title: Breast Ca FNA Q

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

description: RNA obtained from leftovers remained in the syringe used for diagnostic FNA.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalized using cubic spline normalization with the Illumina GenomeStudio software.

Sample B was used by the Beadstudio software as the reference for cubic spline normalization; therefore, the normalized and non-normalized data values for this Sample are identical.

source_name: Breast cancer fine needle aspirate

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s recommendations.

growth_protocol: No in vitro growth. The samples are fine needle aspirates from human breast cancers.

extract_protocol: Standard Trizol total RNA extraction. RNA quality and amounts were assessed with a Bioanalyzer 2100 and by spectrophotometry.

treatment_protocol: After fine needle aspiration and spreading of the material on diagnostic slides, the syringe was rinsed with Trizol to recover and extract RNA from residual material.

tag: tissue

value: breast cancer

tag: cellularity

value: intermediate

tag: nuclear grade

value: low

tag: epithelial cells

tag: stromal cells

value: No

tag: inflammatory cells

tag: histotype

value: ductal

tag: histological grade

tag: pgr (%)

tag: her2 score

tag: sample

value: Q


title: alpha 32

status: Public on Dec 20 2012

type: RNA

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: ventricle of ovariectomized female mice receiving treatment with the estrogen receptor alpha agonist 16 alpha LE2 for 4 week

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and variance stailization (VSN) as normalization method using vsn2 package

label: biotin

molecule: total RNA

organism: Mus musculus

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

growth_protocol: female C57BL/6 mice from Harlan- Germany breeding

extract_protocol: RNA was isolated using the Trizol standard protocol, including Dnase digest (Quiagen)

treatment_protocol: female 8 weeks old mice were ovariectomized and received Alzet minipumps 1004 filled up with cyclodextrinated estrogens or placebo solution

tag: strain

tag: age

value: 8 weeks

tag: gender

value: female

value: ventricle


title: Day12_Thy- M2 [mRNA]

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

description: Sample name: KH195

hyb_protocol: Samples were hybridized to affymetrix MOE430A arrays using the protocol provided by the supplier

scan_protocol: Arrays were scanned on an affymetrix scanner in according to the manufacturers protocol

data_processing: Data were normalized using robust multi array averaging (RMA) and converted to log2 scale

source_name: Sorted cells

label_protocol: Samples were labeled with biotin in the standard way

growth_protocol: Mouse Embryonic fibroblast (MEFF) cultures were established from E13.5 embryos from a reprogrammable mice strain carrying one copy of the OKSM cassette and Rosa26-M2rtTA allele (het/het) or carrying two copies of the OKSM cassette and Rosa26-M2rtTA allele (ho/ho). Reprogramming was performed in ESC medium (KODMEM with 15% FBS, L-Glutamin, penicillin-streptomycin, non-essential amino acids, b-mercaptoethanol and 1000 U/ml LIF) in the presence of doxycycline.

extract_protocol: iPSCs were harvested when they reached about 50% confluency and preplated on non-gelatinized T25 flasks for 45 minutes to remove feeder cells. Intermidiates cell types were harvest after FACS sorting. Cells were then spun down and the pellet used for isolation of total RNA using the miRNeasy Mini Kit (QIAGEN) without DNase digestion. RNA was eluted from the columns using 50 ml RNase-free water or TE buffer, pH7.5 (10 mM Tris-HCl and 0.1 mM EDTA) and quantified using a Nanodrop (Nanodrop Technologies).

treatment_protocol: Harvested cells were incubated with antibodies against Thy1.2 (PE conjugated, 53-2.1, eBiosciences) and SSEA-1 (mouse IgM, MC-480, Developmental Hybridoma Bank) for 20 minutes. Cells were washed in PBS and then incubated for 20 minutes with APC conjugated anti mouse IgM, (eBioscience) and Pacific Blue-conjugated streptavidin (Invitrogen). The cells were washed in PBS, resuspended in propidium iodide 5% FBS/PBS solution and passed through a 40mm cell strainer to achieve single cell suspension. Cells were sorted on a FACSAria (BD Biosciences ) and/or analysed in a LSRII (BD Bioscience).  For analysis and/or sorting of intermediates, cells were stained with Thy1.2 and SSEA1 antibodies and sorted or analyzed as indicated.

tag: time after induction [days]

tag: cell stage

value: Intermediates

value: NEG

tag: gfp


title: Breast Ca FNA M

country: Italy

organism: Homo sapiens

tag: tissue

value: high

value: no

value: papillary

value: M


title: OV4711_CGH

type: genomic

city: Oslo

first: Aslaug

last: Helland

address: Hospital Radiumhospitalet

department: Dept of Genetics

country: Norway

institute: Institute for Cancer Research, Oslo University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44490.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

source_name: universal reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: universal reference

value: Primary tumor, Ovarian

value: 67 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: OV3618_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44823.gif

scan_protocol: Scanner Model: GenePix 4000B

value: 59 years


title: Breast Ca FNA N

value: breast cancer

tag: cellularity

tag: nuclear grade

tag: epithelial cells

tag: stromal cells

tag: inflammatory cells

tag: histotype

tag: histological grade

tag: pgr (%)

value: N


title: alpha 30

source_name: treatment with the estrogen receptor alpha agonist 16 alpha LE2 for 4 week

tag: strain

tag: age

tag: gender


title: Breast Ca FNA P

tag: tissue

value: low

value: intermediate

value: lobular

tag: her2 score

tag: sample

value: P


title: OV3118_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44554.gif

tag: reference

value: 64 years

tag: tumor histology

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)


title: Day12_SSEA1+ M2 [mRNA]

description: Sample name: KH196

tag: time after induction [days]

tag: cell stage

value: Intermediates

value: NEG

value: POS

tag: gfp


title: OV4455_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44825.gif

value: 61 years

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: OV2834_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45110.gif

value: 79 years


title: OV3159_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44820.gif

value: universal reference

value: 73 years


title: Day12_Thy+ M2 [mRNA]

description: Sample name: KH194


title: Day9_SSEA1+ M2 [mRNA]

description: Sample name: KH193


title: Bos taurus_biceps brachii_S56

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

description: Sample of bovine biceps brachii muscle

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R2.11.1 statistical software

label: Cyanine 3

organism: Bos taurus

source_name: Bovine biceps brachii samples collected at the slaughterhouse

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: sample id

value: Bos taurus muscle, S56

tag: status

value: suspected for corticosteroids treatment


title: Breast Ca FNA L

tag: cellularity

tag: nuclear grade

value: high

tag: epithelial cells

tag: stromal cells

tag: inflammatory cells

tag: histotype

value: ductal

tag: histological grade

value: negative

tag: pgr (%)

value: L


title: alpha 29

tag: strain

tag: age

value: 8 weeks

tag: gender

value: female

tag: tissue

value: ventricle


title: Day9_Thy+ M2 [mRNA]

description: Sample name: KH191

tag: time after induction [days]

tag: cell stage

tag: gfp


title: Breast Ca FNA G

value: breast cancer

value: intermediate

tag: her2 score

tag: sample

value: G


title: Breast Ca FNA H

tag: cellularity

value: no

value: H


title: Day9_Thy- M2 [mRNA]

description: Sample name: KH192

value: Intermediates

value: NEG


title: 60hr-B

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with GeneChip 3000.

data_processing: Affymetrix Mouse 430 v2 arrays were analyzed in R, version 2.13, using the packages affy (Gautier et al. 2004), version 1.3, and limma (Smyth et al., 2005), version 3.8.3. Normalization was done using rma.

source_name: KH2 mES

label_protocol: Biotin labelling was done with 200 ng total RNA with the Ambion MessageAmp III kit.

growth_protocol: One day before of thawing, T25 plates with feeders were prepared. Aseptically the cell suspension was transferred into a sterile centrifuge tube containing several ml of warm FCS-ES media. Cells were pelleted by centrifuging at 1000 rpm for 5 minutes. Supernatant was aspirated and cells were resuspended into required quantity of fresh media. Cells were distributed evenly by tilting plates several times and then were placed in incubator (at 370 C and 5% CO2).    Passage/expand of ES cells: Media was changed 3 hours before passaging them. Media was aspirated and washed twice with PBS. 800l of pre warmed Trypsin/EDTA solution were added and placed in incubator at 370 C for 1minute. During this period colonies float off when flicking the plate. Trypsin activity was stopped by adding 5ml of FCS-ES medium to flask. Colonies were dissociated into single cells by pipetting up and down for several times and pelleting the cells by centrifugation at 1000 rpm for 5 minutes. Media was aspirated and the cells were resuspended in appropriate volume of fresh ES cell medium and cells were seeded in 1:6 ratio into T75 flask. Plate was tilted several times to distribute the cells evenly and placed in the incubator.

extract_protocol: RNA for microarray analysis was isolated from ES cells grown on feeder cells. After induction, cells were washed in PBS, trypsinized, and replated onto a fresh gelatinized plate for 30 minutes. Media and unbound cells were aspirated. Adhered cells were resuspended in Trizol, aliquoted and flash frozen until needed. RNA were isolated as described per manufacture’s instruction and cleaned using RNAeasy Kit ( Quiagen). Quality and quantity of RNA were analyzed by Agilent Bioanlayzer 2100.

treatment_protocol: Media was changed 3 hours before passaging them. Media was aspirated and washed twice with PBS. 2 ml of pre warmed Trypsin/EDTA solution were added and placed in incubator at 370 C for 1minute. During this period colonies float off when flicking the plate. Trypsin activity was stopped by adding 5ml of FCS-ES medium to flask. Colonies were dissociated into single cells by pipetting up and down for several times and pelleting the cells by centrifugation at 1000 rpm for 5 minutes. Media was aspirated and the cells were resuspended in appropriate volume of fresh ES cell medium and cells were seeded in 1:6. ratio into fresh  T75 flask with feeders. Plate was tilted several times to distribute the cells evenly and placed in the incubator. Next day media was changed. Cells treated for 2, 4 and and 6  hours with RA  were supplemented with differentiation media ( DMEM + 10% Serum + NAA+ 0.3uM  RA) . After required period of induction, Media was aspirated and washed twice with PBS. 2 ml of pre warmed Trypsin/EDTA solution were added and placed in incubator at 370 C for 1minute. During this, period colonies float off when flicking the plate. Trypsin activity was stopped by adding 5ml of FCS-ES medium to flask. Colonies were dissociated into single cells by pipetting up and down for several times. Additional 15 ml of Differentiation media (without RA) was added and plated into freshly gelatinized plates. For gelatinized plates, Culture plates were treated half an hour before seeding with 0.1% Gelatin. Gelatin was later aspirated just before seeding of cells. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm. Pellets were dislodged by gentle tapping and 2 ml trizol were added.   These tubes were stored at -80 until RNA isolation.

tag: cell line

tag: treatment

value: retinoic acid

tag: time

value: 60 hours


title: 72hr-B

value: 72 hours


title: OV2801_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44819.gif

tag: reference

value: universal reference

value: Primary tumor, Ovarian

value: 47 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: OV3122_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44481.gif

tag: tissue

tag: age

value: 55 years


title: Day6_Thy- M3 [mRNA]

description: Sample name: KH189

tag: strain

tag: time after induction [days]

tag: cell stage


title: Breast Ca FNA E

value: high

tag: nuclear grade

tag: epithelial cells

tag: stromal cells

tag: inflammatory cells

tag: histotype

value: ductal

tag: histological grade

tag: pgr (%)

tag: her2 score

tag: sample

value: E


title: 60hr-C

tag: cell line

tag: treatment

tag: time


title: Day6_SSEA1+ M3 [mRNA]

description: Sample name: KH190

value: POS

tag: gfp


title: Breast Ca FNA C

tag: tissue

value: breast cancer

tag: cellularity

value: intermediate

value: negative

value: C


title: 72hr-A


title: 72hr-C


title: Breast Ca FNA F

value: no

value: endocrine

value: F


title: OV3626_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44559.gif

tag: reference

tag: age

value: 64 years

tag: tumor histology

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: 60hr-A

value: retinoic acid

value: 60 hours


title: Breast Ca FNA B

value: low

tag: nuclear grade

tag: epithelial cells

tag: stromal cells

tag: inflammatory cells

value: No

tag: histotype

tag: histological grade

tag: pgr (%)

value: B


title: OV4070_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44489.gif

value: universal reference

tag: tissue

value: Primary tumor, Ovarian

value: 72 years

value: serous


title: OV3942_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44484.gif

value: 49 years


title: Day6_Thy+ M2 [mRNA]

description: Sample name: KH185

tag: strain

tag: time after induction [days]

tag: cell stage

value: Intermediates

value: POS

value: NEG

tag: gfp


title: Day6_SSEA1+ M2 [mRNA]

description: Sample name: KH187


title: 48hr-C

tag: cell line

tag: treatment

tag: time

value: 48 hours


title: Day3_SSEA1+ M3 [mRNA]

description: Sample name: KH184


title: Day6_Thy- M2 [mRNA]

description: Sample name: KH186


title: Acute-type ATL patient #4

city: miyazaki city

first: kentarou

last: nagai

state: miyazaki

department: Miyazaki university

country: Japan

institute: biochemistry

description:
Acute4
ATL_145.CEL

hyb_protocol: Following linear amplification of cRNA with T7 RNA polymerase, the biotinylated cRNA was cleaned with an RNeasy Mini Column Kit, fragmented to 50 to 200 nucleotides, and then hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChips were scanned using Affymetrics GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: ATL cells_acute-type ATL patients

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: sample group

value: acute-type T-cell leukemia (ATL) patients

value: peripheral blood

tag: cell type

value: Adult T-cell leukemia (ATL) cells


title: OV3658_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44482.gif

tag: reference

tag: age

value: 61 years

tag: tumor histology

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: Acute-type ATL patient #6

description:
Acute6
ATL_162.CEL

tag: tissue


title: OV2857_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44835.gif

value: 65 years


title: Day3_Thy- M3 [mRNA]

description: Sample name: KH183

tag: strain

tag: time after induction [days]


title: 48hr-A

value: retinoic acid


title: Acute-type ATL patient #3

description:
Acute3
ATL 2_061217.CEL


title: Day3_Thy+ M3 [mRNA]

description: Sample name: KH182

tag: cell stage

tag: gfp


title: 36hr-C

tag: cell line

tag: treatment

value: 36 hours


title: Acute-type ATL patient #5

description:
Acute5
ATL_148.CEL

tag: sample group


title: Acute-type ATL patient #7

description:
Acute7
ATL_163.CEL

tag: cell type


title: OV3882_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44483.gif

tag: reference

value: 42 years


title: OV3666_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44602.gif

value: universal reference

tag: age

value: 47 years


title: 36hr-B

tag: time


title: Day6_Thy+ M3 [mRNA]

description: Sample name: KH188


title: OV2853_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45109.gif

value: Primary tumor, Ovarian

value: 70 years

tag: tumor histology

tag: grade of tumor


title: OV3846_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44603.gif

value: 76 years

value: serous

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)


title: Acute-type ATL patient #2

description:
Acute2
ATL 1_061217.CEL


title: Day3_SSEA1+ M2 [mRNA]

description: Sample name: KH181

value: Intermediates

value: POS


title: 24hr-E

value: 24 hours


title: OV3482_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44817.gif

value: 68 years

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: 24hr-F


title: OV3636_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44832.gif

tag: tissue


title: Day3_Thy+ M2 [mRNA]

description: Sample name: KH179

tag: strain

tag: time after induction [days]

value: NEG


title: OV3924_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44532.gif


title: KH2-MEF_m3 [mRNA]

description: Sample name: KH178

tag: cell stage

value: MEF

tag: gfp


title: 24hr-D

tag: cell line

tag: treatment


title: Healthy volunteer #4

description:
CD4+N4
060807 Normal 4.CEL

source_name: CD4+ T lymphocytes_healthy

tag: sample group

value: healthy volunteers

value: peripheral blood

tag: cell type

value: CD4+ T lymphocytes


title: Healthy volunteer #5

description:
CD4+N5
060807 Normal 5.CEL


title: Healthy volunteer #2

description:
CD4+N2
060807 Normal 2.CEL


title: KH2-MEF_m2 [mRNA]

description: Sample name: KH177


title: OV2842_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44826.gif

tag: reference

tag: age

value: 39 years


title: 24hr-B

value: retinoic acid

tag: time


title: 24hr-C


title: Healthy volunteer #3

description:
CD4+N3
060807 Normal 3.CEL


title: Healthy volunteer #1

description:
CD4+N1
060807 Normal 1.CEL


title: 24hr-A


title: Day3_Thy- M2 [mRNA]

description: Sample name: KH180


title: 48hr-B

value: 48 hours


title: OV4126_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44604.gif

value: universal reference

value: 73 years

tag: tumor histology

tag: grade of tumor


title: OV3917_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44833.gif

value: Primary tumor, Ovarian

value: 57 years

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)


title: J LF liver rep3

city: Baton Rouge

first: Brenda

last: Richards

state: LA

address: 6400 Perkins Rd.

department: Basic Science

institute: Pennington Biomedical Research Center

hyb_protocol: Microarray hybridization of each sample (using ten micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.

data_processing: Signal intensities across microarrays were normalized using the quantile-quantile method (www.bioconductor.org).

label: Dig-UTP

source_name: mutant mouse liver 2 days high-fat diet

label_protocol: 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.

growth_protocol: Twelve-week old male mice were singly housed in filter-top cages and kept under 12h light/12h dark conditions in a specific-pathogen free facility fed a Chow diet (LabDiet 5001).

extract_protocol: Tissues were quickly removed and frozen in liquid nitrogen and stored at -80C for subsequent preparation of total RNA. Total RNA was isolated using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O supplemented with the RNase inhibitor Superasin (Ambion, Austin, TX) as per manufacturers directions.  Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).

treatment_protocol: After weaning the offspring were treated the same; from weaning until 12 weeks of age mice were fed a chow diet (LabDiets 5001) ad libitum. Several days prior to initiation of experimental diets, bedding was removed and replaced with stainless steel wire floor inserts. Nesting tubes were provided to reduce time spent on wire flooring. At 12 weeks of age mice were fed ad libitum a high-fat diet D12331 or low-fat diet D12329 (Research Diets) for 2 days.

value: BALB/cByJ (Acads-/-)

tag: genotype

value: Acads-/-

value: liver

value: low-fat diet


title: OV3777_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44818.gif

tag: tissue

value: 59 years

value: serous

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: J LF liver rep2

tag: strain


title: 16hr-C

value: 16 hours


title: cell line_293T_Ago2-IP_miR941

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

description: Ago2-IP after miR941 transfection

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: RMA processing was used to generate expression levels for the probesets. It includes quantile normalization and log2 transformation (R Affy package). MAS5 was used as well to return 'Present/Absent/Marginal' flags and p-values on each probeset, which can be used for filtering ('pam' and 'pvalue' in the data table).

source_name: cell line 293T

label_protocol: Labeling was performed according to standard Affymetrix protocols.

extract_protocol: Total RNA were extracted with Trizol reagent (Invitrogen).

treatment_protocol: Ago2 Immunoprecipitation (Ago2-IP) experiments after miR-941 overexpression were conducted in 293T cell line. Briefly, All transfections were performed using human 293T cells cultured in 6-well tissue culture plates. Lipofectamine 2000 (Invitrogen) was used for a Synthetic miR-941 or a scrambled oligo transfection, at 30 nmol/l each (final concentration) per 1x106 cells/well of a 6-well plate using DharmaFECT (GE Healthcare). Total 5x106 cells were collected and subjected to Ago2 immunoprecipitation (Ago2-IP) using the RNA isolation kit Mouse Ago2 (Wako Chemicals) according to the manufacturer's instructions. For a negative control, immunoprecipitation was performed using nonimmune IgG beads prepared with the antibody immobilization bead kit (Wako Chemicals). The IP pull down RNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA. The cRNA was analyzed on affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions.

tag: transfected with

value: Synthetic miR-941

tag: genotype/variation

value: miR-941 overexpression

tag: ip antibody

tag: ip antibody vendor

value: Wako Chemicals

tag: ip antibody cat. #

tag: ip antibody lot. #


title: 16hr-B

tag: cell line

tag: treatment


title: J LF liver rep1


title: 16hr-A

tag: time


title: cell line_MSF_miR_transfection

description: Gene expression after miR941 transfection

organism: Macaca mulatta

treatment_protocol: miRNA mimics-Lipofectamine 2000 (Invitrogen) complexes were prepared freshly before transfection according to the manufacturer's protocol. Cells were transfected in six-well plates using miRNA mimics-Lipofectamine 2000 with a final oligonucleotide concentration of 10nmol/L. In parallel, negative control transfections with mock oligonucleotides were conducted according to the manufacturer's protocol.

value: MSF

value: miR-941 mimics-Lipofectamine 2000 complexes


title: J HF liver rep3

value: high-fat diet


title: J HF liver rep2


title: 12hr-F

value: retinoic acid

value: 12 hours


title: cell line_FrhK-4_mock_transfection

description: Gene expression after mock transfection

tag: cell type

value: fetal rhesus monkey kidney (FRhK-4) cells

value: mock oligonucleotides


title: cell line_MSF_mock_transfection

description: Gene expression after mock transfection


title: OV4087_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43423.gif

tag: reference

value: universal reference

value: Primary tumor, Ovarian

tag: age

value: 51 years

tag: tumor histology

tag: grade of tumor

tag: event (alive=1, dead=2)


title: cell line_293T_Ago2-IP_control

description: Ago2-IP after mock transfection

value: scrambled oligo

value: control

value: nonimmune IgG beads

value: millipore


title: J HF liver rep1

value: BALB/cByJ (Acads-/-)

tag: genotype

value: Acads-/-

tag: tissue

value: liver


title: OV4520_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs//44486.gif

value: 61 years

value: serous

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: 12hr-D


title: 12hr-C


title: 12hr-E


title: Acute-type ATL patient #1

description:
Acute1
060807 ATL 3.CEL

tag: sample group

value: acute-type T-cell leukemia (ATL) patients

value: peripheral blood

value: Adult T-cell leukemia (ATL) cells


title: cell line_FrhK-4_miR_transfection

value: fetal rhesus monkey kidney (FRhK-4) cells

tag: transfected with

value: miR-941 mimics-Lipofectamine 2000 complexes


title: OV2729_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44834.gif

value: universal reference

value: 68 years


title: KZ LF liver rep2

source_name: control mouse liver 2 days high-fat diet

tag: strain

value: BALB/cByKZ (Acads+/+)

value: Acads+/+

value: low-fat diet


title: KZ LF liver rep3


title: OV3376_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44827.gif

value: Primary tumor, Ovarian

value: 52 years


title: GSCs AntimiR-138 -Replicate-3

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

description:
Isolated from glioma tissue
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalised using quantile normalisation on Illumina Inc. GenomeStudio version 1.9.0

source_name: Glioma stem cells

label_protocol: Biotinylated cRNA were prepared with the Target Amp-Nano kit for Illumina arrays

extract_protocol: Total RNA was extracted by using Exiqon columns as per manufacturer instructions

treatment_protocol: GSCs were transduced either with Scrambled or anti-miR-138

value: Glioma stem cells

tag: transducer


title: cell line_LLCM2_miR_transfection

tag: cell line

value: rhesus monkey kidney cell


title: 12hr-B

tag: treatment

value: retinoic acid

tag: time

value: 12 hours


title: OV3097_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44610.gif

tag: reference

value: 73 years

value: serous


title: KZ LF liver rep1

value: liver


title: cell line_293T_mock_transfection

description: Gene expression after mock transfection

tag: cell type

value: human embryonic kidney cells

value: mock oligonucleotides


title: GSCs AntimiR-138 -Replicate-2

description:
Isolated from glioma tissue
Replicate 2


title: KZ HF liver rep3

value: high-fat diet


title: OV3229_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44821.gif

value: universal reference

tag: age

value: 45 years

tag: tumor histology


title: cell line_LLCM2_mock_transfection

description: Gene expression after mock transfection


title: 12hr-A


title: KZ HF liver rep2

value: BALB/cByKZ (Acads+/+)


title: OV3331_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44479.gif

value: 72 years

tag: grade of tumor

tag: event (alive=1, dead=2)


title: 08hr-B

value: baseline

value: 8 hours


title: OV4015_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44550.gif

tag: tissue

value: Primary tumor, Ovarian

value: 60 years


title: OV3113_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44530.gif

value: 59 years

tag: progression (no progression=1, progression=2)


title: 36hr-A

value: retinoic acid

value: 36 hours


title: 08hr-C


title: KZ HF liver rep1

tag: genotype

value: Acads+/+


title: cell line_293T_miR_transfection

value: miR-941 mimics-Lipofectamine 2000 complexes


title: OV4078_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44531.gif

value: 62 years

value: serous

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: cell line_HSF2_mock_transfection

description: Gene expression after mock transfection

value: human skin fibroblast cells

tag: transfected with

value: mock oligonucleotides


title: J LF brain rep3

source_name: mutant mouse brain 2 days low-fat diet

tag: strain

value: BALB/cByJ (Acads-/-)

value: Acads-/-

value: brain

value: low-fat diet


title: GSCs scrambled-Replicate-3

description:
Isolated from glioma tissue
Replicate 3

value: Glioma stem cells

tag: transducer

value: scrambled


title: cell line_HSF2_miR_transfection

tag: cell line


title: J HF brain rep3

source_name: mutant mouse brain 2 days high-fat diet

tag: treatment

value: high-fat diet


title: 9h_SN_3

city: Shanghai

first: Guohui

last: Ding

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA) with default settings，Dye channel: Green, Scan resolution = 5μm, PMT 100%，10%，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: SN_sciatic nerve resection_9h

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

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion, Austin, TX) according to the manufacturer’s instructions. The quality of the purified RNA was assessed using a BioAnalyzer 2100 (Agilent Technology, Santa Clara, CA). The purified RNA was quantified by determining the absorbance at 260nm using a Nanodrop ND-1000 spectrophotometer (Infinigen Biotechnology Inc., City of Industry, CA).

treatment_protocol: Thirty adult, male Sprague-Dawley (SD) rats (180-220g, supplied by the Experimental Animal Center of Nantong University) were randomly divided into six groups of six rats each. Each animal was anaesthetized by an intraperitoneal injection of complex narcotics (85mg/kg trichloroac etaldehyde monohydrate, 42mg/kg magnesium sulfate, 17mg/kg sodium pentobarbital), and the sciatic nerve was exposed and lifted through an incision on the lateral aspect of the mid-thigh of the left hind limb. A 1cm long segment of sciatic nerve was then resected at the site just proximal to the division of tibial and common peroneal nerves, and the incision sites were then closed. To minimize discomfort and possible painful mechanical stimulation, the rats were housed in large cages with sawdust bedding after surgery. SN tissues (0.5cm) were collected at different time points after injury, respectively. All the experimental procedures involving animals were conducted in accordance with Institutional Animal Care guidelines and ethically approved by the Administration Committee of Experimental Animals, Jiangsu Province, China (Approval ID: SYXK(SU)2007-0021).

value: Sprague-Dawley

tag: weight

value: proximal sciatic nerve (SN)


title: 9h_SN_2


title: rve8_ConstantLight_116hr

city: Durham

first: Polly

middle: Yingshan

last: Hsu

state: NC

address: Duke University

department: Biology

institute: Duke University

hyb_protocol: Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45 C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Analysis was performed in R 2.13.  The raw data were filtered and nonperforming probes were dynamically masked during the analysis, using the scripts provided by Rehrauer et.al. (Rehrauer et al. 2009). Background correction, normalization, and summarization of probe sets were based on the Agronomics1 “all genes” CDF files with TAIR.9 annotation (Rehrauer et al. 2009) and RMA (Irizarry et al., 2003) implemented in the Aroma.Affymetrix package (Bengtsson et al., 2008).

organism: Arabidopsis thaliana

label_protocol: GeneChip 3' IVT Express kit

growth_protocol: Arabidopiss Col and rve8-1 seedlings (~50 plants/ per sample) were grown in 12 hours light/ 12 hours dark for 7 days before releasing to the constant light. After 72 hours in the constant light, samples were harvested every 4 hours for 2 days.

extract_protocol: trizol extraction, and then cleaned using Qiagen mini-elute columns

tag: genotype/variation

tag: circadian time

value: whole seedlings


title: GSCs AntimiR-138 -Replicate-1

description:
Isolated from glioma tissue
Replicate 1

tag: cell type


title: OV4656_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44605.gif

tag: reference

value: universal reference

value: Primary tumor, Ovarian

tag: age

value: 71 years

tag: tumor histology

value: IV


title: J LF brain rep2

tag: tissue


title: rve8_ConstantLight_112hr


title: J LF brain rep1


title: J HF brain rep2


title: sepal stage-3

city: Nagoya

first: Takashi

last: Negishi

state: Aichi

address: Furo-cho, Chikusa-ku

institute: Nagoya University Graduate School

description: Negative control probes (derived from bacteria, plant other than H. macrophylla, and bacteriophage) were spotted on 70 spots, and factory QC probes were spotted on 326 spots. Therefore, signal data from total of 396 control spots were included in 12,396-spot data on the custom-designed H. macrophylla oligo DNA microarray.

hyb_protocol: 5μg of the purified Cy5-aRNA sample was dissolved in 100μl of hybridization solution (CombiMatrix CustomArray 12K Hybridization and Imaging Protocol: PTL006), and hybridization reaction was carried out at 45ºC for 16hours.

scan_protocol: The microarrays went through post-hybridization washes according to CombiMatrix CustomArray 12K Hybridization and Imaging Protocol (PTL006), and they were scaned by Axon Instruments' GenePix 4000B scanner (5μm resolution, PMT gain at 450, Laser power at 100%).

data_processing: The raw data files were obtained from the scanned images using MicroarrayImager ver.6.0.1 (CombiMatrix Corp.), and were background-subtracted and median-normalized by Microsoft Office Excel 2003 within each of the microarray.  We employed simple fold-difference calculation using Microsoft Office Excel 2003 for each of the spot intensities between S1:S2, S1:S3, and S2:S3.  Since sample number (n) was 1 for all of the condition groups, there was no application of statistical analysis for this data processing.

organism: Hydrangea macrophylla

source_name: pooled sepal

label_protocol: 1μg of total RNA was reverse-transcribed using T7-oligo-dT primer and produced cDNA was double-stranded by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, cat#AM1753).  From ds-cDNA, aRNA was amplified and labeled with amino allyl UTP, and then Cy5-coupling to amino allyl modified aRNA was carried out according to the instruction of the Amino Allyl MessageAmp II aRNA Amplification Kit.

growth_protocol: Hydrangea macrophylla flower bouquet (blue sepal) was purchased at a local florist, and among them sepals at different growth stages were sampled for total RNA extraction.

extract_protocol: 100mg of sepal from each growth stage were collected, and total RNA was extracted by RNeasy Plant Mini Kit according to the manufacturer's protocol provided in the kit (QIAGEN, cat#74903).

treatment_protocol: There was no special treatment done on the sepal samples.

value: sepal

tag: growth stage

tag: position

value: Opened

tag: pigmentation

value: Full (dark blue)


title: sepal stage-2

value: Opening

value: Faint (light blue)


title: sepal stage-1

value: Closed

value: No


title: rve8_ConstantLight_108hr


title: KZ LF brain rep3

source_name: control mouse brain 2 days low-fat diet

value: BALB/cByKZ (Acads+/+)

tag: genotype

value: Acads+/+

value: brain

value: low-fat diet


title: 9h_SN_1

value: Sprague-Dawley

value: proximal sciatic nerve (SN)


title: Myxoid LPS-6

city: Houston

first: Hao

last: Hu

state: Texas

address: 1155 Pressler Blvd, Unit 1340

department: Epidemiology

institute: MD Anderson Cancer Center

hyb_protocol: cDNA samples were hybridised to 22K spotted cDNA microarrays.

scan_protocol: Intensity of Cy3 and Cy5 fluorescence for every gene spot on the hybridised arrays was measured with a GenePix 4000 scanner (Axon Instruments, Foster City, USA).

data_processing: Data was analysed with GenePix version 3.0 software (Axon instruments). GenePix calculates a normalization factor which is the mean log2 R/G signal ratio value of all probes in each array. This factor is used to scale the log2 R/G value of each probe.

source_name: myxoid liposarcoma

label_protocol: We prepared Cy3-labelled (green fluorescent) cDNA from reference mRNA and Cy5-labelled (red fluorescent) cDNA from mRNA from every tumour specimen.

growth_protocol: Not applicable.

extract_protocol: Tissue was homogenised in Trizol reagent (GibcoBRL/Invitrogen, Carlsbad, USA) and total RNA was prepared. We isolated mRNA by the FastTrack 2.0 method (Invitrogen).

treatment_protocol: Frozen tissue samples were obtained from soft-tissue tumour specimens resected at the Vancouver Hospital and Health Sciences Centre, the Stanford University Medical Centre, and the Hospital of the University of Pennsylvania between 1993 and 2003. We cut a frozen section from each specimen before RNA isolation to confirm that the sample was representative of the case.

value: myxoid liposarcoma

source_name: Universal Human Reference RNA

growth_protocol: Universal Human Reference RNA (Stratagene; Catalog No. 740000).

tag: sample type

value: reference


title: 6h_SN_1

source_name: SN_sciatic nerve resection_6h

tag: strain


title: SS-3

source_name: synovial sarcoma

value: synovial sarcoma


title: rve8_ConstantLight_100hr

value: whole seedlings


title: GSCs scrambled-Replicate-1

description:
Isolated from glioma tissue
Replicate 1

value: Glioma stem cells

tag: transducer

value: scrambled


title: 6h_SN_3


title: KZ LF brain rep1


title: J HF brain rep1

value: BALB/cByJ (Acads-/-)

value: Acads-/-

value: high-fat diet


title: 3h_SN_3

source_name: SN_sciatic nerve resection_3h


title: 6h_SN_2


title: 08hr-A

source_name: KH2 mES

tag: cell line

value: baseline

tag: time

value: 8 hours


title: 3h_SN_2

tag: weight


title: KZ LF brain rep2

value: BALB/cByKZ (Acads+/+)

tag: treatment


title: KZ HF brain rep3

source_name: control mouse brain 2 days high-fat diet

value: Acads+/+


title: Myxoid LPS-5


title: SFT-7

source_name: solitary fibrous tumor

value: solitary fibrous tumor


title: rve8_ConstantLight_96hr

tag: genotype/variation

tag: circadian time


title: cell line_HEK_miR_transfection

value: HEK

tag: cell type

value: human embryonic kidney cells

tag: transfected with

value: miR-941 mimics-Lipofectamine 2000 complexes


title: rve8_ConstantLight_104hr


title: rve8_ConstantLight_92hr


title: 3h_SN_1

value: Sprague-Dawley

value: proximal sciatic nerve (SN)


title: rve8_ConstantLight_88hr


title: 1h_SN_3

source_name: SN_sciatic nerve resection_1h


title: KZ HF brain rep2

value: brain


title: 1h_SN_2


title: KZ HF brain rep1


title: 1h_SN_1


title: MEL-1

source_name: melanoma

value: melanoma

value: reference


title: rve8_ConstantLight_76hr

value: whole seedlings


title: rve8_ConstantLight_84hr


title: 0.5h_SN_2

source_name: SN_sciatic nerve resection_0.5h


title: CCS-3

source_name: clear cell sarcoma

value: clear cell sarcoma


title: rve8_ConstantLight_80hr


title: SFT-6


title: Myxoid LPS-4

value: myxoid liposarcoma


title: Col_ConstantLight_112hr

value: Col


title: Myxoid LPS-3


title: Col_ConstantLight_116hr


title: CCS-1


title: 0.5h_SN_3


title: Col_ConstantLight_108hr


title: 0h_SN_3

source_name: SN_sciatic nerve resection_0h


title: rve8_ConstantLight_72hr


title: CCS-2


title: GSCs scrambled-Replicate-2

description:
Isolated from glioma tissue
Replicate 2

source_name: Glioma stem cells

value: Glioma stem cells

value: scrambled


title: SS-2

value: synovial sarcoma


title: Col_ConstantLight_104hr


title: OV4818_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43458.gif

source_name: universal reference

tag: reference

value: universal reference

value: Primary tumor, Ovarian

tag: age

value: 67 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: LMS-3

source_name: leiomyosarcoma

tag: tissue

value: leiomyosarcoma

tag: sample type


title: cell line_HEK_mock_transfection

description: Gene expression after mock transfection

tag: cell line

value: HEK

value: human embryonic kidney cells

value: mock oligonucleotides


title: 0.5h_SN_1

tag: strain

value: Sprague-Dawley

tag: weight

value: proximal sciatic nerve (SN)


title: SS-1

value: reference


title: 0h_SN_2


title: OV3743-CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43530.gif

value: 56 years


title: OV4600_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43874.gif

value: 64 years


title: SFT-5

value: solitary fibrous tumor


title: 0h_SN_1


title: Col_ConstantLight_96hr

tag: genotype/variation

value: Col

value: whole seedlings


title: Col_ConstantLight_92hr

tag: circadian time


title: SFT-4


title: rnh201 strain-4

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression at mid-log

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Saccharomyces cerevisiae

source_name: Total RNA, Strain-Δ|(-2)|-7B-YUNI300 (MATa CAN1 his7-2 leu2-Δ::kanMX ura3-Δ trp1-289 ade2-1 lys2-ΔGG2899-2900) rnh201::hphMX4 agp1:: URA3-OR1

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Strains were streaked onto yeast peptone dextrose adenine (YPDA) plates and grown at 30°C for 3 days. Individual colonies were grown in 25 mL YPDA at 30°C for 6-8 hours.  Cells were counted and a calculated volume from the day cultures diluted into 25 ml of YPDA and grown at 30°C overnight with constant shaking to achieve a cell density of 1-3 x 107 cells/ ml.

extract_protocol: Total RNA was isolated using a RiboPure yeast kit (Ambion), as per manufacturer’s instructions.

treatment_protocol: No treatment. In this study we compared a wild-type strain (WT) to a mutant strain lacking RNH201.

value: MUT delta RNH201 yeast


title: Col_ConstantLight_100hr


title: rnh201 strain-3

description: Gene expression at mid-log


title: rnh201 strain-2

description: Gene expression at mid-log

source_name: Total RNA, Strain- Δ|(-2)|-7B-YUNI300 (MATa CAN1 his7-2 leu2-Δ::kanMX ura3-Δ trp1-289 ade2-1 lys2-ΔGG2899-2900) rnh201::hphMX4 agp1:: URA3-OR1


title: SFT-2

source_name: Universal Human Reference RNA


title: Col_ConstantLight_88hr


title: SFT-3


title: rnh201 strain-1

description: Gene expression at mid-log


title: OV3709_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43460.gif

value: universal reference

value: 57 years


title: Col_ConstantLight_80hr


title: OV4762_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43421.gif

value: Primary tumor, Ovarian

value: 60 years


title: WT-4

description: Gene expression at mid-log

source_name: Total RNA, Strain-Δ|(-2)|-7B-YUNI300 (MATa CAN1 his7-2 leu2-Δ::kanMX ura3-Δ trp1-289 ade2-1 lys2-ΔGG2899-2900) agp1:: URA3-OR1

value: WT yeast


title: OV4704_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43094.gif

value: 70 years

value: IIIC


title: Myxoid LPS-1

source_name: myxoid liposarcoma

value: myxoid liposarcoma


title: Col_ConstantLight_72hr


title: Myxoid LPS-2


title: WT-3

description: Gene expression at mid-log


title: OV4488_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43871.gif

value: 71 years

value: serous


title: Col_ConstantLight_76hr


title: OV4305_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43049.gif


title: WT-2

description: Gene expression at mid-log


title: Col_ConstantLight_84hr


title: OV3935_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44488.gif

value: 55 years


title: OV4861-CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43534.gif

value: 66 years


title: WT-1

description: Gene expression at mid-log


title: OV4713_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43164.gif

value: 47 years


title: SFT-1

value: solitary fibrous tumor

value: reference


title: delta rnh201 #3SNM106

description: Gene expression at mid-log


title: OV5025-CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43529.gif


title: LMS-1

value: leiomyosarcoma


title: LMS-2


title: delta rnh201 #2SNM106

description: Gene expression at mid-log

source_name: Total RNA,Strain-Δ|(-2)|-7B-YUNI300 (MATa CAN1 his7-2 leu2-Δ::kanMX ura3-Δ trp1-289 ade2-1 lys2-ΔGG2899-2900) rnh201::hphMX4 agp1:: URA3-OR1

value: MUT delta RNH201 yeast


title: OV4203-CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43891.gif

value: universal reference

value: 73 years


title: WT-B #2 SNM8

description: Gene expression at mid-log

source_name: Total RNA, Strain- Δ|(-2)|-7B-YUNI300 (MATa CAN1 his7-2 leu2-Δ::kanMX ura3-Δ trp1-289 ade2-1 lys2-ΔGG2899-2900) agp1:: URA3-OR1


title: delta rnh201 #1SNM106

description: Gene expression at mid-log


title: OV4589_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44487.gif

value: Primary tumor, Ovarian

value: 81 years


title: WT-B #3 SNM8

description: Gene expression at mid-log

source_name: Total RNA, Strain Δ|(-2)|-7B-YUNI300 (MATa CAN1 his7-2 leu2-Δ::kanMX ura3-Δ trp1-289 ade2-1 lys2-ΔGG2899-2900) agp1:: URA3-OR1

value: WT yeast


title: OV4164-CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43533.gif

value: 57 years


title: Day6_SSEA1+EpCAM- 1

source_name: Sorted cells

treatment_protocol: Harvested cells were incubated with antibodies against Thy1.2 (PE conjugated, 53-2.1, eBiosciences), SSEA-1 (mouse IgM, MC-480, Developmental Hybridoma Bank) and optionally EpCAM (PE, G8.8, eBioscience) for 20 minutes. Cells were washed in PBS and then incubated for 20 minutes with APC conjugated anti mouse IgM, (eBioscience) and Pacific Blue-conjugated streptavidin (Invitrogen). The cells were washed in PBS, resuspended in propidium iodide 5% FBS/PBS solution and passed through a 40mm cell strainer to achieve single cell suspension. Cells were sorted on a FACSAria (BD Biosciences ) and/or analysed in a LSRII (BD Bioscience).  For analysis and/or sorting of intermediates, cells were stained with Thy1.2 and SSEA1 antibodies and sorted or analyzed as indicated.

tag: time after induction[days]

tag: cell stage

value: intermediates

value: NEG

value: POS

tag: epcam

tag: gfp


title: Day6_SSEA1+EpCAM+ 1


title: WT-B #1 SNM8

description: Gene expression at mid-log


title: OV4870_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs//43887.gif

tag: reference

tag: age

value: 65 years

tag: tumor histology

value: serous


title: Day6_SSEA1+EpCAM- 2


title: OV3997_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43431.gif

value: 38 years

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)


title: OV3998_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43045.gif

tag: tissue

value: 42 years

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: Day6_SSEA1+EpCAM+ 2


title: A549_EGFplus_rep1

status: Public on Dec 19 2012

city: Cleveland

first: yu

last: liu

address: 11900 Euclid

institute: Case Western Reserve University

hyb_protocol: Labeled cRNA was purified, fragmented and hybridized to human U133A GeneChip micro-arrays (Affymetrix) for 16 h at 45°C.

scan_protocol: Staining was performed on an Affymetrix fluidics station utilizing streptavidin/phycoerythrin conjugate (Molecular Probes, Invitrogen Life Science), followed by biotinylated antibody to streptavidin (Vector Laboratories, Burlingame, CA) and finally via a second streptavidin/ phycoerythrin conjugate. Stained micro-arrays were scanned on a Hewlett Packard GeneArray Scanner.

data_processing: Software Expander (version5.1) was used for data processing and analysis including RMA normalization and summarization.

source_name: A549 cells EGF stimulated

label_protocol: cDNA was synthesized using SuperScript II Reverse Transcriptase Kit (Invitrogen, Carlsbad, CA) and cRNA was synthesized using the GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA) using biotinylated ribonucleotides (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: Subconfluent A549 cells were seeded in 75-cm2 flasks for 12 h in media supplemented with 10% FBS.

extract_protocol: After 48 h of transfection, cells were harvested and total RNA was isolated using an RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Cells were untreated or transfected separately with either pCMV5 vector encoding human PIAS3 or siRNA against STAT3.

tag: cell line

tag: cell type

value: adenocarcinomic human alveolar basal epithelial cells


title: TUMOR, MANTLE CELL LYMPHOMA  ID6 [Affy_STY]

city: Barcelona

first: Sílvia

last: Beà

state: Barcelona

address: Rossello, 153

department: HematoPathology

country: Spain

institute: Hospital Clinic

description: Tumor, sty array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Image data were analysed
Primary data description: Data files were generated using the Affymetrix gene chip operating (GCOS) and gene chip genotyping analysis (GTYPE) software suites. GTYPE version 4.1 was used for the analysis of signal intensity and to determine genotype calls. Since no matched normal DNA was available, unpaired analysis using an independent reference set was performed. The complete data set was analyzed as combined subarrays (500K) by visual inspection using CNAT 4.0 (Affymetrix) and the copy number analyzer for gene chip (CNAG) v3.0 and by an algorithm described by Lenz and coworkers

label: Biotin

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID6

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from genomic DNA.

extract_protocol: Genomic DNA was extracted from frozen tissue of MCL prior to treatment using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: patient identifier

tag: source type

value: tumor genomic DNA from MCL patient

tag: gender

value: male

tag: translocation status of ccnd2

value: neg

tag: transl

tag: age/gender

tag: ln involvement

value: LN

tag: extranodal

value: BM

tag: ldh

value: Normal

tag: Stage

value: IV

tag: ipi

tag: therapy

value: C

tag: response

value: PR

tag: os (+ indicates alive)


title: TUMOR, MANTLE CELL LYMPHOMA  ID3 [Affy_STY]

description: Tumor, sty array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID3

value: CHOP


title: TUMOR, MANTLE CELL LYMPHOMA  ID4 [Affy_STY]

description: Tumor, sty array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID4

value: LN (multiple)

value: PB, BM, Spleen

value: High

value: COP+FCR


title: A549_PIAS3_rep1

source_name: A549 cell PIAS3 over expressed

tag: transfected with

value: pCMV5 vector encoding human PIAS3


title: TUMOR, MANTLE CELL LYMPHOMA  ID1 [Affy_STY]

description: Tumor, sty array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID1

value: female

value: LN (inguinal)

value: Intestine

value: IIIA

value: CR


title: A549_siRNA_STAT3_rep1

source_name: A549 cell siRNA against STAT3

tag: cell line

value: adenocarcinomic human alveolar basal epithelial cells

value: siRNA against STAT3


title: Airn 16kb truncation

type: mixed

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

hyb_protocol: The labeled ds-cDNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: Airn T16 5d differentiated D3 ESCs

label_protocol: 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol

growth_protocol: D3 ES cell lines were differentiated on gelatinized dishes after feeder cell depletion and LIF withdrawal by 0.27μM retinoic acid for 5 days.

extract_protocol: Total RNA was extracted from different cells. After the treatment of DNase I, total RNA was reverse transcribed, and synthesized to double-stranded cDNA. The genomic DNA isolated from D3 ES cell line was fragmented and used as Input DNA.

tag: cell line background

tag: cell type

value: Murine embryonic stem (ES) cells

tag: genotype/variation

value: polyA cassettes inserted before the Igf2r promoter

tag: day of differentiation

tag: airn length

value: Airn truncated to 16kb (T16)

source_name: wildtype D3 ESCs_sonicated genomic DNA

value: wild type


title: Airn 51kb truncation

source_name: Airn T51 5d differentiated D3 ESCs

value: polyA cassettes inserted after the Igf2r promoter

value: Airn truncated to 51kb (T51)


title: OV4633_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43163.gif

source_name: universal reference

tag: reference

value: universal reference

tag: tissue

value: Primary tumor, Ovarian

tag: age

value: 61 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: OV4641-CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43532.gif

value: 65 years


title: GFP:Gfi1-knock-in granulocytes

city: Montréal

first: Lothar

last: Vassen

state: Quebec

address: 110, avenue des Pins Ouest

department: Hematopoiesis and Cancer

country: Canada

institute: IRCM

description: Gene expression data from bone marrow derived GFP:Gfi1-KI/WT granulocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with Affymetrix Mouse Genome 430A 2.0 Arrays and Scanned using the Afymetrix scanner M10 at the BioChip laboratory of the University Hospital of Essen, Germany

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data was processed using the AltAnalyze software (www.altanalyze.org) using the default parameters.

source_name: Mouse bone marrow derived CD11b+, Gr1-high granulocytes from heterozygous GFP:Gfi1 knock-in mouse

label_protocol: Target RNA was reverse transcried into cDNA and in-vitro transcription was performed according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) to generate biotin-labeled cRNA.

growth_protocol: mice were housed under specific pathogen free (SPF) conditions.

extract_protocol: TRIzol (Invitrogen) was used to isolate total RNA following the manufacturers instructions.

treatment_protocol: untreated

tag: strain

value: C57BL/6 [backcrossings were done for at least 10 generations]

value: bone marrow

tag: genotype

value: GFP:Gfi1 KI/WT

value: 8 weeks


title: A549_siRNA_STAT3_rep2

tag: cell line

value: adenocarcinomic human alveolar basal epithelial cells

tag: transfected with


title: OV3872-CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43531.gif

scan_protocol: Scanner Model: GenePix 4000A

value: 48 years


title: Airn 27kb truncation

source_name: Airn T27 5d differentiated D3 ESCs

tag: cell line background

tag: cell type

value: Murine embryonic stem (ES) cells

value: Airn truncated to 27kb (T27)


title: Airn 31kb truncation

source_name: Airn T31 5d differentiated D3 ESCs

tag: genotype/variation

tag: day of differentiation

value: Airn truncated to 31kb (T31)


title: GFP:Gfi1-knock-in monocytes; Gfi1-high

description: Gene expression data from bone marrow derived GFP-high GFP:Gfi1-KI/WT monocytes

source_name: Mouse bone marrow derived CD11b+, Gr1-low, GFP-high monocytes from heterozygous GFP:Gfi1 knock-in mouse


title: GFP:Gfi1-knock-in monocytes; Gfi1-low

description: Gene expression data from bone marrow derived GFP-low GFP:Gfi1-KI/WT monocytes

source_name: Mouse bone marrow derived CD11b+, Gr1-low, GFP-low monocytes from heterozygous GFP:Gfi1 knock-in mouse


title: Forward Air Promoter (FAP)

source_name: Forward Air Promoter (FAP) ES cells

growth_protocol: ES cell line was differentiated on gelatinized dishes after feeder cell depletion and LIF withdrawal by 0.27μM retinoic acid for 5 days

extract_protocol: Total RNA was extracted from different tissues or cells. After the treatment of DNase I, total RNA was reverse transcribed, and synthesized to double-stranded cDNA. The genomic DNA isolated from D3 ES cell line was fragmented and used as Input DNA.

value: FAP ES cells

tag: airn length

value: wild type


title: A549_EGFplus_rep2

source_name: A549 cells EGF stimulated


title: Airn 3kb truncation

source_name: Airn T3 5d differentiated D3 ESCs

value: polyA cassettes inserted before the Igf2r promoter

value: Airn truncated to 3kb (T3)


title: A549_PIAS3_rep2

value: pCMV5 vector encoding human PIAS3


title: Gale WNV_WT_5_Sp_WN-TX

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse whole genome array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color Quick-Amp labeling kit. The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 6-12 week old mice wildtype C57bl/6 (WT), IFNAR-/-, IPS1-/- and IPS1-/-xIFNAR-/- mice were  subcutaneously infected with 100 PFU of WNV-TX in a 10 microl inoculum diluted in Hanks balanced salt solution (HBSS) supplemented with 1% heat-inactivated FBS or mock. Spleen and liver was isolated from strain and time-matched mock (n=2) and WNV-TX infected WT (n=3; day 4 post-infection), Ips-1-/-(n=3; day 4 post-infection), Ifnar-/- (n=3; day 2 post-infection), and Ips-1-/-xIfnar-/- (DKO; n=3; day 4 post-infection) animals for microarray analysis.

extract_protocol: Samples submerged in RNAlater were thawed and homogenized in TRIzol.  TRIzol lysates  were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Samples for microarray analysis were stored in RNAlater at -80 degrees C prior to RNA extraction.

tag: animal number

value: WT

tag: virus infection

value: WNV-TX

tag: tissue

value: spleen

tag: time

value: 4 days post-infection


title: Gale WNV_WT_4_Lv_WN-TX

value: liver


title: Gfi1 knock-out monocytes

description: Gene expression data from bone marrow derived Gfi1-KI/KI monocytes

source_name: Mouse bone marrow derived CD11b+, Gr1-low monocytes from Gfi1 knock-out mouse

value: C57BL/6 [backcrossings were done for at least 10 generations]

value: bone marrow

value: GFP:Gfi1 KI/KI

tag: age


title: Gale WNV_WT_1_Lv_Mock

value: Mock


title: Gale WNV_WT_2_Lv_Mock


title: Airn wildtype

source_name: wildtype 5d differentiated D3 ESCs

value: Murine embryonic stem (ES) cells

value: wild type; 118kb


title: TUMOR, MANTLE CELL LYMPHOMA  ID5 [Affy_STY]

description: Tumor, sty array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID5

tag: patient identifier

tag: source type

value: tumor genomic DNA from MCL patient

tag: gender

value: male

tag: translocation status of ccnd2

value: neg

tag: transl

tag: age/gender

tag: ln involvement

value: LN

tag: extranodal

value: BM

tag: ldh

value: Normal

tag: Stage

value: IV

tag: ipi

tag: therapy

value: CHOP

tag: response

value: PR

tag: os (+ indicates alive)


title: Gale WNV_IPS1-KO_7_Lv_Mock

tag: animal number

tag: genotype

tag: virus infection

tag: tissue

value: 4 days post-infection


title: Gale WNV_WT_5_Lv_WN-TX

value: WT

value: WNV-TX

value: liver

tag: time


title: Gale WNV_WT_4_Sp_WN-TX

value: spleen


title: Gale WNV_WT_3_Sp_WN-TX


title: Gale WNV_WT_3_Lv_WN-TX


title: Gale WNV_IPS1-KO_6_Sp_Mock

value: Mock


title: Gale WNV_WT_1_Sp_Mock


title: OV3798_CGH

city: Oslo

first: Aslaug

last: Helland

institute: Institute for Cancer Research, Oslo University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43870.gif

hyb_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: universal reference

value: Primary tumor, Ovarian

tag: age

value: 63 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: Gale WNV_WT_2_Sp_Mock


title: Gale WNV_IPS1-KO_8_Sp_WN-TX


title: Gale WNV_IPS1-KO_9_Lv_WN-TX


title: Gale WNV_IPS1-KO_10_Sp_WN-TX


title: Gale WNV_IPS1-KO_6_Lv_Mock_2


title: TUMOR, MANTLE CELL LYMPHOMA  ID45 [Agilent]

description: Tumor  vs normal

hyb_protocol: The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used. Protocol Version 3.1 was followed with slight modifications.

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Raw data were generated from scanned images using Agilent Feature Extraction Software (v10.7). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Genomic Workbench suite (v5.0), using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).  Waves aCGH correction algorithm (WACA), based on GC content and fragment size adjusted was applied in several cases.

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID45

label_protocol: As per manufacturer (Agilent)

extract_protocol: Genomic DNA was extracted from 27 MCL using the phenol-chloroform extraction method according to previously published protocols with minor modification. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis. All extracted DNAs had at least a PCR control gene band of 200 bp.

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: gender

value: male

tag: translocation status of ccnd2

value: neg

source_name: normal, sex-matched control DNA

value: sex-matched control


title: Gale WNV_IPS1-KO_9_Sp_WN-TX


title: TUMOR, MANTLE CELL LYMPHOMA  ID42 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID42

tag: patient identifier

tag: transl

tag: age/gender

tag: ln involvement

value: LN (inguinal)

tag: extranodal

value: Stomach

tag: ldh

value: Normal

tag: Stage

value: IIA

tag: ipi

tag: therapy

value: R

tag: response

value: CR

tag: os (+ indicates alive)


title: Gale WNV_IPS1-KO_10_Lv_WN-TX

tag: animal number

tag: genotype

tag: virus infection

value: WNV-TX

tag: tissue

value: liver

tag: time

value: 4 days post-infection


title: Gale WNV_IPS1-KO_7_Sp_Mock

value: Mock

value: spleen


title: TUMOR, MANTLE CELL LYMPHOMA  ID38 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID38

tag: source type

tag: gender

tag: translocation status of ccnd2

value: LN (mutiple)

value: BM, Spleen, Tonsil

value: III

value: R-CHOP


title: TUMOR, MANTLE CELL LYMPHOMA  ID40 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID40

tag: patient identifier

value: tumor genomic DNA from FFPE tissue of a MCL patient

value: male

tag: transl

tag: age/gender

value: LN (multiple)

value: BM, Spleen, Pleura

value: High

value: IV

value: PD


title: Post-IP scrambled NC-transfected vs. Pre-IP scrambled NC-transfected replicate 2

city: New Haven

first: Alan

last: Fu

state: CT

address: 60 College St.

institute: Yale University

hyb_protocol: Hybrdization was performed by MOGene, LC (St Louis, MO) using standard protocol from Agilent Whole Human Genome Oligo Microarray Kit

scan_protocol: Scanned on an Agilent G2565AA scanner by MOGene, LC (St Louis, MO)

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Human cervical cancer cell line (HeLa) - Post-IP scrambled NC-transfected replicate 2

label_protocol: Labeling was performed by MOGene, LC (St Louis, MO) using standard protocol from Agilent Whole Human Genome Oligo Microarray Kit

growth_protocol: HeLa cells were cultured in (+)-glutamine RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit (QIAGEN) with on-column DNA digestion.

treatment_protocol: Cells were transfected with either a miR-202 mimic or a scrambled negative control (Qiagen) using the Lipofectamine™ RNAiMAX transfection reagent (Invitrogen), according to the manufacturer’s protocol.  120 pmol of miR-202 mimic or negative control was mixed with 20 μl of RNAiMAX reagent in 2 ml of OPTI-MEM (Invitrogen). The complex was then added into a 100mm dish and incubated for 20 min at room temperature. Approximately 4 million cells were then seeded into the dish to a total volume of 10 ml and incubated for 12 hours at 37°C before harvesting.

tag: cell line

value: HeLa

tag: transfection

value: scrambled NC-transfected

tag: ip antibody

value: anti-EIF2C2/Ago2 monoclonal antibody:2E12-1C9, Cat.No:H00027161-M01,  Novus Biologicals, LLC

source_name: Human cervical cancer cell line (HeLa) - Pre-IP scrambled NC-transfected replicate 2

tag: ip

value: Pre-IP


title: Gale WNV_IFNR-KO_13_Lv_WN-TX

value: IFNR-KO

value: WNV-TX

value: liver

value: 2 days post-infection


title: Gale WNV_IPS1-KO_8_Lv_WN-TX

value: 4 days post-infection


title: TUMOR, MANTLE CELL LYMPHOMA  ID36 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID36

value: female

tag: ln involvement

value: LN (mutiple)

tag: extranodal

value: BM, Spleen

tag: ldh

tag: Stage

tag: ipi

tag: therapy

tag: response

value: sex-matched control


title: Gale WNV_IFNR-KO_15_Sp_WN-TX

tag: animal number

tag: genotype

tag: virus infection

tag: tissue

value: spleen

tag: time


title: Post-IP miR-202 mimic-transfected vs. Pre-IP miR-202 mimic-transfected replicate 2

source_name: Human cervical cancer cell line (HeLa) - Post-IP miR-202 mimc-transfected replicate 2

value: miR-202 mimic-transfected

source_name: Human cervical cancer - Pre-IP miR-202 mimc-transfected replicate 2


title: TUMOR, MANTLE CELL LYMPHOMA  ID29 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID29

tag: patient identifier

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: gender

value: male

tag: translocation status of ccnd2

tag: transl

tag: age/gender

value: LN (cervical)

value: BM, PB

value: IV

value: R, Bendamustine

value: NR

tag: os (+ indicates alive)


title: TUMOR, MANTLE CELL LYMPHOMA  ID35 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID35

tag: ln involvement

value: LN (multiple)

tag: extranodal

value: BM, PB, Spleen

tag: ldh

value: FCR


title: TUMOR, MANTLE CELL LYMPHOMA  ID37 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID37

value: BM, Tonsil

value: Normal

tag: Stage

tag: ipi

tag: therapy

value: FC

value: CR


title: DlitR_vs_wild type_repl3 (biofilm)

city: Tromsoe

first: Espen

middle: Mikal

last: Robertsen

address: Breivika

department: Chemistry

institute: University of Tromsoe

description: Biological replicate 3 of 4

hyb_protocol: Samples were hybridised to the microarrays at 42ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in 2×SSC/0.1% SDS for 5 min at 42ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.) Images were quantified using the GenePix v6.1 software

data_processing: The quantified signals were background corrected using “normexp” (LIMMA) with offset value 50 and normalized using print-tip loess and between-array quantile normalization. The expression data were analysed using the LIMMA framework in Bioconductor (http://www.bioconductor.org).

organism: Aliivibrio salmonicida LFI1238

source_name: wild type control grown for 72 hrs as statical biofilm at 4°C

label_protocol: cDNA was generated and labelled with Cy3 and Cy5 by using 15 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).

extract_protocol: Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)

tag: genotype/variation

value: wild type

tag: growth

value: 72 hrs as statical SWT biofilm at 4°C

source_name: DlitR mutant grown for 72 hrs as statical biofilm at 4°C

value: DlitR mutant


title: TUMOR, MANTLE CELL LYMPHOMA  ID30 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID30

value: tumor genomic DNA from FFPE tissue of a MCL patient

value: neg

value: LN (axillary)

value: IVA

value: R

tag: response

value: PD

value: sex-matched control


title: DlitR_vs_wild type_repl4 (biofilm)

description: Biological replicate 4 of 4 Dye swap


title: TUMOR, MANTLE CELL LYMPHOMA  ID39 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID39

value: male

value: LN (cervical)

value: Tonsil

value: IIA

value: R-COP

value: PR


title: Gale WNV_IFNR-KO_11_Sp_Mock

tag: animal number

tag: genotype

value: IFNR-KO

tag: virus infection

value: Mock

tag: tissue

value: spleen

tag: time

value: 2 days post-infection


title: Post-IP miR-202 mimic-transfected vs. Pre-IP miR-202 mimic-transfected replicate 1

source_name: Human cervical cancer cell line (HeLa) - Post-IP miR-202 mimc-transfected replicate 1

tag: cell line

value: HeLa

tag: transfection

value: miR-202 mimic-transfected

tag: ip antibody

value: anti-EIF2C2/Ago2 monoclonal antibody:2E12-1C9, Cat.No:H00027161-M01,  Novus Biologicals, LLC

source_name: Human cervical cancer - Pre-IP miR-202 mimc-transfected replicate 1

tag: ip

value: Pre-IP


title: TUMOR, MANTLE CELL LYMPHOMA  ID34 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID34

tag: patient identifier

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: gender

value: female

tag: translocation status of ccnd2

value: D2-unknown partner

tag: transl

tag: age/gender

tag: ln involvement

value: LN

tag: extranodal

value: BM, PB

value: Normal

value: IV

value: R-CHOP, RDHAP, BMT

value: CR

tag: os (+ indicates alive)

source_name: normal, sex-matched control DNA


title: DlitR_vs_wild type_repl1 (biofilm)

description: Biological replicate 1 of 4

tag: genotype/variation

value: wild type

tag: growth

value: 72 hrs as statical SWT biofilm at 4°C

value: DlitR mutant


title: DlitR_vs_wild type_repl4 (suspension)

description: Biological replicate 4 of 4 Dye swap

hyb_protocol: Samples were hybridised to the microarrays at 42ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in2×SSC/0.1% SDS for 5 min at 42ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.

source_name: DlitR mutant grown at 8°C and harvested at an OD600 of 0.8

value: SWT suspension medium at 8°C and harvested at an OD600 of 0.8

source_name: wild type control grown at 8°C and harvested at an OD600 of 0.8


title: DlitR_vs_wild type_repl2 (biofilm)

description: Biological replicate 2 of 4


title: LPSX3 cell culture

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: cultured cells derived from xenograft tumor of LPSX3

hyb_protocol: Following Agilent Human 44K microarray processing protocol

scan_protocol: Scanned on an Agilent Scanner

data_processing: Agilent Feature Extraction software v.7.5 was used to calculate gene expression values.  For multiple spots representing each unique probe, the average of their intensity ratios (log10 of  Cy5/Cy3) was used to represent the probe.

source_name: Mixed reference pool of fatty tumors

label_protocol: Using Agilent Quick Amp Labeling Kit (Agilent Technologies) and protocol

extract_protocol: Total RNA was extracted using QIAzol RNA Kit following manufacturer's instructions

tag: reference

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX3 cell culture

tag: tissue type

value: cell culture

tag: cell type

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism


title: Gale WNV_IFNR-KO_12_Sp_Mock

tag: animal number

tag: genotype

value: IFNR-KO

tag: virus infection

value: Mock

tag: tissue

value: spleen

tag: time

value: 2 days post-infection


title: DlitR_vs_wild type_repl2 (suspension)

description: Biological replicate 2 of 4


title: DlitR_vs_wild type_repl1 (suspension)

description: Biological replicate 1 of 4


title: TUMOR, MANTLE CELL LYMPHOMA  ID32 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID32

tag: patient identifier

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: gender

value: male

tag: translocation status of ccnd2

tag: transl

value: LN (axillary)

value: BM

tag: ldh

tag: Stage

tag: ipi

tag: therapy

tag: response

value: sex-matched control


title: TUMOR, MANTLE CELL LYMPHOMA  ID16 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID16

value: D2-unknown partner

tag: age/gender

tag: ln involvement

value: LN (multiple)

tag: extranodal

value: BM, Spleen

value: IV

value: R-CHOP

value: CR

tag: os (+ indicates alive)


title: Gale WNV_IFNR-KO_14_Lv_WN-TX

tag: animal number

tag: genotype

tag: virus infection

value: WNV-TX

value: liver


title: LPSX3 Xenograft passage 16

description: Xenograft tumor of LPSX3 at passage 16

tag: reference

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX3 Xenograft passage 16

tag: tissue type

value: xenograft

tag: cell type

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: Post-IP scrambled NC-transfected vs. Pre-IP scrambled NC-transfected replicate 1

source_name: Human cervical cancer cell line (HeLa) - Post-IP scrambled NC-transfected replicate 1

tag: cell line

value: HeLa

tag: transfection

value: scrambled NC-transfected

tag: ip antibody

value: anti-EIF2C2/Ago2 monoclonal antibody:2E12-1C9, Cat.No:H00027161-M01,  Novus Biologicals, LLC

source_name: Human cervical cancer cell line (HeLa) - Pre-IP scrambled NC-transfected replicate 1

tag: tissue

tag: ip

value: Pre-IP


title: Gale WNV_IFNR-KO_14_Sp_WN-TX

value: IFNR-KO

value: spleen

tag: time

value: 2 days post-infection


title: TUMOR, MANTLE CELL LYMPHOMA  ID17 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID17

tag: patient identifier

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: gender

value: female

tag: translocation status of ccnd2

tag: transl

tag: age/gender

tag: ln involvement

value: LN (cervical)

value: BM, Duodenum, Colon

tag: ldh

tag: Stage

value: IVA

tag: ipi

tag: therapy

tag: response

value: sex-matched control


title: TUMOR, MANTLE CELL LYMPHOMA  ID18 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID18

value: male

value: LN

tag: extranodal

value: BM, PB, Tonsil

value: IVB

value: CT and RT

value: PD

tag: os (+ indicates alive)


title: LPSX3 Xenograft passage 6 mechanic dissociation

description: Xenograft tumor of LPSX3 at passage 6; mechanical dissociated cells were used in the subcutaneous injection

tag: reference

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX3 Xenograft passage 6 mechanical dissociation

tag: tissue type

value: xenograft

tag: cell type

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: DlitR_vs_wild type_repl3 (suspension)

description: Biological replicate 3 of 4

source_name: wild type control grown at  8°C and harvested at an OD600 of 0.8

tag: genotype/variation

value: wild type

tag: growth

value: SWT suspension medium at 8°C and harvested at an OD600 of 0.8

value: DlitR mutant


title: Gale WNV_IFNR-KO_15_Lv_WN-TX

tag: animal number

tag: genotype

value: IFNR-KO

tag: virus infection

value: WNV-TX

tag: tissue

value: liver

tag: time

value: 2 days post-infection


title: TUMOR, MANTLE CELL LYMPHOMA  ID27 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID27

tag: patient identifier

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: gender

value: male

tag: translocation status of ccnd2

value: neg

tag: transl

tag: age/gender

tag: ln involvement

value: LN (inguinal)

value: No

tag: ldh

value: Normal

tag: Stage

value: IIIA

tag: ipi

value: sex-matched control


title: TUMOR, MANTLE CELL LYMPHOMA  ID26 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID26

value: female

tag: extranodal

value: BM, Spleen

value: High

value: IV

tag: therapy

value: R-CHOP

tag: response

value: PR

tag: os (+ indicates alive)


title: TUMOR, MANTLE CELL LYMPHOMA  ID8 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID8

value: Colorectal†

value: IIAE


title: TUMOR, MANTLE CELL LYMPHOMA  ID14 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID14

value: LN (multiple)

value: BM, Gastrointestinal tract

source_name: normal, sex-matched control DNA


title: HPHC-4wk-R12

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip mouse genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: The data were normalized using the Robust Multichip Average methods (RMA)

source_name: Liver, 4 weeks feeding

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

extract_protocol: Liver total RNA was extracted from frozen tissue using TriPure Isolation Reagent (Roche Applied Science, Indianapolis, IN, USA), following the instruction of the manufacturer.

value: male

tag: strain

tag: diet

value: HPHC

tag: time point


title: HPHC-4wk-R11


title: HPHC-4wk-R10


title: LPSX3 Xenograft passage 6 frozen/thaw

description: Xenograft tumor of LPSX3 at passage 6; frozen-then-thaw cells were used in the subcutaneous injection

source_name: Mixed reference pool of fatty tumors

tag: reference

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX3 Xenograft passage 6 frozen/thaw

tag: tissue type

value: xenograft

tag: cell type

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: TUMOR, MANTLE CELL LYMPHOMA  ID25 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID25

tag: patient identifier

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: gender

value: female

tag: translocation status of ccnd2

value: neg

tag: transl

tag: age/gender

value: LN (cervical)

value: CR

value: sex-matched control


title: TUMOR, MANTLE CELL LYMPHOMA  ID13 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID13

tag: ln involvement

tag: extranodal

value: BM

tag: ldh

tag: Stage

value: IVB

tag: ipi

tag: therapy


title: TUMOR, MANTLE CELL LYMPHOMA  ID23 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID23

value: LN

value: BM, CNS

value: CHOP

tag: response

tag: os (+ indicates alive)


title: HPHC-4wk-R09

value: male

tag: strain

tag: diet

value: HPHC

tag: time point


title: TUMOR, MANTLE CELL LYMPHOMA  ID31 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID31

tag: patient identifier

value: LN (periaortic)

value: High

value: IVA

value: R CHOP


title: HPHC-4wk-R07


title: Gale WNV_IFNR-KO_12_Lv_Mock

tag: animal number

tag: genotype

value: IFNR-KO

tag: virus infection

value: Mock

tag: tissue

value: liver

tag: time

value: 2 days post-infection


title: HPHC-4wk-R06

tag: gender


title: Gale WNV_IFNR-KO_11_Lv_Mock


title: TUMOR, MANTLE CELL LYMPHOMA  ID12 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID12

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: translocation status of ccnd2

value: neg

tag: transl

tag: age/gender

tag: ln involvement

value: LN (inguinal)

tag: extranodal

value: No

value: Normal

value: IA

value: R-CHOP+RT

value: CR


title: LPSX3 Xenograft passage 6 chunk

description: Xenograft tumor of LPSX3 at passage 6; chunks were used in the subcutaneous injection

tag: reference

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX3 Xenograft passage 6 chunk

tag: tissue type

value: xenograft

tag: cell type

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: Gale_WNV_STI-KO/IFNAR-KO_21_Lv_D4_WN-TX

tag: animal number

value: DKO

value: WNV-TX

value: 4 days post-infection


title: HPHC-4wk-R08

value: male

tag: strain

tag: diet

value: HPHC

tag: time point


title: HPHC-4wk-R05


title: TUMOR, MANTLE CELL LYMPHOMA  ID9 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID9

tag: patient identifier

value: tumor genomic DNA from FFPE tissue of a MCL patient

value: female

value: neg

value: LN

value: BM

tag: ldh

tag: Stage

value: IVA

tag: ipi

tag: therapy

value: R-CHOP

tag: response

tag: os (+ indicates alive)

value: sex-matched control


title: LPSX3 Xenograft passage 6

description: Xenograft tumor of LPSX3 at passage 6

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX3 Xenograft passage 6

value: xenograft


title: TUMOR, MANTLE CELL LYMPHOMA  ID15 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID15

tag: source type

tag: gender

tag: translocation status of ccnd2

tag: transl

tag: age/gender

tag: ln involvement

value: LN (cervical)

tag: extranodal

value: Waldeyer ring, Tonsil

value: IIIB


title: LPSX3 Xenograft passage 6 strainer

description: Xenograft tumor of LPSX3 at passage 6; cells dissociated by straining method before being used in the subcutaneous injection

tag: reference

source_name: LPSX3 Xenograft passage 6 strainer

tag: tissue type

tag: cell type

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: LPSX3 Xenograft passage 1

description: Xenograft tumor of LPSX3 at passage 1

source_name: LPSX3 Xenograft passage 1


title: Gale WNV_IFNR-KO_13_Sp_WN-TX

tag: animal number

tag: genotype

value: IFNR-KO

tag: virus infection

value: WNV-TX

tag: tissue

value: spleen

tag: time

value: 2 days post-infection


title: Gale_WNV_STI-KO/IFNAR-KO_21_Sp_D4_WN-TX_2

value: DKO

value: 4 days post-infection


title: HPHC-4wk-R02

value: male

tag: strain

tag: diet

value: HPHC

tag: time point


title: Gale_WNV_STI-KO/IFNAR-KO_18_Lv_D4_Mock_2

value: Mock

value: liver


title: HPHC-4wk-R01

tag: gender


title: LPSX2 cell culture

description: cultured cells derived from xenograft tumor of LPSX2

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX2 cell culture

value: cell culture


title: HPHC-4wk-R03


title: HPHC-2d-R10

source_name: Liver, 2 days feeding


title: TUMOR, MANTLE CELL LYMPHOMA  ID28 [Agilent]

description: Tumor  vs normal

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID28

tag: patient identifier

tag: source type

value: tumor genomic DNA from FFPE tissue of a MCL patient

tag: translocation status of ccnd2

tag: transl

tag: age/gender

value: LN (inguinal)

value: BM, PB

tag: ldh

tag: Stage

value: IV

tag: ipi

tag: therapy

tag: response

tag: os (+ indicates alive)

source_name: normal, sex-matched control DNA

value: sex-matched control


title: LPSX2 Xenograft from cell culture

description: Xenograft tumor grew from the cultured cells derived from LPSX2 xenograft

source_name: Mixed reference pool of fatty tumors

tag: reference

source_name: LPSX2 Xenograft from cell culture

tag: tissue type

value: xenograft

tag: cell type

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: HPHC-2d-R11

tag: gender

tag: strain

tag: diet

tag: time point


title: HPHC-4wk-R04

source_name: Liver, 4 weeks feeding


title: HPHC-2d-R12


title: Gale_WNV_STI-KO/IFNAR-KO_18_Sp_D4_Mock

tag: animal number

tag: genotype

value: DKO

tag: virus infection

tag: tissue

value: spleen

tag: time


title: HPHC-2d-R09

value: male


title: LPSX2 Xenograft passage 6

description: Xenograft tumor of LPSX2 at passage 6

source_name: LPSX2 Xenograft passage 6


title: Gale_WNV_STI-KO/IFNAR-KO_17_Lv_D4_Mock

value: 4 days post-infection


title: Gale_WNV_STI-KO/IFNAR-KO_20_Lv_D4_WN-TX

value: WNV-TX


title: LPSX2 Xenograft passage 4

description: Xenograft tumor of LPSX2 at passage 4

source_name: LPSX2 Xenograft passage 4


title: HPHC-2d-R07

value: HPHC


title: HPHC-2d-R06


title: HPHC-2d-R05


title: Gale_WNV_STI-KO/IFNAR-KO_20_Sp_D4_WN-TX


title: Gale_WNV_STI-KO/IFNAR-KO_17_Sp_D4_Mock

value: Mock


title: LPSX2 Xenograft passage 0

description: Xenograft tumor of LPSX2 first grew in mouse from the inplantation of the orignal human tumor

value: total RNA from human 8 benign fatty tumors (7 lipomas, 1 hibernoma), 33 well differentitated liposarcoma, 15 de-differentiated liposarcoma, 2 pleomorphic liposarcoma, and 11 myxoid liposarcomas

source_name: LPSX2 Xenograft passage 0


title: Gale_WNV_STI-KO/IFNAR-KO_19_Lv_D4_WN-TX

value: liver


title: Gale_WNV_STI-KO/IFNAR-KO_19_Sp_D4_WN-TX


title: HFHC-4wk-R12

value: HFHC


title: LPSX1 Xenograft passage 15

description: Xenograft tumor of LPSX1 at passage 15

source_name: LPSX1 Xenograft passage 15


title: HPHC-2d-R01


title: DU 145-3

first: Angela

last: Ting

state: Ohio

address: 9500 Euclid Ave/NE50

department: Genomic Medicine

institute: Cleveland Clinic

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalized and analyzed using the Illumina GenomeStudio v2009.1.

source_name: cultured prostate carcinoma cell line

growth_protocol: All cell lines were cultured in media recommended by the distributors at 37oC, 5% CO2.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by DNase I treatment.  RNA quality and concentration was measure using the nanodrop spectrophtometer.

tag: origin

value: ATCC

tag: cell line


title: LPSX3_com_3

description: LPSX3 xenograft tumor after combination (rapamycin & sorafenib) treatment, biological replicate 3

hyb_protocol: Following Agilent SurePrint Human GE 8x60 microarray protocol

scan_protocol: Arrays were scanned with Agilent DNA Microarray Scanner.   Numerical results were extracted with Feature Extraction software version 10.7.1 using 028004_D_F_20110708 grid, GE1_107_Sep09 protocol and GE1_QCMT_Sep09 metric set

data_processing: Text files from Agilent Feature Extraction software were processed and normalized by Agi4x44PreProcess package (version 1.14.0)  downloaded from Bioconductor.  In brief, the signal was adjusted by background correction, and the normalized by quantile method.  Probes were fitered out if their signals were abcent (i.e. not above the background) in more than 75% of samples.

source_name: LPSX3, combo treated

label_protocol: Using Agilent LowInput Quick Amp One Color Labeling Kit (Agilent Technologies) and protocol

extract_protocol: Roche's MagNA Pure Compact Nucleic Acid Purification System was used for automated RNA isolation.


title: HPHC-2d-R03


title: LPSX1 Xenograft passage 10

description: Xenograft tumor of LPSX1 at passage 10

source_name: LPSX1 Xenograft passage 10


title: LPSX1 cell culture

description: cultured cells derived from xenograft tumor of LPSX1

source_name: LPSX1 cell culture

value: cell culture


title: LNCaP-3

description: replicate 3

label_protocol: Standard Illumina hybridization protocol

value: LNCaP


title: HFHC-4wk-R11


title: HFHC-4wk-R07


title: HPHC-2d-R04


title: HFHC-4wk-R05


title: RWPE-1-3

description: replicate 3

source_name: cultured HPV-tranformed normal prostate epithelial cells

value: RWPE


title: HPHC-2d-R02


title: HFHC-4wk-R09


title: LPSX1 Xenograft passage 5

description: Xenograft tumor of LPSX1 at passage 5

source_name: LPSX1 Xenograft passage 5

value: xenograft

value: liposarcoma


title: HFHC-4wk-R10


title: HFHC-4wk-R06


title: HFHC-4wk-R08