title: NHEK duplicate1

status: Public on Dec 03 2010

type: RNA

city: La Jolla

first: Saiyong

last: Zhu

state: CA

address: 10550 North Torrey Pines Road,

country: USA

institute: The Scripps Research Institute

hyb_protocol: BeadChip Hyb Wheel

scan_protocol: Illumina BeadArray Reader

data_processing: Illumina BeadStudio Software

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: keratinocytes

label_protocol: Biotin

growth_protocol: NHEKs were cultured in keratinocytes media; hiPSC-O and HUES 9 were cultured in hESC media

extract_protocol: RNeasy Plus Mini Kit

tag: cell type

value: keratinocytes

tag: cell line

value: NHEK


title: hiPSC-O duplicate2

source_name: iPSCs

value: iPSCs


title: HUES9 duplicate2

source_name: hESCs

value: hESCs


title: RC2 24h 135

city: Bethesda

first: Marcel

last: van der Brug

address: 9000 Rockville Pike

department: NIA

institute: NIH

description: RC 24Hr

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Beadstudio v3.2

source_name: Stable iLRRK2 HEK Cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The Flp-In-Trex vector was used to generate stable cell lines expressing the lrrk2 gene. Doxycyclin (1ug/ml final conc) was used to induce expression.

value: HEK

tag: transfectant

value: LRRK2 with the R1441C mutation

tag: treatment time

value: 24 hr


title: RC2 24h 134

description: RC 24Hr


title: hiPSC-O duplicate1


title: RC2 0h 116

description: RC 00Hr

value: 0 hr


title: RC2 12h 120

description: RC 12Hr

value: 12 hr


title: HUES9 duplicate1


title: RC2 24h 133

description: RC 24Hr


title: NHEK duplicate2


title: RC2 12h 118

description: RC 12Hr


title: RC1 12h 82

description: RC 12Hr


title: RC2 0h 117

description: RC 00Hr


title: RC1 24h 97

description: RC 24Hr


title: RC1 12h 89

description: RC 12Hr


title: RC1 0h 81

description: RC 00Hr


title: RC1 24h 99

description: RC 24Hr


title: RC2 12h 119

description: RC 12Hr


title: RC1 12h 84

description: RC 12Hr


title: RC2 0h 112

description: RC 00Hr


title: RC1 24h 98

description: RC 24Hr


title: wt1 24h 27

description: WT 24Hr

value: wildtype LRRK2


title: wt1 24h 25

description: WT 24Hr


title: wt1 24h 26

description: WT 24Hr


title: wt3 12h 48

description: WT 12Hr


title: wt3 12h 53

description: WT 12Hr


title: wt1 0h 8

description: WT 00Hr


title: wt3 24h 63

description: WT 24Hr


title: wt3 0h 40

description: WT 00Hr


title: wt3 0h 45

description: WT 00Hr


title: wt1 12h 12

description: WT 12Hr


title: wt3 24h 59

description: WT 24Hr


title: wt3 0h 41

description: WT 00Hr


title: wt1 0h 9

description: WT 00Hr


title: wt3 12h 52

description: WT 12Hr


title: wt1 12h 17

description: WT 12Hr


title: wt3 24h 61

description: WT 24Hr


title: wt1 12h 16

description: WT 12Hr


title: wt1 0h 7

description: WT 00Hr


title: RC1 0h 79

description: RC 00Hr


title: G2019S-NTE

description: PD

source_name: fibroblasts

value: patient derived fibroblast cells

tag: disease status

value: parkinson's disease

tag: lrrk2 mutation


title: G2019S-MMU

description: PD


title: RC1 0h 80

description: RC 00Hr


title: G2019S-CBY

description: CN

value: control


title: CON-FMB

description: CN

value: wild type


title: CON-C7

description: PD


title: G2019S-MAN

description: PD


title: CON-EOR

description: CN


title: CON-JEC

description: CN


title: R1441G-VMB

description: PD


title: CON-C5

description: PD


title: CON-ITE

description: CN


title: G2019S-MSN

description: CN


title: CON-C3

description: CN


title: G2019S-NLA

description: PD


title: G2019S-AZO

description: CN


title: R1441G-TMB

description: PD


title: CON-C4

description: PD


title: Non-diabetic islets, rep7

status: Public on Dec 01 2010

city: Pisa

first: Marco

last: Bugliani

address: via Paradisa, 2

department: Dept. Endocrinology and Metabolism

country: Italy

institute: University of Pisa

description:
ND8
Gene expression data from non-diabetic human islets.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip HG U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with R/Bioconductor using affy, affyPLM for quality control, rma for normalization and limma for differential expression analysis.

source_name: human islets, non-diabetic

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA after two-cycle target labeling (GeneChip Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Once isolated, human islets were cultured in M199 culture medium.

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

tag: tissue

value: pancreatic islets

tag: disease state

value: non-diabetic

tag: age

value: 73 yrs

tag: gender

value: female

tag: bmi (kg/m2)


title: Type 2 diabetic islets, rep4

description:
T2D (E)
Gene expression data from type 2 diabetic human islets.

source_name: human islets, diabetic

value: type 2 diabetes

value: 75 yrs


title: Type 2 diabetic islets, rep1

description:
T2D (B)
Gene expression data from type 2 diabetic human islets.

value: 79 yrs

value: male


title: CON-JER

description: CN


title: Non-diabetic islets, rep4

description:
ND4
Gene expression data from non-diabetic human islets.

value: 54 yrs


title: Non-diabetic islets, rep5

description:
ND5
Gene expression data from non-diabetic human islets.

value: 76 yrs


title: Type 2 diabetic islets, rep2

description:
T2D (C)
Gene expression data from type 2 diabetic human islets.


title: Type 2 diabetic islets, rep6

description:
T2D (I)
Gene expression data from type 2 diabetic human islets.

value: 66 yrs


title: Non-diabetic islets, rep6

description:
ND6
Gene expression data from non-diabetic human islets.

value: 77 yrs


title: Non-diabetic islets, rep3

description:
ND3
Gene expression data from non-diabetic human islets.

value: 47 yrs


title: Non-diabetic islets, rep1

description:
ND1
Gene expression data from non-diabetic human islets.


title: Type 2 diabetic islets, rep3

description:
T2D (D)
Gene expression data from type 2 diabetic human islets.


title: Non-diabetic islets, rep2

description:
ND2
Gene expression data from non-diabetic human islets.

value: 33 yrs


title: CON-ALF

description: CN

value: patient derived fibroblast cells


title: Type 2 diabetic islets, rep5

description:
T2D (F)
Gene expression data from type 2 diabetic human islets.


title: Van-0A

type: genomic

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

description: labelled products were hybridized to the array in a total amount of 16ug

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G, GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Bioconductor package Affy. raw intensity was read from .CEL file, log transformed, background corrected, quantile normalzied, then convert back to normal scale.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: genomic DNA

label_protocol: Invitrogen Bioprime random labeling

extract_protocol: Puregen plant DNA extraction kit

value: leaf

tag: genotype


title: G2019S-CWA

description: PD

value: parkinson's disease


title: heart, female casein HCM, rep1

city: Boulder

first: Leslie

last: Leinwand

state: CO

address: 3415 Colorado Ave

department: MCD Biology and BioFrontiers Institute

institute: University of Colorado at Boulder

description: Gene expression data from casein-fed, HCM female hearts

hyb_protocol: cRNA were hybridized 16 hours at 45 degrees Celsius on the Affymetrix MGU74Av2 GeneChip.  Chips were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Hewlett Packard Gene Array Scanner G2500A.

data_processing: The data were analyzed with the Robust Multiarray Averaging (RMA) method in Affymetrix Expression Console using default settings.

organism: Mus musculus

source_name: left ventricle, female, casein, HCM

label_protocol: Biotinylated cRNA were amplified and labeled according to the Affymetrix instructions using 10 μg total RNA.

growth_protocol: Mice were housed until 2 months of age under standard conditions and fed ad libitum either a standard soy-based rodent diet or a casein-based diet, as indicated.

extract_protocol: Total RNA was extracted with TRI reagent according to the manufacturer's instructions. For each sample, RNA from two animals was pooled.

treatment_protocol: At 2 months old, mice were anesthetized with inhaled isoflurane, sacrificed by cervical dislocation, and hearts were rapidly excised.  Hearts were exsanguinated in ice-cold, sterile PBS and left ventricles were flash frozen in liquid nitrogen.

tag: strain

value: left ventricle

tag: genotype/variation

value: HCM

tag: Sex

tag: diet

value: casein


title: heart, female soy HCM, rep3

description: Gene expression data from soy-fed, HCM female hearts

source_name: left ventricle, female, soy, HCM

value: female

value: soy


title: heart, female casein HCM, rep2


title: heart, female soy HCM, rep2


title: heart, female casein wt, rep3

description: Gene expression data from casein-fed, wild-type female hearts

source_name: left ventricle, female, casein, wild-type

value: wild-type


title: heart, female soy HCM, rep1


title: heart, female soy wt, rep3

description: Gene expression data from soy-fed, wild-type female hearts

source_name: left ventricle, female, soy, wild-type


title: heart, female casein wt, rep1


title: heart, female casein wt, rep2


title: heart, female soy wt, rep4


title: heart, female casein HCM, rep3


title: heart, female soy wt, rep2


title: untagged a/alpha cell control

city: San Francisco

first: Lauren

middle: N

last: Booth

address: 600 16th Street, N374

department: Micobiology and Immunology

institute: University of California, San Francisco

hyb_protocol: see Nobile et al. 2009 (PMID: 19529758)

scan_protocol: see Nobile et al. 2009 (PMID: 19529758)

data_processing: see Nobile et al. 2009 (PMID: 19529758)

organism: Kluyveromyces lactis

source_name: ChIP of WT a/alpha cells

label_protocol: see Nobile et al. 2009 (PMID: 19529758)

growth_protocol: YEPD, 30 degrees, to OD600=0.6

extract_protocol: see Nobile et al. 2009 (PMID: 19529758) and for the a1 and α2 ChIPs 2 μL of 5 mg/mL mouse anti-HA antibody clone 12CA5 (Roche) were used.

value: a/alpha cells

tag: sample type

value: untagged control

tag: chip antibody

value: anti-HA

source_name: Input DNA from WT a/alpha cells

growth_protocol: YEPD

value: input DNA


title: Col-0A


title: Ler-1A


title: MATalpha2

source_name: ChIP of HA tagged-MATalpha2 a/alpha cells

growth_protocol: YEPD, 30 degrees, to OD600=0.5

tag: cell type

value: MATalpha2 ChIP fraction

source_name: Input DNA from HA tagged-MATalpha2 a/alpha cells


title: Eden-1


title: Cvi0A


title: heart, female casein HCM, rep4


title: RME1, rep2

source_name: ChIP of myc tagged-RME1 a cells

growth_protocol: phophate-starvation (see Tuch et al. 2008)

value: a cells

value: RME1 ChIP fraction

value: anti-myc

source_name: Input DNA from myc tagged-RME1 a cells

growth_protocol: phosphate-starved


title: Bil-7


title: RME1, rep1

value: a cell

source_name: Input DNA from myc tagged-RME1 a cell


title: MATa1

source_name: ChIP of HA tagged-MATa1 a/alpha cells

growth_protocol: YEPD, 30 degrees, to OD600=0.4

value: MATa1 ChIP fraction

source_name: Input DNA from HA tagged-MATa1 a/alpha cells


title: heart, female soy wt, rep1


title: heart, male soy HCM, rep3

description: Gene expression data from soy-fed, HCM male hearts

source_name: left ventricle, male, soy, HCM

value: male


title: heart, male soy HCM, rep2

value: left ventricle


title: CS28419

value: leaf


title: heart, male casein HCM, rep1

description: Gene expression data from casein-fed, HCM male hearts

source_name: left ventricle, male, casein, HCM

value: HCM

value: casein


title: heart, male casein HCM, rep3


title: heart, male casein HCM, rep2


title: High_S_Se_seg_pool_F2

description:
DNA sample for Bulk Segregant analysis
labelled products were hybridized to the array in a total amount of 30ug

tag: s+se accumulating status

value: high


title: heart, male casein HCM, rep4


title: LitRvsControl_High_repl3

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

description: Technical replicate 3 of 3 at OD600nm 0.8

hyb_protocol: Samples were hybridised to the microarrays at 42 ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in 0.1×SSC/0.1% SDS for 5 min at 42 ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.) Images were quantified using the GenePix v6.1 software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. J-Express Pro v2.7 (Dysvik and Jonassen 2001) software was used.

organism: Aliivibrio salmonicida LFI1238

source_name: Aliivibrio salmonicida LFI1238 LitR mutant

label_protocol: cDNA was generated and labelled with Cy3 and Cy5 by using 15 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).

extract_protocol: Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)

value: LitR mutant

tag: od

source_name: Aliivibrio salmonicida LFI1238 stimulated wild type control

value: wild type


title: LitRvsControl_High_repl2

description: Technical replicate 2 of 3 at OD600nm 0.8


title: LitRvsControl_Med_repl2

description: Technical replicate 2 of 3 at OD600nm 0.5


title: LitRvsControl_Med_repl3

description: Technical replicate 3 of 3 at OD600nm 0.5


title: heart, male casein wt, rep4

description: Gene expression data from casein-fed, wild-type male hearts

source_name: left ventricle, male, casein, wild-type

value: wild-type


title: LitRvsControl_High_repl1

description: Technical replicate 1 of 3 at OD600nm 0.8


title: heart, male casein wt, rep1


title: heart, female casein wt, rep4

value: female


title: LitRvsControl_Med_repl1

description: Technical replicate 1 of 3 at OD600nm 0.5


title: heart, male soy wt, rep4

description: Gene expression data from soy-fed, wild-type male hearts

source_name: left ventricle, male, soy, wild-type

value: soy


title: LitRvsControl_Low_repl3

description: Technical replicate 3 of 3 at OD600nm 0.15


title: LitRvsControl_Low_repl1

description: Technical replicate 1 of 3 at OD600nm 0.15


title: LitRvsControl_Low_repl2

description: Technical replicate 2 of 3 at OD600nm 0.15


title: heart, male casein wt, rep2


title: DPvsControl_60min_repl3

description: Technical replicate 3 of 3 at 60 min

source_name: Aliivibrio salmonicida LFI1238 stimulated (2,2`-dipyridyl)

tag: treatment

value: Stimulated (2,2`-dipyridyl)

tag: time

value: 60 minutes

source_name: Aliivibrio salmonicida LFI1238 control


title: DPvsControl_60min_repl1

description: Technical replicate 1 of 3 at 60 min


title: DPvsControl_30min_repl3

description: Technical replicate 3 of 3 at 30 min

value: 30 minutes


title: Low_S_Se_seg_pool_F2

source_name: genomic DNA

tag: tissue

value: low


title: DPvsControl_60min_repl2

description: Technical replicate 2 of 3 at 60 min


title: heart, male soy wt, rep3


title: heart, male soy wt, rep2


title: DPvsControl_30min_repl1

description: Technical replicate 1 of 3 at 30 min


title: DPvsControl_30min_repl2

description: Technical replicate 2 of 3 at 30 min


title: DPvsControl_15min_repl3

description: Technical replicate 3 of 3 at 15 min

value: 15 minutes


title: DPvsControl_15min_repl2

description: Technical replicate 2 of 3 at 15 min


title: Col-0B

description: labelled products were hybridized to the array in a total amount of 16ug


title: heart, male soy wt, rep1


title: DPvsControl_15min_repl1

description: Technical replicate 1 of 3 at 15 min


title: untagged a cell control

source_name: ChIP of WT a cells

value: a cells

value: untagged control

value: anti-myc

source_name: Input DNA from WT a cells

value: input DNA


title: somite of GFP- rep 3

city: paris

first: mounia

last: lagha

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were normalised using the RMA algorithm and significant differences in gene expression were obtained using a LPE statistical test adjusted using the  BH multiple correction.

source_name: hypaxial part of the dermomyotome of E9.5 interlimb somites of mouse embryo, GFP negative cells

label_protocol: We used the GeneChip Expression Two-Cycle 3'amplification system (Affymetrix)

growth_protocol: mouse embryos were dissected in DMEM medium and Pax3-GFP fluorescence was viewed under a microscope

extract_protocol: Rneasy micro kit (Qiagen)

treatment_protocol: forelimb buds were dissociated by passage through a 2ml syringue and filtered before the flow cytometry sorting

value: E9.5 interlimb somites

value: GFP-


title: somite of GFP- rep 1


title: somite of GFP- rep 2


title: somite of GFP+ rep 3

source_name: hypaxial part of the dermomyotome of E9.5 Pax3GFP/+ interlimb somites of mouse embryo


title: somite of GFP+ rep 2


title: POLA wild lines_N2

city: Kunming

first: LI

last: JUAN

state: Yunnan

address: Black Dragon Pool

department: Rice Research Institute

country: China

institute: Yunnan Agricultural University

description: Gene expression data from panicles of POLA wild lines at ten to fifteen days after pollination stage for ripening stage

hyb_protocol: The hybridization used the GeneChip Hybridization,Wash and Stain Kit according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner G3000.

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

organism: Oryza sativa Japonica Group

source_name: POLA wild lines at ripening stage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, One-Cycle Target Labeling and Control Reagents.

growth_protocol: All of materials were grown in a greenhouse under natural daylight.

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

value: panicles

tag: Stage


title: pola RNAi lines_M2

description: Gene expression data from panicles of pola wild lines at ten to fifteen days after pollination stage for ripening stage

source_name: pola RNAi lines at ripening stage

value: pola RNAi


title: pola mutant_M1

description: Gene expression data from panicles of pola mutant at early to late meiotic stage

source_name: pola mutant at meiotic stage

value: early to late meiotic stage

value: pola mutant


title: somite of PAX3FKHR rep 2

source_name: hypaxial part of the dermomyotome of E9.5 Pax3PAX3-FKHR/GFP interlimb somites of mouse embryo


title: somite of PAX3FKHR rep 1


title: somite of GFP+ rep 1


title: somite of PAX3FKHR rep 3


title: POLA wild lines_N1

description: Gene expression data from panicles of POLA wild lines at early to late meiotic stage

source_name: POLA wild lines at meiotic stage

value: wild type


title: forelimb of GFP- rep 2

source_name: forelimb bud of E10.5 mouse embryo, GFP negative cells

value: E10.5 forelimb buds


title: forelimb of GFP- rep 3


title: forelimb of GFP+ rep 3

description: GFP+D

source_name: forelimb bud of E10.5 Pax3GFP/+ mouse embryo


title: forelimb of GFP- rep 1


title: forelimb of GFP+ rep 1

description: GFP+A


title: forelimb of GFP+ rep 2

description: GFP+C


title: forelimb of PAX3FKHR rep 2

description: GFP _FKHR2

source_name: forelimb bud of E10.5 Pax3PAX3-FKHR/GFP mouse embryo


title: forelimb of PAX3FKHR rep 1

description: GFP _FKHR1


title: forelimb of PAX3FKHR rep 3

description: GFP _FKHR3


title: heart, male soy HCM, rep1

description: Gene expression data from soy-fed, HCM male hearts

source_name: left ventricle, male, soy, HCM

value: left ventricle

value: HCM

value: male

value: soy

tag: age


title: heart, male casein wt, rep3

source_name: left ventricle, male, casein, wild-type

value: wild-type

value: casein


title: MIAML217N_BU

city: Ann Arbor

first: Sami

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

description: Normal

hyb_protocol: The DNA was prepared for hybridization to SNP 6.0 arrays according to the manufacturers’ recommendations.

scan_protocol: SNP 6.0 arrays were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing:
Affymetrix CEL files for each blast and buccal sample were analyzed using Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to generate tab-delimited SNP call files in text format. Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip adapted to operate in a 64-bit environment.
dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using a median-smoothing algorithm.

source_name: primary human: buccal

label_protocol: Biotinylated, fragmented DNA was prepared from genomic DNA according to the standard Affymetrix protocol.

extract_protocol: Highly pure blast cells or buccal swabs were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 56C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

treatment_protocol: Purification: Liquid nitrogen-cryopreserved (liquid phase) peripheral blood or bone marrow mononuclear cells derived from AML patients were washed and recovered by centrifugation and then treated with anti-human CD3 (Miltenyi Biotec #130-050-101), anti-human CD14 microbeads (if blasts were negative for CD14 expression; Miltenyi Biotec #130-050-201), anti-human CD19 (if blasts were negative for CD19 expression; Miltenyi Biotec #130-050-301) and anti-human CD235a (Miltenyi Biotec #130-050-501) per manufacturer’s recommendations.  Cell suspensions were run through Miltenyi MACS LS separation columns (#130-042-401) in order to negatively enrich for AML blasts.  AML blast DNA used for SNP 6.0 profiling was extracted from samples that were further purified as follows:  post-Miltenyi column samples were washed and stained with FITC-conjugated anti-CD33, PE-conjugated anti-CD13, and APC-conjugated anti-CD45 (all antibodies: eBioscience, San Diego, CA).  After final washing, propidium iodide (PI) was added to a concentration of 1 μg/ml to discriminate dead cells.  Sorting of cells was done on a FACS-ARIA high-speed flow cytometer (Becton Dickinson, Mountain View, CA).  Live cells (PI-negative) were gated for blasts by identifying those cells with intermediate-intensity staining for CD45 and low- to moderate-intensity side scatter(20).  CD33 and CD13 were then used in order to further discriminate blasts versus erythroid lineage and mature myeloid lineage cells.

value: primary buccal tissue

tag: tumor vs. normal

value: normal

tag: disease

value: acute myelogenous leukemia (AML)

tag: patient


title: MIAML217T

description: Primary AML

source_name: primary human: blood or bone marrow, FACS sort-purified AML blasts

value: purified AML blasts from blood or bone marrow

value: tumor

tag: aml subtype

value: primary AML


title: MIAML216T

description: Secondary AML

value: secondary AML


title: MIAML201N_BU

description: Normal


title: MIAML214N_BU

description: Normal


title: MIAML214T

description: Secondary AML


title: MIAML216N_BU_031910

description: Normal


title: MIAML200T

description: Secondary AML


title: MIAML199T

description: Primary AML


title: MIAML202N_BU

description: Normal


title: MIAML215T

description: Primary AML


title: MIAML201T

description: Treatment-related AML

value: treatment-related AML


title: MIAML202T

description: Primary AML


title: MIAML204N_BU

description: Normal


title: MIAML215N_BU

description: Normal


title: MIAML212N_BU

description: Normal


title: MIAML200N_BU

description: Normal


title: MIAML210N_BU

description: Normal


title: MIAML198N_BU

description: Normal


title: MIAML197T

description: Primary AML


title: MIAML198T

description: Primary AML


title: MIAML195N_BU

description: Normal


title: MIAML194T

description: Primary AML


title: MIAML199N_BU

description: Normal


title: Valproic acid-treated cells vs. untreated cells at time point 72 hrs, replicate 3

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
T_vs_U_72hrs-Rep3
Replicate 3 of 3. Valproic acid-treated vs. untreated K562 cells at time point 72 hrs

hyb_protocol: 750ng of each cRNA were fragmented in the fragmentation buffer, in presence of blocking agent. Subsequently, samples were hybridized with hybridization buffer on microarrays slides  in a Surhyb gasket for 17h at 65°C.

scan_protocol: Slides were scanned on an Axon GenePix 4100A Images were quantified using Axon GenePix Pro 6.1.0.2

data_processing: Data were processed in the R statistical environement using the Limma package. Background correction was performed using the normexp method and normalization was performed using Loess.

source_name: Untreated K562 cells at time point 72 hrs

label_protocol: According to the manufacturer's instructions, reverse transcription were done with 700ng of RNA and labeling of the samples accured during transcription of cRNA.

growth_protocol: Cells were thawed 10 days before treatment and cultivated in RPMI-1640 complemented with 10%, 1% penecilin/streptomycin, in order to have engouh cells for one serie. Each replicate is made from a different thawing.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions. RNA cleanup was realized with the RNeasy Mini Kit (Qiagen), quantity and quality of RNA were checked with a Nanodrop 1000 spectrophotometer and an Agilent bioanalyzer 4100,  respectively.

treatment_protocol: Cells were seeded the day before treatment in culture medium. At T0, cells were treated with 1mM of VPA. At T+2h, +6h; +10h, +48h and +72h, cells were collected for RNA extraction.

tag: cell line

value: DNSZ K562

tag: agent

value: 72 hrs

source_name: Valproic acid-treated K562 cells at time point 72 hrs

value: Valproic acid


title: MIAML204T

description: Secondary AML


title: MIAML212T

description: Primary AML


title: MIAML197N_BU

description: Normal


title: MIAML195T

description: Primary AML


title: Valproic acid-treated cells vs. untreated cells at time point 48 hrs, replicate 3

description:
T_vs_U_48hrs-Rep3
Replicate 3 of 3. Valproic acid-treated vs. untreated K562 cells at time point 48 hrs

source_name: Untreated K562 cells at time point 48 hrs

value: 48 hrs

source_name: Valproic acid-treated K562 cells at time point 48 hrs


title: MIAML211T

description: Primary AML


title: Valproic acid-treated cells vs. untreated cells at time point 72 hrs, replicate 1

description:
T_vs_U_72hrs-Rep1
Replicate 1 of 3. Valproic acid-treated vs. untreated K562 cells at time point 72 hrs


title: MIAML194N_BU

description: Normal


title: MIAML193T

description: Primary AML


title: MIAML193N

description: Normal


title: Valproic acid-treated cells vs. untreated cells at time point 48 hrs, replicate 2

description:
T_vs_U_48hrs-Rep2
Replicate 2 of 3. Valproic acid-treated  vs. untreated K562 cells at time point 48 hrs


title: MIAML210T

description: Secondary AML


title: Valproic acid-treated cells vs. untreated cells at time point 10 hrs, replicate 3

description:
T_vs_U_10hrs-Rep3
Replicate 3 of 3. Valproic acid-treated vs. untreated K562 cells at time point 10 hrs

source_name: Untreated K562 cells at time point 10 hrs

value: 10 hrs

source_name: Valproic acid-treated K562 cells at time point 10 hrs


title: Valproic acid-treated cells vs. untreated cells at time point 10 hrs, replicate 1

description:
T_vs_U_10hrs-Rep1
Replicate 1 of 3. Valproic acid-treated vs. untreated K562 cells at time point 10 hrs


title: Valproic acid-treated cells vs. untreated cells at time point 10 hrs, replicate 2

description:
T_vs_U_10hrs-Rep2
Replicate 2 of 3. Valproic acid-treated  vs. untreated K562 cells at time point 10 hrs


title: Valproic acid-treated cells vs. untreated cells at time point 6 hrs, replicate 3

description:
T_vs_U_6hrs-Rep3
Replicate 3 of 3. Valproic acid-treated vs. untreated K562 cells at time point 6 hrs

source_name: Untreated K562 cells at time point 6 hrs

value: 6 hrs

source_name: Valproic acid-treated K562 cells at time point 6 hrs


title: MIAML191T

description: Primary AML


title: Valproic acid-treated cells vs. untreated cells at time point 6 hrs, replicate 1

description:
T_vs_U_6hrs-Rep1
Replicate 1 of 3. Valproic acid-treated vs. untreated K562 cells at time point 6 hrs


title: Valproic acid-treated cells vs. untreated cells at time point 6 hrs, replicate 2

description:
T_vs_U_6hrs-Rep2
Replicate 2 of 3. Valproic acid-treated  vs. untreated K562 cells at time point 6 hrs


title: MIAML192N

description: Normal


title: MIAML192T

description: Primary AML


title: MIAML191N

description: Normal


title: Valproic acid-treated cells vs. untreated cells at time point 72 hrs, replicate 2

description:
T_vs_U_72hrs-Rep2
Replicate 2 of 3. Valproic acid-treated  vs. untreated K562 cells at time point 72 hrs


title: MIAML188N_092109

description: Normal


title: Valproic acid-treated cells vs. untreated cells at time point 2 hrs, replicate 3

description:
T_vs_U_2hrs-Rep3
Replicate 3 of 3. Valproic acid-treated vs. untreated K562 cells at time point 2 hrs

source_name: Untreated K562 cells at time point 2 hrs

value: 2 hrs

source_name: Valproic acid-treated K562 cells at time point 2 hrs


title: Valproic acid-treated cells vs. untreated cells at time point 2 hrs, replicate 1

description:
T_vs_U_2hrs-Rep1
Replicate 1 of 3. Valproic acid-treated vs. untreated K562 cells at time point 2 hrs


title: Valproic acid-treated cells vs. untreated cells at time point 48 hrs, replicate 1

description:
T_vs_U_48hrs-Rep1
Replicate 1 of 3. Valproic acid-treated vs. untreated K562 cells at time point 48 hrs


title: MIAML189T_092109

description: Primary AML


title: Valproic acid-treated cells vs. untreated cells at time point 2 hrs, replicate 2

description:
T_vs_U_2hrs-Rep2
Replicate 2 of 3. Valproic acid-treated  vs. untreated K562 cells at time point 2 hrs


title: MIAML189N_BU_031910

description: Normal


title: MIAML188T_092809

description: Primary AML


title: MIAML184N_031910

description: Normal

source_name: primary human: remission bone marrow

value: primary remission bone marrow


title: MIAML180T_031910

description: Secondary AML


title: MIAML182N_032009

description: Normal


title: MIAML179T

description: Primary AML


title: MIAML182T

description: Primary AML


title: MIAML180N_BU_031910

description: Normal


title: MIAML167T

description: Primary AML


title: MIAML174T

description: Primary AML


title: MIAML176T

description: Secondary AML


title: MIAML167N_BU

description: Normal


title: MIAML176N

description: Normal


title: MIAML163T

description: Primary AML


title: MIAML160T

description: Secondary AML


title: MIAML169T

description: Secondary AML


title: MIAML164N

description: Normal


title: MIAML159T

description: Primary AML


title: MIAML160N

description: Normal


title: MIAML163N

description: Normal


title: MIAML158N

description: Normal


title: MIAML174N_031910

description: Normal


title: MIAML179N

description: Normal


title: MIAML157T

description: Treatment-related AML


title: MIAML158T

description: Secondary AML


title: MIAML157N

description: Normal


title: MIAML169N

description: Normal


title: MIAML151T

description: Secondary AML


title: MIAML151N

description: Normal


title: MIAML161N

description: Normal


title: MIAML153T

description: Secondary AML


title: MIAML164T

description: Primary AML


title: MIAML161T

description: Secondary AML


title: MIAML150N

description: Normal


title: MIAML143T

description: Primary AML


title: MIAML159N

description: Normal


title: MIAML145T

description: Primary AML


title: MIAML150T

description: Primary AML


title: MIAML147N

description: Normal


title: MIAML147T

description: Primary AML


title: MIAML145N

description: Normal


title: MIAML142N

description: Normal


title: MIAML142T

description: Primary AML


title: MIAML153N

description: Normal


title: MIAML143N

description: Normal


title: MIAML137T

description: Treatment-related AML


title: MIAML136N

description: Normal


title: MIAML140T

description: Primary AML


title: MIAML131N

description: Normal


title: MIAML136T

description: Treatment-related AML


title: MIAML138N

description: Normal


title: MIAML131T

description: Primary AML


title: MIAML137N

description: Normal


title: MIAML127T

description: Primary AML


title: MIAML128N

description: Normal


title: MIAML138T

description: Primary AML


title: MIAML123N_031910

description: Normal


title: MIAML128T

description: Secondary AML


title: MIAML127N

description: Normal


title: MIAML124T

description: Treatment-related AML


title: MIAML132N

description: Normal


title: MIAML122T

description: Primary AML


title: MIAML140N

description: Normal


title: MIAML124N

description: Normal


title: MIAML123T_021709

description: Primary AML


title: MIAML120T

description: Secondary AML


title: MIAML132T

description: Primary AML


title: MIAML184T_031910

description: Treatment-related AML


title: MIAML122N

description: Normal


title: MIAML115T

description: Treatment-related AML


title: MIAML126N

description: Normal


title: MIAML120N_060908

description: Normal


title: MIAML117N

description: Normal


title: MIAML110N

description: Normal


title: MIAML112T

description: Treatment-related AML


title: MIAML117T

description: Primary AML


title: MIAML113T

description: Primary AML


title: MIAML112N

description: Normal


title: MIAML110T

description: Primary AML


title: MIAML115N

description: Normal


title: MIAML108T

description: Primary AML


title: MIAML109T_072208

description: Primary AML


title: MIAML109N_032009

description: Normal


title: MIAML100N

description: Normal


title: MIAML113N

description: Normal


title: MIAML107N

description: Normal


title: MIAML103N

description: Normal


title: MIAML108N

description: Normal


title: MIAML103T

description: Primary AML


title: MIAML105T

description: Primary AML


title: MIAML100T

description: Primary AML


title: MIAML101T

description: Primary AML


title: MIAML101N

description: Normal


title: MIAML098T

description: Primary AML


title: MIAML102N

description: Normal


title: MIAML099N

description: Normal


title: MIAML098N

description: Normal


title: MIAML126T

description: Secondary AML


title: MIAML102T

description: Primary AML


title: MIAML099T

description: Primary AML


title: MIAML107T

description: Primary AML


title: MIAML096T

description: Primary AML


title: MIAML093T

description: Primary AML


title: MIAML105N

description: Normal


title: MIAML095T

description: Primary AML


title: MIAML095N

description: Normal


title: MIAML090T

description: Primary AML


title: MIAML091T

description: Primary AML


title: MIAML092T

description: Primary AML


title: MIAML089N_031910

description: Normal


title: MIAML088T

description: Treatment-related AML


title: MIAML088N

description: Normal


title: MIAML092N

description: Normal


title: MIAML091N

description: Normal


title: MIAML087N

description: Normal


title: MIAML081T

description: Primary AML


title: MIAML081N

description: Normal


title: MIAML096N

description: Normal


title: MIAML078T

description: Primary AML


title: MIAML080T

description: Primary AML


title: MIAML077N

description: Normal


title: MIAML077T

description: Primary AML


title: Skin.5d.1

first: Corrie

last: Gallant-Behm

address: 347 UCB

department: Molecular, Cellular, and Developmental Biology

description: Tissue is cutaneous, measured time is at 5d

hyb_protocol: standard as recommended by manufacturer

scan_protocol: standard as recommended by manufacturer

data_processing: We used quantile normalization and Bioconductor package Agi4x44Preprocess version 1.6.0 to process the data.

organism: Oryctolagus cuniculus

source_name: cutaneous

label_protocol: standard as recommended by manufacturer

extract_protocol: Following animal euthanasia, samples of all wounds were frozen in RNAlater (Ambion, Austin, TX) at -80oC for molecular analysis. The epithelium of all incisional grid samples was mechanically separated from the underlying mesenchymal tissue using a single-edged razor blade (Schierle et al. 2007), and was homogenized in RLT buffer (Qiagen, Valencia, CA) with 1% beta- mercaptoethanol using a PowerGen Model 500 Homogenizer (Fisher Scientific, Houston, TX). Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA) as previously described (Reno et al. 1997). RNA quality was determined using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: cutaneous

tag: time point


title: Skin.5d.5


title: Skin.5d.4


title: MIAML078N

description: Normal

value: primary buccal tissue


title: Skin.5d.3


title: MIAML073T

description: Primary AML


title: Skin.5d.2


title: MIAML067T_031910

description: Primary AML


title: MIAML076N

description: Normal

value: normal


title: Mucosa.5d.5

description: Tissue is Mucosa, measured time is at 5d

source_name: Mucosa

value: Mucosa


title: MIAML097T

description: Secondary AML

value: purified AML blasts from blood or bone marrow

value: acute myelogenous leukemia (AML)


title: MIAML089T

description: Primary AML

value: tumor

value: primary AML


title: MIAML068T

description: Treatment-related AML

value: treatment-related AML


title: MIAML068N

description: Normal


title: MIAML080N

description: Normal


title: Mucosa.5d.4


title: MIAML064T

description: Primary AML


title: Mucosa.5d.3


title: MIAML067N

description: Normal


title: Mucosa.5d.2


title: Skin.3d.5

description: Tissue is cutaneous, measured time is at 3d


title: Mucosa.5d.1


title: MIAML097N

description: Normal


title: Skin.3d.4


title: MIAML062T

description: Primary AML


title: MIAML087T

description: Primary AML


title: MIAML076T

description: Treatment-related AML


title: Skin.3d.2


title: Skin.3d.1


title: Skin.3d.3


title: MIAML093N

description: Normal


title: Mucosa.3d.6

description: Tissue is Mucosa, measured time is at 3d


title: Mucosa.3d.5


title: Mucosa.3d.4


title: MIAML090N

description: Normal


title: MIAML073N_BU

description: Normal


title: Mucosa.3d.3


title: Mucosa.3d.2


title: Mucosa.3d.1


title: MIAML062N

description: Normal


title: MIAML060N

description: Normal


title: M202 (parental)

city: Los Angeles

first: Ali

last: Jazirehi

address: 10833 LeConte Ave, CHS 54-140

institute: UCLA, Department of Surgery

hyb_protocol: Labeled cDNAs were hybridized to the GeneChip Human Gene 1.0 ST Arrays (Affymetrix) according to the manufacturer's protocol

scan_protocol: Array scanning was carried out with the GeneChip Scanner 3000 7G (Affymetrix) according to the manufacturer's instructions

data_processing: RMA

source_name: Human melanoma cell lines

label_protocol: cDNAs were generated from total RNA and biotinylated according to the standard Affymetrix protocol.

growth_protocol: Selected melanoma cell lines were grown in RPMI supplemented with 10% serum

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Cell lines were either left untreated or grown under lymphocyte selective pressure

tag: genotype

value: V600E BRAF mutant

tag: sensitivity

value: PLX4032 sensitive


title: Skin.12h.4

description: Tissue is cutaneous, measured time is at 12h


title: Skin.12h.6


title: MIAML059N

description: Normal


title: MIAML061T

description: Primary AML


title: Skin.12h.5


title: M202R1 (resistant)

value: PLX4032 resistant


title: MIAML057N

description: Normal


title: Skin.12h.2


title: MIAML057T

description: Primary AML


title: Mucosa.12h.6

description: Tissue is Mucosa, measured time is at 12h


title: MIAML059T

description: Primary AML


title: Skin.12h.1


title: Mucosa.12h.5


title: MIAML053T

description: Primary AML


title: MIAML056N

description: Normal


title: Skin.12h.3


title: MIAML064N

description: Normal


title: MIAML056T

description: Primary AML


title: Mucosa.12h.4


title: MIAML050N

description: Normal


title: MIAML050T

description: Primary AML


title: MIAML053N

description: Normal


title: Mucosa.12h.2


title: MIAML049N

description: Normal


title: Mucosa.12h.1


title: Skin.1d.6

description: Tissue is cutaneous, measured time is at 1d


title: Mucosa.12h.3


title: Skin.1d.4


title: Skin.1d.3


title: Skin.1d.5


title: MIAML049T

description: Primary AML


title: MIAML047T

description: Treatment-related AML


title: MIAML047N_010908

description: Normal


title: MIAML045T

description: Treatment-related AML


title: MIAML060T

description: Primary AML


title: MIAML045N

description: Normal


title: Skin.3d.6


title: Skin.1d.2


title: MIAML061N_BU

description: Normal


title: Mucosa.1d.6

description: Tissue is Mucosa, measured time is at 1d


title: Skin.1d.1


title: MIAML043N

description: Normal


title: MIAML063T

description: Secondary AML

value: secondary AML


title: MIAML063N

description: Normal


title: MIAML044T

description: Primary AML


title: Mucosa.1d.5


title: Mucosa.1d.3


title: Mucosa.1d.4


title: MIAML041N

description: Normal


title: Mucosa.1d.1


title: MIAML040N

description: Normal


title: Skin.0h.5

description: Tissue is cutaneous, measured time is at 0h


title: MIAML036T

description: Primary AML


title: Skin.0h.4


title: Skin.0h.3


title: MIAML040T

description: Primary AML


title: Skin.0h.2


title: Mucosa.0h.5

description: Tissue is Mucosa, measured time is at 0h


title: Skin.0h.1


title: Mucosa.0h.4


title: MIAML044N

description: Normal


title: MIAML032T

description: Primary AML


title: MIAML043T

description: Treatment-related AML


title: Mucosa.0h.2


title: MIAML041T

description: Treatment-related AML


title: Ctrl.3

description: Tissue is unwounded skin, measured time is at 0h

source_name: unwounded skin

value: unwounded skin


title: Mucosa.0h.1


title: Ctrl.4


title: Ctrl.2


title: MIAML030N

description: Normal

source_name: primary human: buccal


title: MIAML032N

description: Normal


title: MIAML030T

description: Secondary AML

source_name: primary human: blood or bone marrow, FACS sort-purified AML blasts


title: Ctrl.1


title: MIAML014T

description: Treatment-related AML


title: MIAML009N

description: Normal


title: MIAML012T

description: Treatment-related AML


title: MIAML036N

description: Normal


title: Mucosa.1d.2


title: MIAML012N

description: Normal


title: MIAML014N

description: Normal


title: MIAML006T

description: Primary AML


title: Mucosa.0h.3


title: MIAML006N

description: Normal


title: MIAML009T

description: Primary AML


title: MIAML001T

status: Public on Nov 30 2010

description: Primary AML


title: MSC - 24 moths of age - (#1)

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

institute: University of Verona

hyb_protocol: Labeled cRNA were hybridized overnight at 60°C with the arrays.

scan_protocol: After washing, hybridization was revealed by chemoluminescence and array image was captured using X-ray film and a flatbed desktop scanner.

data_processing: Data from arrays was analyzed using GEArray Expression Analysis Suite (Superarray Bioscience Corporation)

label: Biotin

source_name: mesenchymal stem cells isolated from the inguinal fat pad of a FVB mouse

label_protocol: TrueLabeling-AMP Linear RNA Amplification Kit (Superarray Bioscience Corporation, Frederick, MD, USA) was used to amplify and label RNA for hybridization.

growth_protocol: DMEM Dulbecco’s Modified Eagle Medium (1X) liquid (High Glucose) [with GlutaMAX 4500 mg/L D-Glucose without Sodium Pyruvate]

extract_protocol: total RNA extracted using QIAGEN Rneasy kit, following the manifacturer's instruction

treatment_protocol: cells cultured within the 5th passage

value: 24 months

tag: strain

value: FVB


title: MSC - 24 months of age - (#2)


title: MSC - 12 months of age - (#3)

value: 12 months


title: MSC - 12 months of age - (#7)


title: CRC patiënt 22

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: germline DNA from suspected familial microsatellite-stable CRC

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA ((Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix scanner 3000.

data_processing: Genotyping information obtained using Affymetrix Genotyping Concole software (v2.1)

source_name: Blood

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

tag: age at diagnosis

tag: #first degree rel.

tag: tumor location

value: Sigmoid colon


title: CRC patiënt 41

value: Colon


title: CRC patiënt 36

value: Descending colon


title: chukchi143

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0   Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

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

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium  Human660W-Quad v1.0 Genotyping BeadChips (Illumina).
Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

label: C-Bio and A-DNP

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Female

tag: population

value: Chukchis

tag: region

value: Siberia

value: blood


title: chukchi123

tag: tissue


title: CRC patiënt 28


title: MSC - 12 months of age - (#2 technical replicate)

tag: age


title: MSC - 12 months of age - (#2)


title: chukchi142


title: chukchi130


title: mongol128

value: Male

value: Mongolians


title: CRC patiënt 5


title: CRC patiënt 21

value: Rectosigmoid colon


title: CRC patiënt 40


title: chukchi114


title: chukchi136


title: CRC patiënt 37

value: Rectum


title: mongol131


title: MSC - 6 moths of age - (#7)

value: 6 months


title: chukchi126


title: MSC - 6 months of age - (#8)


title: chukchi125


title: chukchi116


title: MSC - 3 months of age - (#5)

value: 3 months


title: MSC - 6 months of age - (#6)


title: chukchi117


title: chukchi119


title: mongol123


title: MSC - 3 months of age - (#8)


title: chukchi124


title: MSC - 3 months of age - (#2)


title: MSC - 1 month of age - (#8 technical replicate)

value: 1 month


title: chukchi128


title: MSC - 1 month of age - (#1 technical replicate)


title: MSC - 1 month of age - (#2)


title: MSC - 1 month of age - (#5)


title: MSC - 1 month of age - (#8)


title: MSC - 1 month of age (#1)


title: mongol119


title: mongol120


title: mongol115


title: CRC patiënt 38


title: A188/Oh43/W22/B73 hybrid 4x vs. B73/W22 hybrid 4x Scan3

city: St. Louis

first: Nicole

middle: Christina

last: Riddle

state: MO

address: 1 Brookings Dr.; CB1137

department: Biology

institute: Washington University

description: Sample 45

hyb_protocol: The hybridization mix consisted of DIG Easy Hyb (Roche) supplemented with 500ug/ml yeast tRNA and 500ug/ml salmon sperm DNA for blocking. Two Cy3 and two Cy5 labeled probes were combined with 120 ul of this mix to be used on one slide set. The hybridization mix was heated to 65°C for 5 min and then cooled to room temperature before loading onto the microarray slide. The array surface was covered with a coverslip (Lifterslip, Erie Scientific), the array was moved into a hybridization chamber (Corning) and incubated at 37°C for approximately 15 h. After hybridization, the coverslip was removed by immersing the array into 1x sodium chloride/sodium citrate buffer (SSC) at room temperature. The slide was washed thrice 10– 15 min in 1x SSC, 0.1% SDS at 50°C (10% SDS, 20x SSC from Ambion). After the last wash, residual SDS was removed by a quick rinse in 1x SSC at room temperature. The slide was dried by centrifugation in a slide centrifuge.

scan_protocol: An Axon GenePix 4000B scanner was used to scan all microarrays. Unless otherwise noted, three scans were performed per slide, all at 100% laser power: (1) A scan where the Cy3/Cy5 ratio had been adjusted to approximately 1 using a prescan at low resolution by altering the photo multiplier tube (PMT) gain. (2) A scan where the gain settings were constant among all slides (500 for 532/Cy3 and 600 for 635/Cy5). (3) A scan where the PMT was determined by the automatic setting of the scanner, with a pixel saturation level of 0.005%. For experiments 1 and 2, two additional scans were performed: a scan with the Cy3/Cy5 ratio adjusted to 1 at 33% laser power and a high-intensity scan which had the PMT gain of scan two from above increased by 100 for either channel. GenePix software was used to grid the arrays.

data_processing: Background-subtracted median signal intensity values for each of the 54,492 features were log2 transformed prior to analysis. Two types of analysis of variance (ANOVA) were carried out, one assuming a common variance for all features and one using a feature-specic variance. Statistical significance using a multiple  comparison correction was determined in two ways, a Bonferroni correction (0.05), and false discovery rate (FDR) controlling procedure (0.05; Benjamini and Hochberg 1995). Note,  the data provided is derived from the combined loop analysis, not simply the single comparisons. Due to technical reasons, several slides were excluded from the analysis.  They are MO A1.4.004, MO B1.4.006, MO A.1.4.006, MO B1.4.014, MO B1.4.109, MO B1.4.112, MO A1.4.160, MO A1.4.153, MO B1.4.160, MO B1.4.163 MO A.1.4.186, MO A1.4.188, MO B1.4.242, MO B1.4.244, MO B1.4.254, MO B1.4.256, MO A1.4.262, MO A1.4.264, MO B1.4.273, and MO B1.4.275.

organism: Zea mays

source_name: Adult leaves

label_protocol: An indirect labeling method using amino-allyl-dUTP followed by coupling to Cy3/Cy5 was carried out according to a modified protocol (Catts et al. 2005).

growth_protocol: All plants for tissue collection were grown in the Sears greenhouse at the University of Missouri, Columbia with 16-h light per day. ProMix BX General Purpose Growing Medium (Premier Horticulture) supplemented with iron sulfate, DynaGreenTM 12-12-12 (Hummert) fertilizer and greensand was used and additional liquid fertilizer (a 0.3% solution of Peter’s general purpose 20-20-20 fertilizer; Hummert).

extract_protocol: Total RNA was isolated from the pooled leaf tissue of 10 individuals per genotype using Trizol (Invitrogen) following the manufacturer’s recommendation with minor modifications. Two independent RNA preps were made from each genotype.

treatment_protocol: Treatments were different maize genotypes: B73 monoploids, B73 diploids, B73 triploids, B73 tetraploids, Oh43 tetraploids, W22 tetraploids, A188 tetraploids, A188/Oh43 tetraploid hybrids, B73/W22 tetraploid hybrids, and A188/Oh43/W22/B73 double-cross tetraploid hybrids.

tag: genotype/variation

value: B73/W22 hybrid 4x


title: A188/Oh43/W22/B73 hybrid 4x vs. B73/W22 hybrid 4x Scan2

description: Sample 44


title: A188/Oh43/W22/B73 hybrid 4x vs. B73/W22 hybrid 4x Scan1

description: Sample 43


title: A188/Oh43/W22/B73 hybrid 4x vs. A188/Oh43 hybrid 4x Scan2

description: Sample 41

value: A188/Oh43 hybrid 4x


title: A188/Oh43/W22/B73 hybrid 4x vs. A188/Oh43 hybrid 4x Scan1

description: Sample 40


title: chukchi129


title: A188/Oh43/W22/B73 hybrid 4x vs. A188/Oh43 hybrid 4x Scan3

description: Sample 42


title: B73 4x vs. A188 4x Scan3

description: Sample 39


title: mongol124


title: B73 4x vs. A188 4x Scan2

description: Sample 38


title: mongol114


title: B73 4x vs. A188 4x Scan1

description: Sample 37


title: B73/W22 4x vs. W22 hybrid 4x Scan1

description: Sample 34


title: B73/W22 4x vs. W22 hybrid 4x Scan3

description: Sample 36


title: W22 4x vs. B73 4x Scan3

description: Sample 33


title: B73/W22 4x vs. W22 hybrid 4x Scan2

description: Sample 35


title: koryakE151

value: Koryaks


title: mongol107


title: W22 4x vs. B73 4x Scan2

description: Sample 32


title: koryakE117


title: koryakE131


title: koryakE137


title: B73/W22 4x vs. B73 hybrid 4x Scan3

description: Sample 30


title: koryakE95


title: koryakE66


title: W22 4x vs. B73 4x Scan1

description: Sample 31


title: koryakE78


title: buryat27

value: Buryats


title: koryakE77


title: koryakE6


title: koryakE41


title: koryakE76


title: koryakE35


title: B73/W22 4x vs. B73 hybrid 4x Scan2

description: Sample 29


title: koryakE67


title: koryakE5


title: Oh43 4x vs. A188/Oh43 hybrid 4x Scan3

description: Sample 27

value: Oh43 4x


title: koryakE114


title: Oh43 4x vs. A188/Oh43 hybrid 4x Scan1

description: Sample 25


title: Oh43 4x vs. A188/Oh43 hybrid 4x Scan2

description: Sample 26


title: koryakE102


title: buryat23


title: buryat26


title: A188 4x vs. Oh43 4x Scan2

description: Sample 23


title: A188 4x vs. Oh43 4x Scan3

description: Sample 24


title: B73/W22 4x vs. B73 hybrid 4x Scan1

description: Sample 28


title: buryat25


title: koryakE58


title: A188 4x vs. A188/Oh43 hybrid 4x Scan1

description: Sample 19


title: A188 4x vs. A188/Oh43 hybrid 4x Scan3

description: Sample 21


title: A188 4x vs. A188/Oh43 hybrid 4x Scan2

description: Sample 20


title: A188 4x vs. Oh43 4x Scan1

description: Sample 22


title: B73 4x vs. 3x Scan3

description: Sample 18


title: B73 4x vs. 3x Scan2

description: Sample 17


title: B73 4x vs. 3x Scan1

description: Sample 16


title: buryat20


title: B73 4x vs. 2x Scan3

description:
Sample 15
Calculated based on loop design


title: B73 4x vs. 2x Scan2

description:
Sample 14
Calculated based on loop design


title: B73 4x vs. 2x Scan1

description:
Sample 13
Calculated based on loop design


title: buryat24


title: B73 4x vs. 1x Scan2

description: Sample 11


title: B73 4x vs. 1x Scan3

description: Sample 12


title: buryat18


title: Burya16


title: Buryat15


title: Buryat17


title: B73 3x vs 2x Scan3

description: Sample 9


title: B73 4x vs. 1x Scan1

description: Sample 10


title: Buryat12


title: B73 3x vs 2x Scan1

description: Sample 7


title: B73 1x vs. 3x Scan2

description:
Sample 5
Calculated based on loop design


title: Buryat6


title: B73 1x vs. 3x Scan3

description:
Sample 6
Calculated based on loop design


title: Buryat8


title: Buryat9


title: Dolgan10

value: Dolgans


title: Dolgan8


title: B73 3x vs 2x Scan2

description: Sample 8


title: B73 1x vs. 3x Scan1

description:
Sample 4
Calculated based on loop design


title: Buryat2


title: B73 1x vs. 2x Scan3

description: Sample 3


title: B73 1x vs. 2x Scan2

description: Sample 2


title: Buryat3


title: B73 1x vs. 2x Scan1

description: Sample 1


title: Buryat14


title: Burya10


title: Dolgan5


title: Dolgan7

value: Female


title: Dolgan6


title: Dolgan2


title: Nganassan14

value: Nganassans


title: Nganassan13

value: Siberia


title: Nganassan15

value: blood


title: Buryat4

value: Male


title: Nganassan11


title: Nganassan10


title: Dolgan3


title: Nganassan12


title: Nganassan8


title: Nganassan5


title: Nganassan7


title: Yukagir9

value: Yukaghirs


title: Nganassan1


title: Yukagir7


title: Nganassan3


title: Yukagir10


title: Yukagir3


title: Yukagir2


title: Yukagir5


title: Nganassan9


title: Nganassan6


title: Yukagir6


title: Yukagir4


title: westGreenland11

value: West Greenlanders

value: America


title: westGreenland18


title: westGreenland17


title: westGreenland20


title: eastGreenland14

value: East Greenlanders


title: eastGreenland17


title: westGreenland16


title: eastGreenland9


title: eastGreenland7


title: Nganassan4


title: Nganassan2


title: Yukagir1


title: eastGreenland16


title: eastGreenland10


title: eastGreenland3


title: westGreenland9


title: westGreenland6


title: tuva16

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium Human610-Quad v1.0  Genotyping BeadChips (Illumina).
Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

value: Tuvinians


title: tuva12


title: tuva11


title: tuva15


title: eastGreenland5


title: tuva14


title: eastGreenland1


title: tuva6


title: westGreenland5


title: tuva13


title: eastGreenland6


title: tuva10


title: tuva5


title: tuva8


title: tuva7


title: tuva3


title: tuva4


title: Posterior proximal region of an E5.5 mouse embryo MOE430B rep3

city: Faro

first: Lisa

last: Goncalves

address: Campus de Gambelas, Ed8, Lab 1.17

country: Portugal

institute: CBME UALG

description: Gene expression data from Pp region of an E5.5 mouse embryo

hyb_protocol: 15 µg of biotinylated cRNA was used in a 300-µl hybridization containing added hybridization controls. 200 µl of mixture was hybridized on Affymetrix (Santa Clara, CA, USA) GeneChip Mouse Expression Set 430 arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols were used on an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 2500.

data_processing: Scanned arrays were analyzed first with Affymetrix MAS 5.0 software to obtain Absent/Present calls and for subsequent analysis with dChip 2010. Each set of 5 arrays (430A and 430B type) was analyzed separately from here on. Each set was normalized applying an Invariant Set Normalization Method. Then the normalized probe cell intensities of the 5 arrays were used to obtain model-based gene expression indices based on a PM-only model.

label_protocol: A modified linear amplification protocol was applied to generate the required amount of probe, according to Van Gelder et al., 1990

growth_protocol: Embryos with fluorescently labeled AVE were collected from B6SJLF1×CerlP-GFP matings at 5.5 dpc.

extract_protocol: Ad and Pp regions were isolated from embryos in which the AVE occupied a lateraldistal position. For the isolation of Ad regions, fragments comprising the fluorescently labeled AVE and the underlying epiblast, were microdissected. Pp regions were isolated by dissecting triangular-shaped fragments of proximal visceral endoderm and epiblast from a position diametrically opposed to the fluorescently-labeled domain. The upper limit of the Pp fragments coincided with the embryonic-extraembryonic boundary and extended in depth to roughly one third of the diameter of the egg cylinder, while its lateral limit corresponded to about one third of the height of the embryonic region. The freshly dissected fragments were immediately homogenized with TRIzol® and frozen in liquid nitrogen. The samples were then stored at -80ºC until processing.

treatment_protocol: Embyos suffered no treatment prior to the extraction procedures

value: Posterior proximal region of embryo

tag: genetic background


title: westGreenland1


title: Whole E5.5 mouse embryo MOE430B rep1

description: Gene expression data from an E5.5 mouse embryo

source_name: Whole E5.5 mouse embryo

value: Whole embryo


title: Anterior distal region of an E5.5 mouse embryo MOE430B rep4

description: Gene expression data from Ad region of an E5.5 mouse embryo

value: Anterior distal region of embryo


title: Anterior distal region of an E5.5 mouse embryo MOE430B rep3


title: Posterior proximal region of an E5.5 mouse embryo MOE430B rep4


title: tuva2


title: Whole E5.5 mouse embryo MOE430A rep1


title: tuva9


title: westGreenland2


title: Posterior proximal region of an E5.5 mouse embryo MOE430A rep1


title: Anterior distal region of an E5.5 mouse embryo MOE430A rep2


title: Posterior proximal region of an E5.5 mouse embryo MOE430A rep2


title: evenk13

value: Evenkis


title: evenk12


title: evenk11


title: Anterior distal region of an E5.5 mouse embryo MOE430A rep1


title: evenk8


title: evenk7


title: evenk4


title: evenk14


title: evenk9


title: evenk6


title: M4–

city: Dresden

first: Yoko

last: Arai

address: Pfotenhauerstrasse 108

department: MPI-CBG

country: Germany

institute: Max Planck Institute

description: Gene expression after FACS in the S phase cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4858A-028005) for 17 hours at 65°C and 10 rpm in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). The wash buffers contained 0.005% Triton X-102.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the AgilentG3_GX_1Color scan protocol for 8x60K high densitiy Micorarray Formats (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%, the resulting file is a 20bit tiff image).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20100617) to obtain background subtracted and spatially detrended green Processed Signal intensities.
Normalized signal intensity (log2 transformed and quantile normalized) calculated from the green processed signal after Feature Extraction using the GeneSpring software version 11.0 (Agilent)

source_name: Tis21–GFP negative S phase cells, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng total RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions in the Agilent One-Color Microarray-Based Gene Expression Analysis v.6.5 Manual. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All mouse embryos used were heterozygous Tis21-GFP knock-in mice (C57BL/6 background), obtained by overnight mating of homozygous Tis21-GFP males with wildtype C57BL/6 females. Noon of the day on which the vaginal plug was observed was defined as embryonic day (E) 0.5. All animal studies were performed in strict pathogen-free conditions in the animal facility of the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

extract_protocol: Total RNA was prepared using NucleoSpin RNA XS kit (Macherey-Nagel) following the manufacturer's recommendations. RNA was quantified and quality controlled using the RNA 6000 Pico Kit on the Agilent 2100 Bioanalyzer RNA (Agilent Technologies).

treatment_protocol: Dorsal telencephalon (cerebral cortex) was dissected from E14.5 Tis21-GFP heterozygous mouse embryos in Tyrode’s solution. The tissue was digested with trypsin mix solution (0.13 % trypsin (Sigma–Aldrich), 0.067 % Hyaluronidase (Sigma–Aldrich) and 0.02 % kynurenic acid (Sigma–Aldrich) in serum-free medium consisting of DMEM and F-12 nutrient (1:1; Invitrogen) for 20 min at 37°C. 0.07 % trypsin inhibitor was added to stop the digestion, collect cells at 600 g for 5 min in a centrifuge, dissociate cells in 0.07 % trypsin inhibitor, washed cells with DMEM and F-12 medium and then filtrate cells to obtain single cells. Single cells were incubated with a vital dye (Vybrant DyeCycle Violet stain, Invitrogen) at 37°C for 1 hour and sorted S phase cells by DNA contents between 2N and 4N DNA mass using a FACSAria II cell sorter (Becton, Dickinson).

tag: developmental stage

value: Embryonic day (E) 14.5

value: dorsal telencephalon (cerebral cortex)

tag: cell cycle

value: S phase

value: Tis21 negative


title: evenk10

value: Female


title: M3+

source_name: Tis21–GFP positive S phase cells, replicate 2

value: Tis21 positive


title: evenk15

value: Siberia

value: blood


title: evenk2


title: M2+

source_name: Tis21–GFP positive S phase cells, replicate 1


title: M3–

source_name: Tis21–GFP negative S phase cells, replicate 2


title: M4+

source_name: Tis21–GFP positive S phase cells, replicate 3


title: evenk16

value: Male


title: tuva1


title: M2–

source_name: Tis21–GFP negative S phase cells, replicate 1


title: altai11

value: Altaians


title: altai8


title: altai14


title: altai10


title: evenk1


title: evenk5


title: altai9


title: altai13


title: altai4


title: MSC - 12 months of age (#3)

description: cells cultured at 20th passage

hyb_protocol: Cy3-labeled cDNA was hybridized overnight at 42°C to mus musculus 12x135K Array (Roche NimbleGen)

scan_protocol: arrays were scanned with GenePix 4400A Microarray Scanner

data_processing: the data were extracted from scanned images using NimbleScan software

source_name: MSC from inguinal fat pad

label_protocol: cDNA synthesis followed by Cy3-labeling

treatment_protocol: cells cultured up to the 20th passage

value: FVB

value: 12 month


title: MSC - 1 month of age (#2)

description: cells cultured at 20th passage

value: 1 month


title: MSC - 12 months of age (#2)

description: cells cultured at 20th passage


title: MSC - 12 months of age (#1)

description: cells cultured at 20th passage


title: altai5


title: altai7


title: Liver_LT (agilent)

city: Shanghai

first: Wenchao

last: Hu

address: 320 Yueyang Road

department: Functional Genomics Group

institute: CAS-MPG Partner Institute for Computational Biology

description: 18-30nt RNA in LT stage

hyb_protocol: Same as above. The entire reaction was hybridized to the array for 20 hours at 55°C.

scan_protocol: Microarray results were extracted using Agilent Microarray Scanner (Agilent)

data_processing: The miRNA signals and errors on miRNA microarray were obtained from gTotalGeneSignal and gTotalGeneError respectively in the output files of Agilent Feature Extraction software (v9.5.3.1), subsequently analyzed by Gene-Spring GX 7.3.1 software (Agilent).

organism: Urocitellus parryii

source_name: Liver total RNA, LT stage

label_protocol: Labeling and hybridization of total RNA were performed according to the manufacturer’s protocol with no modification.

extract_protocol: Total RNA from each tissue sample was extracted using TRizol (Invitrogen) according to the manufacturer's instructions. Total RNA quality was assessed by Bioanalyzer 2100 (Agilent). Total RNA of arctic ground squirrels from the same stage were mixed in the equal amount into three pooled samples: EA, LT, and PR.100ng total RNA from three pooled samples was used as input in the labeling reaction.

value: liver

tag: stage

value: late topor


title: MSC - 1 month of age (#5-1)

description: cells cultured at 20th passage


title: altai3


title: Liver_PR (agilent)

description: 18-30nt RNA in PR stage

source_name: Liver total RNA, PR stage

value: post-reproduction


title: MSC - 1 month of age (#5-2)

description: cells cultured at 20th passage


title: Human lung tissue

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v1GeneChip 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: lung

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

value: lung

tag: Sex

value: unknown

value: adult

tag: disease state

value: healthy


title: altai6


title: Liver_EA (agilent)

description: 18-30nt RNA in EA stage

source_name: Liver total RNA, EA stage

value: early arousal


title: liver of M.fortis

first: Weibin

last: Jiang

address: 518,Ziyue ARd

institute: Shanghai Institute of Veterinary Research, Chinese Academy of Agricultural Sciences

description: compare gene expression profiles of control liver and infected liver in M.fortis

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

organism: Alexandromys fortis

source_name: hepatocyte

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: The tissues were preserved in liquid nitrogen for RNA isolation.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: male

tag: infection

value: Schistosoma japonicum


title: liver of rat

description: compare gene expression profiles of control liver and infected liver in rat

organism: Rattus norvegicus

tag: strain

value: Wistar


title: lung of M.fortis

description: compare gene expression profiles of control lung and infected lung in M.fortis

source_name: pneumonocyte


title: HP 26695_Mutant 1_rep2

city: Moscow

first: Kuvat

last: Momynaliev

address: Malaya Pirogovskaya 1A

country: Russia

institute: Research Institute for Phys-Chim Medicine

description: Single resistant colonies grown on selective plates were picked up, transferred onto fresh rif-containing plates which were then incubated for 3 days. Then cells were harvested into 1 ml of saline, collected by centrifugation, and pellet was used for DNA extraction. The mutations in the gene that are responsible for resistance were identified by DNA sequencing and comparison with the sequence of the wild-type strain 26695.

hyb_protocol: Arrays were prehybridized for 2 h at 65°C in 1× hybridization buffer (5× SSC, pH 7.5, 5× Denhardt’s solution, 0.5% SDS) in a Hybridization Oven/Shaker (Amersham). Hybridization was carried out in 5 ml of 1× hybridization buffer containing 5.5•106 cpm/ml cDNA for 20 h at 65°C. After hybridization, the cDNAmacroarray was washed in 2× SSC, 0.1% SDS, then it was incubated for 20 min at 65°C, and finally it was incubated in 0.2× SSC, 0.1% SDS for 1 h at 65°C.

scan_protocol: The arrays were exposed for 2 and 4 days to storage phosphor screens (Molecular Dynamics, Sunnyvale, Calif.) and scanned with a Storm 820 PhosphorImager (Molecular Dynamics) at a resolution of 50 mm and a color depth of 16 bits.

data_processing: Hybridization signals were quantified with ArrayVision software. After subtraction of the background, which was defined as the median of signals surrounding the entire spot fields, the overall spot normalization function was used to calculate the normalized intensity values of individual spots, thus facilitating the comparison of results from different hybridizations and filters. Relative signals from different arrays were normalized by comparing the signal from a gene to the total signal from all spots on the array. The cutoff for significant up- or down-regulation of genes was defined as a twofold difference. Statistical difference between expression of genes in the H. pylori-wild type and H. pylori rpoB mutants N1 and N2  was analyzed by the t-test. A P value of  < 0.05 was considered statistically significant

organism: Helicobacter pylori 26695

source_name: HP 26695, Rif Resistant, clone 1

label_protocol: For cDNA synthesis, 2 mg (8.5 mkl)of total RNA was mixed with 1.5 mkl of a commercially available specific primer mix (AR-OLHP-RT, Eurigentec). The primer mix consisted of 1621 specific oligonucleotide primers complementary to the 3’ ends of all H.pylori  mRNAs (Eurigentec). The sample was heated to 70°C for 10 min and subsequently cooled to 42°C for primer annealing. Reverse transcription was performed in a total volume of 50 mkl with MMLV reverse transcriptase (200 U/ml, Promega), 2.5 µl 0.1 M DTT,  0.25 µl RNasin (40U/ml), 1.25 µl dNTP mix (10 mM dCTP,dGTP, dTTP; 0.1 mM dATP) and 5 mkl [α-33P] dATP (3000 Ci/mmol) in the appropriate reaction buffer for 2 h. After addition of 1 mkl of 10% sodium dodecyl sulfate (SDS), 1 mkl of 0.5 M EDTA (pH 8.0), and 3 mkl of 3 M NaOH, the remaining RNA was hydrolyzed by incubation at 68°C for 30 min and at room temperature for 15 min. Prior to ethanol precipitation, the cDNA solution was neutralized with 3 mkl of 2 N HCl. After a wash with 70% ethanol the pellet was carefuly dried and resolved in 100 mkl of distilled water.

growth_protocol: H.pylori reference strain 26695 was routinely maintained on Columbia agar plates supplemented with 10 % heat-inactivated Horse Serum, 5% yeast extract and H. pylori-selective antibiotic mix Dent. Liquid culture was grown in BHI broth (3,7% brain heart infusion with 10% inactivated Fetal Bovine Serum and 5% yeast extract). Both plates and broth cultures were incubated at 37C under atmosphere enriched with 5% CO2  for 2-3 days

extract_protocol: H.pylori cells were collected in 1.5-ml eppendorf tubes by washing of plates different times  with PBS buffer.  Total mRNA was isolated from two independent cultivations of each clone  and subsequently used for independent cDNA synthesis and hybridization. After centrifugation at  10000 g for  10 min, the pellet was resuspended in 300 ml of the Lysis/Binding solution supplied in the RNAqueous kit (Ambion Inc., Austin, Tex.). The total RNA was subsequently extracted according to the manufacturer’s recommendations. To remove all the genomic DNA, RNA was treated with DNase I (Promega, Madison, Wis.).) and RNasin (Promega, Madison, Wis.) for 20 min at 37°C. RNA concentration was quantitated by determination of the absorbance at 260 and 280 nm, and RNA integrity was verified by visualization on a 1% agarose gel.

treatment_protocol: Mutant strains were selected by culturing  H. pylori 26695 on selective plates containing 20 μg/ml of rifampicin. In 5 days resistant colonies were picked up and passed under rifampicin pressure.

tag: phenotype

value: Rifampicin resistant

tag: rpob mutation 1

tag: rpob mutation 2


title: HP 26695_Mutant 1_rep1


title: altai1

source_name: blood

tag: gender

value: Male

value: Siberia

value: blood


title: HP 26695_Mutant 1_rep3

source_name: HP 26695, Rif Resistant, clone1


title: HP 26695_Mutant 2_rep1

source_name: HP 26695, Rif Resistant, clone 2


title: HP 26695_Mutant 2_rep3


title: HP 26695_Mutant 2_rep2


title: ket2

tag: population

value: Kets


title: Caco2-BBE cells transfected with SPAK

city: Atlanta

first: Yutao

last: Yan

state: Georgia

address: 615 Michael St, WHB/265

department: Medicine

institute: Emory University

description: Gene expression data from Caco2-BBE cells transfected with SPAK, reps 1 and 2 merged.

hyb_protocol: Microarrays containing all oligonucleotides from the Compugen Human Release 2.0 OligoLibrary were resuspended in 150mMol phosphate buffer and arrayed by Microarrays Incorporated on amine-coated glass slides from Genexprex, crosslinked using 80mjoules of ultraviolet energy (Stratagene Stratalinker, LaJolla, CA), baked for two hours at 70C, and stored until use. After the addition of 1 ug of Poly A RNA (Sigma, P9403) the probes were hybridized to the arrays at 42ºC for 16 hours, and washed.

scan_protocol: The microarrays were scanned with a GenePix4000A scanner (Axon Instruments, Union City, CA).

data_processing: Any Cy3 or Cy5 fluorescence level below background or smaller than 60% of the original spotting area was defined as 'absent'. After normalization (Lowess using GeneSpring), all data was filtered to eliminate all data points that may not be reliable. This included flagged spots, lowly expressed spots, and spots with negative signal values. After filtering, the genes were chosen for further analysis on the basis of fold change of treated samples vs. controls (2 and higher up- or down-regulation) in 2 or 3 experiments with P value of <0.05. The data in the VALUE column is expressed as the natural log of the ch1/ch2 ratios.

source_name: Caco2-BBE cells

label_protocol: Total RNA from transfected Caco2-BBE cells were pooled together. 20 µg of total RNA was combined with 5X 1st Strand Buffer, 1 µg Oligo dT20mer, 0.1M DTT (Gibco Invitrogen, Carlsbad, CA), low dTTP/dNTP mix (Amersham Biosciences, Piscataway, NJ), RNasin (Promega Biosciences, San Luis Obispo, CA), and Cyanine 5-dUTP (PerkinElmer, Torrance, CA) in 500 µL tubes. The reactions were heated to 65ºC for 5 minutes and reverse transcribed with SuperScript II RNase H- Reverse Transcriptase (Gibco) at 42ºC for 90 min. Five µL of 0.5 M EDTA was added to stop the reaction and then the mixture was heated to 65ºC for 30 min with 10 µL of 1 M NaOH to hydrolyze the RNA, followed by the addition of 25 µL of 1 M Tris to neutralize the NaOH. The Cy-3 and Cy-5 labeled probes were combined and isolated by running through a Microcon YM-30 size-exclusion column (Millipore), washed with TE buffer, and resuspended in 11 µL of TE.

growth_protocol: Caco2-BBE cells transfected with SPAK or vector were maintained in 37oC incubator with CO2

tag: transfection

value: SPAK

source_name: Universal human reference RNA

label_protocol: Universal human reference RNA was combined with 5X 1st Strand Buffer, 1 µg Oligo dT20mer, 0.1M DTT (Gibco Invitrogen, Carlsbad, CA), low dTTP/dNTP mix (Amersham Biosciences, Piscataway, NJ), RNasin (Promega Biosciences, San Luis Obispo, CA), and Cyanine 3-dUTP (PerkinElmer, Torrance, CA) in 500 µL tubes. The reactions were heated to 65ºC for 5 minutes and reverse transcribed with SuperScript II RNase H- Reverse Transcriptase (Gibco) at 42ºC for 90 min. Five µL of 0.5 M EDTA was added to stop the reaction and then the mixture was heated to 65ºC for 30 min with 10 µL of 1 M NaOH to hydrolyze the RNA, followed by the addition of 25 µL of 1 M Tris to neutralize the NaOH. The Cy-3 and Cy-5 labeled probes were combined and isolated by running through a Microcon YM-30 size-exclusion column (Millipore), washed with TE buffer, and resuspended in 11 µL of TE.

tag: sample type

value: Universal human reference RNA


title: HP 26695_wild type_rep4

source_name: HP 26695, wild type

value: Rifampicin sensitive

value: wild-type

value: no


title: HP 26695_wild type_rep1


title: HP 26695_Mutant 2_rep4


title: HP 26695_wild type_rep2


title: HP 26695_wild type_rep3


title: evenk3

value: Female

value: Evenkis

tag: region

tag: tissue


title: selkup10

value: Selkups


title: selkup9


title: MSC - 24 months of age (sample #2)

hyb_protocol: hybridization has been performed using Tecan hybridization stations

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image analysis was then performed to quantify the signals on the arrays

data_processing: raw data have been normalized using the 'norm-exp' background correction

source_name: mesenchymal stem cells from inguinal fat pad of FVB mice of 24 months of age

label_protocol: RNA samples were Hy3 labeled. A common reference obtained by mixing equal amounts of samples 1 to 6 was Hy5 labeled.

extract_protocol: total RNA extracted using TRIZOL reagent (Invitrogen), following manifacturer's instructions. RNA samples were cleaned using the Rneasy kit (Qiagen) with slight modifications to preserve miRNAs. Basically, 350 ul Buffer RLT and 3.5 volumes of 100% ethanol were added to 50 ul of RNA sample, and the mixture was added to an RNeasy Mini spin column. After centrifugation, the column was washed twice with 500 ul buffer RPE, and the RNA was eluted with 30 ul RNase-free water.

value: FVB mice

tag: age

value: 24 months

source_name: common reference: mix of total RNA from samples 1 to 6


title: MSC - 3 months of age (sample #5)

source_name: mesenchymal stem cells from inguinal fat pad of FVB mice of 3 months of age

value: 3 months


title: MSC - 6 months of age (sample #7)

source_name: mesenchymal stem cells from inguinal fat pad of FVB mice of 6 months of age

value: 6 months


title: MSC - 3 months of age (sample #8)


title: MSC - 1 month of age (sample #8)

source_name: mesenchymal stem cells from inguinal fat pad of FVB mice of 1 month of age

value: 1 month


title: MSC - 12 months of age (sample #2/1)

source_name: mesenchymal stem cells from inguinal fat pad of FVB mice of 12 months of age

value: 12 months


title: HP 26695_Mutant 1_rep4

value: Rifampicin resistant


title: Caco2-BBE cells transfected with Vector

description: Gene expression data from Caco2-BBE cells transfected with Vector, reps 1 and 2 merged.

value: Vector


title: selkup7

value: Siberia

value: blood


title: selkup6

value: Male


title: MSC - 6 months of age (sample #6)


title: MSC - 1 month of age (sample #1)


title: selkup5


title: Liver_infected_9weeks_3

city: Herston

first: Melissa

middle: Louise

last: Burke

state: QLD

address: 300 Herston Road

department: Division of Infectious Diseases and Immunology

country: Australia

institute: Queensland Institute of Medical Research

description:
9wks88_F
Gene expression in the liver of CBA mice 9 weels post infection with Schistosoma japonicum

hyb_protocol: cRNA was hybridised to Illumina MouseWG-6 v2 expression beadchip arrays according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing:
Data was analysed using the GenomeStudio v1.1.1 and Genespring GX 11 programs
Values reported were derived using Illumina GenomeStudio v1.1.1 and represent relative signal intensity normalized to background, Genespring GX 11 was used to normalise each chip to the 50th percentile and each gene to the median and uninfected controls, measurements less than 0.01 were set to 0.01

source_name: Liver homogenate, infected, 9 weeks

label_protocol: cRNA was synthesised from 100ng of total RNA from each individual mouse with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

extract_protocol: Total RNA was extracted from liver tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Mice were euthanized and liver tissue was collected and stored in RNAlater for microarray analysis

value: CBA

value: 6 weeks

value: Liver

value: infection with 12 cercariae

tag: time

value: 9 weeks post infection


title: Liver_infected_9weeks_4

description:
9wks61_D
Gene expression in the liver of BALB/c mice 9 weeks post infection with Schistosoma japonicum

value: BALB/c

value: Female


title: MSC - 12 months of age (sample #1.4)

value: FVB mice


title: Liver_infected_9weeks_1

description:
9wks69_F
Gene expression in the liver of BALB/c mice 9 weeks post infection with Schistosoma japonicum


title: Liver_infected_9weeks_6

description:
9wks56_E
Gene expression in the liver of BALB/c mice 9 weeks post infection with Schistosoma japonicum


title: lung of rat

description: compare gene expression profiles of control lung and infected lung in rat

value: Wistar

value: male

value: lung

value: Schistosoma japonicum


title: selkup8

value: Selkups


title: selkup3


title: Liver_infected_7weeks_4

description:
7wks61_C
Gene expression in the liver of BALB/c mice 7 weeks post infection with Schistosoma japonicum

source_name: Liver homogenate, infected, 7 weeks

value: 7 weeks post infection


title: Liver_infected_7weeks_5

description:
7wks56_C
Gene expression in the liver of CBA mice 7 weeks post infection with Schistosoma japonicum


title: Liver_infected_7weeks_3

description:
7wks88_D
Gene expression in the liver of BALB/c mice 7 weeks post infection with Schistosoma japonicum


title: Liver_infected_4weeks_4

description:
4wks61_B
Gene expression in the liver of BALB/c mice 4 weeks post infection with Schistosoma japonicum

source_name: Liver homogenate, infected, 4 weeks

value: 4 weeks post infection


title: liver of mouse

description: compare gene expression profiles of control liver and infected liver in mouse

source_name: hepatocyte

value: liver


title: Liver_infected_4weeks_3

description:
4wks88_C
Gene expression in the liver of BALB/c mice 4 weeks post infection with Schistosoma japonicum


title: lung of mouse

description: compare gene expression profiles of control lung and infected lung in mouse

source_name: pneumonocyte


title: Liver_infected_4weeks_5

description:
4wks56_B
Gene expression in the liver of CBA mice 4 weeks post infection with Schistosoma japonicum


title: Liver_infected_7weeks_2

description:
7wks69_E
Gene expression in the liver of CBA mice 7 weeks post infection with Schistosoma japonicum


title: Liver_infected_7weeks_6

description:
7wks56_D
Gene expression in the liver of CBA mice 7 weeks post infection with Schistosoma japonicum


title: Liver_infected_9weeks_5

description:
9wks61_E
Gene expression in the liver of CBA mice 9 weels post infection with Schistosoma japonicum


title: Liver_infected_4weeks_2

description:
4wks69_C
Gene expression in the liver of CBA mice 4 weeks post infection with Schistosoma japonicum


title: Liver_uninfected_control_6

description:
Uninfected56_A
Gene expression in the liver of normal CBA mice

source_name: Liver homogenate, uninfected

value: Uninfected

value: control


title: Liver_infected_4weeks_1

description:
4wks69_B
Gene expression in the liver of BALB/c mice 4 weeks post infection with Schistosoma japonicum

value: 6 weeks


title: selkup2

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

source_name: blood

value: Siberia

value: blood


title: Liver_uninfected_control_4

description:
Uninfected61_A
Gene expression in the liver of normal BALB/c mice

value: Liver


title: Liver_uninfected_control_3

description:
Uninfected88_B
Gene expression in the liver of normal CBA mice

value: CBA


title: Liver_uninfected_control_5

description:
Uninfected61_F
Gene expression in the liver of normal CBA mice

value: Female


title: DeltaSpxBAckAWalK_vsWT_rep1

status: Public on Nov 29 2010

city: Bloomington

first: Krystyna

middle: M

last: Kazmierczak

state: IN

address: 1001 E. Third St.

institute: Indiana University

description: Independent biological replicate

hyb_protocol: Fluorescently-labeled cDNAs were resuspended in the manufacturer's salt-based hybridization buffer. Samples were heated for 3 min at 95C, chilled on ice for 3 min, and applied to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed for 5 min in prewarmed (30C) buffers. Buffer 1: 2X SSC, 0.1% SDS; Buffer 2: 1X SSC; Buffer 3: 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635 nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio ~ 1.0). Images were analyzed using GenePix Pro 6.0 software (Molecular Devices).

data_processing: Data were analyzed using software from the TM4 Microarray Software Suite (www.tm4.org). GenePix results files (.gpr) were converted to TIGR MultiExperiment Viewer file format (.mev) using ExpressConverter 2.1 software. Lowess (block) normalization was performed on non-background subtracted data using TIGR MIDAS 2.21 software.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae D39 rpsL1 (Winkler lab strain IU1781)

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer's recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.1

extract_protocol: Total RNA was extracted at OD620~0.1 using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification (RNAeasy mini kit, Qiagen) as described in Robertson et al., J Bact (2002) 184:3508-3520

treatment_protocol: No treatment

tag: serotype

value: Virulent, capsule-producing serotype 2

tag: genotype/variation

value: transformed with the rpsL1 allele conferring streptomycin resistance

source_name: S. pneumoniae D39 rpsL1 delta spxB delta ackA walK::Janus (Winkler lab strain IU4319)

value: virulent, capsule-producing serotype 2

value: the spxb (spd_0636; pyruvate oxidase) and acka (spd_1853; acetate kinase) genes were deleted and the walk gene (spd_1084; histidine kinase) was disrupted using the janus [kanr-rpsl+] cassette described in sung et al., appl environ microbiol (2001) 67:5190-5196


title: altai2

value: Male

value: Altaians


title: DeltaSpxBAckA_vsWT_rep2

description: Independent biological replicate, dye swap

source_name: S. pneumoniae D39 rpsL1 delta spxB delta ackA (Winkler lab strain IU3590)

value: the spxB (SPD_0636; pyruvate oxidase) and ackA (SPD_1853; acetate kinase) genes were deleted


title: DeltaSpxBAckA_vsWT_rep1

description: Independent biological replicate


title: Liver_uninfected_control_1

description:
Uninfected69_A
Gene expression in the liver of normal BALB/c mice

value: BALB/c


title: Liver_uninfected_control_2

description:
Uninfected88_A
Gene expression in the liver of normal BALB/c mice


title: DeltaSpxBPtaAckAWalK_vsWT_rep1

description: Independent biological replicate

source_name: S. pneumoniae D39 rpsL1 delta spxB delta pta delta ackA walK::Janus (Winkler lab strain IU3107)

value: the spxb (spd_0636; pyruvate oxidase), pta (spd_0985; phosphate acetyltransferase), and acka (spd_1853; acetate kinase) genes were deleted and the walk gene (spd_1084; histidine kinase) was disrupted using the janus [kanr-rpsl+] cassette described in sung et al., appl environ microbiol (2001) 67:5190-5196


title: DeltaSpxBPtaAckAWalK_vsWT_rep2


title: DeltaSpxBPtaAckA_vsWT_rep4

source_name: S. pneumoniae D39 rpsL1 delta spxB delta pta delta ackA (Winkler lab strain IU2837)

value: the spxB (SPD_0636; pyruvate oxidase), pta (SPD_0985; phosphate acetyltransferase), and ackA (SPD_1853; acetate kinase) genes were deleted


title: Liver_infected_4weeks_6

description:
4wks56_F
Gene expression in the liver of CBA mice 4 weeks post infection with Schistosoma japonicum

value: infection with 12 cercariae

value: 4 weeks post infection


title: ket1

value: Kets

value: Siberia


title: DeltaSpxBPtaAckA_vsWT_rep2


title: selkup1

value: Selkups

value: blood


title: selkup4


title: DeltaSpxBPta_vsWT_rep2

source_name: S. pneumoniae D39 rpsL1 delta spxB delta pta (Winkler lab strain IU2689)

value: the spxB (SPD_0636; pyruvate oxidase) and pta (SPD_0985; phosphate acetyltransferase) genes were deleted


title: DeltaPta_vsWT_rep3

description: Independent biological replicate

value: Virulent, capsule-producing serotype 2

source_name: S. pneumoniae D39 rpsL1 delta pta (Winkler lab strain IU2687)

value: the pta gene (SPD_0985; phosphate acetyltransferase) was deleted


title: DeltaPta_vsWT_rep1

description: Independent biological replicate

value: transformed with the rpsL1 allele conferring streptomycin resistance


title: DeltaSpxBPta_vsWT_rep1

description: Independent biological replicate


title: WalK-Janus_vsWT_rep1

description: Independent biological replicate

source_name: S. pneumoniae D39 rpsL1 walK::Janus (Winkler lab strain IU1885)

value: virulent, capsule-producing serotype 2

value: the walk gene (spd_1084; histidine kinase) was disrupted using the janus [kanr-rpsl+] cassette described in sung et al., appl environ microbiol (2001) 67:5190-5196


title: DeltaPta_vsWT_rep2


title: DeltaSpxBPtaAckA_vsWT_rep3

description: Independent biological replicate


title: DeltaSpxBPtaAckA_vsWT_rep1

description: Independent biological replicate


title: WalK-Janus_vsWT_rep2


title: DeltaSpxB_vsWT_rep2

source_name: S. pneumoniae D39 rpsL1 delta spxB (Winkler lab strain IU2173)

value: the spxB gene (SPD_0636; pyruvate oxidase) was deleted


title: DeltaSpxB_vsWT_rep1

description: Independent biological replicate


title: Liver_infected_9weeks_2

description:
9wks88_E
Gene expression in the liver of CBA mice 9 weels post infection with Schistosoma japonicum

value: CBA

value: Female

value: 6 weeks

value: Liver

value: 9 weeks post infection


title: Phan_012_KO.bleomycin rep3

first: Tianju

last: Liu

state: Michigan

address: 109 Zina pitcher pl

department: Pathology

description: gene expression profile at day 21 after bleomycin endotracheal injection

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: bleomycin injected mouse lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

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

treatment_protocol: Bleomycin or saline was endotracheally injected into wild type and FIZZ2 knockout mice, then the lungs were purfused with PBS and harvested for total RNA isolation.

value: Lung

tag: agent

value: bleomycin

value: FIZZ2 knockout


title: Phan_007_KO.saline rep1

description: gene expression profile at day 21 after saline endotracheal injection

source_name: saline injected mouse lung

value: saline