomic DNA from liver sample 49

description: NAFLD

source_name: liver tissue 49

tag: group

value: NAFLD

tag: age


title: genomic DNA from liver sample 47

description: control

source_name: liver tissue 47

value: NORMAL

tag: bmi


title: liver, H, A1359-45

source_name: Healthy obese

tag: fat

tag: inflammation

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: ESCs-cont-5

description: Control ESC replicate 5

tag: strain


title: ESCs-cont-4

description: Control ESC replicate 4

tag: cell type


title: liver, N, A1359-46

tag: tissue type

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: tAML patient sample SJTAML076

tag: disease state

tag: chromosome 5q status


title: ESCs-cont-3

description: Control ESC replicate 3

tag: genotype


title: genomic DNA from liver sample 45

description: NASH

source_name: liver tissue 45

tag: group

value: NASH

tag: age

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: ESCs-cont-2

description: Control ESC replicate 2

source_name: Embryonic stem cells

tag: strain


title: liver, N, A1359-44

tag: fat

tag: inflammation

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: tAML patient sample SJTAML081

tag: disease state

tag: cell type


title: genomic DNA from liver sample 46

description: unknown

source_name: liver tissue 46

value: liver


title: liver, H, A1359-43

tag: tissue type

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: tAML patient sample SJTAML070

tag: chromosome 5q status


title: genomic DNA from liver sample 43

description: Healthy Obese

source_name: liver tissue 43

tag: group

tag: age

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: 27-A Healthy control-10

city: Shanghai

first: junjie

last: xiao

address: 150 Ji Mo Road

country: China

institute: Key Laboratory of Arrhythmias, Ministry of Education, China (Tongji University School of Medicine)

description: Tagman-based qRT PCR

hyb_protocol: MiRNAs were reverse-transcribed using the Megaplex Primer Pools (Human Pools A v2.1 and B v2.0), and the products were preamplified according to the ABI preamplification protocol. MiRNAs expression was screened using Taqman miRNA microarrays A and B according to the manufacturer protocol (all from Applied Biosystems, Foster City, CA).

scan_protocol: MiRNAs expression was screened using Taqman miRNA microarrays A and B according to the manufacturer protocol (all from Applied Biosystems, Foster City, CA). All steps were performed using a 7900HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA).

data_processing: For the lack of generally accepted standards all qPCR data of single miRNAs expression were analyzed as unadjusted Ct values and standardized to miR-16 (A plate) or miR-135a*(B plate).

label: Tagman

source_name: Plasma

label_protocol: Tagman-based qRT PCR

extract_protocol: Total RNA was isolated from plasma using mirVana PARIS isolation kit (Ambion, Austin, Texas) according to the manufacturer’s instructions for plasma samples. Briefly, each of 400 μL human plasma was used to extract total RNA. Each sample was eluted in 100 μL of RNAsefree water.

tag: gender

value: male


title: liver, H, A1359-42

tag: fat

tag: inflammation

value: after surgery

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: tAML patient sample SJTAML069

tag: disease state

tag: cell type


title: genomic DNA from liver sample 44

description: Healthy Obese

source_name: liver tissue 44


title: 26-A APE-10

description: Tagman-based qRT PCR


title: genomic DNA from liver sample 41

description: Healthy Obese

source_name: liver tissue 41


title: tAML patient sample SJTAML068

tag: chromosome 5q status


title: 25-A Healthy control-9

description: Tagman-based qRT PCR


title: liver, H, A1359-41

tag: tissue type

tag: group

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: tAML patient sample SJTAML067


title: 24-A Healthy control-8

description: Tagman-based qRT PCR

tag: gender

tag: age


title: genomic DNA from liver sample 40

description: NASH

source_name: liver tissue 40

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: liver, S, A1649-03

source_name: Steatosis, after surgery

value: Steatosis

tag: fat

tag: inflammation

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: genomic DNA from liver sample 42

description: NASH

source_name: liver tissue 42

tag: group


title: tAML patient sample SJTAML065

source_name: RNA extracted from tumor cells

tag: disease state

tag: chromosome 5q status

tag: cell type


title: liver, H, A1359-51

source_name: Healthy obese, after surgery

tag: tissue type

value: Healthy obese

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: genomic DNA from liver sample 38

description: NASH

source_name: liver tissue 38

tag: age

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: 22-A Healthy control-6

description: Tagman-based qRT PCR

tag: gender


title: 21-A Healthy control-5

description: Tagman-based qRT PCR


title: liver, C, A1649-02

source_name: Control, after surgery

value: Control

tag: fat

tag: inflammation

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: genomic DNA from liver sample 39

description: NASH

source_name: liver tissue 39

tag: group


title: tAML patient sample SJTAML063

tag: disease state

tag: chromosome 5q status

value: Chromosome 5q deletion

tag: cell type


title: tAML patient sample SJTAML054


title: 20-A APE-9

description: Tagman-based qRT PCR

tag: age


title: liver, N, A1359-39

source_name: Nash

tag: tissue type

value: Nash

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: tAML patient sample SJTAML057

value: therapy-related myeloid neoplasm (t-MN)


title: tAML patient sample SJTAML061


title: 19-A APE-8

description: Tagman-based qRT PCR

tag: gender


title: genomic DNA from liver sample 37

description: NASH

source_name: liver tissue 37

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: liver, N, A1359-37

tag: fat

tag: inflammation

value: female

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: genomic DNA from liver sample 35

description: NAFLD

source_name: liver tissue 35

tag: group

tag: age


title: tAML patient sample SJTAML055

tag: disease state

tag: chromosome 5q status

value: Chromosome 5q wild type

tag: cell type

value: mononuclear cell


title: liver, H, A1359-38

source_name: Healthy obese

tag: tissue type

value: liver biopsy

tag: bariatric surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar


title: genomic DNA from liver sample 33

description: Healthy Obese

source_name: liver tissue 33

value: Healthy Obese

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: tAML patient sample SJTAML053


title: tAML patient sample SJTAML052


title: tAML patient sample SJTAML050


title: liver, H, A1359-36

tag: fat

tag: inflammation

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin


title: 18-A APE-7

description: Tagman-based qRT PCR

tag: gender

tag: age


title: tAML patient sample SJTAML049

tag: disease state

tag: chromosome 5q status

tag: cell type


title: liver, N, A1359-35

source_name: Nash, before surgery

tag: tissue type

tag: group

tag: bariatric surgery

value: before surgery

tag: Sex

tag: nas

tag: fibrosis

tag: delta adipo


title: genomic DNA from liver sample 36

description: Healthy Obese

source_name: liver tissue 36

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: 23-A Healthy control-7

description: Tagman-based qRT PCR

source_name: Plasma


title: genomic DNA from liver sample 32

description: NASH

source_name: liver tissue 32


title: liver, N, A1359-34

tag: fat

tag: inflammation

tag: lar

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin


title: 15-A APE-5

description: Tagman-based qRT PCR

tag: gender

tag: age


title: liver, C, A1359-40

source_name: Control

tag: tissue type

tag: group

tag: bariatric surgery

tag: Sex


title: 16-A APE-6

description: Tagman-based qRT PCR


title: genomic DNA from liver sample 28

description: Healthy Obese

source_name: liver tissue 28

tag: sex (1 - male, 2 - female)


title: 14-A APE-4

description: Tagman-based qRT PCR


title: genomic DNA from liver sample 31

description: NAFLD

source_name: liver tissue 31

value: NAFLD

tag: bariatric surgery (1 - before surgery, 2 - after)


title: tAML patient sample SJTAML048

source_name: RNA extracted from tumor cells

tag: disease state

tag: chromosome 5q status

tag: cell type


title: genomic DNA from liver sample 30

description: NASH

source_name: liver tissue 30

value: NASH

tag: bmi

tag: tissue


title: genomic DNA from liver sample 29

description: Healthy Obese

source_name: liver tissue 29

value: liver


title: liver, N, A1359-33

tag: fat

tag: inflammation

tag: nas

tag: fibrosis

tag: lar

tag: delta lar

tag: delta adipo


title: 13-A APE-3

description: Tagman-based qRT PCR

tag: gender

value: male

tag: age


title: ESCs-cont-1

description: Control ESC replicate 1

source_name: Embryonic stem cells

tag: strain

value: Embryonic stem cells

tag: genotype


title: genomic DNA from liver sample 27

description: Healthy Obese

source_name: liver tissue 27

tag: group

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)


title: 9-A Healthy control-3

description: Tagman-based qRT PCR


title: 12-A APE-2

description: Tagman-based qRT PCR


title: 10-A Healthy control-4

description: Tagman-based qRT PCR


title: liver, N, A1359-32

source_name: Nash

tag: tissue type

tag: bariatric surgery

tag: Sex

tag: delta leptin

tag: leptin

tag: adiponectin


title: 11-A APE-1

description: Tagman-based qRT PCR


title: genomic DNA from liver sample 34

description: control

source_name: liver tissue 34

value: NORMAL

tag: bmi

tag: tissue


title: genomic DNA from liver sample 25

description: NAFLD

source_name: liver tissue 25


title: liver, H, A1359-31

source_name: Healthy obese, after surgery

value: Healthy obese

tag: fat

tag: inflammation

value: after surgery

tag: nas

tag: fibrosis

tag: lar

tag: delta lar


title: genomic DNA from liver sample 26

description: Healthy Obese

source_name: liver tissue 26

tag: group

tag: age


title: 8-A Healthy control-2

description: Tagman-based qRT PCR

tag: gender


title: tAML patient sample SJTAML043

tag: disease state

tag: chromosome 5q status

value: Chromosome 5q deletion

tag: cell type


title: liver, N, A1359-27

tag: tissue type

value: Nash

tag: bariatric surgery

tag: Sex

tag: delta leptin

tag: delta adipo


title: liver, C, A1359-29

value: Control

tag: fat

tag: bmi

tag: leptin

tag: adiponectin


title: tAML patient sample SJTAML045

value: therapy-related myeloid neoplasm (t-MN)


title: liver, S, A1359-30

source_name: Steatosis, before surgery

value: Steatosis

tag: inflammation

value: female

tag: nas

tag: fibrosis

tag: lar


title: tAML patient sample SJTAML021

value: Chromosome 5q wild type

value: mononuclear cell


title: tAML patient sample SJTAML042


title: tAML patient sample SJTAML046


title: liver, N, A1359-26

value: liver biopsy

tag: group

tag: age

tag: delta lar


title: liver, H, A1359-28


title: tAML patient sample SJTAML047

tag: disease state

tag: chromosome 5q status

tag: cell type


title: tAML patient sample SJTAML040


title: 7-A Healthy control-1

description: Tagman-based qRT PCR

tag: gender


title: genomic DNA from liver sample 24

description: NAFLD

source_name: liver tissue 24

value: NAFLD

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: tissue


title: liver, H, A1359-25

source_name: Healthy obese, before surgery

tag: tissue type

tag: fat

tag: bariatric surgery

value: before surgery

tag: Sex

tag: bmi

tag: delta leptin

tag: delta adipo


title: liver, H, A1359-23

tag: group

tag: inflammation

tag: nas

tag: fibrosis

tag: lar

tag: leptin

tag: adiponectin


title: liver, H, A1359-22

tag: age

tag: delta lar


title: liver, S, A1649-01


title: liver, S, A1359-20


title: tAML patient sample SJTAML015

tag: disease state

tag: chromosome 5q status

tag: cell type


title: tAML patient sample SJTAML030


title: liver, S, A1359-19

source_name: Steatosis

tag: tissue type

tag: fat

tag: bariatric surgery


title: liver, H, A1359-24

source_name: Healthy obese

tag: Sex

tag: bmi

tag: delta leptin


title: tAML patient sample SJTAML028


title: genomic DNA from liver sample 23

description: control

source_name: liver tissue 23

tag: group

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: tissue

value: liver


title: liver, N, A1359-18

source_name: Nash, before surgery

tag: inflammation

tag: nas

tag: fibrosis

tag: lar

tag: leptin

tag: delta adipo


title: genomic DNA from liver sample 20

description: NAFLD

source_name: liver tissue 20

tag: age


title: tAML patient sample SJTAML027

source_name: RNA extracted from tumor cells

tag: disease state

tag: chromosome 5q status

tag: cell type


title: tAML patient sample SJTAML034


title: tAML patient sample SJTAML012


title: genomic DNA from liver sample 22

description: NAFLD

source_name: liver tissue 22


title: genomic DNA from liver sample 18

description: Healthy Obese

source_name: liver tissue 18

value: Healthy Obese


title: genomic DNA from liver sample 19

description: Healthy Obese

source_name: liver tissue 19


title: tAML patient sample SJTAML023


title: genomic DNA from liver sample 21

description: NASH

source_name: liver tissue 21

value: NASH


title: tAML patient sample SJTAML009


title: tAML patient sample SJTAML008


title: genomic DNA from liver sample 16

description: Healthy Obese

source_name: liver tissue 16


title: liver, H, A1359-15

tag: tissue type

tag: fat

tag: bariatric surgery

tag: Sex

tag: delta lar

tag: adiponectin


title: tAML patient sample SJTAML010


title: genomic DNA from liver sample 15

description: Healthy Obese

source_name: liver tissue 15

tag: group

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: liver, H, A1359-13

tag: inflammation

tag: nas

tag: fibrosis

tag: lar

tag: delta leptin

tag: leptin


title: liver, S, A1359-17

tag: tissue type

tag: age

tag: delta adipo


title: liver, H, A1359-14

tag: fat

tag: bariatric surgery

tag: Sex


title: tAML patient sample SJTAML005

tag: disease state

tag: chromosome 5q status

tag: cell type


title: liver, H, A1359-16

tag: group

tag: bmi

tag: delta lar

tag: adiponectin


title: liver, C, A1359-10

source_name: Control

tag: inflammation

tag: nas

tag: fibrosis


title: liver, N, A1359-11

source_name: Nash

tag: lar

tag: delta leptin

tag: leptin


title: genomic DNA from liver sample 14

description: NAFLD

source_name: liver tissue 14

tag: age

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: tissue


title: liver, H, A1359-12

tag: tissue type

tag: fat

tag: bariatric surgery

tag: Sex

tag: delta adipo


title: liver, C, A1359-09

tag: group

tag: bmi

tag: delta lar


title: tAML patient sample SJTAML002

tag: disease state

tag: chromosome 5q status

tag: cell type


title: genomic DNA from liver sample 9

description: control

source_name: liver tissue 9

value: NORMAL


title: genomic DNA from liver sample 8

description: control

source_name: liver tissue 8


title: genomic DNA from liver sample 10

description: Healthy Obese

source_name: liver tissue 10


title: genomic DNA from liver sample 13

description: control

source_name: liver tissue 13


title: genomic DNA from liver sample 12

description: control

source_name: liver tissue 12


title: genomic DNA from liver sample 7

description: control

source_name: liver tissue 7


title: genomic DNA from liver sample 17

description: Healthy Obese

source_name: liver tissue 17


title: liver, H, A1359-07

source_name: Healthy obese

value: Healthy obese

tag: inflammation

tag: nas

tag: fibrosis

tag: lar

tag: delta leptin

tag: adiponectin


title: genomic DNA from liver sample 5

description: control

source_name: liver tissue 5

tag: age

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: tissue


title: liver, C, A1359-08

tag: tissue type

tag: fat

tag: bariatric surgery

tag: Sex

value: male

tag: leptin

tag: delta adipo


title: liver, C, A1359-05

tag: group

tag: bmi

tag: delta lar


title: genomic DNA from liver sample 4

description: control

source_name: liver tissue 4


title: CLL116 + AG + T18

city: Oslo

first: Ludvig

middle: A

last: Munthe

state: Oslo

address: Sognsvannsveien 20

department: Institute of Clinical Medicine

country: Norway

institute: University of Oslo

description: CLL + Th cells in the presence of Ag and BCR ligation

hyb_protocol: 1500ng of biotin labeled cRNA was used to hybridize onto Illumina HumanWG-6 v3 Expression BeadChips

scan_protocol: Standard Illumina scanning protocol. After scanning, the results were imported into Illumina GenomeStudio v. 2010.1, Gene Expression module v. 1.6.0 for quality control and data export.

data_processing: In GeneSpring GX, Logbase 2-transformed data were normalized to the 75 percentile with baseline transformation to median of all samples. Flag Information: Lower cutoff for 'Present' call: 0.8, Upper cutoff for 'Absent' call: 0.6

source_name: Human blood derived CLL cells + human DR0401 restricted Ckappa-specific Th cell clone (T18)

label_protocol: 290ng per sample was amplified and labeled with the TotalPrep™-96 RNA Amplification Kit (Illumina, San Diego, CA, USA). Sample quality was further tested by Agilent 2100 bioanalyzer (Agilent, Santa Clara, CA, USA).

growth_protocol: 32-45 x10e6 PBMC were incubated overnight with or without 2 μg/ml of Ms κ+IgG anti-kappa and anti-lambda mAbs. The PBMC were then cultured in presence or absence of 12.5 x10e6 T18 cells. On day 3, CLL cells were purified by negative selection using CD3 and CD14 Dynabeads (Invitrogen). The purity of CD19+CD4- cells as assessed by Flow cytometry was 93%-99%, median 98%. CD4+ cell contamination was low (0-0.6%, median 0.05%).

extract_protocol: Trizol extracted RNA from purified CLL cells was controlled and quantified on a NanoDrop1000 (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: CLL cells with or without 2 μg/ml of mouse κ+ anti-kappa and anti-lambda IgG antibodies were incubated with T18 Th cells. On day 3, CLL cells were purified

tag: vh mutation

value: Mut, CD38-


title: liver, N, A1359-06

value: Nash

tag: inflammation

tag: nas

tag: fibrosis

tag: lar


title: liver, C, A1359-04

value: Control

tag: age

tag: delta leptin

tag: adiponectin


title: liver, C, A1359-03

tag: tissue type


title: liver, C, A1359-01

tag: fat


title: CLL103 - no Ag + T18

description: CLL + T cells, controll: no antigen

value: Unmut, CD38+


title: genomic DNA from liver sample 1

description: control

source_name: liver tissue 1

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: tissue


title: CLL107 + AG - no Th cells

description: BCR ligation control

source_name: Human blood derived CLL cells


title: CLL106 + AG + T18


title: CLL103 + AG + T18


title: CLL116 - no Ag + T18

description: CLL + T cells, controll: no antigen


title: CLL103 + AG - no Th cells

description: BCR ligation control


title: CLL107 - no Ag + T18

description: CLL + T cells, controll: no antigen


title: CLL106 + AG - no Th cells

description: BCR ligation control


title: CLL116 + AG - no Th cells

description: BCR ligation control


title: genomic DNA from liver sample 6

description: control

source_name: liver tissue 6


title: CLL107 + AG + T18


title: liver, C, A1359-02

source_name: Control

tag: bariatric surgery

tag: Sex

tag: leptin

tag: delta adipo


title: CLL106 - no Ag + T18

description: CLL + T cells, controll: no antigen

tag: vh mutation


title: KB001-ref vs. KB001-SP6

status: Public on Aug 07 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA

data_processing: Features were extracted using Imagene software from Biodiscovery. Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

organism: Canis lupus familiaris

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA isolation using Trizol v1.0 (tissue sections)

tag: ID

value: several canine organs

tag: sample type

value: spleen


title: KB001-ref vs. KB001-SP3


title: KB001-ref vs. KB001-SP5


title: genomic DNA from liver sample 2

description: control

source_name: liver tissue 2

tag: group

tag: bmi


title: KB001-ref vs. KB001-D3

value: Soft Tissue Histiocytic Sarcoma Biopsy


title: KB001-ref vs. KB001-SP2


title: KB001-SP5 vs. KB001-ref


title: KB001-ref vs. KB001-D7


title: KB001-ref vs. KB001-D13

value: Visceral Histiocytic Sarcoma Biopsy


title: KB001-ref vs. KB001-D11


title: KB001-ref vs. KB001-D9


title: KB001-ref vs. KB001-D6


title: KB001-ref vs. KB001-D1


title: genomic DNA from liver sample 3

description: control

source_name: liver tissue 3

tag: age


title: KB001-SP4 vs. KB001-ref


title: KB001-ref vs. KB001-D8


title: KB001-ref vs. KB001-D2


title: KB001-ref vs. KB001-D12


title: KB001-SP6 vs. KB001-ref


title: KB001-D9 vs. KB001-ref


title: KB001-SP2 vs. KB001-ref


title: KB001-SP3 vs. KB001-ref


title: KB001-SP1 vs. KB001-ref


title: KB001-ref vs. KB001-D14


title: KB001-ref vs. KB001-D4


title: KB001-D8 vs. KB001-ref


title: KB001-ref vs. KB001-D5


title: KB001-D6 vs. KB001-ref


title: KB001-D2 vs. KB001-ref


title: VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep4

city: Cardiff

first: Aliaksei

last: Holik

address: Museum Avenue

department: School of Biosciences

institute: Cardiff University

description:
Replicate_4
6816115033_B
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall

hyb_protocol: Samples were hybridised according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide

scan_protocol: Samples were scanned according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and normalised using variance stabilising data transformation (vsn) method (Huber et al. (2002) Bioinformatics 18: S96–S104) from the beadarray package

source_name: Brg1-Apc deficient

label_protocol: 100ng of total RNA was labelled using Illumina TotalPrepTM-96 RNA Amplification Kit (Ambion) according to manufacturer's protocol.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen), purified and on-column DNAse treated using Rneasy mini kit  (Qiagen) according to manufacturer's protocol.

value: Murine small intestine (jejunum)

tag: genotype/variation


title: VillinCreERT2+_Brg1fl/fl_Rep3

description:
Replicate_3
6816115033_G
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall

source_name: Brg1 deficient


title: VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep2

description:
Replicate_2
6816115008_B
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2-_Rep4

description:
Replicate_4
6816115033_F
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall

source_name: Cre-negative (control)


title: VillinCreERT2+_Brg1fl/fl_Rep2

description:
Replicate_2
6816115008_H
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep3

description:
Replicate_3
6816115033_A
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: KB001-D7 vs. KB001-ref


title: KB001-D3 vs. KB001-ref


title: KB001-D12 vs. KB001-ref


title: KB001-D14 vs. KB001-ref


title: KB001-D1 vs. KB001-ref


title: KB001-D4 vs. KB001-ref


title: KB001-D13 vs. KB001-ref


title: VillinCreERT2-_Rep1

description:
Replicate_1
6816115008_E
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2+_Brg1fl/fl_Rep4

description:
Replicate_4
6816115033_H
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2+_Brg1fl/fl_Rep1

description:
Replicate_1
6816115008_G
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2+_Apcfl/fl_Brg1+/+_Rep3

description:
Replicate_3
6816115033_C
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall

source_name: Apc deficient


title: KB001-D11 vs. KB001-ref


title: KB001-D5 vs. KB001-ref


title: KB001-ref vs. KB001-SP4


title: VillinCreERT2+_Apcfl/fl_Brg1+/+_Rep1

description:
Replicate_1
6816115008_C
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2-_Rep2

description:
Replicate_2
6816115008_F
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2+_Apcfl/fl_Brg1+/+_Rep2

description:
Replicate_2
6816115008_D
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep1

description:
Replicate_1
6816115008_A
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: VillinCreERT2-_Rep3

description:
Replicate_3
6816115033_E
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall


title: KB001-ref vs. KB001-SP1


title: Rep1_RSHSeed

city: Corvallis

first: Laurent

middle: Gerard

last: Deluc

state: OR

address: 4017 ALS Building

department: Horticulture

institute: Oregon State University

hyb_protocol: Hybridization was performed by the Center For Genome Research and Biocomputing, OSU  following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the Center For Genome Research and Biocomputing, OSU following their standard operating protocol. See www.nimblegen.com. Each microarray was scanned using an Axon GenePix 4400A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS package software (Simon and Biot, 2011)

organism: Vitis vinifera

source_name: RSH berry Class-Seed

label_protocol: Labeling was performed in Deluc's Lab following NimbleGen cDNA synthesis and labeling reactions operating protocol. See www.nimblegen.com.

growth_protocol: Individual berries of Vitis vinifera Pinot Noir clone 48 berries were sampled from one vineyard at three development stages (prevéraison, midvéraison, and harvest)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: genotype

value: Pinot Noir - clone Pommard


title: Rep3_RSHSeed


title: Rep2_RSHSeed


title: 7.25 MONO

city: Los Angeles

first: Peter

middle: W.

last: Laird

state: California

address: 1450 Biggy St.

department: USC Epigenome Center

institute: USC/Norris Cancer Center

description: Normal human bone marrow cells

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Background corrected against out-of-band signals and dye bias corrected against Illumina internal controls

source_name: Bone marrow cells

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: cell type

value: Monocytes


title: Rep3_PSHSeed

source_name: PSH berry Class-Seed


title: Rep1_PSHSeed


title: 7.25 PMN

description: Normal human bone marrow cells

value: Polymorphonuclear granulocytes


title: 7.11 PMN

description: Normal human bone marrow cells


title: Rep2_PSHSeed


title: Rep3_GSHSeed

source_name: GSH berry Class-Seed


title: Rep2_GSHSeed


title: 7.11 PROS

description: Normal human bone marrow cells

value: Promyelocytes


title: 8.10 CD19

description: Normal human bone marrow cells

value: CD19+ B cells


title: 7.25 PROS

description: Normal human bone marrow cells


title: 9.1 PMN

description: Normal human bone marrow cells


title: 8.24 CD3

description: Normal human bone marrow cells

value: CD3+ T cells


title: 8.10 CD3

description: Normal human bone marrow cells


title: 8.24 CD19

description: Normal human bone marrow cells


title: 7.18 PROS

description: Normal human bone marrow cells


title: Rep2_RSSeed

source_name: RS berry Class-Seed


title: ura3 (2+) t=-240 10ng

city: Durham

first: Horia

last: Todor

state: North Carolina

address: 125 Science Drive

department: Biology

institute: Duke University

description: Cartridge 1

hyb_protocol: Performed by Nanostring (see Geiss, et at. 2008)

data_processing: Genes were normalized by the sum of the positive spike in controls. Genes were then normalized by the geometric mean of the three reference genes (srp19, mrp, vng1670c). Resulting numbers were further normalized by the average sum of all counts per strain (ura3, trmB) in the 100ng samples. Microsoft Excel was used for this normalization.

organism: Halobacterium salinarum NRC-1

source_name: ura3, 240 minutes before glucose

label_protocol: No labeling

growth_protocol: Gene expression was assayed in a previously constructed strain containing an in-frame deletion of VNG1451C (∆ura3∆trmB; Schmid et al., 2009) and its isogenic parent strain (∆ura3). Cells for gene expression were grown in a Complete Defined Medium (CDM), containing 19 amino acids (modified from Schmid et al., 2009) supplemented with 50 mM uracil to complement the ura3 deletion. Cultures were grown at 225 r.p.m. shaking at 42°C under low ambient light.

extract_protocol: Cells were immediately pelleted by centrifugation and snap frozen in liquid nitrogen. RNA was prepared using the Absolutely-RNA miniprep kit (Stratagene/Agilent) according to the manufacturer’s instructions. RNA quality was assessed using the Agilent 2100 BioAnalyzer using the RNA-Nano Chip and the Prokaryotic Nano RNA protocol, and samples were verified to be free of DNA contamination by 25 cycles of PCR amplification on at least 200 ng RNA prior to cDNA conversion in RT-qPCR.

treatment_protocol: Addition of glucose to 5% at t=0

tag: strain

value: ∆ura3  (WT)

tag: timepoint

tag: rna amount (ng)


title: 7.18 MONO

description: Normal human bone marrow cells


title: 9.1 CD19

description: Normal human bone marrow cells


title: 8.24 CD34

description: Normal human bone marrow cells

value: CD34+CD38- cells


title: ura3 (2+) t=180

description: Cartridge 4

scan_protocol: Performed by Nanostring (see Geiss, et at. 2008)

source_name: ura3, 180 minutes after glucose


title: 8.10 PMN

description: Normal human bone marrow cells


title: Rep1_GSHSeed


title: Rep3_PSSeed

source_name: PS berry Class-Seed


title: ura3 (2+) t=90

description: Cartridge 4

source_name: ura3, 90 minutes after glucose


title: ura3 (2+) t=5

description: Cartridge 4

source_name: ura3, 5 minutes after glucose


title: Rep3_RSSeed


title: 7.18 PMN

description: Normal human bone marrow cells


title: ura3 (2+) t=45

description: Cartridge 4

source_name: ura3, 45 minutes after glucose


title: ura3 (1+) t=360

description: Cartridge 4

source_name: ura3, 360 minutes after glucose


title: Rep2_PSSeed


title: ura3 (1+) t=90

description: Cartridge 4


title: ura3 (1+) t=45

description: Cartridge 4


title: ura3 (1+) t=20

description: Cartridge 3

source_name: ura3, 20 minutes after glucose


title: ura3 (2+) t=10

description: Cartridge 4

source_name: ura3, 10 minutes after glucose


title: ura3 (2+) t=20

description: Cartridge 4


title: 563T

city: Melbourne

first: Richard

middle: William

last: Tothill

state: Victoria

address: St Andrews Place

country: Australia

institute: Peter MacCallum Cancer Centre

description: Hybridised to SNP6

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

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

data_processing:
Data files (CEL) were generated using the Affymetrix GeneChip® Command Console (AGCC) v1.0 and normalized using the R package Aroma.Affymetrix (Bengtsson et al., 2008).
All SNP CEL files were normalized in a single batch using the R package 'aroma.affymetrix' and segmented using the circular binary segmentation (CBS) algorithm to improve the signal to noise ratio. Matched normal tissue was not available for normalization, so the average signal from pooled male and female normal samples generated in our laboratory was used as a reference

label: Biotin

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from frozen tissue using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: tissue

value: Cancer of unknown primary


title: 8.24 PMN

description: Normal human bone marrow cells


title: 2864T

description: Hybridised to SNP6


title: 1382T

description: Hybridised to SNP6


title: 1184T

description: Hybridised to SNP6


title: ura3 (1+) t=0

description: Cartridge 3

source_name: ura3, 0 minutes before glucose


title: 4413T

description: Hybridised to SNP6


title: ura3 (2+) t=0

description: Cartridge 4


title: Rep1_RSSeed


title: Rep1_PSSeed


title: ura3 (2+) t=-60

description: Cartridge 4

source_name: ura3, 60 minutes before glucose


title: Rep3_GSSeed

source_name: GS berry Class-Seed


title: Rep3_PVSeed

source_name: PV berry Class-Seed


title: trmB (2+) t=45

description: Cartridge 3

source_name: trmB, 45 minutes after glucose

value: ∆trmB


title: 7.11 MONO

description: Normal human bone marrow cells

source_name: Bone marrow cells


title: 8.10 CD34

description: Normal human bone marrow cells


title: ura3 (1+) t=180

description: Cartridge 4


title: trmB (2+) t=90

description: Cartridge 3

source_name: trmB, 90 minutes after glucose


title: Rep2_GSSeed


title: ura3 (1+) t=10

description: Cartridge 3


title: Rep1_GSSeed


title: ura3 (1+) t=-60

description: Cartridge 3


title: trmB (2+) t=10

description: Cartridge 3

source_name: trmB, 10 minutes after glucose


title: 3461T

description: Hybridised to SNP6


title: 1698T

description: Hybridised to SNP6


title: trmB (3-) t=0

description: Cartridge 2

source_name: trmB, 0 minutes before glucose


title: trmB (2+) t=180

description: Cartridge 3

source_name: trmB, 180 minutes after glucose


title: ura3 (1+) t=-240

description: Cartridge 3

source_name: ura3, 240 minutes before glucose


title: trmB (3-) t=-60

description: Cartridge 2

source_name: trmB, 60 minutes before glucose


title: trmB (2+) t=20

description: Cartridge 3

source_name: trmB, 20 minutes after glucose


title: ura3 (1+) t=5

description: Cartridge 3

source_name: ura3, 5 minutes after glucose


title: Rep2_RSHPulp

source_name: RSH berry Class-Pulp


title: Rep1_PVSeed


title: Rep2_PVSeed


title: trmB (2+) t=5

description: Cartridge 3

source_name: trmB, 5 minutes after glucose


title: trmB (3-) t=-240

description: Cartridge 2

source_name: trmB, 240 minutes before glucose


title: trmB (3+) t=45

description: Cartridge 2


title: trmB (3+) t=360

description: Cartridge 2

source_name: trmB, 360 minutes after glucose


title: trmB (3+) t=90

description: Cartridge 2


title: trmB (3+) t=10

description: Cartridge 2


title: Rep2_PSHPulp

source_name: PSH berry Class-Pulp


title: Rep1_PSHPulp


title: Rep3_PSHPulp


title: Rep1_RSHPulp


title: trmB (3+) t=20

description: Cartridge 2


title: trmB (3+) t=-60

description: Cartridge 2


title: trmB (3+) t=0

description: Cartridge 2


title: trmB (3+) t=5

description: Cartridge 2


title: trmB (3+) t=180

description: Cartridge 2


title: trmB (3+) t=360 1000ng

description: Cartridge 1

source_name: ura3, 360 minutes after glucose


title: trmB (3+) t=360 100ng

description: Cartridge 1


title: trmB (3+) t=-60 1000ng

description: Cartridge 1


title: trmB (3+) t=360 10ng

description: Cartridge 1


title: trmB (3+) t=-60 100ng

description: Cartridge 1


title: trmB (3+) t=-60 10ng

description: Cartridge 1


title: Rep3_RSHPulp


title: Rep3_GSHPulp

source_name: GSH berry Class-Pulp


title: Rep3_RSPulp

source_name: RS berry Class-Pulp


title: Rep2_RSPulp


title: Rep1_GSHPulp


title: ura3 (2+) t=360 100ng

description: Cartridge 1


title: ura3 (2+) t=-240 1000ng

description: Cartridge 1


title: Rep2_PSPulp

source_name: PS berry Class-Pulp


title: Rep3_GSPulp

source_name: GS berry Class-Pulp


title: Rep1_PSPulp


title: ura3 (2+) t=360 10ng

description: Cartridge 1


title: ura3 (2+) t=360 1000ng

description: Cartridge 1


title: ura3 (2+) t=-240 100ng

description: Cartridge 1


title: Rep3_PSPulp


title: Rep2_GSPulp


title: Rep3_PVPulp

source_name: PV berry Class-Pulp


title: Rep1_RSPulp


title: Rep1_PVPulp


title: Rep2_PVPulp


title: Rep2_GSHPulp


title: Rep1_GSPulp


title: Rep1_RSHSkin

source_name: RSH berry Class-Skin


title: Rep3_RSHSkin


title: Rep2_RSHSkin


title: Rep3_PSHSkin

source_name: PSH berry Class-Skin


title: Rep1_PSHSkin


title: R175Q 4

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Goodman Cancer centre

country: Canada

institute: McGill

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software

data_processing: Microarray data were extracted using Feature Extraction Software (Agilent Technologies). The arrays were normalized using normexp background correction, loess within array and quantile between array normalization.

label_protocol: The profiles of resulting amplified RNA (aRNA) were assessed using a 2100 Bioanalyzer (Agilent Technologies). The aRNA samples (5μg) were conjugated to Cy3 dye using an Arcturus Turbo Labeling Kit (Cat. #: KIT0609, Applied Biosystems). Universal human reference RNA (Stratagene) was amplified using the same procedure and labeled with Cy5 dye (CAT # KIT0619, Applied Biosystems).

growth_protocol: NMuMG-NT2197 cells were generated, cultured, and transfected with a pMSCV/hygro expression vector (Clontech) expressing a wildtype ShcA cDNA or a ShcA mutant harbouring an arginine to glutamine substitution at amino acid 175 (R175Q)

extract_protocol: Total RNA (1-2.5ng) from microdissected material was subjected to two rounds of linear amplification using a RiboAmp HSPlus Amplification Kit (Cat. #: KIT0525, Applied Biosystems) following the manufacturer’s protocol.

tag: treatment

value: ShcA R175Q expression

tag: cell line

source_name: Universal Mouse Reference

value: Universal Mouse Reference


title: patient biological replicate1

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: Gene expression data from CGL patient with c-fos promoter mutation

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 h at 45C on HU95A_v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and all prone sets scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: human fibroblasts (cell culture)

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: Human fibroblast initiated from skin biopsies were cultured  in DMEM (10% FCS supplemented with antibiotics and antimycotics). Cells were harvested 48h following last passaging. Cell from 6 control individual’s were used. Of patient 3 independent cell charges were grown to passage 10 and analyzed separately (biological replicate).

extract_protocol: Total RNA was performed according to the GIT, phenol/chloroform extraction protocol (Chomczynski and Sacchi 1987). For Array experiments 8µg total RNA were used.

treatment_protocol: Cells were washed twice in 1x PBS and harvested for RNA extraction by direct lysis in GIT.

tag: health condition

value: lipodystrophy; similar to Werner Syndrome


title: patient biological replicate3


title: patient biological replicate4


title: patient biological replicate4

growth_protocol: Human fibroblast initiated from skin biopsies were cultured to passage 10 in DMEM (10% FCS supplemented with antibiotics and antimycotics). Cells were harvested 48h following last passaging. Cell from 6 control individual’s were used. Of patient 4 independent cell charges were grown to passage 10 and analyzed separately (biological replicate).

value: CGL


title: Rep2_PSHSkin


title: patient biological replicate2


title: Rep3_GSHSkin

source_name: GSH berry Class-Skin


title: patient biological replicate1


title: nT 3

description: nT

source_name: nT 3

value: ShcA wild type expression


title: Rep2_GSHSkin


title: R175Q 3


title: nT 4

description: nT

source_name: nT 4


title: R175Q 1


title: Rep2_RSSkin

source_name: RS berry Class-Skin


title: Rep2_PSSkin

source_name: PS berry Class-Skin


title: Rep1_GSHSkin


title: patient biological replicate3


title: R175Q 2


title: nT 2

description: nT

source_name: nT 2


title: nT 1

description: nT

source_name: nT 1


title: control6

description: Gene expression data from non-diabetic control individual 6

value: non-diabetic control individual 6


title: Rep3_RSSkin


title: Rep1_RSSkin


title: Gene expression in WT megakaryocytes 3

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

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

department: Center for Radioisotope Science

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in WT megakaryocytes

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

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

data_processing: Data was obtained using the Agilent Feature Extraction software (v10.1), using default for all parameters.  The data were analyzed using GeneSpring GX software (v11.5) (Agilent).

source_name: primary megakaryocytes cultured from E13.5 WT fetal liver

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole embryos using Isogen (Nippon Gene).

value: WT


title: Rep3_PSSkin

value: Pinot Noir - clone Pommard


title: control5

description: Gene expression data from non-diabetic control individual 5

value: non-diabetic control individual 5


title: control3

description: Gene expression data from non-diabetic control individual 3

value: non-diabetic control individual 3


title: Rep3_GSSkin

source_name: GS berry Class-Skin


title: Gene expression in WT megakaryocytes 2

description: Gene expression in WT megakaryocytes


title: Rep1_PSSkin


title: Rep1_GSSkin


title: control4

description: Gene expression data from non-diabetic control individual 4

value: non-diabetic control individual 4


title: control2

description: Gene expression data from non-diabetic control individual 2

value: non-diabetic control individual 2


title: Gene expression in WT megakaryocytes 1

description: Gene expression in WT megakaryocytes


title: testes can[3] rep3

status: Public on Aug 06 2013

first: Helen

last: White-Cooper

department: Biosciences

description: gene expression from can mutant testes

hyb_protocol: Hybridisation was perfomed in GeneChip Hybridisation Oven 640, and washed with wash with GeneChip Fluidic Station 400

scan_protocol: scanning and quality control with GeneChip Scanner 3000 7G

data_processing: Data were collected and processed with affymetrix software (GCOS v1.4). An affymetrix t100 normalisation was preformed across replicates

organism: Drosophila melanogaster

source_name: Drosophila testes from can[3] individuals

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

growth_protocol: Flies were grown on standard cornmeal yeast sucrose agar medium, and collected for dissection within one day of eclosion

extract_protocol: Trizol extraction of total RNA following manufacturer's instructions.

treatment_protocol: Testes were manually dissected in testis buffer, snap frozen in liquid nitrogen, and stored at -80C until sufficient sample had been collected. Samples were processed into 1 ml Trizol reagent, then shipped on dry ice to the microarray facility in Glasgow university.

value: adult testis

tag: culture temperature


title: control1

description: Gene expression data from non-diabetic control individual 1

value: non-diabetic control individual 1


title: testes can[3] rep2

description: gene expression from can mutant testes


title: testes comr rep2

description: gene expression from aly mutant testes

source_name: Drosophila testes from aly[5] individuals


title: Gene expression in p45-/- megakaryocytes 1

source_name: primary megakaryocytes cultured from E13.5 p45-/- fetal liver


title: testes can[3] rep1

description: gene expression from can mutant testes


title: testes comr rep3

description: gene expression from aly mutant testes


title: testes red e rep3

description: gene expression from normal testes

source_name: Drosophila testes from red e individuals (control)


title: testes red e rep2

description: gene expression from normal testes


title: testes comr rep1

description: gene expression from aly mutant testes


title: Gene expression in p45-/- megakaryocytes 3


title: Gene expression in p45-/- megakaryocytes 2


title: Rep1_PVSkin

source_name: PV berry Class-Skin


title: Rep3_PVSkin


title: Rep2_PVSkin


title: testes red e rep1

description: gene expression from normal testes


title: CBA Cochlea Mice-1

city: Tampa

first: Robert

last: Frisina

state: FL

address: 4202. E. Fowler Avenue ENB 118

department: Department of Chemical & Biomedical Engineering

institute: university of south florida

description: expression data from mus musculus

hyb_protocol: GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.

scan_protocol: The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.

data_processing: The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.

source_name: CBA mice cochlea

label_protocol: Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1  g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.

growth_protocol: CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet  vivarium room.

extract_protocol: Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The cochleae were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.

treatment_protocol: No treatment, normal aging mice

value: CBA/CaJ

tag: hearing status

value: Severe Presbycusis

tag: gender

value: Female


title: CBA Cochlea Mice-32

description: expression data from mus musculus

value: Male


title: CBA Cochlea Mice-34

description: expression data from mus musculus

value: Mild Presbycusis


title: CBA Cochlea Mice-35

description: expression data from mus musculus


title: CBA Cochlea Mice-37

description: expression data from mus musculus


title: CBA Cochlea Mice-30

description: expression data from mus musculus


title: CBA Cochlea Mice-11

description: expression data from mus musculus


title: CBA Cochlea Mice-31

description: expression data from mus musculus

value: Middle-Aged


title: CBA Cochlea Mice-13

description: expression data from mus musculus

value: Sever Presbycusis


title: CBA Cochlea Mice-22

description: expression data from mus musculus


title: CBA Cochlea Mice-28

description: expression data from mus musculus


title: CBA Cochlea Mice-20

description: expression data from mus musculus


title: CBA Cochlea Mice-3

description: expression data from mus musculus


title: CBA Cochlea Mice-12

description: expression data from mus musculus


title: CBA Cochlea Mice-24

description: expression data from mus musculus


title: CBA Cochlea Mice-29

description: expression data from mus musculus


title: CBA Cochlea Mice-21

description: expression data from mus musculus


title: CBA Cochlea Mice-2

description: expression data from mus musculus


title: CBA Cochlea Mice-39

description: expression data from mus musculus


title: CBA Cochlea Mice-23

description: expression data from mus musculus


title: CBA Cochlea Mice-27

description: expression data from mus musculus


title: CBA Cochlea Mice-38

description: expression data from mus musculus


title: CBA Cochlea Mice-14

description: expression data from mus musculus


title: CBA Cochlea Mice-26

description: expression data from mus musculus


title: CBA Cochlea Mice-33

description: expression data from mus musculus


title: CBA Cochlea Mice-10

description: expression data from mus musculus


title: CBA Cochlea Mice-15

description: expression data from mus musculus


title: CBA Cochlea Mice-7

description: expression data from mus musculus


title: CBA Cochlea Mice-19

description: expression data from mus musculus


title: CBA Cochlea Mice-41

description: expression data from mus musculus

value: Young Control


title: CBA Cochlea Mice-9

description: expression data from mus musculus


title: CBA Cochlea Mice-6

description: expression data from mus musculus


title: CBA Inferior colliculus Mice-11

source_name: CBA mice Inferior colliculus

extract_protocol: Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.


title: CBA Inferior colliculus Mice-1


title: CBA Inferior colliculus Mice-37


title: CBA Inferior colliculus Mice-30


title: CBA Inferior colliculus Mice-22


title: CBA Inferior colliculus Mice-35


title: CBA Cochlea Mice-5

description: expression data from mus musculus


title: CBA Inferior colliculus Mice-33


title: CBA Cochlea Mice-25

description: expression data from mus musculus


title: CBA Inferior colliculus Mice-12


title: CBA Cochlea Mice-40

description: expression data from mus musculus


title: CBA Cochlea Mice-8

description: expression data from mus musculus


title: Rep2_GSSkin


title: CBA Cochlea Mice-18

description: expression data from mus musculus


title: CBA Cochlea Mice-16

description: expression data from mus musculus


title: CBA Inferior colliculus Mice-21


title: CBA Inferior colliculus Mice-34


title: CBA Inferior colliculus Mice-3


title: CBA Inferior colliculus Mice-32


title: CBA Inferior colliculus Mice-40


title: CBA Cochlea Mice-4

description: expression data from mus musculus


title: CBA Cochlea Mice-36

description: expression data from mus musculus


title: CBA Cochlea Mice-17

description: expression data from mus musculus


title: CBA Inferior colliculus Mice-39


title: CBA Inferior colliculus Mice-2


title: CBA Inferior colliculus Mice-38


title: CBA Inferior colliculus Mice-28


title: CBA Inferior colliculus Mice-14


title: CBA Inferior colliculus Mice-36


title: CBA Inferior colliculus Mice-20


title: CBA Inferior colliculus Mice-27


title: CBA Inferior colliculus Mice-23


title: CBA Inferior colliculus Mice-41


title: CBA Inferior colliculus Mice-10


title: CBA Inferior colliculus Mice-7


title: CBA Inferior colliculus Mice-17


title: CBA Inferior colliculus Mice-19


title: CBA Inferior colliculus Mice-15


title: CBA Inferior colliculus Mice-8


title: CBA Inferior colliculus Mice-18


title: CBA Inferior colliculus Mice-31


title: CBA Inferior colliculus Mice-9


title: CBA Inferior colliculus Mice-24


title: CBA Inferior colliculus Mice-26


title: CBA Inferior colliculus Mice-29


title: CBA Inferior colliculus Mice-6


title: erad/d_ovarian tumor_5 months_age

city: Urbana

first: Mary

last: Laws

address: 2001 S. Lincoln Ave.

institute: University of Illinois

hyb_protocol: The Affymetrix Alternative Protocol for Eukaryotic Target Hybridization manual P/N 702232 Revision 2 Appendices B and C was utilized for hybridization, washing, and staining.  A cocktail was prepared with 15 micrograms of aRNA, adding biotinylated, fragmented hybridization controls: four prokaryotic antisense RNAs and one synthetic oligonucleotide.  Following a 16-hour hybridization to an Affymetrix GeneChip 3’ Expression Mouse Genome 430 2.0 Array at 45°C and 60 rpm in a GeneChip model 640 oven, the chip was washed, and stained first with streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA).  The stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and  counterstained with additional conjugated phycoerythrin utilizing a GeneChip Fluidics Station model 450 and the GeneChip Command Console (AGCC) Fluidics Control software version 1.0.

scan_protocol: The chip was scanned with a GeneChip Scanner model 3000 7G Plus.  Raw fluorescence signals for pixels within each probe feature in the image (DAT) file were converted to a single feature fluorescence value utilizing the Cell Analysis algorithm incorporated in the AGCC Scan Control version 1.0 to generate a fluorescence intensity (CEL) file.  The quality of the image file was evaluated visually before further processing.

data_processing: The CEL files in each experiment were analyzed with Affymetrix Expression Console version 1.1 utilizing the MAS5 algorithm, selecting the scaling parameter for all probe sets, and an arbitrary target value of 150 to generate chip and report files.  A quality control summary of metrics, labeling and hybridization controls, and housekeeping genes for all files within the experiment was generated by the Keck Center Functional Genomics staff and results were evaluated for accuracy and consistency.

source_name: ovarian tumor from era d/d mouse 5 months old

label_protocol: Microarrays were processed by the W. M. Keck Center for Comparative and Functional Genomics in the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.  Labeled antisense RNA was prepared utilizing the GeneChip 3' IVT Express Kit Labeling and Control Reagents kit (Affymetrix, Inc., Santa Clara, CA), according to the manufacturer’s manual P/N 702646 Revision 1.  Briefly, 100 nanograms of total RNA was spiked with four prokaryotic polyadenylated sense RNA controls, primed with a T7-(dT) oligonucleotide containing a T7 promoter sequence, and reverse transcribed to synthesize first-strand DNA.  A double-stranded DNA template was then synthesized with DNA polymerase along with RNase H to degrade RNA.  The resulting cDNA was in vitro transcribed with the addition of a biotinylated ribonucleotide analog, and amplified at 40°C for 14 hours.  The resulting biotin-labeled antisense RNA was purified with magnetic beads, quantified, and fragmented to produce lengths of less than 200 nucleotides.

extract_protocol: Total RNA was isolated from ovarian tumor tissue or normal ovary tissue after tissue was homogenized using a bead beater. Total RNA was cleaned up using Qiagen kit and protocol.

treatment_protocol: Ovarian tumor tissue and normal ovarian tissue was snap frozen in liquid nitrogen and then homogenized using a bead beater.

value: female

value: ovarian tumor

value: era d/d_conditional deletion of estrogen receptor alpha mediated by cre driven by progestrogen receptor

value: 10 months


title: nhr-8(hd117)_L3_25degC_NoAddedCholesterol_rep7

city: Cologne

first: Daniel

last: Magner

address: Joseph-Stelzmann-Str. 9b

institute: Max Planck Institute for Biology of Aging

description: Gene expression at mid-L3 larval stage of C. elegans nhr-8(hd117) mutant animals grown at 25 deg C on NGM media (no cholesterol added) and seeded with E. coli strain OP50

hyb_protocol: Hybridization and processing was according to the Agilent microarray protocol.

scan_protocol: Scanning was performed with an Agilent microarray scanner.

data_processing: Expression data was read in the statistical programming environment R and processed for background correction and quantile normalization and summarized for genes that differed in expression between N2 vs nhr-8(hd117) using the Bioconductor Limma package.

organism: Caenorhabditis elegans

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA without amplification

growth_protocol: Seven independent synchronized populations of N2 and nhr-8(hd117) animals were grown from eggs on low cholesterol plates at 25 degrees C until mid-L3 larval stage and collected for microarray RNA expression analysis.

extract_protocol: RNA was prepared using a QIAGEN RNeasy purification kit.

treatment_protocol: Growth of animals was at 25 degrees C on NGM plates with no added cholesterol. An overnight LB culture of E. coli OP50, washed 3 times with M9 buffer, was used to seed the plates. The bacterial lawn was allowed to grown overnight before use.

value: nhr-8(hd117) mutant

tag: developmental stage

value: mid-L3 larval

tag: temperature

value: 25 deg C

tag: growth media

value: NGM with no added cholesterol


title: erad/d_ovarian tumor_10 months_age

source_name: ovarian tumor from era d/d mouse 10 months old

tag: age


title: CBA Inferior colliculus Mice-4


title: N2_L3_25degC_NoAddedCholesterol_rep7

description: Gene expression at mid-L3 larval stage of C. elegans N2 wild-type animals grown at 25 deg C on NGM media (no cholesterol added) and seeded with E. coli strain OP50

tag: genotype/variation

value: wild-type


title: flox_control_ovary_5months_age

source_name: ovary_mouse 5 months old

value: ovary

tag: genotype

value: era f/f_estrogen receptor alpha flox

value: 5 months


title: N2_L3_25degC_NoAddedCholesterol_rep6


title: nhr-8(hd117)_L3_25degC_NoAddedCholesterol_rep6


title: flox_control_ovary_10months_age

source_name: ovary_mouse 10 months old


title: CBA Inferior colliculus Mice-5

value: CBA/CaJ

value: Female


title: CBA Inferior colliculus Mice-25

value: Male


title: nhr-8(hd117)_L3_25degC_NoAddedCholesterol_rep4


title: nhr-8(hd117)_L3_25degC_NoAddedCholesterol_rep3


title: nhr-8(hd117)_L3_25degC_NoAddedCholesterol_rep5


title: nhr-8(hd117)_L3_25degC_NoAddedCholesterol_rep2


title: N2_L3_25degC_NoAddedCholesterol_rep4


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1138

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis kidney

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing:
The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization.
Each of the hybridization was normalized separately and the VALUE column contains the batch-corrected data using Combat.

source_name: Kidney Biopsy from Human Rapidly Progressive Glomerulonephritis

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

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) following manufacturer's protocol.

value: Tubulointerstitium from kidney biopsy

tag: disease status

value: Rapidly Progressive Glomerulonephritis


title: N2_L3_25degC_NoAddedCholesterol_rep3


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1135


title: N2_L3_25degC_NoAddedCholesterol_rep2


title: Tumor Nephrectomy, H7-Tub-TN1185

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy kidney

source_name: Kidney Biopsy from Human Tumor Nephrectomy

value: Tumor Nephrectomy


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1134


title: Tumor Nephrectomy, H7-Tub-TN1186


title: nhr-8(hd117)_L3_25degC_NoAddedCholesterol_rep1


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1131


title: Tumor Nephrectomy, H7-Tub-TN1187


title: N2_L3_25degC_NoAddedCholesterol_rep5


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1128


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1130


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1127


title: N2_L3_25degC_NoAddedCholesterol_rep1


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1129


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1120


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1121


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1122


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1126


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1123


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1119


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1113


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1118


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1106


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1103


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1109


title: Minimal Change Disease, H7-Tub-MCD1163

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease kidney

source_name: Kidney Biopsy from Human Minimal Change Disease

value: Minimal Change Disease


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1107


title: Minimal Change Disease, H7-Tub-MCD1137


title: Minimal Change Disease, H7-Tub-MCD1111


title: Minimal Change Disease, H7-Tub-MCD1116


title: Focal and Segmental Glomerulosclerosis, H7-Tub-FSGS1115

description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis kidney

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis

value: Focal and Segmental Glomerulosclerosis


title: Minimal Change Disease, H7-Tub-MCD1112


title: Focal and Segmental Glomerulosclerosis, H7-Tub-FSGS1125


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Tub-FSGS&MCD1136

description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis and Minimal Change Disease kidney

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis and Minimal Change Disease


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Tub-FSGS&MCD1124


title: Focal and Segmental Glomerulosclerosis, H7-Tub-FSGS1162


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Tub-FSGS&MCD1117


title: Rapidly Progressive Glomerulonephritis, H7-Tub-RPGN1102


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Tub-FSGS&MCD1104


title: Diabetic Nephropathy, H7-Tub-DN1132

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy kidney

source_name: Kidney Biopsy from Human Diabetic Nephropathy

value: Diabetic Nephropathy


title: Diabetic Nephropathy, H7-Tub-DN1133


title: Diabetic Nephropathy, H7-Tub-DN1139


title: Diabetic Nephropathy, H7-Tub-DN1108


title: Diabetic Nephropathy, H7-Tub-DN1101


title: Tumor Nephrectomy, H7-Glom-TN995

description: Gene Expression data from the glomeruli of human Tumor Nephrectomy kidney

value: Glomeruli from kidney biopsy


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN935

description: Gene Expression data from the glomeruli of human Rapidly Progressive Glomerulonephritis kidney


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN934


title: Diabetic Nephropathy, H7-Tub-DN1110


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN942


title: Tumor Nephrectomy, H7-Glom-TN997


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN929


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN943


title: Diabetic Nephropathy, H7-Tub-DN1114


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN937


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN930


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN946


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN924


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN939


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN938


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN936


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN911


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN909


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN925


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN908


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN913


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN926


title: Tumor Nephrectomy, H7-Glom-TN996


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN904


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN907


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN902


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN906


title: Minimal Change Disease, H7-Glom-MCD973

description: Gene Expression data from the glomeruli of human Minimal Change Disease kidney


title: Minimal Change Disease, H7-Glom-MCD903


title: Rapidly Progressive Glomerulonephritis, H7-Glom-RPGN928


title: Minimal Change Disease, H7-Glom-MCD919


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS972

description: Gene Expression data from the glomeruli of human Focal and Segmental Glomerulosclerosis kidney


title: Minimal Change Disease, H7-Glom-MCD945


title: Leaf_T65_C0_rep3

city: Sapporo

first: Yuji

last: Kishima

address: Kita-ku Kita 9 Nishi 9 W105

institute: Hokkaido University

description: Gene expression in no-treatment rice leaves

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA were fragmented and hybridized with the 4x44K microarray at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green : 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for log2 transformation with GenespringGX11(Agilent).

organism: Oryza sativa

source_name: T65, Leaf, C0

label_protocol: One-color spike-mix was added to the total RNA prior to labeling reaction. Labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3-CTP according to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN) and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: The seeds were sown in early May, and the plants were consistently grown under greenhouse conditions at 25°C/19°C (day/night).

extract_protocol: For leaf and anther samples, total RNA was extracted using TRIzol® Plus RNA Purification kit (Invitrogen). The extracted RNA was quantified using NanoDrop ND-2000 UV-VIS spectrophotometer (Thermo Scientific) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The low-temperature treatment was applied for 4 days during the booting stage, which can be estimated by AD. The plants at AD = ± 1 cm, corresponding to the early microspore stage (late tetrad to late uninucleate pollen), were exposed to the low temperature of 12C for 4 days.

tag: strain

value: Leaf

tag: rna extraction day


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS971


title: Leaf_T65_C0_rep2


title: Leaf_T65_C0_rep1


title: Minimal Change Disease, H7-Glom-MCD921


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS970


title: Leaf_Nipponbare_C0_rep3

source_name: Nipponbare, Leaf, C0

value: Nipponbare


title: Leaf_Nipponbare_C0_rep1


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS933


title: p63-excised orthotopic tumor 2

city: Boston

first: Matthew

last: Ramsey

state: MA

address: 77 Ave Louis Pasteur, HIM 668

department: Dermatology

institute: Brigham and Women's Hospital

description: Sample name: p63-excised 2

hyb_protocol: Total RNA was hybridized to Illumina MouseWG-6 v2 BeadChip arrays using standard protocols

scan_protocol: Chips were scanned with Illumina BeadArray Reader

data_processing:
The data were normalised using quantile normalisation with lumi in R statistical software environment version 2.12.0.
See supplemental file 'Microarray sample and processing data.pdf' for R commands.

source_name: orthotopic SCC tumor

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

growth_protocol: Mice were treated once weeklly with 25mg 7,12-Dimethyl-benz[a]anthracene dissolved in acetone until SCC tumors formed.  Primary tumor was disaggregated, and orthotopically transplanted into recipient Nude mice.

extract_protocol: RNA was extracted from whole tumors using Qiagen RNeasy Fibrous Tissue Mini Kit according to manufacturer’s instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Orthotopic tumors were allowed to grow for 13 days, and then mice were treated daily for 5 days with tamoxifen (p63-excised) or vehicle control (p63-intact).  Tumors were harvested 1-3 days after last treatment.

value: mixed c57BL/6 - CD1 background

tag: mouse genotype

tag: tumor inducer

value: Weekly DMBA

tag: tumor type

value: Orthotopic Cutaneous Squamous Cell Carcinoma

tag: recipient mouse

value: Nude

tag: conditional excision of p63 in scc tumor

value: yes


title: Anther_Silewah_C5_rep2

description: Gene expression 5days after cool treatment rice anthers

source_name: Silewah, Anther, C5

value: Silewah

tag: tissue

value: Anther


title: p63-excised orthotopic tumor 3

description: Sample name: p63-excised 3


title: Anther_Silewah_C5_rep3


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS927


title: Leaf_Nipponbare_C0_rep2


title: p63-intact orthotopic tumor 2

description: Sample name: p63-Intact 2

value: no


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS920


title: Anther_Silewah_C5_rep1


title: p63-excised orthotopic tumor 1

description: Sample name: p63-excised 1


title: Tac_JQ1_d28_r3

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: gene expression of TAC surgery mouse heart followed by JQ1 treatment

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 16-18 hours in a GeneChip Hybridization oven 645 at 45C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, the genechip arrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Bioconductor (http://bioconductor.org) packages affyQCReport, rma, and limma were used to perform quality control, normalization and differential expression analysis, respectively.

label: biotin allonamide triphosphate

source_name: 28 day - TAC - JQ1

label_protocol: cDNA was generated using the Ambion WT Expression Kit.  The samples were labeled using the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol.

growth_protocol: All models were conducted in C57Bl/6J mice (Jackson Laboratories), which were maintained in a pathogen-free facility with standard light/dark cycling and access to food and water ad libitum.

extract_protocol: For tissue RNA, a 10-20 mg piece of mouse heart tissue was preserved in RNA Later stabilization reagent (Qiagen) followed by mechanical disruption/homogenization in PureZOL (BioRad) on a TissueLyser (Qiagen) using stainless steel beads (Qiagen). The aqueous phase was extracted with chloroform. RNA was purified from the aqueous phase using the Aurum purification kit (BioRad #732-6830) following manufacturer’s instructions.

treatment_protocol: All mice were C57Bl/6J littermate males aged 10-12 weeks. For TAC, mice were anesthetized with ketamine/xylazine, mechanically ventilated (Harvard apparatus), and subject to thoracotomy. The aortic arch was constricted between the left and right carotid arteries using a 7.0 silk suture and a 27-guage needle as previously described (Hu et al., 2003). In our hands, this protocol created a consistent peak pressure gradient of approximately 50 mmHg across the constricted portion of the aorta. Injections of JQ1 or vehicle were begun 1.5 days postoperatively.

value: heart


title: Anther_Silewah_C3_rep1

description: Gene expression 3days after cool treatment rice anthers

source_name: Silewah, Anther, C3


title: p63-intact orthotopic tumor 1

description: Sample name: p63-Intact 1


title: Tac_JQ1_d28_r2


title: Tac_vehicle_d28_r2

description: gene expression of TAC surgery mouse heart followed by dmso treatment

source_name: 28 day - TAC- vehicle


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS918


title: Anther_Silewah_C3_rep3


title: Tac_vehicle_d28_r3


title: p63-intact orthotopic tumor 3

description: Sample name: p63-Intact 3


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS915


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS917


title: Anther_Silewah_C1_rep2

description: Gene expression 1day after cool treatment rice anthers

source_name: Silewah, Anther, C1


title: Anther_Silewah_C1_rep3


title: Anther_Silewah_C3_rep2


title: Focal and Segmental Glomerulosclerosis, H7-Glom-FSGS912


title: Tac_JQ1_d28_r1


title: Anther_Silewah_C1_rep1


title: Sham_vehicle_d28_r1

description: gene expression of sham surgery mouse heart followed by dmso treatment

source_name: 28 day - sham - vehicle


title: Sham_vehicle_d28_r3


title: Sham_vehicle_d28_r2


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Glom-FSGS&MCD944

description: Gene Expression data from the glomeruli of human Focal and Segmental Glomerulosclerosis and Minimal Change Disease kidney

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis and Minimal Change Disease


title: Anther_Silewah_C0_rep3

description: Gene expression in no-treatment rice anthers

source_name: Silewah, Anther, C0


title: Tac_JQ1_d11_r1

source_name: 11 day - TAC - JQ1


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Glom-FSGS&MCD940


title: Tac_JQ1_d11_r2