title: Black.022807.Mouse 430_2

city: Boston

first: Irit

last: Adini

address: 1 balckfan circle

department: Vascular Biology Department

institute: Boston Children's Hospital

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

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing:
program-name = Expression Console
program-id = 1.3.1.187
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0

source_name: pigmented melanocytes

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

growth_protocol: Cells were grown in RPMI 1640 medium containing FCS 2-ME (2-Mercaptoethanol) and TPA (tetradecanoyl phorbol acetate) at 37°C and 10% CO2.

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

treatment_protocol: Medium is changed twice a week.  Media was supplemented with additional phenol red to maintain pH. Cells are grown to appropriate confluence then rinsed with PBS with 0.7% NaCl, , and placed on ice in the RNeasy Mini Kit from QIAGEN.

value: Balb/c

value: wild type (point mutation corrected)

value: skin

value: pigmented melanocytes


title: Multiple Sclerosis 4_1

status: Public on Sep 21 2013

type: RNA

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Gene expression of initial lesion

hyb_protocol: The Hybridization Mix was prepared using the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) and hybridized to the Arrays using the Agilent Microarray Hybridzation Chamber Kit (G2534A). After the hybridization, the Arrays were washed using the Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326). The Hybridization was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

scan_protocol: The scanning was done with the Agilent Microarray Scanner (Agilent p/n G2565BA). Information from scan data was processed using the Agilent’s Scan Control software, version A.7.0.1 and data were extracted with the Agilent Feature Extraction Software 9.5.1. The scanning as well as the feature extraction was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

data_processing: The 75th percentile signal values were used to normalize the Agilent one-colour microarray signals. BEFORE 2013: Noramlization was done over all the cases included in each comparion (e.g. all 4 controls vs all 3 NAWMs)and log2fold changes were calculated with those normalized data. The log2fold change data matrix for each comparison [Control vs EL (=innate lesion), Control vs LL (=early demyelinated lesion), Control vs NAWM] is provided as a supplementary file on the Series records. Each file is a combination of the 7 Samples for each of the three comparisons described in the manuscript Fischer et al., 2012. UPDATE in 2013: Normalization was done over all 16 arrays.

molecule: total RNA

organism: Homo sapiens

source_name: Initial lesion

label_protocol: For the labeling, the Low RNA Input Linear Amplification Kit, PLUS, One colour was used (Agilent p/n 5188-5339). The labelled cRNA was purified using Quiagen’s RNeasy spin colums (RNeasy Mini Kit, Quiagen p/n 74104) and quantified using a NanoDrop ND-1000 Spectrophotometer. Labeling was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

extract_protocol: Sections from formaldehyde-fixed, paraffin-embedded (FFPE) tissue were used. Consecutively cut sections of 6-10 µm were mounted on glass slides in RNAse-free conditions. The localization of interest was marked in the Klüver-Barrera stained slide which was used as template for the scratching with a scalpel from the unstained slices. The scratched FFPE material was collected, each region of interest to a separate Eppendorf tube. The scratched material in the Eppendorf tubes was deparaffinated with Xylol, afterwards total RNA was isolated using the Roche High Pure FFPE RNA Micro Kit. The mRNA in the isolate was then transcribed to the cDNA using the Paradise® Reagent System (Arcturus, USA). Two rounds of linear amplification were performed and the obtained purified aRNA was then sent to Imagenes (imaGenes GmbH, D-13125 Berlin, www.imagenes-bio.de) where the RNA was Cy 3 labeled and hybridized to human whole genome 4x44K Agilent platforms. The Roche High Pure FFPE RNA Micro Kit as well as the Paradise® Reagent System was used according to the instructions of the manufacturer.

tag: brain tissue

value: White matter

tag: disease state

value: initial lesion


title: HFD + Pio - BLKS Group 6- mouse 2

city: Indianapolis

first: Emily

middle: K

last: Sims

state: IN

address: 705 Riley Hospital Drive, Room 5960

country: USA

institute: Indiana University School of MEdicine

description: islet gene expression after 12 weeks of diet treatment

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocl using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Auburn, CA).  Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridzation bufer was hybridized for 17 hours at 65°C to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.  The microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 for 1 minute.  The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System Agilent Technologies, Auburn, CA).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.  The software determines feature intesities (including background subtraction), rejects outliers and calculates statistical confidences.  For determination of differential gene expression FES derived output data files were further analyzed using the Roseeta Resolver gene expression data analysis system (Rosetta Biosoftware)

organism: Mus musculus

source_name: HFD + Pio - BLKS Group 6- mouse 2

label_protocol: To produce Cy3-labeled cRNA, RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, Auburn, CA) following the manufacterer's protocol.  Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies, Thermo Fisher Scientific, Waltham, MA).

extract_protocol: Mouse islets were isolated from collagenase-perfused pancreata  (CIzyme MA; VitaCyte, Indianapolis, IN) and neutral protease (CIzyme BP Protease; VitaCyte).  RNA was shipped to Miltenyi Biotec on dry ice and was isolated using standard RNA extraction protocols (NucleoSpin RNA II).  Samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Miltenyi Biotec, Agilent Technologies, Auburn, CA)

treatment_protocol: male 8 week-old BL6 and BLKS mice were fed normal chow (18% kcal from fat), HFD (42% kcal from fat), or HFD supplemented with the PPAR-γ agonist pioglitazone (PIO) (140 mg PIO/kg diet) for 12 weeks.

tag: strain

tag: gender

value: male

tag: age

value: 8 week-old

tag: tissue

value: islets


title: BLK.11-22-06 mouse 430_2

state: MA

label: biotin

tag: strain background

tag: genotype/variation

tag: cell type


title: Multiple Sclerosis 4_4

description: Gene expression of early demyelinated lesion

source_name: Early demyelinated lesion

value: early demyelinated lesion


title: HFD + Pio - BLKS Group 6- mouse 1

source_name: HFD + Pio - BLKS Group 6- mouse 1


title: HFD- BLKS Group 5- mouse 3

source_name: HFD- BLKS Group 5- mouse 3


title: HFD- BLKS Group 5- mouse 4

source_name: HFD- BLKS Group 5- mouse 4


title: Albino.022807.Mouse 430_2

source_name: non-pigmented melanocytes

value: homozygous point mutation in tyrosinase gene

value: non-pigmented melanocytes


title: Chow-BLKS Group 4-mouse 4

source_name: Chow-BLKS Group 4-mouse 4


title: HFD- BLKS Group 5- mouse 2

source_name: HFD- BLKS Group 5- mouse 2


title: HFD- BLKS Group 5- mouse 1

source_name: HFD- BLKS Group 5- mouse 1


title: ALB.11-22-06 mouse 430_2


title: HFD + Pio - BL/6 Group 3- mouse 4

source_name: HFD + Pio - BL/6 Group 3- mouse 4


title: HFD + Pio - BLKS Group 6- mouse 4

source_name: HFD + Pio - BLKS Group 6- mouse 4


title: Chow-BLKS Group 4-mouse 1

source_name: Chow-BLKS Group 4-mouse 1


title: HFD- BL/6 Group 2- mouse 4

source_name: HFD- BL/6 Group 2- mouse 4


title: Chow-BL/6 Group 1-mouse 3

source_name: Chow-BL/6 Group 1-mouse 3


title: HFD + Pio - BL/6 Group 3- mouse 1

source_name: HFD + Pio - BL/6 Group 3- mouse 1


title: HFD + Pio - BL/6 Group 3- mouse 2

source_name: HFD + Pio - BL/6 Group 3- mouse 2


title: Multiple Sclerosis 4_3


title: HFD- BL/6 Group 2- mouse 3

source_name: HFD- BL/6 Group 2- mouse 3


title: Chow-BL/6 Group 1-mouse 1

source_name: Chow-BL/6 Group 1-mouse 1


title: HFD + Pio - BLKS Group 6- mouse 3

source_name: HFD + Pio - BLKS Group 6- mouse 3


title: Chow-BLKS Group 4-mouse 3

source_name: Chow-BLKS Group 4-mouse 3


title: HFD- BL/6 Group 2- mouse 1

source_name: HFD- BL/6 Group 2- mouse 1


title: Chow-BLKS Group 4-mouse 2

source_name: Chow-BLKS Group 4-mouse 2


title: spleen_Myd88_PcAS_24h_3

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

description: Sample name: Myd88PcAS-3

hyb_protocol: 600 ng of each Cy3-labeled aaRNA hybridized to a SurePrint G3 Mouse Gene Expression 8x60K microarray (Agilent) as per manufacturers protocol.

scan_protocol: Arrays were scanned on an Agilent scanner, 3 um resolution, 20-bit tiff

data_processing: Custom in-house scripts and the Bioconductor Limma package were used for filtering and normalization.  Control features and sample features with saturated, non-uniform feature, and non-uniform background flags were removed.  Genes present across 70% of arrays were retained, log2 transformed, KNN-imputed, and quantile normalized.  Genes determined to be not expressed were filtered out (expressed genes = log2 intensity >= 7 across all samples within a group).  Arrays were median centered, followed by median centering of genes.

source_name: Myd88 knockout, whole spleen, P. chabaudi infection, 24h

label_protocol: 1.5 ug of aRNA coupled to Cy3 in 0.1 M sodium bicarbonate pH 9 buffer and purified over spin columns

growth_protocol: Total spleen RNA extraction 24h post mock- or P. chabaudi-infection

extract_protocol: RNA was isolated from frozen spleens disrupted in 1mL Trizol at 30/s for 3 min in a TissueLyser II (Qiagen, Valencia, CA), followed by RNA isolation (RNAqueous Micro, Life Technologies).  Purified RNA was amplified (MessageAmp II , Life Technologies) with minor modifications to manufacturer’s instructions to generate amino-allyl incorporated amplified RNA.

treatment_protocol: Mice were either injected ip with 10^6 uninfected or infected erythrocytes from a donor mouse

value: female

tag: background strain

value: Myd88 knockout

value: spleen

tag: infection

value: P. chabaudi

tag: infection duration


title: spleen_Myd88_PcAS_24h_4

description: Sample name: Myd88PcAS-4


title: Chow-BL/6 Group 1-mouse 2

source_name: Chow-BL/6 Group 1-mouse 2


title: Chow-BL/6 Group 1-mouse 4

source_name: Chow-BL/6 Group 1-mouse 4


title: spleen_Myd88_PcAS_24h_1

description: Sample name: Myd88PcAS-1


title: spleen_Myd88_PcAS_24h_2

description: Sample name: Myd88PcAS-2


title: HFD + Pio - BL/6 Group 3- mouse 3

source_name: HFD + Pio - BL/6 Group 3- mouse 3


title: HFD- BL/6 Group 2- mouse 2

source_name: HFD- BL/6 Group 2- mouse 2


title: spleen_Myd88_mock_4

description: Sample name: Myd88mock-4

source_name: Myd88 knockout, whole spleen, mock infection, 24h

value: mock


title: spleen_Myd88_mock_2

description: Sample name: Myd88mock-2


title: spleen_Myd88_mock_3

description: Sample name: Myd88mock-3


title: paediatric low grade glioma_LGG_37

city: Genova

first: annalisa

last: barla

state: GE

address: via Dodecaneso 35

department: DIBRIS

country: Italy

institute: Università degli Studi di Genova

description: Gene expression data from pediatrics low grade gliomas

hyb_protocol: Hybridization was performed according Affymetrix GeneChip Expression Analysis Technical Manual

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: Gene expressions were extracted from the .CEL files and normalized using the Robust Multichip Average method by running an R script based on the aroma package.

source_name: tumour sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted from serial frozen sections of tumour tissue by using the TRIzol reagent combined with silica column purification system

treatment_protocol: Tumour samples were included in HistoGel prior to dissection in 10 μm slices

tag: lesion site

value: supratentorial


title: spleen_Unc93b1_PcAS_24h_3

description: Sample name: UncPcAS-3

source_name: Unc93b1-3d, whole spleen, P. chabaudi infection , 24h

value: Unc93b1 knockout


title: spleen_Unc93b1_PcAS_24h_2

description: Sample name: UncPcAS-2


title: paediatric low grade glioma_LGG_35


title: paediatric low grade glioma_LGG_38


title: paediatric low grade glioma_LGG_34


title: paediatric low grade glioma_LGG_36


title: paediatric low grade glioma_LGG_39


title: paediatric low grade glioma_LGG_40


title: spleen_Myd88_mock_1

description: Sample name: Myd88mock-1


title: spleen_Unc93b1_PcAS_24h_4

description: Sample name: UncPcAS-4


title: paediatric low grade glioma_LGG_33


title: paediatric low grade glioma_LGG_30


title: spleen_Unc93b1_PcAS_24h_1

description: Sample name: UncPcAS-1


title: spleen_Unc93b1_mock_4

description: Sample name: Uncmock-4

source_name: Unc93b1-3d, whole spleen, mock infection, 24h


title: paediatric low grade glioma_LGG_29


title: paediatric low grade glioma_LGG_25


title: spleen_Unc93b1_mock_3

description: Sample name: Uncmock-3


title: paediatric low grade glioma_LGG_28


title: paediatric low grade glioma_LGG_31


title: paediatric low grade glioma_LGG_32


title: paediatric low grade glioma_LGG_26


title: paediatric low grade glioma_LGG_27


title: paediatric low grade glioma_LGG_24


title: spleen_Tlr7_PcAS_24h_2

description: Sample name: T7PcAS-2

source_name: Tlr7 knockout, whole spleen, P. chabaudi infection, 24h

value: Tlr7 knockout


title: spleen_Tlr7_PcAS_24h_3

description: Sample name: T7PcAS-3


title: spleen_Unc93b1_mock_2

description: Sample name: Uncmock-2


title: spleen_Unc93b1_mock_1

description: Sample name: Uncmock-1


title: spleen_Tlr7_mock_3

description: Sample name: T7mock-3

source_name: Tlr7 knockout, whole spleen, mock infection, 24h


title: spleen_Tlr7_mock_2

description: Sample name: T7mock-2


title: paediatric low grade glioma_LGG_22


title: spleen_Tlr7_PcAS_24h_1

description: Sample name: T7PcAS-1


title: paediatric low grade glioma_LGG_17

value: infratentorial


title: paediatric low grade glioma_LGG_19


title: paediatric low grade glioma_LGG_20


title: spleen_Tlr7_mock_1

description: Sample name: T7mock-1


title: spleen_Tlr9_PcAS_24h_3

description: Sample name: T9PcAS-3

source_name: Tlr9 knockout, whole spleen, P. chabaudi infection, 24h

value: Tlr9 knockout


title: spleen_Tlr9_PcAS_24h_4

description: Sample name: T9PcAS-4


title: paediatric low grade glioma_LGG_15


title: paediatric low grade glioma_LGG_23


title: spleen_Tlr9_PcAS_24h_2

description: Sample name: T9PcAS-2


title: spleen_Tlr7_mock_4

description: Sample name: T7mock-4


title: Radio-resistant nasopharyngeal carcinoma patient NO.158

city: shanghai

first: shu

last: yang

address: State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science

country: China

institute: Fudan University

description:
RR-NPC 11
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.

hyb_protocol: The probe was dissolved in 20 µl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide]. Microarrays were pre-hybridized with a hybridization solution containing 0.5 mg/ml denatured salmon sperm DNA at 42C for 6 hrs. Fluorescent probe mixtures were denatured at 90C for 5 minutes, and then applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42C for 15-17 hours. Next, the hybridized chips were each washed at 60C for 10 min in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC, then dried at room temperature.

scan_protocol: The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA) at two wavelengths, 635nm and 532 nm, to detect emission from both Cy5 and Cy3 respectively.

data_processing: The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP. Ratios of Cy5 to Cy3 were computed using the GenePix Pro 3.0 median of ratio method. Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged 'Bad' or 'Not Found' by GenePix software was removed from the final data. Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were selected from each array and used for further analysis.

label_protocol: Total RNA was reverse transcribed using the Superscript III RNase H- Reverse Transcriptase kit (Invitrogen) following the manufacturer’s instructions with Cy3-dUTP for NPCI or Cy5-dUTP for NPC.

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

value: Radio-resistant nasopharyngeal carcinoma tissue

source_name: Nasopharyngeal chronic inflammation patient tissue

value: Nasopharyngeal chronic inflammation tissue


title: Radio-resistant nasopharyngeal carcinoma patient NO.170

description:
RR-NPC 12
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: paediatric low grade glioma_LGG_13


title: Radio-resistant nasopharyngeal carcinoma patient NO.122

description:
RR-NPC 9
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: Radio-resistant nasopharyngeal carcinoma patient NO.109

description:
RR-NPC 8
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: spleen_Tlr9_PcAS_24h_1

description: Sample name: T9PcAS-1


title: paediatric low grade glioma_LGG_16


title: Radio-resistant nasopharyngeal carcinoma patient NO.93

description:
RR-NPC 6
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: paediatric low grade glioma_LGG_11


title: Radio-resistant nasopharyngeal carcinoma patient NO.87

description:
RR-NPC 5
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: Radio-resistant nasopharyngeal carcinoma patient NO.157

description:
RR-NPC 10
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: paediatric low grade glioma_LGG_12


title: spleen_Tlr9_mock_4

description: Sample name: T9mock-4

source_name: Tlr9 knockout, whole spleen, mock infection, 24h


title: Radio-resistant nasopharyngeal carcinoma patient NO.108

description:
RR-NPC 7
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: paediatric low grade glioma_LGG_10


title: paediatric low grade glioma_LGG_21


title: paediatric low grade glioma_LGG_14


title: spleen_Tlr9_mock_1

description: Sample name: T9mock-1


title: spleen_Tlr9_mock_3

description: Sample name: T9mock-3


title: spleen_Tlr9_mock_2

description: Sample name: T9mock-2


title: Radio-resistant nasopharyngeal carcinoma patient NO.60

description:
RR-NPC 3
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: spleen_B6_PcAS_24h_4

description: Sample name: B6PcAS-4

source_name: C57BL/6, whole spleen, P. chabaudi infection, 24h

value: wildtype


title: Radio-resistant nasopharyngeal carcinoma patient NO.84

description:
RR-NPC 4
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: spleen_B6_PcAS_24h_3

description: Sample name: B6PcAS-3


title: paediatric low grade glioma_LGG_8


title: Radio-resistant nasopharyngeal carcinoma patient NO.25

description:
RR-NPC 2
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: spleen_Tlr7_PcAS_24h_4

description: Sample name: T7PcAS-4


title: Radio-sensitive nasopharyngeal carcinoma patient NO.102

description:
RS-NPC 7
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.

value: Radio-sensitive nasopharyngeal carcinoma tissue


title: spleen_B6_PcAS_24h_2

description: Sample name: B6PcAS-2


title: paediatric low grade glioma_LGG_7


title: paediatric low grade glioma_LGG_9


title: Human_Neonatal Stem

city: Philadelphia

first: Olga

last: Igoucheva

state: PA

address: 233 South 10th street

department: Dermatology

institute: Thomas Jefferson University

description: ADSC

hyb_protocol: Agilent Gene Expression Hybridization Kit according to Agilent 60 mer oligo microarray protocol

scan_protocol: Slide was scanned on an Agilent Scanner,  using Agilent feature extraction software.

data_processing: Background correction and normalization were done using Quantile normalization with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA).

source_name: Human foreskin

label_protocol: Linear T-7 based amplification and Agilent low input quick amp labeling kit

growth_protocol: ADSC were isolated from neonatal foreskin and were grown in stem cell defined medium

extract_protocol: Qiagen kit

treatment_protocol: Primary cells with no treatment

value: adipose layer of neonatal foreskin skin

value: stem cells


title: Radio-sensitive nasopharyngeal carcinoma patient NO.130

description:
RS-NPC 8
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.


title: paediatric low grade glioma_LGG_18


title: Radio-sensitive nasopharyngeal carcinoma patient NO.56

description:
RS-NPC 5
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.


title: Radio-sensitive nasopharyngeal carcinoma patient NO.19

description:
RS-NPC 4
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.


title: Radio-resistant nasopharyngeal carcinoma patient NO.22

description:
RR-NPC 1
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.


title: Radio-sensitive nasopharyngeal carcinoma patient NO.83

description:
RS-NPC 6
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.


title: paediatric low grade glioma_LGG_4

description: Gene expression data from pediatrics low grade gliomas


title: spleen_B6_mock_4

description: Sample name: B6mock-4

source_name: C57BL/6, whole spleen, mock infection, 24h


title: paediatric low grade glioma_LGG_5


title: spleen_B6_mock_3

description: Sample name: B6mock-3


title: Radio-sensitive nasopharyngeal carcinoma patient NO.10

description:
RS-NPC 3
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.


title: paediatric low grade glioma_LGG_3


title: paediatric low grade glioma_LGG_6


title: spleen_B6_mock_1

description: Sample name: B6mock-1


title: paediatric low grade glioma_LGG_2


title: Radio-sensitive nasopharyngeal carcinoma patient NO.6

description:
RS-NPC 1
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.


title: Radio-sensitive nasopharyngeal carcinoma patient NO.8

description:
RS-NPC 2
Radio-sensitive nasopharyngeal carcinoma patient tissue before treatment.


title: spleen_B6_mock_2

description: Sample name: B6mock-2


title: spleen_B6_PcAS_24h_1

description: Sample name: B6PcAS-1


title: paediatric low grade glioma_LGG_1


title: 6055424141_R04C01

status: Public on Sep 20 2013

type: genomic

city: London

first: Gianluca

last: Campanella

address: Norfolk Place

department: Epidemiology and Biostatistics

country: United Kingdom

institute: Imperial College London

hyb_protocol: Bisulfite converted DNA (using the EZ-96 DNA Methylation-Gold Kit, Zymo Research) was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using the standard manufacturer's protocol

scan_protocol: Arrays were imaged using the Illumina HiScanSQ system using standard recommended scanner setting

data_processing: Background subtraction and dye bias correction were performed using in-house routines

label: Biotin and 2,4-DNP

molecule: genomic DNA

source_name: Buffy coat

label_protocol: Standard Illumina Infinium HD Methylation assay protocol

extract_protocol: Genomic DNA was extracted and purified from peripheral blood leukocytes using the QIAsymphony DNA Mini Kit (QIAGEN) according to the manufacturer's instructions

value: F

tag: age at menarche

tag: cancer type (icd-10)

tag: time to diagnosis


title: 5809079044_R01C02


title: 5809079085_R03C01


title: 6969568028_R03C01


title: 5809079050_R03C02


title: 6055424026_R03C01


title: 6929726067_R03C02


title: 6969568156_R03C02


title: 6055424083_R05C02

value: M


title: 7766130010_R03C02


title: 6055424130_R03C01


title: 6055424126_R01C01


title: 6055424025_R01C01


title: 5809079064_R04C02


title: 6969568107_R02C01


title: 6042324097_R02C01


title: 6042324097_R05C02


title: 5808922057_R02C02


title: 6042324119_R03C02


title: 5809079068_R02C01


title: 5808922057_R02C01


title: 6969568107_R03C02


title: 6055424026_R04C01


title: 6969568107_R06C01


title: 6969568107_R04C01


title: 6055424126_R05C01


title: 6929697001_R03C02


title: 6042316165_R03C02


title: 6042316165_R02C02


title: 5809079011_R06C01


title: 6969568090_R05C02


title: 6055424114_R05C02


title: 6969568029_R01C02


title: 5809079011_R04C01


title: 6042316165_R05C02


title: 6969568107_R02C02


title: 5809079024_R01C01


title: 6969568090_R05C01


title: 6042324091_R02C01


title: 6055424132_R04C02


title: 6929726067_R01C01


title: 6055424083_R02C02


title: 5809079050_R03C01


title: 6042324098_R04C01


title: 6042324098_R05C01


title: 6969568054_R01C01


title: 6042324098_R03C01


title: 6042324124_R01C01


title: 6042324119_R06C01


title: 6042324098_R06C01


title: 6042324124_R02C02


title: 6055424048_R05C02


title: 6969568107_R04C02


title: 6042324088_R01C01


title: 6042316165_R06C01


title: 6929697006_R06C02


title: 6055424064_R04C02


title: 6042324124_R05C02


title: 6055424064_R04C01


title: 6042324124_R04C02


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title: 6969568099_R01C02


title: 6929697005_R06C01


title: 6969568099_R03C02


title: 6929697005_R05C02


title: 6929697005_R06C02


title: 6969568065_R05C02


title: 6969568065_R02C02


title: 6969568099_R04C01


title: 7766130100_R04C01


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title: 6969568141_R05C01


title: 6969568065_R04C02


title: 6969568052_R01C01


title: TAMs_BLZ945_rep3

first: Robert

middle: L

last: Bowman

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

hyb_protocol: 15 μg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G using the GeneChip Command Console version 3.2 as CEL files.

data_processing: Feature intensity was extracted by Affymetrix GCOS 1.4.  All analysis was completed in R using the Bioconductor suite of packages.  Expression values were computed using the robust multi-array average (RMA) method, and then quantile normalized.

source_name: CD11b+ Gr.1- tumor associated macrophages isolated from 7 day BLZ945 treated murine gliomas

label_protocol: 75 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: All animal studies were approved by the Institutional Animal Care and Use Committee of Memorial Sloan-Kettering Cancer Center

extract_protocol: Sorted cell populations were resuspended in 0.5 mL of Trizol.

treatment_protocol: Nestin-Tv-a;Ink4a/Arf-/-  mice from a mixed background were fully anesthetized with 10 mg/ml ketamine/1 mg/ml xylazine and were subcutaneously injected with 50 μl of the local anesthetic 0.25% bupivacaine at the surgical site. Mice were intracranially injected with 1 μl containing 2 x 105 DF-1:RCAS-PDGF-B-HA cells between 5-6 weeks of age using a fixed stereotactic apparatus (Stoelting). Injections were made to the right frontal cortex, approximately 1.5 mm lateral and 1 mm caudal from bregma, and at a depth of 2 mm.  Mice underwent MRI scans at 4-5 weeks post-injection of RCAS-PDGF-B-HA cells. When tumor volume was in the range of 4.5-40 mm3, animals were randomly assigned to treatment groups.  Mice were dosed with 200mg of BLZ945 or vehicle (20% captisol) by oral gavage once per day for 7 days.  Following treatment, mice were fully anesthetized with avertin and transcardially perfused with 20 ml of PBS. The brain was then isolated and the tumor macrodissected from the surrounding normal tissue.  The tumor was digested to a single cell suspension by incubation with 5 ml of papain digestion solution (0.94 mg/ml papain (Worthington), 0.48 mM EDTA, 0.18 mg/ml N-Acetyl-L-cysteine (Sigma), 0.06 mg/ml DNase I (Sigma), diluted in Earl’s Balanced Salt Solution and allowed to activate at room temperature for at least 30 minutes). Following digestion, the enzyme was inactivated by the addition of 2 ml of 0.71 mg/ml ovomucoid (Worthington). After a 5 min centrifugation at 1100 rpm, the cell pellet was resuspended with 500μL of ovomucoid and 10ml PBS. This cell suspension was then passed through a 40 μm mesh to remove undigested tissue, washed with FACS buffer (1% IgG Free BSA in PBS (Jackson Immunoresearch)), and centrifuged at a low speed of 750 rpm (Sorvall Legend RT), to remove debris and obtain the cell pellet.  After counting, cells were incubated with 1 μl of Fc Block for every million cells for at least 15 minutes at 4°C. Cells were then stained with anti-CD11b and  anti-Gr.1 antibodies,  for 10 minutes at 4°C, washed with FACS buffer, and resuspended in FACS buffer containing DAPI (5 mg/ml diluted 1:5000) for live/dead cell exclusion.  Samples were run on a BD FACSAria (Becton Dickstein) cell sorter and cells were collected into FACS buffer.

tag: genotype

value: Female

tag: age (weeks)

tag: initial tumor volume

tag: agent

value: tumor associated macrophages (TAMs)


title: TAMs_BLZ945_rep8

tag: gender


title: 6929697005_R04C02

tag: age


title: TAMs_BLZ945_rep4


title: 6929697005_R03C02


title: TAMs_BLZ945_rep5


title: 6969568141_R02C02


title: 6969568099_R03C01


title: 6969568099_R01C01


title: TAMs_BLZ945_rep6

value: Male


title: TAMs_BLZ945_rep2


title: TAMs_BLZ945_rep7


title: 6969568156_R06C02


title: 6969568052_R05C02


title: 6969568052_R05C01


title: TAMs_Vehicle_rep8

source_name: CD11b+ Gr.1- tumor associated macrophages isolated from 7 day Vehicle treated murine gliomas

value: Vehicle


title: TAMs_Vehicle_rep7


title: 6969568099_R06C02


title: 6969568141_R02C01


title: TAMs_BLZ945_rep1


title: 7766130010_R06C01


title: ALCL_cell line_Karpas 299 patient 11-0549

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: ALCL_cell line_Karpas 299 patient

hyb_protocol: standard Affymetrix procedures using Fluidics Station

scan_protocol: standard Affymetrix procedures using GeneChip Scanner 3000

data_processing:
Inital array intensity data was obtained using Affymetrix GeneChip Command Console Software (AGCC). Copy number log2 ratio signal and allele difference was extracted from CEL files using Affymetrix Power Tools (APT 1.14.2) with default analysis settings and Affymetrix provided reference profile 'GenomeWideSNP_6.hapmap270.na31.r1.a5.ref' as reference input.
Log2Ratio=copy number log2ratio; Allele.Difference=allele difference signal

source_name: Human tissue from ALCL_cell line_Karpas 299 patient

label_protocol: standard Affymetrix protocol starting from 250 ng of DNA.

extract_protocol: All clinical specimens were derived from involved sites and obtained in the course of routine diagnostic procedures before therapy initiation. Cases were selected based upon the availability of frozen material with a fraction of neoplastic cells in the specimen representing >70% of overall cellularity as determined by morphologic and/or immunophenotypic studies.

tag: tissue

value: Anaplastic Large Cell Lymphoma (ALCL)


title: ALCL_cell line_MAC1 patient 10-1062

description: ALCL_cell line_MAC1 patient

source_name: Human tissue from ALCL_cell line_MAC1 patient


title: ALCL_cell line_(TS) patient 10-1060

description: ALCL_cell line_(TS) patient

source_name: Human tissue from ALCL_cell line_(TS) patient


title: 7766130100_R02C01


title: ALCL_cell line_FE-PD patient 11-0548

description: ALCL_cell line_FE-PD patient

source_name: Human tissue from ALCL_cell line_FE-PD patient


title: ALCL_cell line_SU-DHL 1 patient 11-0551

description: ALCL_cell line_SU-DHL 1 patient

source_name: Human tissue from ALCL_cell line_SU-DHL 1 patient


title: TAMs_Vehicle_rep5


title: TAMs_Vehicle_rep2


title: TAMs_Vehicle_rep3


title: ALK-ALCL patient 10-1052

description: ALK-ALCL patient

source_name: Human tissue from ALK-ALCL patient

tag: disease status

value: ALK-ALCL patient


title: ALK-ALCL patient 10-1050

description: ALK-ALCL patient


title: TAMs_Vehicle_rep4


title: ALCL_cell line_JB6 patient 10-1061

description: ALCL_cell line_JB6 patient

source_name: Human tissue from ALCL_cell line_JB6 patient


title: TAMs_Vehicle_rep6


title: 6969568052_R01C02


title: 6969568141_R06C02


title: ALK+ALCL patient 10-0794

description: ALK+ALCL patient

source_name: Human tissue from ALK+ALCL patient

value: ALK+ALCL patient


title: 6969568065_R06C02


title: ALK-ALCL patient 10-0793

description: ALK-ALCL patient


title: 6929697005_R04C01


title: ALCL_cell line_L82 patient 11-0550

description: ALCL_cell line_L82 patient

source_name: Human tissue from ALCL_cell line_L82 patient


title: TAMs_Vehicle_rep1


title: 6969568052_R02C01


title: 7766130010_R05C01


title: ALK-ALCL patient 10-0789

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0790

description: ALK+ALCL patient


title: 6969568099_R02C02


title: ALK-ALCL patient 10-0763

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0760

description: ALK+ALCL patient


title: 6969568141_R03C01


title: ALK+ALCL patient 10-0753

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0759

description: ALK-ALCL patient


title: ALK-ALCL patient 10-0762

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0572

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0758

description: ALK-ALCL patient


title: 6929697005_R02C02


title: ALK-ALCL patient 10-0757

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0573

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0751

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0750

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0565

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0566

description: ALK-ALCL patient


title: ALK-ALCL patient 10-0754

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0755

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0788

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0571

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0564

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0563

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0568

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0558

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0556

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0557

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0234

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0232

description: ALK-ALCL patient


title: 6969568141_R01C02


title: ALK+ALCL patient 10-0227

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0231

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0229

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0225

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0030

description: ALK-ALCL patient


title: ALK-ALCL patient 10-0014

description: ALK-ALCL patient


title: ALK-ALCL patient 09-858

description: ALK-ALCL patient


title: ALK+ALCL patient 10-0018

description: ALK+ALCL patient


title: ALK+ALCL patient 10-0016

description: ALK+ALCL patient


title: ALK-ALCL patient 09-851

description: ALK-ALCL patient


title: ALK+ALCL patient 09-850

description: ALK+ALCL patient


title: ALK-ALCL patient 09-847

description: ALK-ALCL patient


title: ALK+ALCL patient 09-849

description: ALK+ALCL patient


title: ALK+ALCL patient 09-856

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0222

description: ALK-ALCL patient


title: ALK+ALCL patient 09-038

description: ALK+ALCL patient


title: ALK-ALCL patient 09-845

description: ALK-ALCL patient


title: ALK+ALCL patient 09-042

description: ALK+ALCL patient


title: ALK+ALCL patient 09-037

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0230

description: ALK-ALCL patient


title: ALK-ALCL patient 09-039

description: ALK-ALCL patient


title: ALK+ALCL patient 09-040

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0221

description: ALK-ALCL patient


title: ALK-ALCL patient 09-036

description: ALK-ALCL patient


title: ALK-ALCL patient 09-030

description: ALK-ALCL patient


title: ALK+ALCL patient 09-029

description: ALK+ALCL patient


title: ALK-ALCL patient 09-031

description: ALK-ALCL patient


title: ALK+ALCL patient 09-032

description: ALK+ALCL patient


title: DLBCL patient 10-1026

description: DLBCL patient

source_name: human tissue from DLBCL patient

value: human clinical sample

value: DLBCL patient


title: DLBCL patient 10-1028

description: DLBCL patient


title: DLBCL patient 10-0994

description: DLBCL patient


title: DLBCL patient 10-1023

description: DLBCL patient


title: ALK-ALCL patient 10-0559

description: ALK-ALCL patient


title: DLBCL patient 10-1003

description: DLBCL patient


title: DLBCL patient 10-1006

description: DLBCL patient


title: DLBCL patient 10-1011

description: DLBCL patient


title: DLBCL patient 10-1002

description: DLBCL patient


title: DLBCL patient 10-0998

description: DLBCL patient


title: ALK+ALCL patient 10-0761

description: ALK+ALCL patient


title: ALK-ALCL patient 10-0752

description: ALK-ALCL patient


title: DLBCL patient 10-0959

description: DLBCL patient


title: DLBCL patient 10-0957

description: DLBCL patient


title: DLBCL patient 10-0956

description: DLBCL patient


title: DLBCL patient 10-0990

description: DLBCL patient


title: DLBCL patient 10-0985

description: DLBCL patient


title: DLBCL patient 10-0986

description: DLBCL patient


title: DLBCL patient 10-0984

description: DLBCL patient


title: DLBCL patient 10-0983

description: DLBCL patient


title: DLBCL patient 10-1019

description: DLBCL patient


title: DLBCL patient 10-1009

description: DLBCL patient


title: DLBCL patient 10-0979

description: DLBCL patient


title: DLBCL patient 10-0978

description: DLBCL patient


title: DLBCL patient 10-0976

description: DLBCL patient


title: DLBCL patient 10-0977

description: DLBCL patient


title: DLBCL patient 10-0974

description: DLBCL patient


title: DLBCL patient 10-0973

description: DLBCL patient


title: DLBCL patient 10-0972

description: DLBCL patient


title: DLBCL patient 10-0996

description: DLBCL patient


title: DLBCL patient 10-0969

description: DLBCL patient


title: DLBCL patient 10-0963

description: DLBCL patient


title: DLBCL patient 10-0960

description: DLBCL patient


title: DLBCL patient 11-0040

description: DLBCL patient


title: DLBCL patient 10-1030

description: DLBCL patient


title: DLBCL patient 10-0228

description: DLBCL patient


title: DLBCL patient 10-0991

description: DLBCL patient


title: DLBCL patient 11-0041

description: DLBCL patient


title: DLBCL patient 11-0044

description: DLBCL patient


title: DLBCL patient 10-0955

description: DLBCL patient


title: DLBCL patient 11-0057

description: DLBCL patient


title: DLBCL patient 11-0056

description: DLBCL patient


title: DLBCL patient 11-0053

description: DLBCL patient


title: DLBCL patient 11-0042

description: DLBCL patient


title: DLBCL patient 11-0054

description: DLBCL patient


title: DLBCL patient 11-0043

description: DLBCL patient


title: DLBCL patient 11-0037

description: DLBCL patient


title: DLBCL patient 11-0048

description: DLBCL patient


title: DLBCL patient 11-0051

description: DLBCL patient


title: DLBCL patient 11-0052

description: DLBCL patient


title: DLBCL patient 11-0049

description: DLBCL patient


title: DLBCL patient 10-0971

description: DLBCL patient


title: DLBCL patient 11-0035

description: DLBCL patient


title: DLBCL patient 11-0034

description: DLBCL patient


title: DLBCL patient 11-0050

description: DLBCL patient


title: DLBCL patient 11-0038

description: DLBCL patient


title: DLBCL patient 11-0039

description: DLBCL patient


title: DLBCL patient 11-0047

description: DLBCL patient


title: DLBCL patient 11-0032

description: DLBCL patient


title: CLL-phase patient 09-336

description: CLL-phase patient

source_name: human tissue from CLL-phase patient

value: CLL-phase patient


title: CLL-phase patient 09-291

description: CLL-phase patient


title: CLL-phase patient 09-299

description: CLL-phase patient


title: DLBCL patient 11-0045

description: DLBCL patient


title: CLL-phase patient 09-134

description: CLL-phase patient


title: CLL-phase patient 09-364

description: CLL-phase patient


title: CLL-phase patient 09-352

description: CLL-phase patient


title: ALK-ALCL patient 10-0567

description: ALK-ALCL patient


title: CLL-phase patient 09-1234

description: CLL-phase patient


title: CLL-phase patient 09-1164

description: CLL-phase patient


title: CLL-phase patient 08-879

description: CLL-phase patient


title: CLL-phase patient 09-130

description: CLL-phase patient


title: CLL-phase patient 09-1214

description: CLL-phase patient


title: CLL-phase patient 09-1231

description: CLL-phase patient


title: CLL-phase patient 09-1162

description: CLL-phase patient


title: CLL-phase patient 09-898

description: CLL-phase patient


title: CLL-phase patient 09-1161

description: CLL-phase patient


title: CLL-phase patient 09-1157

description: CLL-phase patient


title: CLL-phase patient 09-945

description: CLL-phase patient


title: CLL-phase patient 09-894

description: CLL-phase patient


title: CLL-phase patient 09-901

description: CLL-phase patient


title: CLL-phase patient 09-896

description: CLL-phase patient


title: CLL-phase patient 09-946

description: CLL-phase patient


title: CLL-phase patient 09-937

description: CLL-phase patient


title: DLBCL patient 11-0033

description: DLBCL patient


title: CLL-phase patient 08-546

description: CLL-phase patient


title: CLL-phase patient 09-437

description: CLL-phase patient


title: CLL-phase patient 08-552

description: CLL-phase patient


title: RS patient 09-949

description: RS patient

source_name: human tissue from RS patient

value: RS patient


title: RS patient 09-948

description: RS patient


title: CLL-phase patient 07-230

description: CLL-phase patient


title: RS patient 09-956

description: RS patient


title: RS patient 09-954

description: RS patient


title: RS patient 09-741

description: RS patient


title: RS patient 09-899

description: RS patient


title: RS patient 09-900

description: RS patient


title: RS patient 09-814

description: RS patient


title: RS patient 09-815

description: RS patient


title: RS patient 09-895

description: RS patient


title: RS patient 09-816

description: RS patient


title: RS patient 09-740

description: RS patient


title: RS patient 09-739

description: RS patient


title: CLL-phase patient 09-951

description: CLL-phase patient


title: CLL-phase patient 09-596

description: CLL-phase patient


title: RS patient 09-734

description: RS patient


title: RS patient 09-730

description: RS patient


title: RS patient 09-732

description: RS patient


title: RS patient 09-737

description: RS patient


title: RS patient 09-728

description: RS patient


title: RS patient 09-738

description: RS patient


title: RS patient 09-725

description: RS patient


title: RS patient 09-723

description: RS patient


title: RS patient 09-724

description: RS patient


title: RS patient 09-597

description: RS patient


title: RS patient 09-542

description: RS patient


title: RS patient 09-541

description: RS patient


title: RS patient 09-540

description: RS patient


title: RS patient 09-510

description: RS patient


title: RS patient 09-281

description: RS patient


title: RS patient 09-511

description: RS patient


title: RS patient 09-284

description: RS patient


title: RS patient 09-1242

description: RS patient


title: RS patient 09-283

description: RS patient


title: RS patient 09-282

description: RS patient


title: RS patient 09-735

description: RS patient


title: RS patient 09-280

description: RS patient


title: RS patient 09-1230

description: RS patient


title: RS patient 09-279

description: RS patient


title: RS patient 09-1228

description: RS patient


title: RS patient 09-1229

description: RS patient


title: RS patient 09-1227

description: RS patient


title: RS patient 09-736

description: RS patient


title: RS patient 09-727

description: RS patient


title: RS patient 09-1211

description: RS patient


title: RS patient 09-1207

description: RS patient


title: RS patient 09-1212

description: RS patient


title: RS patient 09-1210

description: RS patient


title: RS patient 09-1206

description: RS patient


title: RS patient 09-1184

description: RS patient


title: RS patient 09-1181

description: RS patient


title: RS patient 09-722

description: RS patient


title: RS patient 09-1163

description: RS patient


title: RS patient 09-1167

description: RS patient


title: RS patient 09-1172

description: RS patient


title: RS patient 09-1165

description: RS patient


title: RS patient 09-1159

description: RS patient


title: RS patient 09-1208

description: RS patient


title: RS patient 09-015

description: RS patient


title: RS patient 09-012

description: RS patient


title: RS patient 09-014

description: RS patient


title: DLBCL patient 10-1018

description: DLBCL patient


title: LSC with vehicle (DMSO) for 6h_1

city: Cambridge

first: Kimberly

last: Hartwell

address: 7 Cambridge Center

department: Cancer Program

institute: Broad Institute

description:
PrimLeuk_DMSO_1
n5719882018_C
replicate 1

hyb_protocol: See citation; Labeled cRNA was normalized to 150 ng/ µl and hybridized to Illumina's MouseRef-8 v2.0 Expression BeadChip. The labeled RNA strand was hybridized to the bead on the BeadChip containing the complementary gene-specific sequence. After a 16 hour hybridization, the beadchips were washed and stained using a Cy3 streptavidin conjugate.

scan_protocol: See citation; Illumina’s BeadArray Reader was used to measure the fluorescence intensity at each addressed bead location according to manufacturer's instruction.

data_processing: Raw data were normalized by cubic spline method implemented in Illumina Normalizer module of GenePattern analysis tool kit

source_name: LSC with vehicle (DMSO) for 6h

label_protocol: See citation; In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide.

growth_protocol: See citation; Freshly isolated LSCe cells were treated with either 5 µM BRD7116 or DMSO vehicle control for 6 hours in suspension in Iscove's Modified Dulbecco's Medium, 10% FBS, 1% Pen-Strep at 37˚C/ 5% CO2 (250,000 cells in 150µL per 96-well, then drug was added in 20µL media

extract_protocol: See citation; Total RNA was extracted from the cells (RNeasy kit 74104, Qiagen)

value: leukemia stem cell

tag: perturbagen

value: small molecule

tag: type

value: control

tag: name

value: DMSO

tag: concentration

value: 0.2% DMSO (neutral control)

tag: vehicle

tag: duration

value: 6 h


title: LSC with BRD7116 for 6h_3

description:
PrimLeuk_BRD7116_3
n5719882026_B
replicate 3

source_name: LSC with BRD7116 for 6h

tag: cell type

value: treatment

value: 5µM in 0.2% DMSO


title: LSC with BRD7116 for 6h_1

description:
PrimLeuk_BRD7116_1
n5719882016_B
replicate 1


title: LSC with vehicle (DMSO) for 6h_2

description:
PrimLeuk_DMSO_2
n5719882016_A
replicate 2


title: LSC with BRD7116 for 6h_5

description:
PrimLeuk_BRD7116_5
n5719882026_F
replicate 5


title: 823 Normal

city: Heidelberg

first: Nitin

last: Patil

state: BW

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

country: Germany

institute: German Cancer Research Centre (DKFZ)

description:
Sample name: 823 N_4239609006_B
Resected tissue from liposarcoma

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Beadstation array scanner

data_processing: Data extraction was done for beads individually, and outliers with greater than 2.5 median absolute deviation (MAD) were removed. The data was normalized using quantile normalization without background substraction

source_name: fatty tissue

label_protocol: Standard Illumina label protocol

extract_protocol: RNeasy Lipid Tissue kit (Qiagen, Germany)

tag: disease state

value: liposarcoma

value: corresponding normal


title: LSC with BRD7116 for 6h_2

description:
PrimLeuk_BRD7116_2
n5719882018_E
replicate 2


title: TH17-cells-BETi-48h-1

first: Barbara

middle: M

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

hyb_protocol: The fragmented and labelled ST-cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Following the hybridization for 18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000.  Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing:
CEL files were processed by the Affymetrix Expression Console software package using the gene-level RMA algorithm on the core set of probesets and the annotation file Huex-1_0-st-v2_na31_hg19 provided by Affymetrix.
MoEx-1_0-st-v1.r2.pgf

label_protocol: Total RNA was amplified using the NuGEN Applause™ WT Amp Plus ST Amplification System. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity.  A modification step targeting the amplified single-stranded cDNA resulted in the generation of sense target (ST) cDNA product compatible with the Affymetrix  GeneChip® Exon arrays.  The ST-cDNA was purified for accurate quantitation and to ensure optimal performance during the fragmentation and labeling process. The ST- cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer. The appropriate amount of amplified ST-cDNA was fragmented and labeled using the Encore™ Biotin Module. The enzymatically and chemically fragmented product (50-100 nt) was labeled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented ST-cDNA.

growth_protocol: C57BL/6 mice were purchased from Charles River Laboratories.  All mice were kept  under specific pathogen-free conditions in the animal care facility at ViviSource Laboratories, Inc. (Waltham, MA).  Single cell suspension of splenocytes were prepared using 70-μm nylon cell strainers (BD Bioscience).  Red blood cells were lysed using ammonium chloride lysis buffer (R7757; Sigma) and washed with cRPMI 10% FBS (61870-036; Invitrogen). Naïve CD4 T cells were purified using magnetic-activated cell sorting beads (130-093-227; Miltenyi Biotec).  Purity of sorted naive cells was greater than 90%.

extract_protocol: Total RNA was prepared by using a Qiagen RNeasy kit with on-column DNase digestion according to the manufacturer’s instructions.

treatment_protocol: Naïve CD4+ T cells were treated with 150 nM JQ1 or DMSO under TH17 polarizing conditions for 48h.   Naïve CD4 T cells were cultured in 24-well plates (1x106 cells/ml) and stimulated with anti-CD3/CD28 coated beads (Dynabeads 11452D; Invitrogen) for 4 days under TH17, polarizing conditions: 5 ng/ml TGF-β1 (100-B; R&D Biosystems), 20 ng/ml IL-6 (406-ML; R&D Biosystems), 20 ng/ml IL-23 (1887-ML-010; R&D Biosystems), 10 μg/ml anti-IFN-γ antibody (XMG1.1; BD Pharmingen), 10 μg/ml anti-IL-4 antibody (11B11;BD Pharmingen).

tag: strain/background

value: TH17 cells

tag: treatment

value: 150 nM JQ1 (BET inhibitor)

tag: timepoint

value: 48 hours


title: 823 Tumor

description:
Sample name: 823 T_4239609006_A
Resected tissue from liposarcoma

value: tumor


title: 806 Tumor

description:
Sample name: 806 T_4233291196_E
Resected tissue from liposarcoma


title: TH17-cells-untreated-48h-1

value: DMSO (untreated control)


title: LSC with BRD7116 for 6h_4

description:
PrimLeuk_BRD7116_4
n5719882026_C
replicate 4


title: TH17-cells-BETi-48h-2


title: 806 Normal

description:
Sample name: 806 N_4233291196_F
Resected tissue from liposarcoma


title: 823 Tumor_WDH

description:
Sample name: 823T_WDH_4233291197_E
Resected tissue from liposarcoma


title: 185 Tumor

description:
Sample name: 185 T_4233291187_E
Resected tissue from liposarcoma


title: TH17-cells-untreated-48h-2


title: 823 Normal_WDH

description:
Sample name: 823N_WDH_4233291197_F
Resected tissue from liposarcoma


title: 185 Normal

description:
Sample name: 185 N_4233291187_F
Resected tissue from liposarcoma


title: 7766130100_R05C01

source_name: Buffy coat

value: F

tag: age at menarche

tag: cancer type (icd-10)

tag: time to diagnosis


title: 7766130017_R01C01

tag: gender

tag: age


title: 7766130046_R03C01


title: 7766130017_R02C01


title: 6969568099_R04C02


title: 7766130100_R06C01


title: 7766130046_R04C01


title: 6969568099_R05C02


title: 6969568141_R06C01


title: 6969568065_R06C01


title: 7766130046_R03C02


title: 6969568052_R03C02


title: 6969568052_R02C02


title: 6969568065_R03C01


title: 5808922057_R03C02


title: 7766130046_R04C02


title: 6969568065_R04C01


title: 6969568066_R06C01


title: 6969568141_R04C01


title: 6055424035_R05C02


title: 6969568065_R05C01


title: 6969568052_R03C01


title: 6969568052_R04C02


title: 5809079002_R01C02


title: 6055424126_R06C01

value: M


title: 6969568052_R06C01


title: 6055424083_R06C01


title: 7766130010_R05C02


title: 6969568066_R02C01


title: 6969568052_R04C01


title: 6969568066_R04C01


title: 6055424025_R03C02


title: 6929726094_R01C02


title: 6929726094_R05C01


title: 6055424025_R03C01


title: 6055424130_R05C01


title: 6969568090_R01C01


title: 6055424083_R04C01


title: 5809079060_R02C02


title: 6055424083_R03C01


title: 6055424130_R05C02


title: 6929697006_R05C02


title: 6042324124_R03C02


title: 6055424026_R01C01


title: 6969568066_R04C02


title: 6055424141_R02C02


title: 6929697006_R01C01


title: 6969568066_R02C02


title: 6042324119_R04C02


title: 5809079002_R05C02


title: 6042316165_R06C02


title: 5809079002_R01C01


title: 6929726094_R03C01


title: 6042324088_R02C02


title: 6055424119_R06C02


title: 6055424114_R03C02


title: 6055424114_R06C02


title: 6055424154_R06C02


title: 6055424035_R02C02


title: 5809079044_R06C02


title: 6055424083_R04C02


title: 6055424154_R04C02


title: 6055424126_R05C02


title: 5809079087_R01C01


title: 6969568066_R06C02


title: 6969568108_R02C01


title: 6929697015_R03C02


title: 6055424119_R03C01


title: 6055424026_R06C02


title: 5809079002_R02C02


title: 5808922057_R06C02


title: 5809079060_R04C02


title: 5809079002_R02C01


title: 6055424132_R05C02


title: 6969568108_R01C01


title: 6055424119_R02C02


title: 6969568108_R04C01


title: 6055424132_R02C01


title: 5809079050_R06C02


title: 5809079044_R06C01


title: 6055424025_R05C02


title: 6042324097_R04C02


title: 6969568156_R04C01


title: 6929726094_R01C01


title: 6055424026_R04C02


title: 6055424132_R03C01


title: 6929697015_R01C02


title: 6055424114_R04C02


title: 5809079064_R05C02


title: 6969568028_R01C01


title: 5809079002_R05C01


title: 6055424119_R02C01


title: 6042324124_R01C02


title: 6042324091_R03C02


title: 6929697006_R04C01


title: 6969568108_R06C01


title: 6042324088_R03C02


title: 6969568156_R02C02


title: 6969568028_R05C01


title: 5808922057_R03C01


title: 5809079050_R01C02


title: 6042324097_R05C01


title: 6929697015_R05C01


title: 5809079064_R03C02


title: 6042324088_R05C01


title: 6042324094_R01C02


title: 6969568108_R01C02


title: 5809079085_R05C02


title: 6042324097_R06C01


title: 6969568108_R02C02


title: 5809079050_R02C02


title: 5809079024_R05C01


title: 5809079060_R03C02


title: 6969568054_R01C02


title: 5809079011_R01C01


title: 6055424025_R06C02


title: 5809079002_R06C02


title: 5809079060_R06C01


title: 5809079002_R04C02


title: 5809079011_R05C01


title: 6055424048_R04C02


title: 6969568107_R03C01


title: 6042324124_R04C01


title: 5809079011_R02C01


title: 6055424035_R01C02


title: 6929697006_R06C01


title: 6055424126_R03C02


title: 6042324124_R02C01


title: 6969568108_R06C02


title: 5809079044_R05C02


title: 6055424048_R01C02


title: 5809079060_R02C01


title: 6929697006_R02C01


title: 6042324119_R04C01


title: 5809079050_R02C01


title: 6969568108_R04C02


title: 6042324088_R05C02


title: 6929726071_R05C02


title: 6042316165_R04C01


title: 5809079050_R01C01


title: 5809079064_R03C01


title: 6969568054_R02C01


title: 6055424083_R01C02


title: 6042324094_R02C01


title: 6929726071_R03C02


title: 6969568107_R01C02


title: 6055424132_R01C01


title: 6055424064_R01C01


title: 6055424132_R01C02


title: 5809079002_R04C01


title: 6969568066_R01C02


title: 6042324094_R01C01


title: 5809079044_R05C01


title: 6929726071_R01C02


title: 5809079044_R04C01


title: 5809079044_R04C02


title: 6969568156_R01C01


title: 6969568066_R05C01


title: 5809079011_R05C02


title: 5809079044_R01C01


title: 6929697001_R05C01


title: 6969568107_R01C01


title: 6929726067_R03C01


title: 6929697015_R02C01


title: 6969568108_R03C02


title: 6055424119_R01C01


title: 6969568054_R06C01


title: 6969568054_R06C02


title: 6042324098_R01C02


title: 6042324097_R04C01


title: 5809079024_R04C02


title: 6929697006_R02C02


title: 6969568156_R03C01


title: 6055424132_R03C02


title: 6969568054_R04C01


title: 6055424064_R06C02


title: 5809079085_R01C01


title: 6969568108_R05C02


title: 5809079087_R04C01


title: 6969568028_R01C02


title: 6969568107_R05C02


title: 6969568054_R02C02


title: 6969568108_R03C01


title: 6042324088_R03C01


title: 5808922057_R04C01


title: 6042324091_R04C01


title: 5808922057_R05C02


title: 5809079068_R01C02


title: 5809079024_R05C02


title: 5808922057_R05C01


title: 6042324091_R03C01


title: 5809079068_R01C01


title: 5809079085_R02C01


title: 6969568029_R06C01


title: 6042324091_R02C02


title: 6055424119_R01C02


title: 6042324097_R06C02


title: 6929697015_R06C01


title: 6055424048_R06C02


title: 6042324097_R01C02


title: 6969568029_R04C01


title: 6969568108_R05C01


title: 5809079060_R04C01


title: 6969568090_R03C02


title: 6929726071_R05C01


title: 6929697001_R03C01


title: 6969568054_R04C02


title: 6042324119_R03C01


title: 6929726071_R03C01


title: 6929697001_R01C02


title: 6969568029_R02C01


title: 5809079064_R01C01


title: 6055424132_R06C02


title: 6055424132_R06C01


title: 5809079064_R06C01


title: 6042324088_R06C02


title: 5809079044_R03C02


title: 6929726071_R01C01


title: 5809079002_R06C01


title: 6969568029_R02C02


title: 5809079068_R05C02


title: 6055424035_R06C02


title: 5809079064_R02C02


title: 5809079060_R01C01


title: 6969568029_R05C02


title: 5809079044_R03C01


title: 6055424083_R02C01


title: 6055424048_R04C01


title: 6969568029_R04C02


title: 6055424114_R05C01


title: 5809079024_R03C02


title: 5809079024_R01C02


title: 6929697015_R03C01


title: 6042324098_R05C02


title: 6055424114_R06C01


title: 6042316165_R03C01


title: 7766130010_R06C02


title: 6929697006_R05C01


title: 6055424048_R01C01


title: 6055424035_R01C01


title: 6042324097_R02C02


title: 6055424035_R06C01


title: 6969568066_R05C02


title: 6055424083_R01C01


title: 5809079060_R01C02


title: 6929726068_R05C02


title: 6969568066_R03C02


title: 6055424154_R04C01


title: 6055424154_R05C01


title: 6042324091_R06C02


title: 6055424025_R06C01


title: 6042324098_R04C02


title: 5809079064_R06C02


title: 5809079002_R03C02


title: 6929726071_R06C01


title: 6969568066_R03C01


title: 6055424035_R05C01


title: 6042324098_R03C02


title: 6055424154_R06C01


title: 5809079085_R05C01


title: 6042316165_R01C02


title: 6042324097_R03C01


title: 5809079060_R03C01


title: 5809079068_R04C02


title: 6042316165_R04C02


title: 5809079024_R02C02


title: 6929726094_R04C01


title: 5809079068_R06C01


title: 6969568107_R05C01


title: 6929726068_R03C02


title: 6969568054_R03C01


title: 5809079011_R03C02


title: 6969568029_R03C02


title: 5809079068_R03C01


title: 5809079068_R05C01


title: 5809079068_R04C01


title: 6969568029_R06C02


title: 6042324094_R06C02


title: 6929697001_R02C01


title: 5809079024_R04C01


title: 6055424154_R05C02


title: 5809079024_R03C01


title: 6055424141_R03C02


title: 5809079024_R02C01


title: 6042324088_R01C02


title: 6055424130_R06C02


title: 6929697006_R04C02


title: 5809079064_R01C02


title: 6055424114_R01C02


title: 6055424126_R06C02


title: 5809079050_R05C02


title: 6929726068_R01C02


title: 6042324091_R06C01


title: 5809079050_R06C01


title: 6042324119_R01C01


title: 6055424130_R03C02


title: 6055424026_R01C02


title: 5809079050_R05C01


title: 6042324119_R02C01


title: 5809079050_R04C01


title: 6929697015_R06C02


title: 6055424064_R05C01


title: 6929697015_R04C02


title: 6969568028_R03C02


title: 6055424132_R02C02


title: 5809079064_R05C01


title: 6055424025_R01C02


title: 5808922057_R04C02


title: 5809079085_R01C02


title: 6042324098_R01C01


title: 6929697001_R04C01


title: 6042324119_R01C02


title: 6969568156_R01C02


title: 6055424064_R06C01


title: 5808922057_R01C02


title: 6969568090_R01C02


title: 6055424119_R03C02


title: 6055424141_R04C02


title: 6929697001_R02C02


title: 6929726068_R05C01


title: 6055424141_R05C02


title: 6929697001_R06C01


title: 6055424119_R05C01


title: 5809079085_R02C02


title: 6042324088_R02C01


title: 6055424064_R05C02


title: 6929726094_R02C01


title: 6055424026_R03C02


title: Colon tissue -Tumor

city: Columbus

first: Taewan

state: OH

institute: The Ohio State University

description: SAMPLE J

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: Tumor colon tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Cell lines were culture in humidified 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) in accordance with manufacturer's instruction. mRNA was purified from 1 μg total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: tissue

value: Colorectal cancer tissue


title: 6042324088_R04C02


title: 6929697001_R06C02


title: HT29

description: SAMPLE I

source_name: colorectal tumor_HT29

tag: cell line

value: Colorectal cancer cells


title: 6929697001_R04C02


title: SW620

description: SAMPLE H

source_name: colorectal tumor_SW620


title: 7766130010_R04C02


title: HCT116

description: SAMPLE F

source_name: colorectal tumor_HCT116


title: 5809079087_R01C02


title: CCD-841CoN

description: SAMPLE D

value: Normal colorectal cells


title: RKO

description: SAMPLE G

source_name: colorectal tumor_RKO

value: RKO


title: 6929726068_R03C01


title: siMYC RKO replicate-3

description: SAMPLE 12

source_name: RKO_c-MYC siRNA

tag: treated with

value: c-MYC siRNA


title: Colon Tissue -NAT

description: SAMPLE E

source_name: normal Colon tissue_NAT

value: Colon normal tissue


title: CCD-33Co

description: SAMPLE B


title: 6055424114_R04C01


title: CCD-112CoN

description: SAMPLE C


title: 6055424048_R06C01


title: 6929697015_R01C01


title: CCD-18Co

description: SAMPLE A


title: 5809079085_R04C02


title: 6055424126_R01C02


title: siCTRL RKO replicate-3

description: SAMPLE 9

source_name: RKO_Control siRNA

value: Control siRNA


title: siMYC RKO replicate-1

description: SAMPLE 10


title: 6055424114_R01C01


title: 6055424130_R01C02


title: siMYC HCT116 replicate-2

description: SAMPLE 5

source_name: HCT116_c-MYC siRNA


title: 6055424048_R02C01


title: siMYC RKO replicate-2

description: SAMPLE 11


title: ΔsigCDE_high light_30min_biol.rep2

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

hyb_protocol: 500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).

data_processing: The scanned images were analyzed with Agilent's Feature Extraction program version 10.7.3. using  protocol GE1_107_Sep09 and Grid 016989_D_F_20070606. gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method.

organism: Synechocystis sp. PCC 6803

source_name: ΔsigCDE_high light PPFD 750 µmol m-2s-1_30min

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell were grown in BG-11 medium in standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2)

extract_protocol: RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959). RNA was purified and DNase treated using RNeasy mini kit (Qiagen).

treatment_protocol: Cells grown in standard growth conditions (A730=1, 40 mL) were illuminated for 30-min at PPFD of 750 µmol m-2s-1.

tag: genotype/variation

value: ΔsigCDE mutant

tag: phenotype

value: glucose tolerant

tag: growth condition

value: high light PPFD 750 µmol m-2s-1


title: ΔsigCDE_high light_30min_biol.rep3


title: 6929697015_R05C02


title: siMYC HCT116 replicate-3

description: SAMPLE 6


title: 6055424114_R02C01


title: siCTRL RKO replicate-2

description: SAMPLE 8


title: siMYC HCT116 replicate-1

description: SAMPLE 4


title: 6969568054_R03C02


title: siCTRL HCT116 replicate-2

description: SAMPLE 2

source_name: HCT116_Control siRNA


title: ΔsigCDE_high light_30min_biol.rep1


title: 6929726068_R01C01


title: siCTRL HCT116 replicate-3

description: SAMPLE 3


title: siCTRL RKO replicate-1

description: SAMPLE 7


title: 6055424141_R06C01


title: 5809079011_R06C02


title: CS_high light_30min_biol.rep3

source_name: control strain_high light PPFD 750 µmol m-2s-1_30min

value: wild type/control


title: 6929697001_R05C02


title: CS_high light_30min_biol.rep2


title: CS_high light_30min_biol.rep1


title: 6055424154_R03C01


title: 6055424141_R06C02


title: siCTRL HCT116 replicate-1

description: SAMPLE 1


title: Subject LST022,  biological rep2

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

country: Canada

institute: University of British Columbia

hyb_protocol: Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)

scan_protocol: standard Affymetrix protocol

data_processing:
Raw data normalization using the 'farms' package consisted of RMA background correction, quantile normalization and  summarization of probe-level data using Factor Analysis for Robust Microarray Summarization
Data filtering was also performed using the Informative vs. Non-Informative Calls function in the 'farms' package. Differential gene expression was determined using moderated t-tests in limma using an FDR cut-off of 10%.
All statistical analyses were performed in the statistical computing program R.

source_name: Post

label_protocol: standard Affymetrix protocol

extract_protocol:
Samples were stored at -80⁰C until RNA extraction
From PAXgene tube samples, total RNA was purified from 2.5 mL of whole blood using Rneasy mini kit (Qiagen, Chatsworth, CA, USA)
From EDTA tube samples, total RNA was purified from 3.0 mL of whole blood following modified TRIzol-based extraction method.
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

tag: response

value: DR

tag: site

value: Laval

tag: allergen

value: Cat Pelt

tag: Sex

tag: ethnicity

value: Caucasian

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)

value: whole blood


title: 6055424141_R05C01

tag: gender

value: M

tag: age

tag: cancer type (icd-10)

tag: time to diagnosis


title: Subject STS009,  biological rep2

tag: response

tag: site

value: VGH

tag: allergen

value: Cat

tag: Sex

value: F

tag: ethnicity

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: hemoglobin (g/l)

tag: tissue


title: Subject LST017,  biological rep2

value: Cat Hair (Lot)

tag: hematocrit (l/l)

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)


title: Subject LST013,  biological rep2

tag: response

tag: site

tag: allergen

value: Cat Hair

tag: Sex

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)


title: 6055424130_R04C02

tag: gender


title: Subject LST012,  biological rep2

value: ER

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: tissue


title: Subject LST026,  biological rep2

tag: response

tag: site

tag: allergen

tag: Sex

tag: leukocytes (x10^9/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)


title: Subject LST021,  biological rep2

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)


title: 6055424035_R04C01

tag: gender

tag: age at menarche

tag: cancer type (icd-10)

tag: time to diagnosis


title: Subject LST014,  biological rep2

tag: response

tag: site

tag: allergen

tag: Sex

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: tissue


title: Subject STS009,  biological rep1

source_name: Pre

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)


title: Subject LST018,  biological rep2

tag: response

tag: site

tag: allergen

tag: Sex

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)


title: Subject LST018,  biological rep1

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: leukocytes (x10^9/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: tissue


title: 6929726067_R05C02

tag: gender

tag: age at menarche


title: Subject LST020,  biological rep2

tag: response

tag: site

tag: allergen

tag: Sex

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)


title: Subject LST003,  biological rep2

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)


title: Subject LST019,  biological rep2

tag: response

tag: site

tag: allergen

tag: Sex

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: tissue


title: Subject LST020,  biological rep1

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)


title: Subject LST022,  biological rep1

tag: response

tag: site

tag: % fall in fev1 (early)

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)


title: Subject LST017,  biological rep1

tag: allergen

tag: Sex

tag: ethnicity

tag: age

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: tissue


title: Subject LST016,  biological rep2

tag: response

tag: site

value: Cat Pelt (Lot#)

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)


title: Subject STS007,  biological rep1

tag: allergen

tag: Sex

tag: % fall in fev1 (early)

tag: mean cell volume (fl)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)


title: Subject STS007,  biological rep2

tag: response

tag: site

tag: ethnicity

tag: age

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: tissue


title: gDNA_8h_cdc6-mn_2

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description: CGH of 8h gDNA from cdc6-mn cells versus control DNA replicate 2

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

organism: Saccharomyces cerevisiae

source_name: mitotic G1 budding yeast cells

label_protocol: not provided

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours. Samples were isolated after 8 hours.  Control DNA samples were isolated from G1 haploid SK1, which were incubated for 3 hours with 5 μg/ml alpha-factor.

extract_protocol: Cells were lysed by bead beating in 500 µl phenol/chloroform and 500 µl of breakage buffer (10 mM TRIS, pH 8.0, 1 mM EDTA, 100 mM NaCl, 2% Triton X-100, 1% SDS).  After centrifugation, the aqueous phase was precipitated with ethanol and resuspended in 500 µl TE7.6 (10 mM TRIS, pH7.6, 1 mM EDTA) with 30 µg RNase. DNA was resuspended and samples were incubated at 50°C for 3 hours. DNA was sheared by sonicating at 100% output and lowest power for 10 seconds using a Branson sonicator. DNA was extracted with 500 µl phenol/chloroform, precipitated with ethanol and resuspended in 100 µl of TE7.6

tag: strain

tag: genotype/variation

source_name: meiotic budding yeast cells (SPO 8h)


title: gDNA_8h_cdc6-mn_1

description: CGH of 8h gDNA from cdc6-mn cells versus control DNA replicate 1


title: Subject LST026,  biological rep1

tag: allergen

tag: Sex

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: mean cell volume (fl)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)


title: Subject LST021,  biological rep1

tag: response

tag: site

tag: ethnicity

tag: age

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)


title: DSB-pat1.114-rad50S

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

description: IP/Input scaling factor: 1.3

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

scan_protocol: Slides were imaged on an Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.1.1.1 or 10.5.1.1).

data_processing: Dark spot and control probes were removed, as were custom probes for repetitive DNA.  To allow comparisons between strains in the same experiment (the same rad50 allele), log ratios were multiplied by a calibration factor ranging from 1.1-1.3 determined by comparing probes within six prominant DSB hotspots shown by Southern blot to be indistinguishable.  The resulting ratios were then median normalized.

organism: Schizosaccharomyces pombe

source_name: IP Rec12, pat1-114, rad50S

label_protocol: Immunoprecipitated material and whole-cell extracts were PCR amplified to increase signal and Cy3/Cy5-labeled dUTPs were incorporated.

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for 16-18 hours to synchronize cells; nitrogen was added and meiosis was induced by two different methods: addition of a chemical inhibitor (1-NM-PP1) of the pat1-as2 allele or the temperature was shifted to 34°C.

extract_protocol: Cells were collected at the indicated time points following induction of meiosis when DSBs were maximal.  No exogenous crosslinking agent was used; cells were treated with protease inhibitors, broken with a bead beater, chromatin sonicated to ~500-1000 bp, and Rec12-FLAG immunoprecipitated.

tag: time

value: 5 hours

tag: induction method

value: temperature shift

source_name: Whole-cell input for induced pat1-114, rad50S


title: gDNA_8h_WT_1

description: CGH of 8h gDNA from wild-type cells versus control DNA replicate 1

tag: strain

tag: genotype/variation

value: wild-type


title: Sf3b1+/-_BMT_LSK

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

country: Japan

institute: Kumamoto University

description: Gene expression in Sf3b1 LSK cells at 9 months post-transplantation

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner (Agilent Technologies)

data_processing: Standard Agilent protocol

source_name: Bone marrow LSK cells, Sf3b1+/-, BMT, replicate 1

label_protocol: 20 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

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

treatment_protocol: Freshly isolated bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

tag: transplantation

value: Sf3b1+/- bone marrow cells

tag: cell type

value: Bone marrow LSK cells (at 9 months post-transplantation)


title: WT_BMT_LSK

description: Gene expression in WT LSK cells at 9 months post-transplantation

source_name: Bone marrow LSK cells, wild type, BMT, replicate 1

value: wild type

value: wild type bone marrow cells


title: Subject LST016,  biological rep1

tag: response

value: Laval

tag: allergen

tag: Sex

value: Caucasian

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: mean cell volume (fl)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)

tag: tissue


title: gDNA_8h_WT_2

description: CGH of 8h gDNA from wild-type cells versus control DNA replicate 2

tag: strain

tag: genotype/variation


title: DSB-pat1.as2-rad50S-34C

description: IP/Input scaling factor: 1

source_name: IP Rec12, pat1-as2, rad50S, 34C, no inhibitor

tag: time

tag: induction method

source_name: Whole-cell input for induced pat1-as2, rad50S, 34C, no inhibitor


title: DSB-pat1.as2-rad50S-25C

description: IP/Input scaling factor: 1.1

source_name: IP Rec12, pat1-as2, rad50S, 25C, with inhibitor

value: 8.5 hours

value: pat1-as2 inhibitor

source_name: Whole-cell input for induced pat1-as2, rad50S, 25C, with inhibitor


title: Sf3b1+/-_LSK

description: Gene expression in LSK cells from Sf3b1+/- mice at 20 weeks old

source_name: Bone marrow LSK cells, Sf3b1+/-, replicate 1

tag: transplantation

value: no

tag: cell type

value: Bone marrow LSK cells (from mice at 20 weeks old)


title: Control-4 mon

status: Public on Sep 19 2013

city: Beijing

first: Subi

last: Wei

state: Beijing

address: Xueyuan Load

department: Medical Systems Biology Research Center

institute: Tsinghua university

description: low-molecuar-weight RNA derived from total RNA

hyb_protocol: Standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using GenePix Pro 4.0 (Axon Instruments, California, United States). Data processing including local background subtraction, quantile normalization across multiple slides was performed in R package (version 2.5.0).

source_name: wild type mice

label_protocol: 5μg of the Low-molecular-weight RNAs were isolated from total RNAs by a PEG solution precipitation method and labelled with 5-phosphate-cytidyl-uridyl-Cy3-3(Dharmacon, Chicago, United States) using T4 RNA ligase (NEB, Beijing, China) at 4°C for 4 hours in the dark. Eight synthetic small RNAs were spiked in for exogenous control.

growth_protocol: APP/PS1M146V/+ mice were generated by crossed Tg2576 APP transgenic mice with PS1 M146V homozygous (PS1M146V/M146V) mice. All mice were feed and housed according to standard procedures.

extract_protocol: The bilateral hippocampus was dissected from groups of mice (n= 3), pooled, then stored in liquid nitrogen until use. Tissue was homogenized in liquid nitrogen and total RNAs was prepared using TRIzol™ reagent according to the protocol provided by the manufacturer, with an additional 2 h incubation step at -20 °C during isopropanol precipitation. The A260/A280 ratio as well as the banding pattern of RNAs by denaturing gel electrophoresis was used to estimate the quality of the RNAs.

treatment_protocol: No treatment

tag: disease state

value: normal

value: bilateral hippocampus


title: Control-9 mon