title: WT: r1918: 4.0 Days: 10XLD50: Animal B

value: wild-type

value: lung

value: B


title: genomic DNA from swim up sperm 12

status: Public on Jul 16 2013

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description:
normal sperm sample
EPI12_Up.20

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

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

data_processing: Genome studio

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: sperm

label_protocol: Standard Illumina Protocol

extract_protocol: Sperm DNA was extracted with an user-developed version of the QIAamp® DNeasy&Tissue Kit purification protocol according to manufacturer instructions.

tag: gender

value: male

tag: disease state

value: Normal donor


title: genomic DNA from swim up sperm 10

description:
normal sperm sample
EPI10_Up.20


title: WT: r1918: 3.0 Days: 10XLD50: Animal B, dye-swap

type: RNA

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

hyb_protocol: Microarray slide hybridization was performed with Agilent-013326 human microarrays according to the manufacturer's instructions. Each microarray experiment was done with two technical replicates by reverse dye hybridization for experimental and reference samples.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B). Raw images were analyzed using the Agilent Feature Extraction software (version 8.1.1.1) and the GE2-v5_95_Feb07 extraction protocol.

data_processing: Processing was done in R, and background correction (bg=0, none) and loess normalization were performed using the LIMMA package.

molecule: total RNA

organism: Mus musculus

label_protocol: Cy3- and Cy5-labeled cRNA probes were generated by using an Agilent Low RNA Input Linear Amplification kit.

extract_protocol:
Lungs were homogenized in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5 % sarcosyl, 0.1 M β-mercaptoethanol) and kept at -80 degrees C prior to RNA isolation.
Lysates were phase-separated, and RNA was isolated from the aqueous phase.

treatment_protocol: Animals were infected with highly pathogenic A/Vietnam/1203 or fully reconstructed 1918 influenza virus. Lungs were harvested at 1, 3, and 4 days post-infection for microarray.

tag: strain/background

tag: genotype/variation

value: female

tag: tissue

tag: infection status

value: influenza

tag: influenza virus strain

tag: time post-infection

value: day 3

tag: animal

value: mock


title: WT: r1918: 4.0 Days: 10XLD50: Animal A, dye-swap

value: day 4

value: A


title: WT: VN1203: 1.0 Days: 10XLD50: Animal B

value: day 1


title: WT: r1918: 4.0 Days: 10XLD50: Animal A


title: WT: r1918: 3.0 Days: 10XLD50: Animal B


title: WT: r1918: 3.0 Days: 10XLD50: Animal A, dye-swap


title: Seed_RAD_1h_rep1

city: Sutton Bonington

first: Simon

middle: Peter

last: Pearce

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Fragmented cRNA at a final concentration of 0.0375ng/μl was used for hybridization. The GeneChip (#900720) HWS Kit was used for hybridization, washing and staining.

scan_protocol: The scanning was performed using the Affymetrix 3000G scanner

data_processing: The data was analysed using RMA in the affy Bioconductor package in R, using the v14.0.0 Arabidopsis CustomCDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF

label: biotin

organism: Arabidopsis thaliana

source_name: Excised Radicle and Embryonic Axis, 1h after sowing

label_protocol: The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. For each sample 100 ng was used as input.

growth_protocol: Seeds of Arabidopsis accession Columbia-0 (Col-0, N60000) were sown on 0.7% water agarose (Eurogentec) and incubated in a germination cabinet at 22°C with continuous light.

extract_protocol: For RNA extraction a Stratagene kit was used (Agilent Technologies, Absolutely RNA Nanoprep kit, 50 preps, cat# 400753).

treatment_protocol: At eleven stages after sowing seeds were dissected into four parts (as detailed above) using a stereo microscoop, pair of pincers and a scalpel knife.

tag: accession

value: Columbia-0 (Col-0, N60000)

value: Embryo

tag: seed part

value: RAD

tag: time


title: Seed_MCE_20h_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 20h after sowing

value: Endosperm

value: MCE


title: genomic DNA from swim up sperm 1

description:
normal sperm sample
EPI01_Up.20


title: DIS t+ FL_8

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Agilent DNA Microarray scanner G2505B (Agilent Technologies).

data_processing: Median normalization and dewaving as described in van de Wiel et al. Briefings in Bioinformatics 2011 (PMID 20172948). NimbleScan software version 2.5.16 (Roche NimbleGen).

source_name: DNA isolated from disseminated t+ FL

label_protocol: Standard NimbleGen protocol.

extract_protocol: The DNA isolation protocol is described in Buffart et al., J Pathol. 2007 Jan;211(1):45-51 (PMID 17117405).

value: disseminated t+ follicular lymphoma

value: follicular lymphoma (FL)

source_name: DNA isolated from a pool of 100 healthy individuals

value: healthy

value: blood

tag: sample type

value: reference


title: Seed_MCE_25h_TR_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 25h after sowing, with testa rupture

tag: testa/endosperm rupture status

value: with testa rupture


title: WT: r1918: 3.0 Days: 10XLD50: Animal A

value: wild-type

value: female

value: lung

value: influenza


title: Seed_MCE_38h_noER_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, without endosperm rupture

value: without endosperm rupture


title: Seed_MCE_31h_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 31h after sowing


title: WT: r1918: 1.0 Days: 10XLD50: Animal B, dye-swap

value: day 1

value: B

value: mock


title: DIS t+ FL_5


title: WT: r1918: 1.0 Days: 10XLD50: Animal B


title: Seed_MCE_16h_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 16h after sowing

value: Columbia-0 (Col-0, N60000)


title: genomic DNA from swim up sperm 7

description:
normal sperm sample
EPI07_Up.20

value: male

value: Normal donor


title: Seed_MCE_7h_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 7h after sowing

value: Endosperm

value: MCE


title: DIS t+ FL_4

value: disseminated t+ follicular lymphoma

value: follicular lymphoma (FL)

value: healthy


title: Seed_MCE_12h_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 12h after sowing


title: DIS t+ FL_2

value: blood

value: reference


title: Seed_MCE_38h_ER_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, with endosperm rupture

value: with endosperm rupture


title: DIS t+ FL_1


title: WT: r1918: 1.0 Days: 10XLD50: Animal A, dye-swap

value: wild-type

value: female

value: lung

value: A


title: DIS t+ FL_3


title: DIS t+ FL_6


title: Seed_MCE_3h_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 3h after sowing


title: WT: r1918: 1.0 Days: 10XLD50: Animal A

value: influenza

value: day 1


title: LOC t+ FL_15

source_name: DNA isolated from localized t+ FL

value: localized t+ follicular lymphoma


title: Seed_MCE_1h_rep1

source_name: Excised Micropylar & Chalazal Endosperms, 1h after sowing

value: Columbia-0 (Col-0, N60000)


title: LOC t+ FL_16


title: LOC t+ FL_14


title: IFNR1KO: VN1203: 4.0 Days: 10XLD50: Animal B, dye-swap

value: day 4

value: B

value: mock


title: LOC t+ FL_13


title: IFNR1KO: VN1203: 4.0 Days: 10XLD50: Animal C, dye-swap

value: C


title: cell line HDLM-2

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: Gene expression data from established Hodgkin's lymphoma cell line after treatment with vorinostat

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized on Human Exon 1.0ST Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed using the RMA algorithm with Affymetrix Expression Console
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Hodgkin’s lymphoma cell line HDLM-2

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol

growth_protocol: Established Hodgkin's lymphoma cells were grown under standard conditions.

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

tag: cell line


title: Seed_Dry_rep1

source_name: Whole dry seeds

value: Seed

value: Whole dry seed


title: LOC t+ FL_12

value: follicular lymphoma (FL)

value: healthy

value: blood


title: IFNR1KO: VN1203: 4.0 Days: 10XLD50: Animal C

value: wild-type


title: cell line L-428

source_name: Hodgkin’s lymphoma cell line L-428


title: LOC t+ FL_9

value: reference


title: genomic DNA from swim down sperm 1

description:
normal sperm sample
EPI01_Down.20

source_name: sperm

value: male

value: Normal donor


title: LOC t+ FL_10


title: LOC t+ FL_8


title: LOC t+ FL_11


title: genomic DNA from swim down sperm 12

description:
normal sperm sample
EPI12_Down.20


title: IFNR1KO: VN1203: 4.0 Days: 10XLD50: Animal B

value: female

value: lung

value: influenza


title: cell line L-540

description: Gene expression data from established Hodgkin's lymphoma cell line

source_name: Hodgkin’s lymphoma cell line L-540


title: genomic DNA from swim down sperm 18

description:
normal sperm sample
EPI18_Down.20


title: IFNR1KO: VN1203: 4.0 Days: 10XLD50: Animal A, dye-swap

value: A


title: genomic DNA from swim down sperm 14

description:
normal sperm sample
EPI14_Down.20


title: genomic DNA from swim down sperm 20

description:
normal sperm sample
EPI20_Down.20


title: genomic DNA from swim down sperm 16

description:
normal sperm sample
EPI16_Down.20


title: IFNR1KO: VN1203: 3.0 Days: 10XLD50: Animal C, dye-swap

value: day 3


title: IFNR1KO: VN1203: 3.0 Days: 10XLD50: Animal C


title: Adventitious-Root_9-hours_R2

city: Gent

first: boris

last: parizot

address: Technologiepark 927

country: Belgium

institute: VIB Department of Plant Systems Biology

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The RMA normalization procedure was applied to perform a convolution background correction using perfect matched probe intensities, quantile normalization and summarization of perfect matched probe intensities based on a multi-array model fit robustly using the median polish algorithm.

organism: Zea mays

source_name: Pericycle in front of the xylem poles in adventitious roots of seedlings grown on NPA and transfered 9-hours on NAA

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

growth_protocol: For the primary root, plants were germinated and grown 64 hours in NPA 50 µM. For the adventitious roots, plants were germinated and grown in water for 6 days.

extract_protocol: On average, 800 pericycle cells from at least 9 different roots were poole and prepared for the extraction of total RNA for each individual replicate. ARNs were extracted using Ambion technologies, and cDNA were amplified two times.

treatment_protocol: For the primary root, plants were transfered to NAA 50 µM. For the adventitious roots, plants were transfered to NAA 25 µM.

tag: cultivar

tag: root type

value: Adventitious root

tag: growth

value: Germination in water, growth for 6 days, and then transfer to NPA 25 µM for 4 days

tag: treatment

value: 9 hours NAA  25 µM

value: Pericycle in front of the phloem poles


title: LOC t+ FL_6

tag: disease state

value: localized t+ follicular lymphoma

source_name: DNA isolated from a pool of 100 healthy individuals


title: Adventitious-Root_9-hours_R1


title: Adventitious-Root_9-hours_R3


title: IFNR1KO: VN1203: 3.0 Days: 10XLD50: Animal B

tag: strain/background

tag: genotype/variation

tag: gender

value: mock

value: B


title: LOC t+ FL_2

tag: tissue

value: follicular lymphoma (FL)

value: healthy

value: blood


title: IFNR1KO: VN1203: 3.0 Days: 10XLD50: Animal A, dye-swap

tag: infection status

tag: influenza virus strain

tag: time post-infection

value: wild-type


title: Adventitious-Root_6-hours_R2

source_name: Pericycle in front of the xylem poles in adventitious roots of seedlings grown on NPA and transfered 6-hours on NAA

value: 6 hours NAA  25 µM


title: LOC t+ FL_4

value: reference


title: LOC t+ FL_3


title: LOC t+ FL_1


title: genomic DNA from swim down sperm 10

description:
normal sperm sample
EPI10_Down.20

value: male

value: Normal donor


title: LOC t+ FL_5


title: Adventitious-Root_6-hours_R3


title: Adventitious-Root_4-hours_R3

source_name: Pericycle in front of the xylem poles in adventitious roots of seedlings grown on NPA and transfered 4-hours on NAA

value: 4 hours NAA  25 µM


title: IFNR1KO: VN1203: 3.0 Days: 10XLD50: Animal B, dye-swap

value: female

value: lung

value: influenza

value: day 3

tag: animal


title: IFNR1KO: VN1203: 4.0 Days: 10XLD50: Animal A

value: day 4

value: A


title: IFNR1KO: VN1203: 3.0 Days: 10XLD50: Animal A

value: mock


title: t- FL_12

source_name: DNA isolated from t- FL

value: t- follicular lymphoma


title: IFNR1KO: VN1203: 1.0 Days: 10XLD50: Animal B, dye-swap

value: day 1

value: B


title: Adventitious-Root_6-hours_R1

value: Adventitious root

value: Germination in water, growth for 6 days, and then transfer to NPA 25 µM for 4 days

value: Pericycle in front of the phloem poles


title: IFNR1KO: VN1203: 1.0 Days: 10XLD50: Animal C, dye-swap

value: C

value: wild-type


title: Adventitious-Root_4-hours_R1


title: IFNR1KO: VN1203: 1.0 Days: 10XLD50: Animal C


title: IFNR1KO: VN1203: 1.0 Days: 10XLD50: Animal B


title: Adventitious-Root_3-hours_R3

source_name: Pericycle in front of the xylem poles in adventitious roots of seedlings grown on NPA and transfered 3-hours on NAA

value: 3 hours NAA  25 µM


title: Adventitious-Root_3-hours_R2


title: t- FL_10

value: follicular lymphoma (FL)

value: healthy

value: blood

value: reference


title: Adventitious-Root_4-hours_R2

value: 4 hours NAA  25 µM


title: t- FL_9


title: IFNR1KO: VN1203: 1.0 Days: 10XLD50: Animal A

value: female

value: lung

value: influenza


title: IFNR1KO: r1918: 4.0 Days: 10XLD50: Animal B, dye-swap

value: day 4

value: mock


title: t- FL_8

value: t- follicular lymphoma


title: Adventitious-Root_3-hours_R1

value: Adventitious root


title: IFNR1KO: VN1203: 1.0 Days: 10XLD50: Animal A, dye-swap

value: day 1

value: A


title: IFNR1KO: r1918: 4.0 Days: 10XLD50: Animal B

value: B


title: t- FL_7


title: t- FL_11


title: Adventitious-Root_2-hours_R2

source_name: Pericycle in front of the xylem poles in adventitious roots of seedlings grown on NPA and transfered 2-hours on NAA

value: Germination in water, growth for 6 days, and then transfer to NPA 25 µM for 4 days

value: 2 hours NAA  25 µM

value: Pericycle in front of the phloem poles


title: t- FL_5

value: follicular lymphoma (FL)

value: healthy


title: t- FL_4

value: blood

value: reference


title: Adventitious-Root_2-hours_R3


title: IFNR1KO: r1918: 3.0 Days: 10XLD50: Animal B, dye-swap

value: female

value: day 3

value: wild-type


title: IFNR1KO: r1918: 4.0 Days: 10XLD50: Animal A, dye-swap

value: lung

value: influenza

value: day 4


title: IFNR1KO: r1918: 4.0 Days: 10XLD50: Animal A

value: mock


title: IFNR1KO: r1918: 3.0 Days: 10XLD50: Animal A


title: Adventitious-Root_2-hours_R1

value: Adventitious root


title: Primary-Root_4-hours_R2

source_name: Pericycle in front of the xylem poles in the primary root of seedlings grown on NPA and transfered 4-hours on NAA

value: Primary root

value: Germination in NPA 50 µMand growth for 64 hours

value: 4 hours NAA  50 µM


title: IFNR1KO: r1918: 3.0 Days: 10XLD50: Animal A, dye-swap

value: A


title: Adventitious-Root_NPA_R3

source_name: Pericycle in front of the xylem poles in adventitious roots of seedlings grown on NPA

value: Germination in water, growth for 6 days, and then transfer to NPA 25 µM for 4 days

value: Pericycle in front of the phloem poles


title: IFNR1KO: r1918: 1.0 Days: 10XLD50: Animal B, dye-swap

value: day 1

value: B


title: Adventitious-Root_NPA_R1


title: IFNR1KO: r1918: 1.0 Days: 10XLD50: Animal A, dye-swap


title: t- FL_3

value: t- follicular lymphoma

value: follicular lymphoma (FL)

value: healthy

value: blood

value: reference


title: t- FL_2


title: LOC t+ FL_7

value: localized t+ follicular lymphoma


title: t- FL_1


title: Primary-Root_3-hours_R3

source_name: Pericycle in front of the xylem poles in the primary root of seedlings grown on NPA and transfered 3-hours on NAA

value: 3 hours NAA  50 µM


title: NMZL_14

source_name: DNA isolated from NMZL

value: nodal marginal zone B-cell lymphoma

value: nodal marginal zone lymphoma (NMZL)


title: NMZL_13


title: IFNR1KO: r1918: 1.0 Days: 10XLD50: Animal A

value: wild-type

value: female

value: lung

value: mock

value: influenza


title: Adventitious-Root_NPA_R2

value: Adventitious root

value: Germination in water, growth for 6 days, and then transfer to NPA 25 µM for 4 days

value: Pericycle in front of the phloem poles


title: NMZL_11


title: 70W exosomes

city: Houston

first: Laura

last: Camacho

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
SAMPLE 6
Test 3
miRNA profiling

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://pcrdataanalysis.sabiosciences.com/mirna/arrayanalysis.php. The relative quantity of the target miRNA was normalized using Syn-cel-miR-39 miScript miRNA Mimic miRNeasy Spike-In Control (Qiagen, Germantown, MD) that was exogenously added during RNA purification. The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-Change file reports test/control (ie, brain metastatic cell-derived exosomes/non brain metastatic cell derived-exosomes).  Linked as supplementary file on Series record.

label: SYBR Green

source_name: 70W cell-derived exosomes

label_protocol: 10 ng of total RNA were reverse transcribed with miScript II RT kit (Qiagen, Germantown, MD) according to manufacturers’ guidelines. 20 µl of cDNA was diluted with RNase-free water prior to the PCR reaction.  Real-time PCR for mature miRNA expression profiling was developed using the SYBR Green-based human breast cancer pathway-focused miScript miRNA PCR array (Qiagen, Germantown, MD) on a StepOnePlus 96-well RT PCR instrument (Applied Biosystems, Grand Island, NY).

growth_protocol: After 72 hours of cell culturing, 10 ml of culture media was centrifuged at 3000 x g for 15 min to remove cells and cell debris. The supernatant was mixed with 2 ml of ExoQuick-TC, refrigerated for 16 hours and then centrifuged at 1500 x g for 30 min at 4°C to obtain the exosomes pellet.

extract_protocol: Total RNA from exosomes was isolated using mirVana miRNA isolation kit (Life Technologies, Grand Island, NY)

tag: brain-homing cell line

tag: cell type

value: Melanoma


title: MeWo exosomes

description:
SAMPLE 5
Control 3
miRNA profiling

source_name: MeWo cell-derived exosomes

tag: parental non-brain metastatic cell line

value: MeWo


title: NMZL_10

value: healthy

tag: sample type


title: CTC1BMSM exosomes

description:
SAMPLE 4
Test 2
miRNA profiling

source_name: CTC1BMSM cell-derived exosomes

value: Circulating tumor cell


title: t- FL_6

value: t- follicular lymphoma

value: follicular lymphoma (FL)

value: blood

value: reference


title: NMZL_8

value: nodal marginal zone B-cell lymphoma

value: nodal marginal zone lymphoma (NMZL)


title: Primary-Root_3-hours_R1

tag: cultivar

value: Primary root

value: Germination in NPA 50 µMand growth for 64 hours

value: 3 hours NAA  50 µM


title: IFNR1KO: r1918: 1.0 Days: 10XLD50: Animal B

value: wild-type

value: female

value: lung

value: mock

value: influenza

value: day 1

value: B


title: Primary-Root_2-hours_R2

source_name: Pericycle in front of the xylem poles in the primary root of seedlings grown on NPA and transfered 2-hours on NAA

tag: root type

value: 2 hours NAA  50 µM

value: Pericycle in front of the phloem poles


title: MDA-MB-231BR exosomes

description:
SAMPLE 2
Test 1
miRNA profiling

source_name: MDA-MB-231BR cell-derived exosomes

value: Breast cancer


title: NMZL_6

value: healthy

value: blood


title: NMZL_7

value: nodal marginal zone B-cell lymphoma

value: reference


title: NMZL_5

value: nodal marginal zone lymphoma (NMZL)


title: Primary-Root_2-hours_R1

value: Primary root

tag: growth

value: Germination in NPA 50 µMand growth for 64 hours


title: NMZL_12


title: Primary-Root_NPA_R3

source_name: Pericycle in front of the xylem poles in the primary root of seedlings grown on NPA

tag: treatment


title: Primary-Root_NPA_R2


title: Primary-Root_NPA_R1


title: optic nerve head, 3 months, optic nerve crushed, biological rep1

status: Public on Jul 15 2013

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

description:
TJ2012022316
gene expression data from optic nerve heads that experienced optic nerve crush, 3 months after surgery

hyb_protocol: Fragmented cDNA was hybridized to the GeneChip Mouse Genome 430A 2.0 arrays in an Affymetrix hybridization oven 645. Affymetrix GeneChip Fluidics Station 450 was used for array washing and staining.

scan_protocol: Affymetrix GeneChip Scanner 3000 was used for array scanning and generating scan data.

data_processing:
The data were analyzed using DChip software.  The overall intensity of each array was normalized using the “Invariant Set Normalization” method.
The expression values were calculated in DChip using the “PM/MM difference model”.

source_name: optic nerve head, optic nerve crushed, recovered for 3 months

label_protocol: Total RNA from each sample was reversed transcribed and amplified using the Ovation RNA Amplification System V2 (NuGEN).  The amplified cDNA was biotin labeled using Encore Biotin Module (NuGen).

growth_protocol: Mice were housed under standard conditions.

extract_protocol: Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen).  The integrity and concentration of the isolated total RNA was confirmed by analysis on a Bioanalyzer 2100 using PicoChips (Agilent Technologies).  The RNA integrity number (RIN) for all samples was greater than 9.0.

treatment_protocol: The optic nerve of left eye was crushed for 10 seconds at 1 mm behind the globe. The right eye was not operated on. The optic nerve head was collected 3 months after the surgery.

value: mouse optic nerve head

tag: strain

tag: age at surgery

value: 6-8 weeks


title: Primary-Root_4-hours_R1

value: 4 hours NAA  50 µM


title: NMZL_4

tag: disease state

source_name: DNA isolated from a pool of 100 healthy individuals


title: optic nerve head, 3 months, optic nerve crushed, biological rep3

description:
TJ2012022318
gene expression data from optic nerve heads that experienced optic nerve crush, 3 months after surgery

tag: gender

value: female


title: NMZL_3

tag: tissue


title: optic nerve head, 3 months, contralateral control, biological rep5

description:
TJ2012022315
gene expression data from normal contralateral control optic nerve heads, 3 months after surgery

source_name: optic nerve head, contralateral control for 3-month recovery


title: optic nerve head, 3 months, contralateral control, biological rep4

description:
TJ2012022314
gene expression data from normal contralateral control optic nerve heads, 3 months after surgery


title: optic nerve head, 3 months, optic nerve crushed, biological rep5

description:
TJ2012022320
gene expression data from optic nerve heads that experienced optic nerve crush, 3 months after surgery


title: NMZL_2


title: optic nerve head, 3 months, contralateral control, biological rep3

description:
TJ2012022313
gene expression data from normal contralateral control optic nerve heads, 3 months after surgery


title: optic nerve head, 3 months, optic nerve crushed, biological rep4

description:
TJ2012022319
gene expression data from optic nerve heads that experienced optic nerve crush, 3 months after surgery


title: optic nerve head, 3 months, optic nerve crushed, biological rep2

description:
TJ2012022317
gene expression data from optic nerve heads that experienced optic nerve crush, 3 months after surgery


title: optic nerve head, 3 weeks, optic nerve crushed, biological rep5

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 weeks after surgery
TJ2011071445

source_name: optic nerve head, optic nerve crushed, recovered for 3 weeks

treatment_protocol: The optic nerve of left eye was crushed for 10 seconds at 1 mm behind the globe. The right eye was not operated on. The optic nerve head was collected 1 day to 3 weeks after the surgery.


title: optic nerve head, 3 weeks, optic nerve crushed, biological rep3

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 weeks after surgery
TJ2011071443


title: optic nerve head, 3 months, contralateral control, biological rep1

description:
TJ2012022311
gene expression data from normal contralateral control optic nerve heads, 3 months after surgery


title: optic nerve head, 3 weeks, optic nerve crushed, biological rep4

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 weeks after surgery
TJ2011071444


title: optic nerve head, 3 weeks, optic nerve crushed, biological rep2

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 weeks after surgery
TJ2011071442


title: Primary-Root_4-hours_R3


title: optic nerve head, 3 weeks, optic nerve crushed, biological rep1

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 weeks after surgery
TJ2011071441


title: Primary-Root_2-hours_R3


title: optic nerve head, 3 weeks, contralateral control, biological rep5

description:
gene expression data from normal contralateral control optic nerve heads, 3 weeks after surgery
TJ2011071440

source_name: optic nerve head, contralateral control for 3-week recovery


title: optic nerve head, 3 months, contralateral control, biological rep2

description:
TJ2012022312
gene expression data from normal contralateral control optic nerve heads, 3 months after surgery


title: optic nerve head, 3 weeks, contralateral control, biological rep4

description:
gene expression data from normal contralateral control optic nerve heads, 3 weeks after surgery
TJ2011071439


title: Primary-Root_3-hours_R2

value: 3 hours NAA  50 µM


title: optic nerve head, 3 weeks, contralateral control, biological rep2

description:
gene expression data from normal contralateral control optic nerve heads, 3 weeks after surgery
TJ2011071437


title: optic nerve head, 1 week, optic nerve crushed, biological rep3

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 week after surgery
TJ2011071433

source_name: optic nerve head, optic nerve crushed, recovered for 1 week


title: optic nerve head, 3 weeks, contralateral control, biological rep3

description:
gene expression data from normal contralateral control optic nerve heads, 3 weeks after surgery
TJ2011071438


title: optic nerve head, 1 week, optic nerve crushed, biological rep5

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 week after surgery
TJ2011071435


title: optic nerve head, 1 week, optic nerve crushed, biological rep2

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 week after surgery
TJ2011071432


title: optic nerve head, 1 week, contralateral control, biological rep5

description:
gene expression data from normal contralateral control optic nerve heads, 1 week after surgery
TJ2011071430

source_name: optic nerve head, contralateral control for 1-week recovery


title: optic nerve head, 1 week, optic nerve crushed, biological rep4

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 week after surgery
TJ2011071434


title: optic nerve head, 3 days, optic nerve crushed, biological rep5

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 days after surgery
TJ2011071425

source_name: optic nerve head, optic nerve crushed, recovered for 3 days


title: optic nerve head, 1 week, contralateral control, biological rep2

description:
gene expression data from normal contralateral control optic nerve heads, 1 week after surgery
TJ2011071427


title: optic nerve head, 3 days, optic nerve crushed, biological rep4

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 days after surgery
TJ2011071424


title: optic nerve head, 3 weeks, contralateral control, biological rep1

description:
gene expression data from normal contralateral control optic nerve heads, 3 weeks after surgery
TJ2011071436


title: optic nerve head, 3 days, contralateral control, biological rep4

description:
gene expression data from normal contralateral control optic nerve heads, 3 days after surgery
TJ2011071419

source_name: optic nerve head, contralateral control for 3-day recovery


title: optic nerve head, 1 week, optic nerve crushed, biological rep1

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 week after surgery
TJ2011071431


title: optic nerve head, 1 week, contralateral control, biological rep3

description:
gene expression data from normal contralateral control optic nerve heads, 1 week after surgery
TJ2011071428


title: optic nerve head, 3 days, optic nerve crushed, biological rep3

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 days after surgery
TJ2011071423


title: optic nerve head, 1 week, contralateral control, biological rep1

description:
gene expression data from normal contralateral control optic nerve heads, 1 week after surgery
TJ2011071426


title: optic nerve head, 3 days, optic nerve crushed, biological rep2

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 days after surgery
TJ2011071422


title: optic nerve head, 3 days, optic nerve crushed, biological rep1

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 3 days after surgery
TJ2011071421


title: optic nerve head, 1 week, contralateral control, biological rep4

description:
gene expression data from normal contralateral control optic nerve heads, 1 week after surgery
TJ2011071429


title: optic nerve head, 3 days, contralateral control, biological rep2

description:
gene expression data from normal contralateral control optic nerve heads, 3 days after surgery
TJ2011071417


title: optic nerve head, 3 days, contralateral control, biological rep1

description:
gene expression data from normal contralateral control optic nerve heads, 3 days after surgery
TJ2011071416


title: optic nerve head, 1 day, optic nerve crushed, biological rep4

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 day after surgery
TJ2011071414

source_name: optic nerve head, optic nerve crushed, recovered for 1 day


title: optic nerve head, 3 days, contralateral control, biological rep5

description:
gene expression data from normal contralateral control optic nerve heads, 3 days after surgery
TJ2011071420


title: optic nerve head, 1 day, optic nerve crushed, biological rep2

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 day after surgery
TJ2011071412


title: NMZL_9

source_name: DNA isolated from NMZL


title: optic nerve head, 1 day, contralateral control, biological rep5

description:
gene expression data from normal contralateral control optic nerve heads, 1 day after surgery
TJ2011071410

source_name: optic nerve head, contralateral control for 1-day recovery


title: optic nerve head, 1 day, contralateral control, biological rep2

description:
gene expression data from normal contralateral control optic nerve heads, 1 day after surgery
TJ2011071407


title: optic nerve head, 1 day, contralateral control, biological rep4

description:
gene expression data from normal contralateral control optic nerve heads, 1 day after surgery
TJ2011071409


title: optic nerve head, 1 day, optic nerve crushed, biological rep3

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 day after surgery
TJ2011071413


title: optic nerve head, 1 day, contralateral control, biological rep3

description:
gene expression data from normal contralateral control optic nerve heads, 1 day after surgery
TJ2011071408


title: optic nerve head, 3 days, contralateral control, biological rep3

description:
gene expression data from normal contralateral control optic nerve heads, 3 days after surgery
TJ2011071418


title: optic nerve head, 1 day, optic nerve crushed, biological rep5

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 day after surgery
TJ2011071415


title: optic nerve head, naïve control, biological rep2

description:
gene expression data from naïve control optic nerve heads
TJ2011071402

source_name: optic nerve head, naïve control, no surgery


title: optic nerve head, naïve control, biological rep4

description:
gene expression data from naïve control optic nerve heads
TJ2011071404


title: optic nerve head, naïve control, biological rep3

description:
gene expression data from naïve control optic nerve heads
TJ2011071403


title: optic nerve head, 1 day, optic nerve crushed, biological rep1

description:
gene expression data from optic nerve heads that experienced optic nerve crush, 1 day after surgery
TJ2011071411


title: optic nerve head, 1 day, contralateral control, biological rep1

description:
gene expression data from normal contralateral control optic nerve heads, 1 day after surgery
TJ2011071406


title: optic nerve head, naïve control, biological rep5

description:
gene expression data from naïve control optic nerve heads
TJ2011071405


title: optic nerve head, naïve control, biological rep1

description:
gene expression data from naïve control optic nerve heads
TJ2011071401


title: MDA-MB-231P exosomes

description:
SAMPLE 1
Control 1
miRNA profiling

source_name: MDA-MB-231P cell-derived exosomes


title: IFNR1KO: r1918: 3.0 Days: 10XLD50: Animal B

tag: strain/background

tag: genotype/variation

value: wild-type

value: lung

tag: infection status

value: mock

value: influenza

value: day 3


title: CTC1P exosomes

description:
SAMPLE 3
Control 2
miRNA profiling

source_name: CTC1P cell-derived exosomes

value: Circulating tumor cell


title: NMZL_1

value: healthy

value: blood


title: genomic DNA from central chondrosarcoma_set2_sample17

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

description: tumour sample

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

data_processing: GenomeStudio software v2011.1. The non_normalized.txt file contains unmethylated (SignalA) and methylated (SignalB) signal intensities.

source_name: central chondrosarcoma

extract_protocol: genomic DNA was extracted and purified using QiaAMP DNA Mini Kit according to standard instructions

tag: age at presentation

value: male

tag: tumor grade

tag: idh status

value: WT


title: genomic DNA from central chondrosarcoma_set2_sample23

description: tumour sample

value: MUT


title: genomic DNA from central chondrosarcoma_set2_sample18

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample24

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample25

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample8

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample16

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample20

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample6

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample22

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample14

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample3

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample2

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample21

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample7

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample12

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample9

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample19

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample13

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample23

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample5

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample11

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample26

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample15

description: tumour sample


title: genomic DNA from central chondrosarcoma_set2_sample4

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample22

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample27

description: tumour sample


title: Synovial fluid of Rheumatoid arthritis (RA)  sample 6

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

description: Gene expression profiling of synovial fluid derived mononuclear cells from RA patient using whole human genome microarray

hyb_protocol: The Cyanine-3 labeled cRNA molecules were fragmented and hybridized onto human genome DNA microarrays (1X44, 4x44K, Agilent Technologies) for 17 hrs at 65°C with 10 rpm. Later, Arrays were washed using gene expression wash buffers according to the manufacturer’s hybridization protocol (Agilent Oligo Microarray Kit, Agilent Technologies).

scan_protocol: Agilent microarray scanner (G2505B) was used to scan the microarray slides. One color scan settings were used for 4x44 K  and 1x44 K array slides (scan resolution 5 um, dye channel was set to green, green PMT was set to 100%).

data_processing: Agilent feature extraction software was used to processes the images.

source_name: Knee aspirated synovial fluid RA sample6

label_protocol: Total RNA (~500ng) was reverse transcribed from each sample and linear amplification carried out using the low RNA input linear amplification kit (Agilent Technologies , Palo Alto, CA) to synthesize the first and second strands of cDNA and this cDNA was used as a template for generating cRNAs. Simultaneous amplification and Cyanine-3 (Perkin Elmer) dye incorporstion was done for labeling of cRNA as per the manufacturer’s protocol (Agilent Quick Amp Labeling Kit (Catalog #.51900442, Agilent technologies). The labeled cRNA molecules were purified using RNeasy spin columns (Qiagen, Valencia, CA).

extract_protocol: Total RNA extraction carried out from approximately 5 X 100000 synovial fluid derived mononuclear cells from  both the disease types. Purification was done using RNeasy Lipid Tissue Mini kit (Catalog # 74804, QIAGEN, CA 91355, USA) as per manufacturer’s protocol. The range of RNA concentration isolated form samples was 1-5 µg/ 5X105 cells and 2-5 µg/5X100000 cells in SpA and RA respectively. Integrity of the isolated RNA was checked by 2100 Bioanalyzer (Agilent Technologies) that measures the ratio of 28S and 18S ribosomal RNAs to compute the integrity of total mRNA.

treatment_protocol: Some RA patients were under going drug treatment with either methotrexate or Hydroxychloroquinone and the rest on none or on some generic pain killers

tag: date of collection

tag: fluid

value: Non turbid, viscous and nonbloody

value: Female

tag: age (y)

tag: case history

value: suffering from past 11 yrs and came with pain and swollen knees

value: Methotreaxate, Hydroxychloroquinone

tag: cell type

value: mononuclear cells from synovial fluid

value: Rheumatoid arthritis


title: Synovial fluid of Spondyloarthritis (SpA) of  sample 3

description: Gene expression profiling of synovial fluid derived mononuclear cells from SpA patient using whole human genome microarray

source_name: Knee aspirated synovial fluid SpA sample 3

value: Turbid, highly viscous and non bloody

value: Male

value: suffering from past 4 months had  back ache, knee swellings and an Ankylosing spondylitis case

tag: treatment

value: spondyloarthropathy


title: genomic DNA from central chondrosarcoma_set2_sample10

description: tumour sample


title: Synovial fluid of Rheumatoid arthritis (RA)  sample 7

source_name: Knee aspirated synovial fluid RA sample7

value: suffering from past 2 yrs and came with pain and swollen knees


title: Synovial fluid of Spondyloarthritis (SpA) of  sample 1

source_name: Knee aspirated synovial fluid SpA sample 1

value: Suffering from Viral infection and an undifferentiated spondyloarthropathy case


title: genomic DNA from central chondrosarcoma_Sample19

description: tumour sample

value: female


title: Synovial fluid of Rheumatoid arthritis (RA)  sample 2

source_name: Knee aspirated synovial fluid RA sample2

value: Came with pain and swollen knees

value: Pain killers


title: Synovial fluid of Rheumatoid arthritis (RA)  sample 5

source_name: Knee aspirated synovial fluid RA sample5

value: No details available


title: genomic DNA from central chondrosarcoma_set2_sample1

description: tumour sample

value: MUT


title: genomic DNA from central chondrosarcoma_Sample17

description: tumour sample

value: male


title: genomic DNA from central chondrosarcoma_Sample20

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample14

description: tumour sample

value: WT


title: genomic DNA from central chondrosarcoma_Sample15

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample12

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample13

description: tumour sample


title: Synovial fluid of Spondyloarthritis (SpA) of  sample 5

source_name: Knee aspirated synovial fluid SpA sample 5

value: suffering from past 8 yrs had  back ache, knee swellings and an Ankylosing spondylitis case


title: genomic DNA from central chondrosarcoma_Sample16

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample10

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample18

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample11

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample8

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample9

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample24

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample7

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample5

description: tumour sample


title: RARS_71-Tumor

city: Tokyo

first: Ayana

last: Kon

address: Hongo 7-3-1, Bunkyo-ku

department: Cancer Genomics Project

country: Japan

institute: The University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR software.

label: Biotin

source_name: MDS primary sample

label_protocol: Affymetrix standard protocol.

extract_protocol: Genomic DNA was obtained from bone marrow or peripheral blood samples.

tag: disease status

value: myelodysplastic syndrome

value: tumor


title: genomic DNA from central chondrosarcoma_Sample4

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample3

description: tumour sample


title: genomic DNA from central chondrosarcoma_Sample6

description: tumour sample


title: AML-129-Tumor

description: Hybridized to 50K_Xba

source_name: AML primary sample

value: acute myeloid leukemia


title: genomic DNA from central chondrosarcoma_Sample1

description: tumour sample


title: RARS_70-Tumor

description: Hybridized to 250K_Nsp


title: genomic DNA from central chondrosarcoma_Sample2

description: tumour sample


title: RARS_72-Tumor

description: Hybridized to 250K_Nsp


title: genomic DNA from central chondrosarcoma_Sample21

description: tumour sample


title: AML-128-Tumor

description: Hybridized to 50K_Xba


title: RARS_68-Tumor

description: Hybridized to 250K_Nsp


title: RARS_60-Tumor

description: Hybridized to 250K_Nsp


title: RARS_69-Tumor

description: Hybridized to 250K_Nsp


title: RARS_67-Tumor

description: Hybridized to 250K_Nsp


title: RARS_53-Tumor

description: Hybridized to 250K_Nsp


title: RARS_66-Tumor

description: Hybridized to 250K_Nsp


title: RARS_61-Tumor

description: Hybridized to 250K_Nsp


title: RARS_62-Tumor

description: Hybridized to 250K_Nsp


title: RARS_57-Tumor

description: Hybridized to 250K_Nsp


title: RARS_65-Tumor

description: Hybridized to 250K_Nsp


title: AML-092-Tumor

description: Hybridized to 50K_Xba


title: RARS_56-Tumor

description: Hybridized to 250K_Nsp


title: AML-053-Tumor

description: Hybridized to 50K_Xba


title: AML-125-Tumor

description: Hybridized to 50K_Xba


title: AML-089-Tumor

description: Hybridized to 50K_Xba


title: RARS_59-Tumor

description: Hybridized to 250K_Nsp


title: AML-127-Tumor

description: Hybridized to 50K_Xba


title: RARS_51-Tumor

description: Hybridized to 250K_Nsp


title: RARS_55-Tumor

description: Hybridized to 250K_Nsp


title: Control 6h biological rep3

city: Kiev

first: Andrii

last: Droni

address: Zabolotnogo 150

country: Ukraine

institute: IMBG

description: SAMPLE 12

hyb_protocol: Following fragmentation, 16 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: Bioconductor’s affy package was used for data pre-processing and normalization (Bioconductor v.2.5, R v.2.10.0). Data preprocessing was performed using RMA method for background correction, quantile for normalization, PM-only for PM-correction, and medianpolish for probe set summary. Normalization was carried out in 2 steps – first within the 4 groups of biological replicas, followed by normalization across all microarrays.

organism: Rattus norvegicus

source_name: primary rat hepatocytes control_incubated for 6 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions with additional purification on RNeasy mini kit columns (Quiagen).

tag: strain background

value: wistar

value: liver

value: primary hepatocytes

tag: treated with

value: none (untreated control) for 6hrs


title: RARS_54-Tumor

description: Hybridized to 250K_Nsp


title: RARS_58-Tumor

description: Hybridized to 250K_Nsp


title: Interferon alpha 6h biological rep3

description: SAMPLE 11

source_name: primary rat hepatocytes_interferon alpha for 6 hrs

value: 250u/ml rat interferon alpha for 6hrs


title: AML-044-Tumor

description: Hybridized to 50K_Xba


title: AML-047-Tumor

description: Hybridized to 50K_Xba


title: AML-052-Tumor

description: Hybridized to 50K_Xba


title: Control 6h biological rep2

description: SAMPLE 10


title: RARS_52-Tumor

description: Hybridized to 250K_Nsp


title: RARS_63-Tumor

description: Hybridized to 250K_Nsp


title: RARS_50-Tumor

description: Hybridized to 250K_Nsp


title: Interferon alpha 6h biological rep2

description: SAMPLE 9


title: RARS_48-Tumor

description: Hybridized to 250K_Nsp


title: RARS_47-Tumor

description: Hybridized to 250K_Nsp


title: Control 6h biological rep1

description: SAMPLE 8


title: AML-028-Tumor

description: Hybridized to 50K_Xba


title: RARS_45-Tumor

description: Hybridized to 250K_Nsp


title: RARS_44-Tumor

description: Hybridized to 250K_Nsp


title: RARS_41-Tumor

description: Hybridized to 250K_Nsp


title: RARS_43-Tumor

description: Hybridized to 250K_Nsp


title: AML-041-Tumor

description: Hybridized to 50K_Xba


title: Interferon alpha 6h biological rep1

description: SAMPLE 7


title: RARS_40-Tumor

description: Hybridized to 250K_Nsp


title: AML-006-Tumor

description: Hybridized to 50K_Xba


title: RARS_38-Tumor

description: Hybridized to 250K_Nsp


title: RARS_39-Tumor

description: Hybridized to 250K_Nsp


title: tAML-001-Tumor

description: Hybridized to 50K_Hind


title: AML-029-Tumor

description: Hybridized to 50K_Xba


title: RARS_32-Tumor

description: Hybridized to 250K_Nsp


title: RARS_37-Tumor

description: Hybridized to 250K_Nsp


title: RARS_49-Tumor

description: Hybridized to 250K_Nsp


title: Control 3h biological rep3

description: SAMPLE 6

source_name: primary rat hepatocytes control_incubated for 3 hrs

value: none (untreated control) for 3hrs


title: RARS_42-Tumor

description: Hybridized to 250K_Nsp


title: RARS_36-Tumor

description: Hybridized to 250K_Nsp


title: RARS_34-Tumor

description: Hybridized to 250K_Nsp


title: RARS_46-Tumor

description: Hybridized to 250K_Nsp


title: Interferon alpha 3h biological rep3

description: SAMPLE 5

source_name: primary rat hepatocytes_interferon alpha for 3 hrs

value: 250u/ml rat interferon alpha for 3hrs


title: RARS_35-Tumor

description: Hybridized to 250K_Nsp


title: AML-038-Tumor

description: Hybridized to 50K_Xba


title: RARS_30-Tumor

description: Hybridized to 250K_Nsp


title: AML-093-Tumor

description: Hybridized to 50K_Hind


title: AML-134-Tumor

description: Hybridized to 50K_Hind


title: Control 3h biological rep1

description: SAMPLE 2


title: AML-054-Tumor

description: Hybridized to 50K_Hind


title: AML-091-Tumor

description: Hybridized to 50K_Hind


title: Interferon alpha 3h biological rep2

description: SAMPLE 3


title: Control_zVAD_rep2_exp3

first: Deborah

last: Flusberg

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard University

hyb_protocol: Samples (biotin-labeled cRNA) were hybridized onto arrays for approximately 18 hours. The arrays were then washed and stained with strepatavidin-Cy3 before being scanned in the array readers (Microarray Core Facility, Children's Hospital, Boston, MA).

scan_protocol: Arrays were scanned using an Illumina BeadArray Reader (Microarray Core Facility, Children's Hospital, Boston, MA).

data_processing: data were log-transformed and quantile normalized using the Bioconductor Lumi package in R.  In cases of multiple probes for the same gene, the probe with the highest value for that gene was included in the final analysis-- these are marked yes in the column labeled MPG (max-per-gene; column AH) of the Matrix normalized worksheet.

label: biotin-cRNA + Streptavidin-Cy3

source_name: cells surviving a 6h treatment with caspase inhibitor zVAD-fmk alone (100% of cells), one day after the treatment

label_protocol: Total RNA underwent a reverse transcription reaction to generate double-stranded cDNA. The cDNA then underwent an in-vitro transcription reaction in which biotin-labeled cRNA was created (Microarray Core Facility, Children's Hospital, Boston, MA).

growth_protocol: Cells were maintained and treated in MCF10A growth media (Debnath et al., 2003)

extract_protocol: RNA was extracted using the Nucleospin Total RNA Isolation kit (Macherey-Nagel) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: origin tissue

value: breast epithelial

tag: transformation

value: nontransformed


title: Interferon alpha 3h biological rep1

description: SAMPLE 1

tag: tissue


title: Control_zVAD_rep1_exp3

treatment_protocol: cells surviving a 6h treatment with caspase inhibitor zVAD-fmk alone (100% of cells), one day after the treatment


title: Control 3h biological rep2

description: SAMPLE 4


title: RARS_27-Tumor

description: Hybridized to 250K_Nsp


title: arf2-8 gnc gnl_rep3

city: Freising-Weihenstephan

first: Claus

last: Schwechheimer

address: WZW - Lehrstuhl Systembiologie der Pflanzen, Am Hochanger 4

institute: Claus Schwechheimer

description: Gene expression of whole seedlings at day 10.

hyb_protocol: The probes were hybridized in rotating hybridization chambers (Agilent Technologies) and incubated at 65 °C for 17 h overnight in a hybridization oven. Subsequently, the arrays were washed according to the manufacturer’s instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1. (Agilent) using default parameters (protocol GE1-v1_107_Sep09 and Grid: 021169_D_F_20110524) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: 10-day-old seedlings, arf2-8 gnc gnl

label_protocol: Cy3-labeled cRNA was prepared from 0.5 µg total RNA.

growth_protocol: Seedlings were grown in 150 µE white light on GM medium for 10 days in long day conditons (16 hrs light/8 hrs dark). Material was harvested in the middle of the light period.

extract_protocol: RNA was prepared using the Machery-Nagel Nucleo Spin RNA Plant Kit.

treatment_protocol: No treatment.

tag: ecotype

tag: genotype

value: arf2 gnc gnl

value: whole seedling

tag: age

value: 10 days


title: RARS_28-Tumor

description: Hybridized to 250K_Nsp


title: Survivors_zVAD_rep2_exp3

source_name: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL + caspase inhibitor zVAD-fmk (100% of cells), one day after the treatment


title: RARS_29-Tumor

description: Hybridized to 250K_Nsp


title: RARS_31-Tumor

description: Hybridized to 250K_Nsp


title: RARS_26-Tumor

description: Hybridized to 250K_Nsp


title: arf2-8 gnc gnl_rep2


title: RARS_21-Tumor

description: Hybridized to 250K_Nsp


title: RARS_25-Tumor

description: Hybridized to 250K_Nsp


title: gnc gnl_rep3

source_name: 10-day-old seedlings, gnc gnl

value: gnc gnl


title: RARS_23-Tumor

description: Hybridized to 250K_Nsp


title: Control_IETD_rep1_exp3

source_name: cells surviving a 6h treatment with caspase inhibitor IETD-fmk alone (100% of cells), one day after the treatment


title: gnc gnl_rep2


title: arf2-8 gnc gnl_rep1


title: Control_IETD_rep2_exp3

treatment_protocol: cells surviving a 6h treatment with caspase inhibitor IETD-fmk alone (100% of cells), one day after the treatment


title: RARS_24-Tumor

description: Hybridized to 250K_Nsp


title: RARS_16-Tumor

description: Hybridized to 250K_Nsp


title: Survivors_IETD_rep2_exp3

source_name: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL + caspase inhibitor IETD-fmk (100% of cells), one day after the treatment


title: RARS_22-Tumor

description: Hybridized to 250K_Nsp


title: RARS_15-Tumor

description: Hybridized to 250K_Nsp


title: RARS_19-Tumor

description: Hybridized to 250K_Nsp


title: RARS_13-Tumor

description: Hybridized to 250K_Nsp


title: RARS_17-Tumor

description: Hybridized to 250K_Nsp


title: RARS_20-Tumor

description: Hybridized to 250K_Nsp


title: RARS_12-Tumor

description: Hybridized to 250K_Nsp


title: RARS_8-Tumor

description: Hybridized to 250K_Nsp


title: RARS_14-Tumor

description: Hybridized to 250K_Nsp


title: arf2-8 (Col)_rep1

source_name: 10-day-old seedlings, arf2-8


title: arf2-8 (Col)_rep2


title: arf2-8 (Col)_rep3


title: IKB_survivors_rep1_exp3

source_name: Day 1 Survivor cells stably expressing the IKB-super-repressor plasmid


title: RARS_11-Tumor

description: Hybridized to 250K_Nsp


title: Survivors_zVAD_rep1_exp3

treatment_protocol: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL + caspase inhibitor zVAD-fmk (100% of cells), one day after the treatment


title: IKB_survivors_rep2_exp3

treatment_protocol: Day 1 Survivor cells stably expressing the IKB-super-repressor plasmid


title: RARS_7-Tumor

description: Hybridized to 250K_Nsp


title: Survivors_IETD_rep1_exp3

treatment_protocol: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL + caspase inhibitor IETD-fmk (100% of cells), one day after the treatment


title: gnc gnl_rep1


title: IKB_control_rep2_exp3

source_name: untreated cells stably expressing the IKB-super-repressor plasmid


title: RARS_2-Tumor

description: Hybridized to 250K_Nsp


title: RARS_18-Tumor

description: Hybridized to 250K_Nsp


title: RARS_10-Tumor

description: Hybridized to 250K_Nsp


title: wild type (Col)_10 days_rep3

source_name: 10-day-old seedlings, wild type

value: wild type


title: RARS_9-Tumor

description: Hybridized to 250K_Nsp

value: myelodysplastic syndrome


title: wild type (Col)_10 days_rep2


title: IKB_control_rep1_exp3

treatment_protocol: untreated cells stably expressing the IKB-super-repressor plasmid


title: wild type (Col)_10 days_rep1


title: RARS_5-Tumor

description: Hybridized to 250K_Nsp

value: tumor


title: Survivors_rep6_exp3

source_name: surviving cells (50ng/ml SuperKiller TRAIL, 6h) re-treated with same dose/time TRAIL on Day 1 and Day 2


title: Liver Day 6 Post Hepatectomy C

city: New York

first: Daniel

middle: J

last: Nolan

state: NY

address: 1300 York Ave

department: Genetic Medicine

institute: Weill Cornell Medical College

description: Liver Day 6 Post Hepatectomy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
All Data was processed using GeneSpring 11 software with RMA normalization
MoGene-1_0-st-v1, HuGene-1_0-st-v1
MoGene-1_0-st-v1-r3, HuGene-1_0-st-v1-r3

source_name: C57BL/6 Adult Male post hepatectomy

label_protocol: Nugen Ovation Amplification, Ovation Exon Module, Encore Biotin Module for preparation, fragmentation, and labeling.

extract_protocol: PicoPure RNA isolation kit

tag: marker

value: VEGFR3+ Isolectin+ CD34- IgG-

tag: strain

tag: gender

value: male

value: Hepatectomy

tag: time

value: 6 d


title: Survivors_rep5_exp3

source_name: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL (10-20% of cell population), 7 days after the treatment


title: Control_rep7_exp3

source_name: untreated cells

treatment_protocol: untreated cells


title: AML-165-Tumor

description: Hybridized to 250K_Nsp

source_name: AML primary sample

value: acute myeloid leukemia


title: dcl1-9 dark treatment, rep3

city: Oeiras

first: Elena

last: Baena-Gonzalez

address: Rua da Quinta Grande 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

description: Gene expression data from dcl1-9 leaves under starvation conditions (darkness)

hyb_protocol: 3,5 µg of end-labeled, fragmented cDNA was used in a 150-µl hybridization cocktail containing added hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix), of which 120 µl were hybridized on array strips for 20 h at 48°C. Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system, followed by scanning of the array strips.

scan_protocol: GeneAtlas station and protocol

data_processing:
Scanned arrays were analyzed first with Affymetrix Expression Console software for quality control. Subsequent analysis was carried out with DNA-Chip Analyzer (dChip; http://www.dchip.org, Wong Lab, Harvard) using custom cdf file aragene11st_At_TAIRG.cdf and respective annotations as available from Brainarray database version 15 (Vazquez et al., 2004;Sandberg and Larsson, 2007). The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the 12 arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model (Li and Hung Wong, 2001). Replicate data for the same sample type were weighted gene-wise by using inverse squared standard error as weights.
Lower bound of fold-change (FC). All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2. The lower confidence bound criterion means that we can be 90% confident that the fold change is a value between the lower confidence bound and a variable upper confidence bound. Li and Hung Wong (Li and Hung Wong, 2001) have shown that the lower confidence bound is a conservative estimate of the fold change and therefore more reliable as a ranking statistic for changes in gene expression.

source_name: Detached leaves of Arabidopsis dcl1-9 mutant plants (4-5 week-old) were floated on MilliQ water and incubated for 6h under darkness (22ºC)

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) Arabidopsis Gene 1.1 ST Array Strips by using the Ambion WT Expression Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal Labeling Kit, according to the manufacturer’s protocols. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Ambion WT Expression Kit) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (Ambion WT Expression Kit). 15 µg of this cRNA was used for a second cycle of first-strand cDNA synthesis (Ambion WT Expression Kit). 5.5 µg of single stranded cDNA was fragmented and end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: All Arabidopsis thaliana (Arabidopsis) plants used in this study are in the Columbia (Col-0) background. dcl1-9 was originally isolated in ecotype Wassilewskija (Feldmann, 1992) and has been backcrossed five times to Col-0 ecotype (Vazquez et al., 2004). Sterilized seeds were stratified in the dark at 4ºC for 2 days, and sowed on plates containing 0.5X Murashige and Skoog medium with 0.1% MES, 0.8% phytoagar and 1% sucrose. Plates were sealed and incubated in short day conditions (12 h light 100 µE/12 h dark) at 22ºC during the light period and 18ºC during the dark period. After 10 days, seedlings were transferred to 1:3 vermiculite:soil mixture and kept in the same photoperiod and temperature conditions.

extract_protocol: Total RNA from three biological replicates was extracted using TRIzol® reagent (Life Technologies) and treated with RNase-Free DNase (Promega). The concentration and purity of DNased RNA were determined by spectrophotometry and integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Well-expanded leaves from 4-5 week-old plants (true leaf numbers five to seven) were detached and incubated in Petri dishes with 20 mL of sterile MilliQ water for 6h either in the light or in dark. Dark treatment started 2h after the onset of the light period. After the treatment, leaves were quickly pat-dried, flash-frozen in liquid N2 and kept at -80ºC until RNA extraction.

value: mature leaves

value: dcl1-9 mutant

tag: genetic background

value: 4-5 week old plants

value: dark


title: AML-164-Tumor

description: Hybridized to 250K_Nsp


title: AML-161-Tumor

description: Hybridized to 250K_Nsp


title: RARS_1-Tumor

description: Hybridized to 250K_Nsp

source_name: MDS primary sample


title: Repeat_rep3_exp2

treatment_protocol: surviving cells (50ng/ml SuperKiller TRAIL, 6h) re-treated with same dose/time TRAIL on Day 1 and Day 2

value: breast epithelial

value: nontransformed


title: dcl1-9 dark treatment, rep2


title: Control_rep6_exp3


title: Liver Day 6 Post Hepatectomy A

description: Liver Day 6 Post Hepatectomy

value: liver


title: dcl1-9 dark treatment, rep1


title: AML-166-Tumor

description: Hybridized to 250K_Nsp


title: AML-159-Tumor

description: Hybridized to 250K_Nsp


title: AML-160-Tumor

description: Hybridized to 250K_Nsp


title: AML-162-Tumor

description: Hybridized to 250K_Nsp


title: AML-153-Tumor

description: Hybridized to 250K_Nsp


title: RARS_4-Tumor

description: Hybridized to 250K_Nsp


title: Liver Day 6 Post Hepatectomy B

description: Liver Day 6 Post Hepatectomy


title: AML-156-Tumor

description: Hybridized to 250K_Nsp


title: AML-157-Tumor

description: Hybridized to 250K_Nsp


title: AML-154-Tumor

description: Hybridized to 250K_Nsp


title: dcl1-9 light control, rep3

description: Gene expression data from dcl1-9 leaves in control conditions (light)

source_name: Detached leaves of Arabidopsis dcl1-9 mutant plants (4-5 week-old) were floated on MilliQ water and incubated for 6h under control light conditions (100 µE, 22ºC)

value: light


title: Liver Day 4 Post Hepatectomy A

description: Liver Day 4 Post Hepatectomy

value: 4 d


title: Reset_rep3_exp2

treatment_protocol: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL (10-20% of cell population), 7 days after the treatment


title: AML-141-Tumor

description: Hybridized to 250K_Nsp


title: RARS_3-Tumor

description: Hybridized to 250K_Nsp


title: Survivors_rep4_exp2

source_name: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL (10-20% of cell population), one day after the treatment


title: wild-type dark treatment, rep2

description: Gene expression data from WT leaves under starvation conditions (darkness)

source_name: Detached leaves of Arabidopsis WT Col-0 plants (4-5 week-old) were floated on MilliQ water and incubated for 6h under darkness (22ºC)

value: wild-type


title: AML-167-Tumor

description: Hybridized to 250K_Nsp


title: AML-158-Tumor

description: Hybridized to 250K_Nsp


title: Liver Day 2 Post Hepatectomy B

description: Liver Day 2 Post Hepatectomy

value: 2 d


title: Liver Day 4 Post Hepatectomy C

description: Liver Day 4 Post Hepatectomy


title: AML-152-Tumor

description: Hybridized to 250K_Nsp

value: tumor


title: AML-163-Tumor

description: Hybridized to 250K_Nsp


title: wild-type dark treatment, rep3


title: Liver Day 4 Post Hepatectomy B

description: Liver Day 4 Post Hepatectomy

value: VEGFR3+ Isolectin+ CD34- IgG-


title: Survivors_rep3_exp2

treatment_protocol: cells surviving a 6h treatment with 50ng/ml SuperKiller TRAIL (10-20% of cell population), one day after the treatment


title: Liver Day 2 Post Hepatectomy C

description: Liver Day 2 Post Hepatectomy

value: male


title: Liver Day 2 Post Hepatectomy A

description: Liver Day 2 Post Hepatectomy

value: Hepatectomy


title: wild-type light control, rep3

description: Gene expression data from WT leaves in control conditions (light)

source_name: Detached leaves of Arabidopsis WT Col-0 plants (4-5 week-old) were floated on MilliQ water and incubated for 6h under control light conditions (100 µE, 22ºC)


title: Reset_rep2_exp2


title: Control_rep4_exp2


title: dcl1-9 light control, rep2


title: AML-137-Tumor

description: Hybridized to 250K_Nsp


title: RARS_6-Tumor

description: Hybridized to 250K_Nsp

value: myelodysplastic syndrome


title: wild-type dark treatment, rep1


title: AML-138-Tumor

description: Hybridized to 250K_Nsp

value: acute myeloid leukemia


title: Liver Steady State A v2

description: Liver Steady State

source_name: WT C57BL/6 adult Male


title: Control_rep5_exp2


title: dcl1-9 light control, rep1

value: mature leaves


title: Liver Steady State B v2

description: Liver Steady State


title: Repeat_rep2_exp2


title: Reset_rep1_exp1


title: Control_rep3_exp1


title: Liver Steady State C v2

description: Liver Steady State


title: Bone Marrow Day 28 C

description: Bone Marrow Day 28 Post 650R

source_name: C57BL/6 Adult Male post irradiation

value: Ve-Cad+ Isolectin+ IgG-

value: bone marrow


title: wild-type light control, rep2

value: 4-5 week old plants


title: wild-type light control, rep1


title: AML-139-Tumor

description: Hybridized to 250K_Nsp


title: AML-136-Tumor

description: Hybridized to 250K_Nsp


title: Bone Marrow Day 28 B

description: Bone Marrow Day 28 Post 650R


title: Survivors_rep2_exp1

value: breast epithelial


title: Bone Marrow Day 28 A

description: Bone Marrow Day 28 Post 650R


title: PAO1-AMV-2

city: Aurora

last: Schurr

state: CO

institute: University of Colorado School of Medicine

data_processing:
program-name = ArrayStar
program-version = 5.0.0.56
program-company = DNASTAR
affymetrix-algorithm-name = RMA
affymetrix-algorithm-version = 1.0
Microarray analysis was performed using DNASTAR Array Star version 5.0.  The software was used to normalize the raw expression data and generate gene lists with fold-change values.  CLC WorkBench version 6 was used to generate the Volcano plot comparing the p values to the fold changes of the gene expression dataset.  Gene lists were compiled with relevant information from the PAO1 annotation (25) in Microsoft Excel 2007.  Graphs were exported and annotated in Adobe Illustrator CS5.  Microarray data from Tart et al. 2005 (27) was compared to the dataset compiled in this study with a p value cutoff of >0.01.  The resulting Venn was further annotated and color-coded in Adobe Illustrator CS5

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa grown on PIAAMV for 18hr at 37°C

label_protocol: Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.  End labeled with biotin-ddUTP with use of the Enzo BioArray Terminal Labeling kit (Affymetrix).

extract_protocol: Cells were treated with RNAprotect (Qiagen) and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions.  RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.

tag: growth protocol

value: PIA-AMV


title: PAO1-AMV-3

hyb_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: PAO1-AMV-1

scan_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: Repeat_rep1_exp1

value: nontransformed


title: PAO1-3

source_name: P. aeruginosa grown on PIA for 18hr at 37°C

value: PIA


title: Bone Marrow Day 21 C

description: Bone Marrow Day 21 Post 650R

tag: treatment


title: Control_rep2_exp1


title: Bone Marrow Day 21 A

description: Bone Marrow Day 21 Post 650R


title: Control_rep1_exp1


title: Bone Marrow Day 21 B

description: Bone Marrow Day 21 Post 650R


title: Survivors_rep1_exp1


title: PAO1-2


title: PAO1-1


title: AML-130-Tumor

description: Hybridized to 250K_Nsp

tag: disease status


title: SupB15-MR cells, biological rep1

city: Manchester

first: jizhong

last: LIU

address: wilmslow road

institute: THE UNIVERSITY OF MANCHESTER

description: Gene expression data from normal cultured SupB15-MR cells

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

data_processing: The data were analyzed with RMA.

source_name: SupB15-MR cells grow in normal medium

label_protocol: 2 ug of total RNA were labelled with Nugen Ovation Biotin labelling system (NuGEN Technologies)

growth_protocol: Cells were incubated in RPMI1640 medium containing 10% FBS, cell density were about 0.7-1.0 million cells/ml

extract_protocol: Total RNA were purified by Qiagen RNeasy Micro kit

treatment_protocol: same passages of cells were normal cultured

tag: cell type

value: lymphocyte

tag: drug sensitivity

value: multiple drug resistant


title: Bone Marrow Day 10 C

description: Bone Marrow Day 10 Post 650R


title: AML-114-Tumor

description: Hybridized to 250K_Nsp


title: Aspergillus oryzae grown on the substrate I9_Shake Flask 3

city: Gothenburg

first: D.B.R.K. Gupta

last: Udatha

state: Sweden

address: Medicinaregatan 9C

department: Department of Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

description:
Processed data file: ctrl_vs_I9.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 32

hyb_protocol: cRNA was quantified in a spectrophotometer. cRNA quality was assessed using a BioAnalyzer. A GeneChip Fluidics Station FS-400 (fluidics protocol FS450_001) and a GeneChip Scanner 3000 were used for hybridization and scanning.

scan_protocol: Arrays were washed and stained using a GeneChip Fluidics Station FS-400, and scanned on an Agilent GeneArray Scanner 3000.

data_processing: The scanned probe array images were converted into data files using the Agilent software.

organism: Aspergillus oryzae RIB40

label_protocol: Standard Agilent protocol

growth_protocol:
The composition of the batch cultivation medium was the following (in g L-1): 20 g glucose monohydrate, 2.0 g MgSO4.7H2O, 2 g K2SO4, 2.0 g KH2PO4, 5.0 g (NH4)2SO4, 0.5 ml L-1 pluronic acid (PE-6100) (BASF SE, Ludwigshafen, Germany) and 0.6 ml L-1 of trace elements solution. Trace elements solution composition (in g L-1): 14.3 g ZnSO4.7H2O, 8.5 g MnSO4.H2O, 13.8 g FeSO4.7H2O, 2.5 g CuSO4.5H2O, 3 g citric acid monohydrate (as a chelating agent) and 0.5 g NiCl2.6H2O. A. oryzae spore propagation medium (Cove-N-Gly) (in g L-1): 218 g sorbitol, 10 g glycerol 99.5%, 2.02 g KNO3, 25 g agar and 50 ml L-1 of salt solution. Cove-N-Gly salt solution (in g L-1): 26 g KCl, 26 g MgSO4.7H2O, 76 g KH2PO4 and 50 ml L-1 of trace elements solution. Cove-N-Gly trace elements solution (in mg L-1): 40 mg Na2B4O7.10H2O, 400 mg CuSO4.5H2O, 1,200 mg FeSO4.7H2O, 700 mg MnSO4.H2O, 800 mg Na2MoO4.2H2O and 10 g ZnSO4.7H2O.
A. oryzae RIB40 batch fermentations were inoculated with spores propagated on Cove-N-Gly spore propagation medium plates incubated for 5 days at 30 C. To obtain enough mycelia with well dispersed filamentous growth grown under the same conditions to start enzyme induction with ten different protein inducing oligosaccharides in 250 mL shake flask cultivations, two consecutive batch cultivations were carried out. A. oryzae batch fermentations were performed in 3.6 L Infors bioreactors with a working volume of 2.8 L. Reactors were equipped with two Rushton four-blade disc turbines, no baffles, pH and temperature control. The temperature was maintained at 30 C and the pH was controlled by automatic addition of by addition of 10% H3PO4 or 10% NH3 solution. The pH was set to 3.5 to prevent spore aggregation and kept constant throughout the cultivation. The stirring speed was initially set at 200 rpm and the aeration rate to 0.1 vvm (volume of gas per volume of liquid per minute). After germination, these parameters were increased to 1000 rpm and 1 vvm and kept steady throughout all the rest of the fermentation. The batch cultivation was used to harvest biomass for consecutive induction by any of the different oligosaccharides at the final concentration listed in brackets: 1,3:1,4-β-glucohexaose (66.67 mg L-1), Glc-Maltotriosyl-maltotriose (333.33 mg L-1), 1,4-β-D-xylopentaose (66.67 mg L-1), 1,5-alpha-L-Arabinoheptaose (100 mg L-1), Galactosyl-mannotriose (133.33 mg L-1), sophorose (66.67 mg L-1), D-turanose (333.33 mg L-1), D-melibiose (333.33 mg L-1), 1,4-β-D-mannohexaose (133.33 mg L-1), cellohexaose (200 mg L-1), xyloglucan reduced (X3GLC4) (333.33 mg L-1) and glucose (as control, 20 g L-1). Unless otherwise stated, the oligosaccharides used were obtained from Megazyme (Megazyme, International Ireland Ltd, Wicklow, Ireland); solely sophorose, D-melibiose and D-turanose were obtained from Sigma (Sigma-Aldrich Inc., St. Louis, MO, United States). Oligosaccharides were very well dissolved in water, filtered sterilized and added to each of the three shake flask replicates. Mycelium was harvested after ~32 h cultivation in mid-exponential phase. Mycelium was washed with sterile mineral media without carbon source, squeezed and weighed under sterile conditions. 800 mg of wet weighed mycelia were used for inoculation of each shake flask cultivation.

extract_protocol: For gene expression analysis, mycelium was harvested after 2 h cultivation with the respective inducer from each of the three biological replicates. The cultures were filtered through sterile Miracloth (Calbiochem, San Diego, CA, USA) and washed with a suitable amount of 0.9 % NaCl solution. The mycelium was quickly dried by squeezing and subsequently frozen in liquid nitrogen. Samples were stored at -80°C until RNA extraction. A. oryzae total RNA was extracted using the Qiagen RNeasy Mini Kit (QIAGEN Nordic, Ballerup, Denmark), according to the protocol for isolation of total RNA from plant and fungi. For the purpose, approximately 500 mg of frozen mycelium was ground to powder using a ceramic mortar and pestle. Mycelium was kept in liquid nitrogen throughout the grinding processing. All samples were inspected for good quality of total RNA extracted with a BioAnalyzer (2100 BioAnalyzer, Agilent Technologies Inc., Santa Clara, CA, USA). RNA quantification was performed in a spectrophotometer (Biophotometer 6131, Eppendorf AG, Hamburg, Germany) and total RNA was stored at -80 oC until further processing.

tag: genotype/variation

value: Wild-type

tag: phenotype

value: normal

tag: accession

value: Aspergillus oryzae sequenced strain RIB40

tag: grown on substrate

tag: substrate description

value: Mannohexaose

value: mycelium


title: Aspergillus oryzae grown on the substrate I9_Shake Flask 2

description:
Processed data file: ctrl_vs_I9.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 31

tag: tissue


title: Bone Marrow Day 10 B

description: Bone Marrow Day 10 Post 650R

value: male


title: Aspergillus oryzae grown on the substrate I9_Shake Flask 1

description:
Processed data file: ctrl_vs_I9.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 30


title: Bone Marrow Steady State C v2

description: Bone Marrow Steady State


title: Bone Marrow Day 10 A

description: Bone Marrow Day 10 Post 650R


title: AML-131-Tumor

description: Hybridized to 250K_Nsp

value: acute myeloid leukemia

value: tumor


title: Aspergillus oryzae grown on the substrate I7_Shake Flask 3

description:
Processed data file: ctrl_vs_I7.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 29

value: Turanose


title: Bone Marrow Steady State B v2

description: Bone Marrow Steady State

value: Ve-Cad+ Isolectin+ IgG-

value: bone marrow


title: AML-133-Tumor

description: Hybridized to 250K_Nsp


title: SupB15 cells

description: Gene expression data from normal cultured SupB15 cells

source_name: SupB15 cells grow in normal medium

tag: cell line

value: drug sensitive


title: AML-126-Tumor

description: Hybridized to 250K_Nsp


title: Bone Marrow Steady State A v2

description: Bone Marrow Steady State

tag: marker


title: AML-132-Tumor

description: Hybridized to 250K_Nsp


title: Kasumi1_RAD21WT_Exp2_rep3

data_processing: Raw array signals were processed using dCHIP.

source_name: Kasumi-1 cells, wild-type

growth_protocol: Kasumi-1 cells were retrovirally transduced with either mock or wild-type RAD21. The cells were sorted by GFP-marking using a MoFlo® FACS cell sorter (Beckman Coulter) 48 hrs after retroviral transduction.

extract_protocol: Total RNA from cultured cells was isolated with the RNeasy Total RNA kit (Qiagen) using RNase-free DNase set (Qiagen) to reduce contamination of genomic DNA according to the manufacturer's protocol.

tag: transduction

value: wild-type RAD21


title: Aspergillus oryzae grown on the substrate I7_Shake Flask 2

description:
Processed data file: ctrl_vs_I7.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 28


title: Kasumi1_RAD21WT_Exp2_rep2


title: SupB15-MR cells, biological rep2

description: Gene expression data from normal cultured SupB15-MR5 cells


title: Aspergillus oryzae grown on the substrate I7_Shake Flask 1

description:
Processed data file: ctrl_vs_I7.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 27


title: Aspergillus oryzae grown on the substrate I6_Shake Flask 3

description:
Processed data file: ctrl_vs_I6.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 26

value: Sophorose


title: Kasumi1_RAD21WT_Exp2_rep1


title: Kasumi1_Mock_Exp2_rep2

source_name: Kasumi-1 cells, mock

value: mock


title: Kasumi1_Mock_Exp2_rep1


title: Liver Steady State C

description: Liver Steady State

value: VEGFR3+ Isolectin+ CD34- IgG-

tag: strain

tag: gender

value: liver


title: Aspergillus oryzae grown on the substrate I5_Shake Flask 3

description:
Processed data file: ctrl_vs_I5.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 23

value: Wild-type

value: Galactosyl-mannotriose


title: Aspergillus oryzae grown on the substrate I6_Shake Flask 2

description:
Processed data file: ctrl_vs_I6.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 25

value: normal

value: Aspergillus oryzae sequenced strain RIB40


title: Kasumi1_Mock_Exp2_rep3


title: AML-110-Tumor

description: Hybridized to 250K_Nsp


title: AML-112-Tumor

description: Hybridized to 250K_Nsp


title: AML-094-Tumor

description: Hybridized to 250K_Nsp


title: Liver Steady State B

description: Liver Steady State


title: Aspergillus oryzae grown on the substrate I6_Shake Flask 1

description:
Processed data file: ctrl_vs_I6.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 24

value: mycelium


title: AML-113-Tumor

description: Hybridized to 250K_Nsp


title: Bone Marrow Steady State B

description: Bone Marrow Steady State

value: male


title: AML-109-Tumor

description: Hybridized to 250K_Nsp

value: acute myeloid leukemia


title: Aspergillus oryzae grown on the substrate I5_Shake Flask 2

description:
Processed data file: ctrl_vs_I5.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 22


title: AML-108-Tumor

description: Hybridized to 250K_Nsp

value: tumor


title: Liver Steady State A

description: Liver Steady State


title: Glomerulus C

description: Kidney Glomeruli Endothelial Cells

value: VE-Cad+ CD34+ IgG-

value: Kidney Glomeruli Endothelial Cells


title: Kasumi1_RAD21WT_Exp1_rep1


title: Aspergillus oryzae grown on the substrate I4_Shake Flask 3

description:
Processed data file: ctrl_vs_I4.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 20


title: Kasumi1_RAD21WT_Exp1_rep3


title: Kasumi1_RAD21WT_Exp1_rep2


title: Aspergillus oryzae grown on the substrate I5_Shake Flask 1

description:
Processed data file: ctrl_vs_I5.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 21


title: Bone Marrow Steady State C

description: Bone Marrow Steady State

value: Ve-Cad+ Isolectin+ IgG-

value: bone marrow


title: AML-088-Tumor

description: Hybridized to 250K_Nsp


title: Glomerulus B

description: Kidney Glomeruli Endothelial Cells


title: AML-087-Tumor

description: Hybridized to 250K_Nsp


title: Kasumi1_Mock_Exp1_rep1


title: Kasumi1_Mock_Exp1_rep3


title: Bone Marrow Steady State A

description: Bone Marrow Steady State


title: Kasumi1_Mock_Exp1_rep2


title: Aspergillus oryzae grown on the substrate I4_Shake Flask 2

description:
Processed data file: ctrl_vs_I4.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 19


title: Glomerulus A

description: Kidney Glomeruli Endothelial Cells


title: Aspergillus oryzae grown on the substrate I3_Shake Flask 3

description:
Processed data file: ctrl_vs_I3.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 17

value: D-Xylopentaose


title: Heart C

description: Heart Endothelial Cells

value: Heart Endothelial Cells


title: AML-111-Tumor

description: Hybridized to 250K_Nsp


title: Aspergillus oryzae grown on the substrate I4_Shake Flask 1

description:
Processed data file: ctrl_vs_I4.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 18


title: Aspergillus oryzae grown on the substrate I3_Shake Flask 1

description:
Processed data file: ctrl_vs_I3.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 15


title: Synovial fluid of Spondyloarthritis (SpA) of  sample 2

description: Gene expression profiling of synovial fluid derived mononuclear cells from SpA patient using whole human genome microarray

source_name: Knee aspirated synovial fluid SpA sample 2

tag: date of collection

tag: fluid

value: Turbid, highly viscous and non bloody

value: Male

tag: age (y)

tag: case history

value: Two weeks  back patient had bloody diarrhoea and an undifferentiated spondyloarthropathy case

value: mononuclear cells from synovial fluid

tag: disease state

value: spondyloarthropathy


title: Heart B

description: Heart Endothelial Cells

tag: cell type


title: Synovial fluid of Spondyloarthritis (SpA) of  sample 4

source_name: Knee aspirated synovial fluid SpA sample 4

value: suffering from past 6 yrs had  back ache, knee swellings and an Ankylosing spondylitis case

tag: treatment

value: Pain killers


title: Heart A

description: Heart Endothelial Cells


title: Lung C

description: Lung Endothelial Cells

value: Lung Endothelial Cells


title: Aspergillus oryzae grown on the substrate I2_Shake Flask 3

description:
Processed data file: ctrl_vs_I2.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 14

tag: genotype/variation

value: Wild-type

tag: phenotype

value: normal

value: Aspergillus oryzae sequenced strain RIB40

value: Glc-Maltotriosyl-maltotriose

value: mycelium


title: AML-084-Tumor

description: Hybridized to 250K_Nsp

source_name: AML primary sample

tag: disease status

value: acute myeloid leukemia

value: tumor


title: AML-085-Tumor

description: Hybridized to 250K_Nsp


title: Leaf_07506-01versus12120-03 dye swap_rep1

city: Fredericton

first: Helen

middle: H.

last: Tai

state: New Brunswick

address: P. O. Box 20280, 850 Lincoln Rd.

department: Potato Research Centre

institute: Agriculture and Agri-Food Canada

description: both clones are diploids

hyb_protocol: Hybridization and slide processing were performed using the 1 × 44 k POCI array (Kloosterman et al. 2008) using the Arrayit microarray hybridization cassette (Arrayit Corp, Sunnyvale, CA, USA) according to manufacturer specifications. Slides were scanned on the GenePix 4000B Microarray Scanner (MDS Analytical Technologies, Ottawa, ON, Canada), and data were extracted using the manufacturer’s software.

data_processing:
Microarray data were analyzed using the Genowiz 4.0 software (Ocimum Biosolutions, Gaithersburg, MD, USA). Double channel analysis of 07506-01 and 12120-03 data was done using print-tip loess normalization with a smoothing factor of 0.1.
Normalized log2 transformation of 07506-01/12120-03 (Cy5/Cy3) fluorescence ratio for each gene with negative ratio values retained.

organism: Solanum tuberosum

label_protocol: Total RNA was purified using RNeasy MinElute Spin Columns (Qiagen, Toronto, ON, Canada) and DNAse I treated before first- and second-strand synthesis following the Ambion MessageAmp™ II aRNA amplification kit protocol (Life Technologies, Burlington, ON, Canada) using the following minor modifications. For first-strand synthesis, 2 μg of total RNA was used in the reaction followed by second-strand synthesis with half of the recommended enzyme concentrations. Purified cDNA was used for in vitro transcription using an indirect amino-allyl-labeling method with a 1:3 incorporation ratio of uridine triphosphate (UTP)/5-(3-aminoallyl)-UTP. In vitro transcription was performed at 37°C with a lid temperature of 40°C for a period of 15 h, after which samples were purified according to the manufacturer’s protocol. Unincorporated nucleotides were removed using filter cartridges provided with the kit.  Purified aminoallyl RNA (aRNA) samples were dried using a speedvac at 45 oC and stored at -80 oC.  For sample labeling, 5-7 μg of aRNA was resuspended in 5 μl freshly made carbonate buffer (0.1 M Na2CO3) adjusted to pH 9. Equal amounts of either Cy5 or Cy3 dye (GE Healthcare, Mississauga, ON, Canada) were added to aRNA from 07506-01 or 12120-03, respectively, and incubated for 2 h at room temperature. Each of the three replicate Cy5-labelled sRNA samples (1 μg each) from 07506-01 was paired with a Cy3-labelled aRNA sample from 12120-03 and co-hybridized on a single slide. A fourth slide consisted of swapping dye labels between 07506-01 and 12120-03 for replicate 1.  Samples were purified using RNeasy MinElute Spin Columns (Qiagen, Toronto, ON, Canada) prior to application on slides.  Dye incorporation was measured using a ND-100 Spectrophotometer v3.3 (Nanodrop Technologies, Wilmington, DE, USA).

growth_protocol: Two diploid potato clones, 07506-01 and 12120-03, were developed at the Agriculture and Agri-Food Canada Potato Research Centre (AAFC-PRC) in Fredericton, New Brunswick, Canada. The diploid clones were primarily based on hybrids between Solanum phureja or S. stenotomum and Solanum. tuberosum L. Phureja Group and Stenotomum Group (De Jong 1987).  The experiment was performed at the Potato Research Centre, Agriculture and Agri-Food Canada (AAFC), Fredericton, NB, Canada (45° 52' N, 66° 31' W) during 2008.  Seed tubers were obtained from the Benton Ridge Substation of AAFC in Benton, New Brunswick, Canada, which is a certified virus-free breeding farm.   07506-01 and 12120-03 seed tubers were sown in a plot carrying V. dahliae on May 15, 2008.  Fertilizer was banded about 7.5 cm to each side and 5 cm below the potato seed pieces at planting according to normal production practices at 200 kg N ha-1 as ammonium nitrate, 150 kg P2O5 ha-1 and 150 kg K2O ha-1. The plants were hilled on July 10, 2008. Standard commercial practices were used for control of diseases, insects and weeds. No irrigation was applied.

extract_protocol: Clones 07506-01 and 12120-03 were planted in three replicates in the field in a randomized block design with five plants per replicate plot.  The plants from the field were used for gene expression analysis.  One leaflet 1 to 1.5 cm in width was collected from the expanding top leaf from each plant at ten weeks after planting in the field.  The leaflets from the five plants for each replicate plot were combined and immediately frozen in liquid nitrogen and stored at -80oC until processed. Frozen leaflets from field plants was ground using bead matrix 4, speed 6, for 40 s in a FastPrep instrument (MP Biomedicals, Montreal, PQ, Canada).  Total RNA and DNA were co-extracted using a scaled-down hot borate extraction method (Tai et al. 2007, Wan and Wilkins 1994) and .  quality was checked using a BioAnalyzer (Agilent, Mississauga, ON, Canada).  The nucleic acid extract was split: for RNA extraction the samples were treated with DNase I and for DNA extraction the samples were treated with RNAse A.

treatment_protocol: Experiment was a comparison between two potato genotypes.

value: leaf

tag: age

value: 10 weeks after planting


title: Aspergillus oryzae grown on the substrate I2_Shake Flask 2

description:
Processed data file: ctrl_vs_I2.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 13

tag: accession

tag: grown on substrate

tag: substrate description

tag: tissue


title: Lung B

description: Lung Endothelial Cells

tag: marker

value: Ve-Cad+ Isolectin+ IgG-

tag: strain

value: male


title: Lung A

description: Lung Endothelial Cells

tag: gender


title: AML-086-Tumor

description: Hybridized to 250K_Nsp


title: Leaf_07506-01versus12120-03_rep3

description: both clones are diploids

scan_protocol: Slides were scanned on the GenePix 4000B Microarray Scanner (MDS Analytical Technologies, Ottawa, ON, Canada), and data were extracted using the manufacturer’s software.


title: AML-055-Tumor

description: Hybridized to 250K_Nsp


title: Brain C

description: Brain Endothelial Cells

value: CD34+ Ve-Cad+ IgG-

value: Brain Endothelial Cells


title: Synovial fluid of Rheumatoid arthritis (RA)  sample 4

description: Gene expression profiling of synovial fluid derived mononuclear cells from RA patient using whole human genome microarray

source_name: Knee aspirated synovial fluid RA sample4

tag: date of collection

tag: fluid

value: Non turbid, viscous and nonbloody

value: Female

value: suffering from past 2 yrs and came with pain and swollen knees

value: Methotrexate

value: mononuclear cells from synovial fluid

value: Rheumatoid arthritis


title: Synovial fluid of Rheumatoid arthritis (RA)  sample 3

source_name: Knee aspirated synovial fluid RA sample3

value: Turbid, highly viscous and non bloody

tag: age (y)

tag: case history

value: suffering from past 8 months and came with pain and swollen knees

value: Pain killers


title: Aspergillus oryzae grown on the substrate I11_Shake Flask 2

description:
Processed data file: ctrl_vs_I11.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 10

value: Wild-type

value: normal

value: Aspergillus oryzae sequenced strain RIB40

value: Xyloglucan

value: mycelium


title: AML-082-Tumor

description: Hybridized to 250K_Nsp

value: acute myeloid leukemia

value: tumor


title: Brain B

description: Brain Endothelial Cells

value: CD34+ Ve-Cad+ IgG-

tag: cell type

value: Brain Endothelial Cells

value: male


title: AML-081-Tumor

description: Hybridized to 250K_Nsp


title: Aspergillus oryzae grown on the substrate I2_Shake Flask 1

description:
Processed data file: ctrl_vs_I2.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 12

value: Glc-Maltotriosyl-maltotriose


title: Brain A

description: Brain Endothelial Cells


title: Aspergillus oryzae grown on the substrate I10_Shake Flask 3

description:
Processed data file: ctrl_vs_I10.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 8

value: Cellohexaose


title: Aspergillus oryzae grown on the substrate I10_Shake Flask 2

description:
Processed data file: ctrl_vs_I10.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 7


title: Muscle C

description: Muslce Endothelial Cells

value: CD34+ Isolectin+ IgG-

value: Muslce Endothelial Cells


title: Aspergillus oryzae grown on the substrate I11_Shake Flask 1

description:
Processed data file: ctrl_vs_I11.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 9


title: Aspergillus oryzae grown on the substrate I3_Shake Flask 2

description:
Processed data file: ctrl_vs_I3.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 16

value: D-Xylopentaose


title: AML-050-Tumor

description: Hybridized to 250K_Nsp