title: dt_48 weeks_fasted_rep_3 [muscle]

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: Sample name: 48M

data_processing: The data were quantile normalised using lumi library in R

source_name: muscle

label_protocol: Standard Illumina labeling protocol

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

value: 48 weeks

tag: fasting status

value: fasted

tag: diet

value: muscle


title: 5713384061_A

status: Public on May 01 2013

type: RNA

city: Seoul

first: Yuyoung

last: Lee

address: 50 Irwon-Dong, Gangnam-Gu

country: South Korea

institute: SMC

description: SAMPLE 65

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The software package to extract raw data was Genomestudio. The intensity of the probes was transformed by binary logarithm and then was normalized using the quantile normalization method.

molecule: total RNA

organism: Homo sapiens

source_name: cervical cancer

label_protocol: RNA was labelled using the WG-DASL kit from Illumina.

extract_protocol: RNA was extracted using a High Pure RNA Paraffin Kit protocol - Roche.

tag: Stage

tag: largest diameter


title: dt_48 weeks_fasted_rep_2 [muscle]

description: Sample name: 47M

label: biotin

organism: Mus musculus

tag: age

tag: strain

tag: tissue


title: T2

city: Nottingham

first: David

last: Archer

address: University Park

department: School of Biology

country: United Kingdom

institute: Nottingham University

description: gene expression data from conidia germinated for 2h in liquid ACM media

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: standard Affymetrix protocol

data_processing: GeneSpring GX 11 (Agilent Technologies, Inc), Data were normalized using the RMA algorithm. Raw intensity signal values were normalized per chip to the 75th percentile and baseline transformation to the median of all samples (time points) was used.

organism: Aspergillus niger

source_name: conidia germinated for 2h

label_protocol: GeneChip® IVT Express Kit

growth_protocol: A. niger strain N402, a cpsA1 derivative of A. niger N400 (Bos et al. 1988) was grown on Aspergillus complete medium (ACM) (containing per litre: NaNO3 6g, KCl, 0.52 g; MgSO4.7H2O, 0.52 g; KH2PO4, 1.52 g; Na2B4O7.10H2O, 0.008 mg; CuSO4.5H2O, 0.16 mg; FePO4.H2O, 0.16 mg; MnSO4.4H2O, 0.16 mg; NaMoO4.2H2O, 0.16 mg; ZnSO4, 1.6 mg, Bacto casamino acids, 1g, yeast extract, 1g, Bacto peptone, 2g, glucose, 10g, vitamins: p-aminobenzoic acid, 4mg, thiamine HCl, 0.5mg, D-biotin, 0.02mg, nicotinic acid, 1mg,  pyridoxine hydrochloride, 2.5mg, choline chloride, 0.014g, riboflavin, 1mg, agar 20g where applicable  ) for 6 days at 28oC to develop mature conidia. Conidia were harvested by washing the agar slopes with a 0.01% (w/v) Tween 80 solution. The conidial suspension was filtered through sterile synthetic wool and conidia were counted using a haemocytometer. Conidia (104/ml) were germinated in liquid ACM media for 1, 2, 4 and 6 hours at 28˚C, in 2L conical flasks containing 1000 ml of medium, shaken at 150rpm.  Germinated conidia were recovered by filtration into 0.5 ml RNA extraction buffer (0.6M NaCl, 0.2M sodium acetate, 0.1M EDTA, 4% w/v SDS) and snap frozen in liquid nitrogen. Frozen dormant or germinated conidia were mixed with 0.5ml glass beads and disintegrated in a Sartorius dismembranator (4 min, 2000rpm).

extract_protocol: RNA was extracted using the TRIzol reagent protocol (Invitrogen) according to manufacturer’s instructions, followed by an additional clean-up using RNeasy columns (Qiagen) including the on-column DNAase treatment step.

tag: developmental stage

value: conidia germinated for 2h


title: HH14 right sinus venosus slide 3 rep 2

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: HH14_Right sinus  venosus _ slide 3 _ rep2

hyb_protocol: Slides were pre-hybridized (5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 1% (w/v) bovine serum albumin, fraction V (Sigma)) for 45 minutes at 42°C to block the remaining reactive epoxide groups and reduce background signal. Cy3 and Cy5 labelled RNA samples were combined as described in the experimental design and mixed with 2x hybridization mixture to a final concentration of 5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 0.2 \mug/\muL herring sperm DNA (Invitrogen). Target-RNA mix was denatured for 5 minutes at 70°C and incubated at 42°C for 30 minutes. Hybridization was done in a GeneTAC hybridization station (Genomic Solutions) for 16 hours at 42°C with agitation. The arrays were washed at room temperature in 5 successive buffers, i.e., 1x SSC + 0.2% SDS, 0.1x SSC + 0.2% SDS, 1x SSC, 0.1x SSC and 0.001x SSC, each step lasting 4 minutes. The slides were finally pressure-air dried and stored in the dark.

scan_protocol: Slides were scanned using an Agilent G2565BA microarray scanner on a 10 micro m resolution. The resulting images were split into the red and green channels prior to feature extraction with the GenePix Pro 6.1.0.2 (Axon Instruments Inc.) software.

data_processing: Median spot intensities were imported from the genepix results files using the Limma package. Flagged spots were assigned a weight of 0.1, control spots were removed and the remaining data were normalized with lowess (parameters: span = 0.25, iterations = 2) and aquantile transformations using the R/Limma package in Bioconductor

organism: Gallus gallus

source_name: Right sinus

label_protocol: 1500 ng amplified RNA ( Ambion MessageAmp-II ) wasd labelled with either Cy3 or Cy5 as decribed by 't Hoen PA ( Nucleic Acids Res. 2003 Mar 1;31(5):e20 )

growth_protocol: Embryonic chicken were staged according to Hamburger and Hamilton. HH14 Left and Right sinus horns were isolated.

extract_protocol: Total RNA was isolated using Macherey-Nagel nucleospin columns and DnaseI treated. Quantified with the Nanodrop ND1000 and QC with an Agilent nanoChip.

value: right sinus venosus


title: 12_post

type: other

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

country: USA

institute: Oberlin College

hyb_protocol: We blocked printed peptide arrays with 0.1 mg ml-1 biotin (Sigma) in PBS for 10 min at RT with 500 rpm orbital agitation. After rinsing the arrays six times in peptide binding buffer (PBB): [50 mM Tris (Mallinckrodt Baker, Phillipsburg, NJ) pH 7.5, 150 mM NaCl (Mallinckrodt AR, Phillipsburg NJ), 0.05% NP-40 (Sigma) + 2.5% FCS), we applied mAb and pAb antibodies diluted to 1.0 μg ml–1 or patient serum diluted 1:80 in PBB. Following primary incubation for 3 h at RT with 500 rpm orbital agitation, we rinsed the arrays six times with PBB then six times in PBST before applying secondary antibody reagents (goat anti-mouse IgG, goat anti-rabbit IgG or goat anti-human IgG conjugated to Cy3, Jackson ImmunoResearch) diluted to 0.375 μg ml–1 in PBST plus 20% FCS for 30 min at RT with 500 rpm orbital agitation. We then rinsed arrays six times in PBST, three times in PBS and three times in diH20 and dried arrays in microscope slide racks centrifuged at 300 g for 5 min at RT.

scan_protocol: We immediately scanned processed peptide arrays with an Axon digital scanner and analyzed scanned images with Genepix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

label: Goat anti-Human IgG/IgM conjugated to Cy3 (Jackson Immunoresearch, West Grove, PA)

molecule: other

source_name: serum

extract_protocol: All individuals were ambulatory and generally healthy as determined by clinical history. Females of childbearing potential were tested for pregnancy by a urine sample. Volunteers at initial enrollment had no active systemic or serious concurrent illness, no history of immunodeficiency, nor any known or suspected impairment of immunologic function, including clinically significant liver disease, diabetes mellitus treated with insulin, moderate to severe renal disease, blood pressure >150/95 at screening, chronic hepatitis B or C, recent or current use of systemic immunosuppressive medication. In addition, none of the volunteers were recipients of blood or blood products within the past 6 months or blood donors within 6 weeks prior to immunization. Volunteers were screened to assure that they did not have signs of febrile illness on day of enrollment and baseline blood draw. A total of ~120 ml peripheral blood was obtained in three visits (~40 ml/visit): at day 0 (pre-vaccine), 5-7 and 28 7 days after receiving a single intramuscular dose of trivalent seasonal influenza vaccine Fluzone (Sanofi Pasteur, Swiftwater, PA). Each dose of the vaccine contained a total of 45  g of antigen corresponding to 15  g HA each of H1N1, H3N2 and B strains of the seasonal viruses included for that year. Serum was separated by centrifugation of clotted blood, and stored at -80 C before use. Serum samples from visit 1 (day 0) and 3 (day 28   7) were used for array experiments and microneutralization titer determination.

tag: h1n1 cpost

tag: h3n2 cpost

tag: b cpost

tag: molecule

value: IgG/IgM


title: MPM Epithelioid_84

city: Boston

first: Assunta

last: De Rienzo

state: Massachusetts

address: 75 Francis Street

department: Surgery

institute: Brigham and Women's Hospi

description: SAMPLE 84

hyb_protocol: 0.75 ug of total RNA was amplified using Illumina TotalPrep RNA amplification kit (Applied Biosystems, Foster City, CA, USA).  cRNA was hybridized to Illumina Human-6 Expression BeadChip (Illumina, San Diego, CA, USA) as recommended by the manufacturer

scan_protocol: The arrys were scanned by the Bead Station (Illumina, San Diego, CA, USA) as recommended by the manufacturer

data_processing: Array data processing was performed with Illumina BeadStudio software.

source_name: Tumor

label_protocol: Cy3-streptavidin (Amersham Biosciences, Little Chalfont, United Kingdom) as recommended by the manufacturer

extract_protocol: RNA was extracted using Triazol reagent (Invitrogen Corporation, Carlsbad, CA, USA) according to the manufacturer’s instructions.  DNase I (Invitrogen Corporation, Carlsbad, CA, USA) treatment was performed according to the manufacturer’s instructions

value: MPM Epithelioid


title: dt_48 weeks_fasted_rep_1 [muscle]

description: Sample name: 46M


title: 5713384049_J

description: SAMPLE 56


title: HH14 left sinus venosus slide 1 rep 4

description: HH14_Left Sinus  venosus _ slide 1 _ rep4

source_name: Left Sinus

value: left sinus venosus


title: 5713384028_K

description: SAMPLE 49


title: 5713384051_E

description: SAMPLE 61


title: MPM Epithelioid_83

description: SAMPLE 83


title: 11_post


title: 5713384028_L

description: SAMPLE 50


title: MPM Epithelioid_89

description: SAMPLE 89


title: HH14 right sinus venosus slide 4 rep 5

description: HH14_Right sinus  venosus _ slide 4 _ rep5


title: MPM Epithelioid_88

description: SAMPLE 88


title: T4

description: gene expression data from conidia germinated for 4h in liquid ACM media

source_name: conidia germinated for 4h

value: conidia germinated for 4h


title: HH14 right sinus venosus slide 6 rep 6

description: HH14_Right sinus  venosus _ slide 6 _ rep6


title: 5713384049_L

description: SAMPLE 58

value: IIA


title: 5713384049_K

description: SAMPLE 57


title: T1

description: gene expression data from conidia germinated for 1h in liquid ACM media

source_name: conidia germinated for 1h

value: conidia germinated for 1h


title: HH14 left sinus venosus slide 5 rep 6

description: HH14_Left Sinus  venosus _ slide 5 _ rep6


title: 5713384049_G

description: SAMPLE 54


title: HH14 right sinus venosus slide 2 rep 4

description: HH14_Right sinus  venosus _ slide 2 _ rep4


title: 12_pre


title: 5713384049_H

description: SAMPLE 55


title: HH14 left sinus venosus slide 6 rep 3

description: HH14_Left Sinus  venosus _ slide 6 _ rep3


title: 5713384051_C

description: SAMPLE 59


title: HH14 left sinus venosus slide 3 rep 5

description: HH14_Left Sinus  venosus _ slide 3 _ rep5


title: HH14 left sinus venosus slide 4 rep 2

description: HH14_Left Sinus  venosus _ slide 4 _ rep2


title: HH14 left sinus venosus slide 2 rep 1

description: HH14_Left Sinus  venosus _ slide 2 _ rep1


title: HH14 right sinus venosus slide 5 rep 3

description: HH14_Right sinus  venosus _ slide 5 _ rep3


title: 10_pre


title: 10_post


title: 11_pre


title: 5713384028_J

description: SAMPLE 48


title: 9_pre


title: 8_post


title: 8_pre


title: 9_post


title: 7_post


title: 5713384028_D

description: SAMPLE 44


title: kn_48 weeks_fasted_rep_3 [muscle]

description: Sample name: 42M


title: 5713384028_E

description: SAMPLE 45


title: MPM Epithelioid_78

description: SAMPLE 78


title: 7_pre


title: MPM Biphasic_81

description: SAMPLE 81

value: MPM Biphasic


title: 6_post


title: MPM Epithelioid_82

description: SAMPLE 82


title: kn_48 weeks_fasted_rep_1 [muscle]

description: Sample name: 40M


title: MPM Epithelioid_77

description: SAMPLE 77


title: 6_pre


title: kn_48 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 38M

value: non-fasted


title: MPM Epithelioid_80

description: SAMPLE 80


title: MPM Epithelioid_74

description: SAMPLE 74


title: 5713384028_B

description: SAMPLE 42


title: 5713384028_I

description: SAMPLE 47


title: kn_48 weeks_fasted_rep_2 [muscle]

description: Sample name: 41M


title: dt_48 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 45M


title: 5713384028_F

description: SAMPLE 46


title: kn_48 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 37M


title: MPM Epithelioid_79

description: SAMPLE 79


title: 5713384027_K

description: SAMPLE 39


title: 5713384028_C

description: SAMPLE 43


title: 5713384028_A

description: SAMPLE 41


title: db_48 weeks_fasted_rep_3 [muscle]

description: Sample name: 36M

value: B6.BKS(D)-Lep rdb/J


title: MPM Epithelioid_75

description: SAMPLE 75


title: 5_pre


title: 5_post


title: dt_48 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 44M


title: 4_post


title: 5713384027_L

description: SAMPLE 40


title: MPM Sarcomatoid_71

description: SAMPLE 71

value: MPM Sarcomatoid


title: 4_pre


title: 5713384027_I

description: SAMPLE 37


title: 5713384027_C

description: SAMPLE 32


title: 3_post


title: db_48 weeks_fasted_rep_1 [muscle]

description: Sample name: 34M


title: 5713384027_F

description: SAMPLE 34


title: MPM Epithelioid_67

description: SAMPLE 67


title: 3_pre


title: 5713384027_J

description: SAMPLE 38


title: db_48 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 32M


title: MPM Epithelioid_68

description: SAMPLE 68


title: 2_post


title: MPM Sarcomatoid_72

description: SAMPLE 72


title: MPM Sarcomatoid_69

description: SAMPLE 69


title: db_48 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 33M


title: ob_48 weeks_fasted_rep_2 [muscle]

description: Sample name: 29M

value: B6.V-Lep ob/J


title: MPM Sarcomatoid_66

description: SAMPLE 66


title: MPM Epithelioid_64

description: SAMPLE 64


title: 5713384008_L

description: SAMPLE 30


title: 5713384027_G

description: SAMPLE 35


title: 5713384027_H

description: SAMPLE 36


title: 5713384027_E

description: SAMPLE 33


title: MPM Sarcomatoid_73

description: SAMPLE 73


title: 2_pre


title: 1_pre


title: db_48 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 31M


title: ob_48 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 27M


title: 1_post


title: ob_48 weeks_fasted_rep_1 [muscle]

description: Sample name: 28M


title: kn_48 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 39M


title: dt_48 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 43M


title: MPM Epithelioid_65

description: SAMPLE 65


title: MPM Epithelioid_76

description: SAMPLE 76


title: MPM Sarcomatoid_70

description: SAMPLE 70


title: db_48 weeks_fasted_rep_2 [muscle]

description: Sample name: 35M


title: ob_48 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 25M


title: dt_16 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 21M

value: 16 weeks


title: 5713384008_J

description: SAMPLE 29


title: MPM Epithelioid_63

description: SAMPLE 63


title: dt_16 weeks_fasted_rep_3 [muscle]

description: Sample name: 24M


title: 5713384027_A

description: SAMPLE 31


title: ob_48 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 26M

value: 48 weeks


title: Sarcoma_59

description: SAMPLE 59

value: Sarcoma


title: 5713384008_G

description: SAMPLE 26


title: MPM Epithelioid_62

description: SAMPLE 62


title: Metastatic Thyroid Cancer_61

description: SAMPLE 61

value: Metastatic Thyroid Cancer


title: Synovial Sarcoma_60

description: SAMPLE 60

value: Synovial Sarcoma


title: 5713384008_C

description: SAMPLE 23


title: Melanoma-Malignant_56

description: SAMPLE 56

value: Melanoma-Malignant


title: Renal Cell Carcinoma - Chromophobe_58

description: SAMPLE 58

value: Renal Cell Carcinoma - Chromophobe


title: 5713384008_H

description: SAMPLE 27


title: dt_16 weeks_fasted_rep_2 [muscle]

description: Sample name: 23M

value: fasted

value: muscle


title: dt_16 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 19M


title: ob_48 weeks_fasted_rep_3 [muscle]

description: Sample name: 30M


title: 5713384008_I

description: SAMPLE 28


title: dt_16 weeks_fasted_rep_1 [muscle]

description: Sample name: 22M


title: 5713384008_F

description: SAMPLE 25


title: Synovial Sarcoma_57

description: SAMPLE 57


title: dt_16 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 20M


title: Metastatic Prostate Cancer_55

description: SAMPLE 55

value: Metastatic Prostate Cancer


title: 5713384008_B

description: SAMPLE 22

value: IIA


title: kn_16 weeks_fasted_rep_1 [muscle]

description: Sample name: 16M


title: AHY136 Opaque Untagged 136

type: genomic

city: San Francisco

first: Aaron

last: Hernday

state: Ca

institute: UC San Francisco

hyb_protocol: Hybridization followed the Agilent protocol

scan_protocol: Arrays were scanned with an Axon 4000B scanner

data_processing: Data was extracted and lowess normalized using Agilent ChIP analytics v1.3 software.

molecule: genomic DNA

organism: Candida albicans

label_protocol: Aminoallyl dUTP was incorporated during linear amplification of the genomic DNA using exo- Klenow fragment

extract_protocol: Crosslinked cells were lysed by mechanical disruption.  Genomic DNA was sheared by sonication then immunoprecipitated with monoclonal or polyclonal antibodies.

treatment_protocol: formaldehyde crosslinking

tag: phenotype

value: Opaque

tag: chip antibody

value: myc

tag: antibody vendor/catalog#

value: Biosource, AHO0062

value: No antibody


title: 5713384006_K

description: SAMPLE 19


title: Non-Hodgkins Lymphoma_53

description: SAMPLE 53

value: Non-Hodgkins Lymphoma


title: 5713384006_L

description: SAMPLE 20


title: kn_16 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 15M

value: non-fasted


title: kn_16 weeks_fasted_rep_3 [muscle]

description: Sample name: 18M

value: 16 weeks


title: AHY135 White Untagged 135

value: White


title: AHY342 White AHR1 118


title: kn_16 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 14M


title: 5713384008_D

description: SAMPLE 24


title: Renal Cell Carcinoma-Clear Cell_52

description: SAMPLE 52

value: Renal Cell Carcinoma-Clear Cell


title: AHY135 White Wor2 155


title: Metastatic Meningeal Hemangiopericytoma_54

description: SAMPLE 54

value: Metastatic Meningeal Hemangiopericytoma


title: AHY122 White Czf1-delete 69


title: AHY135 White Untagged 117


title: kn_16 weeks_fasted_rep_2 [muscle]

description: Sample name: 17M


title: 5713384008_A

description: SAMPLE 21


title: 5713384006_J

description: SAMPLE 18


title: db_16 weeks_fasted_rep_2 [muscle]

description: Sample name: 11M

value: B6.BKS(D)-Lep rdb/J


title: 5713384006_H

description: SAMPLE 16


title: db_16 weeks_fasted_rep_3 [muscle]

description: Sample name: 12M


title: Renal Cell Carcinoma-Clear Cell_51

description: SAMPLE 51


title: 5713384006_I

description: SAMPLE 17


title: AHY346 Opaque AHR1 116


title: 5713384006_F

description: SAMPLE 14


title: 5713384006_G

description: SAMPLE 15


title: kn_16 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 13M


title: Sarcoma_50

description: SAMPLE 50

value: Sarcoma


title: db_16 weeks_fasted_rep_1 [muscle]

description: Sample name: 10M


title: Rhabdomyosarcoma_47

description: SAMPLE 47

value: Rhabdomyosarcoma


title: ob_16 weeks_fasted_rep_2 [muscle]

description: Sample name: 05M

value: fasted

value: B6.V-Lep ob/J


title: db_16 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 07M

value: muscle


title: Thymoma_48

description: SAMPLE 48

value: Thymoma


title: AHY136 Opaque Czf1 68

value: Opaque


title: Myofibrosarcoma_49

description: SAMPLE 49

value: Myofibrosarcoma


title: 5713384006_E

description: SAMPLE 13


title: db_16 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 09M


title: Metastatic Meningeal Hemangiopericytoma_43

description: SAMPLE 43


title: AHY231 Opaque Wor3 059

value: myc

value: Biosource, AHO0062


title: Follicular Lymphoma_44

description: SAMPLE 44

value: Follicular Lymphoma


title: db_16 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 08M

value: non-fasted


title: Synovial Sarcoma_45

description: SAMPLE 45

value: Synovial Sarcoma


title: AHY174 Opaque Czf1-delete 70

value: No antibody


title: 5713384006_A

description: SAMPLE 9


title: Thymoma_42

description: SAMPLE 42


title: 5713384006_B

description: SAMPLE 10


title: AHY231 Opaque Wor3 056


title: AHY135 White Czf1 67

value: White


title: AHY136 Opaque Untagged 060


title: 5713384006_C

description: SAMPLE 11


title: ob_16 weeks_fasted_rep_1 [muscle]

description: Sample name: 04M

value: 16 weeks


title: ob_16 weeks_fasted_rep_3 [muscle]

description: Sample name: 06M


title: AHY205 Opaque Wor1 053


title: 5713384006_D

description: SAMPLE 12


title: Metastatic Melanoma_40

description: SAMPLE 40

value: Metastatic Melanoma


title: Monophasic Synovial Sarcoma_37

description: SAMPLE 37

value: Monophasic Synovial Sarcoma


title: Follicular Lymphoma_46

description: SAMPLE 46


title: Sarcoma_41

description: SAMPLE 41

value: Sarcoma


title: AHY203 Opaque Wor1 Wor2-delete 052


title: 5713384004_G

description: SAMPLE 5


title: 5713384004_L

description: SAMPLE 8


title: RZY219 White Wor1-delete 054


title: AHY189 Opaque Wor2 047


title: ob_16 weeks_non-fasted_rep_3 [muscle]

description: Sample name: 03M


title: 5713384004_D

description: SAMPLE 4


title: Spindle Cell Sarcoma_39

description: SAMPLE 39

value: Spindle Cell Sarcoma


title: AHY136 Opaque Untagged 048


title: AHY136 Opaque Czf1 055


title: Thymoma_36

description: SAMPLE 36


title: ob_16 weeks_non-fasted_rep_1 [muscle]

description: Sample name: 01M

value: B6.V-Lep ob/J


title: 5713384004_H

description: SAMPLE 6


title: Thyroid Carcinoma_35

description: SAMPLE 35

value: Thyroid Carcinoma


title: ob_16 weeks_non-fasted_rep_2 [muscle]

description: Sample name: 02M

value: muscle


title: AHY135 White Wor2 045


title: dt_48 weeks_fasted_rep_2 [liver]

description: Sample name: 47W

source_name: liver

extract_protocol: RNA was extracted with QIAGEN  RNeasy Lipid Tissue mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: 48 weeks

value: fasted

value: liver


title: dt_48 weeks_fasted_rep_3 [liver]

description: Sample name: 48W


title: 5713384004_C

description: SAMPLE 3


title: dt_48 weeks_fasted_rep_1 [liver]

description: Sample name: 46W


title: dt_48 weeks_non-fasted_rep_1 [liver]

description: Sample name: 43W


title: dt_48 weeks_non-fasted_rep_3 [liver]

description: Sample name: 45W


title: 5713384004_B

description: SAMPLE 2


title: 5713384004_K

description: SAMPLE 7


title: AHY135 White Efg1 042


title: AHY123 White Efg1-delete 044


title: kn_48 weeks_fasted_rep_1 [liver]

description: Sample name: 40W


title: AHY136 Opaque Efg1 037

value: Opaque


title: dt_48 weeks_non-fasted_rep_2 [liver]

description: Sample name: 44W


title: Hemangiopericytoma_34

description: SAMPLE 34

value: Hemangiopericytoma


title: AHY174 Opaque Czf1-delete 041


title: Young base -Test (Cy5) vs.Mature tip- Control (Cy3)- [Mutant cy5 , Control Cy3]

city: Bangalore

first: Mainak

last: Das Gupta

state: Karnataka

address: C.V. Raman Avenue

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description:
Young base vs Mature tip
RNA from proliferative base of 5 mm WT leaf compared with that of mature tip of 20 mm WT leaf

hyb_protocol: Agilent Arabidopsis  thaliana Gene expression Microarray 22k (AMADID: 013324): 750ng of each Cyanine-3 and Cyanine-5 labeled cRNA were combined with 50μl of 10x Blocking agent. The volume is made upto 240 ul using Nuclease free water. 10μl of 25x Fragmentation buffer (Agilent) were added and incubated at 60°C for 30 minutes in dark. The fragmented cRNA were mixed with 250μl of 2x Hybridization Buffer (Agilent). About 490μl of the resulting mixture was applied to the Gene Expression Microarray (Agilent Technologies), and hybridized at 65°C for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer-I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer-II at 37ºC. Slides were finally rinsed with Acetonitrile for cleaning up and drying.Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226)& Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) : 825ng of cy3 labeled  samples and 825ng of cy5 labeled samples were pooled, fragmented and hybridized and data from these channels were used for comparison to test hybridizations of respective channels.  Fragmentation of labeled aRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1

data_processing: Data Analysis was performed using Genespring GX Software using LOWESS normalization.

organism: Antirrhinum majus

source_name: Leaf 20 mm (Mature tip)

label_protocol: Agilent Arabidopsis  thaliana Gene expression Microarray 22k (AMADID: 013324):Low RNA Input Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2μl of oligo dT-T7 Promoter Primer in nuclease-free water at 65ºC for 10 min followed by incubation with 4.0μl of 5× First strand buffer, 2μl of 0.1M DTT, 1 μl of 10mM dNTP mix, 1μl of 200 U/μl MMLV RT, and 0.5μl of 40U/μl RNaseOUT, at 40ºC for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 μl of 10 mM Cyanine-3 CTP or 2.4 μl of 10 mM Cyanine-5 CTP (Perkin-Elmer, Boston, MA), 20μl of 4X Transcription buffer, 8 μl of NTP mixture, 6 μl of 0.1M DTT, 0.5 μl of RNaseOUT, 0.6μl of Inorganic pyrophosphatase, 0.8 μl of T7 RNA polymerase, and 15.3μl of nuclease-free water at 40 ºC for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization.Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226)& Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) : The samples for Gene expression were labeled using Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523).  Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 42°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dyes Cy3 CTP(Agilent) for control samples and Cy5 CTP(Agilent) for test samples were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Wild type Antirrhinum plants (stock JI-98) and cin-756 mutants were grown in continuous light or 16/8 hrs light/dark regime at 25 ºC.  Third and fourth leaves were used for all the experimental analysis.

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

tag: genotype/variation

value: leaf

tag: leaf length

value: 20 mm (Mature tip)

source_name: Leaf 3-5 mm (Young base)

value: 3-5 mm (Young base)


title: AHY123 White Efg1-delete 038

value: White

value: No antibody


title: Metastatic Melanoma_33

description: SAMPLE 33

value: Metastatic Melanoma


title: AHY122 White Czf1-delete 040


title: Melanoma-Malignant_29

description: SAMPLE 29

value: Melanoma-Malignant


title: Metastatic Prostate Cancer_30

description: SAMPLE 30

value: Metastatic Prostate Cancer


title: Synovial Sarcoma_32

description: SAMPLE 32

value: Synovial Sarcoma


title: Sarcoma_31

description: SAMPLE 31

value: Sarcoma


title: kn_48 weeks_fasted_rep_2 [liver]

description: Sample name: 41W

tag: fasting status


title: CIN (cy3) vs. WT (cy5)  Dye Swap-[Mutant cy3 , Control Cy5]_Rep2 (US45103024_251634110001_S01_GE2-v5_95_Feb07_1_2.txt)

description:
Mutant vs WT
RNA extracted from 3-5 mm long (young) cin and wild type leaves

source_name: Leaf 3-5 mm


title: 5713384004_A

description: SAMPLE 1


title: Metastatic Alveolar Soft Part Sarcoma_38

description: SAMPLE 38

value: Metastatic Alveolar Soft Part Sarcoma


title: AHY136 Opaque Efg1 043


title: AHY135 White Efg1 036


title: CIN (cy5) vs. WT (cy3)- [Mutant cy5 , Control Cy3] (20mm _leaves mature)

description:
Mutant vs WT
RNA extracted from 20 mm long (mature) cin and wild type leaves

source_name: Leaf 20 mm

value: 20 mm


title: kn_48 weeks_non-fasted_rep_1 [liver]

description: Sample name: 37W

value: 48 weeks

value: non-fasted

tag: diet


title: db_48 weeks_fasted_rep_1 [liver]

description: Sample name: 34W

value: fasted

value: B6.BKS(D)-Lep rdb/J

value: liver


title: kn_48 weeks_non-fasted_rep_2 [liver]

description: Sample name: 38W


title: Metastatic Thyroid Cancer_25

description: SAMPLE 25

value: Metastatic Thyroid Cancer


title: Lymphocytic Lymphoma_26

description: SAMPLE 26

value: Lymphocytic Lymphoma


title: Papillary Thyroid Carcinoma_28

description: SAMPLE 28

value: Papillary Thyroid Carcinoma


title: CIN (cy5) vs. WT (cy3)- [Mutant cy5 , Control Cy3]_Rep1

value: leaf


title: Papillary Thyroid Carcinoma_23

description: SAMPLE 23


title: kn_48 weeks_fasted_rep_3 [liver]

description: Sample name: 42W


title: db_48 weeks_fasted_rep_2 [liver]

description: Sample name: 35W


title: Papillary Thyroid Carcinoma_24

description: SAMPLE 24


title: kn_48 weeks_non-fasted_rep_3 [liver]

description: Sample name: 39W


title: db_48 weeks_fasted_rep_3 [liver]

description: Sample name: 36W


title: Thymoma_27

description: SAMPLE 27

value: Thymoma


title: AHY136 Opaque Czf1 035

value: Opaque

value: No antibody


title: AHY135 White Czf1 034

value: White


title: db_48 weeks_non-fasted_rep_3 [liver]

description: Sample name: 33W


title: ob_48 weeks_fasted_rep_2 [liver]

description: Sample name: 29W

value: B6.V-Lep ob/J


title: Metastatic Prostate Cancer_18

description: SAMPLE 18

value: Metastatic Prostate Cancer


title: AHY136 Opaque Wor2 031


title: Tissue from normal bladder_Normal_5

city: Grand Rapids

first: Jacob

last: Zhang

state: MI

address: 333 Bostwick Ave

department: Cancer Genetics

institute: Van Andel Institute

description: Gene expression data from Tissue from normal bladder

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

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 10 entrez gene ID CDF was used. Data were then rma normalized using R and the bioconductor suite of analysis tools (eset <- rma(ab))

source_name: Tissue from normal bladder

label_protocol: 10 ug of Qiagen-purified total RNA was labeled with 6ul of 1mg/ml R-Phycoerythrin Streptavidin (SAPE)

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's protocol

value: normal bladder


title: AHY122 White Wor2-delete 032


title: AHY136 Opaque Wor2 030


title: Pleomorphic Sarcoma_21

description: SAMPLE 21

value: Pleomorphic Sarcoma


title: db_48 weeks_non-fasted_rep_2 [liver]

description: Sample name: 32W

value: 48 weeks


title: Tissue from normal bladder_Normal_6


title: ob_48 weeks_fasted_rep_1 [liver]

description: Sample name: 28W


title: Stomach Cancer-Stromal Sarcoma_17

description: SAMPLE 17

value: Stomach Cancer-Stromal Sarcoma


title: ob_48 weeks_fasted_rep_3 [liver]

description: Sample name: 30W

value: fasted


title: Tissue from normal bladder_Normal_8


title: AHY69 Opaque Czf1


title: Tissue from normal bladder_Normal_7


title: Sarcoma_22

description: SAMPLE 22

value: Sarcoma


title: Hemangioendothelioma_20

description: SAMPLE 20

value: Hemangioendothelioma


title: Non-Hodgkins Lymphoma_19

description: SAMPLE 19

value: Non-Hodgkins Lymphoma


title: db_48 weeks_non-fasted_rep_1 [liver]

description: Sample name: 31W

value: non-fasted

value: B6.BKS(D)-Lep rdb/J

value: liver


title: AHY69 Opaque Wor2


title: AHY122 White Wor2-delete 033


title: Metastatic Melanoma_16

description: SAMPLE 16

value: Metastatic Melanoma


title: ob_48 weeks_non-fasted_rep_1 [liver]

description: Sample name: 25W


title: RZY511 Opaque Wor1 031

value: Opaque


title: Metastatic Thymoma_14

description: SAMPLE 14

value: Metastatic Thymoma


title: RZY219 White Wor1-delete 032

value: White

value: No antibody


title: Metastatic Prostate Cancer_15

description: SAMPLE 15

value: Metastatic Prostate Cancer


title: Synovial Sarcoma_12

description: SAMPLE 12

value: Synovial Sarcoma


title: ob_48 weeks_non-fasted_rep_3 [liver]

description: Sample name: 27W

value: B6.V-Lep ob/J


title: ob_48 weeks_non-fasted_rep_2 [liver]

description: Sample name: 26W

value: 48 weeks


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_ EGDeΔprfA in MEM_replicate1

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description: Gene expression in biofilm-grown cells from EGDeΔprfA collected  from  cultivated statically at 37°C for 48 h in MEM.

hyb_protocol: Fluorescence dye labeled cDNA was hybridized to Agilent Listeria monocytogenes customized Whole Genome 8×*15K array according to the instructions of Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 8.0.0.0 was used for background subtraction and signal median normalization.

organism: Listeria monocytogenes EGD-e

label_protocol: RNA was amplified and labeled using Agilentagilent FairPlay III Microarray Labeling Kit.

growth_protocol: Listeria monocytogenes EGDe (serotype 1/2a) and its prfA isogenic deletion strain EGDeΔprfA are gifts from Prof. W. Goebel of Department of Microbiology in Wuerzburg University in Germany. Individual colonies of the stock culture were inoculated into 5 mL of brain heart infusion (BHI) broth (Difco, Sparks, MD) and incubated at 37oC with shaking (180 rpm) for overnight.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacture’s instructions. The quantity of RNA in each sample was assessed spectrophotometerically (NanoDrop Technologies, Wilmington, DE) and RNA integrity was assessed by formaldehyde agarose gel electrophoresis.

treatment_protocol: Biofilms for the microarray analysis were grown on 10 cm diameter, 2 cm deep sterile polystyrene petri dishes (Nest Biotechnology Co., Ltd) filled with 20 mL of minimal essential medium (MEM) or BHI and cultivated statically at 37°C for 48 h. The planktonic cells were collected in exponential phase by centrifugation when the optical density of cells at 600 nm reached 0.6.

tag: genotype

value: ΔprfA

tag: cell

value: biofilm-grown cells

tag: growth condition


title: RZY219 White Wor1-delete 006

tag: strain


title: dt_16 weeks_fasted_rep_2 [liver]

description: Sample name: 23W

tag: age

value: 16 weeks

value: fasted

tag: tissue


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_EGDe in MEM_replicate2

description: Gene expression in biofilm-grown cells from EGDe collected  from  cultivated statically at 37°C for 48 h in MEM.

value: wildtype


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_ EGDeΔprfA in MEM_replicate2

value: cultivated statically at 37°C for 48 h in MEM


title: Renal Cell Carcinoma-Clear Cell_13

description: SAMPLE 13

value: Renal Cell Carcinoma-Clear Cell


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_EGDe in MEM_replicate3


title: AHY136 Opaque Wor2 018


title: RZY511 Opaque Wor1 003


title: RZY219 White Wor1-delete 033


title: Tissue from normal bladder_Normal_4

value: normal bladder


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_ EGDeΔprfA in MEM_replicate3


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_EGDe in BHI_replicate2

description: Gene expression in biofilm-grown cells from EGDe collected  from  cultivated statically at 37°C for 48 h in BHI.


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_EGDe in MEM_replicate1


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_EGDe in BHI_replicate3

value: cultivated statically at 37°C for 48 h in BHI


title: Tissue from normal bladder_Normal_2


title: Tissue from normal bladder_Normal_1


title: Pleomorphic Sarcoma_9

description: SAMPLE 9

value: Pleomorphic Sarcoma


title: RZY511 Opaque Wor1 034

value: Opaque


title: dt_16 weeks_fasted_rep_1 [liver]

description: Sample name: 22W

value: liver


title: dt_16 weeks_fasted_rep_3 [liver]

description: Sample name: 24W


title: dt_16 weeks_non-fasted_rep_2 [liver]

description: Sample name: 20W

value: non-fasted


title: dt_16 weeks_non-fasted_rep_3 [liver]

description: Sample name: 21W


title: Tissue from normal bladder_Normal_3


title: biofilm-grown cells_10 ml_cultivated statically at 37°C for 48 h_EGDe in BHI_replicate1


title: Renal Cell Carcinoma-Clear Cell_10

description: SAMPLE 10


title: planktonic cells_10 ml_OD0.6_EGDe in MEM_replicate3

description: Gene expression in planktonic cells from EGDe collected  from exponential phase in MEM with OD0.6

value: planktonic cells

value: exponential phase in MEM with OD0.6


title: Sarcoma_11

description: SAMPLE 11

value: Sarcoma


title: tissue from urothelial cell carcinoma_UCa_27

description: Gene expression data from tissue from urothelial cell carcinoma

source_name: tissue from urothelial cell carcinoma

value: urothelial cell carcinoma


title: planktonic cells_10 ml_OD0.6_EGDe in MEM_replicate2


title: dt_16 weeks_non-fasted_rep_1 [liver]

description: Sample name: 19W


title: RZY511 Opaque Wor1 022

value: No antibody


title: tissue from urothelial cell carcinoma_UCa_23


title: tissue from urothelial cell carcinoma_UCa_21


title: tissue from urothelial cell carcinoma_UCa_25


title: planktonic cells_10 ml_OD0.6_EGDe in MEM_replicate1


title: tissue from urothelial cell carcinoma_UCa_20


title: tissue from urothelial cell carcinoma_UCa_22


title: tissue from urothelial cell carcinoma_UCa_26


title: Sarcoma_6

description: SAMPLE 6


title: kn_16 weeks_fasted_rep_3 [liver]

description: Sample name: 18W


title: planktonic cells_10 ml_OD0.6_EGDe in BHI_replicate3

description: Gene expression in planktonic cells from EGDe collected  from exponential phase in BHI with OD0.6

value: exponential phase in BHI with OD0.6


title: Sarcoma_7

description: SAMPLE 7


title: tissue from urothelial cell carcinoma_UCa_24


title: Spindle Cell Sarcoma_5

description: SAMPLE 5

value: Spindle Cell Sarcoma


title: kn_16 weeks_fasted_rep_2 [liver]

description: Sample name: 17W

value: 16 weeks

value: fasted


title: kn_16 weeks_fasted_rep_1 [liver]

description: Sample name: 16W


title: tissue from urothelial cell carcinoma_UCa_18


title: cMAQC b_4

description: SAMPLE 4

source_name: RNA control

value: control


title: tissue from urothelial cell carcinoma_UCa_19


title: planktonic cells_10 ml_OD0.6_EGDe in BHI_replicate1

value: wildtype


title: iMAQCb_2

description: SAMPLE 2


title: Metastatic Melanoma_8

description: SAMPLE 8

value: Metastatic Melanoma


title: kn_16 weeks_non-fasted_rep_3 [liver]

description: Sample name: 15W


title: cMAQC a_3

description: SAMPLE 3


title: planktonic cells_10 ml_OD0.6_EGDe in BHI_replicate2


title: kn_16 weeks_non-fasted_rep_2 [liver]

description: Sample name: 14W


title: db_16 weeks_fasted_rep_1 [liver]

description: Sample name: 10W

value: B6.BKS(D)-Lep rdb/J


title: kn_16 weeks_non-fasted_rep_1 [liver]

description: Sample name: 13W


title: EndothelialCells_High WSS_24hrs_Rep1

city: Buffalo

first: Jennifer

last: Dolan

state: NY

address: 3435 Main Street

department: Neuroscience

institute: University at Buffalo

description: High WSS2

hyb_protocol: Standard protocol described in Affymetrix GeneChip 3' IVT Express Kit.

scan_protocol: Affymetrix GeneChip Scanner and software.

data_processing: All analyses were performed in R/Bioconductor. Affymetrix bovine CEL files were preprocessed and normalized using RMA [see supplementary file on Series record]. Informative, valid probe sets were determined using FARMS (Talloen et al., 2007, Bioinformatics 23(21):2897-2902). FARMS represents an unbiased approach to remove non-informative probe sets based on their intra-probe set correlation. Sample to sample data exploration was performed using unsupervised hierarchial clustering and principle component analysis. Differential gene expression analysis was performed using a linear model approach and employing an empirical Bayes method for calculation of statistical significance (Bioconductor,limma package). We identified those probe sets whose expression were significantly enriched or depleted by at least two fold change and statistically significant following 5% FDR adjustment of p-values.

organism: Bos taurus

source_name: endothelial cells exposed to a high wall shear stress for 24 hrs

label_protocol: Conducted using Affymetrix standard protocols.

growth_protocol: Bovine aortic endothelial cells were seeded on glass coverslips and allowed to grow to confluence for 5 days. Cells were maintained in DMEM with 10% FBS and 1% penicilin/streptomycin.

extract_protocol: Total RNA was extracted following Qiagen RNeasy Mini Kit protocol using spin column technology. Purity and integrity were confirmed.

treatment_protocol: 24 hrs before the flow experiments started culture media was changed and cells were allowed to equilibrate in flow media containing DMEM, 5% FBS, 1% pen/strep, and 8% Dextran 70. For treatment, cells were subjected to either positive wall shear stress gradient or a negative wall shear stress gradient by placement in a flow loop system in which media was circulated over the cells to produce the mentioned flow conditions. After 24 hours the experiment was ended and coverslips of cells removed from the chamber.

value: aorta

tag: cell type

value: endothelial cell

tag: passage

tag: stress

value: High wall shear stress


title: FsrB mutant after 0 min, without GBAP addition, biological rep2

city: Oeiras

first: Neuza

last: Teixeira

address: Av. da República, Estação Agronómica Nacional

country: Portugal

institute: ITQB

description: Gene expression data from E. faecalis ∆fsrB after 0 minutes, without GBAP addition.

hyb_protocol: Samples were hybridized to a previously described custom E. faecalis Affymetrix GeneChip.

scan_protocol: GeneChips were scanned at the University of Iowa DNA Core Facility.

data_processing: Data was analyzed using Affymetrix GeneChip Operating Software, which identifies probe sets with statistically significant hybridization over background (i.e. presence versus absence calls) and among those, identifies probe sets for which hybridization is significantly increased or decreased in pairwise comparisons of microarray experiments. Signal log ratios for differentially expressed probe sets were averaged and converted to fold change values.

organism: Enterococcus faecalis V583

label_protocol: Biotinylated cRNA were prepared with the BioArray Terminal Labeling Kit (Enzo Life Sciences).

growth_protocol: E. faecalis strains were grown in BHI, at 37ºC, until 0.4 OD (600nm). At this point, purified GBAP was added to a final concentration of 10nM in the culture. For others samples we did the same protocol but without GBAP.

extract_protocol: RNA was stabilized with RNA protect (Qiagen) and RNA was isolated with RNeasy columns per the manufacturer's instructions (Qiagen). Samples were treated with RNase-free DNase I (Roche) to remove contaminating DNA

value: ∆fsrB


title: db_16 weeks_fasted_rep_2 [liver]

description: Sample name: 11W

value: liver


title: iMAQC a_1

description: SAMPLE 1


title: FsrB mutant after 0 min, without GBAP addition, biological rep1

description: Gene expression data from E. faecalis ∆fsrB after  0 minutes, without  GBAP addition.


title: db_16 weeks_fasted_rep_3 [liver]

description: Sample name: 12W


title: ∆fsrB∆gelE∆sprE mutant after 0 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis ∆fsrB∆gelE∆sprE after 0 minutes of GBAP addition.

value: ∆fsrB∆gelE∆sprE


title: exponential E. coli after SHX rep1

city: frederick

first: cedric

last: cagliero

address: 1050 boyles street

institute: NCI/NIH

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: SHX 30min.

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Growth in LB at 37C until OD600 = 0.2

extract_protocol: The total RNA is purified by a hot phenol method

treatment_protocol: serine hydroxamate 500 ug/ml is added to induce stringent response

value: SHX 30min.


title: FsrB mutant after 10 min, without GBAP addition, biological rep1

description: Gene expression data from E. faecalis ∆fsrB after 10 minutes, without GBAP addition.


title: EndothelialCells_Baseline WSS_24hrs_Rep2

description: Baseline WSS3

source_name: endothelial cells exposed to a baseline wall shear stress for 24 hrs

value: Baseline wall shear stress


title: EndothelialCells_Baseline WSS_24hrs_Rep3

description: Baseline WSS4


title: CD16bright/CD62Ldim t=4, rep4

city: Nijmegen

first: Stan

middle: de

last: Kleijn

address: Kapittelweg 29

department: Laboratory of pediatric infectious diseases

institute: Radboud University Nijmegen Medical Centre

hyb_protocol: Standard Affymetrix hybridization and wash protocol.

scan_protocol: GeneChip scanner 3000 using the Affymetrix scan protocol.

data_processing:
Affymetrix Expression Console 1.1 core RMA sketch. Core exons from the hg18 genome were used in the analysis.
Probe group file: HuEX-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: CD16bright/CD62Ldim neutrophils, LPS, 4 hr

label_protocol: Affymetrix terminal labeling protocol.

extract_protocol: Qiagen RNeasy total RNA isolation.

treatment_protocol: After LPS infusion, blood was taken from healthy volunteers at t=0 and t=4 hours. Neutrophils were FACS sorted based on CD16 and CD62L expression.

tag: disease state

value: healthy

tag: treatment

value: lipopolysaccharide (LPS)

tag: treatment duration

value: 4 hr

value: isolated circulating neutrophils

tag: neutrophil subset


title: EndothelialCells_High WSS_24hrs_Rep3

description: High WSS4


title: FsrB mutant after 10 min, without GBAP addition, biological rep2

source_name: E. faecalis ∆fsrB after 10 minutes, without GBAP addition

tag: genotype/variation


title: exponential E. coli in LB rep2

source_name: exp. phase

value: exp. phase


title: ∆fsrB∆gelE∆sprE mutant after 10 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis ∆fsrB∆gelE∆sprE after 10 minutes of GBAP addition.


title: ∆fsrB∆gelE∆sprE mutant after 0 min of GBAP addition, biological rep1

description: Gene expression data from E. faecalis ∆fsrB∆gelE∆sprE after  0 minutes of GBAP addition.


title: EndothelialCells_High WSS_24hrs_Rep2

description: High WSS3


title: CD16dim/CD62Lbright t=4, rep4

source_name: CD16dim/CD62Lbright neutrophils, LPS, 4 hr


title: exponential E. coli in LB rep1

source_name: exp. Phase

value: exp. Phase


title: ∆fsrB∆gelE∆sprE mutant after 10 min of GBAP addition, biological rep1

source_name: E. faecalis ∆fsrB∆gelE∆sprE after 10 minutes of GBAP addition


title: CD16bright/CD62Lbright t=4, rep4

source_name: CD16bright/CD62Lbright neutrophils, LPS, 4 hr


title: db_16 weeks_non-fasted_rep_3 [liver]

description: Sample name: 09W

source_name: liver

value: 16 weeks

value: non-fasted


title: exponential E. coli after SHX rep2


title: db_16 weeks_non-fasted_rep_2 [liver]

description: Sample name: 08W

value: B6.BKS(D)-Lep rdb/J


title: EndothelialCells_Positive WSSG_24hrs_rep3

description: Positive Gradient4

source_name: endothelial cells exposed to a positive wall shear stress gradient for 24 hrs

value: aorta

value: positive wall shear stress gradient


title: EndothelialCells_Baseline WSS_24hrs_Rep1

description: Baseline WSS2

value: endothelial cell


title: ob_16 weeks_fasted_rep_3 [liver]

description: Sample name: 06W

value: fasted

value: B6.V-Lep ob/J


title: EndothelialCells_Negative WSSG_24hrs_rep1

description: Negative Gradient2

source_name: endothelial cells exposed to a negative wall shear stress gradient for 24 hrs

value: negative wall shear stress gradient


title: ∆fsrB∆sprE mutant after 0 min of GBAP addition, biological rep1

description: Gene expression data from E. faecalis ∆fsrB∆sprE after  0 minutes of GBAP addition.

value: ∆fsrB∆sprE


title: db_16 weeks_non-fasted_rep_1 [liver]

description: Sample name: 07W

value: liver


title: ∆fsrB∆sprE mutant after 0 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis ∆fsrB∆sprE after 0 minutes of GBAP addition.


title: EndothelialCells_Positive WSSG_24hrs_rep2

description: Positive Gradient3


title: EndothelialCells_Negative WSSG_24hrs_rep2

description: Negative Gradient3


title: ob_16 weeks_fasted_rep_1 [liver]

description: Sample name: 04W


title: ∆fsrB∆sprE mutant after 10 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis ∆fsrB∆sprE after 10 minutes of GBAP addition.


title: EndothelialCells_Negative WSSG_24hrs_rep3

description: Negative Gradient4


title: CD16dim/CD62Lbright t=4, rep2

value: healthy


title: CD16bright/CD62Lbright t=4, rep3

value: lipopolysaccharide (LPS)


title: CD16bright/CD62Lbright t=0, rep3

source_name: CD16bright/CD62Lbright neutrophils, LPS, 0 hr

value: 0 hr


title: EndothelialCells_Positive WSSG_24hrs_rep1

description: Positive Gradient2


title: CD16dim/CD62Lbright t=4, rep3

value: 4 hr

value: isolated circulating neutrophils


title: ob_16 weeks_non-fasted_rep_1 [liver]

description: Sample name: 01W


title: ∆fsrB∆gelE mutant after 0 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis  ∆fsrB∆gelE after 0 minutes of GBAP addition.

value: ∆fsrB∆gelE


title: CD16bright/CD62Lbright t=0, rep4


title: ∆fsrB∆gelE mutant after 0 min of GBAP addition, biological rep1

description: Gene expression data from E. faecalis  ∆fsrB∆gelE after  0 minutes of GBAP addition.


title: ob_16 weeks_fasted_rep_2 [liver]

description: Sample name: 05W

value: 16 weeks


title: ∆fsrB∆sprE mutant after 10 min of GBAP addition, biological rep1

source_name: E. faecalis ∆fsrB∆sprE after 10 minutes of GBAP addition


title: CD16bright/CD62Ldim t=4, rep2


title: ob_16 weeks_non-fasted_rep_2 [liver]

description: Sample name: 02W

value: non-fasted


title: HIV-CP-6

city: Shenyang

first: zining

last: zhang

state: Liaoning

address: No 155, Nanjingbei street, Heping District

department: 1st affiliated hospital

institute: China Medical University

description: This sample is from one of the total seven HIV chronic disease progressors enrolled in this study.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249)

source_name: Peripheral blood mononuclear cell

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using NucleoSpin® RNA clean-up (MACHEREY-NAGEL, Germany) according to the manufacturer's instructions.

tag: gender

value: Male

tag: disease progression

value: CP

tag: estimated days after hiv infection


title: CD16bright/CD62Lbright t=4, rep2


title: CD16bright/CD62Ldim t=4, rep3


title: ∆fsrB∆gelE mutant after 10 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis  ∆fsrB∆gelE after 10 minutes of GBAP addition.


title: ∆fsrB∆gelE mutant after 10 min of GBAP addition, biological rep1

source_name: E. faecalis ∆fsrB∆gelE after 10 minutes of GBAP addition


title: cells expressing the marker NG2: NG2-III

city: Grenoble

first: jacques

last: Baudier

address: 17 Rue des Martyrs

department: iRTSV

country: France

institute: INSERM

hyb_protocol: Ten micrograms of biotin-labeled aRNA was fragmented using 5 µl of fragmentation buffer in a final volume of 20 µl, then was mixed with 240 µl of Amersham hybridization solution (GE Healthcare Europe GmbH, Freiburg, Germany) and injected onto CodeLink Uniset Rat Whole Genome bioarrays (40K) containing 36000 rat oligonucleotide gene probes (both from GE Healthcare Europe GmbH, Freiburg, Germany). Arrays were hybridized overnight at 37°C at 300 rpm in an incubator. The slides were washed in stringent TNT buffer at 46°C for 1 hour, and then a streptavidin-cy5 (GE Healthcare) detection step was performed. Each slide was incubated for 30 min in 3.4 ml of streptavidin-cy5 solution as described previously (10), then was washed 4 times in 240 ml of TNT buffer, rinsed twice in 240 ml of water containing 0.2% Triton X-100, and dried by centrifugation at 600 rpm.

scan_protocol: The slides were scanned using a Genepix 4000B scanner (Axon, Union City, USA) and Genepix software, with the laser set at 635 mm, the laser power at 100%, and the photomultiplier tube voltage at 60%. The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and normalized hybridization signal for each spot on the array.

data_processing: Fluorescence intensity signal of each spot and threshold of detection were measured using Codelink Expression Analysis v4.2 software (Amersham GE). Fluorescence data were normalized using the global method of the 50th percentile (median). Detection threshold was calculated using the normalized signal intensity of the 100 negative control samples in the array + 3 standards deviations (SD); spots with signal intensities below this threshold were referred as ‘absent’. The quality of processing was evaluated by generating scatter plots of positive signal distribution. Signal intensities were then converted to log base 2 values. Filtering was performed using Genespring software 7.0 (Agilent Technology®, Santa Clara, CA, USA).

organism: Rattus norvegicus

source_name: cell population NG2 derived from OPC isolated from newborn rats and expressing only NG2

label_protocol: Total RNAs (10 ng, initial quantity) were amplified and biotin labeled by two rounds of in vitro transcription (dIVT) with MessageAmp® II aRNA Amplification kit (Ambion®) following the manufacturer’s protocol and as described previously (Van Gelder R.N., et al., 1990). Different concentrations of synthetic mRNA (spikes) were added to all samples before amplification; these positive controls were used to ascertain sensibility, quality and to normalize data. aRNA quantity and quality were measured with NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) at 260 nm and 280 nm in water. aRNA quality was assessed with Agilent 2100 BioAnalyser (Agilent) using RNA 6000 Nano LabChip kit (Agilent®) and following the manufacturer’s protocol.

extract_protocol: Total RNA were extracted from frozen cells with the Qiagen RNeasy minikit (Qiagen®, Hilden, Germany) following manufacturer’s protocol and quantified with Qubit (Invitrogen)- using  Quant-IT RNA assay (Molecular Probes). Quality of total RNA was verified by microchips on Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). The 28S / 18S ratio was between 1.8 and 2.1 and RIN was 8.7 minimum.

value: newborn

value: oligodendrocyte progenitor cells (OPC)

tag: cell subpopulation


title: FsrB mutant after 0 min of GBAP addition, biological rep1

description: Gene expression data from E. faecalis ∆fsrB after  0 minutes of GBAP addition.

value: ∆fsrB


title: FsrB mutant after 0 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis ∆fsrB after 0 minutes of GBAP addition.


title: HIV-CP-5


title: CD16dim/CD62Lbright t=4, rep1


title: ob_16 weeks_non-fasted_rep_3 [liver]

description: Sample name: 03W

tag: fasting status

value: B6.V-Lep ob/J

tag: diet


title: cells expressing the marker A2B5 and are NG2 positive: NG2/A2B5-III

source_name: cell population NG2/A2B5 derived from OPC isolated from newborn rats and expressing A2B5 and NG2


title: HIV-RP-5

description: This sample is from one of the total six HIV rapid disease progressors enrolled in this study.

value: RP


title: FsrB mutant after 10 min of GBAP addition, biological rep2

description: Gene expression data from E. faecalis ∆fsrB after 10 minutes of GBAP addition.


title: HIV-CP-7


title: CD16bright/CD62Lbright t=4, rep1


title: HIV-CP-3


title: CD16bright/CD62Lbright t=0, rep2


title: CD16bright/CD62Ldim t=4, rep1


title: cells expressing the marker A2B5 and are NG2 positive: NG2/A2B5-II


title: cells expressing the marker NG2: NG2-I


title: FsrB mutant after 10 min of GBAP addition, biological rep1

source_name: E. faecalis ∆fsrB after 10 minutes of GBAP addition


title: cells expressing the marker NG2: NG2-II


title: CD16bright/CD62Lbright t=0, rep1


title: cells expressing the marker A2B5 and are NG2 positive: NG2/A2B5-I


title: cells expressing the marker O4 and are NG2 negative: O4-III

source_name: cell population O4 derived from OPC isolated from newborn rats and expressing O4


title: cells expressing the marker O4 and are NG2 negative: O4-II


title: HIV-CP-2


title: HIV-Validation cohort-CP-7

data_processing: Preprocessing of raw data and statistical analyses were performed using RealTime StatMiner software. U1 and U6 were used in the training cohort and RNY3 and U6 was used in the validation cohort for normalization.

label: SYBR Green

label_protocol: With this universal tag, SYBR-based real-time quantitative PCR method was performed with miRNA-specific forward primers and a reverse universal primer mix.

extract_protocol: Total RNA of PBMCs was isolated with Trizol reagent (Invitrogen). E coli polyA polymerase was used to add adenines at the 3' end of RNA molecules lacking a polyA tail. After oligodT annealing, a universal tag was attached to the 3' end of cDNAs during cDNA synthesis using retro-transcriptase Superscript III (Invitrogen).

value: control

value: male


title: HIV-Validation cohort-CP-9


title: HIV-Validation cohort-CP-10


title: HIV-Validation cohort-CP-8


title: HIV-RP-6


title: HIV-CP-1


title: HIV-Validation cohort-CP-6


title: HIV-CP-4


title: HIV-RP-4


title: HIV-Validation cohort-CP-5


title: cells expressing the marker O4 and are NG2 negative: O4-I


title: HIV-RP-3


title: HIV-Validation cohort-CP-1


title: HIV-Validation cohort-CP-4


title: HIV-Validation cohort-CP-2


title: HIV-Validation cohort-CP-3


title: HIV-RP-2


title: Striatum_6-OHDA_STN-HFS_sample3_rep1

city: MARSEILLE

first: Sylviane

last: Lortet

address: parc scientifique de Luminy

institute: IBDML

description: Striatum gene expression of STN-HFS treated rat

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), 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 9.1 (Agilent) using default parameters (protocol: GE1-v5_95_Feb07  and Grid: 014879_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: Striatum, 6-OHDA, STN-HFS

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

extract_protocol: Total RNA was isolated using the Rneasy Mini  Kit (Qiagen) with DNAse treatment on the column according to manufacturer's recommantation RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The RNA samples selected for microarray and for real time PCR experiments had an >8.0 RNA integrity number on a scale of 10. Each RNA was stored at -80°C until use cRNA labeling and array hybridization.

treatment_protocol: Unilateral injection of 9 μg of 6-OHDA dissolved in 4.5 μL of 0.9% sterile NaCl containing 0.1% ascorbic acid, in the left SNc. Chronic L-DOPA treatment for 19 days, two injections per day, at a 12-h interval, of 25 mg/kg L-DOPA and 12.5 mg/kg benserazide dissolved in 0.9% NaCl. Deep brain stimulation: unilateral implantation of one platinum-iridium electrode in the STN ipsilateral to the lesion side. STN-HFS was applied continuously for 5 days in freely moving rats. The stimulation parameters were: frequency:130 Hz; pulse width 80 μs; intensity 60 μA.

value: Striatum

tag: stn-hfs

value: yes

tag: l-dopa treatment

value: no


title: HIV-RP-1


title: CAY3853 a WOR1 OE 2

city: Providence

first: Richard

middle: J

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

description:
Candida tropicalis a cells (ATCC 34139 ST-120 his-)
Biological replicate 2 of 2, CAY1503 Wor1 overexpression cells

hyb_protocol: 300ng of Cy3 and Cy5 samples were mixed together in a total volume of 25uL ddH2O, heated to 95C for 3 min, and cooled to room temperature. 25uL GE hybridization buffer was added to samples, mixed, and spun down. 40uL of hybridization sample was loaded onto slide, slide sealed, and incubated at 65C rotating at 10rpm for ~17 hours. Slide washed using Agilent Wash Buffers and Drying and Stabilization Solution.

scan_protocol: Scanned using Axon 4000b scanner, pixel size = 5 um, Lines to average = 2, Focus position = 15. Scanned for count ratio = 1.

data_processing: Data normalized using Goulphar. Fold change values were averaged for each spot.

organism: Candida tropicalis

source_name: C. tropicalis TDH3-WOR1 cells

label_protocol: cDNA synthesized with Oligo(dT)20 + pdN9, with aa-dUTP/dNTPs using Superscript RT III. RNA hydrolyzed with 0.2M NaOH/0.03M EDTA and neutralized with 0.3M HCl. Samples cleaned using Zymo Columns. Sample dye-coupled in 0.1 M Na Bicarbonate, pH 9.0 and adding 1.25uL Cy3 (reference) or Cy5 (experimental). Samples were incubated at room temperature for 1 hour in darkness and cleaned up using Zymo columns.

growth_protocol: For experimental biofilm samples: Cultures were inoculated in 3 ml of Spider medium then incubated at 25°C overnight.  2 ODs of cells were spun down and resuspended in 1 ml of Lee's + Glucose medium and transferred to the well of a 12-well polystyrene plate.  Plates were incubated at 25°C for 1-2 days without shaking, and cells were removed ands spun down; For universal reference samples: Cells grown overnight in liquid Spider media, diluted to 0.2 OD600, and grown to 1.0 - 1.2. Cells spun down and flash frozen in an ethanol/dry ice bath.

extract_protocol: RNA extracted using Ribopure Yeast Kit.

tag: strain

source_name: Universal reference

value: Mixed white and opaque grown in liquid Spider medium


title: CAY3853 a WOR1 OE 1

description:
Candida tropicalis a cells (ATCC 34139 ST-120 his-)
Biological replicate 1 of 2, CAY1503 Wor1 overexpression cells


title: CAY3378 a opaque 2

description:
Candida tropicalis a cells (ATCC 34139 ST-120 his-)
Biological replicate 1 of 2, CAY1503 opaque cells

source_name: C. tropicalis opaque cells

value: CAY1503 opaque (CAY3378)


title: RpoS_FWAF_stationary_3

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description:
Ch1(Cy5): RpoS_FWAF_stationary_3p.pair
Ch2(Cy3): RpoS_FWAF_stationary_3m.pair
ChIP-chip G.sulfurreducens, RpoS, FWAF, Stationary phase

hyb_protocol: Hybridization was performed by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scan was performed with an Axon GenePix 4000B scanner by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: IP/mock-IP ratio computation and enriched region identification as implemented in the NimbleScan software package, version 2.4.27 (www.nimblegen.com).

organism: Geobacter sulfurreducens PCA

label_protocol: Labeling was performed following Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF (fresh water acetate-fumarate) medium, under strictly anoxic conditions at 30°C, and harvested at early stationary phase

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 - 1000 bp. Specific antibody against the target protein was used to immunoprecipitate the chromatin protein complex.  [RpoH, RpoN and RpoS antibodies are produced by polycolonal rabbit antibodies produced by Katy Juarez] For the control (mock-IP), no antibody was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR.

treatment_protocol: Cross-linked and sonicated chromatin complex of RpoS and DNA was immunoprecipitated by RpoS antibody.

value: Wild type

tag: chip antibody

value: RpoS antibody

source_name: G.sulfurreducens RpoS ChIP DNA FWAF starionary phase mock

treatment_protocol: Cross-linked and sonicated chromatin complex was processed without any antitbody as control.

tag: sample type

value: no-antibody control (mock-IP)


title: HIV-Validation cohort-RP-18

value: test


title: HIV-Validation cohort-RP-19


title: CAY3378 a opaque 1

description:
Candida tropicalis a cells (ATCC 34139 ST-120 his-)
Biological replicate 2 of 2, CAY1503 opaque cells


title: HIV-Validation cohort-RP-17


title: Striatum_6-OHDA_sample3_rep1

description: Striatum gene expression of 6-OHDA lesioned rat

source_name: Striatum, 6-OHDA

tag: tissue


title: Striatum_6-OHDA_L-DOPA_STN-HFS_sample3_rep1

description: Striatum gene expression of L-DOPA and STN-HFS treated rat

source_name: Striatum, 6-OHDA, L-DOPA, STN-HFS


title: Striatum_6-OHDA_L-DOPA_sample3_rep1

description: Striatum gene expression of L-DOPA treated rat

source_name: Striatum, 6-OHDA, L-DOPA


title: Striatum_6-OHDA_STN-HFS_sample1_rep1


title: AHY205b vs reference (normalized low intensity scan)

hyb_protocol: A pooled reference was created from the Cy5 labelled fractions. Equal amounts of Cy3 labelled sample and Cy5 labelled reference were hybridized overnight to custom designed Agilent-020166 Ca21_GE_plus_tiling_2.0 arrays (PMID20735781)

scan_protocol: Following hybridization, slides were processed and then scanned on a Genepix 4000A or 4000B Axon Instrument Scanner (Axon/Molecular Devices, Sunnyvale, CA USA) (PMID20735781).

data_processing: Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (Lemoine et al., 2006) for R (The R Foundation for Statistical Computing) (PMID20735781).

source_name: C. albicans opaque plus WOR1 a/a cells

label_protocol: Following cDNA synthesis, samples were dye coupled to both Cy3 and Cy5 in separate reactions (PMID20735781).

growth_protocol: log phase, synthetic complete, 25 degrees

extract_protocol: RNA was extracted using the RiboPure-Yeast RNA kit (Ambion, number AM1926) according to the manufacturer's instruction (PMID 19529758).

value: plus WOR1 a/a cells

tag: cell phenotype

value: opaque cells

source_name: Mixed reference

value: mixed white and opaque, wild-type and mutant


title: Striatum_6-OHDA_STN-HFS_sample2_rep1


title: HIV-Validation cohort-RP-16


title: Striatum_6-OHDA_sample2_rep1


title: Striatum_6-OHDA_L-DOPA_sample2_rep1


title: Normortensive control_Sample 16

city: Augusta

first: Xiaoling

last: Wang

state: GA

address: 1120 15th streeet

department: Pediatrics

institute: Medical College of Georgia

description: match with sample 15

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 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

label: Cy5 and Cy3

source_name: peripheral leukocyte

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from buffy coat using Qiagen® QiAamp® Blood Kit according to standard instructions

value: Male

tag: cell type

value: peripheral leukocyte

tag: disease state

value: Normortensive control

tag: match

value: match with sample 15


title: Hypertensive case_Sample 15

description: match with sample 16

value: Hypertensive case

value: match with sample 16


title: Striatum_6-OHDA_sample1_rep1

value: Striatum

value: male


title: Striatum_6-OHDA_L-DOPA_STN-HFS_sample1_rep1

value: yes


title: RpoS_FWAF_stationary_2

description:
Ch1(Cy5): RpoS_FWAF_stationary_2p.pair
Ch2(Cy3): RpoS_FWAF_stationary_2m.pair
ChIP-chip G.sulfurreducens, RpoS, FWAF, Stationary phase

source_name: G.sulfurreducens RpoS ChIP DNA FWAF starionary phase

tag: genotype/variation

value: polycolonal rabbit antibodies produced by Katy Juarez


title: CIN-1 (cy5) vs. AMA-1 (cy3)- [Mutant cy5 , Control Cy3]_Rep1

description:
Mutant vs WT
RNA extracted from 3-5 mm long (young) cin and wild type leaves

organism: Arabidopsis thaliana

source_name: Leaf 3-5 mm

value: leaf

tag: leaf length


title: HIV-Validation cohort-RP-15

source_name: Peripheral blood mononuclear cell

tag: gender


title: Striatum_6-OHDA_L-DOPA_STN-HFS_sample2_rep1


title: AHY205a vs reference (normalized low intensity scan)


title: Striatum_6-OHDA_L-DOPA_sample1_rep1

value: no


title: HIV-Validation cohort-RP-14

tag: estimated days after hiv infection


title: HIV-Validation cohort-RP-12


title: HIV-Validation cohort-RP-10


title: HIV-Validation cohort-RP-11

value: female


title: Hypertensive case_Sample 13

description: match with sample 14

value: match with sample 14


title: Normortensive control_Sample 14

description: match with sample 13

value: match with sample 13


title: AHY212b vs reference (normalized low intensity scan)

source_name: C. albicans opaque wor3 delete a/a cells

value: wor3 delete a/a cells

value: opaque cells


title: HIV-Validation cohort-RP-13

value: test


title: AHY203a vs reference (normalized low intensity scan)

source_name: C. albicans opaque wor2 delete plus WOR1 a/a cells

value: wor2 delete plus WOR1 a/a cells

value: mixed white and opaque, wild-type and mutant


title: RpoS_electrode_2

description:
Ch1(Cy5): RpoS_electrode_2p.pair
Ch2(Cy3): RpoS_electrode_2m.pair
ChIP-chip G.sulfurreducens, RpoS, electrode

growth_protocol: G.sulfurreducens PCA strain was cultured on electrode, under strictly anoxic conditions at 30°C, and harvested after one week

value: Wild type

value: RpoS antibody

source_name: G.sulfurreducens RpoS ChIP DNA electrode mock

value: no-antibody control (mock-IP)


title: AHY203b vs reference (normalized low intensity scan)


title: RpoH_FWAF_logphase_heatshock_2

description:
Ch1(Cy5): RpoH_FWAF_logphase_heatshock_2p.pair
Ch2(Cy3): RpoH_FWAF_logphase_heatshock_2m.pair
ChIP-chip G.sulfurreducens, RpoH, FWAF, Logphase, Heatshock

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF (fresh water acetate-fumarate) medium, under strictly anoxic conditions at 30°C, and heatshock to 42C for 15 min at mid-exponential phase

treatment_protocol: Cross-linked and sonicated chromatin complex of RpoH and DNA was immunoprecipitated by RpoH antibody.

value: RpoH antibody

source_name: G.sulfurreducens RpoH ChIP DNA FWAF Logphase heatshock mock


title: RpoN_electrode_2

description:
Ch1(Cy5): RpoN_electrode_2p.pair
Ch2(Cy3): RpoN_electrode_2m.pair
ChIP-chip G.sulfurreducens, RpoN, electrode

treatment_protocol: Cross-linked and sonicated chromatin complex of RpoN and DNA was immunoprecipitated by RpoN antibody.

value: RpoN antibody

source_name: G.sulfurreducens RpoN ChIP DNA electrode mock


title: RpoH_FWAF_logphase_heatshock_3

description:
Ch1(Cy5): RpoH_FWAF_logphase_heatshock_3p.pair
Ch2(Cy3): RpoH_FWAF_logphase_heatshock_3m.pair
ChIP-chip G.sulfurreducens, RpoH, FWAF, Logphase, Heatshock

source_name: G.sulfurreducens RpoH ChIP DNA FWAF Logphase heatshock


title: RpoS_FWAF_stationary_1

description:
Ch1(Cy5): RpoS_FWAF_stationary_1p.pair
Ch2(Cy3): RpoS_FWAF_stationary_1m.pair
ChIP-chip G.sulfurreducens, RpoS, FWAF, Stationary phase


title: RpoS_electrode_1

description:
Ch1(Cy5): RpoS_electrode_1p.pair
Ch2(Cy3): RpoS_electrode_1m.pair
ChIP-chip G.sulfurreducens, RpoS, electrode

source_name: G.sulfurreducens RpoS ChIP DNA electrode


title: Hypertensive case_Sample 12

description: match with sample  4

value: Male

value: peripheral leukocyte

value: Hypertensive case

value: match with sample  4


title: HIV-Validation cohort-RP-9

value: male


title: AHY212a vs reference (normalized low intensity scan)


title: HASMCs of Subject 11: TNFa

city: Bochum

first: Jurgen

last: Knobloch

address: Bürkle-De-La-Camp-Platz 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bergmannsheil

description:
Gene expression after 8 hours
P11(H02)

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized for 17 hours at 65° C to Agilent Whole-Human-Genome Oligo Microarrays 4x44k. The microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with preheated 0.06x SSPE buffer containing 0.005% N-lauroylsarcosine at 37° C for 1 min. A final washing step was performed with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized microarrays were detected with the Agilents Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Software (FES 10.5.1.1) was used to read out and process the microarray image files. FES determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES-derived output data files were further analyzed with the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware) in order to compare two single intensity profiles in a ratio experiment. The ratios were calculated by dividing sample signal intensity (TNFa stimulation) through unstimulated control signal intensity.

source_name: ex-vivo cultivated HASMCs, TNFa (20 ng/ml)

label_protocol: 1 µg of each total RNA sample was used to produce Cy3-labeled cRNA via T7-based amplification using the Agilent Quick Amp Labeling Kit (Agilent Technologies) according to the instructions of the manufacturer. cRNA yield and Cy3-incorporation rates (13-15 fmol/ng) were measured with an ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: HASMCS were grown in Dulbecco's modifed Eagle's medium (DMEM; Invitrogen, Karlsruhe, Germany, cat#-31885-023) with 10% FCS (Sigma-Aldrich; cat#-N-4637), sodium pyruvate (1 mM; Invitrogen cat#-11360-039), L-glutamine (2 mM; Sigma-Aldrich cat#-G-7513), non-essential amino acids (1%; Invitrogen cat#-11140-035), penicillin (100 U/ml), streptomycin (100 μg/ml; Sigma-Aldrich cat#-P-4333), and amphotericin B (1.5 μg/ml; Sigma-Aldrich cat#-A-2942).

extract_protocol: RNA was isolated with standard protocols (NucleoSpin RNAII; Macherey-Nagel, Düren, Germany) and quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).  Results were visualized in gel images and electropherograms with the Agilent 2100 Bioanalyzer expert software that was also used to check RNA quality by the generation of RNA Integrity numbers (RIN) (1, low quality - 10, high quality). All samples revealed RIN values between 9 and 10 and thus had sufficient quality for gene expression profiling experiments.

treatment_protocol: For stimulation, HASMCs were plated out at equal density in 6-well plates. Before stimulation, subconfluent cell monolayers (approximately 80% confluence) in six-well cell culture plates were deprived of serum for 24 h in serum-free and low-glucose (1g/l) DMEM (Invitrogen; cat#-41966-029) supplemented with 1 mM sodium pyruvate, 2 mM L-glutamine, 1% non-essential amino acids, 100 U/ml penicillin, 100 μg/ml streptomycin, 1.5 μg/ml amphotericin B, 1 mM insulin (Sigma-Aldrich cat#-I1882), 5 mg/ml, apo-transferrin (Sigma-Aldrich cat#-T1147) and 100 μM ascorbic acid (Sigma-Aldrich cat#-A4403).   HASMC stimulation was done in serum-free and low-glucose (1 g/l) DMEM supplemented with 1 mM sodium pyruvate, 2 mM L-glutamine, 1% nonessential amino acids, 100 U/ml penicillin, 100 μg/ml streptomycin, and 1.5 μg/ml amphotericin B. HASMCs at passages 2 to 7 were left untreated, stimulated with recombinant human TNFa (20 ng/ml; R&D Systems, Mineapolis, MN, USA, cat#-210-TA)

value: female

tag: age


title: Normortensive control_Sample 8

description: match with sample 10

value: Normortensive control

value: match with sample 10


title: HIV-Validation cohort-RP-8


title: HASMCs of Subject 09: TNFa

description:
Gene expression after 8 hours
P09(H02)


title: Hypertensive case_Sample 10

description: match with sample 8

value: match with sample 8


title: HIV-Validation cohort-RP-7

value: test


title: Hypertensive case_Sample 11

description: match with sample 6

value: match with sample 6


title: AHY207b vs reference (normalized low intensity scan)

source_name: C. albicans white wor3 delete a/a cells

value: wor3 delete a/a cells

value: white cells

value: mixed white and opaque, wild-type and mutant


title: HASMCs of Subject 10: control

description:
Gene expression after 8 hours
P10(H01)

source_name: ex-vivo cultivated HASMCs, unstimulated


title: RpoH_FWAF_logphase_heatshock_1

description:
Ch1(Cy5): RpoH_FWAF_logphase_heatshock_1p.pair
Ch2(Cy3): RpoH_FWAF_logphase_heatshock_1m.pair
ChIP-chip G.sulfurreducens, RpoH, FWAF, Logphase, Heatshock

value: Wild type

value: polycolonal rabbit antibodies produced by Katy Juarez

value: no-antibody control (mock-IP)


title: HIV-Validation cohort-RP-6


title: HASMCs of Subject 10: TNFa

description:
Gene expression after 8 hours
P10(H02)


title: AHY554b vs reference (normalized low intensity scan)

source_name: C. albicans opaque efg1 delete a/a cells

value: efg1 delete a/a cells

value: opaque cells


title: HIV-Validation cohort-RP-5


title: AHY207a vs reference (normalized low intensity scan)


title: RpoN_electrode_1

description:
Ch1(Cy5): RpoN_electrode_1p.pair
Ch2(Cy3): RpoN_electrode_1m.pair
ChIP-chip G.sulfurreducens, RpoN, electrode

source_name: G.sulfurreducens RpoN ChIP DNA electrode

value: RpoN antibody


title: HASMCs of Subject 08: control

description:
Gene expression after 8 hours
P08(H01)


title: AHY554a vs reference (normalized low intensity scan)

source_name: Mixed reference


title: HASMCs of Subject 11: control

description:
Gene expression after 8 hours
P11(H01)


title: HIV-Validation cohort-RP-4


title: Hypertensive case_Sample 9

description: match with sample 5

source_name: peripheral leukocyte

value: Male

value: peripheral leukocyte

value: Hypertensive case

value: match with sample 5


title: Normortensive control_Sample 7

description: match with sample 1

value: Normortensive control

value: match with sample 1


title: HASMCs of Subject 09: control

description:
Gene expression after 8 hours
P09(H01)

value: female


title: HIV-Validation cohort-RP-1

value: test

value: male


title: HIV-Validation cohort-RP-2


title: Normortensive control_Sample 3

description: match with sample 2

value: match with sample 2


title: Normortensive control_Sample 5

description: match with sample 9

value: match with sample 9


title: HASMCs of Subject 07: TNFa

description:
Gene expression after 8 hours
P07(H02)


title: AHY174a vs reference (normalized low intensity scan)

source_name: C. albicans opaque czf1 delete a/a cells

value: czf1 delete a/a cells

value: mixed white and opaque, wild-type and mutant


title: HIV-Validation cohort-RP-3


title: AHY121b vs reference (normalized low intensity scan)

source_name: C. albicans white wor2 delete a/a cells

value: wor2 delete a/a cells

value: white cells


title: Normortensive control_Sample 4

description: match with sample 12

value: match with sample 12


title: HASMCs of Subject 08: TNFa

description:
Gene expression after 8 hours
P08(H02)


title: AHY123b vs reference (normalized low intensity scan)

source_name: C. albicans white efg1 delete a/a cells

value: efg1 delete a/a cells


title: Hypertensive case_Sample 2

description: match with sample 3

value: Male

value: match with sample 3


title: HASMCs of Subject 06: TNFa

description:
Gene expression after 8 hours
P06(H02)


title: HASMCs of Subject 07: control

description:
Gene expression after 8 hours
P07(H01)


title: Normortensive control_Sample 6

description: match with sample 11

value: peripheral leukocyte

value: match with sample 11


title: AHY174b vs reference (normalized low intensity scan)

value: opaque cells


title: AHY122a vs reference (normalized low intensity scan)

source_name: C. albicans white czf1 delete a/a cells


title: AHY123a vs reference (normalized low intensity scan)


title: AHY122b vs reference (normalized low intensity scan)


title: Training cohort-NC-3

source_name: Peripheral blood mononuclear cell

value: control


title: Training cohort-NC-2


title: HIV-Training cohort-CP-5


title: Training cohort-NC-1


title: HASMCs of Subject 06: control

description:
Gene expression after 8 hours
P06(H01)

value: female


title: HIV-Training cohort-CP-6

value: test


title: HASMCs of Subject 02: control

description:
Gene expression after 8 hours
P02(H01)

value: male


title: Gene Expression in Forebrain of Male Goldfish Following Exposure to Waterborne Sex Pheromones Replicate 4

city: Ottawa

first: Wudu

middle: E.

last: Lado

state: ON

address: 30 Marie Private

department: Biology

country: Canada

institute: University of Ottawa

description: Biological replicate 4 of 4.

hyb_protocol: Array 900MPX Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers. Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Positive and negative control spots are removed prior to the normalization step. LOWESS (SAS software) normalized VALUE data obtained from log of processed Green signal/processed Red signal.

organism: Carassius auratus

source_name: telencephalon of male goldfish treated with vehicles labeled with Cyanine-5 (red)

extract_protocol: Qiagen's RNeasy Plus Mini Kit

tag: tissue origin

value: brain

value: telencephalonic tissue

source_name: telencephalon of male goldfish treated with PGF2alpha labeled with Cyanine-3 (Green)


title: Gene Expression in Forebrain of Male Goldfish Following Exposure to Waterborne Sex Pheromones Replicate 3

description: Biological replicate 3 of 4.

data_processing: Positive and negative control spots are removed prior to the normalization step. LOWESS (SAS software) normalized VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: telencephalon of male goldfish treated with vehicles labeled with Cyanine-3 (green)

label_protocol: Array 900MPX Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

treatment_protocol: vehicles

source_name: telencephalon of male goldfish treated with PGF2alpha labeled with Cyanine-5 (red)

treatment_protocol: PGF2alpha treatment


title: Gene Expression in Forebrain of Male Goldfish Following Exposure to Waterborne Sex Pheromones Replicate 2

description: Biological replicate 2 of 4.


title: Hypertensive case_Sample 1

description: match with sample 7

value: Hypertensive case

value: match with sample 7


title: HASMCs of Subject 03: TNFa

description:
Gene expression after 8 hours
P03(H02)


title: HASMCs of Subject 03: control

description:
Gene expression after 8 hours
P03(H01)


title: HIV-Training cohort-CP-4


title: RZY219 vs reference (normalized low intensity scan)

source_name: C. albicans white wor1 delete a/a cells

value: wor1 delete a/a cells

value: mixed white and opaque, wild-type and mutant


title: AHY121a vs reference (normalized low intensity scan)

value: wor2 delete a/a cells

value: white cells


title: AHY136b vs reference (normalized low intensity scan)

source_name: C. albicans opaque a/a cells

value: a/a cells


title: RZY235 vs reference (normalized low intensity scan)


title: OCK partial iPS clone siTcf3-A day2

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

description:
overall design 'D'
cell culture

hyb_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)

data_processing: Robust Multichip Analysis (RMA) using R Bioconductor

growth_protocol: standard cell culture

extract_protocol: Trizol and RNEasy purification

treatment_protocol: as described in publication

value: partially reprogrammed clone (partial iPS clone)

tag: agent (reprogramming factor)

value: OCK

value: Tcf3 wt

tag: sirna treatment

tag: time


title: HIV-Training cohort-CP-3


title: HIV-Training cohort-CP-2


title: AHY136a vs reference (normalized low intensity scan)

city: San Francisco

first: Aaron

last: Hernday

institute: UC San Francisco

value: opaque cells


title: AHY135b vs reference (normalized low intensity scan)

source_name: C. albicans white a/a cells


title: Gene Expression in Forebrain of Male Goldfish Following Exposure to Waterborne Sex Pheromones Replicate 1

description: Biological replicate 1 of 4

data_processing: Positive and negative control spots are removed prior to the normalization step. LOWESS (SAS software) normalized VALUE data obtained from log of processed Green signal/processed Red signal


title: OCK partial iPS clone siTcf3-B day2

description:
overall design 'D'
cell culture

scan_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)


title: OCK Tcf3 wt day26

description:
overall design 'C'
cell culture

label_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)

value: reprogramming cultures


title: HASMCs of Subject 02: TNFa

description:
Gene expression after 8 hours
P02(H02)

source_name: ex-vivo cultivated HASMCs, TNFa (20 ng/ml)


title: OCK partial iPS clone siCtrl day2

description:
overall design 'D'
cell culture

value: siCtrl


title: HCC827_IkB

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

description: MiG IkB

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 alorighthm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: lung adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocl using 100 ng of total RNA (Ambion).

growth_protocol: LLC grown in DMEM+10% FBS. Human lines grown in RPMI+10% FBS.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: Cells were transduced with control retrovirus (MiG) or MiG retrovirus expressing IkB alpha super-repressor (SR) mutant or activated IKK beta (S177, S181 to E mutations). Cells were FACS sorted by GFP expression.

tag: cell line

tag: cell line type

value: lung adenocarcinoma

value: IkB


title: Training cohort-NC-4

value: control

value: male


title: PC9_MIG

description: MiG Control

value: Control


title: OCK Tcf3 ko day26

description:
overall design 'C'
cell culture

value: Tcf3 ko


title: AHY135a vs reference (normalized low intensity scan)

tag: sample type


title: HCC827_IKK

description: MiG IKK

value: IKK


title: OCK Tcf3 wt day22

description:
overall design 'C'
cell culture


title: AHY205b vs reference (normalized high intensity scan)

source_name: C. albicans opaque plus WOR1 a/a cells

value: plus WOR1 a/a cells

value: mixed white and opaque, wild-type and mutant


title: HIV-Training cohort-RP-11

value: test


title: HIV-Training cohort-CP-1


title: PC9_IkB

description: MiG IkB


title: AHY205a vs reference (normalized high intensity scan)

source_name: Mixed reference


title: PC9_IKK

description: MiG IKK


title: H358_IKB

description: MiG IkB

source_name: bronchioalveolar carcinoma

value: bronchioalveolar carcinoma


title: HCC827_MIG

description: MiG Control


title: AHY203b vs reference (normalized high intensity scan)

source_name: C. albicans opaque wor2 delete plus WOR1 a/a cells

value: wor2 delete plus WOR1 a/a cells


title: HIV-Training cohort-RP-10


title: H358_IKK

description: MiG IKK


title: HIV-Training cohort-RP-8


title: HIV-Training cohort-RP-9


title: HIV-Training cohort-RP-7


title: AHY203a vs reference (normalized high intensity scan)


title: OCK Tcf3 wt day19

description:
overall design 'C'
cell culture

value: OCK


title: OCK Tcf3 ko day15

description:
overall design 'C'
cell culture


title: HIV-Training cohort-RP-5


title: HIV-Training cohort-RP-4


title: HIV-Training cohort-RP-6


title: AHY212a vs reference (normalized high intensity scan)

source_name: C. albicans opaque wor3 delete a/a cells

value: wor3 delete a/a cells


title: H358_MIG

description: MiG Control


title: H23_IKK

description: MiG IKK


title: OCK Tcf3 ko day19

description:
overall design 'C'
cell culture


title: OCK Tcf3 wt day11

description:
overall design 'C'
cell culture

value: Tcf3 wt


title: OCK Tcf3 ko day11

description:
overall design 'C'
cell culture

value: reprogramming cultures


title: AHY212b vs reference (normalized high intensity scan)

value: opaque cells


title: OCK Tcf3 ko day22

description:
overall design 'C'
cell culture


title: AHY554b vs reference (normalized high intensity scan)

source_name: C. albicans opaque efg1 delete a/a cells

value: efg1 delete a/a cells


title: OCK Tcf3 wt day15

description:
overall design 'C'
cell culture


title: OSK iPS Tcf3 wt

description:
overall design 'A'
cell culture

value: iPS Clone

value: OSK


title: A549_IKK

description: MiG IKK

source_name: lung carcinoma

value: lung carcinoma


title: AHY207a vs reference (normalized high intensity scan)

source_name: C. albicans white wor3 delete a/a cells

value: white cells


title: HIV-Training cohort-RP-2

source_name: Peripheral blood mononuclear cell

value: male


title: OSK iPS Tcf3 ko clone #1

description:
overall design 'A'
cell culture

value: Tcf3 ko


title: H23_IkB

description: MiG IkB

value: lung adenocarcinoma

value: IkB


title: AHY207b vs reference (normalized high intensity scan)

value: mixed white and opaque, wild-type and mutant


title: AHY554a vs reference (normalized high intensity scan)


title: HIV-Training cohort-RP-1

value: test


title: AHY123b vs reference (normalized high intensity scan)

source_name: C. albicans white efg1 delete a/a cells


title: MB231/miR-203

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

description: Gene expression data in MDA-MB-231 cell infected with miR-203 over-expression virus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix human Genome 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Bioconductor and R language were used for pre-processing the two hybridizations. The robust multi-array analysis(RMA) was used for bacjground adjustment,normalization and log2 transformation of the signal intensity

source_name: miR-203 overexpression

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

growth_protocol: Cells were grown in humidified 5% CO2 incubator in DMEM supplemented with 10% FBS

extract_protocol: Rneasy kit (Qiagen) extraction of total RNA was performed according to the manufacture's protocol

tag: overexpression


title: HIV-Training cohort-RP-3


title: AHY174b vs reference (normalized high intensity scan)

source_name: C. albicans opaque czf1 delete a/a cells

value: czf1 delete a/a cells

tag: cell phenotype


title: AHY174a vs reference (normalized high intensity scan)


title: AHY123a vs reference (normalized high intensity scan)


title: A549_MIG

description: MiG Control

value: Control


title: OSK iPS Tcf3 ko clone #2

description:
overall design 'A'
cell culture

tag: cell type


title: A549_IKB

description: MiG IkB


title: H23_MIG

description: MiG Control


title: AHY122b vs reference (normalized high intensity scan)

source_name: C. albicans white czf1 delete a/a cells


title: MB231/EV

description: Gene expression data in MDA-MB-231 cell infected with control virus

source_name: control vector

value: empty vector


title: OCK iPS Tcf3 ko clone #2

description:
overall design 'B'
cell culture

value: OCK


title: OCK iPS Tcf3 ko clone #1

description:
overall design 'B'
cell culture