title: unpaired normal_N15

city: Boston

first: Zhigang

last: Wang

address: 450 Brookline Ave SM936A

department: Cancer Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: initially performed by DFCI microarray core using softwares from Affymetrix. The data for allelic signals in the sample data table were directly exported by dChip software (dChip_2010_1.exe) after the processing the data from cel files.

source_name: unpaired normal

label_protocol: Affymetrix standard protocol

extract_protocol: DNA extracted by proteinase K disgestion-phenochloroform extraction or Qigen DNA extraction kit from ovarian cancer cells enriched from tumor tissues by needle-microdissection or from ascites by affinity enrichment with anti-EPCAM-conjugated beads.

value: Blood (unpaired to tumors)


title: unpaired normal_N21

status: Public on Nov 06 2012

type: genomic

middle: C

state: MA

country: USA

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

tag: tissue


title: unpaired normal_N20


title: PCNSL patient 31

type: RNA

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: Tumor tissue from female patient, 72 years old, KPS 70, HD-MTX chemotherapy treated.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The data were log2-transformed.

molecule: total RNA

source_name: Human brain tumor tissue from PCNSL patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: brain tumor

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: female

tag: age

value: 72 years

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX chemotherapy

tag: outcome

value: alive

tag: survival time

value: more than 3 years


title: unpaired normal_N17


title: PCNSL patient 32

description: Tumor tissue from male patient, 64 years old, KPS 70, HD-MTX chemotherapy treated.

value: male

value: 64 years


title: unpaired normal_N16


title: unpaired normal_N18


title: PCNSL patient 30

description: Tumor tissue from female patient, 71 years old, KPS 40, HD-MTX chemotherapy treated.

value: 71 years

value: dead

value: 1-2 years


title: unpaired normal_N8


title: unpaired normal_N9


title: unpaired normal_N11


title: high grade serous ovarian cancer_HGSC50

description:
PFSTx: progression free survival (months) from the end of primary platinum/taxol treatment
BPM: BRCA1 promoter methylation
Grade H/L: high grade (grade 2, 3) / low (grade 1) grade

source_name: high grade serous ovarian cancer

value: ovarian tumor tissue

tag: pathologic subtype

value: Serous

tag: Stage

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Omentum

tag: tso (tumor sample origin)

tag: residual disease

tag: resistance

tag: progressed

tag: pfstx (months)

tag: floh%

tag: bpm


title: unpaired normal_N13

tag: tissue

value: Blood (unpaired to tumors)


title: unpaired normal_N14


title: PCNSL patient 33

description: Tumor tissue from female patient, 67 years old, KPS 50, HD-MTX chemotherapy treated.

value: brain tumor

tag: disease state

tag: gender

tag: age

value: 67 years

tag: karnofsky performance status (kps)


title: unpaired normal_N12


title: unpaired normal_N5


title: unpaired normal_N19


title: high grade serous ovarian cancer_HGSC52

tag: pathologic subtype

value: Ovary


title: high grade serous ovarian cancer_HGSC44

tag: Stage

value: Uterus


title: unpaired normal_N4


title: unpaired normal_N10


title: unpaired normal_N6


title: unpaired normal_N7


title: PCNSL patient 27

description: Tumor tissue from male patient, 44 years old, KPS 50, HD-MTX chemotherapy treated.

value: primary central nervous system lymphoma (PCNSL)

value: 44 years

tag: therapy

value: HD-MTX chemotherapy

tag: outcome

tag: survival time

value: 2-3 years


title: high grade serous ovarian cancer_HGSC45

tag: grade

tag: grade h/l

tag: primary site

tag: tso (tumor sample origin)


title: high grade serous ovarian cancer_HGSC49

tag: residual disease

tag: resistance

tag: progressed

tag: pfstx (months)


title: high grade serous ovarian cancer_HGSC51

tag: tissue

value: mix (S/E)

tag: floh%

tag: bpm


title: PCNSL patient 29

description: Tumor tissue from male patient, 50 years old, KPS 70, HD-MTX chemotherapy treated.

tag: disease state

tag: gender

value: male

tag: age

value: 50 years

tag: karnofsky performance status (kps)

value: alive

value: more than 3 years


title: high grade serous ovarian cancer_HGSC46

value: ovarian tumor tissue

tag: pathologic subtype

value: Serous

tag: Stage


title: shp63 OFF Nutlin-3 treatment replicate 2

city: Boulder

first: Corrie

last: Gallant-Behm

state: CO

address: 347 UCB

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado at Boulder

description: Gene expression data from H226 cells, shp63 OFF

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Differential gene expression was determined with Partek software using one-way ANOVA.

label: biotin

source_name: shp63 OFF, Nutlin-3 treatment, replicate 2

label_protocol: standard Affymetrix protocol

growth_protocol: H226 cells were plated in RPMI medium supplemented with 10% fetal calf serum 24hrs prior to treatment as indicated

extract_protocol: total RNA was extracted from cells using Tri reagent according to manufacturer's instructions

treatment_protocol: normal growth; 10uM Nutlin-3 12hrs; 1ug/mL doxycycline for 48hrs (to turn on shp63)

tag: cell line

tag: shRNA

value: shp63 OFF

tag: treatment


title: PCNSL patient 23

description: Tumor tissue from female patient, 59 years old, KPS 50, HD-MTX chemotherapy treated.

value: female

value: 59 years

tag: therapy

tag: outcome

value: dead

tag: survival time


title: PCNSL patient 25

description: Tumor tissue from male patient, 63 years old, KPS 80, HD-MTX chemotherapy treated.

value: brain tumor

value: 63 years


title: PCNSL patient 24

description: Tumor tissue from male patient, 64 years old, KPS80, HD-MTX chemotherapy treated.

value: primary central nervous system lymphoma (PCNSL)

value: 64 years

value: survival


title: Fish oil

city: Nashville

first: Viswanathan

last: Saraswathi

state: TN

address: 702 Light Hall, 23rd Ave and Pierce

institute: Vanderbilt University

description: Gene expression data from mice fed a fish oil diet for 12 weeks.

hyb_protocol: The targets in hybridization cocktail were heat denatured at 99°C for 5 minutes, cooled to 45°C for 5 minutes, centrifuged and then loaded on the Affymetrix cartridge arrays for a hybridization period of 16 hours at 45°C, with rotation of 60 RPM in Affymetrix Model 645 Hybridization Oven

scan_protocol: GeneChips were scanned using Affymetrix 7G plus scanner.

data_processing: The data were analyzed with GCOS software and by using Affymetrix default analysis settings and RMA as normalization method, signal intensity values are calculated

organism: Mus sp.

source_name: Fish oil fed mice

label_protocol: Affymetrix WT Sense reactions, using the Affymetrix WT Sense reaction kit (catalog#900652)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. We pooled 6 RNA samples in each group for the microarray experiment.

treatment_protocol: LDLR-/- mice were fed a high fat diet supplemented with 6% olive oil or fish oil in the presence or absence of indomethacin for 12 weeks. Olive oil and fish oil were mixed with diet whereas indomethacin ( 6mg/liter) was administered in drinking water.

value: Liver

tag: genotype

value: LDLR-/-

tag: diet

value: 6% fish oil

tag: drug

value: Placebo

tag: experimental period

value: 12 weeks


title: shp63 ON replicate 2

description: Gene expression data from H226 cells, shp63 ON

source_name: shp63 ON, replicate 2

value: shp63 ON

value: untreated


title: shp63 OFF normal growth replicate 2

source_name: shp63 OFF, normal growth, replicate 2


title: PCNSL patient 28

description: Tumor tissue from female patient, 68 years old, KPS 50, HD-MTX chemotherapy treated.

tag: tissue

value: 68 years

value: HD-MTX chemotherapy

value: 2-3 years


title: shp63 ON replicate 1

source_name: shp63 ON, replicate 1


title: Olive oil+indomethacin

description: Gene expression data from mice fed an olive oil diet in the presence of indomethacin

source_name: Mice received Olive oil + indomethacin

value: 6% olive oil

value: Indomethacin


title: shp63 OFF normal growth replicate 1

source_name: shp63 OFF, normal growth, replicate 1

value: shp63 OFF


title: PCNSL patient 20

description: Tumor tissue from female patient, 68 years old, KPS 40, HD-MTX chemotherapy treated.

value: brain tumor

tag: disease state

value: female

value: less than 1 year


title: PCNSL patient 22

description: Tumor tissue from male patient, 63 years old, KPS.50

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: male

value: 63 years

value: survival


title: Fish oil+Indomethacin

description: Gene expression data from mice fed a fish oil diet in the presence of indomethacin

source_name: Mice received Fish oil + indomethacin

value: Liver

value: LDLR-/-

value: 6% fish oil


title: high grade serous ovarian cancer_HGSC43

value: ovarian tumor tissue

value: Serous

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Ovary

tag: tso (tumor sample origin)

tag: age

tag: residual disease

tag: resistance

tag: progressed

tag: pfstx (months)

tag: floh%

tag: bpm


title: high grade serous ovarian cancer_HGSC40

tag: pathologic subtype

tag: Stage

value: Omentum


title: PCNSL patient 21

description: Tumor tissue from male patient, 57 years old, KPS 60, HD-MTX chemotherapy treated.

value: 57 years

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX chemotherapy

tag: outcome

value: dead

tag: survival time


title: PCNSL patient 26

description: Tumor tissue from male patient, 76 years old, KPS 60, HD-MTX chemotherapy treated.

tag: tissue

value: brain tumor

tag: disease state

tag: gender

value: 76 years

value: 1-2 years


title: Olive oil (Control)

description: Gene expression data from mice fed an olive oil diet for 12 weeks.

organism: Mus musculus

source_name: Olive oil fed mice

tag: genotype

tag: diet

value: 6% olive oil

tag: drug

value: Placebo

tag: experimental period

value: 12 weeks


title: high grade serous ovarian cancer_HGSC42

description:
PFSTx: progression free survival (months) from the end of primary platinum/taxol treatment
BPM: BRCA1 promoter methylation
Grade H/L: high grade (grade 2, 3) / low (grade 1) grade

tag: grade

tag: grade h/l

tag: primary site

tag: tso (tumor sample origin)

tag: age

tag: residual disease

tag: resistance

tag: progressed


title: shp63 OFF Nutlin-3 treatment replicate 1

source_name: shp63 OFF, Nutlin-3 treatment, replicate 1

tag: cell line

tag: shRNA

value: shp63 OFF

tag: treatment


title: high grade serous ovarian cancer_HGSC41

tag: tissue

tag: pathologic subtype

tag: Stage

tag: pfstx (months)

tag: floh%

tag: bpm


title: brcell_96h_control [MCF7m-C]

city: Shanghai

first: Yingyan

last: Yu

address: Shanghai Ruijin 2nd Road No.197

department: Department of Surgery

country: China

institute: Shanghai Ruijin Hospital

description: Gene expression after 96hr saRNA transfection to cell line

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: transfection


title: PCNSL patient 19

description: Tumor tissue from male patient, 62 years old, KPS 100, HD-MTX containing polychemotherapy treated.

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: male

value: 62 years

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX-containing polychemotherapy

tag: outcome

tag: survival time

value: more than 3 years


title: high grade serous ovarian cancer_HGSC38

value: ovarian tumor tissue

value: Serous

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Fallopian

tag: tso (tumor sample origin)

tag: age

tag: residual disease

value: < 1 cm

tag: resistance

tag: progressed


title: brcell_96h_saRNA [MCF7H-B]

tag: cell line

value: 50 nM saRNA


title: brcell_96h_control [MCF7m-A]


title: high grade serous ovarian cancer_HGSC35

tag: tissue

tag: pathologic subtype

tag: Stage

value: IIIC

value: Ovarian

value: Omentum

tag: pfstx (months)

tag: floh%

tag: bpm


title: high grade serous ovarian cancer_HGSC36

value: IIIA

value: R ovary


title: brcell_96h_saRNA [MCF7H-C]

tag: transfection


title: brcell_96h_saRNA [MCF7H-A]


title: high grade serous ovarian cancer_HGSC33


title: high grade serous ovarian cancer_HGSC37

value: IV

value: Surface of right diaphragm


title: brcell_96h_control [MCF7m-B]


title: OX1

city: guelph

first: Yong Mei

last: Bi

address: 50 Stone Road E.

department: Molecular and Cellular Biology

country: Canada

institute: University of Guelph

description: gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rice Genome array

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis

organism: Oryza sativa

source_name: OsCGA1 OX rice plant

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

growth_protocol: Plants were grown in growth chambers with 16 hr of light (500µmol/m2-s) at 28C and 8 hr dark at 23C.

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

value: 4 week old plant

value: leaf

tag: genotype/variation

value: transgenic rice over-expressing this OsCGA1


title: OX2

description: gene expression data


title: high grade serous ovarian cancer_HGSC34

value: IC

tag: grade


title: PCNSL patient 15

description: Tumor tissue from female patient, 59 years old, KPS 70, HD-MTX containing polychemotherapy treated.

value: brain tumor

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: female

value: 59 years

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX-containing polychemotherapy

tag: outcome

value: dead

tag: survival time

value: 1-2 years


title: WT3

description: gene expression data

source_name: wild type rice plant

value: wild type


title: PCNSL patient 17

description: Tumor tissue from female patient, 57 years old, KPS 90, HD-MTX chemotherapy treated.

tag: age

value: 57 years

value: HD-MTX chemotherapy

value: 2-3 years


title: OX3

description: gene expression data


title: high grade serous ovarian cancer_HGSC32

value: ovarian tumor tissue

value: Serous

value: IIC

tag: grade h/l

value: H

tag: primary site

value: Fallopian

tag: tso (tumor sample origin)

value: R ovary

tag: residual disease

value: < 1 cm

tag: resistance

tag: progressed


title: WT2

description: gene expression data

tag: Stage

value: 4 week old plant

tag: tissue

value: leaf


title: PCNSL patient 18

description: Tumor tissue from female patient, 68 years old, KPS 60, HD-MTX containing polychemotherapy treated.

value: brain tumor

value: primary central nervous system lymphoma (PCNSL)

value: female

value: 68 years

value: more than 3 years


title: PCNSL patient 16

description: Tumor tissue from male patient, 74 years old, KPS 70, HD-MTX chemotherapy treated.

value: male

value: 74 years

value: survival


title: PCNSL patient 13

description: Tumor tissue from male patient, 47 years old, KPS 70.

value: 47 years

value: dead


title: high grade serous ovarian cancer_HGSC31

value: ovarian tumor tissue

tag: pathologic subtype

value: Serous

value: IIIC

value: Ovarian

value: Omentum

value: > 1 cm

tag: pfstx (months)

tag: floh%

tag: bpm


title: PCNSL patient 14

description: Tumor tissue from female patient, 68 years old, KPS90 , HD-MTX containing polychemotherapy treated.

tag: disease state

tag: gender

tag: karnofsky performance status (kps)

value: HD-MTX-containing polychemotherapy


title: SMARC1N-PN1 StageVIII R2

city: London

first: Frederic

last: Marsolais

address: 1391 Sandford Street

institute: Southern Crop Protection & Food Research Centre

hyb_protocol: Four µg of purified aRNA was labelled using RNA ampULSe  labeling kit with Cy5 following Kreatech ULS labelling procedure and hybridized to the arrays according to CustomArray (formerly Combimatrix)protocolshttp://cores.montana.edu/index.php?page=combimatrix-arrays.

scan_protocol: The images were scanned on a GenePix 4000B scanner (Axon Instruments, CA) at values of 5 micron resolution, a focal depth of 150 microns, 100% laser power, and 400 PMT.

data_processing: Data was extracted using GenePix Pro 6.1.0.4, adjusted with local background median values and filtered to remove poor or “absent” probes with median signals < negative control median values plus twice the standard deviation. Four slides (one slide from the last two developmental stages of each line) were removed from final analysis. The probes with six slides out of 28 samples passing the filtering were included in the normalization and further analysis. Probe intensities were adjusted with local background subtraction, log2 transformed and then applied to a quantile normalization at the probe level with GeneSpring GX v. 11.5 (Agilent Technologies, Mississauga, ON). The final single expression value of a given transcript on each array was determined by averaging probe intensities after Tukey's median polish and then applied to baseline-transformation to obtain gene-level normalized signal values.

organism: Phaseolus vulgaris

source_name: SMARC1N-PN1 Seed stage VIII

label_protocol: aRNA was synthesized from 1 µg of DNase I-treated total RNA using RNA ampULSe amplification kit (Kreatech Diagnostics, Netherlands) according to manufacturer instructions

growth_protocol: Phaseolus vulgaris wild-type line SARC1 and seed storage protein deficient line SMARC1N-PN1 were grown in the field in 2009 in London, ON

extract_protocol: Total RNA was extracted from 0.5 g~1 g of pulverized seed powder using a  lithium chloride precipitation method

treatment_protocol: Normal cultivation management

value: seeds with fresh weight of 380 mg

tag: weight

tag: developmental stage

value: seed stage VIII

tag: genotype

tag: genetic background


title: high grade serous ovarian cancer_HGSC26

value: III

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Fallopian

tag: tso (tumor sample origin)

tag: age

value: < 1 cm


title: high grade serous ovarian cancer_HGSC30

tag: tissue

tag: Stage

tag: residual disease

tag: resistance

tag: progressed


title: high grade serous ovarian cancer_HGSC29

tag: pathologic subtype

value: R ovary

value: no

tag: pfstx (months)

tag: floh%

tag: bpm


title: high grade serous ovarian cancer_HGSC27

value: II

value: ovarian

value: uterus


title: PCNSL patient 12

description: Tumor tissue from male patient, 58 years old, KPS 80, HD-MTX containing polychemotherapy treated.

value: brain tumor

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: male

value: 58 years

tag: karnofsky performance status (kps)

tag: therapy

tag: outcome

value: alive

tag: survival time

value: more than 3 years


title: WT1

description: gene expression data

value: 4 week old plant

value: leaf

tag: genotype/variation

value: wild type


title: SMARC1N-PN1 StageVI R2

source_name: SMARC1N-PN1 Seed stage VI

value: seeds with fresh weight of 150 mg

tag: weight

tag: developmental stage

value: seed stage VI

tag: genotype

tag: genetic background


title: SMARC1N-PN1 StageVI R3

tag: tissue


title: SMARC1N-PN1 StageVIII R3

value: seeds with fresh weight of 380 mg

value: seed stage VIII


title: SMARC1N-PN1 StageV R4

source_name: SMARC1N-PN1 Seed stage V

value: seeds with fresh weight of 50 mg

value: 50 mg

value: seed stage V


title: SMARC1N-PN1 StageVIII R1


title: SMARC1N-PN1 StageV R2


title: PCNSL patient 11

description: Tumor tissue from male patient, 69 years old, KPS 50.

source_name: Human brain tumor tissue from PCNSL patient

tag: age

value: 69 years

value: dead


title: PCNSL patient 10

description: Tumor tissue from male patient, 68 years old, KPS 100, HD-MTX containing polychemotherapy treated.

value: brain tumor

value: primary central nervous system lymphoma (PCNSL)

value: 68 years

value: HD-MTX-containing polychemotherapy

value: less than 1 year


title: SMARC1N-PN1 StageV R3


title: SMARC1N-PN1 StageVI R1


title: PCNSL patient 9

description: Tumor tissue from female patient, 66 years old, KPS 60, HD-MTX containing polychemotherapy treated.

value: female

value: 66 years

value: more than 3 years


title: cdc55_24_Msn2DNES_20min

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

hyb_protocol: 325ng of both Cy3 and Cy5 labeled cRNA were hybridized to the S. cerevisiae AMADID GE 8x15K G4813A arrays. Samples were hybridized for 17 hours in G2545A Hybridization Oven.

scan_protocol: Agilent G2565A Microarray Scanner System was used to scan the arrays.

data_processing: Agilent Feature Extraction program (Version FE 10.5.1.1). Features with signals below 100 units were discarded. Technical replicates were averaged.

organism: Saccharomyces cerevisiae W303

source_name: reference: untreated W303 msn2msn4

label_protocol: 1 µg of total RNA was used for labeling reaction (Agilent Quick Amp Labeling Kit, two-color, Cat.Nr. 5190-0444). The standard Agilent Protocol for two-color labeling was used, Publication Number: G4140-90050 v.6.0). W303msn2msn4 untreated is Cy3 labelled reference

growth_protocol: Cells were grown for 4 generations in 50ml cultures in YPD at 30°C to OD600nm of about 1. before NaCl was added to a final concentration of 0.4M. After 0(untreated control), 10, 20 and 30 minutes cells were harvested and immediately frozen.

extract_protocol: Total RNA was isolated using glass beads and phenol/chloroform extraction.

treatment_protocol: Hyperosmotic stress: NaCl was added to a final concentration of 0.4M.

tag: cell type

value: whole cell extract

value: msn2msn4 pMsn2pMsn2DNES

tag: treatment

source_name: Saccharomyces cerevisiae strain W303 msn2msn4cdc55

value: msn2msn4cdc55 pMsn2pMsn2DNES

value: 0.4M NaCl


title: cdc55_24_Msn2DNES_30min


title: high grade serous ovarian cancer_HGSC24

source_name: high grade serous ovarian cancer

value: ovarian tumor tissue

tag: pathologic subtype

value: mix (S/E)

tag: Stage

value: IV

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Ovarian

tag: tso (tumor sample origin)

value: R ovary

tag: residual disease

value: no

tag: resistance

tag: progressed

tag: pfstx (months)

tag: floh%


title: PCNSL patient 8

description: Tumor tissue from female patient, 70 years old, KPS 100, HD-MTX containing polychemotherapy treated.

value: brain tumor

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: 70 years

tag: karnofsky performance status (kps)

tag: therapy

tag: outcome

value: dead

tag: survival time

value: 2-3 years


title: SMARC1N-PN1 StageV R1

tag: tissue

value: seeds with fresh weight of 50 mg

tag: weight

value: 50 mg

tag: developmental stage

value: seed stage V

tag: genotype

tag: genetic background


title: high grade serous ovarian cancer_HGSC25

tag: pathologic subtype

value: Serous

tag: Stage

value: IIIC

tag: grade

tag: grade h/l

tag: primary site

tag: tso (tumor sample origin)

value: L ovary

tag: age

tag: bpm


title: cdc55_24_Msn2DNES_10min

tag: cell type

value: whole cell extract

tag: genotype/variation

value: msn2msn4 pMsn2pMsn2DNES

tag: treatment

value: msn2msn4cdc55 pMsn2pMsn2DNES

value: 0.4M NaCl


title: cdc55_24_Msn2DNES_0min


title: M24_Msn2DNES_30min

source_name: Saccharomyces cerevisiae strain W303 msn2msn4


title: PCNSL patient 7

description: Tumor tissue from male patient, 70 years old, KPS 70, HD-MTX containing polychemotherapy treated.

tag: disease state

tag: gender

value: male

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX-containing polychemotherapy

tag: outcome

tag: survival time


title: M24_Msn2DNES_10min


title: SMARC1N-PN1 StageIV R1

source_name: SMARC1N-PN1 Seed stage IV

tag: tissue

value: seeds with fresh weight of 25mg

tag: weight

value: 25 mg

tag: developmental stage

value: seed stage IV

tag: genotype

tag: genetic background


title: high grade serous ovarian cancer_HGSC21

value: ovarian tumor tissue

tag: pathologic subtype

tag: Stage

value: IIIB

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Ovarian

tag: tso (tumor sample origin)

tag: residual disease

value: < 1 cm

tag: resistance

tag: progressed

tag: pfstx (months)

tag: floh%


title: high grade serous ovarian cancer_HGSC19

value: Serous

value: R ovary

tag: age

value: no

tag: bpm


title: PCNSL patient 6

description: Tumor tissue from female patient, 63 years old, KPS 70, HD-MTX containing polychemotherapy treated.

tag: tissue

value: brain tumor

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: female

value: 63 years

tag: karnofsky performance status (kps)

tag: therapy

tag: outcome

value: dead

tag: survival time

value: 1-2 years


title: SMARC1N-PN1 StageIV R3

value: seeds with fresh weight of 25mg

tag: weight

tag: developmental stage

tag: genotype

tag: genetic background


title: PCNSL patient 5

description: Tumor tissue from female patient, 71 years old, KPS 80, HD-MTX containing polychemotherapy treated.

value: 71 years

value: HD-MTX-containing polychemotherapy

value: alive

value: more than 3 years


title: PCNSL patient 4

description: Tumor tissue from male patient, 62 years old, KPS 100.

value: male

value: 62 years


title: SMARC1N-PN1 StageIV R2

value: 25 mg

value: seed stage IV


title: M24_Msn2DNES_20min

tag: cell type

value: whole cell extract

tag: genotype/variation

value: msn2msn4 pMsn2pMsn2DNES

tag: treatment

value: 0.4M NaCl


title: high grade serous ovarian cancer_HGSC22

description:
PFSTx: progression free survival (months) from the end of primary platinum/taxol treatment
BPM: BRCA1 promoter methylation
Grade H/L: high grade (grade 2, 3) / low (grade 1) grade

value: ovarian tumor tissue

tag: pathologic subtype

value: Serous

tag: Stage

value: IIIC

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Ovarian

tag: tso (tumor sample origin)

value: L tube and ovary

tag: residual disease

value: < 1 cm

tag: resistance

tag: progressed

tag: pfstx (months)

tag: floh%


title: PCNSL patient 3

description: Tumor tissue from male patient, 55 years old, KPS 70, HD-MTX containing polychemotherapy treated.

tag: tissue

value: brain tumor

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

tag: age

value: 55 years

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX-containing polychemotherapy

tag: outcome

value: dead

tag: survival time

value: less than 1 year


title: SMARC1N-PN1 StageIV R4

value: seeds with fresh weight of 25mg

tag: weight

value: 25 mg

tag: developmental stage

value: seed stage IV

tag: genotype

tag: genetic background


title: high grade serous ovarian cancer_HGSC23

tag: pathologic subtype

tag: Stage

value: IV

tag: grade

tag: grade h/l

tag: primary site

value: Fallopian

tag: tso (tumor sample origin)

value: Omentum

tag: residual disease

tag: bpm


title: SARC1 StageVIII R3

source_name: SARC1 Seed stage VIII

tag: tissue

value: seeds with fresh weight of 380 mg

value: seed stage VIII

value: wild type


title: M24_Msn2DNES_0min

tag: cell type

value: whole cell extract

tag: genotype/variation

value: msn2msn4 pMsn2pMsn2DNES

tag: treatment


title: PCNSL patient 2

description: Tumor tissue from male patient, 73 years old, KPS 70, HD-MTX containing polychemotherapy treated.

value: brain tumor

tag: disease state

tag: gender

value: male

tag: age

value: 73 years

tag: karnofsky performance status (kps)

tag: therapy

tag: outcome

tag: survival time

value: more than 3 years


title: SARC1 StageVIII R1

tag: weight

tag: developmental stage

tag: genotype

tag: genetic background


title: SARC1 StageVIII R2


title: high grade serous ovarian cancer_HGSC18

value: ovarian tumor tissue

tag: pathologic subtype

value: Serous

tag: Stage

value: IIIC

tag: grade

tag: grade h/l

value: H

tag: primary site

value: Ovarian

tag: tso (tumor sample origin)

tag: residual disease

value: < 1 cm

tag: resistance

tag: progressed

tag: pfstx (months)

tag: floh%


title: high grade serous ovarian cancer_HGSC14

tag: tissue

value: ovarian cancer ascites

value: Ascites

tag: age

tag: bpm


title: high grade serous ovarian cancer_HGSC17

value: III

value: L ovary


title: SARC1 StageVI R3

source_name: SARC1 Seed stage VI

value: seeds with fresh weight of 150 mg

tag: weight

tag: developmental stage

value: seed stage VI

value: wild type


title: Stump vs Blastema [LC]

city: New Haven

first: Edna

last: Holman

state: CT

address: 266 Whitney Ave. KBT-442

department: Molecular, Cellular and Developmental Biology

institute: Yale University

description:
Biological Replicate 1 of 3:
368bl vs. 368st
Blastema_17dpa_rep1 vs. Stump_rep1
Chip: 01_YU_081977. Sample A: 368bl - Cy3. Sample B: 368st - Cy5.
Raw: 01_YU_081977-1107-Crews-368bl+368st-425-495_Data.txt.

Biological Replicate 2 of 3:
369bl vs. 369st
Blastema_17dpa_rep2 vs. Stump_rep2
Chip: 02_YU_081978. Sample A: 369st - Cy3. Sample B: 369bl - Cy5.
Raw: 02_YU_081978-1107-Crews-369st+369bl-435-505_Data.txt.

Biological Replicate 3 of 3:
378bl vs. 378st
Blastema_17dpa_rep3 vs. Stump_rep3
Chip: 03_YU_081979. Sample A: 378st - Cy3. Sample B: 378bl - Cy5.
Raw: 03_YU_081979-1107-Crews-378st+378bl-450-485_Data.txt.

hyb_protocol: using µParaflo® Microfluidic Biochip Technology

scan_protocol: Axon GenePix 4000B Microarray Scanner

data_processing: ArrayPro software-Global Normalization

organism: Ambystoma mexicanum

source_name: Mid-bud regenerating blastema

label_protocol: Cy3 or Cy5 (Outsourced to LC Sciences)

extract_protocol: Total RNA extracted using mirVana miRNA Isolation Kit (Ambion) manufacturer's instructions

tag: days post amputation

value: Mid-bud regenerating blastema

source_name: Non-regenerating stump

value: Non-regenerating stump


title: SARC1 StageVI R1

tag: genotype

tag: genetic background


title: PCNSL patient 1

description: Tumor tissue from male patient, 65 years old, KPS 60, HD-MTX containing polychemotherapy treated.

value: brain tumor

tag: disease state

value: primary central nervous system lymphoma (PCNSL)

tag: gender

value: male

value: 65 years

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX-containing polychemotherapy

tag: outcome

value: dead

tag: survival time


title: SARC1 StageV R3

source_name: SARC1 Seed stage V

value: seeds with fresh weight of 50 mg

value: 50 mg

value: seed stage V


title: SARC1 StageV R2


title: high grade serous ovarian cancer_HGSC15

value: ovarian cancer ascites

tag: pathologic subtype

value: Serous

tag: Stage

value: IV

tag: grade

tag: grade h/l

value: H

tag: tso (tumor sample origin)

value: Ascites

tag: residual disease

tag: resistance

tag: progressed


title: KO 541 L2

city: Orlando

first: Steven

middle: N.

last: Ebert

state: Florida

address: 6900 Lake Nona Blvd

department: Biomedical Sciences

institute: Univ of Central Florida

description: Dopamine beta-hydroxylase (Dbh)

data_processing: Performed by GeneLogic (Gaithersburg, MD). See Quality Control file from GeneLogic for more information.

source_name: adrenergic-deficient

growth_protocol: Age- and size-matched E10.5 mouse hearts were isolated and total RNA was extracted

extract_protocol: Standard Trizol-based extraction of total RNA

treatment_protocol: Ultrasound analysis was used to confirm viability and heart rate data in vivo immediately before isolation

tag: tissue

value: heart

tag: developmental stage

tag: genotype/variation

value: Dbh-/-


title: PCOS, biological rep 4

city: Delhi

first: Rita

last: Singh

address: Department of Zoology

department: Department of Zoology

country: India

institute: University of Delhi

description: Gene expression using RMA method

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 C on the HG-133 Plus 2 Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 7G by Affymetrix.

data_processing: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

source_name: PCOS, biological rep 4

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

growth_protocol: Ovarian aspirates were collected after oocyte retrieval from the consented normal and PCOS patients in the operating room and processed immediately for granulosa cell isolation and RNA extraction to minimize RNA degradation. RNA was stored at -80°C until use.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).

treatment_protocol: Normal and PCOS women were treated with FSH after pituitary downregulation until E2 levels reached 300 pg/mL per dominant follicles. hCG  was then administered followed by transvaginal oocyte retrieval.

tag: cell type

value: granulosa cells

tag: disease

value: Polycystic ovary Syndrome


title: SARC1 StageVI R2

value: seeds with fresh weight of 150 mg

tag: weight

value: seed stage VI

tag: genotype

value: wild type

tag: genetic background


title: PCOS, biological rep 7

description: Gene expression using RMA method

source_name: PCOS, biological rep 7


title: high grade serous ovarian cancer_HGSC20

value: ovarian tumor tissue

value: IIIC

tag: primary site

value: Fallopian

value: Omentum

tag: age

value: < 1 cm

tag: pfstx (months)

tag: floh%

tag: bpm


title: PCOS, biological rep 2

description: Gene expression using RMA method

source_name: PCOS, biological rep 2


title: PCOS, biological rep 6

description: Gene expression using RMA method

source_name: PCOS, biological rep 6


title: KO 569 R4

description: Dopamine beta-hydroxylase (Dbh)

hyb_protocol: Performed by GeneLogic (Gaithersburg, MD)


title: SARC1 StageV R4

value: seeds with fresh weight of 50 mg

value: 50 mg

value: seed stage V


title: PCOS, biological rep 1

description: Gene expression using RMA method

source_name: PCOS, biological rep 1


title: high grade serous ovarian cancer_HGSC16

tag: pathologic subtype

value: Serous

tag: Stage

tag: grade

tag: grade h/l

value: H

tag: tso (tumor sample origin)


title: KO 541 L1

description: Dopamine beta-hydroxylase (Dbh)

scan_protocol: Performed by GeneLogic (Gaithersburg, MD)

tag: tissue

value: heart

tag: developmental stage


title: SARC1 StageV R1


title: high grade serous ovarian cancer_HGSC11

value: ovarian cancer ascites

value: Ovarian

value: Ascites

tag: residual disease

tag: resistance

tag: progressed


title: high grade serous ovarian cancer_HGSC13

value: mix (S/E)

value: III

value: ovarian


title: PCOS, biological rep 5

description: Gene expression using RMA method

source_name: PCOS, biological rep 5

tag: cell type

value: granulosa cells

tag: disease

value: Polycystic ovary Syndrome


title: high grade serous ovarian cancer_HGSC8

tag: primary site

value: peritoneal


title: high grade serous ovarian cancer_HGSC10

tag: age


title: KO 569 R2

description: Dopamine beta-hydroxylase (Dbh)

label_protocol: Performed by GeneLogic (Gaithersburg, MD)

tag: genotype/variation

value: Dbh-/-


title: WT 541 L5

description: Dopamine beta-hydroxylase (Dbh)

source_name: control

value: Dbh+/+


title: high grade serous ovarian cancer_HGSC9

tag: pfstx (months)

tag: floh%


title: Normal, biological rep 3

description: Gene expression using RMA method

source_name: Normal, biological rep 3

value: normal


title: Normal, biological rep 2

description: Gene expression using RMA method

source_name: Normal, biological rep 2


title: SARC1 StageIV R3

source_name: SARC1 Seed stage IV

value: seeds with fresh weight of 25mg

tag: weight

value: 25 mg

value: seed stage IV

tag: genotype

value: wild type

tag: genetic background


title: WT 569 R3

description: Dopamine beta-hydroxylase (Dbh)

value: heart


title: WT 570 R2

description: Dopamine beta-hydroxylase (Dbh)


title: SARC1 StageIV R1


title: high grade serous ovarian cancer_HGSC7

source_name: high grade serous ovarian cancer

value: ovarian cancer ascites

tag: pathologic subtype

value: Serous

tag: Stage

tag: grade

tag: grade h/l

value: H

value: endometrial

tag: bpm


title: Normal, biological rep 1

description: Gene expression using RMA method

source_name: Normal, biological rep 1


title: COV434 Wildtype [RR1022]

status: Public on Nov 05 2012

city: Auckland

first: Roseanne

last: Rosario

address: 85 Park Road, Grafton

country: New Zealand

institute: University of Auckland

hyb_protocol: 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.

scan_protocol: Affymetrix protocol

data_processing: RMA normalisation method

label_protocol: 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).

growth_protocol: Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.

extract_protocol: Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ).  Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.

treatment_protocol: For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate.  Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ).  RNAi-lipid complexes were removed 7h post transfection and replaced with complete media.  For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate.  Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media.  Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.

tag: cell line

tag: transfection


title: COV434 Mutant [RR1017]


title: PCOS, biological rep 3

description: Gene expression using RMA method

source_name: PCOS, biological rep 3

tag: cell type


title: COV434 Control [RR1023]

value: empty vector


title: COV434 Wildtype [RR1018]


title: COV434 Control [RR1021]


title: t=72, shMYCN#3, B

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

treatment_protocol: IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA

value: Neuroblastoma cell line

tag: viral transduction status

value: with shMYCN virus (duplo)

tag: time

value: 72 hrs


title: COV434 Wildtype [RR1020]


title: SARC1 StageIV R4

tag: tissue

tag: developmental stage


title: KGN Knockdown [RR1007]

source_name: KGN

value: KGN

value: FOXL2 stealth RNAi


title: WT 541 L3

description: Dopamine beta-hydroxylase (Dbh)

tag: genotype/variation

value: Dbh+/+


title: KGN Control  [RR1009]

value: GC matched control


title: t=24, shMYCN#3, A

value: with shMYCN virus

value: 24 hrs


title: KGN Control  [RR1003]


title: t=24, shMYCN#3, B


title: KGN Knockdown [RR1004]


title: t=48, shMYCN#3, B

value: 48 hrs


title: COV434 Control [RR1016]


title: t=72, shMYCN#3, A


title: t=48,SHC002,IMR32

value: with control virus


title: t=72,SHC002,IMR32


title: t=0, no virus, rep 2

value: control

value: 0 hrs


title: KGN Knockdown [RR1008]


title: COV434 Mutant [RR1024]


title: t=24,SHC002,IMR32


title: COV434 Mutant [RR1019]

value: Mutant


title: t=0, no virus, rep 1


title: t=48, shMYCN#3, A


title: KGN Control  [RR1006]


title: PatientID: 16306

city: Little Rock

middle: J

last: Heuck

state: AR

address: 4301 W Markham

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciences

hyb_protocol: As recommended by manufacturer

scan_protocol: As recommended by manufacturer

data_processing: Microarray data were normalized using the MAS 5.0 algorithm using GCOS 1.1 and Expression Console 1.2.

source_name: CD138+ selected bone marrow plasma cells

label_protocol: As recommended by manufacturer

extract_protocol: Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). Total More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA).

tag: disease

value: Multiple Myeloma

tag: status

value: Relapsed

tag: treatment

tag: randomized to thal

tag: female gender

tag: age ≥ 65

tag: ldh≥190 u/l

tag: ldh≥250 u/l

tag: b2m≥ 3.5 mg/l

tag: b2m≥ 5.5 mg/l

tag: corresponding bl sample


title: PatientID: 16274


title: PatientID: 16279


title: PatientID: 16263


title: PatientID: 16323


title: PatientID: 15639


title: PatientID: 15573


title: PatientID: 15768


title: PatientID: 15980


title: PatientID: 15739


title: PatientID: 16185


title: PatientID: 16309


title: SARC1 StageIV R2

value: seeds with fresh weight of 25mg

tag: weight

value: 25 mg

value: seed stage IV

tag: genotype

value: wild type

tag: genetic background


title: PatientID: 16116


title: PatientID: 15843


title: PatientID: 15417


title: PatientID: 15356


title: PatientID: 15414


title: PatientID: 15019


title: PatientID: 15484


title: PatientID: 15503


title: PatientID: 15820


title: PatientID: 15190


title: PatientID: 15053


title: PatientID: 14899


title: PatientID: 15359


title: PatientID: 15244


title: PatientID: 15168


title: PatientID: 14941


title: PatientID: 15199


title: PatientID: 15714


title: PatientID: 14869


title: PatientID: 14893


title: PatientID: 14777


title: PatientID: 14830


title: PatientID: 14765


title: PatientID: 14053


title: PatientID: 14174


title: PatientID: 13966


title: PatientID: 14134


title: PatientID: 14723


title: PatientID: 14073


title: PatientID: 13782


title: PatientID: 14106


title: PatientID: 13681


title: PatientID: 13507


title: PatientID: 13569


title: PatientID: 14766


title: PatientID: 12938


title: PatientID: 13451


title: PatientID: 13233


title: PatientID: 13316


title: PatientID: 13149


title: PatientID: 13399


title: PatientID: 12809


title: PatientID: 14562


title: PatientID: 13533


title: PatientID: 13064


title: PatientID: 14133


title: PatientID: 13429


title: PatientID: 13746


title: PatientID: 13289


title: PatientID: 12813


title: PatientID: 12865


title: PatientID: 12766


title: PatientID: 12583


title: PatientID: 12761


title: PatientID: 12661


title: PatientID: 12695


title: PatientID: 12517


title: PatientID: 12566


title: PatientID: 12389


title: PatientID: 12492


title: PatientID: 12366


title: PatientID: 12248


title: PatientID: 12017


title: PatientID: 12523


title: PatientID: 12393


title: PatientID: 12259


title: PatientID: 12061


title: PatientID: 12603


title: PatientID: 11928


title: PatientID: 12324


title: PatientID: 11862


title: PatientID: 11609


title: PatientID: 11979


title: PatientID: 11898


title: PatientID: 10473


title: PatientID: 12041


title: PatientID: 10357


title: PatientID: 10405


title: PatientID: 10256


title: PatientID: 10335


title: PatientID: 11869


title: PatientID: 11952


title: PatientID: 11891


title: PatientID: 11666


title: PatientID: 10504


title: PatientID: 11537


title: PatientID: 10162


title: PatientID: 10338


title: PatientID: 10451


title: PatientID: 11810


title: PatientID: 10195


title: PatientID: 10247


title: PatientID: 10107


title: PatientID: 10021


title: PatientID: 9844


title: PatientID: 10099


title: PatientID: 10098


title: PatientID: 8134


title: PatientID: 7527


title: PatientID: 7156


title: PatientID: 9957


title: PatientID: 6592


title: PatientID: 9996


title: PatientID: 7716


title: PatientID: 9835


title: PatientID: 7307


title: PatientID: 7695


title: PatientID: 3407


title: PatientID: 6608


title: PatientID: 7095


title: PatientID: 9315


title: PatientID: 6526


title: PatientID: 7742


title: PatientID: 9514


title: MM1S_untreated_rep1

first: Michele

last: Cea

address: 450 Brookline Av

department: Medical oncology

institute: Dana farber Cancer institute

hyb_protocol: Fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

scan_protocol: cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: The data were analyzed with DNA-chip analyzer (dChip program) Arrays were normalized based on relative signal produced for an invariant subset of genes

source_name: Human Multiple Myeloma cell line MM1S

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: MM1s were cultured in RPMI-1640 medium supplemented with 10% of FBS, 100U/ml penicillin, 100µg/ml streptomycin and 2mMol/L L-glutamine.

extract_protocol: RNAasi plus mini kit from Qiagen according to the manufactor's instruction

treatment_protocol: Treated cells were cultured in presence of FK866 at concentration of 10nM for 6 and 24 hours.

tag: time of treatment with fk866

value: 0 hours


title: PatientID: 7437


title: PatientID: 1649


title: MM1S_fk866 6h_rep1

value: 6 hours


title: PatientID: 3866


title: PatientID: 7538


title: genomic DNA from CD8- NK cells 1

first: William

middle: P

last: Accomando

address: Kresge Bldg 911, 677 Huntington Ave

department: Epidemiology

institute: Harvard School of Public Health

description: MACS purified CD8- CD56+ NK cells

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
Illumina GenomeStudio v2010.3
normalized data: Average Beta (0-1 contrained)
non-normalized data: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: CD8- NK cells 1

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using QIAGEN Dneasy blood and tissue kit according to standard instructions

treatment_protocol: Leukocyte subtypes were purified via magnetic activated cell sorting (MACS) using kits from Miltenyi Biotec

tag: sample type

value: MACS purified leukocyte subtype

tag: disease state

value: normal

tag: purified leukocyte subtype

value: CD8- NK cells

tag: barcode


title: MM1S_fk866 24h_rep1

value: 24 hours


title: genomic DNA from CD16- CD56bright NK cells 1

description: MACS purified CD16- CD56bright NK cells

source_name: CD16- CD56bright NK cells 1

value: CD16- CD56bright NK cells


title: genomic DNA from CD16+ CD56dim NK cells 2

description: MACS purified CD16+ CD56dim NK cells

source_name: CD16+ CD56dim NK cells 2

value: CD16+ CD56dim NK cells


title: genomic DNA from Pan NK cells 4

description: MACS purified CD56+ NK cells

source_name: Pan NK cells 4

value: Pan NK cells


title: genomic DNA from CD16- CD56bright NK cells 2

description: MACS purified CD16- CD56bright NK cells

source_name: CD16- CD56bright NK cells 2


title: genomic DNA from neutrophils 4

description: MACS purified neutrophils

source_name: neutrophils 4

value: neutrophils


title: genomic DNA from CD4+ T-cells 1

description: MACS purified CD4+ T-cells

source_name: CD4+ T-cells 1

value: CD4+ T-cells


title: genomic DNA from B-cells 5

description: MACS purified B-cells

source_name: B-cells 5

value: B-cells


title: genomic DNA from CD4+ T-cells 2

description: MACS purified CD4+ T-cells

source_name: CD4+ T-cells 2


title: genomic DNA from Pan NK cells 5

description: MACS purified CD56+ NK cells

source_name: Pan NK cells 5


title: genomic DNA from CD16+ CD56dim NK cells 1

description: MACS purified CD16+ CD56dim NK cells

source_name: CD16+ CD56dim NK cells 1


title: genomic DNA from Pan NK cells 6

description: MACS purified CD56+ NK cells

source_name: Pan NK cells 6


title: genomic DNA from CD8+ NK cells 1

description: MACS purified CD8+ CD56+ NK cells

source_name: CD8+ NK cells 1

value: CD8+ NK cells


title: genomic DNA from C1 whole blood 24

description: normal whole blood from control donor C1

source_name: whole blood control

value: whole blood control

value: not applicable


title: genomic DNA from C1 whole blood 25


title: genomic DNA from C1 whole blood 27


title: genomic DNA from C1 whole blood 22


title: genomic DNA from NKT cells 1

description: MACS purified CD3+ CD56+ NKT cells

source_name: NKT cells 1

value: NKT cells


title: genomic DNA from C1 whole blood 26


title: genomic DNA from C1 whole blood 23


title: genomic DNA from C1 whole blood 21


title: genomic DNA from CD8+ T-cells 1

description: MACS purified CD8+ T-cells

source_name: CD8+ T-cells 1

value: CD8+ T-cells


title: genomic DNA from C1 whole blood 19


title: genomic DNA from C1 whole blood 20


title: genomic DNA from CD8+ T-cells 2

description: MACS purified CD8+ T-cells

source_name: CD8+ T-cells 2


title: genomic DNA from C1 whole blood 18


title: genomic DNA from C1 whole blood 17


title: genomic DNA from C1 whole blood 14


title: Female PGC, embryonic day 12.5, biological rep1

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

description:
PGC12F_EA1013_04
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

source_name: Female primordial germ cell (PGC), embryonic day 12.5

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).

growth_protocol: PGCLCs were induced from ES cells.

extract_protocol: Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.

treatment_protocol: PGCLCs and PGCs were purified with FACS based on reporter fluorescence.

tag: strain/background

value: mix (C57BL/6, BDF1)

tag: transgene

value: stella-EGFP

tag: Sex

value: female

tag: age

value: embryonic day 12.5

tag: cell type

value: primordial germ cell (PGC)


title: genomic DNA from C1 whole blood 16

value: normal


title: PGC, embryonic day 9.5, biological rep2

description:
PGC9_EA0842_07
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

source_name: Primordial germ cell (PGC), embryonic day 9.5

value: unknown

value: embryonic day 9.5


title: Male PGCLC, day 6, biological rep1

description:
PGCLCd6M_EA0831_06
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

source_name: Male PGC-like cell, day 6

value: BVSC

value: male

value: primordial germ cell-like cell (PGCLC), day 6


title: Female PGC, embryonic day 12.5, biological rep2

description:
PGC12F_EA1013_08
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).


title: genomic DNA from C1 whole blood 9


title: Female PGCLC, day 3, biological rep2

description:
PGCLCd3_EA1013_05
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

source_name: Female PGC-like cell, day 3

value: primordial germ cell-like cell (PGCLC), day 3


title: genomic DNA from C1 whole blood 12


title: genomic DNA from C1 whole blood 15


title: genomic DNA from C1 whole blood 10


title: genomic DNA from C1 whole blood 11


title: genomic DNA from C1 whole blood 7


title: Female PGCLC, day 3 agg-day 6, biological rep2

description:
PGCLCd3ag6_EA1013_07
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

source_name: Female PGC-like cell, day 3-agg day 6

value: primordial germ cell-like cell (PGCLC), day 3-agg day 6


title: Female PGCLC, day 6, biological rep2

description:
PGCLCd6F_EA1013_06
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

source_name: Female PGC-like cell, day 6


title: genomic DNA from Tregs 6

description: MACS purified Tregs

source_name: Tregs 6

value: MACS purified leukocyte subtype

value: Tregs


title: Female PGCLC, day 3 agg-day 6, biological rep1

description:
PGCLCd3ag6_EA1013_03
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).


title: genomic DNA from C1 whole blood 8

value: whole blood control

value: not applicable


title: genomic DNA from Tregs 5

description: MACS purified Tregs

source_name: Tregs 5


title: genomic DNA from C1 whole blood 13


title: Kidney tissue after aliskiren treatment mouse 4

city: Hamburg

first: Thomas

last: Streichert

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

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Tissue of 20 weeks old mice treated with 50 mg/kg aliskiren for six weeks, treatment started six weeks after 2/3 kidney ablation and four weeks after afiliated uninephrectomy

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

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

data_processing: The data were analyzed with Expression Console version 1.1 (Affymetrix) using RMA as normalization method and TMeV version 4.6.1 (Dana-Faber-Cancer-Institute) for T-Test and SAM analysis.

label: Biotinylated Nucleotides

source_name: Kidney tissue after aliskiren treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT Express Kit User Manual , Affymetrix).

extract_protocol: Total RNA of renal cortex was prepared according to standard laboratory methods

tag: tissue

value: kidney

tag: strain

value: FVB/N

value: 20 weeks

tag: treatment

value: 50 mg/kg aliskiren


title: genomic DNA from Tregs 4

description: MACS purified Tregs

source_name: Tregs 4


title: Female PGCLC, day 6, biological rep1

description:
PGCLCd6F_EA1013_02
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

value: female


title: Female PGCLC, day 3, biological rep1

description:
PGCLCd3_EA1013_01
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).


title: genomic DNA from neutrophils 3

description: MACS purified neutrophils

source_name: neutrophils 3

value: normal

value: neutrophils


title: Kidney tissue after aliskiren treatment mouse 3


title: genomic DNA from Pan T-cells 5

description: MACS purified CD3+ T-cells

source_name: Pan T-cells 5

value: Pan T-cells


title: Kidney tissue after losartan treatment mouse 5

description: Tissue of 20 weeks old mice treated with 500 mg/l losartan for six weeks, treatment started six weeks after 2/3 kidney ablation and four weeks after afiliated uninephrectomy

source_name: Kidney tissue after losartan treatment

value: 500 mg/l losartan


title: genomic DNA from B-cells 4

description: MACS purified B-cells

source_name: B-cells 4

value: B-cells


title: genomic DNA from granulocytes 4

description: MACS purified granulocytes

source_name: granulocytes 4

value: granulocytes


title: Kidney tissue after aliskiren treatment mouse 5


title: PGC, embryonic day 9.5, biological rep1

description:
PGC9_EA0831_07
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

value: mix (C57BL/6, BDF1)

value: stella-EGFP

value: unknown

value: embryonic day 9.5

value: primordial germ cell (PGC)


title: genomic DNA from monocytes 5

description: MACS purified monocytes

source_name: monocytes 5

value: MACS purified leukocyte subtype

value: monocytes


title: Kidney tissue after aliskiren treatment mouse 2

value: kidney

value: FVB/N


title: genomic DNA from neutrophils 2

description: MACS purified neutrophils

source_name: neutrophils 2


title: genomic DNA from C1 whole blood 6

source_name: whole blood control

value: whole blood control

value: not applicable


title: Kidney tissue after losartan treatment mouse 3

value: 20 weeks


title: Kidney tissue after losartan treatment mouse 4


title: Kidney tissue after losartan treatment mouse 2


title: genomic DNA from Tregs 2

description: MACS purified Tregs

source_name: Tregs 2

value: normal

value: Tregs


title: genomic DNA from Tregs 3

description: MACS purified Tregs

source_name: Tregs 3


title: Kidney tissue after losartan treatment mouse 1

value: 500 mg/l losartan


title: genomic DNA from granulocytes 3

description: MACS purified granulocytes

source_name: granulocytes 3


title: genomic DNA from C1 whole blood 5


title: Kidney tissue after aliskiren treatment mouse 1

value: 50 mg/kg aliskiren


title: Foxp3(+)epigenetics(+) T cells, rep2

city: Suita

first: Hiromasa

last: Morikawa

state: Osaka

address: 3-1 Yamadaoka

department: IFReC

institute: Osaka university

description: 06_DEREG GFP+ Mock 2_No_1201_(Mouse430_2)

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 18 hr on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner3000 G7 (Affymetrix).

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software (Affymetrix) and CHP files were generated by Affymetrix Expression Console Software (Affymetrix).

source_name: Foxp3(+)epigenetics(+) T cells

label_protocol: Biotinylated cDNA were prepared using the FL-Ovation cDNA Biotin Module V2 (NuGEN) according to the manufacturer's instructions.

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

treatment_protocol: GFP+CD4+ and GFP-CD4+ splenocytes were sorted from DEREG and DEREG/Scurfy mice. These cells were activated with anti-CD3/CD28 antibodies, and then transduced with Foxp3-expressing retrovirus (pGCSamIN, NGFR marker). NGFR+ T cells sorted were subjected to microarray analysis. To normalize the experimental conditions, Tregs (GFP+ T cells from DEREG) and Tconv (GFP- T cells from DEREG) were also activated and transduced with empty vector.

value: spleen

value: T cell


title: Foxp3 transduced epigenetics(-) T cells, rep1

description: 07_DEREG GFP- Foxp3 1_No_1201_(Mouse430_2)

source_name: Foxp3 transduced epigenetics(-) T cells


title: Foxp3(+)epigenetics(+) T cells, rep1

description: 05_DEREG GFP+ Mock 1 No_1201_(Mouse430_2)


title: genomic DNA from Pan T-cells 4

city: Boston

description: MACS purified CD3+ T-cells

source_name: Pan T-cells 4

value: Pan T-cells


title: Foxp3(-)epigenetics(-) T cells, rep1

description: 09_DEREG GFP- Mock 1_No_1201_(Mouse430_2)

source_name: Foxp3(-)epigenetics(-) T cells


title: Foxp3(-)epigenetics(-) T cells, rep2

description: 10_DEREG GFP- Mock 2_No_1201_(Mouse430_2)


title: Foxp3 transduced epigenetics(-) T cells, rep2

description: 08_DEREG GFP- Foxp3 2_No_1201_(Mouse430_2)


title: genomic DNA from Pan NK cells 3

description: MACS purified CD56+ NK cells

source_name: Pan NK cells 3

value: Pan NK cells


title: genomic DNA from Pan T-cells 3

description: MACS purified CD3+ T-cells

source_name: Pan T-cells 3


title: Foxp3 transduced epigenetics(+) T cells, rep2

description: 02_D_S GFP+ Foxp3 2 No_1201-2_(Mouse430_2)

source_name: Foxp3 transduced epigenetics(+) T cells


title: genomic DNA from C1 whole blood 4

description: normal whole blood from control donor C1


title: Foxp3(-)epigenetics(+) T cells, rep2

description: 04_D_S GFP+ Mock 2 No_1201_(Mouse430_2)

source_name: Foxp3(-)epigenetics(+) T cells


title: gastric cancer tissue sample 1

city: San Francisco

first: Xin

last: Chen

state: CA

institute: UCSF

hyb_protocol: The hybridization solution was denatured for 10 min at 72°C and then incubated for 1 h at 37°C. Hybridization was performed for 48-72 h in a moist chamber on a slow rocking table. Next, Arrays were washed for 10 min in 50% formamide and 2 × SSC at 45°C, and 10 min in phosphate buffer at room temperature. Slides were mounted in mounting solutions containing 0.3 microgram/ml DAPI.

scan_protocol: Three single-color intensity images (DAPI, Cy3 and Cy5) were collected for each array using a charge coupled device camera.

data_processing: The UCSF SPOT software [PMID: 11827952] was used to automatically segment the spots based on the DAPI images, perform local background correction and calculate various measurement parameters, including log2 ratios of the total integrated Cy3 and Cy5 intensities for each spot.

label_protocol: For hybridization, 1 microgram of tumor DNA and 1 microgram of gender matched reference DNA was labeled by random priming using Cy3-dCTP and Cy5- dCTP, respectively, using Bioprime Kit (Invitrogen).

extract_protocol: Genomic DNA was extracted using the Genomic DNA purification Kit (Qiagen, Valencia, CA).

value: gastric cancer tissue sample 1

source_name: Three mixed normal blood sample

tag: reference

value: Three mixed normal blood sample


title: gastric cancer cell line MNK45

tag: cell line


title: gastric cancer cell line KATOIII

source_name: KATOIII

value: KATOIII


title: genomic DNA from monocytes 4

description: MACS purified monocytes

source_name: monocytes 4

value: MACS purified leukocyte subtype

value: monocytes


title: genomic DNA from B-cells 3

description: MACS purified B-cells

source_name: B-cells 3

value: B-cells


title: gastric cancer tissue sample 5

value: gastric cancer tissue sample 5


title: genomic DNA from neutrophils 1

description: MACS purified neutrophils

source_name: neutrophils 1

value: neutrophils


title: Foxp3 transduced epigenetics(+) T cells, rep1

description: 01_D_S GFP+ Foxp3 1_No_1201_(Mouse430_2)


title: genomic DNA from Pan T-cells 2

description: MACS purified CD3+ T-cells

source_name: Pan T-cells 2


title: P3s2

city: Turku

first: Tuomas

last: Nikula

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology

description: Total RNA extracted acording to manufacturer's protocol

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation with Illumina bead studio v 1.5.0.34

source_name: PAXgene Blood RNA System

label_protocol: 1 µg of total RNA was first amplified with RiboAmp® OA 1 Round RNA Amplification Kit (Arcturus) and purified cDNA was then used as a template for In Vitro transcription to synthesize labeled cRNA with Illumina® RNA Amplification Kit (Ambion®).

extract_protocol: RNA was extracted using the "PAXgene Blood RNA System" which consists of a blood collection tube (PAXgene Blood RNA Tube) and nucleic acid purification kit (PAXgene Blood RNA Kit).

tag: gender

value: Male


title: gastric cancer tissue sample 3

value: gastric cancer tissue sample 3


title: genomic DNA from Pan T-cells 1

description: MACS purified CD3+ T-cells

source_name: Pan T-cells 1

value: normal


title: F2

description: PBMCs were first isolated by Ficoll gradient centrifugation (Amersham Biosciences) from which total RNA was isolated with Trizol (Gibco BRL®) and stored at -70 ?C. Total RNA samples were then combined for purification in Qiagen's RNeasy Maxi kit, using on column DNAse treatment. Purified total RNA from different columns was pooled again and aliquots were stored for later use at -70 ?C

source_name: PBMC

extract_protocol: PBMCs were first isolated by Ficoll gradient centrifugation (Amersham Biosciences) from which total RNA was isolated with Trizol (Gibco BRL®) and stored at -70 oC. Total RNA samples were then combined for purification in Qiagen's RNeasy Maxi kit, using on column DNAse treatment. Purified total RNA from different columns was pooled again and aliquots were stored for later use at -70 oC

value: Mixed


title: Male PGCLC, day 6, biological rep2

description:
PGCLCd6M_EA0842_06
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).

source_name: Male PGC-like cell, day 6

value: BVSC

value: male

value: primordial germ cell-like cell (PGCLC), day 6


title: P3s1


title: F1


title: P2s2

value: Female


title: P1s2


title: gastric cancer tissue sample 4

value: gastric cancer tissue sample 4


title: P1s1


title: T3s2

source_name: Tempus Blood RNA Tube

extract_protocol: RNA was extracted using the "Tempus Blood RNA Tube Stabilization and Isolation of RNA From Whole Blood" protocol on the ABI Prism 6100 Nucleic Acid PrepStation


title: genomic DNA from granulocytes 2

description: MACS purified granulocytes

source_name: granulocytes 2

value: granulocytes


title: gastric cancer cell line SNU5

value: Three mixed normal blood sample


title: P2s1


title: T1s2


title: T3s1


title: T2s2


title: gastric cancer cell line SNU16


title: T2s1


title: genomic DNA from monocytes 3

description: MACS purified monocytes

source_name: monocytes 3


title: MCIP W210 versus input

city: Bristol

first: Anthony

last: Dallosso

address: University Walk

department: School of Cellular & Molecular Medicine

country: United Kingdom

institute: University of Bristol

hyb_protocol: The labeled experimental IP and control DNAs were co-hybridized to the array for 16 - 20 hours (Nimblegen Inc)

scan_protocol: Nimblegen Inc

data_processing:
Nimblegen Inc
Each feature on the array has a corresponding scaled log_ratio of input and test samples. Log2-ratio (ChIP/input) is scaled to centre the data around zero.

source_name: W210+ p29 MCIP

label_protocol: 4 micrograms of MCIP DNA was labelled using Klenow fragment-catalyzed primer extension using Cy dye coupled 9mer primers (Nimblegen Inc).

extract_protocol: Standard phenol/chloroform method was used for DNA extraction. MCIP protocol as described in related publication.

tag: cell line origin

tag: fraction

value: MCIP

source_name: W210+ p29 input

label_protocol: 4 micrograms of input DNA was labelled using Klenow fragment-catalyzed primer extension using Cy dye coupled 9mer primers (Nimblegen Inc).

extract_protocol: Standard phenol/chloroform method was used for DNA extraction. Protocol as described in related publication.

value: input


title: genomic DNA from monocytes 2

description: MACS purified monocytes

source_name: monocytes 2

tag: sample type

value: MACS purified leukocyte subtype

value: monocytes


title: MCIP IP100 versus input

source_name: IP100+ p29 MCIP

source_name: IP100+ p29 input


title: T1s1


title: Huh7 99

city: Tokushima city

first: toshihito

last: tanahashi

address: Kuramoto-cho 3-18-15

institute: Tokushima University

hyb_protocol: Hybridization were performed in accordance with the manufacturer’s procedure

scan_protocol: The array was scanned with a laser scanner (G2565BA; Agilent).

data_processing: Feature Extraction 9.5 software (Agilent) was used to obtain the microarray raw data.

source_name: Exosome

label_protocol: One-color microRNA labeling with Cy3 fluorescence were performed in accordance with the manufacturer’s procedure.

extract_protocol: The ExoQuicki kit (System Biosciences) was used to extract total RNA including microRNA from exosome fraction.


title: gastric cancer cell line NUGC3

source_name: Three mixed normal blood sample


title: gastric cancer cell line N87


title: Huh7 98


title: Huh7 97


title: gastric cancer tissue sample 9

value: gastric cancer tissue sample 9


title: Huh7 96


title: genomic DNA from Pan NK cells 2

description: MACS purified CD56+ NK cells

source_name: Pan NK cells 2

tag: disease state

value: Pan NK cells


title: gastric cancer tissue sample 92

value: gastric cancer tissue sample 92


title: Huh7 94


title: Huh7 95


title: genomic DNA from granulocytes 1

description: MACS purified granulocytes

source_name: granulocytes 1

tag: purified leukocyte subtype


title: Huh7 93


title: genomic DNA from C1 whole blood 3

source_name: whole blood control

value: whole blood control

value: not applicable

tag: barcode


title: Huh7 91

hyb_protocol: Hybridization were performed in accordance with the manufacturer’s procedure.


title: Huh7 100


title: Huh7 90


title: Huh7 88


title: gastric cancer tissue sample 91

value: gastric cancer tissue sample 91


title: NASH 82

scan_protocol: The array was scanned with a laser scanner (G2565BA; Agilent)

value: exosome rich fraction from sera

value: NASH

value: female


title: NASH 83

value: male


title: NASH 84


title: gastric cancer tissue sample 77

value: gastric cancer tissue sample 77


title: gastric cancer tissue sample 76

value: gastric cancer tissue sample 76


title: gastric cancer tissue sample 78

value: gastric cancer tissue sample 78

value: Three mixed normal blood sample


title: gastric cancer tissue sample 8

value: gastric cancer tissue sample 8


title: gastric cancer tissue sample 90

value: gastric cancer tissue sample 90


title: gastric cancer tissue sample 7

value: gastric cancer tissue sample 7


title: NASH 81


title: genomic DNA from Pan NK cells 1

description: MACS purified CD56+ NK cells

source_name: Pan NK cells 1

value: MACS purified leukocyte subtype

value: normal


title: Chronic hepatitis B 80

value: Chronic hepatitis B


title: Chronic hepatitis B 79


title: genomic DNA from B-cells 2

description: MACS purified B-cells

source_name: B-cells 2

value: B-cells


title: Huh7 89


title: genomic DNA from C1 whole blood 2

value: whole blood control

value: not applicable


title: Huh7 92


title: gastric cancer tissue sample 73

value: gastric cancer tissue sample 73


title: Chronic hepatitis B 78

value: exosome rich fraction from sera


title: gastric cancer tissue sample 72

value: gastric cancer tissue sample 72


title: genomic DNA from C1 whole blood 1


title: Chronic hepatitis B 77

value: female


title: genomic DNA from B-cells 1

description: MACS purified B-cells

source_name: B-cells 1


title: Chronic hepatitis C 75

value: Chronic hepatitis C

value: male


title: gastric cancer tissue sample 6

value: gastric cancer tissue sample 6


title: Chronic hepatitis C 74


title: genomic DNA from Tregs 1

description: MACS purified Tregs

value: Tregs


title: Chronic hepatitis C 73


title: Chronic hepatitis C 71


title: gastric cancer tissue sample 68

value: gastric cancer tissue sample 68

value: Three mixed normal blood sample


title: Foxp3(-)epigenetics(+) T cells, rep1

description: 03_D_S GFP+ Mock 1 No_1201_(Mouse430_2)

source_name: Foxp3(-)epigenetics(+) T cells

tag: strain/background

value: spleen

value: T cell


title: Chronic hepatitis C 70


title: NASH 85

value: NASH


title: NASH 86


title: NASH 87


title: IB3-1, IDR-1018 + flagellin (CFI_D_8)

city: Vancouver

first: Christopher

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

institute: University of British Columbia

description: IB3-1, IDR-1018 + flagellin

hyb_protocol: Amplified cRNA was hybridized to human HT-12 expression bead chips (Illumina) and raw data were first processed with Illumina BeadStudio version 3.4.0 to produce summary gene expression values by the Prostate Centre Microarray Facility, Vancouver, Canada.

data_processing: Microarray values were normalized using quantile normalization with the beadarray Bioconductor package.

source_name: Cell line, IB3-1

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Total RNA was isolated from airway epithelial cells and PBMCs (RNeasy Plus Mini Kit, Qiagen), and was transcribed to cDNA with oligo-dT primers (High-Capacity cDNA Reverse Transcription Kit, Applied Biosystems). RNA quality was determined using Bioanalyzer 2100 (Agilent Technologies). mRNA was amplified using the RNA ampULSe kit (Kreatech) according to manufacturer’s instructions.

treatment_protocol: C38 and IB3-1 cells were seeded in Primaria plates (BD) at a density of 2.5 x 105 cells/ml, and were allowed to grow for 16-18 hr until confluent.

value: confluent in Primaria plates

value: IDR-1018 + flagellin


title: Chronic hepatitis C 76


title: C38, IDR-1018 (NA_B_8)

description: C38, IDR-1018

source_name: Cell line, C38


title: genomic DNA from monocytes 1

description: MACS purified monocytes

source_name: monocytes 1

value: MACS purified leukocyte subtype

value: normal

value: monocytes


title: C38, flagellin (NA_C_6)

description: C38, flagellin

value: flagellin


title: gastric cancer tissue sample 61

value: gastric cancer tissue sample 61


title: gastric cancer tissue sample 66

value: gastric cancer tissue sample 66


title: Chronic hepatitis C 72

value: exosome rich fraction from sera

value: Chronic hepatitis C

value: female


title: IB3-1, IDR-1018 (CFI_B_6)

description: IB3-1, IDR-1018


title: IB3-1, IDR-1018 + flagellin (CFI_D_5)

description: IB3-1, IDR-1018 + flagellin


title: IB3-1, IDR-1018 (CFI_B_8)

description: IB3-1, IDR-1018


title: C38, IDR-1018 (NA_B_5)

description: C38, IDR-1018


title: gastric cancer tissue sample 49

value: gastric cancer tissue sample 49


title: gastric cancer tissue sample 57

value: gastric cancer tissue sample 57


title: Chronic hepatitis C 69

value: male


title: Chronic hepatitis C 68


title: Chronic hepatitis C 66


title: Chronic hepatitis C 64


title: Chronic hepatitis C 65


title: Chronic hepatitis C 62


title: gastric cancer tissue sample 42

value: gastric cancer tissue sample 42

value: Three mixed normal blood sample


title: gastric cancer tissue sample 39

value: gastric cancer tissue sample 39


title: IB3-1, untreated control (CFI_A_6)

description: IB3-1, untreated control

value: confluent in Primaria plates


title: Chronic hepatitis C 60


title: Chronic hepatitis C 63


title: gastric cancer tissue sample 36

value: gastric cancer tissue sample 36


title: Chronic hepatitis C 56


title: Chronic hepatitis C 57


title: Chronic hepatitis C 58


title: gastric cancer tissue sample 47

value: gastric cancer tissue sample 47


title: gastric cancer tissue sample 32

value: gastric cancer tissue sample 32


title: Chronic hepatitis C 59


title: Chronic hepatitis C 54


title: Chronic hepatitis C 53


title: C38, untreated control (NA_A_8)

description: C38, untreated control


title: gastric cancer tissue sample 28

value: gastric cancer tissue sample 28


title: Chronic hepatitis C 52


title: C38, untreated control (NA_A_6)

description: C38, untreated control


title: C38, IDR-1018 + flagellin (NA_D_5)

description: C38, IDR-1018 + flagellin

value: IDR-1018 + flagellin


title: gastric cancer tissue sample 23

value: gastric cancer tissue sample 23


title: IB3-1, flagellin (CFI_C_5)

description: IB3-1, flagellin

value: flagellin


title: Chronic hepatitis C 51

value: exosome rich fraction from sera


title: Chronic hepatitis C 61

value: Chronic hepatitis C


title: C38, flagellin (NA_C_8)

description: C38, flagellin


title: Chronic hepatitis C 55

value: female


title: Chronic hepatitis C 50


title: C38, flagellin (NA_C_5)

description: C38, flagellin


title: IB3-1, flagellin (CFI_C_8)

description: IB3-1, flagellin


title: C38, IDR-1018 + flagellin (NA_D_6)

description: C38, IDR-1018 + flagellin


title: IB3-1, untreated control (CFI_A_8)

description: IB3-1, untreated control


title: Chronic hepatitis C 49


title: gastric cancer tissue sample 21

value: gastric cancer tissue sample 21


title: Chronic hepatitis C 48


title: Chronic hepatitis C 46


title: Chronic hepatitis C 47


title: gastric cancer tissue sample 19

value: gastric cancer tissue sample 19


title: Chronic hepatitis C 44


title: Chronic hepatitis C 45


title: gastric cancer tissue sample 16

value: gastric cancer tissue sample 16


title: gastric cancer tissue sample 15

value: gastric cancer tissue sample 15


title: gastric cancer tissue sample 14

value: gastric cancer tissue sample 14

value: Three mixed normal blood sample


title: gastric cancer tissue sample 13

value: gastric cancer tissue sample 13


title: Chronic hepatitis C 35

value: male


title: Chronic hepatitis C 37


title: Chronic hepatitis C 38


title: Chronic hepatitis C 41


title: Chronic hepatitis C 42


title: Chronic hepatitis C 40


title: Chronic hepatitis C 39


title: Chronic hepatitis C 43


title: Chronic hepatitis C 33


title: IB3-1, flagellin (CFI_C_6)

description: IB3-1, flagellin

value: confluent in Primaria plates


title: gastric cancer tissue sample 11

value: gastric cancer tissue sample 11


title: Patient 36 post-treatment serum

type: protein

first: Serena

middle: S

last: Kwek

address: 513 Parnassus Ave.

description: Serum was diluted 1:500 and used to hybridize Invitrogen protoarray v4.0. Bound antibodies were detected with anti-human IgG conjugated with Alexafluor 647. Array was scanned with an Axon scanner.

scan_protocol: Arrays were scanned with an Axon scanner.

data_processing: The raw data for all arrays were quantile-normalized, median-centered, and log2 transformed using R version 2.14.1

label: Alexafluor 647

molecule: protein

source_name: Serum

label_protocol: Commercially available anti-human IgG conjugated with Alexafluor647 was purchased from Invitrogen.

extract_protocol: Serum was obtained from the supernatant of whole blood with the red blood cells spun down and was frozen in aliquots and stored at -80C. Protein is purified from baculovirus using either GST or His tags.

tag: cancer

value: hormone refractory prostate cancer

tag: designation

value: Responder

tag: treatment status

value: post

tag: protein

value: Human IgG


title: Chronic hepatitis C 32

value: exosome rich fraction from sera

tag: age


title: Chronic hepatitis C 31

value: Chronic hepatitis C


title: C38, IDR-1018 + flagellin (NA_D_8)

description: C38, IDR-1018 + flagellin

value: IDR-1018 + flagellin


title: gastric cancer tissue sample 12

tag: tissue

value: gastric cancer tissue sample 12


title: Chronic hepatitis C 30

value: female


title: gastric cancer tissue sample 10

value: gastric cancer tissue sample 10


title: Chronic hepatitis C 34


title: Chronic hepatitis C 36


title: Patient 36 pre-treatment serum

hyb_protocol: Serum was diluted 1:500 and used to hybridize Invitrogen protoarray v4.0. Bound antibodies were detected with anti-human IgG conjugated with Alexafluor 647.

value: pre


title: gastric cancer cell line AGS

source_name: AGS

value: AGS


title: gastric cancer tissue sample 56

value: gastric cancer tissue sample 56

value: Three mixed normal blood sample


title: gastric cancer cell line BGC823


title: IB3-1, IDR-1018 (CFI_B_5)

description: IB3-1, IDR-1018

tag: treatment


title: Patient 35 post-treatment serum

value: Non-responder


title: C38, untreated control (NA_A_5)

description: C38, untreated control

value: confluent in Primaria plates


title: Patient 34 pre-treatment serum


title: Patient 35 pre-treatment serum


title: Patient 34 post-treatment serum


title: C38, IDR-1018 (NA_B_6)

description: C38, IDR-1018


title: Chronic hepatitis C 29

value: male


title: Chronic hepatitis C 28


title: gastric cancer tissue sample 54

value: gastric cancer tissue sample 54

tag: reference


title: gastric cancer tissue sample 53

value: gastric cancer tissue sample 53


title: Chronic hepatitis C 26


title: Chronic hepatitis C 25


title: IB3-1, untreated control (CFI_A_5)

description: IB3-1, untreated control

tag: cell line


title: IB3-1, IDR-1018 + flagellin (CFI_D_6)

description: IB3-1, IDR-1018 + flagellin


title: gastric cancer tissue sample 45

value: gastric cancer tissue sample 45


title: Chronic hepatitis C 23

tag: gender


title: Normal oral keratinocyte replicate 2

city: Bangkok

first: Chureerat

last: Phokaew

address: 1873 Phayathai Road

department: Department of Medicine

country: Thailand

institute: Chulalongkorn Univerisity

description: replicate 2

data_processing: The data were normalised using cubic spline normalisation with Beadstudio program.

source_name: Normal oral keratinocyte

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

growth_protocol: Head and neck squamous cell cancer (HNSCC) cell lines (WSU-HN) [REF], WSU- HN 17 and 31, were afforded by Dr. Silvio Gutkind, NIH, USA. Hacat (Human keratinocyte immortal cell line) was purchased from ATCC (Manassas, VA, USA). All cell line were cultured in Dulbecco's modified Eagle's medium (Gibco BRL, Life Technologies, Pairly, UK) supplemented with 10% heat- inactivated fetal bovine serum (Sigma, St. Louis,MO, USA). Cells were incubated at 37oC in 5% CO2 and subculture before reach 80% of cell culture area.  Primary normal human oral keratinocytes was isolate from normal healthy gingiva tissue and culture on Collagen from human placenta, Bornstein and Traub Type IV coat plate (C5533,Sigma) in KGMTM-2 Bullet Kit TM media (©Lonza Walkersville, Inc.) according to the suggest protocol from company until cell number reach to target size.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Deoxyribonulease I (DNase I), RNase-free (Fermentas) accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: To inhibit DNMTs, WSU-HN17 and Hacat cells were treated every 24 hours with 4 μM 5-aza-2- deoxycytidine for up to 16 days for genomic demethylation (Sigma-Aldrich). Oligosynthesis siRNA specific to DICER1 (sc-40489) purchased from Santa Cruz biotechnology for transient tranfection, was dilute with RNASE free dH2O to reach 10μM. In a 12 well plate, seed 6 x 105 WSU-HN17 cells per well in 1 ml antibiotic-free normal growth medium supplemented with 10% FBS. In next day, perform transfection those siRNA at 100 nM with Lipofectamine 2000 reagent according to the manufacturer's instructions. Cell was collect at 48h after transfection step by Trizol reagent (Life technologies, Inc.) in order to collect RNA for further study. For WSU-HN31 si-LINE-1 stable cell , after 48 h of transfection with LINE-1 siRNA constructs, cell was switch to culture with 50 ug/ml Hygromycin B (Cat. No. 10 843 555 001, Roche Applied Science) in Dulbecco's modified Eagle's medium (Gibco BRL, Life Technologies, Pairly, UK) supplemented with 10% heat- inactivated fetal bovine serum (Sigma, St. Louis, MO, USA). Cell was collect by Trizol reagent (Life technologies, Inc.) to RNA extraction for further study.

tag: cell type

value: Normal oral keratinocyte

tag: cell stage

value: Normal stage

tag: transfection type

value: Stable

value: Cell culture


title: Normal oral keratinocyte replicate 3

description: replicate 3


title: Chronic hepatitis C 27

tag: sample type

value: exosome rich fraction from sera

tag: disease state

value: Chronic hepatitis C


title: Patient 33 pre-treatment serum

value: hormone refractory prostate cancer

value: Responder

value: Human IgG


title: gastric cancer tissue sample 25

value: gastric cancer tissue sample 25


title: gastric cancer tissue sample 85

value: gastric cancer tissue sample 85

value: Three mixed normal blood sample


title: Patient 28 post-treatment serum

value: Non-responder

value: post


title: Patient 33 post-treatment serum


title: HN17 si-dicer1 48h replicate 2

description: replicate 1

source_name: Head and Neck cancer cell line

value: Tumor stage

value: tranfection with DICER1 (sc-40489)


title: Patient 24 post-treatment serum


title: gastric cancer tissue sample 86

value: gastric cancer tissue sample 86


title: Chronic hepatitis C 67

value: female


title: Normal oral keratinocyte replicate 1

description: replicate 2

value: Normal oral keratinocyte

value: Normal stage


title: HN17 scramble 48h replicate 2

description: replicate 1

value: Stable

value: Cell culture


title: Chronic hepatitis C 21

value: exosome rich fraction from sera

value: Chronic hepatitis C


title: Chronic hepatitis C 22


title: gastric cancer tissue sample 81

value: gastric cancer tissue sample 81


title: gastric cancer tissue sample 83

value: gastric cancer tissue sample 83


title: gastric cancer tissue sample 84

value: gastric cancer tissue sample 84


title: gastric cancer tissue sample 71

value: gastric cancer tissue sample 71


title: Patient 28 pre-treatment serum

value: hormone refractory prostate cancer

value: pre

value: Human IgG


title: gastric cancer tissue sample 65

value: gastric cancer tissue sample 65

value: Three mixed normal blood sample


title: Patient 23 post-treatment serum

value: Non-responder

value: post


title: Patient 22 pre-treatment serum


title: Patient 22 post-treatment serum


title: Chronic hepatitis C 20

value: female


title: Patient 23 pre-treatment serum


title: Chronic hepatitis C 17


title: Chronic hepatitis C 18


title: Chronic hepatitis C 24


title: HN17 si-dicer1 48h replicate 1

description: replicate 2

value: Tumor stage

value: tranfection with DICER1 (sc-40489)


title: Patient 21 post-treatment serum


title: Chronic hepatitis C 16

value: male


title: Chronic hepatitis C 19

source_name: Exososme

value: exosome rich fraction from sera


title: Patient 24 pre-treatment serum

value: Responder


title: gastric cancer tissue sample 75

value: gastric cancer tissue sample 75


title: HN17 aza treatment replicate 1

description: replicate 1

value: Stable

value: Cell culture

value: treated every 24 hours with 4 uM 5-aza-2- deoxycytidine for up to 16 days


title: Patient 21 pre-treatment serum

value: hormone refractory prostate cancer


title: HN17 scramble 48h replicate 1

description: replicate 1


title: Chronic hepatitis C 15

source_name: Exosome

value: Chronic hepatitis C


title: HN17 aza treatment replicate 2

description: replicate 2


title: HN17 control replicate 3

description: replicate 3


title: HN17 control replicate 1

description: replicate 1


title: HN17 control 1 at singapore

description: replicate 4


title: Chronic hepatitis C 14


title: HN17 aza treatment replicate 3

description: replicate 3


title: HN17 control replicate 2

description: replicate 2


title: gastric cancer tissue sample 62

value: gastric cancer tissue sample 62

source_name: Three mixed normal blood sample


title: Normal 12

value: normal liver


title: Normal 11


title: Normal 10


title: Chronic hepatitis C 13


title: Normal 8


title: Patient 19 post-treatment serum

value: Human IgG


title: gastric cancer tissue sample 40

value: gastric cancer tissue sample 40

value: Three mixed normal blood sample


title: gastric cancer tissue sample 55

value: gastric cancer tissue sample 55


title: gastric cancer tissue sample 58

value: gastric cancer tissue sample 58


title: gastric cancer tissue sample 38

value: gastric cancer tissue sample 38


title: gastric cancer tissue sample 60

value: gastric cancer tissue sample 60


title: Patient 20 pre-treatment serum

value: pre


title: Normal 7

value: exosome rich fraction from sera

value: female


title: Patient 20 post-treatment serum

value: Responder

value: post


title: Hacat aza treatment replicate 2

description: replicate 2

source_name: Immortal keratinocyte cell line

value: Hacat

value: Immortal stage

value: Stable

value: Cell culture

value: treated every 24 hours with 4 uM 5-aza-2- deoxycytidine for up to 16 days


title: Hacat aza treatment replicate 3

description: replicate 3


title: Patient 19 pre-treatment serum

value: hormone refractory prostate cancer

value: Human IgG


title: Normal 6

value: normal liver

value: male


title: Hacat control replicate 2

description: replicate 2


title: Normal 9


title: Hacat aza treatment replicate 1

description: replicate 1


title: HN31 si-3LINE-1s stable replicate 2

description: replicate 2

value: Tumor stage

value: 48 h of transfection with LINE-1 siRNA constructs


title: HN31 si-3LINE-1s stable replicate 1

description: replicate 1


title: Normal 4


title: HN31 si-negative stable replicate 2

description: replicate 2


title: HN31 si-negative stable replicate 1

description: replicate 1


title: Normal 3


title: gastric cancer tissue sample 17

value: gastric cancer tissue sample 17

value: Three mixed normal blood sample


title: gastric cancer tissue sample 26

value: gastric cancer tissue sample 26


title: gastric cancer tissue sample 24

value: gastric cancer tissue sample 24


title: gastric cancer tissue sample 29

value: gastric cancer tissue sample 29


title: gastric cancer tissue sample 27

value: gastric cancer tissue sample 27


title: gastric cancer tissue sample 30

value: gastric cancer tissue sample 30


title: gastric cancer tissue sample 34

value: gastric cancer tissue sample 34


title: Normal 1

value: exosome rich fraction from sera


title: Normal 2

label_protocol: One-color microRNA labeling with Cy3 fluorescence were performed in accordance with the manufacturer’s procedure


title: Normal 5

value: female


title: Hacat control replicate 1

description: replicate 1

value: Hacat

value: Immortal stage

value: Stable

value: Cell culture


title: B19-infected CD36+ EPCs

status: Public on Nov 04 2012

city: Gainesville

first: Igor

last: Ignatovich

state: FL

department: Psychiatry

institute: University of Florida

description:
Test
SAMPLE 2

data_processing:
The normalization and all the data analysis were performed using ABI 7500 Software v.2.0.5 and DataAssist Software v.3.0.
For the normalization it uses the average of four housekeeping genes: 18S, HPRT1, GAPDH, GUSB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: FAM

source_name: CD36+ erythroid progenitor cells

label_protocol: PCR assays were performed using TaqMan nuclear receptor signature fast plate (Applied biosystems) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the Verso cDNA kit (Thermo Scientific). Quantitative real-time PCR were performed (Applied Biosystems 7500 Fast) with 40 cycles at 95 oC for 3 seconds and 60 oC for 30 seconds.

growth_protocol: Cells were incubated in StemSpan media (StemCell Technologies, cat number 09600) supplemented with cytokine cocktail (StemCell Technologies, cat number 02690) and human recombinant erythropoietin (StemCell Technologies, cat number 02625) (full media)

extract_protocol: total RNA was extracted using Rneasy Plus Mini Kit (Qiagen)

treatment_protocol: Cells were either mock-infected or infected with a serum containing wtB19 for 2 hours at +4C. Washed two times with StemSpan media, and resuspended in full StemSpan media

value: CD36+ erythroid progenitor cells

tag: infection

value: parvovirus B19


title: mock-infected CD36+ EPCs

description:
Control
SAMPLE 1

value: control


title: Hacat control replicate 3

description: replicate 3