title: hiPSCs, K10M15 rep2

description: Gene expression data form hiPSCs (K10M15, retorvirous)


title: genomic DNA from whole blood of HIV+ man 109

status: Public on Nov 03 2014

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: SAMPLE 109

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

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

data_processing: BeadStudio software v3.2. The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Standard Illumina Protocol

growth_protocol: Fresh frozen blood

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: male

tag: tissue

value: whole blood

tag: age (yrs)

tag: dnamage

tag: hivstatus

value: positve

tag: logviralloadadjustedforage

tag: bmi

tag: lymphocytesperc

tag: whitebloodcellperc

tag: granulocyteperc

tag: monocytesperc

tag: lymphocyteabscount

tag: stripe


title: genomic DNA from whole blood of HIV+ man 108

description: SAMPLE 108


title: hiPSCs, K21S4 rep1

type: RNA

city: Kurashiki

first: Hiroyuki

last: Kamao

state: Okayama

address: 577 Matsushima

department: Ophthalmology

country: Japan

institute: Kawasaki Medical School

description: Gene expression data form hiPSCs (K21S4, retorvirous)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃, washed, and stained on GeneChip® Hybridization, Wash and Stain Kit.

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

data_processing: The data were analyzed with RMA (Rafael A, et al, 2003) algorithm in the R/Bioconductor (http://www.bioconductor.org/) package using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

source_name: hiPSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (0.05ug/ul) (3' IVT Express Kit).

growth_protocol: Selected tissues were incubated in each medium at 37℃.

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

treatment_protocol: Selected tissues were rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (Invitrogen).

tag: source

value: RP patient (K21)

tag: generation method

value: retrovirous (iPSCs from fibroblast)


title: h-RPE2 (lot-0F32920, Lonza)

description: Gene expression data form hRPE (fetal)

source_name: human fetal RPE

value: fetal RPE

value: purchased from Lonza Group Ltd.


title: hiPSC-RPE, K31M28, SDIA

description: Gene expression data form hiPSC-RPE (K31M28, retorvirous, SDIA)

source_name: hiPSC-RPE

value: RP patient (K31)

value: SDIA (RPE from iPSCs)


title: genomic DNA from whole blood of HIV+ man 111

description: SAMPLE 111


title: hiPSC-RPE, K21S4, SDIA

description: Gene expression data form hiPSC-RPE (K21S4, retorvirous, SDIA)


title: KU_41T

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export gene expression data based on unique genes, we used the Sample Gene Profile option of Illumina BeadStudio software. All 47231 probes on the Human-12 BeadChip ver.4 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

data_processing: Array data processing was performed on Illumina BeadStudio software. We normalized gene expression data using quantile normalization and log2 transformation. To export to a data matrix, the Sample Gene Profile option of this software was used.

label: Biotin

source_name: HCC tumor

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 750 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, Inc., Austin, TX). cRNA concentrations were determined using a spectrophotometer (Nanodrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with the mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer's protocol. RNA quality and integrity were confirmed by the ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: age

value: M

tag: disease state

value: hepatocellular carcinoma (HCC)

value: tumor


title: h-RPE3 (lot-181239, Lonza)

description: Gene expression data form hRPE (fetal)


title: hiPSCs, K10M15 rep1

value: RP patient (K10)


title: hiPSCs, K11PD17

description: Gene expression data form hiPSCs (K11PD17, retorvirous)

value: RP patient (K11)


title: HVC_Testosterone, biological rep6

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

country: Germany

institute: Max Planck Institute for Ornithology

description: HVC was dissected from cryosections

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing:
The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: E26R1204 Genomatix GmbH (http://www.genomatix.de)
ChipInspector fold changes are directly generated from the CEL files. Thus there is no normalization file, ChipInspector carries out significance analysis on the single probe level and the resulting file is Erubecula_female_HVCtestovsHVCcontrol.txt.

organism: Erithacus rubecula

source_name: HVC

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Adult robins housed in short light cycles in sound-proofed boxes

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with micro-scalpels under a stereo-microscope, transferred into Qiazol (Qiagen) and stored at -80 C till RNA preparation.

treatment_protocol: Testosterone

value: adult

tag: gender

value: female

tag: origin

value: wild

tag: treatment

value: Testosterone treatment

tag: duration of treatment

value: 40 days

value: HVC


title: hiPSC-RPE, K31M28, SFEB

description: Gene expression data form hiPSC-RPE (K31M28, retorvirous, SFEB)

value: SFEB (RPE from iPSCs)


title: HVC_Testosterone, biological rep5

description: HVC was dissected from cryosections

value: 32 days

tag: tissue


title: HVC_Testosterone, biological rep4

description: HVC was dissected from cryosections

value: 12 days


title: genomic DNA from whole blood of HIV+ man 113

description: SAMPLE 113

value: male

value: whole blood

tag: age (yrs)

tag: dnamage

tag: hivstatus

value: positve

tag: logviralloadadjustedforage


title: KU_44T

value: M


title: genomic DNA from whole blood of HIV+ man 114

description: SAMPLE 114

tag: bmi

tag: lymphocytesperc

tag: whitebloodcellperc

tag: granulocyteperc


title: KU_40T

value: hepatocellular carcinoma (HCC)


title: KU_39T

value: tumor


title: genomic DNA from whole blood of HIV+ man 106

description: SAMPLE 106

tag: monocytesperc

tag: lymphocyteabscount

tag: stripe


title: HVC_Testosterone, biological rep3

description: HVC was dissected from cryosections

tag: age

value: 9 days


title: hiPSC-RPE, K21S4, SFEB

description: Gene expression data form hiPSC-RPE (K21S4, retorvirous, SFEB)

tag: source

value: RP patient (K21)

tag: generation method


title: HVC_Testosterone, biological rep2

description: HVC was dissected from cryosections

value: adult

tag: gender

tag: origin

tag: treatment

value: 8 days


title: hiPSC-RPE, K10M15, SDIA

description: Gene expression data form hiPSC-RPE (K10M15, retorvirous, SDIA)

value: RP patient (K10)

value: SDIA (RPE from iPSCs)


title: hiPSC-RPE, K11PD17, SFEB

description: Gene expression data form hiPSC-RPE (K11PD17, retorvirous, SFEB)

value: RP patient (K11)


title: hiPSC-RPE, K11PD17, SDIA

description: Gene expression data form hiPSC-RPE (K11PD17, retorvirous, SDIA)


title: genomic DNA from whole blood of HIV+ man 105

description: SAMPLE 105

tag: tissue

tag: age (yrs)


title: genomic DNA from whole blood of HIV+ man 104

description: SAMPLE 104

tag: dnamage

tag: hivstatus


title: genomic DNA from whole blood of HIV+ man 103

description: SAMPLE 103

tag: logviralloadadjustedforage

tag: bmi


title: hiPSC-RPE, K10M15, SFEB

description: Gene expression data form hiPSC-RPE (K10M15, retorvirous, SFEB)


title: KU_37T

tag: disease state


title: HVC, biological rep6

description: HVC was dissected from cryosections

value: female

value: wild

value: No treatment

value: HVC


title: HVC_Testosterone, biological rep1

description: HVC was dissected from cryosections

value: Testosterone treatment

tag: duration of treatment

value: 7 days


title: genomic DNA from whole blood of HIV+ man 107

description: SAMPLE 107

value: male

value: whole blood

value: positve

tag: lymphocytesperc

tag: whitebloodcellperc

tag: granulocyteperc

tag: monocytesperc


title: KU_35T

tag: age

value: M

value: hepatocellular carcinoma (HCC)

value: tumor


title: HVC, biological rep5

description: HVC was dissected from cryosections

value: adult


title: hiPSC-RPE, 59SV4, SDIA

description: Gene expression data form hiPSC-RPE (59SV4, Sendai rvirous, SDIA)

tag: source

value: RP patient (59)

tag: generation method


title: KU_36T

tag: gender


title: hiPSC-RPE, 59SV9, SDIA

description: Gene expression data form hiPSC-RPE (59SV9, Sendai virous, SDIA)


title: KU_34T


title: hiPSC-RPE, 59SV3, SDIA

description: Gene expression data form hiPSC-RPE (59SV3, Sendai virous, SDIA)


title: HVC, biological rep4

description: HVC was dissected from cryosections

tag: origin

tag: treatment


title: genomic DNA from whole blood of HIV+ man 101

description: SAMPLE 101

tag: tissue

tag: age (yrs)

tag: lymphocyteabscount

tag: stripe


title: HVC, biological rep2

description: HVC was dissected from cryosections


title: HVC, biological rep1

description: HVC was dissected from cryosections


title: KU_38T


title: hiPSC-RPE, 59M8, SDIA

description: Gene expression data form hiPSC-RPE (59M8, retorvirous, SDIA)


title: KU_32T


title: genomic DNA from whole blood of HIV+ man 99

description: SAMPLE 99

tag: dnamage

tag: hivstatus

tag: logviralloadadjustedforage

tag: bmi


title: KU_31T

tag: disease state


title: hiPSC-RPE, 59SV9, SFEB

description: Gene expression data form hiPSC-RPE (59SV9, Sendai virous, SFEB)

value: SFEB (RPE from iPSCs)


title: KU_28T


title: KU_33T


title: hiPSC-RPE, 59M8, SFEB

description: Gene expression data form hiPSC-RPE (59M8, retorvirous, SFEB)


title: KU_30T


title: genomic DNA from whole blood of HIV+ man 97

description: SAMPLE 97

tag: lymphocytesperc

tag: whitebloodcellperc

tag: granulocyteperc


title: KU_26T

tag: age


title: genomic DNA from whole blood of HIV+ man 95

description: SAMPLE 95

tag: monocytesperc


title: genomic DNA from whole blood of HIV+ man 96

description: SAMPLE 96

tag: gender


title: KU_29T


title: genomic DNA from whole blood of HIV+ man 93

description: SAMPLE 93


title: genomic DNA from whole blood of HIV+ man 102

description: SAMPLE 102


title: KU_27T


title: KU_25T

value: F


title: KU_22T


title: KU_23T


title: KU_24T


title: genomic DNA from whole blood of HIV+ man 100

description: SAMPLE 100


title: genomic DNA from whole blood of HIV+ man 92

description: SAMPLE 92


title: KU_19T


title: KU_20T


title: genomic DNA from whole blood of HIV+ man 91

description: SAMPLE 91


title: genomic DNA from whole blood of HIV+ man 94

description: SAMPLE 94


title: genomic DNA from whole blood of HIV+ man 90

description: SAMPLE 90


title: KU_21T


title: KU_17T


title: genomic DNA from whole blood of HIV+ man 86

description: SAMPLE 86


title: genomic DNA from whole blood of HIV+ man 89

description: SAMPLE 89


title: KU_16T


title: Wild-type strain of Sphingomonas sp. A1 grown on alginate medium

city: Uji

first: Wataru

last: Hashimoto

state: Kyoto

address: Gokasho

department: Graduate School of Agriculture

institute: Kyoto University

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, according to 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: Sphingomonas sp. A1

source_name: wild-type strain of Sphingomonas sp. A1 grown on alginate medium

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

growth_protocol: Wild-type and motile strains of Sphingomonas sp. A1 were grown to mid-log phase (O.D.600nm 0.5 to 0.6) at 30°C in 0.5% alginate medium (0.1% (NH4)2SO4, 0.1% KH2PO4, 0.1% Na2HPO4, 0.01% MgSO4•7H2O, 0.01% yeast extract, and 0.5% sodium alginate (pH 7.2)) .

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Bacterial cells were treated with RNA Protect Bacteria Reagent (Quiagen Inc., Valencia, CA, USA)

tag: strain

value: wild-type


title: MEF(Rosa26ERT2 Cre: THOC5 (flox/flox)) 2d Tamoxifen +/- 1h FCS

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the 'Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7' (Agilent), except that 1000ng of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values was performed with the 'Feature Extraction Software V10.7.3.1' by using the recommended default extraction protocol file: 'GE2_107_Sep09.xml'. For inter-array normalization, processed intensity values as generated in the Feature Extraction process, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array I’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold was defined as 1% of the reference 75th Percentile value (= 15). All of those normalized PS values that fell below this intensity border, were substituted by the respective surrogate value of 15.

organism: Mus musculus

label_protocol: Synthesis of Cy3- or Cy5-labeled cRNA was performed with the 'Quick Amp Labeling kit, two color' (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations.

extract_protocol: Total RNA was extracted by use of the Rneasy Mini Kit (Qiagen).

treatment_protocol: Mouse embryo fibroblast (MEF) cells derived from Rosa26ERT2 Cre: Ola126 THOC5 (flox/flox).

tag: strain (genetic background)

tag: cell type

value: immortalized Murine Embryonic Fibroblasts (MEF)

tag: genotype/variation

value: THOC5 knockdown

tag: protocol

value: unstimulated

source_name: MEF(Rosa26ERT2 Cre: THOC5 (flox/flox)) 2d Tamoxifen 1h FCS

value: FCS stimulation


title: genomic DNA from whole blood of HIV+ man 88

description: SAMPLE 88

tag: tissue

tag: age (yrs)

tag: lymphocyteabscount

tag: stripe


title: KU_15T


title: genomic DNA from whole blood of HIV+ man 87

description: SAMPLE 87

tag: dnamage

tag: hivstatus

tag: logviralloadadjustedforage

tag: bmi


title: KU_18T

tag: disease state


title: MEF(Rosa26ERT2 Cre: THOC5 (flox/flox)) +/- 1h FCS

source_name: MEF(Rosa26ERT2 Cre: THOC5 (flox/flox))

value: wildtype

source_name: MEF(Rosa26ERT2 Cre: THOC5 (flox/flox)) 1h FCS


title: genomic DNA from whole blood of HIV+ man 84

description: SAMPLE 84

tag: lymphocytesperc

tag: whitebloodcellperc

tag: granulocyteperc


title: KU_14T

tag: age

tag: gender


title: genomic DNA from whole blood of HIV+ man 79

description: SAMPLE 79

tag: monocytesperc


title: genomic DNA from whole blood of HIV+ man 83

description: SAMPLE 83


title: KU_13T


title: KU_11T


title: genomic DNA from whole blood of HIV+ man 82

description: SAMPLE 82


title: genomic DNA from whole blood of HIV+ man 80

description: SAMPLE 80


title: KU_12T


title: KU_09T


title: genomic DNA from whole blood of HIV+ man 76

description: SAMPLE 76


title: genomic DNA from whole blood of HIV+ man 81

description: SAMPLE 81


title: KU_08T


title: genomic DNA from whole blood of HIV+ man 98

description: SAMPLE 98


title: genomic DNA from whole blood of HIV+ man 72

description: SAMPLE 72


title: genomic DNA from whole blood of HIV+ man 73

description: SAMPLE 73


title: genomic DNA from whole blood of HIV+ man 77

description: SAMPLE 77


title: genomic DNA from whole blood of HIV+ man 74

description: SAMPLE 74


title: genomic DNA from whole blood of HIV+ man 70

description: SAMPLE 70


title: KU_05T


title: KU_07T


title: C.albicans infected zebrafish_15dpi+12hr_rep2

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

description:
Gene expression after 15dpi+12hr in C. albicans infected zebrafish
H+P 15dpi+12hr

hyb_protocol: The fragmented labeled cRNA was then hybridized to oligo microarray at 60°C for 17 h.

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

data_processing: Scanned images are analyzed by Feature extraction 9.5.3 software (Agilent Technologies, USA),  image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Danio rerio

source_name: C.albicans infected zebrafish, 15dpi+12hr, repeat2

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

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's recommendations. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

treatment_protocol: Each fish was intraperitoneally injected with 1×108 C. albicans cells suspended in 10μL sterile 1× phosphate-buffered saline (PBS)

value: whole fish

value: 9 months

tag: infection

tag: time

value: 36 hours post second injection


title: KU_06T

tag: tissue


title: C.albicans infected zebrafish_15dpi+6hr_rep2

description:
Gene expression after 15dpi+6hr in C. albicans infected zebrafish
H+P 15dpi+6hr

source_name: C.albicans infected zebrafish, 15dpi+6hr, repeat2

value: male

value: 30 hours post second injection


title: C.albicans infected zebrafish_15dpi+18hr_rep2

description:
Gene expression after 15dpi+18hr in C. albicans infected zebrafish
H+P 15dpi+18hr

source_name: C.albicans infected zebrafish, 15dpi+18hr, repeat2

value: 42 hours post second injection


title: C.albicans infected zebrafish_15dpi_rep2

description:
Gene expression after 15dpi in C. albicans infected zebrafish
H+P 15dpi

source_name: C.albicans infected zebrafish, 15dpi, repeat2

value: 24 hours post second injection


title: genomic DNA from whole blood of HIV+ man 71

description: SAMPLE 71

value: whole blood

tag: age (yrs)

value: positve


title: C.albicans infected zebrafish_14dpi+18hr_rep2

description:
Gene expression after 14dpi+18hr in C. albicans infected zebrafish
H+P 14dpi+18hr

source_name: C.albicans infected zebrafish, 14dpi+18hr, repeat2

value: 18 hours post second injection


title: KU_03T

description: To export gene expression data based on unique genes, we used the Sample Gene Profile option of Illumina BeadStudio software. All 47231 probes on the Human-12 BeadChip ver.4 were used.

value: M

value: hepatocellular carcinoma (HCC)

value: tumor


title: genomic DNA from whole blood of HIV+ man 78

description: SAMPLE 78

tag: lymphocyteabscount


title: genomic DNA from whole blood of HIV+ man 85

description: SAMPLE 85

tag: stripe


title: genomic DNA from whole blood of HIV+ man 75

description: SAMPLE 75

tag: dnamage


title: genomic DNA from whole blood of HIV+ man 69

description: SAMPLE 69

tag: hivstatus


title: KU_10T


title: genomic DNA from whole blood of HIV+ man 68

description: SAMPLE 68

tag: logviralloadadjustedforage


title: genomic DNA from whole blood of HIV+ man 67

description: SAMPLE 67

tag: bmi


title: genomic DNA from whole blood of HIV+ man 66

description: SAMPLE 66


title: genomic DNA from whole blood of HIV+ man 64

description: SAMPLE 64


title: KU_04T

tag: disease state


title: C.albicans infected zebrafish_14dpi+6hr_rep2

description:
Gene expression after 14dpi+6hr in C. albicans infected zebrafish
H+P 14dpi+6hr

source_name: C.albicans infected zebrafish, 14dpi+6hr, repeat2

value: 6 hours post second injection


title: C.albicans infected zebrafish_14dpi+2hr_rep2

description:
Gene expression after 14dpi+2hr in C. albicans infected zebrafish
H+P 14dpi+2hr

source_name: C.albicans infected zebrafish, 14dpi+2hr, repeat2

value: 2 hours post second injection


title: KU_02T

value: F


title: KM_079T


title: genomic DNA from whole blood of HIV+ man 65

description: SAMPLE 65

source_name: whole blood

tag: lymphocytesperc


title: C.albicans infected zebrafish_14dpi_rep2

description:
Gene expression after 14dpi in C. albicans infected zebrafish
H 14dpi

source_name: C.albicans infected zebrafish, 14dpi, repeat2

value: 336 hours post first injection


title: C.albicans infected zebrafish_14dpi+12hs_rep2

description:
Gene expression after 14dpi+12hr in C. albicans infected zebrafish
H+P 14dpi+12hr

source_name: C.albicans infected zebrafish, 14dpi+12hr, repeat2

value: whole fish

value: 12 hours post second injection


title: KU_01T


title: genomic DNA from whole blood of HIV+ man 63

description: SAMPLE 63

tag: whitebloodcellperc


title: KM_103T


title: KM_075T


title: KM_069T


title: C.albicans infected zebrafish_17.5dpi_rep2

description:
Gene expression after 17.5dpi in C. albicans infected zebrafish
H 17dpi+12hr

source_name: C.albicans infected zebrafish, 17.5dpi, repeat2

value: 9 months

value: 420 hours post first injection


title: KM_076T

source_name: HCC tumor


title: KM_066T


title: C.albicans infected zebrafish_21dpi_rep2

description:
Gene expression after 21dpi in C. albicans infected zebrafish
H 21dpi

source_name: C.albicans infected zebrafish, 21dpi, repeat2

value: male

value: 504 hours post first injection


title: C.albicans infected zebrafish_15dpi+18hr_rep1

source_name: C.albicans infected zebrafish, 15dpi+18hr, repeat1

value: 42 hours post second injection


title: KM_065T


title: C.albicans infected zebrafish_1dpi_rep2

description:
Gene expression after 1dpi in C. albicans infected zebrafish
H 1dpi

source_name: C.albicans infected zebrafish, 1dpi, repeat2

value: 24 hours post first injection


title: C.albicans infected zebrafish_2dpi_rep2

description:
Gene expression after 2dpi in C. albicans infected zebrafish
H 2dpi

source_name: C.albicans infected zebrafish, 2dpi, repeat2

value: 48 hours post first injection


title: genomic DNA from whole blood of HIV+ man 62

description: SAMPLE 62

value: whole blood

value: positve

tag: granulocyteperc


title: KM_053T

tag: age

value: M

value: hepatocellular carcinoma (HCC)


title: genomic DNA from whole blood of HIV+ man 61

description: SAMPLE 61

tag: gender


title: KM_057T

value: tumor


title: genomic DNA from whole blood of HIV+ man 60

description: SAMPLE 60

tag: monocytesperc


title: C.albicans infected zebrafish_15dpi+6hr_rep1

source_name: C.albicans infected zebrafish, 15dpi+6hr, repeat1

tag: infection

value: 30 hours post second injection


title: C.albicans infected zebrafish_15dpi+12hr_rep1

source_name: C.albicans infected zebrafish, 15dpi+12hr, repeat1

tag: time

value: 36 hours post second injection


title: KM_051T

tag: tissue


title: genomic DNA from whole blood of HIV+ man 58

description: SAMPLE 58

tag: age (yrs)


title: KM_056T


title: C.albicans infected zebrafish_14dpi+18hr_rep1

source_name: C.albicans infected zebrafish, 14dpi+18hr, repeat1

value: 18 hours post second injection


title: genomic DNA from whole blood of HIV+ man 57

description: SAMPLE 57

tag: lymphocyteabscount


title: KM_050T

value: F


title: KM_049T


title: genomic DNA from whole blood of HIV+ man 59

description: SAMPLE 59

tag: stripe


title: KM_032T


title: C.albicans infected zebrafish_15dpi_rep1

source_name: C.albicans infected zebrafish, 15dpi, repeat1

value: whole fish

value: 24 hours post second injection


title: genomic DNA from whole blood of HIV+ man 56

description: SAMPLE 56

tag: dnamage


title: C.albicans infected zebrafish_14dpi+12hs_rep1

source_name: C.albicans infected zebrafish, 14dpi+12hr, repeat1

value: 9 months

value: 12 hours post second injection


title: KM_028T


title: genomic DNA from whole blood of HIV+ man 55

description: SAMPLE 55

value: male

tag: hivstatus


title: C.albicans infected zebrafish_14dpi+6hr_rep1

source_name: C.albicans infected zebrafish, 14dpi+6hr, repeat1

value: 6 hours post second injection


title: C.albicans infected zebrafish_6dpi_rep2

description:
Gene expression after 6dpi in C. albicans infected zebrafish
H 6dpi

source_name: C.albicans infected zebrafish, 6dpi, repeat2

value: 144 hours post first injection


title: KM_025T


title: C.albicans infected zebrafish_21dpi_rep1

source_name: C.albicans infected zebrafish, 21dpi, repeat1

value: 504 hours post first injection


title: C.albicans infected zebrafish_14dpi+2hr_rep1

source_name: C.albicans infected zebrafish, 14dpi+2hr, repeat1

value: 2 hours post second injection


title: C.albicans infected zebrafish_17.5dpi_rep1

source_name: C.albicans infected zebrafish, 17.5dpi, repeat1

value: 420 hours post first injection


title: C.albicans infected zebrafish_14dpi_rep1

source_name: C.albicans infected zebrafish, 14dpi, repeat1

value: 336 hours post first injection


title: C.albicans infected zebrafish_3dhpi_rep2

description:
Gene expression after 3 dpi in C. albicans infected zebrafish
H 3dpi

source_name: C.albicans infected zebrafish, 3dpi, repeat2

value: 72 hours post first injection


title: genomic DNA from whole blood of HIV+ man 52

description: SAMPLE 52

source_name: whole blood

value: whole blood

value: positve

tag: logviralloadadjustedforage


title: KM_012T

source_name: HCC tumor

value: hepatocellular carcinoma (HCC)

value: tumor


title: C.albicans infected zebrafish_3dhpi_rep1

source_name: C.albicans infected zebrafish, 3dpi, repeat1


title: KM_009T

value: M


title: C.albicans infected zebrafish_6dpi_rep1

source_name: C.albicans infected zebrafish, 6dpi, repeat1

value: whole fish


title: KM_015T


title: genomic DNA from whole blood of HIV+ man 53

description: SAMPLE 53

tag: bmi


title: genomic DNA from whole blood of HIV+ man 54

description: SAMPLE 54


title: genomic DNA from whole blood of HIV+ man 48

description: SAMPLE 48


title: genomic DNA from whole blood of HIV+ man 51

description: SAMPLE 51


title: genomic DNA from whole blood of HIV+ man 49

description: SAMPLE 49


title: genomic DNA from whole blood of HIV+ man 50

description: SAMPLE 50


title: genomic DNA from whole blood of HIV+ man 47

description: SAMPLE 47


title: KM_008T

tag: disease state


title: KM_001T

value: F


title: KM_019T


title: C.albicans infected zebrafish_2dpi_rep1

source_name: C.albicans infected zebrafish, 2dpi, repeat1

value: 9 months

value: 48 hours post first injection


title: genomic DNA from whole blood of HIV+ man 45

description: SAMPLE 45

value: male

tag: lymphocytesperc


title: genomic DNA from whole blood of HIV+ man 46

description: SAMPLE 46

tag: whitebloodcellperc


title: hCD2-T-bet_tg/tg_lung_rep2

city: Kyoto

first: Shin

last: Kaneko

address: 53 kawaharacho shogoin, sakyo-ku

description: T-bet tg/tg-2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul  containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) 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 treatment of acetnitrile (Sigma-Aldrich) and, Stabilization and.Drying Solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B US45102874) using one color scan setting for 4x44k 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: 014868_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hCD2-T-bet tg/tg_lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.8 ug RNA using the Quick Amp Labeling Kit,one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the Gene Quant pro (GE Healthcare ).

extract_protocol: The RNAs from the lungs were extracted using RNeasy Mini Kit (Qiagen, Venlo, the Netherland).

tag: strain background

tag: genotype/variation

value: hCD2-T-bet tg/tg

value: lung


title: hCD2-T-bet_tg/wt_lung_rep2

description: T-bet tg/wt-2

source_name: hCD2-T-bet tg/wt_lung

value: hCD2-T-bet tg/wt


title: hCD2-T-bet_tg/tg_lung_rep1

description: T-bet tg/tg-1


title: WT_lung_rep1

value: WT


title: genomic DNA from whole blood of HIV+ man 42

description: SAMPLE 42

tag: gender

tag: granulocyteperc


title: genomic DNA from whole blood of HIV+ man 43

description: SAMPLE 43

tag: monocytesperc


title: genomic DNA from whole blood of HIV+ man 41

description: SAMPLE 41


title: genomic DNA from whole blood of HIV+ man 40

description: SAMPLE 40


title: genomic DNA from whole blood of HIV+ man 39

description: SAMPLE 39


title: C.albicans infected zebrafish_1dpi_rep1

source_name: C.albicans infected zebrafish, 1dpi, repeat1

tag: age

tag: infection

tag: time

value: 24 hours post first injection


title: WT_lung_rep2

tag: tissue


title: hCD2-T-bet_tg/wt_lung_repl1

description: T-bet tg/wt-1


title: GM19240_TN

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

country: Canada

institute: McGill University and Génome Québec Innovation Centre

description: Y117 trio, daughter

hyb_protocol: according to manufacturer's instructions

data_processing: using GenomeStudio from illumina

label: Cy3 and Cy5

growth_protocol: The LCLs were grown in T75 flasks in 1X RPMI 1640 Media (invitrogen, Burlington, ON), With 2 mM L-glutamine, 15% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2. At 70%-80% confluence, the cells were harvested.

extract_protocol: total RNA was extracted from cell lysates resuspended in 600 mL RLT lysis buffer using the Rneasy Mini Kit (Qiagen. DNA was extracted from cell lysates resuspended in 200 mL PBS using the GenElute DNA Miniprep Kit (SigmaAldrich).

treatment_protocol: Cells were plated in 6-well plates with 500,000 cells/mL in 2 mL one day prior to the experiment. Cells were either directly treated with TNF-α (3 ng/ul) for NFkB activation or primarily transfected for one hour with Helenalin (5uM) (EMD Chemicals, USA) in order to inhibit the activation of NFκB (p65). Helenalin is a sesquiterpene lactone that acts as a specific NFκB DNA binding inhibitor by irreversibly alkylating free sulfhydruls of the cysteine residues on the p65 subunit. Following this inhibition, cells were stimulated with TNF-α (3 ng/ul) for 8 hours.

value: female

value: Lymphoblasts

tag: population

value: YRI


title: GM19240_notmt

description: Y117 trio, daughter

scan_protocol: according to manufacturer's instructions


title: genomic DNA from whole blood of HIV+ man 30

description: SAMPLE 30

value: whole blood

tag: age (yrs)

tag: dnamage

value: positve

tag: lymphocyteabscount

tag: stripe


title: genomic DNA from whole blood of HIV+ man 34

description: SAMPLE 34

tag: hivstatus

tag: logviralloadadjustedforage

tag: bmi


title: GM19240_tnfalpha

description: Y117 trio, daughter

label_protocol: according to manufacturer's instructions


title: genomic DNA from whole blood of HIV+ man 35

description: SAMPLE 35

tag: lymphocytesperc

tag: whitebloodcellperc


title: genomic DNA from whole blood of HIV+ man 25

description: SAMPLE 25

tag: gender


title: genomic DNA from whole blood of HIV+ man 16

description: SAMPLE 16

tag: granulocyteperc


title: genomic DNA from whole blood of HIV+ man 24

description: SAMPLE 24

tag: monocytesperc


title: genomic DNA from whole blood of HIV+ man 44

description: SAMPLE 44


title: genomic DNA from whole blood of HIV+ man 37

description: SAMPLE 37


title: genomic DNA from whole blood of HIV+ man 18

description: SAMPLE 18


title: genomic DNA from whole blood of HIV+ man 36

description: SAMPLE 36


title: genomic DNA from whole blood of HIV+ man 19

description: SAMPLE 19


title: genomic DNA from whole blood of HIV+ man 20

description: SAMPLE 20


title: genomic DNA from whole blood of HIV+ man 32

description: SAMPLE 32


title: genomic DNA from whole blood of HIV+ man 33

description: SAMPLE 33


title: genomic DNA from whole blood of HIV+ man 22

description: SAMPLE 22


title: genomic DNA from whole blood of HIV+ man 15

description: SAMPLE 15


title: genomic DNA from whole blood of HIV+ man 26

description: SAMPLE 26


title: genomic DNA from whole blood of HIV+ man 28

description: SAMPLE 28


title: genomic DNA from whole blood of HIV+ man 31

description: SAMPLE 31


title: genomic DNA from whole blood of HIV+ man 29

description: SAMPLE 29


title: GM19240_DMSO

description: Y117 trio, daughter


title: GM19238_notmt

description: Y117 trio, mother


title: genomic DNA from whole blood of HIV+ man 13

description: SAMPLE 13


title: genomic DNA from whole blood of HIV+ man 23

description: SAMPLE 23


title: genomic DNA from whole blood of HIV+ man 17

description: SAMPLE 17


title: genomic DNA from whole blood of HIV+ man 21

description: SAMPLE 21


title: genomic DNA from whole blood of HIV+ man 38

description: SAMPLE 38


title: GM19239_tnfalpha

description: Y117 trio, father


title: GM19238_DMSO

description: Y117 trio, mother


title: GM19238_TN

description: Y117 trio, mother


title: GM19239_TN

description: Y117 trio, father


title: genomic DNA from whole blood of HIV+ man 27

description: SAMPLE 27


title: GM19239_DMSO

description: Y117 trio, father


title: genomic DNA from whole blood of HIV+ man 14

description: SAMPLE 14


title: GM12878_tnfalpha

description: XC01463 trio, maternal mother

value: CEU


title: GM19239_notmt

description: Y117 trio, father


title: ALL22089 PDGF-BB stimulation 6h

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
b 22089 +PDGF 6h

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and target value scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: B precursor acute lymphoblastic leukemia

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3'IVT Express Kit and Affymetrix Hybridization Wash and Stain Kit from 100 ng total RNA.

growth_protocol: Cell were grown in serum free RPMI1640 Medium supplemented with antibiotics.

extract_protocol: Cell were isolated from spleen and bone marrow of xenotransplanted leukemic mice containing more than 90% primary human lymphoblasts and subjected to density gradient centrifugation. Cell were cultured in serum free conditions for 2h prior to stimulation. Cell lysates were prepared by washing in ice cold PBS and lysis in ice cold KLB lysis buffer.

treatment_protocol: Cells were stimulated with 50ng/ml recombinant human PDGF-BB or FLT3L, respectively, for indicated time points and lysed immediately

tag: primary all sample

tag: agent

value: PDGF-BB

tag: cell type

value: primary B cell precursor leukemia cells


title: ALL22089 PDGF-BB stimulation 2h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
b 22089 +PDGF 2h

tag: time


title: ALL22089 PDGF-BB stimulation 30min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
b 22089 +PDGF 30min


title: GM12878_TN

description: XC01463 trio, maternal mother

tag: tissue

tag: population


title: ALL22089 FLT3L stimulation 2h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
22089 +FLT3 2h


title: ALL22089 FLT3L stimulation 4h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
22089 +FLT3 4h


title: ALL22089 FLT3L stimulation 30min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
22089 +FLT3 30min


title: ALL22089 FLT3L stimulation 6h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
22089 +FLT3 6h


title: GM12878_notmt

description: XC01463 trio, maternal mother


title: ALL22089 PDGF-BB stimulation 0min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
b 22089 +PDGF 0min


title: GM12878_DMSO

description: XC01463 trio, maternal mother


title: ALL22089 PDGF-BB stimulation 1h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
b 22089 +PDGF 60min


title: GM12878_gdna

description: XC01463 trio, maternal mother


title: ALL22089 FLT3L stimulation 1h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
22089 +FLT3 60min


title: genomic DNA from whole blood of HIV+ man 12

description: SAMPLE 12

tag: age (yrs)

tag: dnamage


title: ALL22089 PDGF-BB stimulation 4h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
b 22089 +PDGF 4h


title: ALL22089 FLT3L stimulation 0min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
22089 +FLT3 0min


title: genomic DNA from whole blood of HIV+ man 9

description: SAMPLE 9

tag: lymphocyteabscount

tag: stripe


title: genomic DNA from whole blood of HIV+ man 7

description: SAMPLE 7

tag: hivstatus

tag: logviralloadadjustedforage


title: GM12892_TN

description: XC01463 trio, maternal grandmother


title: GM12892_notmt

description: XC01463 trio, maternal grandmother


title: genomic DNA from whole blood of HIV+ man 11

description: SAMPLE 11

tag: bmi

tag: lymphocytesperc


title: GM19238_tnfalpha

description: Y117 trio, mother

tag: gender


title: ALL109 PDGF-BB stimulation 6h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
109 +PDGF 6h


title: genomic DNA from whole blood of HIV+ man 8

description: SAMPLE 8

tag: whitebloodcellperc

tag: granulocyteperc


title: ALL109 PDGF-BB stimulation 1h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
109 +PDGF 60min

tag: primary all sample


title: T215P_eh0027

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled targets were hybridized on the mogene2st array and processed using the Affymetrix system.

scan_protocol: Scanning uses the Affymetrix scanner

data_processing: The data were analyzed with Partek Genomics Suite 6.6 by the RMA method.

source_name: BALB/c_PR8 NS1 T215P variant_lung

label_protocol: RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module.

growth_protocol: BALB/c mice were infected with Influenza A virus PR8 wt and PR8 NS1 T215P variant (100PFU). PBS inoculated mice served as control

extract_protocol: On d5 after Infection, lungs were collected in Trizol. RNA isolation was done using Trizol method and PureLink RNA Mini kit (Ambion)

tag: strain background

value: BALB/c

tag: infected with

value: Influenza A virus PR8 NS1 T215P variant

tag: time point

value: 5 dats after infection


title: genomic DNA from whole blood of HIV+ man 4

description: SAMPLE 4

value: male

tag: tissue

tag: monocytesperc


title: T215P_eh0028


title: T215P_eh0026


title: ALL109 PDGF-BB stimulation 0min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
109 +PDGF 0min

tag: agent

tag: time

tag: cell type


title: ALL109 PDGF-BB stimulation 2h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
109 +PDGF 2h


title: genomic DNA from whole blood of HIV+ man 10

description: SAMPLE 10

tag: age (yrs)

tag: dnamage

tag: lymphocyteabscount

tag: stripe


title: genomic DNA from whole blood of HIV+ man 6

description: SAMPLE 6

tag: hivstatus

tag: logviralloadadjustedforage

tag: bmi

tag: lymphocytesperc


title: ALL109 PDGF-BB stimulation 30min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
109 +PDGF 30min

tag: primary all sample


title: genomic DNA from whole blood of HIV+ man 3

description: SAMPLE 3

tag: gender

tag: whitebloodcellperc

tag: granulocyteperc


title: genomic DNA from whole blood of HIV+ man 5

description: SAMPLE 5

tag: tissue


title: GM12892_DMSO

description: XC01463 trio, maternal grandmother

tag: population


title: genomic DNA from whole blood of HIV+ man 2

description: SAMPLE 2

tag: monocytesperc


title: GM12891_tnfalpha

description: XC01463 trio, maternal grandfather


title: GM12892_gdna

description: XC01463 trio, maternal grandmother


title: GM12891_TN

description: XC01463 trio, maternal grandfather


title: ALL109 PDGF-BB stimulation 4h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
109 +PDGF 4h

tag: agent

tag: time


title: ALL114 FLT3L stimulation 2h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
IIb 114 +FLT3 2h

tag: cell type


title: GM12891_notmt

description: XC01463 trio, maternal grandfather


title: wt_eh0022

source_name: BALB/c_PR8 WT_lung

tag: strain background

tag: infected with

value: Influenza A virus PR8 wt

tag: time point


title: GM12891_DMSO

description: XC01463 trio, maternal grandfather


title: genomic DNA from whole blood of HIV+ man 1

description: SAMPLE 1

tag: age (yrs)

tag: dnamage

tag: hivstatus

tag: lymphocyteabscount

tag: stripe


title: wt_eh0023

value: lung


title: genomic DNA from sample N4

city: guangzhou

first: xufeng

last: li

state: guangdong

address: gongye avenue 253

department: oncology center of zhujiang hospital

country: China

institute: Southern Medical University

data_processing: BeadStudio software 2011.1

source_name: normal esophagus mucosa from heathy individual

extract_protocol: genomic DNA was extracted and purifiedusing QIAamp DNA Mini Kit according to standard instructions

tag: disease state

value: normal

tag: gender


title: wt_eh0021


title: ALL114 FLT3L stimulation 1h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
IIb 114 +FLT3 60min

tag: primary all sample


title: genomic DNA from sample N2

tag: tissue

value: normal esophagus mucosa from heathy individual


title: ALL114 FLT3L stimulation 6h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
IIb 114 +FLT3 6h


title: genomic DNA from sample N3


title: GM12892_tnfalpha

description: XC01463 trio, maternal grandmother

tag: population


title: GM12891_gdna

description: XC01463 trio, maternal grandfather


title: PBS_eh0018

value: PBS (control)


title: ALL114 FLT3L stimulation 4h

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
IIb 114 +FLT3 4h


title: C57BL/6 lung, 2 days post pMT tumor cell injection IV(rep 2)

status: Public on Nov 01 2014

city: Hamilton

first: Ali

middle: A

last: Ashkar

address: 1280 Main St. West

institute: McMaster University

description: Control

data_processing: The normalization and all data analysis were performed according to manufacturers instructions using the web based software package :  http://sabiosciences.com/pcrarraydataanalysis.php.  Data was normalized to the average of the following 5 housekeeping genes:  gusb,hprt, hsp90ab1,gapdh and actb. Target gene signals were normalized to housekeeping genes(2^n - ΔCt where ΔCt= (Ct(target or GOI) - Ave Ct (HKG)) .  The software package automatically performs all fold change calculations based upon the original raw data submitted.  Raw Ct values are available on the series record in the file Non-normalized_data.txt. Normalized data are available in the sample tables and on the series record in the file Normalized_data.txt. Fold-Change data are available on the series record in the file Fold-Change_data.txt. The fold change data reports the fold change between the test (IL-15KO)/control(C57BL/6) ratios.

label: SYBR green

label_protocol: PCR Arrays were performed using the RT^2 Profiler PCR Array for Mouse Cytokines and Chemokines (SABiosciences).  1 ug of RNA per sample was used to create cDNA following the procedure outlined in the RT^2 First Strand Kit (3304011,Qiagen).  The plate was run on the Applied Biosystems 7900 RT machine as outlined in the manufacturers instructions.

extract_protocol: To extract RNA, Trizol (Invitrogen) was used initially (as per manufacturers instruction), followed by Qiagen Rneasy Mini Kit and on column DNAse treatment (Rnase-Free Dnase Set #79254)

tag: strain

tag: genotype

value: wildtype

value: female

tag: age

value: 6-8 weeks

tag: time post tumor cell iv injection

value: 2 days


title: ALL114 FLT3L stimulation 30min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
IIb 114 +FLT3 30min

tag: agent

tag: time

tag: cell type


title: PBS_eh0016

tag: strain background

tag: infected with

tag: time point


title: IL-15 KO lung, 2 days post pMT tumor cell injection IV (rep 1)

description: Test

data_processing: The normalization and all data analysis were performed according to manufacturers instructions using the web based software package :  http://sabiosciences.com/pcrarraydataanalysis.php.  Data was normalized to the average of the following 5 housekeeping genes:  gusb,hprt, hsp90ab1,gapdh and actb. Target gene signals were normalized to housekeeping genes(2^n - ΔCt where ΔCt= (Ct(target or GOI) - Ave Ct (HKG)) .  The software package automatically performs all fold change calculations based upon the original raw data submitted.  Raw Ct values are available on the series record in the file "Non-normalized_data.txt". Normalized data are available in the sample tables and on the series record in the file "Normalized_data.txt". Fold-Change data are available on the series record in the file "Fold-Change_data.txt". The fold change data reports the fold change between the test (IL-15KO)/control(C57BL/6) ratios.

value: IL-15 Knock Out


title: IL-15 KO lung, 2 days post pMT tumor cell injection IV (rep 2)

description: Test


title: C57BL/6 lung, 2 days post pMT tumor cell injection IV(rep 1)

description: Control


title: ALL114 FLT3L stimulation 0min

description:
Gene Expression data from PDGF-BB or FLT3L-stimulated primary human B cell precursor leukemia cells isolated from spleen and bone marrow of leukemic mice
IIb 114 +FLT3 0min


title: genomic DNA from sample N1


title: PBS_eh0017


title: OX17vsWT (dye-swap)

status: Public on Nov 02 2014

city: Sapporo

first: Ryozo

last: Imai

address: Hitsujigaoka 1, Toyohira-ku

department: Hokkaido Agricultural Research Center

institute: National Agriculture and Food Research Organization (NARO)

description: Comparison of gene expression between 35s:TaSK5 transgenic line OX17 and wild-type plants (Col-0). Replication 2 (dye swap)

hyb_protocol: Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridisation and wasshing waspreformed according to Agilent 60-mer oligo microarray processing protocol v.4.1 (PN: G4140-90030)

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Spot intensities on the DNA microarray were quantified by Agilent Feature-extraction software version A.7.5.1 with default parameters. Global lowess normalization was done with package limma of the Bioconductor project.

organism: Arabidopsis thaliana

source_name: TaSK expressing plant no. OX17

label_protocol: Total RNA (500 ng) was fluorescently labeled using a Low Input RNA Fluorescent Linear Amplification Kit version 3.3  (Agilent Technologies).

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown in a mixed soil (2:1 mixture of Jiffy mix and vermiculite) in a growth chamber maintained at 22 °C under 16/8 photoperiod from cool-white fluorescent lights (approximately 100 µmol m-2 sec-1)

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

treatment_protocol: No treatment

tag: ecotype

value: Rosette leaf of 3-week-old plant

tag: genotype/variation

value: TaSK expressing

source_name: wild type plant

value: wild type


title: genomic DNA from sample S2

source_name: normal adjacent tissue

value: normal adjacent tissue

tag: disease state


title: OX7vsWT (dye-swap)

description: Comparison of gene expression between 35s:TaSK5 transgenic line OX7 and wild-type plants (Col-0). Replication 2 (dye swap)

source_name: TaSK expressing plant no. OX7


title: OX7vsWT

description: Comparison of gene expression between 35s:TaSK5 transgenic line OX7 and wild-type plants (Col-0). Replication 1.


title: genomic DNA from sample T4

source_name: esophageal squamous cell carcinoma

value: esophageal squamous cell carcinoma

value: tumor

tag: gender


title: genomic DNA from sample S3


title: DES357507B_635: Male_2

city: Bet Dagan

first: Orly

last: Eshel

address: The Volcani Center POB 6

department: Institute of Animal Science

country: Israel

institute: ARO

description:
DES357507B_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos

hyb_protocol: Agilent hybridization protocol

scan_protocol: Axon 4000B GenePix 6.1

data_processing: Feature Extraction software-GenePix 6.1. Data from each slide was background corrected and Lowess normalized with the LIMMA 2.8 package. All slides were then subjected to aquantile normalization with a single channel analysis design. The repeating probes were represented by their median for analysis.

organism: Oreochromis niloticus

source_name: Pool of whole embryo Males at 2 days post fertilization

label_protocol: A total of 56 biological samples were hybridized to the eArray. For  each  sample  200  ng  of  total  RNA  was  labeled  using  the  Agilent  2-color  low  input quickamp  labeling  kit  according  to  the manufacturer's protocols  (Agilent Technology, Santa Clara, CA).

extract_protocol: Total RNA was extracted from a pool of 5-15 whole embryos withmirVana™ miRNA Isolation Kit, Ambion.

value: Male

tag: days post fertilization

tag: sire

tag: dam


title: DES357505D_635: Female_5

description:
DES357505D_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos

source_name: Pool of whole embryo Females at 5 days post fertilization

value: Female


title: DES357505C_635: Male_9

description:
DES357505C_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos

source_name: Pool of whole embryo Males at 9 days post fertilization


title: DES357505B_635: Male_5

description:
DES357505B_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos

source_name: Pool of whole embryo Males at 5 days post fertilization


title: DES357507D_635: Male_9

description:
DES357507D_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: genomic DNA from sample S1

tag: tissue

value: male


title: OX17vsWT

description: Comparison of gene expression between 35s:TaSK5 transgenic line OX17 and wild-type plants (Col-0). Replication 1.


title: genomic DNA from sample S4

value: normal


title: DES357504C_635: Male_5

description:
DES357504C_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357505A_635: Male_2

description:
DES357505A_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357504D_635: Female_2

description:
DES357504D_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos

source_name: Pool of whole embryo Females at 2 days post fertilization


title: DES357504B_635: Male_5

description:
DES357504B_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357504A_635: Female_5

description:
DES357504A_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357506B_635: Male_9

description:
DES357506B_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357506C_635: Female_9

description:
DES357506C_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos

source_name: Pool of whole embryo Females at 9 days post fertilization


title: DES357502C_635: Female_9

description:
DES357502C_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357502B_635: Male_5

description:
DES357502B_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357502A_635: Female_9

description:
DES357502A_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: genomic DNA from sample T1


title: genomic DNA from sample T3


title: genomic DNA from sample T2


title: 1uM Iso

city: San Francisco

first: Nikoleta

last: Tsvetanova

address: 600 16th street

institute: University of California, San Francisco

description: Sample 3

hyb_protocol: Cy5- and Cy3-labeled aRNA were combined in 3× SSC, 50 mM Hepes (pH 7.0), 20 µg of poly(A) RNA, 20 µg Cot-1 DNA, 20 µg tRNA, and 0.3% SDS to a total volume of 50uL. Samples were then heated to 70°C for 5 min, spun at 14,000rpm at room temperature in a microfuge for 5 min, then hybridized at 65°C using the MAUI hybridization system (BioMicro) for 12-16 hrs

scan_protocol: Microarrays were scanned using AxonScanner 4000B (Molecular Devices), and PMTs were manually adjusted for every slide scanned to maximize signal without saturation

data_processing: GenePix was used to extract data from scanned microarray images. Log2 (Treated/Untreated) from duplicate spots were averaged and all log2 ratios were median-centered on an array-by-array basis

source_name: HEK293_1uM Iso

label_protocol: Amersham Cy dye kit

growth_protocol: HEK293 cells were grown in a CO2 incubator at 37C in DMEM+FBS medium; before treatment with drug, cells were washed once in DMEM without serum, then DMEM without serum was added together with drug for 2 hrs

extract_protocol: RNeasy Mini Kit

treatment_protocol:
1uM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium

tag: cell line

tag: treated with

value: 1uM isoproterenol for 2hrs

tag: sample group

value: Agonist response

source_name: HEK293_untreated cells

value: none (untreated control)

value: reference


title: 10nM Iso rep1

description: Sample 4

source_name: HEK293_10nM Iso

treatment_protocol:
10nM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium

value: 10uM isoproterenol for 2hrs


title: Dyngo/1uM Iso

description: Sample 1

source_name: HEK293_Dyngo_1uM Iso

treatment_protocol:
Cells were pre-treated with Dyngo for 15 min, then 1uM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium

tag: pre-treated with

value: Dyngo for 15 min


title: DES357503C_635: Female_5

description:
DES357503C_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357503D_635: Male_9

description:
DES357503D_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: Dyngo/10nM Iso

description: Sample 2

source_name: HEK293_Dyngo_10nM Iso

treatment_protocol:
Cells were pre-treated with Dyngo for 15 min, then 10nM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium


title: DES357503B_635: Male_2

description:
DES357503B_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357506D_635: Female_5

description:
DES357506D_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357506A_635: Male_5

description:
DES357506A_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357503A_635: Female_5

description:
DES357503A_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357501D_635: Male_2

description:
DES357501D_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357501B_635: Female_2

description:
DES357501B_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357507A_635: Female_2

description:
DES357507A_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357501C_635: Male_5

description:
DES357501C_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357501A_635: Male_9

description:
DES357501A_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357507B_532: Male_5

description:
DES357507B_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357507C_532: Male_9

description:
DES357507C_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357507A_532: Male_5

description:
DES357507A_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357507D_532: Female_5

description:
DES357507D_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357505B_532: Male_9

description:
DES357505B_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP51-T

city: Toronto

first: Diana

middle: M

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Normalization of raw intensities was conducted with the BMIQ algorithm. Filtering was conducted for probes whose detection p-values were over 0.01, probes containing a SNP, and all probes mapping to the X and Y chromosomes.

source_name: brain tumor

label_protocol: Standard Illumina protocol (Biotin/DNP)

growth_protocol: DNA was isolated from fresh-frozen tumor soon after tumor resection

extract_protocol: DNA from choroid plexus tumor (CPT) tissue was obtained by proteinase K digestion and phenol/chloroform extraction

treatment_protocol: Tumor samples were snap frozen in liquid nitrogen upon resection and stored at -80 oC until DNA extraction.

tag: p53 status

value: mut

tag: tumor type

value: choroid plexus carcinomas


title: DES357505A_532: Female_2

description:
DES357505A_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357502D_635: Male_9

description:
DES357502D_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP62-T

value: wt

value: choroid plexus papilloma


title: DES357505C_532: Female_5

description:
DES357505C_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357507C_635: Female_9

description:
DES357507C_635
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357504C_532: Female_5

description:
DES357504C_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357505D_532: Male_2

description:
DES357505D_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357504A_532: Male_5

description:
DES357504A_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP3-T


title: DES357504D_532: Female_5

description:
DES357504D_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357506D_532: Male_5

description:
DES357506D_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP151-T

value: atypical choroid plexus papilloma


title: CP136-T


title: DES357506A_532: Female_9

description:
DES357506A_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP153-T


title: DES357504B_532: Male_2

description:
DES357504B_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357502D_532: Male_5

description:
DES357502D_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357506B_532: Female_2

description:
DES357506B_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357502C_532: Female_2

description:
DES357502C_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357502B_532: Male_9

description:
DES357502B_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP159-T


title: CP114-T


title: DES357506C_532: Male_9

description:
DES357506C_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP148-T


title: CP119-T


title: CP140-TB


title: CP139-TB


title: CP57-T


title: CP56-T


title: DES357503D_532: Female_9

description:
DES357503D_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP108-T


title: DES357503B_532: Male_5

description:
DES357503B_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP110-T


title: post-operative serum-24

city: Odense

first: Annette

middle: Raskov

last: Kodahl

address: Sdr. Boulevard 29

department: Oncology R

country: Denmark

institute: Odense University Hospital

description: breast cancer

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Assay efficiencies were determined by analysis of the amplification curves using algorithms similar to the LinReg software package.
Normalization was performed based on the average of the assays detected in all samples (n=107). The formula used to calculate the normalized Cp values was: Normalized Cp = average Cp (n= 107) – assay Cp (sample).
Matrix normalized worksheet reports normalized signal (against average of the assays detected in all samples).
Fold Change worksheet reports pre-operative/post-operative ratios.

label: SYBR Green

source_name: serum

label_protocol: RNA was reverse-transcribed using the miRCURY LNA™ Universal RT microRNA PCR, polyadenylation and cDNA synthesis kit (Exiqon). cDNA was diluted 50 x and assayed in 10 µl PCR reactions according to the manufacture’s protocol for miRCURY LNA™ Universal RT microRNA PCR.

extract_protocol: Total RNA was extracted using the miRNeasy® Mini Kit (Qiagen, Hilden, Germany) according to manufacturer's instructions.

value: serum


title: post-operative serum-23

description: breast cancer


title: DES357502A_532: Male_9

description:
DES357502A_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP141-TB


title: DES357503A_532: Female_9

description:
DES357503A_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357501D_532: Female_5

description:
DES357501D_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: DES357501C_532: Male_2

description:
DES357501C_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP146-T


title: post-operative serum-22

description: breast cancer


title: CP133-T


title: DES357501A_532: Female_9

description:
DES357501A_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP107-T


title: post-operative serum-21

description: breast cancer


title: post-operative serum-20

description: breast cancer


title: CP138-T


title: post-operative serum-19

description: breast cancer


title: CP107-TA


title: post-operative serum-18

description: breast cancer


title: post-operative serum-17

description: breast cancer


title: CP104-T


title: post-operative serum-16

description: breast cancer


title: CP55-T


title: DES357503C_532: Male_5

description:
DES357503C_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos


title: CP106-T


title: CP115-T


title: PGC_rep3

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

country: France

institute: U1208, INSERM

hyb_protocol: 1.65 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 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture. A volume of 100 µl were hybridized to Microarrays (G2519F-026441) for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Genepix  Scanner (4000B) using the following parameters (PixelSize=5, Wavelengths=532  and  PMTGain=550).

data_processing: The scanned images were analyzed with limma in R

organism: Gallus gallus

source_name: primordial germ cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input QuickAmp labelling  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 Spectrophotometer.

extract_protocol: RNA was extracted from cell pellets using 1 ml of TRIzol ® Reagent (Invitrogen) for 5x10 6 cells according to the manufacturer’s recommendations

tag: passages

tag: cell type

value: primordial germ cells


title: PGC_rep2


title: post-operative serum-14

description: breast cancer


title: CP111-T


title: CP66-T


title: CP50-T


title: PGC_rep1


title: post-operative serum-12

description: breast cancer


title: BM2_rep3

source_name: monocytic cell line

value: monocytic cell line


title: post-operative serum-13

description: breast cancer


title: post-operative serum-15

description: breast cancer


title: post-operative serum-11

description: breast cancer


title: post-operative serum-10

description: breast cancer


title: CP152-T


title: CP157-T


title: CP47-T


title: post-operative serum-9

description: breast cancer


title: post-operative serum-8

description: breast cancer


title: BM2_rep2


title: post-operative serum-7

description: breast cancer


title: post-operative serum-5

description: breast cancer


title: post-operative serum-6

description: breast cancer


title: post-operative serum-4

description: breast cancer


title: post-operative serum-3

description: breast cancer


title: DES357501B_532: Female_2

description:
DES357501B_532
Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX; sire 10,40) or genetically-modified YY 'supermales' (sires 20,30,50) resulted in all-female and all-male embryos

value: Female


title: cEF_rep1

source_name: primary culture

value: embryonic fibroblasts


title: cEF_rep3


title: CP112-T


title: CP143-TB


title: cES_rep3

source_name: embryonic stem cells

value: embryonic stem cells


title: CP59-T


title: cES_rep2


title: cBC_rep1

source_name: Blastodermal cells

value: p0(non cultured)

value: Blastodermal cells


title: cBC_rep2


title: cEF_rep2


title: pre-operative serum-23

description: breast cancer

tag: er status

value: positive

tag: age

tag: menopausal status

value: post

tag: surgery

value: lumpectomy

tag: tumor size (mm)

tag: nodal status

value: negative

tag: who diagnosis

value: ductal carcinoma

tag: tumor grade

tag: her2 status


title: pre-operative serum-24

description: breast cancer

tag: tissue

value: positive (1)


title: post-operative serum-1

description: breast cancer


title: post-operative serum-2

description: breast cancer


title: pre-operative serum-21

description: breast cancer


title: cES_rep1


title: cBC_rep3


title: A08 P12-200AICAR

city: Taipei

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

description: This sample is of wild-type HFDPCs in passage 12 and add 200 microM AICAR in culcural media.

hyb_protocol: Each labeled cDNA was hybridized with 135,000 probes and scanned by MS200 microarray scanner performed according to the procedures recommended from Roche NimbleGen gene expression array's user guide.

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

label_protocol: The Cy3 labeled cDNA was then performed using NimbleGen human gene expression array(Cat. No.05543789001, Roche NimbleGen, Madison, WI, USA).

growth_protocol: Human follicle dermal papilla cells (HFDPCs) were cultured in follicle dermal papilla cell growth medium containing 4.5% follicle dermal papilla cell growth medium supplement mix-fetal calf serum, 2 mM sodium pyruvate, 4 mM L-glutamine, and 0.01% penicillin/streptomycin with 95% humidity and 5% CO2 at 37 °C.

extract_protocol: Total RNA was extracted by using TRIzol® reagent (Life technology) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA). The extracted RNA passed the quality test done by the Agilent 2100 Bioanalyzer instrument was used for cDNA synthesis.

treatment_protocol: Total mRNAs from cultured HFDPCs between passage 10 (P10) and passage 12 (P12) under indicated treatments were studied in this project. Five set of cultured HFDCs including untreated control, 60 and 200 microM adenine treatments, and 60 and 200 microM AICAR treatments were cultured in follicle dermal papilla cell growth medium as described above for RNA extraction.

value: follicle dermal papilla cells

value: Passage 12

tag: treatment

value: 200 microM AICAR


title: pre-operative serum-22

description: breast cancer

value: serum


title: pre-operative serum-19

description: breast cancer


title: pre-operative serum-16

description: breast cancer

value: positive (2)


title: CP53-T

value: wt

value: choroid plexus papilloma


title: pre-operative serum-15

description: breast cancer

value: mastectomy


title: pre-operative serum-20

description: breast cancer


title: A07 P12-200adenine

description: This sample is of wild-type HFDPCs in passage 12 and add 200 microM adenine in culcural media.

source_name: Human follicle dermal papilla cells (HFDPCs)

value: 200 microM Adenine


title: A04 P12-Ctrl

description: This sample is of wild-type HFDPCs in passage 12 for control.

value: control


title: A03 P10-200adenine

description: This sample is of wild-type HFDPCs in passage 10 and add 200 microM adenine in culcural media.

value: Passage 10


title: A06 P12-60AICAR

description: This sample is of wild-type HFDPCs in passage 12 and add 60 microM AICAR in culcural media.

value: 60 microM AICAR


title: A05 P12-60adenine

description: This sample is of wild-type HFDPCs in passage 12 and add 60 microM adenine in culcural media.

value: 60 microM Adenine


title: A01 P10-Ctrl

description: This sample is of wild-type HFDPCs in passage 10 for control.


title: pre-operative serum-10

description: breast cancer

value: positive

value: post

value: lumpectomy


title: pre-operative serum-12

description: breast cancer

value: negative

value: ductal carcinoma


title: genomic DNA from human podocyte with KLF4 expression vector

city: Shinjuku-ku

first: Hiroyuki

last: Sasamura

state: Tokyo

address: 35 Shinanomachi

department: Internal Medicine

institute: Keio University School of Medicine

description: KLF4-overexpressing podocytes

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: iScan Control Software version 3.2.45

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Takara Nucleospin tissue kit according to standard instructions

value: human cultured podocytes

value: KLF4 overexpression


title: pre-operative serum-9

description: breast cancer

value: serum


title: pre-operative serum-11

description: breast cancer


title: pre-operative serum-18

description: breast cancer


title: pre-operative serum-8

description: breast cancer


title: pre-operative serum-17

description: breast cancer


title: pre-operative serum-5

description: breast cancer


title: pre-operative serum-6

description: breast cancer


title: pre-operative serum-3

description: breast cancer


title: pre-operative serum-14

description: breast cancer


title: pre-operative serum-4

description: breast cancer


title: pre-operative serum-13

description: breast cancer

value: positive (1)


title: genomic DNA from human podocyte with empty control vector

description: control podocytes

value: vector control


title: pre-operative serum-2

description: breast cancer


title: pre-operative serum-7

description: breast cancer


title: CPP, CP120-T

description:
CP120-T
Brain tumor

hyb_protocol: 20 tumor DNA samples were hybridized to Affymetrix OncoScan™ FFPE Express 2.0 arrays at St. Jude Children's Research Hospital.

scan_protocol: Standard Affymetrix protocol.

data_processing:
Undertaken using the SNP-FASST2 Segmentation Algorithm within Nexus Copy number software (Discovery Edition 7.0, BioDiscovery, Hawthorne, CA) and NCBI genome build 37.
*probes.txt: Log2 ratio per probe generated by Nexus Copy Number Software.

source_name: choroid plexus tumor, CPP

extract_protocol: Tumor genomic DNA was extracted using standard phenol-chloroform extraction from fresh-frozen samples, and the RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion, Carlsbad, USA) for FFPE samples.

treatment_protocol: DNA was isolated from fresh-frozen samples (snapped frozen in liquid nitrogen) (n=17) and an optimal cutting temperature compound (OCT)-embedded fresh frozen sample (n=1), and formalin-fixed paraffin-embedded (FFPE) samples (n=2).

value: choroid plexus tumor

tag: subgroup

value: choroid plexus papilloma

value: wt

tag: tissue type

value: OCT


title: CPP, CP152-T

description:
CP152-T
Brain tumor

tag: p53 status

value: frozen


title: CPP, CP125-T

description:
CP125-T
Brain tumor


title: BM2_rep1

value: monocytic cell line


title: pre-operative serum-1

description: breast cancer


title: CPC, CP64-T

description:
CP64-T
Brain tumor

source_name: choroid plexus tumor, CPC

value: choroid plexus carcinoma

value: mut


title: Human podocyte with KLF4 expression vector

hyb_protocol: 0.6ug 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 Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: differenciated human cultured podocytes

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: RNA was prepared using ISOGEN (NIPPON GENE) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: human cultured podocyte

tag: gender

value: male

tag: vector

value: KLF4 expression vector


title: Human podocyte with empty control vector

value: control


title: WT 8w rep 3

first: Andrew

last: Emili

address: 160 College St #602

department: Donnelly Centre

institute: University of Toronto

description: miRNA expression in healthy littermate control mice heart ventricle tissue

hyb_protocol: The samples were hybridized on a hybridization station

scan_protocol: not provided

data_processing: The quantified (background correction) signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm

source_name: Mus musculus ventricle healthy littermate 8w

label_protocol: the samples were labelled using the miRCURY™ Hy3™/Hy5™ power labelling kit

value: ventricle

tag: strain

value: FVB/N

source_name: Common reference pool

tag: sample

value: Common reference pool


title: R9C 8w rep 4

description: miRNA expression in PLN 08w mice heart ventricle tissue

source_name: Mus musculus ventricle PLN 8w

value: PLN


title: CPC, CP5-TC

description:
CP5-TC
Brain tumor


title: CPC, CP39-T

description:
CP39-T
Brain tumor


title: WT 8w rep 2


title: R9C 8w rep 3


title: WT 8w rep 1


title: R9C 8w rep 1


title: CPC, CP22-TB

description:
CP22-TB
Brain tumor


title: CPC, CP6-T

description:
CP6-T
Brain tumor

value: FFPE


title: CPC, CP22-TA

description:
CP22-TA
Brain tumor

value: choroid plexus tumor


title: CPC, CP58-T

description:
CP58-T
Brain tumor


title: Berry_skin_25˚brix

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skin. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 25˚Brixs.

hyb_protocol: Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock) berry skin

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

growth_protocol: A vineyard from a commercial winery (J. Lohr Vineyards & Wines) in Paso Robles, CA, planted with Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock), was dedicated to the study. Thirty-three vineyard rows, established as three separate blocks of 11 consecutive rows, were assigned to the project based on a completely randomized block design. The orientation of the vineyard was north-south.

extract_protocol: Skins were peeled from frozen berries with a razor blade for all berries on the clusters of each biological replicate. Separated skins and pulp of all the berries of each biological replicate were pooled (without seeds) and ground in a frozen mortar and pestle. Total RNA was extracted from the finely ground skins and pulp in liquid nitrogen using Qiagen RNeasy Plant MidiKit columns . The total RNA was further purified using a Qiagen RNeasy Plant Mini Kit according to the manufacturers’ instructions. RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).

treatment_protocol: IBMP concentrations of berries during maturation were determined. Twenty bunches per row were picked at each harvest date. Samples were collected from six assigned rows at each harvest date in the first five harvest dates and from three assigned rows in the last harvest. Two clusters per vine were sampled from the west arm on the cordon every ten plants (six biological replicates per harvest date). Clusters were carried in a cooler with dry ice to the laboratory and stored at -80 °C until analysis.

tag: cultivar

value: berry skin

tag: brix level

tag: year

tag: vineyard name

value: J. Lohr Vineyards & Wines

tag: vineyard location

value: Paso Robles, CA, USA


title: R9C 8w rep 2


title: CPC, CP2-T

description:
CP2-T
Brain tumor

value: frozen


title: CPC, CP158-T

description:
CP158-T
Brain tumor

value: wt


title: Berry_pulp_25˚brix

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry pulp. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 25˚Brixs.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock) berry pulp

value: berry pulp


title: Berry_skin_36.7˚brix

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skin. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 36.7˚Brixs.

value: Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock)


title: Berry_skin_23.2˚brix

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skin. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 23.2˚Brixs.


title: CPC, CP153-T

description:
CP153-T
Brain tumor

value: choroid plexus carcinoma


title: 546738A04 - 44B1.3-52h_BR2 vs 43A10.6-52h_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: To observe the effects of guanosine penta/tetraphosphate on gene expression

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Media=MS/2 hygrometry Temperature=21°C Light=80 µE

treatment_protocol: Name:Dex induction 52h - compound based treatment - flooding with a solution of dexomethasone  ,dexamethasone:time 52hour . Plants were treated at 10:30 in the morning (Time 0; 10:30 is 3 and a half hours after the onset of the light period) by flooding with 30uM dexamethasone (in aqueous solution with 0,3 % DMSO and 0,033 % Silwet L-77) for 5 minutes . Samples were taken at 4 hrs and 52 hrs after T0. Aerial parts of the seedlings were rapidly harvested and frozen in liquid nitrogen.

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)

extract_protocol: 44B1.3-52h_BR2:5ug. (Qiagen_RNeasy.pdf)


title: 546738A03 - 43A10.6-52h_BR2 vs 44B1.3-52h_BR2


title: Berry_pulp_36.7˚brix

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry pulp. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 36.7˚Brixs.