title: Lhx2-HSC-like cells

city: Kamakura

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: The mouse ES cells used in this study were derived from 129/Ola strain (male). In the rosa26 locus, tet-transactivator (rtTA) has been inserted and in hprt locus, Lhx2 cDNA was inserted by Cre/loxP system under tetracycline regulatory element.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: iLhx2-ES cells derived from A2lox-cre ES cells (E14tg2a ES cell-derivertive) without Dox

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: The HSC-like cells were cultured in the presence of 1 microg/ml dox, 10 ng/ml IL-6, and 50 ng/ml SCF on OP9 stromal cells in alfa-MEM supplemented with 20% fetal bovine serum, non-essential amino acids, penicillin G, and streptomycin. The HSC-like cells (+dox) and the HSC-like cells cultured in the absence of dox for 3 days (-Dox) were compared.

extract_protocol: Total RNA was extracted by RNeasy mini kit (Qiagen) as manufacture's recommendations

treatment_protocol: The ES cells with inducible Lhx2 (iLhx2-ES cells) were differentiated by OP9 co-culture. One microg/ml dox was added from day 5 of the co-culture, and on day 20, the  lineage-/c-Kit+ cells were isolated (+dox) and these cells were further cultured in the absence of dox for 3 days (-dox)

value: iLhx2-ES cells

value: no Dox

source_name: iLhx2-ES cells derived from A2lox-cre ES cells (E14tg2a ES cell-derivertive) with Dox

value: One microg/ml dox


title: TGBsiHic3

status: Public on Aug 26 2013

type: RNA

city: Adelaide

first: damien

last: leach

address: woodville road

country: Australia

institute: the university of adelaide

description:
Immortalized myofibroblast stably transfected with short hairpin RNA against Hic-5
replicate 3

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Raw data was processed in in R using Bioconductior and Limma. Array data was normalized using RMA, filtered by mapped probes and an arbitary minimum threshold.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: WPMY-1 Sh2 TGFB1I1

label_protocol: Biotinylated cRNA were prepared from 300ng RNA according to the standard Affymetrix protocol

growth_protocol: WPMY-1 cells were maintained in RPMI 1640 medium containing 5% fetal bovine serum.

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Plated 2x10e4 cells/well in 6-well dishes for 48h in RPMI 1640 containing 5% hormone striped fetal bovine serum. Media was replaced with  fresh hormone stripped 5% FBS with TGFB or equivalent vehicle (ethanol)

tag: cell line

tag: cell type

value: Immortalized myofibroblast

tag: transfection

value: short hairpin RNA against Hic-5

tag: treatment

value: 16hr TGFB


title: LSEC sham operated-2

city: Heidelberg

first: Junhao

last: Hu

address: Im Neuenheimer Feld 280

department: Division of Vascular Oncology and Metastasis

country: Germany

institute: German Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Mus musculus

source_name: LSEC

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

growth_protocol: no in vitro culture. LSEC were directly lysed in TRIZOL after isolation.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Then RNA were dissoved in Rnase-free water. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment. LSEC were directly lysed in TRIZOL after isolation.

tag: strain

value: liver sinusoidal endothelial cells

value: sham

tag: age

value: 8 weeks


title: TGBscr2

description:
Immortalized myofibroblast stably transfected with negative control short hairpin RNA
replicate 2

source_name: WPMY-1 SCR

value: negative control short hairpin RNA


title: LSEC hepatectomized-2

value: hepatectomized


title: TGBsiHic5

description:
Immortalized myofibroblast stably transfected with short hairpin RNA against Hic-5
replicate 5


title: TGBscr3

description:
Immortalized myofibroblast stably transfected with negative control short hairpin RNA
replicate 3


title: TGBsiHic1

description:
Immortalized myofibroblast stably transfected with short hairpin RNA against Hic-5
replicate 1


title: LSEC sham operated-3


title: TGBscr4

description:
Immortalized myofibroblast stably transfected with negative control short hairpin RNA
replicate 4


title: TGBscr5

description:
Immortalized myofibroblast stably transfected with negative control short hairpin RNA
replicate 5


title: TGBsiHic4

description:
Immortalized myofibroblast stably transfected with short hairpin RNA against Hic-5
replicate 4


title: TGBsiHic2

description:
Immortalized myofibroblast stably transfected with short hairpin RNA against Hic-5
replicate 2


title: TGBscr1

description:
Immortalized myofibroblast stably transfected with negative control short hairpin RNA
replicate 1


title: LSEC hepatectomized-1


title: LSEC sham operated-1


title: siHic3

value: 16hr vehicle


title: siHic4


title: siHic1


title: siHic5


title: siHic2


title: LSEC hepatectomized-4


title: patid_9

type: genomic

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

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

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

data_processing: Beadstudio

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Glioma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated from 5-40 cryostat sections of 40 μm thickness using the QIAamp DNA mini kit

tag: os (years)

tag: os event

value: deceased

tag: pfs (years)

tag: pfs event

value: prog

tag: cimp

value: CIMP-

tag: igs

value: wt

value: no loss

tag: egfr

tag: mgmt

value: meth

tag: or diagn

value: AOD

tag: rev diagn

tag: surgery

tag: gender

value: F

tag: tum loc

tag: perf

tag: trt

value: RT/PCV


title: scr5

tag: cell line

tag: cell type

value: Immortalized myofibroblast

tag: transfection

tag: treatment


title: patid_91

tag: os (years)

tag: os event

tag: pfs (years)

value: CIMP+

value: LOH

tag: age

value: M


title: patid_125 [27K]

description: glioma

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

data_processing: Beadstudio. The 'non-normalized.txt' data matrix contains Unmethylated (Signal A) and methylated (signal B) signal intensities.

label: Cy5 and Cy58

source_name: glioma

tag: pfs event

tag: cimp

tag: igs

tag: egfr

value: LGG

tag: Sex


title: scr1

value: negative control short hairpin RNA


title: patid_290 [27K]

description: glioma

label: Cy5 and Cy51

tag: mgmt

tag: or diagn

value: AOA

tag: rev diagn

value: AA/GBM

tag: surgery

value: RT


title: scr2

tag: cell line

value: 16hr vehicle


title: patid_302

value: deceased

value: prog

value: mut

tag: gender

tag: tum loc

tag: perf

tag: trt


title: siHic5 DHT 3

description: PShTert-AR

source_name: 24hr Hic5 siRNA, 16hr 10nM DHT treatment replicate 3

growth_protocol: PShTert-AR cells were maintained in RPMI 1640 medium containing 5% fetal bovine serum.

treatment_protocol: Plated 2x10e4 cells/well in 6-well dishes for 24h in RPMI 1640 containing 5% hormone striped fetal bovine serum. Cells were transfected with 10nM non-specific siRNA or Hic-5 specific siRNA using LTX-plus transfection reagent in phenol red-free RPMI 1640. Twenty-four hours following transfection, media was replaced with  fresh hormone stripped 5% FBS. Fourtyeight hours post transfection cells were treated with 10nM hormone or equivalent vehicle (ethanol)

tag: cell type

value: Immortalized AR positive myofibroblast


title: patid_224

tag: os (years)

tag: os event

value: alive

tag: pfs (years)

value: no prog

value: wt

value: meth

value: AOD


title: patid_54 [27K]

description: glioma

label: Cy5 and Cy59

tag: pfs event

tag: cimp

value: CIMP+

value: LOH

tag: age


title: scr3

value: Immortalized myofibroblast

tag: transfection

tag: treatment


title: scr4

value: negative control short hairpin RNA


title: patid_15 [27K]

description: glioma

label: Cy5 and Cy52

tag: igs

tag: egfr

tag: mgmt

tag: or diagn

value: LGG

tag: Sex

value: F


title: patid_109 [27K]

description: glioma

label: Cy5 and Cy55

tag: rev diagn

tag: surgery

value: M

tag: tum loc

value: RT/PCV


title: patid_174 [27K]

description: glioma

label: Cy5 and Cy49

value: deceased

value: no loss

value: unmeth

value: AOA

tag: perf

tag: trt

value: RT


title: patid_84 [27K]

description: glioma

label: Cy5 and Cy54

tag: os (years)

tag: os event

value: prog

value: mut


title: patid_182 [27K]

description: glioma

label: Cy5 and Cy56

tag: pfs (years)

tag: pfs event

value: CIMP-

value: wt

value: amp


title: patid_147 [27K]

description: glioma

label: Cy5 and Cy50

tag: cimp

value: CIMP+

value: LOH

value: meth

value: AOD

tag: age


title: patid_30 [27K]

description: glioma

label: Cy5 and Cy53

value: F


title: patid_507

tag: gender

value: M


title: patid_58 [27K]

description: glioma

label: Cy5 and Cy60

value: alive

value: no prog

tag: igs

value: RT/PCV


title: patid_218

value: deceased

value: no loss

tag: egfr


title: patid_259 [27K]

description: glioma

label: Cy5 and Cy46

tag: mgmt


title: siHic5 VC 3

description: PShTert-AR

source_name: 24hr Hic-5 siRNA, 16hr vehicle treatment replicate 3

tag: cell type

value: Immortalized AR positive myofibroblast


title: patid_299

value: prog

value: unmeth

tag: or diagn

value: AOA

value: RT


title: patid_57 [27K]

description: glioma

label: Cy5 and Cy43

value: mut

value: wt

tag: rev diagn

tag: Sex


title: patid_27 [27K]

description: glioma

label: Cy5 and Cy44

value: CIMP+

value: LGG

tag: surgery

tag: tum loc


title: siHic5 DHT 2

description: PShTert-AR

source_name: 24hr Hic5 siRNA, 16hr 10nM DHT treatment replicate 2


title: siHic5 DHT 1

description: PShTert-AR

source_name: 24hr Hic5 siRNA, 16hr 10nM DHT treatment replicate 1


title: patid_31 [27K]

description: glioma

label: Cy5 and Cy47

value: LOH

value: meth

value: AOD

tag: perf

tag: trt


title: patid_99 [27K]

description: glioma

label: Cy5 and Cy48

tag: os (years)

tag: os event

value: amp

value: AA/GBM

value: F


title: patid_72 [27K]

description: glioma

label: Cy5 and Cy45

value: deceased

tag: pfs (years)

tag: pfs event

value: CIMP-


title: patid_301 [27K]

description: glioma

label: Cy5 and Cy42

value: alive

value: no prog

tag: cimp

tag: age

value: RT/PCV


title: patid_242 [27K]

description: glioma

label: Cy5 and Cy40

value: prog

tag: igs

value: M


title: patid_239 [27K]

description: glioma

label: Cy5 and Cy41

value: no loss

tag: egfr

value: RT


title: siHic5 VC 1

description: PShTert-AR

label: biotin

source_name: 24hr Hic-5 siRNA, 16hr vehicle treatment replicate 1

value: Immortalized AR positive myofibroblast


title: patid_270

label: Cy5 and Cy3

value: CIMP+

value: mut

value: wt

tag: mgmt

tag: gender


title: patid_200

value: meth

tag: or diagn

value: AOD


title: patid_64 [27K]

description: glioma

label: Cy5 and Cy39

tag: rev diagn


title: patid_60 [27K]

description: glioma

label: Cy5 and Cy38

value: LOH

tag: Sex


title: patid_246

value: amp

tag: surgery

value: F


title: siHic5 VC 2

description: PShTert-AR

source_name: 24hr Hic-5 siRNA, 16hr vehicle treatment replicate 2

tag: cell type


title: ns DHT 2

description: PShTert-AR

source_name: 24hr non-specific siRNA, 16hr 10nM DHT treatment replicate 2


title: patid_206 [27K]

description: glioma

label: Cy5 and Cy36

value: AOA

tag: tum loc

tag: perf


title: patid_3

tag: os (years)

value: deceased

tag: trt


title: patid_96 [27K]

description: glioma

label: Cy5 and Cy37

tag: os event

tag: pfs (years)

value: unmeth


title: patid_215

tag: pfs event

tag: cimp

value: LGG

value: RT/PCV


title: ns DHT 3

description: PShTert-AR

source_name: 24hr non-specific siRNA, 16hr 10nM DHT treatment replicate 3


title: patid_213 [27K]

description: glioma

label: Cy5 and Cy34

value: prog

value: CIMP-

tag: igs

tag: age


title: Xpatid_4

tag: egfr

tag: mgmt


title: Xpatid_175

value: no loss

tag: or diagn

tag: gender


title: Xpatid_171

tag: rev diagn

value: RT


title: ns DHT 1

description: PShTert-AR

source_name: 24hr non-specific siRNA, 16hr 10nM DHT treatment replicate 1

value: Immortalized AR positive myofibroblast


title: ns VC 3

description: PShTert-AR

source_name: 24hr non-specific siRNA, 16hr vehicle treatment replicate 3


title: Xpatid_324

value: CIMP+

value: mut

tag: surgery

value: M


title: patid_118 [27K]

description: glioma

label: Cy5 and Cy33

value: alive

value: no prog

value: wt

value: meth

value: AOD

tag: Sex


title: ns VC 2

description: PShTert-AR

source_name: 24hr non-specific siRNA, 16hr vehicle treatment replicate 2

tag: cell type


title: patid_326a [27K]

description: glioma

label: Cy5 and Cy57

value: deceased

value: LOH

tag: tum loc

tag: perf


title: Xpatid_194

tag: os (years)

value: amp

value: AOA

tag: trt


title: Xpatid_135

tag: os event

tag: pfs (years)

value: prog


title: patid_104 [27K]

description: glioma

label: Cy5 and Cy32

tag: pfs event

tag: cimp

value: unmeth

value: F


title: patid_214a [27K]

description: glioma

label: Cy5 and Cy31

value: CIMP-

tag: igs

value: no loss

tag: age

value: RT


title: patid_312 [27K]

description: glioma

label: Cy5 and Cy30

tag: egfr

tag: mgmt


title: patid_248 [27K]

description: glioma

label: Cy5 and Cy28

value: CIMP+

value: mut

tag: or diagn


title: patid_266 [27K]

description: glioma

label: Cy5 and Cy27

value: alive

tag: rev diagn

value: M

value: RT/PCV


title: patid_164 [27K]

description: glioma

label: Cy5 and Cy29

value: wt

value: AA/GBM

tag: surgery


title: patid_338 [27K]

description: glioma

label: Cy5 and Cy26

value: deceased

value: meth

tag: Sex


title: lacZ shRNA 2

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description: lacZ-48 hrs-2

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Array quality was verified before background correction, RMA normalization and log2 conversion using the Bioconductor R package affy (URL: http://www.bioconductor.org).

source_name: A673 Ewing sarcoma cells

label_protocol: 100 ng of total RNA was submitted to the DFCI Microarray Core Facility for biotin labelling and hybridization to Affymetrix HuGene 1.0 ST Arrays.

growth_protocol: A673 cells were obtained from American Type Culture Collection (ATCC) and cultured in DMEM with 10% FCS and RPMI-1640 20 with 15% FCS.

extract_protocol: RNA was extracted with Agilent's Absolutely RNA kit.

treatment_protocol:
For knock down experiments,  A673 cells were grown to 30-35% confluence in 100 mm dishes at which point growth medium was removed and 5 ml fresh medium added along with 5 ml of virus and Polybrene at a final concentration of 8 μg/ml. After 24 hours, medium was replaced with 2 ml fresh growth medium containing puromycin at 4 μg/ml. Cells were selected for 48 hours, then harvested for Western-blot and RNA extraction.
For drug treatment experiments, A673 cells were grown to 65% confluence and then were either left untreated or treated for 24hrs with DMS0 or actinomycin D at low- (5nM) or high-dose (50nM).

tag: source material

value: EWS-FLI1-rearranged cell line

tag: cell line

tag: treatment

value: lacZ shRNA


title: WT648

city: Chicago

first: Bohao

last: Chen

state: IL

address: 5841 S. Maryland Ave

department: Medicine

country: USA

institute: University of Chicago

description: WT biological rep3

hyb_protocol: Following fragmentation, 35 ug of cRNA were hybridized for 16 hr at 45C in a hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Raw data were processed by Affymetrix Expression Console Build v1.3.0.187 using RMA and MAS5 Algorithm. Average intensity data at probe level were background subtracted, log2 transformed, and Quantile normalized.

source_name: Mouse lung wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (GeneChip Expression Analysis Technical Manual Rev5, Affymetrix).

growth_protocol: mouse left lungs were collected from 8-week-old Gata5 KO and wt mice.

extract_protocol: Trizol extraction of total RNA and RNeasy kit cleanup were performed according to the manufacturer's instructions

tag: tissue

value: left lung

tag: genotype

value: Wild Type


title: lacZ shRNA 1

description: lacZ-48 hrs-1


title: FLI1 shRNA 2

description: Fli-1917-48 hrs-2

value: FLI1 shRNA


title: FLI1 shRNA 1

description: Fli-1917-48 hrs-1


title: WT659

description: WT biological rep4


title: patid_103 [27K]

description: glioma

label: Cy5 and Cy25

tag: os (years)

tag: os event

value: prog

value: AOD

value: AOA

value: F

tag: tum loc

tag: perf

tag: trt


title: Xpatid_196

tag: pfs (years)

tag: pfs event

tag: cimp

value: CIMP-

tag: igs

value: no loss

value: unmeth

tag: age

tag: gender

value: RT


title: Xpatid_326

value: CIMP+

value: mut

value: LOH

tag: egfr

value: wt

tag: mgmt

tag: or diagn

tag: rev diagn

tag: surgery

value: M

value: RT/PCV


title: Xpatid_145

value: deceased

value: meth


title: Xpatid_309


title: patid_298 [27K]

description: glioma

label: Cy5 and Cy24

value: alive

value: no prog

tag: Sex


title: patid_111 [27K]

description: glioma

label: Cy5 and Cy35

tag: os (years)

value: prog

value: amp

value: AOD


title: WT619

description: WT biological rep1

label: biotin

tag: tissue

value: left lung

tag: genotype

value: Wild Type


title: Xpatid_259

label: Cy5 and Cy3

tag: os event

value: no loss

value: unmeth

value: AOA

tag: tum loc

tag: perf


title: 50nM actinomycin D 2

description: 50 nM-24 hrs-2

tag: source material

value: EWS-FLI1-rearranged cell line

tag: cell line

tag: treatment

value: 50 nM actinomycin D


title: patid_212 [27K]

description: glioma

label: Cy5 and Cy23

tag: pfs (years)

tag: pfs event

tag: cimp

value: CIMP+

tag: igs

value: mut

value: LOH

value: wt

tag: age

value: F

tag: trt


title: KO618

description: KO biological rep1

source_name: Mouse lung Gata5 knockout

value: Gata5 KO


title: patid_176 [27K]

description: glioma

label: Cy5 and Cy21

value: deceased

value: CIMP-

tag: egfr

tag: mgmt

value: meth

tag: or diagn

tag: rev diagn

tag: surgery

value: RT/PCV


title: KO624

description: KO biological rep3

tag: tissue

value: left lung

tag: genotype


title: Xpatid_85

tag: os (years)

tag: os event

value: prog

value: amp

value: AOD

tag: gender

tag: tum loc

tag: perf


title: Xpatid_149

value: alive

tag: pfs (years)

tag: pfs event

value: no prog

value: no loss

value: AOA

value: M


title: Xpatid_33

tag: cimp

value: CIMP+

tag: igs

value: mut


title: Xpatid_170

value: wt

tag: age

tag: trt


title: 5nM actinomycin D 1

description: 5 nM-24 hrs-1

tag: source material

value: EWS-FLI1-rearranged cell line

tag: cell line

tag: treatment

value: 5 nM actinomycin D


title: KO621

description: KO biological rep2

value: Gata5 KO


title: Xpatid_154

tag: egfr

tag: mgmt

value: meth

tag: or diagn

tag: rev diagn

tag: surgery


title: C.albicans infected zebrafish_18hpi_rep2

city: Hsin-chu

first: Yan-Yu

address: No. 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

country: Taiwan

institute: NTHU

description: Gene expression after 18hr in C. albicans infected zebrafish

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

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

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

organism: Danio rerio

source_name: C.albicans infected zebrafish_18hpi

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

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

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

tag: tissue

value: whole fish

tag: gender

value: male

value: 6 months


title: patid_236 [27K]

description: glioma

label: Cy5 and Cy20

tag: os (years)

tag: os event

value: LOH

tag: Sex

tag: tum loc

tag: perf

value: RT


title: C.albicans infected zebrafish_18hpi_rep3

treatment_protocol: Each fish was intraperitoneally injected with 1×10^8 C. albicans cells suspended in 10μL sterile 1× phosphate-buffered saline (PBS)

tag: age


title: WT623

description: WT biological rep2

value: left lung

tag: genotype

value: Wild Type


title: DMSO control 1

description: DMSO-24 hrs-1

tag: source material

value: DMSO


title: DMSO control 2

description: DMSO-24 hrs-2

tag: cell line


title: C.albicans infected zebrafish_18hpi_rep1


title: 50nM actinomycin D 1

description: 50 nM-24 hrs-1

tag: treatment

value: 50 nM actinomycin D


title: C.albicans infected zebrafish_16hpi_rep3

description: Gene expression after 16hr in C. albicans infected zebrafish

source_name: C.albicans infected zebrafish_16hpi


title: untreated control 2

description: 0 time control-2

value: control


title: ns VC 1

description: PShTert-AR

source_name: 24hr non-specific siRNA, 16hr vehicle treatment replicate 1

tag: cell type

value: Immortalized AR positive myofibroblast


title: patid_249 [27K]

description: glioma

label: Cy5 and Cy19

source_name: glioma

value: deceased

tag: pfs (years)

tag: pfs event

value: prog

tag: cimp

value: CIMP-

tag: igs

value: no loss

tag: egfr

value: amp

tag: mgmt

value: AOD

value: M

tag: trt

value: RT/PCV


title: Xpatid_335

source_name: Glioma

tag: os (years)

tag: os event

value: CIMP+

value: mut

value: meth

tag: or diagn

value: AOA

tag: rev diagn

value: AA/GBM

tag: surgery

tag: gender


title: Xpatid_1

tag: age

value: F

tag: tum loc

tag: perf

value: RT


title: 5nM actinomycin D 2

description: 5 nM-24 hrs-2

tag: source material

value: EWS-FLI1-rearranged cell line

tag: cell line

tag: treatment

value: 5 nM actinomycin D


title: patid_187 [27K]

description: glioma

label: Cy5 and Cy22

value: deceased

tag: pfs (years)

tag: pfs event

tag: cimp

value: wt

tag: Sex


title: Xpatid_53

value: alive

value: no prog

tag: igs

value: LOH

tag: egfr

tag: mgmt

value: LGG

tag: trt


title: patid_190 [27K]

description: glioma

label: Cy5 and Cy17

tag: os (years)

tag: os event

value: prog

value: no loss

tag: or diagn

tag: rev diagn

value: M


title: C.albicans infected zebrafish_16hpi_rep2

tag: tissue

value: whole fish

tag: gender

value: male

tag: age

value: 6 months


title: patid_110 [27K]

description: glioma

label: Cy5 and Cy15

value: CIMP-

value: amp

value: unmeth

value: AOD

value: AOA

tag: surgery

tag: tum loc

tag: perf

value: RT/PCV


title: patid_42 [27K]

description: glioma

label: Cy5 and Cy14

value: deceased

tag: pfs (years)

tag: pfs event

value: wt

value: F

value: RT


title: Heart_3wks_female_transgenic_mildline_rep1

city: Cleveland

first: Andrea

last: Ladd

state: OH

address: 9500 Euclid Avenue

department: Cell Biology

hyb_protocol: Hybridization protocol cRNA was quantified using a nanodrop spectrophotometer and the cRNA quality (size distribution) was further analyzed on a 1% agarose gel. cRNA was hybridized to the Illumina RatRef-12 v1 Expression BeadChip using standard protocols (provided by Illumina, San Diego, CA). Individual hybridizations were performed on each sample, and no pooling of samples took place. Hybridization performed by the Cleveland Clinic Lerner Research Institutes Genomics Core.

scan_protocol: Scan protocol Scan and Imaging procedures adhered strictly to standard protocols provided by Illumina, San Diego, CA.

data_processing: Illumina Genome Studio was used to generate the raw datafiles. The summarized data from the raw microarray data were log2 transformed and processed with force-positive background correction and quantile normalized, all using R statistical packages. Further, linear models and empirical Bayes method in Limma (Smyth, 2004) were used to access the differential expression between the wild types and transgenics. Quality control analyses were applied to detect the outlier samples.

label: Biotin

source_name: heart, MHC-CELF∆ transgenic, mild line

label_protocol: Label protocol 250 ng of RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX). cDNA library preparation performed by the Cleveland Clinic Lerner Research Institutes Genomics Core.

growth_protocol: Mice were housed in microinsular cages in a dedicated mouse room in the Lerner Research Institute’s Biological Resources Unit. Animals were fed a standard diet.

extract_protocol: Mice were euthanized by carbon dioxide inhalation followed by cervical dislocation, and hearts were excised postmortem. Hearts were homogenized in Trizol (Invitrogen) and total RNA was extracted following the manufacturer’s protocol. RNA samples were DNase-treated using the DNA-free Kit (Ambion) and cleaned up using the RNeasy Kit (Qiagen) following manufacturer’s protocols. RNA concentrations and quality were confirmed on a Nanodrop ND-1000 spectrophotometer and Agilent Bio-analyzer.

tag: strain

value: FVB/N

tag: transgenic line

tag: genotype/variation

value: transgenic

value: female

value: 3 weeks

value: heart


title: C.albicans infected zebrafish_16hpi_rep1

value: whole fish

value: male


title: Xpatid_199

value: alive

value: no prog

tag: cimp

value: CIMP+

tag: igs

value: LOH

tag: egfr

tag: mgmt

value: meth

value: M


title: patid_197 [27K]

description: glioma

label: Cy5 and Cy18

tag: os (years)

tag: os event

value: deceased

value: prog

value: CIMP-

value: no loss

value: unmeth

tag: or diagn

value: AOA

tag: Sex

tag: trt


title: Heart_3wks_female_transgenic_mildline_rep3

institute: Cleveland Clinic Lerner Research Institute

value: FVB/N

value: transgenic

tag: gender

value: female

tag: age

tag: tissue


title: untreated control 1

description: 0 time control-1

tag: source material

value: EWS-FLI1-rearranged cell line

tag: cell line

tag: treatment

value: control


title: Heart_3wks_female_transgenic_mildline_rep2

tag: strain

tag: transgenic line

value: 3 weeks

value: heart


title: C.albicans infected zebrafish_12hpi_rep3

description: Gene expression after 12hr in C. albicans infected zebrafish

source_name: C.albicans infected zebrafish_12hpi

value: whole fish

value: male

value: 6 months


title: Xpatid_189

tag: pfs (years)

tag: pfs event

tag: cimp

value: CIMP+

value: mut

tag: rev diagn

tag: surgery

value: M

tag: tum loc

tag: perf

value: RT


title: patid_152 [27K]

description: glioma

label: Cy5 and Cy16

tag: os (years)

tag: os event

value: alive

value: no prog

value: CIMP-

tag: igs

value: wt

value: no loss

tag: egfr

tag: mgmt

value: meth

tag: or diagn

value: AOD

tag: Sex

value: RT/PCV


title: patid_100 [27K]

description: glioma

label: Cy5 and Cy13

value: deceased

value: prog

tag: age

value: F

tag: trt


title: C.albicans infected zebrafish_12hpi_rep2

tag: tissue

value: whole fish

tag: gender

value: male


title: Heart_3wks_female_wildtype_mildline_rep3

source_name: heart, wild type

tag: strain

value: FVB/N

tag: transgenic line

tag: genotype/variation

value: wild type

value: female

value: 3 weeks

value: heart


title: C.albicans infected zebrafish_12hpi_rep1

value: 6 months


title: patid_73 [27K]

description: glioma

label: Cy5 and Cy12

value: alive

tag: pfs (years)

tag: pfs event

value: no prog

tag: cimp

value: CIMP-

value: unmeth

tag: rev diagn

tag: surgery


title: Heart_3wks_female_wildtype_mildline_rep1


title: patid_26 [27K]

description: glioma

label: Cy5 and Cy11

tag: os (years)

tag: os event

tag: igs

value: wt

value: no loss

value: amp

value: meth

value: AOD

value: M

tag: tum loc

tag: perf

value: RT


title: patid_22 [27K]

description: glioma

label: Cy5 and Cy10

value: deceased

value: prog

tag: egfr

tag: mgmt

tag: or diagn

value: AOA

tag: age

tag: Sex


title: Xpatid_129

value: CIMP+

value: LGG

tag: gender

value: F

tag: trt


title: C.albicans infected zebrafish_8hpi_rep2

description: Gene expression after 8hr in C. albicans infected zebrafish

source_name: C.albicans infected zebrafish_8hpi

tag: tissue

value: whole fish

value: male

value: 6 months


title: Xpatid_339

tag: pfs (years)

tag: pfs event

value: mut


title: C.albicans infected zebrafish_8hpi_rep3


title: C.albicans infected zebrafish_8hpi_rep1


title: Heart_3wks_female_transgenic_sevline_rep3

source_name: heart, MHC-CELF∆ transgenic, severe line

tag: strain

value: FVB/N

tag: transgenic line

tag: genotype/variation

value: transgenic

value: female

value: 3 weeks

value: heart


title: C.albicans infected zebrafish_6hpi_rep2

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

source_name: C.albicans infected zebrafish_6hpi


title: Heart_3wks_female_transgenic_sevline_rep2


title: Heart_3wks_female_transgenic_sevline_rep1


title: Xpatid_67

tag: os (years)

tag: os event

tag: cimp

value: CIMP-

value: wt

value: no loss

tag: rev diagn

value: AA/GBM

tag: surgery


title: Xpatid_12

value: deceased

value: prog

tag: igs

value: LOH

tag: egfr

tag: mgmt

value: AOD

tag: tum loc

tag: perf

value: RT


title: Xpatid_20

value: alive

value: no prog

value: CIMP+

tag: or diagn

tag: age

tag: gender

value: M

tag: trt

value: RT/PCV


title: C.albicans infected zebrafish_6hpi_rep3

tag: tissue

value: whole fish

value: male

value: 6 months


title: Xpatid_75

tag: pfs (years)

tag: pfs event

value: mut


title: Heart_3wks_female_wildtype_mildline_rep2

tag: strain

value: FVB/N

tag: transgenic line

tag: genotype/variation

value: wild type

value: female

value: 3 weeks

value: heart


title: patid_32 [27K]

description: glioma

label: Cy5 and Cy7

tag: os (years)

tag: os event

value: deceased

value: prog

tag: cimp

value: LOH

value: wt

value: meth

tag: rev diagn

tag: Sex

value: F


title: patid_94 [27K]

description: glioma

label: Cy5 and Cy8

value: CIMP+

tag: igs

tag: egfr

tag: mgmt

value: AOD

tag: surgery

value: M

tag: tum loc


title: C.albicans infected zebrafish_6hpi_rep1

value: whole fish

tag: gender

value: male

tag: age


title: Xpatid_314

label: Cy5 and Cy3

tag: pfs (years)

value: mut

tag: or diagn

value: AOA

tag: perf

tag: trt

value: RT


title: C.albicans infected zebrafish_4hpi_rep3

description: Gene expression after 4hr in C. albicans infected zebrafish

source_name: C.albicans infected zebrafish_4hpi

tag: tissue

value: 6 months


title: C.albicans infected zebrafish_4hpi_rep2


title: patid_143 [27K]

description: glioma

label: Cy5 and Cy6

tag: os (years)

tag: pfs event

value: CIMP-

value: no loss

value: amp

value: RT/PCV


title: Xpatid_155

tag: os event

value: alive

value: prog

tag: cimp

value: unmeth

value: AA/GBM


title: Heart_3wks_female_wildtype_sevline_rep3

tag: strain

value: FVB/N

tag: transgenic line

tag: genotype/variation

value: wild type

value: female

value: 3 weeks

value: heart


title: patid_208 [27K]

description: glioma

label: Cy5 and Cy5

value: deceased

tag: igs

value: wt

tag: egfr

tag: mgmt

value: meth

tag: rev diagn

value: AOD

tag: Sex

value: M


title: Heart_3wks_female_wildtype_sevline_rep1

growth_protocol: Mice were housed in microinsular cages in a dedicated mouse room in the Lerner Research Institute’s Biological Resources Unit.  Animals were fed a standard diet.

extract_protocol: Mice were euthanized by carbon dioxide inhalation followed by cervical dislocation, and hearts were excised postmortem.  Hearts were homogenized in Trizol (Invitrogen) and total RNA was extracted following the manufacturer’s protocol.  RNA samples were DNase-treated using the DNA-free Kit (Ambion) and cleaned up using the RNeasy Kit (Qiagen) following manufacturer’s protocols.  RNA concentrations and quality were confirmed on a Nanodrop ND-1000 spectrophotometer and Agilent Bio-analyzer.

tag: gender

tag: age


title: Xpatid_139

tag: pfs (years)

value: CIMP-

value: no loss

tag: or diagn

tag: surgery

tag: tum loc

tag: perf


title: Xpatid_138

tag: os (years)

tag: os event

tag: pfs event

tag: trt

value: RT/PCV


title: C.albicans infected zebrafish_4hpi_rep1

tag: tissue

value: whole fish

value: male

value: 6 months


title: patid_122 [27K]

description: glioma

label: Cy5 and Cy4

value: prog

tag: cimp

value: CIMP+

tag: igs

value: mut

value: AOA


title: C.albicans infected zebrafish_2hpi_rep3

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

source_name: C.albicans infected zebrafish_2hpi


title: patid_262 [27K]

description: glioma

tag: egfr

tag: mgmt

value: unmeth


title: Xpatid_257

tag: rev diagn


title: CarotidBif_IPH_pDC

city: Maastricht

first: Marco

last: Manca

state: Limburg

address: P. Debyelaan 25

department: CARIM

institute: University of Maastricht

description:
Array1
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid

hyb_protocol: 2.5 μg of labeled cDNA of each sample was applied to Affymetrix GeneChip Human Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA, USA).

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G and feature extraction was done by Gene Chip® Command Console 3.2 (AGCC) software.

data_processing:
The data were analyzed with R (v.2.13)/Bioconductor (v.2.8) using the package xps (v.1.12.1) and the most up to date .CDF (HuGene-1_0-st-v1.r3.cdf) available from the Affymetrix website at the time. .
The 'HuGene10stv1_Hs_ENTREZG_14.1.0' was used to summarize the probesets to Entrez Genes.

label: biotin

label_protocol: cDNA samples were enzymatically fragmented (input: 3 μg per sample) using the Ovation Pico WTA System V2 and biotin-labeled to the 3-hydroxyl end of the fragmented cDNA using the Encore Biotin Module (NuGEN Technologies).

extract_protocol: RNeasy Micro kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for extraction of RNA from microdissected cryosections. DNA was removed by using 50U DNase I (Qiagen). RNA samples were speed vacuum centrifuged to increase RNA concentration. Total RNA (500-750pg) of pDC-enriched and pDC-deficient plaque fractions was cDNA transcribed (double strand cDNA synthesis), purified (RNAClean beads) and amplified (Ribo-SPIA amplification process) using the Ovation Pico WTA System V2 (NuGEN Technologies, Bemmel, The Netherlands).

treatment_protocol: 4 mm thick OCT frozen sections were cut at -20°C in a cryostat (Leica CM 3050S) and placed on MembraneSlides (NF 1.0 PEN; Carl Zeiss Micro Imaging, Munich, Germany). Sections were fixed and dehydrated for 10 minutes in ice-cold sterile acetone before LCM (Palm Microlaser Technologies, Zeiss Microscope Palm Robo 4.3, Munich, Germany) to improve tissue catapulting. pDC-enriched and pDC-deficient plaque fractions from the very same plaque slices were isolated by LCM from 6-10 frozen tissue sections, respectively pooled and collected in nuclease and nucleid acid free tubes with an adhesive cap covered with tissue lysis buffer (RLT buffer) containing β-mercaptoethanol to improve RNA yield and minimize RNA degradation.

tag: age (yrs)

tag: gener

value: Human atherosclerotic plaque


title: Carotid_shoulder_NOpDC_4

description:
Array10
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid

source_name: Carotid_plaque shoulder_pDC-less

value: female


title: Carotid_shoulder_NOpDC_5

description:
Array11
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid


title: Xpatid_291

value: alive

tag: pfs (years)

value: no prog

value: LOH

value: wt

tag: age

tag: gender

value: RT


title: C.albicans infected zebrafish_2hpi_rep1


title: Carotid_shoulder_NOpDC_3

description:
Array9
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid


title: Xpatid_21

value: deceased

value: CIMP-

value: no loss

value: meth

tag: or diagn

value: AOD

tag: surgery

value: M

tag: tum loc


title: Carotid_shoulder_NOpDC_1

description:
Array7
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid


title: Carotid_shoulder_NOpDC_2

description:
Array8
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid

value: male


title: C.albicans infected zebrafish_1hpi_rep3

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

source_name: C.albicans infected zebrafish_1hpi

value: whole fish

value: 6 months


title: Carotid_shoulder_pDC

description:
Array6
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid

source_name: Carotid_plaque shoulder_pDC-enriched


title: Xpatid_216

tag: os (years)

tag: os event

value: prog

value: CIMP+

tag: perf


title: C.albicans infected zebrafish_2hpi_rep2

tag: tissue


title: Carotid_media_pDC_2

description:
Array5
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid

source_name: Carotid_between media and plaque_pDC-enriched

value: Human atherosclerotic plaque


title: Xpatid_271

value: alive

tag: pfs event

tag: cimp

value: mut

value: F

tag: trt


title: C.albicans infected zebrafish_0.5hpi_rep3

description: Gene expression after 0.5hr in C. albicans infected zebrafish

source_name: C.albicans infected zebrafish_0.5hpi


title: Xpatid_276

tag: igs

value: wt

tag: egfr

value: amp

tag: mgmt

value: AOA


title: C.albicans infected zebrafish_1hpi_rep2


title: Xpatid_36

value: deceased

value: CIMP-

tag: rev diagn

value: RT


title: Carotid_media_pDC_1

description:
Array4
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid

tag: age (yrs)

tag: gener


title: C.albicans infected zebrafish_0.5hpi_rep2

tag: gender

tag: age


title: C.albicans infected zebrafish_1hpi_rep1


title: Carotid_shoulder_pDC_2

description:
Array3
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid


title: Heart_3wks_female_wildtype_sevline_rep2

tag: strain

value: FVB/N

tag: transgenic line

tag: genotype/variation

value: wild type

value: female

value: 3 weeks

value: heart


title: Xpatid_300

tag: os (years)

tag: os event

tag: pfs (years)

value: no prog

value: LOH

value: meth

tag: or diagn

value: AOD

value: LGG

tag: surgery

tag: tum loc

value: RT/PCV


title: C.albicans infected zebrafish_0.5hpi_rep1

tag: tissue

value: whole fish

value: male

value: 6 months


title: Xpatid_115

value: alive

tag: pfs event

tag: cimp

value: CIMP+

tag: igs

value: mut

tag: egfr

value: wt

value: M

tag: perf

tag: trt


title: Carotid_shoulder_pDC_1

description:
Array2
Gene expression data from inflammatory region within human atherosclerotic plaques obtained from endarterectomy of the carotid

data_processing:
The data were analyzed with R (v.2.13)/Bioconductor (v.2.8) using the package xps (v.1.12.1), the most up to date .CDF (HuGene-1_0-st-v1.r3.cdf) available from the Affymetrix website at the time.
The 'HuGene10stv1_Hs_ENTREZG_14.1.0' was used to summarize the probesets to Entrez Genes.

tag: age (yrs)

tag: gener

value: female

value: Human atherosclerotic plaque


title: Xpatid_203

value: no loss

tag: mgmt

value: AOA

tag: rev diagn

tag: age

tag: gender

value: F


title: patid_217 [27K]

description: glioma

label: Cy5 and Cy9

tag: os (years)

tag: os event

value: deceased

tag: pfs (years)

value: prog

value: LOH

value: meth

tag: Sex

value: RT


title: Xpatid_220

value: no prog

tag: or diagn

value: LGG

tag: surgery

tag: tum loc


title: Xpatid_209

value: alive

tag: pfs event

tag: cimp

tag: igs

value: AOD

value: RT/PCV


title: GBM-C214

status: Public on Aug 25 2013

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
Gene expression data from surgical tumor sample of glioblastoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes.

source_name: brain tumor (glioblastoma)

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

extract_protocol: RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: brain tumor

tag: tissue

value: glioblastoma


title: GBM-868


title: GBM-873


title: GBM-C513


title: GBM-C313


title: GBM-D612


title: Xpatid_285

value: CIMP+

value: wt

tag: egfr

value: AA/GBM

value: M

tag: perf

tag: trt


title: GBM-B441


title: EPN-909

description:
Gene expression data from surgical tumor sample of ependymoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

source_name: brain tumor (ependymoma)

value: ependymoma


title: GBM-933


title: GBM-481


title: Xpatid_89

value: deceased

value: CIMP-

value: no loss

tag: mgmt

value: unmeth

value: AOA

tag: rev diagn

tag: age

value: F


title: GBM-C532


title: EPN-871


title: Xpatid_48

tag: os (years)

tag: os event

value: prog

value: mut

tag: gender

value: RT


title: Xpatid_185

tag: pfs (years)

value: meth

tag: or diagn


title: GBM-889

value: brain tumor


title: GBM-273

value: glioblastoma


title: GBM-012


title: GBM-C231


title: GBM-496


title: EPN-930


title: GBM-478


title: EPN-943


title: EPN-848


title: EPN-821


title: EPN-859


title: EPN-870


title: EPN-812


title: EPN-816


title: EPN-790


title: EPN-811


title: EPN-770


title: EPN-700


title: EPN-781


title: EPN-727


title: EPN-723


title: EPN-758


title: DeltaRacA.rep3

city: Leiden

first: Benjamin

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

institute: Leiden University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction, normalization and probe summarization steps were performed according to the default setting of the RMA package as implemented in Bioconductor.

organism: Aspergillus niger

source_name: whole fungal mycelium, racA deletion mutant, exponential growth phase

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol: Maltose-limited batch cultivation of the racA deletion mutant was initiated by inoculation of 5 L (kg) ammonium based minimal medium with conidial suspension to give 10 to the power of 9 conidia L per L. Maltose was sterilized separately from the MM and final concentration was 0.8% (w/v). Temperature was 30 °C and pH 3, kept constant by computer controlled addition of 2 M NaOH or 1 M HCl. Acidification of the culture broth was used as an indirect growth measurement (Iversen et al., 1994). Submerged cultivation was performed with 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific, NJ, USA). A more detailed description of the fermentation medium and cultivation is given in Jorgensen et al. (2010).  Batch cultivation for PglaA-RacAG18V or PglaA-RacA were run similarly as the maltose-limited batch cultivations of the racA deletion mutant cultures except that 0.75% xylose was used as a initial carbon source instead of maltose. When the exponential growth phase was over (indicated by sharp rise of dissolved oxygen tension as well as the pH value), 0.75% maltose was added to induce expression of PglaA-RacAG18V or PglaA-RacA. Samples for the analysis of morphological properties, biomass formation, protein yield and RNA were taken every hour.

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen) followed column purification including a DNAse I treatment.

tag: genotype

value: racA deletion

tag: time point

value: exp


title: EPN-534


title: EPN-507


title: EPN-483


title: wt.rep3

source_name: whole fungal mycelium, wild type, exponential growth phase

value: wild type


title: EPN-80


title: DeltaRacA.rep1


title: EPN-419


title: DeltaRacA.rep2


title: EPN-820


title: EPN-459


title: EPN-416


title: EPN-64


title: EPN-492


title: wt.rep2


title: GBM-C142


title: EPN-691


title: wt.rep1


title: EPN-393


title: EPN-392


title: EPN-388


title: PglA-RacA(G18V).4h.rep1

source_name: whole fungal mycelium, exponential growth phase, 4 hours after induction of racA G18V mutant allele expression


title: PglA-RacA(G18V).2h.rep1

source_name: whole fungal mycelium, exponential growth phase, 2 hours after induction of racA G18V mutant allele expression


title: PglA-RacA(G18V).4h.rep2


title: PglA-RacA(G18V).2h.rep2


title: PglA-RacA(wt).2h.rep1

source_name: whole fungal mycelium, exponential growth phase, 2 hours after induction of racA wild type allele expression

value: PglA-RacA(wt)


title: EPN-364

value: ependymoma


title: PglA-RacA(wt).4h.rep1

source_name: whole fungal mycelium, exponential growth phase, 4 hours after induction of racA wild type allele expression


title: EPN-321


title: EPN-318


title: Station GD 126 m Baltic #8B

status: Public on Aug 24 2013

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

description: 1000 ng random priming amplified DNA from Baltic seawater

hyb_protocol: Samples were hybridized to single or duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4200) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features in which the Cy3 signal was not at least twice the value of the control probes

molecule: other

organism: artificial sequences

source_name: 70-mer probe

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa.  The amplified product was post labeled by conjugation of Cy3 to the dUaa

extract_protocol: DNA was extracted from filtered samples using the Qiagen Allprep kit

tag: sample type

value: Universal Internal Standard + 70-mer

tag: std. molecule

value: 20-mer DNA oligo

tag: description

value: 70-mer probe

organism: aquatic metagenome

source_name: estuary seawater

tag: location, date

tag: location

tag: molecule

value: random priming amplified DNA


title: Station GD 126 m Baltic #7B


title: Station GD 123 m Baltic #6B


title: Pgla-RacA(wt).4h.rep2


title: Station GD 123 m Baltic #5B


title: PglA-RacA(wt).2h.rep2


title: EPN-333

tag: disease state

tag: tissue


title: EPN-319


title: EPN-246


title: Station LD 73 m Baltic #4B


title: SCFA receptor response (G43KO-1)

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled forHigh-Resolution Scanning. The instruments were controlled using GCOS version1.4 software.

data_processing: The data were condensed with MAS 5.0 using the GeneChip Operation Software.

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences Intl. Plymouth Meeting, PA).

extract_protocol: Trizol and Qiagen Total RNA isolation kit

tag: genotype/variation

value: GPR43 KO

tag: strain

value: 6-8 weeks

value: Colon


title: Station LD 73 m Baltic #3B


title: Station GB1 57 m Baltic #2B


title: SCFA receptor response (WT-2)

tag: age


title: EPN-135


title: EPN-195


title: SCFA receptor response (G43KO-2)


title: Bladder_HG7 [mRNA]

city: Berlin

first: Hellmuth-A

last: Meyer

address: Charitéplatz 1

department: Department of Urology

institute: Charite

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881461

hyb_protocol: Labeled samples were hybridized on human catalog 8-plex 15K miRNA microarrays (Agilent Technologies)  according to the supplier’s protocol.

scan_protocol: Microarrays were washed and subsequently scanned at 5 µm resolution with DNA microarray laser scanner (Agilent Technologies) and processed according to the supplier’s protocol.

data_processing: Expression files were generated using Agilent's Genespring GX software

source_name: Bladder

label_protocol: Samples were labeled using the miRNA Complete Labelling and Hyb Kit from Agilent Technologies. In brief, 100 ng total RNA was dephosphorylated with Calf Intestine Alkaline Phosphatase, denaturated with DMSO and used as RNA acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3’, 5’-cytidine bisphosphate (Cy3-pCp). The labeling reaction was column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.

extract_protocol: Total RNA including  mRNA and miRNA were extracted using the miRNAeasy Mini Kit (Qiagen, Hilden, Germany) following manufacturer`s instructions. An additional DNA digestion step on the RNA binding silica gel membrane of the spin column was performed with DNase I. RNA concentration and the absorbance ratio of 260 nm to 280 nm were measured on the NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of isolated RNA was determined by the RNA integrity number (RIN) with an Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

value: high-grade papillary urothelial carcinoma

tag: tumor stage

value: male


title: Station GD 126 m Baltic #8A


title: SCFA receptor response (G41KO-2)

value: GPR41 KO


title: Station GD 123 m Baltic #6A


title: Station GD 126 m Baltic #7A


title: EPN-285

value: brain tumor


title: SCFA receptor response (G41KO-1)


title: Station GD 123 m Baltic #5A


title: EPN-110


title: Bladder_HG6 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881460

tag: gender


title: Bladder_HG8 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881462


title: SCFA receptor response (WT-1)


title: Station LD 73 m Baltic #3A


title: Station GB1 57 m Baltic #2A


title: Bladder_HG4 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881458

value: femal


title: Station GB1 57 m Baltic #1A


title: Bladder_LG8 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881454

value: low-grade papillary urothelial carcinoma


title: Bladder_LG6 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881452


title: Bladder_HG5 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881459


title: Bladder_HG1 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881455


title: Bladder_HG3 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881457


title: Bladder_LG4 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881450


title: Bladder_HG2 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881456


title: Bladder_LG5 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881451


title: Station GB1 57 m Baltic #1B


title: Station LD 73 m Baltic #4A


title: Bladder_LG7 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881453


title: Rame Head RameJ08

description: PCR fragment,  amoA gene from ammonia oxidizing archaea, amplified from DNA extracted from marine sediments

data_processing: Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).

label_protocol: PCR amplification using the primers of Francis et al (2005) for array BC012 and the primers of Stephen et al 1996 and Hornek et al 2006 for array BC009.  The PCR fragments were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from homogenized sediments by bead beating followed by phenol:chloroform extraction (as in Laverock et al 2010).  Then cleaned using the PowerClean DNA Clean-Up Kit (MoBio, Carlsbad, CA, USA).

organism: marine sediment metagenome

source_name: marine sediment

value: Rame Head sediment sample July 2008

value: PCR fragment


title: Rame Head RameM09

value: Rame Head sediment sample March 2009


title: L4 WCO L4M09

value: L4 WCO sediment sample March 2009


title: L4 WCO L4J08

value: Universal Internal Standard + 70-mer

value: L4 WCO sediment sample July 2008


title: Bladder_N7 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881445

value: nonmaligant bladder


title: Station GD 126 m Baltic #7B

value: 20-mer DNA oligo

value: 70-mer probe

value: random priming amplified DNA


title: Bladder_LG3 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881449


title: Station LD 73 m Baltic #4B

description: 1000 ng random priming amplified DNA from Baltic seawater


title: Bladder_N8 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881446


title: Station GD 126 m Baltic #8B


title: Bladder_LG1 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881447


title: Station GD 123 m Baltic #6B


title: Bladder_N4 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881442


title: Station LD 73 m Baltic #3B


title: Station GB1 57 m Baltic #2B


title: Bladder_N5 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881443


title: Bladder_LG2 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881448


title: Wildtype liver_saline-injected 12weeks repl2

city: Bethesda

first: Yuri

last: Postnikov

state: MD

address: 37 Convent Dr

institute: NIH

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit: Affymetrix, P/N 900720, suppliers recommendations, mouse 430.2 Affymetrix expression array

scan_protocol: Agilent GeneArray Scanner

data_processing: Mouse Genome 430 2.0 array has 45101 probe sets associated with approximately 20000 Mouse Genome Informatics (MGI) gene identifiers. Probe sets were mapped to MGI identifiers using information provided by the Jackson Laboratory (http://www.informatics.jax.org/). Values in the Sample data tables were derived from MAS5 algorithm.

label_protocol: GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix, P/N 900493).

growth_protocol: Hmgn1+/+ and Hmgn1-/- littermates were generated by crossing heterozygous Hmgn1+/- male and female, DNA-tail-genotyping F1 mice and further propagating Hmgn1+/+ and Hmgn1-/- homozygotes separately

extract_protocol: Total RNA was isolated from frozen liver tissue with TRIzol followed by purification using RNeasy Kit.

treatment_protocol: At age of 4 weeks HMGN1 wildtype and knockout males received an injection of 10 µg/g body weight of N-nitrosodiethylamine or saline as a control.

value: Liver

tag: treatment

value: injection of 10 µg/g body weight of saline


title: CD11c

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
AR1264_04
FACS-sorted CD14- CD11c high cells derived from HLA-DRhigh lineage- (Lin-) lamina propria cell (LPC) subsets in non-invaded colonic tissue samples from individual colorectal cancer patient (n=10).

hyb_protocol: After labeling, the labeled 2 ug of each cDNA sample was then hybridized on Agilent-039494 SurePrint G3 Human GE 8x60K v2 Microarray at 65°C for 17 h with rotation in the dark. Hybridization was performed using a Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturer's instructions. Slides were washed in GE washing buffer.

scan_protocol: Slides were scanned with an Agilent Microarray Scanner G2505C.

data_processing: Agilent Feature Extraction software (Version 10.10.1.1) was used to convert images into gene expression data. Raw data were imported into GeneSpring GX 11.0 (Agilent Technologies) for database management and quality control. This normalized data without the threshold raw signal and the global normalization algorithm was used for identifying differentially expressed genes.

source_name: FACS-sorted CD14- CD11c high cells

label_protocol: Twenty nanogram of total RNA was reverse transcribed into double strand cDNAs by using an Ovation® Pico WTA System V2 (NuGen) following manufacturer's protocol. Resulting cDNAs were subsequently used for in vitro transcription by DNA polymerase and labeled with cyanine-3 using a Genomic DNA Enzymatic Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA extracted using RNeasy following manufacturer's instructions.

treatment_protocol: Intestinal mucosa samples were obtained from patients who underwent resection of colorectal cancer or CD. Lamina propria cells (LPCs) were obtained by enzymatic digestion, and were analyzed for expression of HLA-DR, lineage markers (Lin), CD14, and CD163 using flow cytometry.

tag: tissue source

value: non-invaded colonic tissue from colorectal cancer patient

tag: cell source

value: HLA-DRhigh lineage- (Lin-) lamina propria cell (LPCs)

tag: cell type

value: CD14- CD11c high cells


title: Bladder_N3 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881441

value: male


title: Bladder_N6 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881444


title: Knockout liver_saline-injected 12weeks repl3


title: Wildtype liver_saline-injected 12weeks repl3


title: Knockout liver DEN-injected 12weeks repl2

value: injection of 10 µg/g body weight of N-nitrosodiethylamine


title: Wildtype liver_saline-injected 12weeks repl1


title: Bladder_N1 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881439


title: Knockout liver_saline-injected 12weeks repl1


title: Station GD 126 m Baltic #8A

tag: sample type


title: CD163 high

description:
AR1264_01
FACS-sorted CD14+ CD163 high cells derived from HLA-DRhigh lineage- (Lin-) lamina propria cell (LPC) subsets in non-invaded colonic tissue samples from individual colorectal cancer patient (n=10).

source_name: FACS-sorted CD14+ CD163 high cells

value: CD14+ CD163 high cells


title: CD163 low

description:
AR1264_02
FACS-sorted CD14+ CD163 low cells derived from HLA-DRhigh lineage- (Lin-) lamina propria cell (LPC) subsets in non-invaded colonic tissue samples from individual colorectal cancer patient (n=10).

source_name: FACS-sorted CD14+ CD163 low cells

value: CD14+ CD163 low cells


title: Station GD 126 m Baltic #7A

tag: std. molecule


title: Knockout liver DEN-injected 12weeks repl3


title: DN

description:
AR1264_03
FACS-sorted CD14- CD11c low cells derived from HLA-DRhigh lineage- (Lin-) lamina propria cell (LPC) subsets in non-invaded colonic tissue samples from individual colorectal cancer patient (n=10).

source_name: FACS-sorted CD14- CD11c low cells

value: CD14- CD11c low cells


title: Station GD 123 m Baltic #6A

tag: description


title: Knockout liver DEN-injected 12weeks repl1


title: Station GD 123 m Baltic #5A

tag: location, date


title: Station LD 73 m Baltic #4A

tag: location


title: Wildtype liver DEN-injected 12weeks repl3


title: Station GB1 57 m Baltic #2A

tag: molecule


title: Station GB1 57 m Baltic #1A


title: Rame Head RameM09B

description: PCR fragment,  amoA gene from ammonia oxidizing bacteria amplified from DNA extracted from marine sediments

value: Rame Head sediment sample July 2008

value: PCR fragment


title: L4 WCO L4M09B

value: Universal Internal Standard + 70-mer

value: L4 WCO sediment sample March 2009


title: Station LD 73 m Baltic #3A

value: 20-mer DNA oligo


title: Knockout liver_saline-injected 12weeks repl2


title: Bladder_N2 [mRNA]

description: mRNA Gene expression corresponds to miRNA Data archived under: GSM881440

value: nonmaligant bladder


title: L4 WCO L4J08B

value: 70-mer probe

value: L4 WCO sediment sample July 2008


title: Rame Head RameJ08A


title: Rame Head RameM09A

value: Rame Head sediment sample March 2009


title: Wildtype liver DEN-injected 12weeks repl2

value: Liver


title: Knockout liver non-injected 4weeks rep2

source_name: Knockout liver non-injected 4weeks rep2


title: L4 WCO L4J08A


title: L4 WCO L4M09A


title: Knockout liver non-injected 4weeks rep3

source_name: Knockout liver non-injected 4weeks rep3


title: Wildtype liver DEN-injected 12weeks repl1


title: Wildtype liver non-injected 4weeks rep3

source_name: Wildtype liver non-injected 4weeks rep3


title: Knockout liver non-injected 4weeks rep1

source_name: Knockout liver non-injected 4weeks rep1


title: OC8-MDSC-2 (set2)

status: Public on Aug 23 2013

city: Ann Arbor

first: Ilona

last: Kryczek

address: 1150 W. Medical Center Dr.

institute: University of Michigan

description:
Sample name: Array 4 (Set 2)
primary ovarian caner cell line (OC8) primed with Myeloid supressor cells from patient 2 (MDSC2) (MDSC for set 2)

data_processing: miRNAs were normalized to the average U6 from the pool in which they were processed. "NA" in raw Ct indicates non-detectable miRs in our cells.

label: FAM

source_name: OC8 cells primed with MDSC

label_protocol: Samples were processed using the Manufaturers protocol titled: TaqMan OpenArray MicroRNA Panels Publication, Part Number 4461306 Rev. C, Revision Date June 2011

extract_protocol: RNA was extracted from the cancer cells by Trizol reagent.

tag: set

tag: cell line

value: Primary ovarian cancer cells (OC8)

tag: co-cultured with

value: MDSC


title: OC8-Control (set 1)

description:
Sample name: Array 1 (Set 1)
primary ovarian caner cell line (OC8) primed with medium (Control for set 1)

source_name: OC8 cells primed with medium

value: medium


title: OC8-Monocytes-3 (set 2)

description:
Sample name: Array 5 (Set 2)
primary ovarian caner cell line (OC8) primed with monocytes from healthy donor (monocytes for set 2)

source_name: OC8 cells primed with monocytes

value: monocytes


title: OC8-Control (set 2)

description:
Sample name: Array 3 (Set 2)
primary ovarian caner cell line (OC8) primed with medium (Control for set 2)


title: OC8-MDSC-1 (set 1)

description:
Sample name: Array 2 (Set 1)
primary ovarian caner cell line (OC8) primed with Myeloid supressor cells (MDSC1) (MDSC for set 1)


title: Wildtype liver non-injected 4weeks rep1

source_name: Wildtype liver non-injected 4weeks rep1

tag: tissue

tag: genotype/variation


title: Wildtype liver non-injected 4weeks rep2

source_name: Wildtype liver non-injected 4weeks rep2


title: S. paradoxus CBS432

city: Rehovot

first: Zvi

last: Tamari

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Samples were hybridized using standard Agilent protocol

scan_protocol: Images were analyzed using Agilent's Feature Extraction software

data_processing: Agilent Feature Extraction Software was used for background detrending and linear LOWESS normalization.

organism: Saccharomyces paradoxus

source_name: S. paradoxus CBS432

label_protocol: The samples were amplified and labeled using agilent two-color Low Input QuickAmp Labeling Kit

growth_protocol: Strains were grown to mid-log phase in YP-glucose or YP-xylulose medium.

extract_protocol: Total RNA was extracted using MasterPure™ Yeast RNA purification Kit (Epicentre)

tag: strain

tag: condition

value: xylulose

value: glucose


title: S. paradoxus YPS138

source_name: S. paradoxus YPS138


title: S. paradoxus DBVPG6466

source_name: S. paradoxus DBVPG6466


title: S. paradoxus N45

source_name: S. paradoxus N45


title: S. paradoxus UWOPS91-917.1

source_name: S. paradoxus UWOPS91-917.1


title: S. paradoxus Z1

source_name: S. paradoxus Z1


title: S. paradoxus N17

source_name: S. paradoxus N17


title: S. paradoxus Q69.8

source_name: S. paradoxus Q69.8


title: S. paradoxus N43

source_name: S. paradoxus N43


title: S. paradoxus Q31.4

source_name: S. paradoxus Q31.4


title: S. paradoxus Y8.1

source_name: S. paradoxus Y8.1


title: Blood_DSA_rejection_28

city: Bronx

first: Pilib

last: Ó Broin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Gene expression data from DSA blood sample

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term. Biopsy and blood sample were processed separately.

source_name: DSA+ and acute or chronic rejection

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Biopsy cores were immediately placed into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation.  Renal tissue content in all cores was verified using a dissecting microscope and non-renal tissue was removed. For whole blood gene expression analysis, 2.5 ml of patient’s peripheral blood was collected into one PAXgene RNA Tube (Qiagen, Valencia, CA) containing lysis buffer and RNA-stabilizing solution. Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA) and QIAGEN PAXgene Blood RNA Kit (Catalog Number 762164, Qiagen, Valencia, CA) for biopsy and blood samples respectively.

treatment_protocol: Biopsies were examined by light microscopy using hematoxylin and eosin, periodic acid-Schiff, trichrome and C4d immunoperoxidase stains and scored using the Banff criteria. Immunoperoxidase staining for C4d was performed on paraffin embedded sections using a polyclonal rabbit anti-human antibody (Cell Marque) at a dilution of 1:100 with the Dako Envision system. Positive peritubular capillary C4d staining was scored minimal (c4d1), focal (c4d2) or diffuse (c4d3) when there was uniform finely granular decoration involving more than 1-10%, 11-50% and greater than 50% for minimal, focal and diffuse respectively. Anti-HLA antibodies were studied by Luminex HLA Single Antigen Bead assays (LABScreen, One Lambda Inc., Canoga Park, CA) that utilize a panel of color-coded beads coated with purified single HLA antigens. The beads include HLA A, B, Cw, DR, and DQ antigens. The antibody specificity and strength were analyzed with HLA Fusion software V2.0 (One Lambda Inc.). The cutoff value for a positive DSA was a mean fluorescence intensity (MFI)  ≥1000.

value: blood


title: Blood_DSA_rejection_24


title: Blood_DSA_rejection_26


title: S. paradoxus DBVPG6304

source_name: S. paradoxus DBVPG6304


title: Blood_DSA_rejection_27


title: ES_undifferentiated_BR1

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

country: United Kingdom

institute: IGMM

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Prior to normalization probes not detected (Illumina detection p-value <0.01) on any sample within the experiment were removed from the analysis. The remaining data was quantile normalized in R with the LIMMA package.

source_name: Undifferentiated embryonic stem cells

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

growth_protocol: OS25s were cultured in Glasgow Minimal Essential Medium (GMEM) (Gibco)  supplemented with 10% (v/v) foetal calf serum (FCS), 0.1mM β-mercaptoethanol, penicillin  (10,000 units/mL) and streptomycin (650μg/mL), 0.3mg/mL L-Glutamine, 1mM sodium  pyruvate, and non-essential amino acids (Sigma) and 1000 units/mL  human recombinant LIF and 0.1mg/mL hygromycin (Roche)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment.  Quality control was performed with Agilent Bioanalyser.

value: Undifferentiated embryonic stem cells


title: ES_undifferentiated_BR2


title: Blood_DSA_rejection_25


title: ES_undifferentiated_BR3


title: Blood_DSA_rejection_23


title: Blood_DSA_rejection_20


title: Blood_DSA_rejection_19


title: Blood_DSA_rejection_18


title: Blood_DSA_rejection_14


title: Blood_DSA_rejection_13


title: Blood_DSA_rejection_22


title: Blood_DSA_rejection_21


title: Blood_DSA_rejection_17


title: Blood_DSA_rejection_15


title: Blood_DSA_rejection_11


title: Blood_DSA_rejection_9


title: Blood_DSA_rejection_12


title: Blood_DSA_rejection_16


title: Blood_DSA_rejection_6


title: Blood_DSA_rejection_7


title: Blood_DSA_rejection_5


title: Blood_DSA_rejection_10


title: Blood_DSA_rejection_2


title: Blood_DSA_rejection_3


title: Blood_DSA_rejection_8


title: Blood_DSA_rejection_4


title: Station GB1 57 m Baltic #1B

description: 1000 ng random priming amplified DNA from Baltic seawater

source_name: 70-mer probe

source_name: estuary seawater

value: random priming amplified DNA


title: Blood_DSA_normal_10

source_name: DSA+ and normal biopsy/mild IF/TA


title: Blood_DSA_rejection_1


title: Blood_DSA_normal_12


title: Blood_DSA_normal_11


title: Blood_DSA_normal_14


title: Blood_DSA_normal_9


title: Blood_DSA_normal_13


title: Blood_DSA_normal_3


title: Blood_DSA_normal_6


title: Blood_No_DSA_12

source_name: No DSA, PRA 0% and normal Biopsy/Mild IF/TA


title: Blood_DSA_normal_8


title: Blood_DSA_normal_4


title: Blood_DSA_normal_2


title: Blood_No_DSA_6


title: Blood_No_DSA_8


title: Blood_DSA_normal_7


title: Blood_No_DSA_11


title: Blood_No_DSA_7


title: Blood_DSA_normal_5


title: Blood_No_DSA_9


title: Blood_DSA_normal_1


title: Blood_No_DSA_5


title: Blood_No_DSA_10


title: Blood_No_DSA_1


title: Blood_No_DSA_2


title: Blood_No_DSA_3


title: Biopsy_DSA_rejection_25

description: Gene expression data from DSA biopsy sample

value: biopsy


title: Biopsy_DSA_rejection_28


title: Biopsy_DSA_rejection_22


title: Biopsy_DSA_rejection_27


title: Blood_No_DSA_4


title: Biopsy_DSA_rejection_23


title: Biopsy_DSA_rejection_21


title: Biopsy_DSA_rejection_26


title: Biopsy_DSA_rejection_20


title: Biopsy_DSA_rejection_12


title: D3EScell_BR3_TR1

hyb_protocol: 1.34μg cRNA was hybridized to Agilent whole mouse genome 4x44k oligomicroarrays  (Agilent cat# G4122F) according to manufacturer instructions (hybridisation proceeded for  63  17 hours).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner at 5μm resolution and spot  intensities were extracted using Array-Pro Analyser.

data_processing: mean net intensity values were quantile normalisation. The arrays were analysed using R version 2.15.0,    using Bioconductor, packages Limma, beadarray, and Ringo.

source_name: stem cells differentiated with 3 days exposure to retinoic acid

label_protocol: labelled with Cy3 after one round of amplification using an Amino Allyl Message Amp II aRNA Amplification kit

extract_protocol: RNA was extracted using standard Trizol protocol, and RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: differentiation

value: 3 days treatment with retinoic acid


title: Biopsy_DSA_rejection_18


title: Biopsy_DSA_rejection_17


title: UDEScell_BR3_TR1

source_name: undifferentiated embryonic stem cells

value: undifferentiated


title: Biopsy_DSA_rejection_15


title: Biopsy_DSA_rejection_9


title: Biopsy_DSA_rejection_10


title: Biopsy_DSA_rejection_16


title: Biopsy_DSA_rejection_8


title: Biopsy_DSA_rejection_19


title: Biopsy_DSA_rejection_14


title: UDEScell_BR3_TR2


title: Biopsy_DSA_rejection_24


title: D3EScell_BR2_TR1


title: Biopsy_DSA_rejection_13


title: Biopsy_DSA_rejection_11


title: Biopsy_DSA_rejection_7


title: D3EScell_BR3_TR2


title: Biopsy_DSA_rejection_6


title: Biopsy_DSA_rejection_5


title: D3EScell_BR2_TR2


title: UDEScell_BR2_TR1


title: UDEScell_BR2_TR2


title: D3EScell_BR1_TR2


title: D3EScell_BR1_TR1


title: Caco-2 control, 120 minutes incubation, replicate 2

city: Davis, CA

first: Carolyn

last: Slupsky

address: One Shields Ave

department: Department of Nutrition, Department of food science and technology

institute: University of California, Davis

description: control, 120min

hyb_protocol: 15 ug in 40 µL of fragmented and labeled aRNA from Caco-2 samples were prepared for hybridization on the GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix).GeneChips were submitted for hybridization to UC Davis School of Medicine Microarray Core Facility equipped with Fluidics Station 450 and Hybridization oven 640. All samples were processed according to Affymetrix protocols

scan_protocol: 3,000 GeneChip Scanner with Autoloader (Affymetrix). All samples were processed according to Affymetrix protocols

data_processing: All data were processed using Bioconductor and normalized via robust multi-array average (RMA) method. Significantly differentially expressed genes were determined using Significance Analysis of Microarrys (SAM) v.3.11

source_name: Caco-2 cell culture

label_protocol: Double-stranded cDNA was synthesized and biotinylated aRNA was generated using GeneChip 3’ IVT Express Kit (Affymetrix, Fremont, CA). GeneChip Sample Cleanup Module (Affymetrix) was used to clean up aRNA according to the manufacturer’s protocol. For the final fragmentation of labeled aRNA, GeneChip 3’ IVT Express Kit was used.

growth_protocol: Caco-2 cells(passages 26-30), was grown at 37 °C and 5% CO2 in a humidified atmosphere in 75 cm2 flasks with Dulbecco’s modified Eagle’s essential medium (DMEM) containing high glucose and supplemented with 2 mM L-glutamine (in the form of Glutamax), 1 mM sodium pyruvate, 16.6 % fetal bovine serum (FBS) v/v, 10 IU/mL penicillin, 0.10 mg/mL streptomycin and 1X non-essential amino acids in accordance with ATCC recommendations. Due to the fact that these cells were co-cultured with bacterial cells an additional buffer composed of 10 mM 3-morpholinopropanesulfonic acid (MOPS), 10 mM N-(Tris(hydroxymethyl)methyl)-2-aminoethanesulfonic acid (TES), 15 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), and 2 mM sodium phosphate was added to further buffer the media (pH 7.2). Media was changed every 2-3 d. All assays were using differentiated the Caco-2 (typically 21-22 d post inoculation).

extract_protocol: Samples of Caco-2 cells in Trizol were first freeze-thawed and centrifuged. The supernatant was used to extract total Caco-2 RNA according to the manufacturer’s protocol (Invitrogen, Carlsbad, CA). Total RNA extracted from Caco-2 cells was then purified using RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Caco-2 cells were incubated with bacteria in a cell culture media lacking antibiotics and serum. Controls included flasks with Caco-2 or bacterial cells alone. Flasks with Caco-2 cells alone and with co-culture were centrifuged at low speed to ensure bacterial adherence with the monolayer.

tag: treatment

value: control, 120min


title: AGM-X809-antimiR-33a/b treated

city: Charlestown

first: Veerle

last: Rottiers

state: MA

address: 149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

description: Female obese African Green Monkey on a high fat diet, treated with antimir-33a/b, RNA from liver biopsy

hyb_protocol: Six μg of labeled cDNA was hybridized to the array for 20 hours following the manufacturer’s protocol. Arrays were washed using the NimbleGen wash buffer kit following the manufacturer’s protocol.

scan_protocol: Arrays were scanned on the ms200 scanner. Images were aligned and features were extracted using Nimblescan 2.6 software.

data_processing: Data were analyzed with the Agilent Genespring GX 11.0

organism: Chlorocebus aethiops

source_name: AGM-antimiR-33a/b treated

label_protocol: DsDNA was labeled with Cy3 using the Roche One Color DNA Labeling kit following the manufacturer’s protocol.

growth_protocol: Twenty moderately obese adult female African green monkeys were selected for the study and fed a high-fat diet for 12 weeks. All monkeys were housed at the RxGen primate facility on the St. Kitts Biomedical Research Foundation campus, St. Kitts

extract_protocol: Double-stranded cDNA (ds cDNA) was prepared from 1 µg of total RNA using the cDNA Synthesis System (Roche).

treatment_protocol: Before the administration of the antimiR compounds the animals were randomly divided into 4 groups of 5 animals. The antimiR-33a, antimiR-33b and antimiR-33a/b compounds were subcutaneously delivered at a dose of 20 mg/kg on day 0, and a 5 mg/kg maintenance dose at weekly intervals.  Vehicle controls received a 0.9% NaCl solution. At day 57 (after 8 weeks of treatment) liver biopsies were taken for this microarray analysis)

value: liver biopsy


title: Caco-2 control, 60 minutes incubation, replicate 1

description: control, 60min

value: control, 60min


title: Biopsy_DSA_rejection_1


title: Biopsy_DSA_normal_12


title: AGM-Y014-antimiR-33a/b treated


title: Caco-2 control, 90 minutes incubation, replicate 2

description: control, 90min

value: control, 90min


title: Caco-2 cocultured with E.coli O157:H7, 120 minutes incubation, replicate 1

description: with O157:H7, 120min


title: Caco-2 control, 90 minutes incubation, replicate 1

description: control, 90min


title: Biopsy_DSA_rejection_2


title: Biopsy_DSA_rejection_4


title: Caco-2 cocultured with E.coli O157:H7, 60 minutes incubation, replicate 1

description: with O157:H7, 60min


title: Caco-2 cocultured with E.coli O157:H7, 120 minutes incubation, replicate 2

description: with O157:H7, 120min


title: Caco-2 control, 60 minutes incubation, replicate 2

description: control, 60min


title: UDEScell_BR1_TR2


title: Caco-2 control, 120 minutes incubation, replicate 1

description: control, 120min


title: Caco-2 cocultured with E.coli O157:H7, 90 minutes incubation, replicate 1

description: with O157:H7, 90min


title: AGM-V555-antimiR-33a/b treated


title: Biopsy_DSA_normal_10


title: Caco-2 cocultured with E.coli K12, 120 minutes incubation, replicate 1

description: with K12, 120min


title: Biopsy_DSA_rejection_3


title: AGM-X077-antimiR-33a/b treated


title: Caco-2 cocultured with E.coli K12, 90 minutes incubation, replicate 2

description: with K-12, 90min


title: Biopsy_DSA_normal_13


title: Caco-2 cocultured with E.coli K12, 120 minutes incubation, replicate 2

description: with K12, 120min


title: Caco-2 cocultured with E.coli O157:H7, 90 minutes incubation, replicate 2

description: with O157:H7, 90min


title: Biopsy_DSA_normal_11


title: UDEScell_BR1_TR1


title: Caco-2 cocultured with E.coli K12, 90 minutes incubation, replicate 1

description: with K-12, 90min


title: Biopsy_DSA_normal_9


title: AGM-V410-antimiR-33a/b treated


title: Caco-2 cocultured with E.coli K12, 60 minutes incubation, replicate 2

description: with K-12, 60min


title: Caco-2 cocultured with E.coli K12, 60 minutes incubation, replicate 1

description: with K-12, 60min


title: AGM-Y865-vehicle treated

description: Female obese African Green Monkey on a high fat diet, treated with vehicle only, RNA from liver biopsy

source_name: AGM-vehicle treated

value: vehicle


title: AGM-Y039-vehicle treated


title: Biopsy_DSA_normal_8


title: dnaJ-ala-2

first: Alison

last: Hottes

address: 220 Carl Icahn Lab Washington Road

department: Lewis-Sigler Institute for Integrative Genomics

description: Comparison of strains in M9-alanine media

hyb_protocol: Samples were then hybridized to E. coli Agilent E. coli Gene Expression Microarray (8x15K format, Catalog # G4813A-020097) according to the manufacturer’s instructions.  Washing was also carried out according to the manufacturer’s instructions.

scan_protocol: Slides were scanned using a High-Resolution C Scanner (Agilent), and then features were extracted using Agilent’s Feature Extraction Software version 9.5 using protocol GE2-v5_95_Feb07 without spike-in controls.

data_processing: The ‘LogRatio’ value was used in subsequent analyses.  All values for the same ORF were averaged as were the values from the two biological replicates performed for each comparison.

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

source_name: dnaJ mutant in Ala media

label_protocol: RNA was poly-adenylated by combining the 31 ul RNA (undiluted from the extract step) with 4 ul 10X Poly(A) Polymerase Reaction Buffer (New England Biolabs), 4 ul 10 mM ATP, and 1 ul (5 U) E. coli Poly(A) polymerase (New England Biolabs) and incubating at 37C for 30 minutes.  Samples were then cleaned with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions.  Samples were labeled with cyanine 3-CTP or cyanine 5-CTP dye using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions starting with 200 ng of RNA per sample.

growth_protocol: LB-grown overnight cultures were pelleted by centrifugation, washed, and resuspended in M9-glutamine of M9-alanine media.  Cultures were shaken at 250 rpm at 37C.  Samples were taken in mid-exponential phase (OD600 =0.15 for glutamine and OD600=0.2 for alanine on an Ultraspec 3100 pro) after ~5 generations of growth in the media.

extract_protocol: When the cultures reached the desired density, 2 ml of culture was added to 4 ml of RNAprotect Bacteria Reagent (Qiagen).  The mixture was incubated at room temperature for 5 min and then centrifuged at 5000 g for 10 min.  The supernatant was removed and the pellets were stored at -80C.  RNA was isolated using the Norgen Total RNA Purification Kit (Product #17200) according to the manufacturer’s directions except in the last step the RNA was eluted in 35 uL.

value: dnaJ mutant

source_name: wild-type in ala media_2

value: wild type


title: Biopsy_DSA_normal_7


title: pgi-ala-1

source_name: pgi mutantin Gln media

value: pgi mutant

source_name: wild-type in ala media_1


title: AGM-Z067-vehicle treated


title: cpxA-ala-2

source_name: cpxA mutant in Ala media

value: cpxA mutant


title: pgi-ala-2

source_name: pgi mutantin Ala media


title: AGM-W433-vehicle treated


title: Biopsy_DSA_normal_6


title: Biopsy_DSA_normal_2


title: cpxA-ala-1

source_name: cpxA mutant in Gln media


title: gcvT-ala-2

source_name: gcvT mutant in Ala media

value: gcvT mutant


title: AGM-W552-vehicle treated


title: Biopsy_DSA_normal_5


title: gcvT-ala-1

source_name: gcvT mutant in Gln media


title: Biopsy_DSA_normal_3


title: dnaJ-ala-1

source_name: dnaJ mutant in Gln media


title: Biopsy_No_DSA_20


title: Biopsy_DSA_normal_4

source_name: DSA+ and normal biopsy/mild IF/TA


title: Biopsy_No_DSA_19

source_name: No DSA, PRA 0% and normal Biopsy/Mild IF/TA


title: Biopsy_DSA_normal_1


title: Biopsy_No_DSA_17


title: Biopsy_No_DSA_18


title: cysQ-gln-2

description: Comparison of strains in M9-glutamine media

source_name: cysQ mutantin Ala media

value: cysQ mutant

source_name: wild-type in gln media_2


title: hfq-gln-2

source_name: hfq mutant in Ala media

value: hfq mutant


title: lrp-gln-2

source_name: Irp mutant in Ala media

value: Irp mutant


title: dnaJ-gln-2


title: cysQ-gln-1

source_name: cysQ mutantin Gln media

source_name: wild-type in gln media_1


title: Biopsy_No_DSA_16


title: Biopsy_No_DSA_15


title: dnaJ-gln-1


title: lrp-gln-1

source_name: Irp mutant in Gln media


title: hfq-gln-1

source_name: hfq mutant in Gln media


title: 4-deoxy-GlcNAc treated SKOV3, biol rep3

city: Nijmegen

first: Xander

last: van Wijk

address: Geert Grooteplein 26-28

department: Biochemistry

institute: Radboud University Nijmegen Medical Centre

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing:
Quantile normalization, with RMA, GC correction and median polish, log2 values from Partek Genomic Suite 6.5
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: ovarian tumor cells, 4-deoxy-GlcNAc treated

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: SKOV3 cells were grown in T75 flasks for three days in McCoys5A medium (Invitrogen) + 10% FBS

extract_protocol: RNA was isolated from SKOV3 cells of three separate culture flasks per experimental condition (control, 50 µM GlcNAc (Ac4) or 50 µM 4-deoxy-GlcNAc (Ac3)) using the Qiagen RNeasy Mini Kit (Qiagen GmbH), including a  DNase digestion step. RNA concentration and purity were measured with a Nanodrop spectrophotometer (Thermo Scientific) and  RNA integrity was confirmed on an Agilent Bioanalyzer.

treatment_protocol: untreated, 50 microM peractylated GlcNAc, 50 microM peractylated 4-deoxy-GlcNAc

value: 50 microM 4-deoxy-GlcNAc


title: Biopsy_No_DSA_11

value: biopsy


title: GlcNAc treated SKOV3, biol rep3

source_name: ovarian tumor cells, GlcNAc treated

value: 50 microM GlcNAc


title: Biopsy_No_DSA_13


title: Biopsy_No_DSA_9


title: Biopsy_No_DSA_12


title: Biopsy_No_DSA_14


title: 4-deoxy-GlcNAc treated SKOV3, biol rep2


title: Biopsy_No_DSA_10


title: GlcNAc treated SKOV3, biol rep2


title: S. cerevisiae YJM269 xylulose Cy5

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae YJM269 xylulose

value: xyulose


title: GlcNAc treated SKOV3, biol rep1


title: Biopsy_No_DSA_8


title: S. cerevisiae CLIB215 xylulose Cy5

source_name: S. cerevisiae CLIB215 xylulose


title: 4-deoxy-GlcNAc treated SKOV3, biol rep1


title: untreated SKOV3, biol rep3

source_name: ovarian tumor cells, untreated

value: untreated


title: Biopsy_No_DSA_7


title: WT vs. Δydr374c rep_2

city: Seoul

first: Hyun-Jun

last: Kang

address: 145, Anam-ro, Seongbuk-gu

country: South Korea

institute: Korea University

description: WT vs. Δydr374c rep_2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization. The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

source_name: wild type cells

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: For the analysis, wild-type and YDR374C deleted cells were harvested at the mid-exponential phase in SD medium.

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

tag: strain background

tag: growth stage

value: mid-exponential phase

source_name: YDR374C deleted cells

value: Δydr374c (YDR374C deletion)


title: untreated SKOV3, biol rep2


title: Caco-2 cocultured with E.coli O157:H7, 60 minutes incubation, replicate 2

description: with O157:H7, 60min

source_name: Caco-2 cell culture


title: untreated SKOV3, biol rep1


title: Biopsy_No_DSA_6

source_name: No DSA, PRA 0% and normal Biopsy/Mild IF/TA


title: WT vs. Δydr374c rep_1

description: WT vs. Δydr374c rep_1


title: Biopsy_No_DSA_5


title: S. cerevisiae T7 xylulose Cy5

source_name: S. cerevisiae T7 xylulose


title: Biopsy_No_DSA_3


title: Rubrum-17α-ethinylestradiol (EE2)-rep1

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description:
Induction with 17α-ethinylestradiol (EE2)
13943605-Rubrum-ethinylest-2.gpr

hyb_protocol: The two differentially labeled cDNAs were resuspended in the universal hybridization buffer (Pronto kit; Corning-Promega, United States), mixed, and added jointly to the surface of the spotted microarray glass slide for overnight hybridization at 42°C using a HS 4800 Pro automated hybridization station (TECAN, Switzerland). The slide was washed according to the Pronto kit’s protocol and then dried in the hybridization station.

scan_protocol: Microarray spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to built-in quality criteria.

data_processing: Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15  as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide technical triplicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fit to a linear model and moderated t-statistics were calculated using empirical Bayes method . P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Rhodospirillum rubrum

source_name: non-induced culture (reference)

label_protocol: Ten micrograms of RNA was reverse transcribed by random priming according to the Pronto kit’s instructions (Corning-Promega, United States) and directly labeled by incorporation of Cy3-dCTP or Cy5-dCTP nucleotides (Amersham Bioscience, United Kingdom) for respectively control and experimental samples.

growth_protocol: Rhodospirillum rubrum S1H was obtained from the American Type Culture Collection (ATCC 25903) and grown in Sistrom Medium A (SIS) with 0.2% (w/v) succinate as sole carbon source in dark aerobic conditions at 30°C and 50 rpm [3]. Early stationary phase cells were inoculated at 2% (v/v) inoculum in 50 mL SIS.

extract_protocol: Ten mL of R. rubrum S1H culture was harvested at OD680 of 0.4 from all test cultures with and without pharmaceuticals, and 20 mL RNAProtect Bacteria Reagent (QIAGEN) was added to preserve the RNA. The fixed cell suspensions were centrifuged at 3500 rpm for 10 min, the supernatant was removed, and cell pellets were stored at -80°C. The RNA extraction was performed using the RNeasy Midi Kit (QIAGEN), following the manufacturer’s guidelines. RNA quantity and quality was assessed using the Nanodrop ND-1000 and the 2100 Bioanalyzer (Agilent) using the RNA 6000 Nano Chip Kit following the manufacturer’s instructions. Only RNA with a RNA Integrity Number (RIN-) value of 9.5 and higher was used for microarray analysis.

treatment_protocol: In accordance with a previous exposure experiment with the biocide triclosan [3], the R. rubrum S1H cultures were exposed to 86 nM of diclofenac (DCF), acetylsalicylic acid (ASA), and 17α-ethinylestradiol (EE2), which corresponded to 27.4 µg/L DCF, 15.5 µg/L ASA, and 25.5 µg/L EE2. Prior to inoculation, SIS was spiked from a stock solution of DCF or EE2 in methanol and the different samples were supplemented with equal final volumes of methanol to nullify the potential effect of differential solvent concentrations. In addition, a solvent control (with methanol) and growth control (without methanol) was prepared. ASA was spiked in the growth medium from a stock solution in water. Subsequently, SIS with and without DCF, EE2, or ASA was inoculated with early stationary phase cells.

tag: ATCC

tag: pharmaceutical agent

source_name: culture induced with 17α-ethinylestradiol (EE2)

value: induction with 17α-ethinylestradiol (EE2)


title: Rubrum-Diclofenac (DCF)-rep3

description:
Induction with diclofenac (DCF)
13943598-Rubrum-Diclofenac-4.gpr

source_name: culture induced with diclofenac (DCF)

value: diclofenac (DCF)


title: Rubrum-17α-ethinylestradiol (EE2)-rep2

description:
Induction with 17α-ethinylestradiol (EE2)
13943602-Rubrum-ethinylest-3.gpr


title: Biopsy_No_DSA_4