title: Neuro_Krainc_P01_B10_L3293

description:
Neuro_Krainc_P01_B10_L3293.CEL
Whole blood gene expression from CONTROL patient.


title: Neuro_Krainc_P01_A03_L2123_RPT

status: Public on May 20 2017

type: RNA

city: Tel Aviv

first: David

last: Amar

address: Haim Levanon

department: Computer Science

country: Israel

institute: Tel Aviv University

description:
Neuro_Krainc_P01_A03_L2123_RPT.CEL
Whole blood gene expression from GPD patient.

hyb_protocol: Samples were processed according to manufacturer’s protocols.

data_processing: Data were preprocessed using RMA. Then the data were log2 transformed and quantile normalized. RMA was selected as it produced better patient correlations than MAS5 and GC-RMA.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol: We collected samples of venous blood using a standardized blood withdrawal protocol. PaxGene (Qiagen) and EDTA tubes were obtained. As participants were recruited at different time points, samples were frozen at -80° C first and RNA was extracted after patient recruitment at all centers was completed.

tag: tissue

value: whole blood

tag: disease label

value: GPD

tag: batch

tag: learning set

value: VALIDATION

tag: Sex

value: Male

tag: genetic (mutated pd genes)

tag: age at 1st symptoms

tag: updrs i

tag: updrs ii

tag: updrs iii score on

tag: updrs iii score off

tag: updrs iv

tag: hoehn & yahr (on)

tag: hoehn & yahr (off)

tag: moca score


title: E8R_012a41

description:
E8R_012a41_(HG-U133_Plus_2).CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.

scan_protocol: Samples were processed according to manufacturer’s protocols.


title: Neuro_Krainc_P01_A11_L2152_RPT

description:
Neuro_Krainc_P01_A11_L2152_RPT.CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.

label_protocol: Samples were processed according to manufacturer’s protocols.


title: Neuro_Krainc_P01_A12_L2153

description:
Neuro_Krainc_P01_A12_L2153.CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.


title: E8R_012a36

description:
E8R_012a36_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

value: IPD

value: TRAINING

value: Female


title: E8R_012a37

description:
E8R_012a37_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.

value: CONTROL


title: Neuro_Krainc_P01_A6_L2126

description:
Neuro_Krainc_P01_A6_L2126.CEL
Whole blood gene expression from GPD patient.


title: Neuro_Krainc_P01_B12_L3329

description:
Neuro_Krainc_P01_B12_L3329.CEL
Whole blood gene expression from CONTROL patient.


title: E8R_012a29

description:
E8R_012a29_(HG-U133_Plus_2).CEL
Whole blood gene expression from PSP patient.

value: PSP


title: E8R_012a26

description:
E8R_012a26_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a24

description:
E8R_012a24_(HG-U133_Plus_2).CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.


title: E8R_012a22

description:
E8R_012a22_(HG-U133_Plus_2).CEL
Whole blood gene expression from MSA patient.

value: MSA


title: E8R_012a30

description:
E8R_012a30_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a20

description:
E8R_012a20_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a21

description:
E8R_012a21_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E8R_012a33

description:
E8R_012a33_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a35

description:
E8R_012a35_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a34

description:
E8R_012a34_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E8R_012a23

description:
E8R_012a23_(HG-U133_Plus_2).CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.

value: ATP13A2+ LRRK2


title: E8R_012a11

description:
E8R_012a11_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a19

description:
E8R_012a19_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a25

description:
E8R_012a25_(HG-U133_Plus_2).CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.


title: E8R_012a06

description:
E8R_012a06_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E8R_012a18

description:
E8R_012a18_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a12

description:
E8R_012a12_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a09

description:
E8R_012a09_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a05

description:
E8R_012a05_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a16

description:
E8R_012a16_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a03

description:
E8R_012a03_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a17_2

description:
E8R_012a17_2_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a08

description:
E8R_012a08_(HG-U133_Plus_2).CEL
Whole blood gene expression from GPD patient.

value: PARKIN


title: E8R_012a14

description:
E8R_012a14_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a02

description:
E8R_012a02_(HG-U133_Plus_2).CEL
Whole blood gene expression from MSA patient.


title: E8R_012a01

description:
E8R_012a01_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a90

description:
E7R_039a90_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a92

description:
E7R_039a92_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a89

description:
E7R_039a89_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a95

description:
E7R_039a95_(HG-U133_Plus_2).CEL
Whole blood gene expression from GPD patient.


title: E7R_039a91

description:
E7R_039a91_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a07

description:
E8R_012a07_(HG-U133_Plus_2).CEL
Whole blood gene expression from GPD patient.


title: E7R_039a99

description:
E7R_039a99_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a98

description:
E7R_039a98_(HG-U133_Plus_2).CEL
Whole blood gene expression from GPD patient.


title: E7R_039a79

description:
E7R_039a79_(HG-U133_Plus_2).CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.


title: E7R_039a71

description:
E7R_039a71_(HG-U133_Plus_2)_2.CEL
Whole blood gene expression from GPD patient.


title: E7R_039a64

description:
E7R_039a64_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a60

description:
E7R_039a60_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a80

description:
E7R_039a80_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a81

description:
E7R_039a81_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a96

description:
E7R_039a96_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a87

description:
E7R_039a87_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a35

description:
E7R_039a35_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.

value: NMF


title: E7R_039a85

description:
E7R_039a85_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a20

description:
E7R_039a20_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a14

description:
E7R_039a14_(HG-U133_Plus_2)_2.CEL
Whole blood gene expression from IPD patient.


title: E7R_039a13

description:
E7R_039a13_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a82

description:
E7R_039a82_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E8R_012a31

description:
E8R_012a31_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a112

description:
E7R_039a112_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a72

description:
E7R_039a72_(HG-U133_Plus_2)_2.CEL
Whole blood gene expression from GPD patient.


title: E8R_012a04_2

description:
E8R_012a04_2_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a57

description:
E7R_039a57_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a94

description:
E7R_039a94_(HG-U133_Plus_2).CEL
Whole blood gene expression from PSP patient.


title: E7R_039a113

description:
E7R_039a113_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a23

description:
E7R_039a23_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a104

description:
E7R_039a104_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a108

description:
E7R_039a108_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a16

description:
E7R_039a16_(HG-U133_Plus_2).CEL
Whole blood gene expression from GPD patient.


title: E7R_039a30

description:
E7R_039a30_(HG-U133_Plus_2).CEL
Whole blood gene expression from GPD patient.


title: E7R_039a105

description:
E7R_039a105_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a103

description:
E7R_039a103_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: E7R_039a111

description:
E7R_039a111_(HG-U133_Plus_2).CEL
Whole blood gene expression from MSA patient.


title: E7R_039a63

description:
E7R_039a63_(HG-U133_Plus_2).CEL
Whole blood gene expression from Vascular dementia patient.

value: Vascular dementia


title: E7R_039a11

description:
E7R_039a11_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a34

description:
E7R_039a34_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a49

description:
E7R_039a49_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.


title: E7R_039a102

description:
E7R_039a102_(HG-U133_Plus_2).CEL
Whole blood gene expression from DRD patient.

value: DRD


title: E7R_039a69

description:
E7R_039a69_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.


title: H4R6 B43_rep3

city: Taichung

first: San

middle: Yuan

last: Huang

address: Kuo-Kuang Rd.

department: Animal science

country: Taiwan

institute: National Chung Hsing University

description: Gene expression at 6 h of recovery after acute heat stress

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent chicken V2 Oligo 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Gallus gallus

label_protocol: 1.65 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

extract_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

treatment_protocol: Hens were treated to acute heat stress (36℃) for 4 h, and recovered at 25℃ for 0, 2, and 6 h. Control goup was non-heat stressed chicken which stayed at 25℃.

value: Small yellow follicles

tag: strain

value: L2 strain Taiwan country chicken

tag: age

value: 30 wk

tag: stress

value: 6 h of recovery after acute heat stress


title: E7R_039a68

description:
E7R_039a68_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

tag: tissue

value: whole blood

tag: disease label


title: E7R_039a106

description:
E7R_039a106_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.

tag: batch

tag: learning set


title: H4R2 B44_rep3

description: Gene expression at 2 h of recovery after acute heat stress

value: 2 h of recovery after acute heat stress


title: H4R2 B35_rep2


title: E7R_039a18

description:
E7R_039a18_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.

tag: Sex

tag: genetic (mutated pd genes)


title: E7R_039a10

description:
E7R_039a10_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

value: IPD

value: Male

tag: age at 1st symptoms

tag: updrs i


title: E7R_039a09

description:
E7R_039a09_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

value: VALIDATION

tag: updrs ii

tag: updrs iii score on


title: H4R6 B33_rep2


title: E7R_039a109

description:
E7R_039a109_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

value: TRAINING

tag: updrs iii score off

tag: updrs iv


title: E7R_039a110

description:
E7R_039a110_(HG-U133_Plus_2).CEL
Whole blood gene expression from CBD patient.

value: CBD

value: Female

tag: hoehn & yahr (on)

tag: hoehn & yahr (off)


title: H4R6 B27_rep1

tag: strain


title: E7R_039a08

description:
E7R_039a08_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

tag: moca score


title: E7R_039a114

description:
E7R_039a114_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.

value: CONTROL


title: Control rep1

city: Suzhou

first: Jiajia

last: Chen

address: Kerui Road

country: China

institute: Suzhou University of Science and Technology

hyb_protocol: The chip contained unique probes of rice miRNAs from miRBase (version 19.0). Each probe was repeated twice on a microarray. A nonhomologous nucleotide acid PUC2MM-20B and rice 5S rRNA served as positive controls. Blank cells and other non-homologous nucleic acid probes served as negative controls. Hybridization was performed overnight on a single-channel mParaFlo microfluidic chip using a microcirculation pump (Atactic Technologies) at 34 °C. Hybridization buffer was 6×SSPE (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity.

organism: Oryza sativa

source_name: rice leaf_control

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

growth_protocol: Seeds of the rice cultivar Nipponbare were rinsed with distilled water and pre-germinated in moist filter paper for two days at 30°C in the dark, then transferred to standard soil and grown for 4 weeks.

extract_protocol: The leaf disks (6 mmϕ) were excised from the uppermost rice leaf blades of 4 week-old rice. Total RNA was isolated by using the mirVanaTM miRNA Isolation Kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s manual.

treatment_protocol: In the drought stressed group, four week old rice seedlings were exposed to simulated drought by treating with treated with 20% polyethylene glycol 6000 (PEG-6000) for 48h to simulate drought stress of -0.5 MPa osmotic potential. In the As stressed group, four week old rice seedlings were subjected to 10 mM As(III) solution (NaAsO2) and 50 mM As(V) solution (Na2HAsO4) for seven days. The control group were grown under normal condition without suffering drought or As stress.

tag: cultivar

value: Nipponbare

tag: age

value: 4 week-old

tag: sample group

value: untreated control

value: leaf


title: As stress rep3

source_name: rice leaf_As stressed_7 days

value: As stressed for 7 days

tag: tissue


title: Drought rep3

source_name: rice leaf_dehyrated_48h

value: PEG dehydration for 48 hrs


title: H4R2 B23_rep1

value: Small yellow follicles

value: L2 strain Taiwan country chicken

value: 30 wk

tag: stress


title: Control rep2


title: E7R_039a04

description:
E7R_039a04_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.

value: whole blood

tag: disease label

tag: batch

tag: learning set

tag: Sex


title: As stress rep2


title: Drought rep2


title: E7R_039a07

description:
E7R_039a07_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

value: IPD

tag: genetic (mutated pd genes)

tag: age at 1st symptoms

tag: updrs i

tag: updrs ii


title: E7R_039a03

description:
E7R_039a03_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

tag: updrs iii score on

tag: updrs iii score off

tag: updrs iv

tag: hoehn & yahr (on)


title: As stress rep1

tag: cultivar


title: H4R0 B45_rep3

description: Gene expression at 0 h of recovery after acute heat stress

tag: strain

tag: age

value: 0 h of recovery after acute heat stress


title: E7R_039a05

description:
E7R_039a05_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

tag: tissue

tag: hoehn & yahr (off)

tag: moca score


title: H4R0 B22_rep1

tag: stress


title: E7R_039a01

description:
E7R_039a01_(HG-U133_Plus_2).CEL
Whole blood gene expression from CONTROL patient.

tag: disease label

tag: batch

tag: learning set


title: E7R_039a02

description:
E7R_039a02_(HG-U133_Plus_2).CEL
Whole blood gene expression from IPD patient.

tag: Sex

value: Male

tag: genetic (mutated pd genes)

tag: age at 1st symptoms


title: Control rep3

tag: sample group


title: CTL A51_rep2

description: Gene expression without heat stress

source_name: CTL A51

value: without heat stress


title: Apc1-/- midgut sample 1

status: Public on May 19 2017

city: Glasgow

first: Julia

last: Cordero

address: Garscube Estate. Switchback Road

country: United Kingdom

institute: University of Glasgow

description: Apc 1

hyb_protocol: Microarray hybridization was done following the protocol publish for the corresponding Affymetrix array. https://tools.thermofisher.com/content/sfs/manuals/expression_analysis_technical_manual.pdf

scan_protocol: Microarray scanning was done following the protocol publish for the corresponding Affymetrix array. https://tools.thermofisher.com/content/sfs/manuals/expression_analysis_technical_manual.pdf

data_processing: Data is Analysed using the Microarray Suite Expression Analysis window. CEL files were subject to RMA normalization and log2 transformation followed by differential gene expression analysis using Anova. All p-values were corrected for multiple testing using Bonferroni.

organism: Drosophila melanogaster

source_name: Apc1-/- midgut

label_protocol: Biotin labeling was done following the protocol publish for the corresponding Affymetrix array. https://tools.thermofisher.com/content/sfs/manuals/expression_analysis_technical_manual.pdf

growth_protocol: Parental lines were maintained at room temperature. Adult wild type and Apc1-/- females where aged for seven days after eclosion at 25ºC. This was followed by whole midgut dissections.

extract_protocol: RNA extraction was done with Trizol and following manufacturer's instructions.

tag: genotype/variation

tag: gender

value: female

value: 7 day old; adult

value: whole adult midguts


title: CTL A43_rep3

description: Gene expression without heat stress

source_name: CTL A43


title: Apc1-/- midgut sample 3

description: Apc 3

treatment_protocol: Adult wild type and Apc1-/- females where aged for seven days after eclosion at 25ºC.


title: wild type midguts- sample  3

description: Con 3

source_name: wild type midgut

value: wild type


title: Apc1-/- midgut sample 2

description: Apc 2


title: Drought rep1

value: Nipponbare

value: 4 week-old


title: CTL A50_rep1

description: Gene expression without heat stress

source_name: CTL A50


title: SFV_RDR_3

city: Liverpool

first: Bahram

last: Ebrahimi

address: Crown Street

institute: Liverpool University

description: Gene expression data from NIH/3T3 cells infected with mutant  SFV-RDR at MOI=10

hyb_protocol: Following labelling and fragmentation, 10ug of aRNA was hybridised for 16 hours at 450C on GeneChip Mouse Genome 430 2.0 arrays in the GeneChip hybridisation oven 640. The arrays were washed and stained using the GeneChip Hybridisation wash and stain kit on the Affymetrix Fluidics station 450 using protocol FS450_0001

scan_protocol: Genechips were scanned using the Affymetrix GeneChip scanner 3000 or 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and displayed using Genespring GXv10.0 (Agilent Technologies).

label: Biotin

organism: Mus musculus

source_name: Mutant RDR virus infection 3

label_protocol: Biotinylated aRNA was prepared according to standard Affymetrix protocols from either 4ug total RNA (GeneChip One-Cycle Target Labelling kit) or 100ng total RNA (GeneChip 3'IVT Express kit)

growth_protocol: Murine NIH/3T3 cells were grown in DMEM (Sigma)containing 10% FBS (Pierce), 2% anti-mycotic/anti-biotic (Sigma), 1% penicillin/streptomycin (Sigma) and 1% non-essential amino acids (Sigma)

extract_protocol: At 8 hours post-infection, NIH/3T3 cells were trysenized and total RNA extracted using an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: NIH/3T3 cells  were grown in  DMEM (Sigma) containing 10% FBS (Pierce), 2% anti-mycotic/anti-biotic (Sigma), 1% penicillin/streptomycin (Sigma) and 1% non-essential amino acids (Sigma) and either mock-infected (no virus) or infected with either Infectious SFV4 (SFV) and SFV-RDR mutant viruses at MOI of 10 anf for 8 hours.

tag: cell line

tag: agent

value: SFV_RDR mutant virus


title: SFV_RDR_2

source_name: Mutant RDR virus infection 2


title: SFV_2

description: Gene expression data from NIH/3T3 cells infected with wildtype SFV4 (SFV) at MOI=10

source_name: Wild type virus infection 2

value: SFV4 (SFV) wildtype virus


title: wild type midguts- sample  1

description: Con 1


title: SRM11-Log phase-Rep 3

city: Istanbul

first: Zeynep

middle: Petek

last: Cakar

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression in the log phase of cell growth

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 h at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed using Feature Extraction Software 9.1 (Agilent) with default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Long-lived Saccharomyces cerevisiae, log. Phase, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 200 ng RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked using the NanoDrop-2000 spectrophotometer.

growth_protocol: Precultures of SRM11 and reference strain were prepared in yeast minimal medium (2% glucose and 0.67% yeast nitrogen base without amino acids (Difco)), and incubated at 30°C and 150 rpm for ~ 16 h. Precultures were then inoculated in triplicate into fresh yeast minimal medium, to an initial OD600 of 0.1. Cultures were incubated at 30°C and 150 rpm. When the culture OD600 values reached 1.0,  cells were harvested and total RNA extraction was done.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit (QIAGEN), according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality (RNA Integrity Number-RIN) was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: There is no treatment protocol in this study

tag: background strain

value: CEN.PK 113.7D (MATa)


title: Control_2

description: Gene expression data from NIH/3T3 cells mock-infected

source_name: Mock infection 2

value: Control


title: SRM11-Log phase-Rep 2

source_name: Long-lived Saccharomyces cerevisiae, log. Phase, replicate 2


title: SFV_3

source_name: Wild type virus infection 3


title: SFV_RDR_1

source_name: Mutant RDR virus infection 1


title: SRM11-Log phase-Rep 1

source_name: Long-lived Saccharomyces cerevisiae, log. Phase, replicate 1


title: SFV_1

source_name: Wild type virus infection 1


title: Control_1

source_name: Mock infection 1


title: epididymal fat, HFn-6 GC+, biological rep1

city: fort collins

first: Jessica

middle: Lynn

last: Hill

state: colorado

address: 502 west lake street

department: Food Science and Human Nutrition

country: USA

institute: Colorado State University

description: RMA expression value derived from Expression Console software

hyb_protocol: Following fragmentation, 3.5 ug of labled ss-DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G system, and following the manufactureres instructions (Affymetrix).

data_processing: Raw data were processed with the GeneChip Command Console software (affymetrix) and Expression Console software (Affymetrix) for background correction and normalization (RMA method). Data analaysis and statistical evaluations were performed with Partek Genomics Suite 6.6 software (Partek).

source_name: epididymal adipose tissue, high fat n-6 rich diet, with prednisolone

label_protocol: Biotinylated cDNA, with Affymetrix DNA labeling reagent, were prepared according to the Affymetrix protocol from 5.5 ug  of ss-cDNA [from 100 ng of total RNA] (GeneChip WT plus reagent kit manual for WT expression arrays, 2013-2015, Affymetrix).

growth_protocol: Breeder pairs obtained (Envigo Labratories, Inc.), mice then bred and housed in a conventional animal facility at the University of Memphis. Starting at 3 wk of age, male progeny mice were placed into individual cages and weaned onto n-6 rich high fat (45% Kcal) diet. Mice had access to food and water ad libitum. Mice were sacrificed by CO2 inhilation at 10 wk of age (point of epididymal fat extraction).

extract_protocol: QIAzol lysis reagant (Qiagen) and RNeasy Lipid Tissue Mini Kit (Qiagen) extraction of total RNA from epididymal adipose tissue was performed according to the manufacturer's instructions.

treatment_protocol: At 6 wk of age, male mice fed the n-6 rich high fat (HFn-6) diet ad libitum started receiving either the glucocorticoid Prednisolone (40mg/kg/m^2) daily (GC+) using sweet potate puree as the vehicle or just the sweet potate puree (GC-). Mice were maintained on the HFn-6 diet as either GC+ or GC- for a total of 4 wk, and then sacrificed when 10 wk of age. Aproxamitly 0.5 mg aliqoutes of adipose tissue were harvested from the left epididymal fat pad, snap frozen in liquid nitrogen, and stored at -80C until time for total RNA extraction.

tag: strain

value: epididymal adipose tissue

value: male


title: epididymal fat, HFn-6 GC-, biological rep2

source_name: epididymal adipose tissue, high fat n-6 rich diet, without prednisolone

tag: tissue


title: epididymal fat, HFn-6 GC-, biological rep1


title: epididymal fat, HFn-6 GC+, biological rep4


title: epididymal fat, HFn-6 GC+, biological rep2


title: Liver, Female HCFD Ikbkb-deleted in hepatocyte

status: Public on May 18 2017

city: Los Angeles

first: Hidekazu

last: Tsukamoto

state: CA

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol in an Affymetrix GeneChip Hybridization Oven 640. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data were analyzed with Affymetrix Expression Console using Robust Multichip Average (RMA) using Affymetrix default analysis settings.

label_protocol: Ambion WT Expression Kit was used to generate ssDNA targets. Fragmentation and biotin labeling were performed using the Affymetrix WT Terminal Labeling and Hybridization Kit.

extract_protocol: Total RNA was extracted from liver using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

value: liver

value: Ikbkb-deleted


title: epididymal fat, HFn-6 GC+, biological rep3


title: Liver, Female HCFD Wildtype

source_name: Liver, Female HCFD Wildtype


title: wild type midguts- sample  2

description: Con 2

tag: age


title: epididymal fat, HFn-6 GC-, biological rep3


title: Liver, Male HCFD Wildtype

source_name: Liver, Male HCFD Wildtype


title: IL10_hNSCs

city: Seoul

first: Mira

last: Cho

address: Yonsei-ro 50, GS Caltex Research hall 206

department: Chemical and Biomolecular Engineering

country: South Korea

institute: Yonsei Univeristy

description: Gene expression data from AAV r3.45 IL10 infected human neural stem cells

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: homo sapiens

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit  The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: human neural stem cells were cultured in DMEM/F12 supplemented with N-2 (1% (v/v); Thermo Fisher Scientific), 8 μg/mL heparin (Sigma-Aldrich, St. Louis, MO, USA), 20 ng/mL fibroblast growth factor-2 (FGF-2; R&D Systems, Minneapolis, MN, USA), 10 ng/mL leukemia inhibitory factor (LIF; Chemicon, Temecula, CA, USA), and 2% P/S at 37°C and 6.5% CO2.

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

treatment_protocol: human neural stem cells were infected by AAV r3.45-NT(no transgene) with multiplicity of infection 5000

value: telencephalon

value: 13 weeks of gestation

tag: treatment

value: AAV r3.45 IL10 infected


title: epididymal fat, HFn-6 GC-, biological rep4


title: hNSCs_NC

description: Gene expression data from normal human neural stem cells

value: normal


title: Liver, Male HCFD Ikbkb-deleted in hepatocyte


title: Control_3

source_name: Mock infection 3


title: thymospheres

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

institute: Weizmann Institute

description: Gene expression data from sorted MHC-II mTEC isolated from WT mice

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mo1ST. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Raw data were processed with the RMA algorithm for probe-level normalization and analyzed using GenePattern software

source_name: thymospheres

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

growth_protocol: Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2.

treatment_protocol: Thymi were surgically removed from mice and placed into cold 1× PBS supplemented with 2% Fetal Bovine Serum (FBS, Invitrogen). Thymi were trimmed of fat and connective tissues, chopped into small pieces and then disintegrated by sequential enzymatic digestion using Collagenase D (Roche #1088858) and Collagenase-Dispase cocktail (Roche #269638). Thymic stroma, containing the TEC fraction, was enriched using a Percoll gradient (Sigma #P1644) and was subjected to staining with anti CD45 beads. Cells were then enriched by MACS columns, and grown in specific culture medium untill collection for RNA extraction.

tag: genotype

value: WT


title: 1990-M1

city: GUANGZHOU

first: LIANG

middle: JIAN

last: KAI

state: GUANGDONG

address: NO.74 ZHONGSHAN NO.2 ROAD YUEXIU DISTRICT

department: PHARMACOLOGY

institute: SUN YAT-SEN UNIVERSITY

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

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

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

source_name: SW1990_M1 infected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: DMEM added with 10%FBS

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Mock infected or infected with M1 virus

tag: cell type

value: pancreatic cancer cell line

tag: infected with

value: M1 virus


title: H4R0 B28_rep2

value: Small yellow follicles

value: L2 strain Taiwan country chicken

value: 30 wk

tag: stress

value: 0 h of recovery after acute heat stress


title: rat_mia_day2_rep6

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description: replicate 6

hyb_protocol: Affymetrix GeneChip™ hybridization protocol

scan_protocol: Affymetrix GeneChip™ scanning protocol

data_processing: The data were processed using rma() function implemented in the oligo R package (v. 1.36.1) with default parameters (background correction and quantile normalization)

organism: Rattus norvegicus

source_name: rat mia day2 rep6

label_protocol: DNA was labeled using Affymetrix GeneChip™ labeling protocol

extract_protocol: RNA was isolated following the manufacturer’s protocol and further purified using the RNeasy Mini Kit (Qiagen Inc.). The total RNA concentration was measured using an ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

tag: day

value: monosodium iodoacetate (MIA)

tag: animal


title: rat_nai_day28_rep2

description: replicate 2

source_name: rat nai day28 rep2

value: naive


title: human neural stem cell_normal

source_name: human neural stem cells

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit


title: rat_mia_day21_rep6

description: replicate 6

source_name: rat mia day21 rep6


title: rat_mia_day0_rep6

description: replicate 6

source_name: rat mia day0 rep6


title: rat_mia_day14_rep2

description: replicate 2

source_name: rat mia day14 rep2


title: rat_nai_day28_rep4

description: replicate 4

source_name: rat nai day28 rep4


title: human neural stem cell_AAV infected

description: Gene expression data from AAV r3.45 infected human neural stem cells

value: infected by AAV r3.45


title: rat_mia_day2_rep3

description: replicate 3

source_name: rat mia day2 rep3


title: rat_mia_day28_rep4

description: replicate 4

source_name: rat mia day28 rep4


title: 1990-con

value: none (control)


title: rat_nai_day21_rep1

description: replicate 1

source_name: rat nai day21 rep1


title: rat_nai_day14_rep2

description: replicate 2

source_name: rat nai day14 rep2


title: rat_mia_day0_rep5

description: replicate 5

source_name: rat mia day0 rep5


title: rat_nai_day21_rep4

description: replicate 4

source_name: rat nai day21 rep4


title: rat_mia_day14_rep1

description: replicate 1

source_name: rat mia day14 rep1


title: rat_mia_day2_rep5

description: replicate 5

source_name: rat mia day2 rep5


title: rat_nai_day0_rep4

description: replicate 4

source_name: rat nai day0 rep4


title: rat_mia_day21_rep1

description: replicate 1

source_name: rat mia day21 rep1


title: rat_mia_day28_rep2

description: replicate 2

source_name: rat mia day28 rep2


title: rat_nai_day21_rep3

description: replicate 3

source_name: rat nai day21 rep3


title: rat_mia_day28_rep3

description: replicate 3

source_name: rat mia day28 rep3


title: rat_nai_day14_rep1

description: replicate 1

source_name: rat nai day14 rep1


title: rat_mia_day14_rep5

description: replicate 5

source_name: rat mia day14 rep5


title: rat_nai_day0_rep3

description: replicate 3

source_name: rat nai day0 rep3


title: rat_mia_day0_rep4

description: replicate 4

source_name: rat mia day0 rep4


title: rat_mia_day2_rep2

description: replicate 2

source_name: rat mia day2 rep2


title: rat_nai_day2_rep4

description: replicate 4

source_name: rat nai day2 rep4


title: rat_nai_day14_rep3

description: replicate 3

source_name: rat nai day14 rep3


title: rat_mia_day28_rep6

description: replicate 6

source_name: rat mia day28 rep6


title: rat_nai_day0_rep2

description: replicate 2

source_name: rat nai day0 rep2


title: rat_mia_day14_rep4

description: replicate 4

source_name: rat mia day14 rep4


title: rat_mia_day21_rep5

description: replicate 5

source_name: rat mia day21 rep5


title: rat_nai_day2_rep1

description: replicate 1

source_name: rat nai day2 rep1


title: rat_mia_day2_rep4

description: replicate 4

source_name: rat mia day2 rep4


title: rat_mia_day0_rep3

description: replicate 3

source_name: rat mia day0 rep3


title: rat_mia_day21_rep4

description: replicate 4

source_name: rat mia day21 rep4


title: rat_nai_day14_rep4

description: replicate 4

source_name: rat nai day14 rep4


title: rat_mia_day28_rep5

description: replicate 5

source_name: rat mia day28 rep5


title: rat_nai_day28_rep1

description: replicate 1

source_name: rat nai day28 rep1


title: rat_nai_day2_rep3

description: replicate 3

source_name: rat nai day2 rep3


title: rat_nai_day21_rep2

description: replicate 2

source_name: rat nai day21 rep2


title: rat_nai_day28_rep3

description: replicate 3

source_name: rat nai day28 rep3


title: rat_mia_day0_rep2

description: replicate 2

source_name: rat mia day0 rep2


title: rat_nai_day2_rep2

description: replicate 2

source_name: rat nai day2 rep2


title: rat_mia_day21_rep3

description: replicate 3

source_name: rat mia day21 rep3


title: GB0893_GFPN-rep2

status: Public on May 17 2017

type: SRA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

description: bPPI-seq

library_source: transcriptomic

data_processing:
library strategy: bait Protein-Protein Interaction-sequencing (bPPI-seq)
Basecalls performed using RTA 1.7 or Illumina Casava1.7
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed for further analysis in each library.
Filtered reads that are mapped in the last exons
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plan text file. Each line is a read. The six columns are chrom, start position, end position, fragment size, index, strand direction

source_name: NIH/3T3 tet-on 3G cells_expressing GFPN alone

extract_protocol:
Total RNAs of sorted cells were extracted using QIAzol (Qiagen) and purified with miRNeasy micro kit (Qiagen) and DNase set (Qiagen). Purified RNAs were reverse transcribed using PrimeScript Reverse Transcriptase (Takara) with an oligo dT primer. The cDNAs were amplified by VNC-specific and T7 primers and fragmented to 200 to 500bp by sonication. The DNA ends were repaired using End-It DNA End-repair Kit (Epicentre), followed by treatment with Klenow Fragment exo- (New England Biolabs) to generate a protruding 3’A base used for adaptor ligation. Following ligation of a pair of top-Phops-oligo-17bp/T7MmeI-18bp adaptors, the fragments between 250-650bp were isolated from agarose gel. Then the DNA was amplified by MmeI-SD1/2/3 and T7 primers to add an MmeI recognition site at both ends, followed by digestion with MmeI (New England Biolabs).
After treatment with Klenow Enzyme (New England Biolabs), indexed libraries were prepared with a Multiplexing Sample Preparation Oligonucleotide Kit (Illumina) according to the user's manual. The fragments between 250-500bp were idolated for sequencing on an Illumina next generation sequencing platform.

tag: cell line origin

value: NIH/3T3 tet-on 3G cells

value: expressing GFPN alone

tag: facs population

value: GFP-positive cells


title: GB0892_GFPN-rep1

description: bPPI-seq

tag: genotype/variation


title: GB0888_H2AZ-rep2

description: bPPI-seq

source_name: NIH/3T3 tet-on 3G cells_expressing GFPN-H2A.Z

value: expressing GFPN-H2A.Z


title: rat_mia_day2_rep1

description: replicate 1

source_name: rat mia day2 rep1


title: GB0887_H2AZ-rep1

description: bPPI-seq


title: rat_nai_day0_rep1

description: replicate 1

source_name: rat nai day0 rep1


title: GB0881_H2A-rep1

description: bPPI-seq

source_name: NIH/3T3 tet-on 3G cells_expressing GFPN-H2A

value: expressing GFPN-H2A


title: rat_mia_day0_rep1

description: replicate 1

source_name: rat mia day0 rep1


title: rat_mia_day14_rep3

description: replicate 3

source_name: rat mia day14 rep3


title: rat_mia_day14_rep6

description: replicate 6

source_name: rat mia day14 rep6


title: NP 34w

city: Fukuoka

first: Takako

last: Ohmaru

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Gynecology and Obstetrics

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

description: Gene expression

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: fibroblast, normal pregnancy, 34w

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was purified with the RNeasy Mini Kit (QIAGEN).

value: placenta

value: fibroblast

tag: gender

value: female

tag: diagnosis

value: normal pregnancy

tag: gestational age (weeks)


title: GB0883_H2A-rep2

description: bPPI-seq

tag: cell line


title: PE 37w

description: Gene expression

source_name: fibroblast, preeclampsia, 37w

value: preeclampsia


title: PE 25w

description: Gene expression

source_name: fibroblast, preeclampsia, 25w


title: NP 38w

description: Gene expression

source_name: fibroblast, normal pregnancy, 38w


title: PE 29w

description: Gene expression

source_name: fibroblast, preeclampsia, 29w


title: PE 40w

description: Gene expression

source_name: fibroblast, preeclampsia, 40w


title: NP 32w

description: Gene expression

source_name: fibroblast, normal pregnancy, 32w


title: rat_mia_day21_rep2

description: replicate 2

source_name: rat mia day21 rep2


title: Intima-media ascending aorta, miRNA, transplant donor, rep5

city: Saitama

first: Naoyuki

last: Kimura

state: Saitama

address: 1-847, Amanuma, Omiya-ku

department: Cardovascular Surgery

institute: Saitama Medical Center, Jichi Medical University

description: miRNA expression of healthy aorta

hyb_protocol: The Labeled cRNA was hybridized using miRNA complete Labeling and Hyb kit (Agilent) according to the manufacturer’s protocol. Briefly, Cy3-labelled RNA samples were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. 45ul of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human miRNA 8X60K, V16.0 Microarrays (G4870A Agilent Technologies) and then rotated at 20 rpm at 55°C for 20 hr.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C, Agilent Technologies) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) with default settings. Raw data were normalized by 90th percentile algorithm, Gene Spring Software 12.5 (Agilent Technologies).

source_name: Intima-media ascending aorta, donor

label_protocol: Total RNA (100 ng) was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase, denatured by DMSO at 100°C for 5 min, and labeled with pCp-Cy3 in the Ligation Master Mix at 16°C for 2 hr. The labeled RNA was purified using Micro Bio-Spin 6 columns (Bio-Rad) and the desalted samples were completely dried up in a vacuum concentrator with heater at 55°C for 55 min to remove DMSO.

extract_protocol: Frozen tissue specimens were homogenized, and total RNA, including miRNA, was extracted with an miRNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer’s instructions.

treatment_protocol: Specimens of aortic tissue were obtained from both study groups. The aortic dissection of all ATAAD patients extended along the entire ascending aorta, and all specimens of dissected aorta were obtained intraoperatively from the mid-portion of the ascending aorta. These specimens were 1.5 to 2.0 cm in diameter. None of the specimens collected were of intact aorta. Specimens obtained from the control group were also 1.5 to 2.0 cm in diameter and from the mid-portion of the ascending aorta.

value: healthy aorta

value: male


title: Intima-media ascending aorta, miRNA, transplant donor, rep3

description: miRNA expression of healthy aorta


title: Intima-media ascending aorta, miRNA, transplant donor, rep4

description: miRNA expression of healthy aorta


title: Intima-media ascending aorta, miRNA, transplant donor, rep2

description: miRNA expression of healthy aorta


title: rat_mia_day28_rep1

description: replicate 1

source_name: rat mia day28 rep1


title: Intima-media ascending aorta, miRNA, ATAAD, rep5

description: miRNA expression of dissected aorta

source_name: Intima-media ascending aorta, ataad patient

value: dissected aorta


title: Intima-media ascending aorta, miRNA, transplant donor, rep1

description: miRNA expression of healthy aorta


title: Intima-media ascending aorta, miRNA, ATAAD, rep4

description: miRNA expression of dissected aorta


title: Intima-media ascending aorta, miRNA, ATAAD, rep6

description: miRNA expression of dissected aorta


title: Intima-media ascending aorta, miRNA, ATAAD, rep3

description: miRNA expression of dissected aorta


title: UCN 34 159.13 collagen

city: Bad Oeynhausen

first: Imke

last: Grimm

address: Georgstraße 11

department: Institut für Laboratoriums- und Transfusionsmedizin

country: Germany

institute: Herz- und Diabeteszentrum NRW; Universitätsklinikum der Ruhr-Universität Bochum

description: SAMPLE 6

hyb_protocol: The Hybridization was also carried out with the Quick Amp WT Labeling Kit, one-color (Agilent, Santa Clara, USA) according to the manufacturer’s recommendations. Hybridization was performed at 65 °C for 17 h. The slides were washed and hybridization was stabilized with Stabilization & Drying solution (Agilent, Santa Clara, USA).

scan_protocol: After drying, the hybridized microarrays were scanned with the high resolution Agilent microarray scanner G2565CA with a resolution of 3 µm and analyzed with the Feature extraction software (Agilent, Santa Clara, USA).

data_processing:
Raw data were quantile-normalized and gene expression data were generated by the Direct Array software (OakLabs, Hennigsdorf, Germany).
All log2 values between -1 and 1 were ignored and only statistically significant values (p<0.05) have been taken.

organism: Streptococcus gallolyticus UCN34

source_name: S. gallolyticus UCN 34; adhered to collagen type I in BHI medium

label_protocol: The cDNA and cRNA synthesis with Cy3 labelling was carried out with the Quick Amp WT Labeling Kit, one-color (Agilent, Santa Clara, USA), following the manufacturer’s recommendations.

growth_protocol: Bacterial cultures in the exponential growth phase were generated by inoculating 5 ml BHI medium with 100 µl overnight culture. The exponential growth phase was reached after 2.5 h at 37 °C and 220 rpm. The bacterial titer was determined by serial dilutions in Dulbecco’s phosphate-buffered saline (DPBS) and plating 100 µl of an adequate concentration in triplicate on tryptone soya agar (Thermo Scientific, Waltham, USA). Tryptone soya agar plates were incubated at 37 °C and the colonies grown were counted using an aCOLyte colony counter (Synbiosis, Cambridge, UK).

extract_protocol: The RNA was extracted with the peqGOLD Bacterial RNA Kit (VWR, Radnor, USA). Bacterial cells were suspended in TE buffer and lysis buffer T and transferred into Lysing Matrix B tubes (MP Biomedicals, Santa Ana, USA). The bacterial cells were disrupted by using Vortex-Genie 2 (scientific industries, New York, USA) for 3 min at full speed. Further RNA extraction was carried following the manufacturer’s instructions. The RNA was eluted with 30 µL RNase-free water and quantified using the NanoDrop 2000 (VWR).

treatment_protocol: An amount of 2 ml of bacterial culture (exponential phase) was added to 6-well plates with immobilized collagen type I (human) in comparison to 2 ml of bacterial culture in 6-well without collagen (planktonic). After incubation for 2 h, the supernatant with the non-adhered bacterial cells (planktonic) and the collagen-adhered bacterial cells were removed for RNA extraction.

tag: growth type

value: BHI medium, adhered to collagen type I

tag: time point

value: 2 h incubation


title: UCN 34 159.13 planktonic

description: SAMPLE 5

source_name: S. gallolyticus UCN 34; planktonic BHI medium 2 hrs

value: BHI medium, planktonic


title: Intima-media ascending aorta, miRNA, ATAAD, rep1

description: miRNA expression of dissected aorta

tag: tissue

tag: age


title: amnion 4 at term

type: genomic

city: San Francisco

first: Joseph

last: Costello

department: NeuroSurgery

institute: UCSF

description:
normal sample
CTL12_amnion

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

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

data_processing:
BeadStudio software v3.2
Methylumi R package normalization option noob (normal-exponential convolution using out-of-band probes)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from amnion

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit or pheno chloroform extraction according to standard instructions

value: amnion

tag: gestational stage

value: term


title: UCN 34 159.10b collagen

description: SAMPLE 4


title: chorion 5 at term

description:
normal sample
CTL12_chorion

source_name: genomic DNA from chorion

value: chorion


title: amnion 3 at term

description:
normal sample
CTL11_amnion


title: trophoblast 3 at second trimester

description:
normal sample
CTL05_trophoblast

source_name: genomic DNA from trophoblast

value: trophoblast

value: second trimester


title: Colon_Normal_17803

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

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

data_processing:
Background subtraction and dye bias correction
Unmethylated and methylated signal intensities

source_name: colon normal tissue

extract_protocol: Standard Illumina Protocol

value: adjacent normal of colon cancer


title: trophoblast 4 at term

description:
normal sample
CTL07_trophoblast


title: Intima-media ascending aorta, miRNA, ATAAD, rep2

description: miRNA expression of dissected aorta


title: chorion 4 at term

description:
normal sample
CTL11_chorion


title: chorion 1 at term

description:
normal sample
CTL01_chorion


title: UCN 34 159.10b planktonic

description: SAMPLE 3


title: chorion 2 at second trimester

description:
normal sample
CTL02_chorion


title: villi 1 at term

description:
normal sample
CTL01_villi

source_name: genomic DNA from villi

value: villi


title: Colon_Tumor_17771

source_name: colon tumor

value: colon cancer


title: amnion 2 at second trimester

description:
normal sample
CTL10_amnion


title: Zymo_Meth_DKO_MsssI

source_name: methylated control sample

value: DKO cell line treated with MsssI


title: villi 2 at second trimester

description:
normal sample
CTL02_villi


title: Zymo_NonMeth_DKO

source_name: non-methylated control sample

value: DKO cell line


title: Intima-media ascending aorta, mRNA, transplant donor, rep3

description: Gene expression of healthy aorta

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6.0 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 Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8×60K array slides (G4851A, Agilent Technologies) at 65 °C with rotation at 10 rpm for 17 hours in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were normalized by 75th percentile algorithm, Gene Spring Software 12.5 (Agilent Technologies).

label_protocol: Cy3-labelled cRNA was prepared from 200 ng total RNA using Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

value: female


title: trophoblast 2 at term

description:
normal sample
CTL04_trophoblast


title: UCN 34 159.5 planktonic

description: SAMPLE 1


title: basal plate 1 at term

description:
normal sample
CTL01_basal_plate

source_name: genomic DNA from basal plate

value: basal plate


title: UCN 34 159.5 collagen

description: SAMPLE 2


title: amnion 1 at second trimester

description:
normal sample
CTL02_amnion


title: DSM 16831 4.15a collagen

description: SAMPLE 6

organism: Streptococcus gallolyticus subsp. gallolyticus DSM 16831

source_name: S. gallolyticus DSM 16831; adhered to collagen type I in BHI medium


title: Colon_Tumor_17777


title: Intima-media ascending aorta, mRNA, transplant donor, rep2

description: Gene expression of healthy aorta

value: healthy aorta

value: male


title: Intima-media ascending aorta, mRNA, transplant donor, rep4

description: Gene expression of healthy aorta


title: basal plate 2 at second trimester

description:
normal sample
CTL02_basal_plate


title: DSM 16831 4.12b collagen

description: SAMPLE 4

value: BHI medium, adhered to collagen type I


title: Colon_Normal_17797


title: NEB_HeLa

source_name: cervical cancer cell line

value: HeLa cell line


title: chorion 3 at second trimester

description:
normal sample
CTL10_chorion


title: trophoblast 1 at second trimester

description:
normal sample
CTL02_trophoblast


title: DSM 16831 4.10b collagen

description: SAMPLE 2

value: 2 h incubation


title: DSM 16831 4.12b planktonic

description: SAMPLE 3

source_name: S. gallolyticus DSM 16831; planktonic BHI medium 2 hrs

value: BHI medium, planktonic


title: Intima-media ascending aorta, mRNA, transplant donor, rep5

description: Gene expression of healthy aorta

source_name: Intima-media ascending aorta, donor


title: Intima-media ascending aorta, mRNA, ATAAD, rep6

description: Gene expression of dissected aorta

value: dissected aorta


title: DSM 16831 4.10a planktonic

description: SAMPLE 1


title: UCN 34 g LYZ

description: SAMPLE 6

scan_protocol: After drying, the hybridized microarrays were scanned with the high resolution Agilent microarray scanner G2565CA with a resolution of 5 µm and analyzed with the Feature extraction software (Agilent, Santa Clara, USA).

source_name: S. gallolyticus UCN34; BHI medium supplemented with lysozyme after 5 hrs

treatment_protocol: An amount of 20 µl of bacterial culture (exponential phase) was added to 980 µl BHI medium in 24-well plates supplemented with lysozyme from chicken egg white (Sigma, Steinheim, Germany; 0 mg/ml; 10 mg/ml), incubated at 37 °C and 70 rpm. After incubation for 5 h, the supernatant with the non-adhered bacterial cells was removed and used for RNA extraction.

tag: growth media

value: BHI medium with 10 mg/ml lysozyme

value: 5 h growth


title: Intima-media ascending aorta, mRNA, ATAAD, rep3

description: Gene expression of dissected aorta

source_name: Intima-media ascending aorta, ataad patient


title: UCN 34 a LYZ

description: SAMPLE 2


title: UCN 34 a BHI

description: SAMPLE 1

source_name: S. gallolyticus UCN34; BHI medium 5 hrs

value: BHI medium


title: UCN 34 e LYZ

description: SAMPLE 4


title: Intima-media ascending aorta, mRNA, ATAAD, rep2

description: Gene expression of dissected aorta


title: UCN 34 e BHI

description: SAMPLE 3


title: Intima-media ascending aorta, mRNA, ATAAD, rep4

description: Gene expression of dissected aorta


title: Intima-media ascending aorta, mRNA, transplant donor, rep1

description: Gene expression of healthy aorta


title: Intima-media ascending aorta, mRNA, ATAAD, rep1

description: Gene expression of dissected aorta


title: Illumina_Control

source_name: Illumina control

value: Illumina control


title: BAA-2069 g BHI

description: SAMPLE 5

organism: Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069

source_name: S. gallolyticus BAA-2069; BHI medium 5 hrs


title: BAA-2069 g LYZ

description: SAMPLE 6

source_name: S. gallolyticus BAA-2069; BHI medium supplemented with lysozyme after 5 hrs


title: BAA-2069 e LYZ

description: SAMPLE 4


title: BAA-2069 a BHI

description: SAMPLE 1


title: BAA-2069 a LYZ

description: SAMPLE 2


title: BAA-2069 e BHI

description: SAMPLE 3


title: AE104(delta zur) with 100 µM ZnCl2, rep 3

status: Public on May 16 2017

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

hyb_protocol: Hybridisation was done by the service provider IMGM Laboratories GmbH (Martinsried)

scan_protocol: Agilent DNA microarray Scanner were used by the service provider IMGM Laboratories GmbH (Martinsried)

data_processing: The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength

organism: Cupriavidus metallidurans CH34

source_name: cells of C. metallidurans

label_protocol: Labeling was done by the service provider IMGM Laboratories GmbH (Martinsried)

growth_protocol: C. metallidurans strains were grown in Mineral salts medium + 0.2 % Na-gluconate to a cell turbidity of 100 Klett, ZnCl2 was added and after 10 min  cells were harvest by centrifugation for 1' at RT in 2.0 ml Tubes.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: ZnCl2 was added at a cell turbitity of 100 Klett for 10 min

tag: genotype

value: AE104 (delta zur)


title: AE104(delta zur) without treatment, rep1


title: AE104 with 100 µM ZnCl2, rep3


title: AE104(delta zur) without treatment, rep2


title: AE104(delta zur) with 100 µM ZnCl2, rep 1


title: AE104(delta zur) without treatment, rep3


title: HEK293T_without Riboflavin

city: Shantou

first: Lin

last: Long

state: Guangdong

address: No.22, Xinling Road

department: Department of Biochemistry and Molecular Biology

institute: Shantou University Medical College

description: RMA expression value derived from Expression Console software (Affymetrix).

hyb_protocol: Array hybridization and washing was performed using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) in a Hybridization Oven 645 (Affymetrix) and a Fluidics Station 450 (Affymetrix) followed the manufacturer’ s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip Scanner 3000 (Affymetrix).

data_processing: Command Console Software 3.1 (Affymetrix) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console (Affymetrix).

source_name: HEK293T, without Riboflavin

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Cells sub-cultured in Dulbecco’s Modified Eagle’s medium (DMEM) or riboflavin-deficient DMEM medium for 25 generations.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit (QIAGEN) following the manufacturer’ s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies).


title: AE104 with 100 µM ZnCl2, rep2


title: HEK293T_with Riboflavin

source_name: HEK293T, with Riboflavin


title: AE104(delta zur) with 100 µM ZnCl2, rep 2


title: TCP_Untreated_3

city: Cologne

first: H. Christian

last: Reinhardt

address: Weyertal 115B

department: Department I of Internal Medicine

institute: University Hospital of Cologne

hyb_protocol: Standard affymetrix gene chip array protocol

scan_protocol: Gene Chip Scanner 3000 7G

data_processing: Matlab Bioinformatics package

source_name: Splenocytes of TCP animal_no stimulation

treatment_protocol: injection of 200mg/kg cyclophosphamide i.p. (dissolved at 20mg/mL)

tag: mouse model

tag: cell type

value: Leukemia cells isolated from infiltrated spleen

tag: stimulated with


title: TCP_CTX_2

source_name: Splenocytes of TCP animal_cyclophosphamide stimulation 12 hrs prior to splenocyte isolation

label_protocol: Standard affymetrix gene chip array protocol


title: TCA_CTX_3

source_name: Splenocytes of TCA animal_cyclophosphamide stimulation 12 hrs prior to splenocyte isolation

value: cyclophosphamide 200mg/kg i.p.


title: TCA_CTX_2


title: TC_CTX_1

source_name: Splenocytes of TC animal_cyclophosphamide stimulation 12 hrs prior to splenocyte isolation


title: TC_CTX_2


title: TCA_Untreated_2

source_name: Splenocytes of TCA animal_no stimulation


title: TC_Untreated_3

source_name: Splenocytes of TC animal_no stimulation


title: TCP_Untreated_2


title: TCP_CTX_1


title: TCA_Untreated_3


title: TC_CTX_3


title: TCA_CTX_1


title: Intima-media ascending aorta, mRNA, ATAAD, rep5

description: Gene expression of dissected aorta


title: TCP_Untreated_1


title: TCA_Untreated_1


title: AE104 with 100 µM ZnCl2, rep1


title: TC_Untreated_2


title: DSM 16831 4.15a planktonic

description: SAMPLE 5

source_name: S. gallolyticus DSM 16831; planktonic BHI medium 2 hrs


title: TC_Untreated_1


title: UCN 34 g BHI

description: SAMPLE 5


title: EDDA_74

status: Public on May 13 2017

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, color-correction)

extract_protocol: Genomic DNA was isolated using the QIAamp DNA Mini Kit (Qiagen) as per manufacturer’s instructions.

tag: Sex

value: M

tag: sample group

value: control

tag: cigarettes per day

tag: gsi score

tag: audit score

tag: ocds score

tag: years addicted

tag: days since last drink

tag: nationality

value: german

tag: sentrix id

tag: sentrix position


title: 64_T2

tag: age


title: EDDA_89


title: EDDA_25


title: EDDA_85


title: 122_T2


title: 68_T2


title: EDDA_73


title: 84_T2


title: EDDA_105

value: polish


title: EDDA_78


title: EDDA_100


title: EDDA_55


title: EDDA_64


title: EDDA_93


title: EDDA_54


title: EDDA_77


title: 104_T2


title: EDDA_120


title: 100_T2


title: EDDA_21


title: EDDA_52


title: EDDA_68


title: EDDA_92


title: EDDA_82


title: EDDA_107


title: 82_T2


title: EDDA_83


title: 105_T2


title: EDDA_50


title: EDDA_96


title: EDDA_121


title: EDDA_70


title: 83_T2


title: 49_T2


title: EDDA_104


title: EDDA_103


title: 123_T2


title: 66_T2


title: 107_T2


title: 121_T2


title: 61_T2


title: EDDA_94


title: EDDA_47


title: 31_T2


title: EDDA_69


title: EDDA_29


title: 47_T2


title: EDDA_49


title: 85_T2


title: EDDA_67


title: EDDA_87


title: EDDA_28


title: EDDA_123


title: EDDA_75


title: EDDA_31


title: EDDA_95


title: EDDA_122


title: EDDA_61


title: 87_T2


title: EDDA_84


title: 120_T2


title: whole_blood_case_127

status: Public on May 12 2017

city: Cambridge

first: Gwenael

last: Leday

address: Forvie Site, Robinson Way

department: School of Clinical Medicine

institute: University of Cambridge

description: SAMPLE 188

hyb_protocol: standard Affymetrix protocol

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip® Operating Software (Affymetrix, Santa Clara, CA, USA).  Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip® Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: The data were read and RMA-normalized using the Bioconductor package affy (default parameters).

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated from all samples using the standard PAXgene protocol on the Qiagen Biorobot 8000.

tag: subject group

value: CASE; major depressive disorder (MDD) patient

tag: anxiety

value: no

tag: gender

value: F

tag: tissue

value: whole blood

tag: batch


title: whole_blood_case_128

description: SAMPLE 190

value: yes


title: 89_T2

tag: Sex


title: EDDA_90

tag: sample group


title: whole_blood_control_62

description: SAMPLE 189

value: CNTL; healthy control


title: 67_T2

tag: cigarettes per day


title: whole_blood_control_61

description: SAMPLE 185


title: whole_blood_control_63

description: SAMPLE 191


title: whole_blood_control_58

description: SAMPLE 180


title: whole_blood_case_122

description: SAMPLE 179


title: 103_T2

tag: gsi score


title: whole_blood_control_64

description: SAMPLE 192


title: whole_blood_control_57

description: SAMPLE 177


title: whole_blood_case_126

description: SAMPLE 187


title: whole_blood_case_125

description: SAMPLE 186


title: whole_blood_control_60

description: SAMPLE 184


title: whole_blood_control_59

description: SAMPLE 183


title: whole_blood_case_124

description: SAMPLE 182


title: whole_blood_control_56

description: SAMPLE 173


title: whole_blood_case_123

description: SAMPLE 181


title: EDDA_66

tag: audit score


title: whole_blood_case_121

description: SAMPLE 178


title: EDDA_97

tag: ocds score


title: whole_blood_case_120

description: SAMPLE 176


title: whole_blood_case_118

description: SAMPLE 174


title: whole_blood_case_117

description: SAMPLE 172


title: EDDA_79

tag: years addicted


title: whole_blood_case_112

description: SAMPLE 167


title: whole_blood_control_55

description: SAMPLE 164


title: whole_blood_case_119

description: SAMPLE 175


title: whole_blood_case_110

description: SAMPLE 165


title: whole_blood_case_115

description: SAMPLE 170


title: whole_blood_case_113

description: SAMPLE 168


title: whole_blood_case_108

description: SAMPLE 162


title: 69_T2

tag: days since last drink


title: whole_blood_case_107

description: SAMPLE 161


title: whole_blood_case_116

description: SAMPLE 171


title: whole_blood_case_109

description: SAMPLE 163


title: EDDA_20

tag: nationality


title: whole_blood_case_111

description: SAMPLE 166


title: whole_blood_control_51

description: SAMPLE 153


title: whole_blood_control_54

description: SAMPLE 157


title: whole_blood_case_114

description: SAMPLE 169


title: whole_blood_case_104

description: SAMPLE 158


title: whole_blood_case_105

description: SAMPLE 159


title: whole_blood_case_103

description: SAMPLE 154


title: whole_blood_control_52

description: SAMPLE 155


title: whole_blood_case_101

description: SAMPLE 151


title: whole_blood_control_53

description: SAMPLE 156


title: whole_blood_case_100

description: SAMPLE 149


title: whole_blood_case_102

description: SAMPLE 152


title: whole_blood_control_50

description: SAMPLE 150


title: whole_blood_case_99

description: SAMPLE 148


title: whole_blood_case_97

description: SAMPLE 145


title: whole_blood_control_47

description: SAMPLE 143


title: whole_blood_control_49

description: SAMPLE 146


title: whole_blood_control_48

description: SAMPLE 144


title: whole_blood_control_43

description: SAMPLE 138


title: whole_blood_case_95

description: SAMPLE 137


title: whole_blood_case_94

description: SAMPLE 136


title: whole_blood_case_98

description: SAMPLE 147


title: whole_blood_case_93

description: SAMPLE 134


title: whole_blood_case_89

description: SAMPLE 129


title: whole_blood_case_96

description: SAMPLE 140


title: whole_blood_control_42

description: SAMPLE 135


title: whole_blood_control_45

description: SAMPLE 141


title: whole_blood_control_46

description: SAMPLE 142


title: whole_blood_case_87

description: SAMPLE 127


title: whole_blood_case_84

description: SAMPLE 124


title: whole_blood_case_85

description: SAMPLE 125


title: whole_blood_control_40

description: SAMPLE 123


title: whole_blood_case_90

description: SAMPLE 130


title: whole_blood_case_91

description: SAMPLE 131


title: whole_blood_control_41

description: SAMPLE 132


title: whole_blood_control_44

description: SAMPLE 139


title: whole_blood_case_88

description: SAMPLE 128


title: whole_blood_case_92

description: SAMPLE 133


title: whole_blood_case_86

description: SAMPLE 126


title: whole_blood_control_39

description: SAMPLE 122


title: whole_blood_case_83

description: SAMPLE 120


title: whole_blood_case_81

description: SAMPLE 118


title: whole_blood_case_80

description: SAMPLE 117


title: whole_blood_case_76

description: SAMPLE 113


title: whole_blood_case_106

description: SAMPLE 160


title: whole_blood_case_77

description: SAMPLE 114


title: whole_blood_case_78

description: SAMPLE 115


title: whole_blood_case_73

description: SAMPLE 109


title: whole_blood_case_79

description: SAMPLE 116


title: whole_blood_case_74

description: SAMPLE 110


title: whole_blood_case_75

description: SAMPLE 112


title: whole_blood_control_37

description: SAMPLE 111


title: whole_blood_case_72

description: SAMPLE 107


title: whole_blood_case_70

description: SAMPLE 105


title: whole_blood_case_82

description: SAMPLE 119


title: whole_blood_case_71

description: SAMPLE 106


title: whole_blood_control_34

description: SAMPLE 102


title: whole_blood_case_69

description: SAMPLE 103


title: whole_blood_control_35

description: SAMPLE 104


title: whole_blood_case_65

description: SAMPLE 98


title: whole_blood_case_63

description: SAMPLE 95


title: whole_blood_control_33

description: SAMPLE 97


title: whole_blood_case_58

description: SAMPLE 90


title: whole_blood_case_55

description: SAMPLE 87


title: whole_blood_control_36

description: SAMPLE 108


title: whole_blood_case_61

description: SAMPLE 93


title: whole_blood_case_66

description: SAMPLE 99


title: whole_blood_case_67

description: SAMPLE 100


title: whole_blood_case_68

description: SAMPLE 101


title: whole_blood_case_62

description: SAMPLE 94


title: whole_blood_case_59

description: SAMPLE 91


title: whole_blood_case_64

description: SAMPLE 96


title: whole_blood_case_60

description: SAMPLE 92


title: whole_blood_case_51

description: SAMPLE 83


title: whole_blood_case_56

description: SAMPLE 88


title: whole_blood_case_57

description: SAMPLE 89


title: whole_blood_case_54

description: SAMPLE 86


title: whole_blood_case_44

description: SAMPLE 76


title: whole_blood_case_50

description: SAMPLE 82


title: whole_blood_case_47

description: SAMPLE 79


title: whole_blood_case_49

description: SAMPLE 81


title: whole_blood_case_43

description: SAMPLE 75


title: whole_blood_case_48

description: SAMPLE 80


title: whole_blood_case_53

description: SAMPLE 85


title: whole_blood_case_45

description: SAMPLE 77


title: whole_blood_case_32

description: SAMPLE 64


title: whole_blood_case_40

description: SAMPLE 72


title: whole_blood_case_46

description: SAMPLE 78


title: whole_blood_case_39

description: SAMPLE 71


title: whole_blood_case_41

description: SAMPLE 73


title: whole_blood_case_31

description: SAMPLE 63


title: whole_blood_case_52

description: SAMPLE 84


title: whole_blood_case_42

description: SAMPLE 74


title: whole_blood_case_36

description: SAMPLE 68


title: whole_blood_case_35

description: SAMPLE 67


title: whole_blood_case_37

description: SAMPLE 69


title: whole_blood_case_34

description: SAMPLE 66


title: whole_blood_case_38

description: SAMPLE 70


title: whole_blood_case_33

description: SAMPLE 65


title: whole_blood_case_30

description: SAMPLE 62


title: whole_blood_case_29

description: SAMPLE 61


title: whole_blood_case_27

description: SAMPLE 59


title: whole_blood_control_38

description: SAMPLE 121


title: whole_blood_case_28

description: SAMPLE 60


title: whole_blood_case_23

description: SAMPLE 55


title: whole_blood_case_24

description: SAMPLE 56


title: whole_blood_case_22

description: SAMPLE 54


title: Control LPS 8

city: Perth

first: Kim

middle: Warwick

last: Carter

state: Western Australia

address: 100 Roberts Road, Subiaco

country: Australia

institute: Telethon Kids Institute

hyb_protocol: At least 500 ng at 50 ng/ml (evaluated by the absorbance 260/280 ratio using a NanoDrop ND 1000 spectrophotometer, NanoDrop Technologies, Wilmington, DE) was sent to the Ramaciotti Centre, UNSW, for analysis using Affymetrix GeneChip HT MG-430 PM Array.

scan_protocol: At least 500 ng at 50 ng/ml (evaluated by the absorbance 260/280 ratio using a NanoDrop ND 1000 spectrophotometer, NanoDrop Technologies, Wilmington, DE) was sent to the Ramaciotti Centre, UNSW, for analysis using Affymetrix Genechip HT MG-430 PM Array.

data_processing: The Affy Bioconductor package was used to read the Affymetrix CEL files into R and to pre-process the arrays using robust multichip average methodology.  We made use of custom CDF annotations for the array from the BrainArray project version 19 using Entrez Gene mappings, available from for 17856 probesets as defined by an alternate CDF for this platform from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/entrezg.asp . Quality control of the arrays was performed using the arrayQualityMetrics package.  The limma package was used to conduct differential expression analysis between UV vs. Control and UV-LPS vs. Control-LPS groups after initial data exploration, adjusting for sampling date. We assessed significance of differential expression analysis using Benjamini Hochberg adjusted p-values.

source_name: macrophages differentiated for 9 days from BM

extract_protocol: Total RNA was extracted from macrophages differentiated for 9 days from bone marrow using TRIzol (Life Technologies) followed by an RNeasy plus mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Recipient mice were gamma-irradiated and injected with 2 x 10e6 BM cells from naïve congenic B6.SJL-Ptprca mice (shaved but not UV-irradiated). Chimeric exposed to LPS.

tag: donor strain

value: B6.SJL-Ptprca (CD45.1 alloantigen)

tag: recipient strain

value: C57BL/6J (CD45.2 alloantigen)

value: Female

tag: cell type

tag: treatment

value: LPS

tag: sample type

value: Control chimeric


title: UV irradiated LPS 7

label_protocol: At least 500 ng at 50 ng/ml (evaluated by the absorbance 260/280 ratio using a NanoDrop ND 1000 spectrophotometer, NanoDrop Technologies, Wilmington, DE) was sent to the Ramaciotti Centre, UNSW, for analysis using Affymetrix Genechip HT MG-430 PM Array.

treatment_protocol: Recipient mice were gamma-irradiated and injected with 2 x 10e6 BM cells from 8 kJ/m2 UV-irradiated congenic B6.SJL-Ptprca mice. Chimeric exposed to LPS.

value: macrophages differentiated for 9 days from BM

value: UV irradiated chimeric


title: whole_blood_case_15

description: SAMPLE 47

tag: subject group

tag: anxiety

tag: gender

tag: age


title: whole_blood_case_25

description: SAMPLE 57

value: M

tag: tissue

tag: batch


title: Control LPS 7

tag: Sex


title: UV irradiated LPS 6


title: whole_blood_case_19

description: SAMPLE 51


title: whole_blood_case_21

description: SAMPLE 53


title: whole_blood_case_26

description: SAMPLE 58


title: whole_blood_case_20

description: SAMPLE 52


title: whole_blood_case_17

description: SAMPLE 49


title: UV irradiated LPS 5


title: whole_blood_case_14

description: SAMPLE 46


title: Control LPS 6


title: whole_blood_case_18

description: SAMPLE 50


title: UV irradiated LPS 8


title: whole_blood_case_16

description: SAMPLE 48


title: UV irradiated LPS 4


title: Control LPS 5


title: whole_blood_case_11

description: SAMPLE 43


title: whole_blood_case_10

description: SAMPLE 42


title: whole_blood_case_12

description: SAMPLE 44


title: whole_blood_case_13

description: SAMPLE 45


title: whole_blood_case_9

description: SAMPLE 41


title: UV irradiated LPS 3


title: Control LPS 4


title: UV irradiated LPS 2


title: Control LPS 2


title: UV irradiated 8

treatment_protocol: Recipient mice were gamma-irradiated and injected with 2 x 10e6 BM cells from 8 kJ/m2 UV-irradiated congenic B6.SJL-Ptprca mice.


title: Control LPS 3


title: whole_blood_case_5

description: SAMPLE 37


title: Control LPS 1


title: whole_blood_control_32

description: SAMPLE 32


title: UV irradiated LPS 1


title: whole_blood_control_30

description: SAMPLE 30


title: whole_blood_case_8

description: SAMPLE 40


title: whole_blood_case_1

description: SAMPLE 33


title: whole_blood_case_4

description: SAMPLE 36


title: whole_blood_case_2

description: SAMPLE 34


title: whole_blood_case_6

description: SAMPLE 38


title: whole_blood_control_29

description: SAMPLE 29


title: UV irradiated 7


title: whole_blood_case_7

description: SAMPLE 39


title: whole_blood_control_31

description: SAMPLE 31


title: whole_blood_case_3

description: SAMPLE 35


title: UV irradiated 5


title: Control 6

treatment_protocol: Recipient mice were gamma-irradiated and injected with 2 x 10e6 BM cells from naïve congenic B6.SJL-Ptprca mice (shaved but not UV-irradiated).


title: whole_blood_control_27

description: SAMPLE 27


title: UV irradiated 6


title: whole_blood_control_28

description: SAMPLE 28


title: Control 8


title: Control 7


title: UV irradiated 4


title: whole_blood_control_26

description: SAMPLE 26


title: Control 5


title: UV irradiated 2


title: whole_blood_control_19

description: SAMPLE 19


title: whole_blood_control_24

description: SAMPLE 24


title: Control 2


title: whole_blood_control_25

description: SAMPLE 25


title: UV irradiated 3


title: UV irradiated 1


title: whole_blood_control_17

description: SAMPLE 17


title: whole_blood_control_20

description: SAMPLE 20


title: whole_blood_control_22

description: SAMPLE 22


title: whole_blood_control_18

description: SAMPLE 18


title: Control 4


title: whole_blood_control_23

description: SAMPLE 23


title: Control 1


title: whole_blood_control_13

description: SAMPLE 13


title: whole_blood_control_16

description: SAMPLE 16


title: whole_blood_control_14

description: SAMPLE 14


title: whole_blood_control_11

description: SAMPLE 11


title: Control 3


title: whole_blood_control_6

description: SAMPLE 6


title: whole_blood_control_7

description: SAMPLE 7


title: whole_blood_control_21

description: SAMPLE 21


title: whole_blood_control_8

description: SAMPLE 8


title: whole_blood_control_5

description: SAMPLE 5


title: whole_blood_control_10

description: SAMPLE 10


title: whole_blood_control_12

description: SAMPLE 12


title: whole_blood_control_15

description: SAMPLE 15


title: whole_blood_control_9

description: SAMPLE 9


title: whole_blood_control_4

description: SAMPLE 4


title: NK318-IEC

city: Tianjin

first: Rongcun

last: Yang

address: Weijin Road 94

institute: Nankai university

description: Gene expression data from germ-free  monocolonized with L.NK318.1 mice intestinal epithelial cells

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

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.

growth_protocol: Mice were maintained in vinyl isolators within the gnotobiotic facility.

treatment_protocol: GF mice monocolonized with 1*10^8 L.NK318.1, two weeks later, intestinal epithelial cells and peyer's patches cells were isolated.

tag: strain

tag: mouse status

value: L.NK318.1-colonized mouse

value: intestinal epithelial cells (IECs)


title: whole_blood_control_3

description: SAMPLE 3


title: NK318.1-PP

description: Gene expression data from germ-free mice monocolonized with L.NK318.1 mice peyer's patches cells

source_name: NK318.1 mice Peyer's patches cells

value: Peyer's patches (PP) cells


title: whole_blood_control_2

description: SAMPLE 2


title: atrap, biological rep3

status: Public on May 11 2017

city: Riverside

first: Huan

last: Wang

address: 900 University Ave

institute: UC Riverside

description: Gene expression data from 3-week old rosette leaves of atrap

hyb_protocol: The biotinylated ribonucleotides were hybridized at 45C for 16 hr according to the manufacturer’s instructions

scan_protocol: Genechip scanner 3000

data_processing:
For Affymetrix GeneChip array analysis, we normalized expression profiles with the RMA method (Irizarry et al., 2003). A list of genes with statistically significant changes in expression between the genotypes was generated by the SAM method in which multiple testing was taken into account through q-value (Schwender et al., 20012).
We used a threshold q-value of 0.05 to select the genes whose expression levels are statistically significantly changed

organism: Arabidopsis thaliana

source_name: Arabidopsis atrap 3-week old rosette leaves

label_protocol: Biotinylated ribonucleotides were synthesized according to the manufacturer’s instructions

growth_protocol: Arabidopsis plants were grown in a controlled growth room at 23°C, with a 12 h light/12 h dark photoperiod

extract_protocol: Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions

treatment_protocol: No treatment

value: 3-weeks old

tag: genotype/variation

value: atrap mutant

value: rosette leaves


title: whole_blood_control_1

description: SAMPLE 1

value: no

value: whole blood


title: GF-IEC

description: Gene expression data from germ-free mice  intestinal epithelial cells

source_name: GF mice intestinal epithelial cells

value: Germ-Free (GF)


title: WT, biological rep1

description: Gene expression data from 3-week old rosette leaves of WT

source_name: Arabidopsis WT 3-week old rosette leaves

value: WT


title: RAW 264.7 cells treated with Bacillus clausii MTCC-8326 for 4 hours  vs untreated cells.

status: Public on May 10 2017

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

country: India

institute: National Institute of Science Education and Research Bhubaneswar

description: RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India

hyb_protocol: 825 ng each of test and reference Cy dye  labeled RNA was mixed together and was fragmented using Agilent fragmentation kit in the presence of blocking reagent for 30 minutes in 60 degree celsius. Equal volume of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture to stop the reaction. 100 μl of the mixture was added to each of the chamber of the hybridization gasket and the array slide was sandwitched over it. The hybridization reaction was done for 17 hours in 65 degree celsius with moist condition in a hybridization oven.

scan_protocol: Scanned on an Agilent G2505C scanner using Agilent Scan control (version 8.3.1.1). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: 500 ng of total RNA were primed with 1.2 µl (3rd dilution) of  T7 promoter primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of MMLV Rtase. The c-DNA was then transcribed by T7 RNA Polymerase in the presence of NTPs and labeled with Cy3-CTP (For Rererence) and Cy5-CTP (For test).

growth_protocol: Cells were grown in DMEM medium (Himedia, India) supplemented with 10% heat inactivated fetal bovine serum (Himedia, India) (without any antibiotic) in 75 cm2 tissue culture flasks (BD Biosciences, USA) at 37 degree Celcius in a humidified atmosphere containing 5% CO2.

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

tag: cell line

tag: background strain

value: BALB/c

source_name: time-matched untreated control


title: RAW 264.7 cells treated with Bacillus clausii MTCC-8326 for 2 hours  vs untreated cells.


title: atrap, biological rep1


title: GF-PP

description: Gene expression data from germ-free mice peyer's patches cells

source_name: GF mice Peyer's patches cells


title: RAW 264.7 cells treated with Bacillus clausii MTCC-8326 for 1 hour  vs untreated cells.


title: RAW 264.7 cells treated with Bacillus clausii MTCC-8326 for 6 hours  vs untreated cells.


title: atrap, biological rep2


title: RAW 264.7 cells treated with Lactobacillus acidophilus MTCC-10307 for 2 hours  vs untreated cells.


title: RAW 264.7 cells treated with Lactobacillus acidophilus MTCC-10307 for 1 hour  vs untreated cells.


title: WT, biological rep3


title: WT, biological rep2


title: RAW 264.7 cells treated with Lactobacillus acidophilus MTCC-10307 for 6 hours vs untreated cells.


title: CD161- NK cell donor 4

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

description: Gene expression in FACS sorted CD161- NK T cells

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17hrs, 65degrees celsius) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing:
Raw data microarray features were normalized using variance stabilizing normalization (vsn) using R and Bioconductor packages.
After  data were normalized (vsn), control probes were removed and then low detected probes removed too.  Negative controls were used to asses the background level and only probes having a signal above background in at least four samples were retained.

source_name: Peripheral Blood, FACS sorted CD19-CD14-CD3-CD56+ NK cells

label_protocol: 10ng of each total RNA sample was used to produce Cy3-labeled cRNA using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and dye-incorporation rate were measured with the ND-100 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Cells taken ex vivo from healthy donors and separated using Ficoll centrifugation

extract_protocol: Rneasy® Mini Kit, Qiagen following manufacturer's protocol. RNA samples were quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies)

treatment_protocol: Live CD3-CD19-CD14-CD56+ NK cell subsets were sorted using a FACS sorter

tag: individual

value: Donor 4

value: Peripheral Blood

tag: cell subtype

value: CD161 Negative


title: RAW 264.7 cells treated with Lactobacillus acidophilus MTCC-10307 for 4 hours  vs untreated cells.


title: p53+/+_dox_48h

city: Tokyo

first: Koichi

last: Matsuda

address: Shirokanedai

institute: The University of Tokyo

description:
p53+/+ 48h
Gene expression after 48h in doxorubicin-treated wild-type p53 cells.

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction containing Agilent Fragmentation Buffer and Gene Expression Blocking Agent following the manufacturer's instructions. Hi-RPM Hybridization Buffer was added to stop the fragmentation. Samples were hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays for 17 hours at 65°C with rotation. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 and 1 minute with 37°C pre-warmed Gene Expression Wash Buffer 2.

scan_protocol: Slides were scanned on the Agilent Microarray Scanner using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MCF10A p53+/+, doxorubicin, 48h-RNA

label_protocol: The fluorescent cRNA using cyanine 3-labelled (Cy3) targets was generated following the Agilent’s One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp labeling) protocol. The Cy3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen) and quantified by Nanodrop-2000 Spectrophotometer.

extract_protocol: Non-treated cells were harvested for total RNA immediately at the time of treatment. Treated cells were harvested at 12, 24, and 48 hours after treatment using RNeasy Plus Mini Kits (Qiagen). The integrity and purity of the RNA templates were determined using a 2100 Bioanalyzer (Agilent).

treatment_protocol: Twenty-four hours after plating, cells were treated with 0.5 μg/ml of doxorubicin for 2 hours.

value: doxorubicin

tag: time to harvest

value: 48 hours


title: p53−/−_dox_48h

description:
p53-/- 48h
Gene expression after 48h in doxorubicin-treated p53-null cells.

source_name: MCF10A p53−/−, doxorubicin, 48h-RNA

tag: treatment


title: p53+/+_no-dox_0h

description:
p53+/+ 0h
Gene expression in non-treated wild-type p53 cells.

source_name: MCF10A p53+/+, no doxorubicin, 0h-RNA

value: 0 hour


title: CD161+ NK cell donor 4

description: Gene expression in FACS sorted CD161+ NK T cells

tag: cell type

value: FACS sorted CD19-CD14-CD3-CD56+ NK cells

value: CD161 Positive


title: p53−/−_no-dox_0h

description:
p53-/- 0h
Gene expression in non-treated p53-null cells.

source_name: MCF10A p53−/−, no doxorubicin, 0h-RNA


title: p53+/+_dox_24h

description:
p53+/+ 24h
Gene expression after 24h in doxorubicin-treated wild-type p53 cells.

source_name: MCF10A p53+/+, doxorubicin, 24h-RNA

value: 24 hours


title: CD161- NK cell donor 3

value: Donor 3


title: CD161+ NK cell donor 2

value: Donor 2


title: p53+/+_dox_12h

description:
p53+/+ 12h
Gene expression after 12h in doxorubicin-treated wild-type p53 cells.

source_name: MCF10A p53+/+, doxorubicin, 12h-RNA

value: 12 hours


title: CD161- NK cell donor 2


title: CD161+ NK cell donor 3


title: p53−/−_dox_24h

description:
p53-/- 24h
Gene expression after 24h in doxorubicin-treated p53-null cells.

source_name: MCF10A p53−/−, doxorubicin, 24h-RNA


title: p53−/−_dox_12h

description:
p53-/- 12h
Gene expression after 12h in doxorubicin-treated p53-null cells.

source_name: MCF10A p53−/−, doxorubicin, 12h-RNA


title: CD161+ NK cell donor 1

value: Donor 1


title: CD161- NK cell donor 1


title: CD14+CD16++ monocytes, day 26 post-SIV infection, biological rep 1

city: Chestnut Hill

first: Kenneth

middle: C

last: Williams

state: MA

address: 140 Commonwealth Ave

department: Biology

institute: Boston College

description: Gene expression data from sorted CD14+CD16++ rhesus macaque peripheral blood monocytes, day 26 post-SIV infection

hyb_protocol: 20 ug of fragmented cRNA was hybridized with a preequilibrated Affymetrix GeneChip Rhesus Macaque Genome Array at 45°C for 16 hours

scan_protocol: GeneChips were scanned in an HP ChipScanner

data_processing: The data were analyzed with Partek Express Genomics Suite software. The data were normalized by using a robust multi-chip average (RMA) algorithm.

organism: Macaca mulatta

source_name: peripheral blood monocytes, CD14+CD16++, day 26 post-SIV infection

label_protocol: Biotinylated cRNA was prepared using the BioArray High Yield RNA Transcript Labeling kit from Enzo Diagnostics according to the manufacturer's instructions

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) according to the manufacturer’s instructions

treatment_protocol: Mononuclear cells were isolated from 10mL EDTA treated whole blood by density gradient centrifugation over Ficoll-Hypaque and stained for 15 minutes with anti-CD14-PacificBlue, anti-CD16-PE, anti-HLA-DR-PerCP-Cy-5.5, anti-CD3-FITC, and anti-CD20-APC in PBS containing 2% FBS. Monocytes were isolated by forward and side scatter characteristics and HLA-DR+CD3-CD20-CD14+ expression and sorted by FACS into subpopulations by CD14 and CD16 expression. Sorted monocytes were washed in PBS and vacuum pelleted.

tag: animal number

tag: stage of siv infection

value: day 26 post-SIV infection

value: sorted CD14+CD16++ peripheral blood monocytes


title: CD14+CD16++ monocytes, day 26 post-SIV infection, biological rep 2


title: CD14+CD16++ monocytes, day 26 post-SIV infection, biological rep 4


title: CD14+CD16++ monocytes, before SIV infection, biological rep 2

description: Gene expression data from sorted CD14+CD16++ rhesus macaque peripheral blood monocytes, pre-SIV infection

source_name: peripheral blood monocytes, CD14+CD16++, pre-SIV infection

value: pre-SIV infection