title: MCC, metastatic, tumor MetMCC543, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC543

value: equivocal


title: MCC, metastatic, tumor MetMCC578, renormalized

status: Public on Oct 18 2012

type: RNA

city: Ann Arbor

first: Paul

last: Harms

address: 1301 Catherine

department: Pathology

country: USA

institute: University of Michigan

description: gene expression data from Merkel cell carcinoma, metastatic

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC578

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.

treatment_protocol: All tumor tissue was procured from the University of Michigan Hospitals Cutaneous Surgery and Oncology Program.  At time of collection, tumor tissue was flash-frozen in liquid nitrogen and stored at -80oC until RNA extraction.  Biopsies of normal skin were flash-frozen at the time of collection and stored at -80oC until time of extraction.

tag: normal or tumor

value: tumor

tag: tissue

value: Merkel cell carcinoma

tag: metastasis, primary, or cell line

value: metastatic tumor

tag: merkel cell polyomavirus status (dna and rna)

value: positive


title: EEEV-105

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

institute: Washington University in St. Louis, School of Medicine

description: hybridization of infected culture for use in training VIPR HMM

hyb_protocol: 70 degree incubation for 12 hours

scan_protocol: scanned using GenePix 4000B scanner

data_processing: None. Regarding the submission of raw (not normalized) data, the microarray data provided represents an unconventional use of microarrays as a diagnostic tool as opposed to the conventional use of microarrays to study gene expression patterns. Each software tool that has been developed to analyze diagnostic microarray data employs its own normalization method. Thus, the standard input to these programs is non-normalized data which is then independently processed by whatever software tool is chosen.

organism:
Chlorocebus aethiops
Alphavirus

source_name: infected culture

label_protocol: amino-allyl Cy3 dye coupled to cDNA

extract_protocol: RNA extracted using Trizol extraction protocol

tag: cell line

value: Vero

tag: infection

value: EEEV FL93-939

tag: purpose

value: Training


title: MCC, metastatic, tumor MetMCC547, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC547

value: negative


title: VEEV-104

value: VEEV TC-83


title: normal skin GSM337260.CEL renormalized

description: gene expression data from normal skin from controls

value: normal skin from controls

value: normal skin


title: normal skin GSM337259.CEL renormalized


title: VEEV-103


title: VEEV-100

value: VEEV 68U201


title: normal skin GSM337257.CEL renormalized


title: Ctrl_C_96h

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

description: Gene expression control

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and by Agilent Feature Extraction Software (v10.5.1.1). Data preprocessing was performed with the Agi4x44PreProcess R package using quantile normalization and quality filtering.

source_name: hNT2 control differentiation

label_protocol: standard Agilent protocol

growth_protocol: Undifferentiated hNT2 cells were cultured in 75 cm2 flasks at the density of 3 x 10 6 cells with 5% heat-inactivated foetal bovine serum (FBS) plus 50 U/ml penicillin and 100 µg/ml streptomycin in Opti-MEM media. After 24 hours and for initiating differentiation, a differentiation medium with 10 µM retinoic acid, 10% of FBS and antibiotics in DMEM-Glutamax was applied during 4 days. The medium was replaced at the beginning of day 3.

extract_protocol: RNA from hNT2 cells previously was purified using the RNeasy Plus kit (Qiagen, Germantown, MD, USA).

treatment_protocol: Paraoxon (1 µM) and mipafox (5 µM) were applied to cells freshly dissolved in the differentiation medium.

tag: treatment

value: Ctrl


title: Ctrl_A_96h

description: Gene expression control


title: VEEV-101


title: EEEV-097


title: normal skin GSM337252.CEL renormalized


title: normal skin GSM337258.CEL renormalized


title: normal skin GSM337246.CEL renormalized


title: normal skin GSM337256.CEL renormalized


title: normal skin GSM337251.CEL renormalized


title: Ctrl_B_96h

description: Gene expression control


title: normal skin GSM337255.CEL renormalized


title: BM_C

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data were quantile normalised using Lumi for R [64-bit R version 2.15.1 (2012-06-22), lumi version 2.8.0].

label: Biotin

source_name: BM

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted with Trizol and amplified using Illumina® TotalPrepTM-96 RNA Amplification Kit

value: Bone Marrow

tag: culture condition

value: Normal bone marrow plasma cells from staging marrows

tag: gender

value: Female


title: VEEV-102


title: BM_A

value: Male


title: BM_MIX

value: Normal bone marrow plasma cells from staging marrows; mixture from 10 donors

value: Mixed


title: normal skin GSM337254.CEL renormalized


title: VEEV-099


title: normal skin GSM337245.CEL renormalized


title: normal skin GSM337250.CEL renormalized


title: EEEV-098


title: normal skin GSM337247.CEL renormalized


title: BM_B


title: Day41_C

value: Peripheral blood

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 28 days of IL-6, IFN-α and supplemented media, with M2-10B4 in the lower compartment.


title: normal skin GSM337249.CEL renormalized


title: VEEV-096

value: Vero

value: VEEV ZPC738


title: normal skin GSM337248.CEL renormalized


title: normal skin GSM337253.CEL renormalized


title: Day41_B


title: normal skin GSM337243.CEL renormalized


title: normal skin GSM337244.CEL renormalized


title: VEEV-095

value: Training


title: Day20_B

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 7 days of IL-6, IFN-α and supplemented media, with M2-10B4 in the lower compartment.


title: normal skin GSM337241.CEL renormalized


title: VEEV-094


title: normal skin GSM337237.CEL renormalized


title: normal skin GSM337240.CEL renormalized


title: Day41_A


title: normal skin GSM337242.CEL renormalized


title: normal skin GSM337239.CEL renormalized


title: Day13_B

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 7 days of IL-6, IL-21, IFN-α and supplemented media, with M2-10B4 in the lower compartment.


title: Day13_C


title: VEEV-092


title: VEEV-090

value: VEEV TRD


title: normal skin GSM337234.CEL renormalized

value: normal skin from controls

value: normal skin


title: normal skin GSM337236.CEL renormalized


title: normal skin GSM337238.CEL renormalized


title: VEEV-091


title: normal skin GSM337235.CEL renormalized


title: Day20_A


title: VEEV-093

value: VEEV 68U201


title: Day13_A


title: normal skin GSM337231.CEL renormalized


title: normal skin GSM337232.CEL renormalized


title: normal skin GSM337233.CEL renormalized


title: Day6_C

value: Plasmablasts generated after 3 days of IL-2, IL-21 in supplemented media.


title: Day6_B


title: VEEV-089


title: normal skin GSM337229.CEL renormalized


title: EEEV-088

value: EEEV BeAr436087


title: normal skin GSM337228.CEL renormalized


title: normal skin GSM337230.CEL renormalized


title: EEEV-087


title: normal skin GSM337227.CEL renormalized


title: normal skin GSM337226.CEL renormalized


title: Day3_C

value: Activated Total B cells following 3 days of F(ab')2, IL-2, IL-21 and CD40L (feeder layer).


title: Day6_A

value: Male


title: normal skin GSM337222.CEL renormalized


title: normal skin GSM337225.CEL renormalized


title: EEEV-086


title: normal skin GSM337220.CEL renormalized


title: EEEV-084

value: EEEV FL93-939


title: normal skin GSM337224.CEL renormalized


title: EEEV-083

description: hybridization of infected culture for use in validating VIPR HMM

value: Validation


title: EEEV-085


title: Day3_B

value: Peripheral blood

value: Female


title: normal skin GSM337215.CEL renormalized


title: Day0_B

value: MACS purified (negative selection) Total B cells from healthy donors.


title: normal skin GSM337219.CEL renormalized


title: Day3_A


title: normal skin GSM337223.CEL renormalized


title: normal skin GSM337216.CEL renormalized


title: normal skin GSM337218.CEL renormalized


title: normal skin GSM337221.CEL renormalized


title: normal skin GSM337217.CEL renormalized


title: Day0_C


title: normal skin GSM337214.CEL renormalized


title: VEEV-081

value: Vero


title: normal skin GSM337213.CEL renormalized


title: Day0_A


title: normal skin GSM337212.CEL renormalized


title: normal skin GSM337211.CEL renormalized


title: CHIKV-071

value: CHIKV LR

value: Training


title: CHIKV-070


title: normal skin GSM337209.CEL renormalized


title: normal skin GSM337210.CEL renormalized


title: normal skin GSM337206.CEL renormalized


title: CHIKV-069


title: normal skin GSM337208.CEL renormalized


title: normal skin GSM337207.CEL renormalized


title: normal skin GSM337205.CEL renormalized


title: aa.3

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

country: Canada

institute: Université du Québec à Chicoutimi

description: SAMPLE 7

hyb_protocol: Hybridation was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples

scan_protocol: Scanning was done using a GeneArray Scanner at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples

data_processing: The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix) and the raw image fils obtained (.CEL) were used for statistical analyses. To calculate gene expression, the robust multiarray analysis (RMA) was used. To identify significant differences in gene expression, a pairwise comparison between control and allergic asthmatic subjects was performed with the microarray results, in the first case with the Limma package available in Bioconductor. However, no correction was applied when using the U133A GeneChips since the RMA method is more stringent. However, Smyth’s moderated t test was used.

source_name: allergic_asthmatic_bronchial biopsies

label_protocol: Probe labelling was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples.

growth_protocol: Biopy protocol: 8 biopsies evaluated as acceptable by the research assistant were taken from bronchi of the right lung using alligator forceps (Olympus FB-15C-1). Biopsies were obtained from the  ubsegmental and segmental bronchial carinae of the lower (3 to 5 biopsies) and upper (1 to 2 biopsies) lobes, as well as the lobar carinae of the middle (2 biopsies) and upper (1 to 2 biopsies) lobes to provide adequate samples of the large airways (3rd to 5th bronchial generation). The samples were immediately placed in RNAlater.

extract_protocol: The samples were mechanically homogenized (Rotor/Stator homogenizer; PowerGen) and total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer’s instructions.

tag: disease status

value: allergic asthmatic subjects

value: bronchial biopsies


title: SINV-067

value: SINV AR339


title: normal skin GSM337203.CEL renormalized

value: normal skin from controls

value: normal skin


title: SINV-068


title: VEEV-082

value: VEEV ZPC738


title: aa.2

description: SAMPLE 6


title: normal skin GSM337201.CEL renormalized


title: normal skin GSM337204.CEL renormalized


title: c.4

description: SAMPLE 4

source_name: control_bronchial biopsies

value: non allergic non asthmatic subject, without any stimulation


title: aa.4

description: SAMPLE 8


title: normal skin GSM337200.CEL renormalized


title: normal skin GSM337202.CEL renormalized


title: aa.1

description: SAMPLE 5


title: WEEV-066


title: normal skin GSM337198.CEL renormalized


title: c.3

description: SAMPLE 3


title: WEEV-065


title: normal skin GSM337199.CEL renormalized


title: c.2

description: SAMPLE 2


title: c.1

description: SAMPLE 1


title: MCC, metastatic, tumor MetMCC624

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

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC624

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5)

treatment_protocol: All tumor tissue was procured from the University of Michigan Hospitals Cutaneous Surgery and Oncology Program.  At time of collection, tumor tissue was flash-frozen in liquid nitrogen and stored at -80oC until RNA extraction. Merkel cell carcinoma cell lines were established at the University of Michigan from tumor tissue procured as described above.

value: Merkel cell carcinoma

value: metastatic tumor

value: negative


title: Pten-/-KrasG12D female biological replicate 3

city: Bronx

first: Antonio

last: Di Cristofano

state: NY

address: 1301 Morris Park Ave Price 302

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

description: Pten-/-KrasG12D female 3

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Analized with Expression Console (RMA): affymetrix-algorithm-name = rma-gene-default; affymetrix-algorithm-version = 1.0; program-name = Expression Console; program-version = 1.1.2800.19935

organism: Mus musculus

source_name: Pten-/-KrasG12D female_tyroid gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

extract_protocol: Trizol extraction followed by Quiagen Rneasy column purification.

tag: strain background

tag: genotype/variation

value: female

tag: age

value: 2 months

value: thyroid gland


title: MCC, metastatic, tumor MetMCC599

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC599

value: positive


title: normal skin GSM337197.CEL renormalized


title: MCC, metastatic, tumor MetMCC614

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC614


title: Pten-/-KrasG12D female biological replicate 2

description: Pten-/-KrasG12D female 2


title: MCC, metastatic, tumor MetMCC603

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC603


title: WEEV-062

value: Vero

value: WEEV McMillan


title: SINV-063

value: Training


title: SINV-064


title: Pten-/-KrasG12D female biological replicate 1

description: Pten-/-KrasG12D female 1


title: WEEV-060


title: MCC, cell line MCC19

description: gene expression data from Merkel cell carcinoma, cell line

source_name: Merkel cell carcinoma, cell line MCC19

value: cell line

value: not done


title: MCC, primary, tumor MCC622

description: gene expression data from Merkel cell carcinoma, primary

source_name: Merkel cell carcinoma, primary, tumor MCC622

value: primary tumor


title: WEEV-061


title: MCC, cell line MCC565

source_name: Merkel cell carcinoma, cell line MCC565


title: MCC, primary, tumor MCC601

source_name: Merkel cell carcinoma, primary, tumor MCC601


title: MCC, cell line MCC21

source_name: Merkel cell carcinoma, cell line MCC21


title: HP7 tumor

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

description: gene expression data from tumors injected with GFAP-CRE in the hippocampus

hyb_protocol: Fragmented cRNA are hybridized using a GeneChip Fluidics Station 450 in aGeneChip Hybridization Oven 640.

scan_protocol: Gene chips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Gene chips were analyzed using Affymetrix power tools using MAS 5 background correction, RMA probeset summarization, and median normalization (-a mas5-bg,med-norm,pm-only,med-polish).

source_name: tumor

label_protocol: total RNA was labeled with the Ambion Affymetrix WT expression kit for Affymetrix whole transcript arrays, product #4411974. Product number 4411974

extract_protocol: total RNA was harvested with Trizol according to manufacturer's instructions

tag: location

value: hippocampus

tag: promoter

value: GFAP


title: MCC, primary, tumor MCC623

source_name: Merkel cell carcinoma, primary, tumor MCC623


title: WEEV-059

source_name: infected culture


title: HP6 tumor


title: MCC, cell line MCC13

source_name: Merkel cell carcinoma, cell line MCC13


title: MCC, metastatic, tumor MetMCC564

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC564


title: MCC, primary, tumor MCC521

source_name: Merkel cell carcinoma, primary, tumor MCC521


title: SYN4 tumor

description: gene expression data from tumors injected with SYN1-CRE in the cortex

value: cortex


title: CHIKV-072

value: CHIKV LR


title: MCC, primary, tumor MCC611

source_name: Merkel cell carcinoma, primary, tumor MCC611

value: Merkel cell carcinoma


title: WEEV-058


title: MCC, primary, tumor MCC506

source_name: Merkel cell carcinoma, primary, tumor MCC506


title: MCC, primary, tumor MCC304

source_name: Merkel cell carcinoma, primary, tumor MCC304

value: insufficient DNA


title: Vero-047

organism: Chlorocebus aethiops

source_name: uninfected culture


title: MCC, primary, tumor MCC592

source_name: Merkel cell carcinoma, primary, tumor MCC592

value: negative


title: SYN3 tumor


title: Vero-045


title: MCC, metastatic, tumor MetMCC591

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC591

value: metastatic tumor


title: Vero-043


title: HP5 tumor


title: Vero-046


title: SYN2 tumor


title: MCC, primary, tumor MCC582

source_name: Merkel cell carcinoma, primary, tumor MCC582


title: SVZ3 tumor

description: gene expression data from tumors injected with GFAP-CRE in the subventricular zone

value: subventricular zone


title: Vero-044


title: SVZ2 tumor


title: SYN1 tumor


title: Recombinant 4-041

value: Validation


title: Recombinant 7-042

value: VEE/CHIK


title: NHP4 normal

description: gene expression data from normal hippocampus tissue

source_name: normal


title: MCC, primary, tumor MCC571

source_name: Merkel cell carcinoma, primary, tumor MCC571

value: positive


title: MCC, primary, tumor MCC470

source_name: Merkel cell carcinoma, primary, tumor MCC470


title: SVZ1 tumor


title: NHP3 normal


title: MCC, primary, tumor MCC569

source_name: Merkel cell carcinoma, primary, tumor MCC569


title: MCC, primary, tumor MCC576

source_name: Merkel cell carcinoma, primary, tumor MCC576


title: VEEV-040

value: Vero

value: VEEV 68U201


title: MCC, primary, tumor MCC529

source_name: Merkel cell carcinoma, primary, tumor MCC529


title: MCC, primary, tumor MCC439

source_name: Merkel cell carcinoma, primary, tumor MCC439


title: NHP2 normal


title: NHP1 normal


title: VEEV-039

source_name: infected culture

value: VEEV ZPC738


title: MCC, primary, tumor MCC437

source_name: Merkel cell carcinoma, primary, tumor MCC437


title: NES4 tumor

description: gene expression data from tumors injected with NES-CRE in the hippocampus

source_name: tumor

value: NES


title: NES2 tumor


title: VEEV-037

value: VEEV TRD


title: VEEV-038

value: VEEV TC-83


title: MCC, primary, tumor MCC412

source_name: Merkel cell carcinoma, primary, tumor MCC412

value: primary tumor


title: Recombinant 12-036


title: NES3 tumor

value: hippocampus


title: MCC, metastatic, tumor MetMCC562

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC562


title: Recombinant 5-035

value: SIN/SAEEE


title: Recombinant 3-034

value: SIN/CHIK


title: Recombinant 1-033

value: EEE/CHIK


title: MCC, primary, tumor MCC345

source_name: Merkel cell carcinoma, primary, tumor MCC345

value: Merkel cell carcinoma


title: Recombinant 14-028

value: SIN/ZPC


title: Recombinant 6-029

value: SIN/TRD


title: MCC, metastatic, tumor MetMCC547

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC547

value: metastatic tumor

value: negative


title: MCC, metastatic, tumor MetMCC543

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC543

value: equivocal


title: Recombinant 15-032

value: Vero

value: SIN/EEE/McM

value: Validation


title: NCTX3 normal

description: gene expression data from normal cortex tissue

value: cortex


title: HP4 tumor

value: GFAP


title: MCC, primary, tumor MCC274

source_name: Merkel cell carcinoma, primary, tumor MCC274


title: NCTX4 normal


title: MCC, metastatic, tumor MetMCC456

source_name: Merkel cell carcinoma, metastatic tumor MetMCC456


title: MCC, metastatic, tumor MetMCC578

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC578

value: positive


title: BCC, tumor BTD133

description: gene expression data from basal cell carcinoma

source_name: basal cell carcinoma, tumor BTD133

value: basal cell carcinoma

value: not done


title: NES1 tumor

value: hippocampus

value: NES


title: NCTX2 normal

source_name: normal


title: Recombinant 13-031

value: SIN/NAEEE


title: Inhibitor treated-cultivations, replicate 3

city: Göteborg

first: Magnus

last: Ask

address: Kemivägen 10

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Samples were hybridized for 16 h.

scan_protocol: Scanning was performed with a GeneChip Scanner 3000 7G.

data_processing: R/Bioconductor GCRMA. Statistical analysis using the limma package.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae VTT C-10883, inhibitors

label_protocol: 3'IVT expression kit (Affymetrix).

growth_protocol: Anaerobic chemostat.

extract_protocol: Qiagen RNeasy kit.

treatment_protocol: Step-change to furfural- and HMF-containing medium.

tag: strain

tag: growth type

value: anaerobic

value: hydroxymethylfurfural (HMF) and furfural


title: NCTX1 normal


title: WEEV-057

value: Training


title: HP2 tumor


title: Inhibitor treated-cultivations, replicate 2


title: Inhibitor treated-cultivations, replicate 1


title: HP3 tumor


title: EEEV-012

value: EEEV FL93-939


title: No inhibitors, replicate 3

source_name: Saccharomyces cerevisiae VTT C-10883, no inhibitors


title: CHIKV-023

value: CHIKV LR


title: BCC, tumor BTD125

source_name: basal cell carcinoma, tumor BTD125

tag: tissue


title: CTX4 tumor

description: gene expression data from tumors injected with GFAP-CRE in the cortex


title: SCC, tumor STD318

description: gene expression data from primary cutaneous squamous cell carcinoma

source_name: primary cutaneous squamous cell carcinoma, tumor STD318

value: insufficient DNA


title: HP1 tumor


title: WEEV-022

source_name: infected culture

value: Vero


title: SINV-007

value: SINV AR339


title: SCC, tumor STD135

source_name: primary cutaneous squamous cell carcinoma, tumor STD135


title: SCC, tumor STD262

source_name: primary cutaneous squamous cell carcinoma, tumor STD262

value: negative


title: No inhibitors, replicate 2


title: No inhibitors, replicate 1


title: CTX1 tumor

source_name: tumor

value: cortex


title: Recombinant 2-005

value: Validation


title: SCC, tumor STD113

source_name: primary cutaneous squamous cell carcinoma, tumor STD113


title: CTX3 tumor

value: GFAP


title: WEEV-004

value: WEEV McMillan


title: CTX2 tumor


title: Gene expression in gastric epithelial cells: CDX1 induction +, 24 h

city: Tokyo

first: Yumiko

last: FUJII

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

department: Depertment of Microbiology, Graduate School of Medicine

country: Japan

institute: University of Tokyo

description: Gene expression data in CDX1-inducible MKN28 cells expressing CDX1 for 24 h.

hyb_protocol: Array hybridization was performed as described previously (Ishii et al., Genomics:136-143, 2000).

scan_protocol: Array scanning was performed as described previously (Ishii et al., Genomics:136-143, 2000).

data_processing: Microarray Suite software 5.0 (Affymetrix) was used to calculate the average differentiation (AD) for each gene probe set, which was shown as an intensity value of the gene expression (Ishii et al., Genomics:136-143, 2000).

source_name: CDX1-inducible MKN28 cells, doxycycline - (CDX1 +), 24 h

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeld cRNA by using a BioArray HighYield RNA Transcription Labeling Kit (Affymetrix) according to the manufacturer's instructions (Ishii et al., Genomics:136-143, 2000).

growth_protocol: CDX1-inducible MKN28 cells were cultured in RPMI 1640 medium (Nissui PharmaCeutical Co.) supplemented with 10% fetal bovine serum and 1 μg/ml doxycycline. Cells were grown in a humidified atomosphere with 5% CO2 at 37°C.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen).

treatment_protocol: CDX1-inducible MKN28 cells, which inducibly express Flag-tagged CDX1 with the use of a tetracycline-regulated Tet-Off System (Clontech), were established from MKN28 human gastric epithelial cells. CDX1-inducible MKN28 cells were cultured in the absence of Doxycycline (Clontech), a tetracycline analog, for 24 h before harvest (induction +).

tag: cell type

value: gastric epithelial cells

tag: transgene

value: pTet-Off, Flag-tagged CDX1

tag: expression


title: Gene expression in gastric epithelial cells: CDX1 induction -, 24 h

description: Gene expression data in CDX1-inducible MKN28 cells not expressing CDX1.

source_name: CDX1-inducible MKN28 cells, doxycycline + (CDX1 -), 24 h

treatment_protocol: CDX1-inducible MKN28 cells, which inducibly express Flag-tagged CDX1 with the use of a tetracycline-regulated Tet-Off System (Clontech), were established from MKN28 human gastric epithelial cells. CDX1-inducible MKN28 cells were cultured in the presence of Doxycycline (Clontech), a tetracycline analog, for 24 h before harvest (induction -).

tag: cell line


title: SU 5 Days_Rep2

status: Public on Oct 17 2012

city: Berlin

first: smita

last: sudheer

address: Ihnestraße 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Biological Replicate 2

hyb_protocol: The labelled cRNA samples were hybridised onto HumanRef-8 v3 chips following the manufacturer’s instructions (Ilumina).

scan_protocol: The hybridized chips were scanned following the manufacturer’s instructions (Ilumina).

data_processing: Rank invariant normalization method from BeadStudio 3.0 software (Illumina) was used for data normalization.

source_name: hESCs treated with SU5402 (20 µM) for 5 Days

label_protocol: 500 ng DNAse-free total RNA was biotin-labelled to generate cRNA employing a linear amplification kit (Ambion).

growth_protocol: The experiments were carried out using the Human Embryonic Stem Cell line H9 obtained from WiCell and cultured on matrigel-coated plates. The cells were passaged and maintained in MEF-conditioned medium (Xu et al., 2001) till they reached a confluency of ~40-50%. They were rinsed with PBS, followed by the various treatments under defined conditions (N2B27) (Yao et al., 2006).

extract_protocol: RNA isolations were performed using the RNeasy Mini Kit (Qiagen). The cells were directly lysed with lysis buffer in the cell-culture wells, after rinsing with PBS. Total RNA from human Placenta was purchased from Clontech (636527).

treatment_protocol: The cells were passaged and maintained in MEF-conditioned medium (Xu et al., 2001) till they reached a confluency of ~40-50%. They were rinsed with PBS, followed by the various treatments under defined conditions (N2B27) (Yao et al., 2006): BMP4 (10 ng/ml) for 3 Hours and 5 Days; BMP4 (10 ng/ml) + SB431542 (20 µM) for 3 Hours, 1 Day, 3 Days and 5  Days; BMP4 (10 ng/ml) + SB431542 (20 µM) + SU5402 (20 µM) for 3 Hours, 1 Day, 3 Days and 5  Days; BMP4 (10 ng/ml) + SB431542 (20 µM) + FGF2 (20 ng/ml) for 3 Hours, 1 Day, 3 Days and 5  Days; SU5402 (20 µM) for 1 Day, 3 Days and 5  Days

value: hESC

value: SU5402 (20 µM) for 5 days


title: SU 5 Days_Rep1

description: Biological Replicate 1


title: SU 3 Days_Rep2

description: Biological Replicate 2

source_name: hESCs treated with SU5402 (20 µM) for 3 Days

value: SU5402 (20 µM) for 3 days


title: Undifferentiated hESCs_Rep2

description: Biological Replicate 2

source_name: hESCs treated with FGF2 (20 ng/ml)

value: FGF2 (20 ng/ml)


title: B/SB/F 5 Days_Rep2

description: Biological Replicate 2

source_name: hESCs treated with BMP4 (10 ng/ml) + SB431542 (20 µM) + FGF2 (20 ng/ml) for 5 Days

value: BMP4 (10 ng/ml) + SB431542 (20 µM) + FGF2 (20 ng/ml) for 5 days


title: SU 1 Day_Rep2

description: Biological Replicate 2

source_name: hESCs treated with SU5402 (20 µM) for 1 Day

value: SU5402 (20 µM) for 1 day


title: Undifferentiated hESCs_Rep1

description: Biological Replicate 1


title: B 5 Days_Rep2

description: Biological Replicate 2

source_name: hESCs treated with BMP4 (10 ng/ml) for 5 Days

value: BMP4 (10 ng/ml) for 5 days


title: B/SB/SU 5 Days_Rep1

description: Biological Replicate 1

source_name: hESCs treated with BMP4 (10 ng/ml) + SB431542 (20 µM) + SU5402 (20 µM) for 5 Days


title: SU 1 Day_Rep1

description: Biological Replicate 1


title: B/SB/SU 1 Day_Rep1

description: Biological Replicate 1

source_name: hESCs treated with BMP4 (10 ng/ml) + SB431542 (20 µM) + SU5402 (20 µM) for 1 Day


title: B/SB/SU 5 Days_Rep2

description: Biological Replicate 2


title: B/SB/SU 3 Hours_Rep1

description: Biological Replicate 1

source_name: hESCs treated with BMP4 (10 ng/ml) + SB431542 (20 µM) + SU5402 (20 µM) for 3 Hours


title: B 5 Days_Rep1

description: Biological Replicate 1


title: B/SB/SU 3 Hours_Rep2

description: Biological Replicate 2


title: B/SB/SU 3 Days_Rep1

description: Biological Replicate 1

source_name: hESCs treated with BMP4 (10 ng/ml) + SB431542 (20 µM) + SU5402 (20 µM) for 3 Days


title: Placenta_Rep2

description: Technical Replicate 2

source_name: Human Placenta

value: Human placenta

tag: vendor

value: Clontech (636527)


title: B/SB/F 5 Days_Rep1

description: Biological Replicate 1

tag: treatment


title: SU 3 Days_Rep1

description: Biological Replicate 1


title: B/SB 5 Days_Rep1

description: Biological Replicate 1

source_name: hESCs treated with BMP4 (10 ng/ml) + SB431542 (20 µM) for 5 Days

value: BMP4 (10 ng/ml) + SB431542 (20 µM) for 5 days


title: Placenta_Rep1

description: Technical Replicate 1


title: B/SB 5 Days_Rep2

description: Biological Replicate 2


title: B/SB/SU 3 Days_Rep2

description: Biological Replicate 2


title: CUL4B

type: genomic

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

country: China

institute: Tianjin Medical School

description: Chip-chip KYSE410 cells CUL4B

hyb_protocol: The labeled ChIP DNA 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.

molecule: genomic DNA

source_name: CUL4B ChIP DNA from KYSE410 cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: KYSE410 cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Invitrogen). All media contained 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin (Gibco BRL).

extract_protocol: 1x10E7 cells were washed twice with PBS and cross-linked with 1% formaldehyde at room temperature for 10 min. Cells then were rinsed with ice-cold PBS twice and collected into 100 mM Tris-HCl (pH 9.4), 10 mM DTT and incubated for 15 min at 30°C and centrifuged for 5 min at 2000 g. Cells were washed sequentially with 1 ml of ice-cold PBS, buffer I (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5), and buffer II (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5). Cells were then resuspended in 0.3 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.1, 1× protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN) and sonicated three times for 10 s each at the maximum setting (Fisher Sonic Dismembrator, Model 300) followed by centrifugation for 10 min. Supernatants were collected and diluted in buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1) followed by immunoclearing with 2 μg sheared salmon sperm DNA, 20 μl preimmune serum and protein A-sepharose (45 μl of 50% slurry in 10 mM Tris-HCl, pH 8.1, 1 mM EDTA) for 2 hr at 4°C. Immunoprecipitation was performed for 6 hr or overnight at 4°C with specific antibodies. After immunoprecipitation, 45 μl protein A-Sepharose and 2 μg of salmon sperm DNA were added and the incubation was continued for another 1 hr. Precipitates were washed sequentially for 10 min each in TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), and buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1). Precipitates were then washed three times with TE buffer and extracted three times with 1% SDS, 0.1 M NaHCO3. Eluates were pooled and heated at 65°C for at least 6 hr to reverse the formaldehyde cross-linking. DNA fragments were purified with a QIAquick Spin Kit (Qiagen, CA). For PCR, 1 μl from a 50 μl DNA extraction and 21–25 cycles of amplification were used.

treatment_protocol: 1x10E7 cells were collected for ChIP assay per antibody

value: KYSE410 cells

tag: chip antibody

source_name: Input DNA from KYSE410 cells

value: none, input DNA


title: B/SB/SU 1 Day_Rep2

description: Biological Replicate 2


title: EZH2

description: Chip-chip KYSE410 cells EZH2

source_name: EZH2 ChIP DNA from KYSE410 cells

growth_protocol: KYSE410 cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Invitrogen). All media contained 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin


title: BMI

description: Chip-chip KYSE410 cells BMI

source_name: BMI ChIP DNA from KYSE410 cells

value: BMI


title: Ire1 ko, biological rep2

city: Boston

first: Ann-Hwee

last: Lee

state: MA

address: 651 Huntington Ave, FXB/205

institute: Harvard School of public health

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: AGCC GeneTitan Wash and Scan

data_processing: We use the R bioconductor suite to normalize the Affymetrix data. The package we use for RMA is in the affy package and the version we currently use is 1.20.2 .

source_name: Ire1 ko, fed state, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.2 ug of total RNA.

extract_protocol: Trizol (Invitrogen) extraction of total RNA followed by cleanup using RNeasy MinElute Cleanup Kit (Qiagen) was performed according to the manufacturer's instructions.

value: Liver

tag: gender

value: male

tag: stain

value: mixed stain

tag: genotype

value: Ire1 ko

value: 14 weeks


title: Ire1 ko, biological rep3


title: WT, tunicamycin, biological rep4

source_name: WT, tunicamycin, 2 mg/kg, 6 hr

value: WT


title: PMN-MDSC RMA-S tumor, repl.3

city: Heidelberg

first: Christian

last: Eisen

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: RMA-S mouse tumor

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

extract_protocol: RNA was extracted using Rneasy Mini Kit (Qiagen), followed by  DNase I treatment (TURBO DNA-free kit, Ambion). Quality control was performed with Agilent Bioanalyser.

value: polymorphnuclear-MDSC from RMA-S tumor

value: RMA-S cell line

tag: genetic background

value: 9 wk


title: WT, littermate of Ire1 ko, biological rep4

source_name: WT, fed state, untreated

tag: age


title: PMN-MDSC RMA-S blood, repl. 3

description: replicate 3

source_name: RMA-S mouse blood

value: polymorphnuclear-MDSC from blood


title: WT, tunicamycin, biological rep2


title: WT, tunicamycin, biological rep3


title: Ire1 ko, tunicamycin, biological rep1

source_name: Ire1 ko, tunicamycin, 2 mg/kg, 6 hr


title: Ire1 ko, biological rep1


title: Ire1 ko, tunicamycin, biological rep3


title: Ire1 ko, tunicamycin, biological rep2


title: MO-MDSC RMA-S blood, repl. 2

description: replicate 2

value: monocytic-MDSC from blood


title: MO-MDSC RMA-S tumor, repl.2

description: replicate 2

value: monocytic-MDSC from RMA-S tumor


title: Ire1 ko, tunicamycin, biological rep4


title: WT, tunicamycin, biological rep1


title: PMN-MDSC RMA-S tumor, repl.2

description: replicate 2


title: PMN-MDSC RMA-S tumor, repl.1

description: replicate 1


title: MO-MDSC RMA-S blood, repl. 1

description: replicate 1


title: MO-MDSC RMA-S tumor, repl.3

description: replicate 3


title: PMN-MDSC RMA-S blood, repl. 2

description: replicate 2


title: MO-MDSC RMA-S blood, repl. 3

description: replicate 3


title: WT, littermate of Ire1 ko, biological rep2


title: WT, littermate of Ire1 ko, biological rep1


title: WT, littermate of Ire1 ko, biological rep3


title: PMN-MDSC RMA-S blood, repl. 1

description: replicate 1


title: MO-MDSC RMA-S tumor, repl.1

description: replicate 1


title: Flag-CDX1 ChIP-chip in gastric epithelial cells: CDX1 induction +, 24 h

description: Flag-CDX1 ChIP-chip on promoter regions in CDX1-inducible gastric epithelial cells using anti-Flag (M2) monoclonal antibody.

hyb_protocol: Each sample was hybridized to the array in 200 μl containing 1X Hybridization buffer (Affymetrix), 50 pM control oligonucleotide (control oligo B2, Affymetrix), 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml acetylated BSA, and 7% DMSO. Samples were denatured for 10 min at 100°C, and then put on ice before being hybridized for 16 h at 45°C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: Array intensity data of ChIP and input fraction were compared by MAT (Model-based Analysis of Tiling-array) algorithm, using the software provided by the laboratory of X.Shirley Liu (http://chip.dfci.harvard.edu/~wli/MAT/). We calculated MAT score and mapped the results to genomic positions in human genome assembly hg 17 (NCBI Build 35). Bandwidth and MaxGap parameters were set to 275 and 275, respectively.

source_name: Flag-CDX1 ChIP in CDX1-inducible MKN28 cells, doxycycline - (CDX1 +), 24 h

label_protocol: DNA was amplified by IVT (in vitro transcription) method. For the labeling, DNA was fragmented by DNaseI, and then end-labeled by Terminal Transferase with biotin-11-ddATP.

extract_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature with swirling. Glycine was added to a final concentration of 0.2 M, and the incubation was continued for an additional 5 min. Cells were washed twise with ice-cold PBS, harvested by scraping, pelleted, and resuspended in SDS lysis buffer [10 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1% SDS, 1 mM EDTA]. Samples were sonicated with Branson SONIFIER 450 for 5 cycles of 1 min (60% duty, output control 1) with an interval of 1 min. Then, samples were centrifuged at 13,000 g for 10 min at 4°C and diluted fivefold in ChIP dilution buffer [20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, and protease inhibitors]. After removal of a control aliquot (Input_DNA), samples were incubated at 4°C overnight with protein G-Sepharose beads that had been incubated overnight with anti-Flag antibody, and then were washed twise with ChIP dilution buffer, once with wash buffer 1 [20 mM Tris-HCl (pH 8.0), 500 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% SDS, 1 mM PMSF], once with wash buffer 2 [10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.25 M LiCl, 0.5% Na-Deoxycholate, 0.5% NP-40, 1 mM PMSF], and three times with TE buffer (pH 8.0). After being washed, the immunoprecipitated samples were eluted from the beads by incubation for 30 min at 65°C in elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS]. The cross-links were then reversed with incubation with Proteinase K for 2 h at 42°C followed by incubation at 65°C overnight. The DNA samples were further purified by phenol-chloroform extraction, and then extracted by ethanol precipitation.

treatment_protocol: CDX1-inducible MKN28 cells, which inducibly express Flag-tagged CDX1 with the use of a tetracycline-regulated Tet-Off System (Clontech), were established from MKN28 human gastric epithelial cells. CDX1-inducible MKN28 cells were cultured in the absence of Doxycycline(Clontech), a tetracycline analog, for 24 h before fixation (induction +).

value: gastric epithelial cells

value: pTet-Off, Flag-tagged CDX1

tag: antibody

value: anti-Flag (M2) monoclonal antibody

source_name: Input DNA in CDX1-inducible MKN28 cells, doxycycline - (CDX1 +), 24 h

extract_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature with swirling. Glycine was added to a final concentration of 0.2 M, and the incubation was continued for an additional 5 min. Cells were washed twise with ice-cold PBS, harvested by scraping, pelleted, and resuspended in SDS lysis buffer [10 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1% SDS, 1 mM EDTA]. Samples were sonicated with Branson SONIFIER 450 for 5 cycles of 1 min (60% duty, output control 1) with an interval of 1 min. Then, samples were centrifuged at 13,000 g for 10 min at 4°C and diluted fivefold in ChIP dilution buffer [20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, and protease inhibitors]. Aliquot of the supernatant was reverse-crosslinked by incubation with Proteinase K for 2 h at 42°C followed by incubation at 65°C overnight in elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS]. The DNA samples were further purified by phenol-chloroform extraction, and then extracted by ethanol precipitation.

treatment_protocol: CDX1-inducible MKN28 cells, which inducibly express Flag-tagged CDX1 with the use of a tetracycline-regulated Tet-Off System (Clontech), were established from MKN28 human gastric epithelial cells. CDX1-inducible MKN28 cells were cultured in the absence of Doxycycline (Clontech), a tetracycline analog, for 24 h before fixation (induction +).

value: none (input DNA)


title: Tinman early

city: Cambridge

first: Boris

last: Adryan

address: Tennis Court Road

department: Cambridge Systems Biology Centre

institute: University of Cambridge

description: Tinman binding in early embryos

hyb_protocol: Approximately 2.7 μg of labeled DNA was hybridized to each GeneChip Drosophila Tiling 1.0R Array (Affymetrix) in 1X MES, 3 M Tetramethylammonium Chloride (TMAC), 40 pM of control oligo B2 (Affymetrix), 100 μg/ml of sonicated salmon sperm DNA and 0.02% Triton X-100 for 18 hours at 45oC with 45 rpm rotation. The hybridized arrays were processed using GeneChip Fluidics Station 450 with the EukGE-WS2v4 protocol (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Genechip Scanner 3000-7G.

data_processing:
Sample groups were analysed in MAT (version 2.09232006.linux) with default parameters, using the .TAG files submitted with the .CEL files.
Auxiliary output files from MAT are included in this submission
This is standard MAT output as detailed in http://liulab.dfci.harvard.edu/MAT/. The .SGR files are human readable log2 enrichment ratios per chromosomal position.

organism: Drosophila melanogaster

source_name: Tinman ChIP DNA from early embryos

label_protocol: 3.0 μg of amplified DNA per sample was reduced to a size of 50-100 bp by incubation with DNase I for 5 min at 37°C. After heat inactivation of DNase I, the fragmented DNA was end-labeled with bio-11-ddATP (Perkin Elmer) using recombinant Terminal Transferase by incubation at 37°C for 2 hr.

extract_protocol: 3-5.5-h-old and 5-8-h-old Drosophila embryos were formaldehyde crosslinked and chromatin was isolated by CsCl gradient ultracentrifugation according to the detailed protocol of Li et al., 2008. The isolated chromatin was sonicated to an average size of about 600 bp. The chromatin solution was precleared by incubating with normal rabbit IgG and Protein A/G beads (Pierce). IP reactions were carried out by incubating 100 μg of chromatin with 1 μg of affinity-purified rabbit anti-Tin antibody or control IgG overnight at 4°C. The immunoprotein–chromatin complexes were captured by incubating with Protein A/G beads, followed by consecutive washes and then eluted with a buffer containing 1% SDS and 0.1 M NaHCO3 (pH 10.0) as described (Li et al., 2008). In each ChIP experiment, a portion of the chromatin solution corresponding to 1% of that used in the ChIP reaction was used as input DNA control. The IP samples along with the inputs were purified by phenol/chloroform extraction and ethanol precipitation after the protein/DNA crosslinks had been reversed by incubation at 65 °C for 6 hrs. At this step, enrichment of known Tin targets was validated using qPCR. Finally, the DNA samples were amplified using a random primer-based DNA amplification protocol (Li et al., 2008). -- Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27.

value: embryo

value: Tinman polyclonal from Yin et al. 1998

source_name: IgG ChIP DNA from early embryos

value: rabbit IgG


title: Tinman late

description: Tinman binding in late embryos

source_name: Tinman ChIP DNA from late embryos

value: 5-8h AEL

source_name: IgG ChIP DNA from late embryos


title: Xbp1 ko, IRE1 siRNA, biological rep2

source_name: Xbp1 ko, IRE1 siRNA injected, 8 days

value: Liver

value: male

value: Xbp1 ko

value: 9 weeks


title: Xbp1 ko, luciferase siRNA, biological rep3

source_name: Xbp1 ko, luciferase siRNA injected, 8 days


title: PMN-MDSC naive blood, repl.2

description: replicate 2

source_name: naive mouse blood

value: naïve


title: Xbp1 ko, IRE1 siRNA, biological rep1


title: Xbp1 ko, biological rep3

source_name: Xbp1 ko, fed state

value: 14 weeks


title: Xbp1 ko, IRE1 siRNA, biological rep4


title: MO-MDSC naive blood, repl.1

description: replicate 1

value: 9 wk


title: Xbp1 ko, luciferase siRNA, biological rep1


title: Xbp1 ko, luciferase siRNA, biological rep4


title: Xbp1 ko, biological rep4


title: Xbp1 ko, IRE1 siRNA, biological rep3


title: WT, littermate of Xbp1 ko, biological rep2

source_name: WT, fed state

value: WT


title: WT, littermate of Xbp1 ko, biological rep3


title: WT, littermate of Xbp1 ko, biological rep4


title: Xbp1 ko, luciferase siRNA, biological rep2


title: Xbp1 ko, biological rep2


title: PMN-MDSC naive blood, repl.3

description: replicate 3

value: polymorphnuclear-MDSC from blood


title: MO-MDSC naive blood, repl.3

description: replicate 3

value: monocytic-MDSC from blood


title: WT NK, steady state, replicate 2

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

description:
Sample name: MDD_12-NK
WT spleen natural killer (NK) cells from untreated mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low)

hyb_protocol: Following fragmentation, 1.875 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix GeneChip® fluidics station 450 with the FS450-0007 protocol.

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

data_processing: The data were RMA normalized in R and Bioconductor, using the limma package.

label_protocol: 150 ng of RNA from each sample was used to synthesize biotinylated probes, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 8x10E5 and 4x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: injection of 100 ug of poly(I:C). Cells were isolated from the mouse spleen 3 hours after injection.

tag: genotype/variation

value: natural killer (NK) cells

tag: agent


title: PMN-MDSC naive blood, repl.1

description: replicate 1


title: MO-MDSC naive blood, repl.2

description: replicate 2


title: WT, littermate of Xbp1 ko, biological rep1


title: Xbp1 ko, biological rep1


title: IFNAR-/- NK, MCMV, replicate 2

description:
Sample name: MDD_A14
IFNAR-KO spleen natural killer (NK) cells from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.2(pos)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430.2 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

label_protocol: Except for sample A7 where only 8 ng was available, 50 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 5x10E4 and 3x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Mice were infected intraperitoneally with salivary gland-murine cytomegalovirus (5x10e4 pfu/mouse). Spleens were harvested at 36 hours post-infection and digested with collagenase (Liberase CI), erythrocytes were lysed with NH(4)Cl, and leukocytes were resuspended in PBS EDTA 5mM before sorting by flow cytometry

tag: strain

tag: chimera description

value: IFNAR-KO

tag: infection

value: murine cytomegalovirus


title: IFNAR-/- NK, steady-state, replicate 2

description:
Sample name: MDD_C37
IFNAR-KO spleen natural killer (NK) cells from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.2(pos)

tag: cell type


title: WT NK, p(I:C), replicate 2

description:
Sample name: MDD_16-NK
WT spleen natural killer (NK) cells from poly(I:C)-injected mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low)


title: WT NK, steady state, replicate 1

description:
Sample name: MDD_4-NK
WT spleen natural killer (NK) cells from untreated mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low)


title: dHstD_KA4days_1

city: Higashihiroshima

first: Kazuhiro

last: Iwashita

state: Hiroshima

address: 3-7-1, Kagamiyama

institute: National Research Institute of Brewing

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridyzed for 16h at 45C on GeneChip. GeneChip were washed and stained in the Affymetrix Fludiscs Station 450

scan_protocol: Scanned according to Affymetrix protocol

data_processing: The data were analyzed GCOS program (version 1.4 affymetrix) using Affymetrix default setting and global scaling as normalization method.  The trimed mean each array was arbitrarily set to 500.

organism: Aspergillus oryzae

source_name: 4day _cultivated_in_KA_dHstD_1

label_protocol: Biotinylated cRNA were prepared from 5ug total RNA using GeneChip IVT Express kit

growth_protocol: KA culture was performed in 20ml KA liquid medium(1g yeast extract, 0.5g KCl, 1.52g KH2PO4, 1.5g L-methionine,. 0.5g MgSO4・7H2O, 100g glucose, 0.5g adenine pH6.0 in1L) inoculated with 200ul of 1*108 /ml conidia suspension, and was incubated at 30oC for 4 or 7days, shaking at 130rpm.

extract_protocol: Mycelia were immediately frozen in liquid nitrogen and powdered to prepare total RNA using isogen.  Then total RNA was purified by Rneasy mini kit.

treatment_protocol: Mycelia were harvested by filtration and washed by ice-cold ddH2O

value: dHstD


title: dHstD_KA4days_2

source_name: 4day _cultivated_in_KA_dHstD_2


title: WT NK, p(I:C), replicate 1

description:
Sample name: MDD_8-NK
WT spleen natural killer (NK) cells from poly(I:C)-injected mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low)


title: LRRK2 mutant knockin H9 hESC derived NSC treated with inhibitor 3

city: La Jolla

first: Fei

last: Yi

state: CA

address: 10010 North Torrey Pines Road

institute: Salk Institute

description: H9 hESC derived NSC with LRRK2 (G2019S) mutation knockin

hyb_protocol: After hybridization cocktails preparation, the Affymetrix HG-U133A 2.0 arrays were hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The statistical analysis of the data was performed using GenePattern platform from Broad Institute. Briefly, raw CEL files were imported into GenePattern platform and normalized using RMA algorithm. The Hierarchical Clustering analysis was performed using the HierarchicalClustering module of the software. The dendrograms and the heat map of the clustered gene expression data were visualized by the HierarchicalClusteringViewer module.

label_protocol: The Affymetrix GeneChip microarray was performed by the Functional Genomics Core Facility at The Salk Institute for Biological Studies following the manufacturer’s protocol (Affymetrix, Santa Clara, CA). Briefly, 100 ng of total RNA of each sample were processed using Affymetrix GeneChip 3’ IVT Expression Kit following the manufacturer’s protocol. For each sample, 12.5 μg fragmented and labeled aRNA were hybridized to the Affymetrix HG-U133A 2.0 chips.

growth_protocol: Cells were cultured in NSC maintainance medium.

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Qiagen).

treatment_protocol: The LRRK2 mutant knockin H9 hESC derived NSC were mock treated or treated with 3µM LRRK2-IN-1 for 5 days.

tag: lrrk2 genotype

value: WT / LRRK2 GS


title: IFNAR-/- NK, steady-state, replicate 1

description:
Sample name: MDD_A4
IFNAR-KO spleen natural killer (NK) cells from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.2(pos)


title: LRRK2 mutant knockin H9 hESC derived NSC 3


title: activated NK cells, replicate 2

city: Marseille

first: Marc

last: DALOD

address: Parc scientifique de Luminy, Case 906

department: Dendritic cells and antiviral defense

institute: Center of Immunology of Marseille Luminy (CIML)

description:
MD_20_430_2
Gene expression data from purified splenic NK cells from 6-10 WT C57BL6 mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE-430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

data_processing: RMA normalization

source_name: activated NK cells, replicate 2

label_protocol: 100 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 7.5x10E5 and 1.5x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol, yielding between 200 and 700 ng of total RNA for each sample.

treatment_protocol: Mice were infected intraperitoneally with salivary gland-murine cytomegalovirus (5x10e4 pfu/mouse). Spleens were harvested at 36 hors post-infection and digested with collagenase (Liberase CI), erythrocytes were lysed with NH(4)Cl, and leukocytes were resuspended in PBS EDTA 5mM before magnetic separation

value: Spleen Natural Killer (NK) Cells from WT mice, positively enriched with anti-DX5-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as TCRbeta(neg), NK1.1(positive)

value: C57BL/6 mice

value: Female

value: 6-8 weeks


title: LRRK2 mutant knockin H9 hESC derived NSC treated with inhibitor 1


title: LRRK2 mutant knockin H9 hESC derived NSC treated with inhibitor 2


title: activated pDCs, replicate 2

description:
MD_14_430_2
Gene expression data from purified splenic DCs from 10-15 WT C57BL6 mice

source_name: activated pDCs, replicate 2

value: Spleen plasmacytoid dendritic cells from WT mice, positively enriched with a cocktail of anti-CD11c- and PDCA1-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as CD19(neg), CD3(neg), NK1.1(neg), 120G8(high), CD11c(intermediate)


title: Control_KA4days_2

source_name: 4day _cultivated_in_KA_control_2

value: Control


title: IFNAR-/- NK, MCMV, replicate 1

description:
Sample name: MDD_B21
IFNAR-KO spleen natural killer (NK) cells from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.2(pos)


title: activated pDCs, replicate 1

description:
MD_11_430_2
Gene expression data from purified splenic DCs from 10-15 WT C57BL6 mice

source_name: activated pDCs, replicate 1


title: activated NK cells, replicate 1

description:
MD_18_430_2
Gene expression data from purified splenic NK cells from 6-10 WT C57BL6 mice

source_name: activated NK cells, replicate 1


title: activated CD11b cDCs, replicate 2

description:
MD_C3_430_2
Gene expression data from purified splenic DCs from 10-15 WT C57BL6 mice

source_name: activated CD11b cDCs, replicate 2

value: Spleen dendritic cells from WT mice, positively enriched with a cocktail of anti-CD11c- and PDCA1-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as CD19(neg), CD3(neg), NK1.1(neg), 120G8(neg/low), CD11c(high), CD11b(positive)


title: activated CD8alpha cDCs, replicate 1

description:
MD_A2_430_2
Gene expression data from purified splenic DCs from 10-15 WT C57BL6 mice

source_name: activated CD8alpha cDCs, replicate 1

value: Spleen dendritic cells from WT mice, positively enriched with a cocktail of anti-CD11c- and PDCA1-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as CD19(neg), CD3(neg), NK1.1(neg), 120G8(neg/low), CD11c(high), CD8alpha(positive)


title: activated CD8alpha cDCs, replicate 2

description:
MD_15_430_2
Gene expression data from purified splenic DCs from 10-15 WT C57BL6 mice

source_name: activated CD8alpha cDCs, replicate 2


title: activated CD11b cDCs, replicate 1

description:
MD_A3_430_2
Gene expression data from purified splenic DCs from 10-15 WT C57BL6 mice

source_name: activated CD11b cDCs, replicate 1


title: activated B lymphocytes, replicate 1

description:
MD_22_430_2
Gene expression data from purified splenic B lymphocytes from 3 WT C57BL6 mice

source_name: activated B lymphocytes, replicate 1

value: Spleen B lymphocytes from WT mice, FACS sorted as CD19(positive) and low in autofluorescence


title: LRRK2 mutant knockin H9 hESC derived NSC 2


title: Wildtype H9 hESC derived NSC 2

description: H9 hESC derived NSC

source_name: Wildtype H9 hESC derived NSC 2

value: WT / WT


title: Human H1 ESC sample 1

description: Gene expression data from human H1 ESC

source_name: Human H1 embryonic stem cells

growth_protocol: Human fibroblasts were maintained in DMEM with 10% FBS. Human iPSC and ESC were cultured in Matrigel (BD Biosciences) with mTeSR medium (Stem Cell Technologies).

treatment_protocol: All iPSC lines were generated by retrovirus mediated cell reprogramming, and expanded in feeder-free Matrigel and mTesR conditions. No additonal treatment was performed before sample extraction.


title: Wildtype H9 hESC derived NSC 1

description: H9 hESC derived NSC

source_name: Wildtype H9 hESC derived NSC 1


title: LRRK2 mutant knockin H9 hESC derived NSC 1


title: MCF-7 breast cancer cell line, ALK over-expressed clones, 3D

city: Houston

first: Annie

middle: Z

last: Luo

state: Texas

address: 1901 East Road 4SCR3.1004

department: Experimental Therapeutics

institute: M D Anderson Cancer Center

description: Gene expression data from MCF-7 breast cancer cell line, ALK over-expressed clones in three dimension

hyb_protocol: The cRNA was then purified using a GeneChip® Sample Cleanup Module Kit (Affymetrix) and fragmented before hybridization. Then, hybridization cocktail containing the fragmented target cRNAs and probe array controls using the GeneChip® Hybridization Control Kit (Affymetrix) was hybridized to probe array.

scan_protocol: The arrays were washed and stained according to protocol and scanned using the GeneChip® Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with using DNA-Chip Analyzer software (dChip; Harvard School of Public Health, Boston, MA) using Affymetrix default analysis settings and global scaling as normalization method. dChipVersion=dChip (DNA-Chip Analyzer), Build date: Dec 17 2010.

source_name: Human MCF-7 breast cancer cell line, ALK over-expressed clones in three dimension

label_protocol: Using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA), total RNA was reverse transcripted to cDNA and synthesized to cRNA using the GeneChip® IVT Labeling kit (Affymetrix) and biotin labeled.

growth_protocol: MCF-7-Ctrl1, MCF-7-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells are plated into ultra-low adherence culture plates (Corning Co-Star, Tewksbury, MA) in serum-free mammary epithelial growth medium (MEBM, Lonza/Clonetics) supplemented with B27 (Invitrogen/Life Technologies Grand Island, NY), 20 ng/ml epidermal growth factor (EGF), 40 ng/ml bFGF (BD Biosciences, San Jose, CA), 4 mg/ml heparin (Sigma-Aldrich, St. Louis, MO) L-glutamine, and 100 U/ml penicillin and streptomycin. These culture conditions support self-renewal as well as formation and propagation of cells as 3 dimensional tumor spheroids.

extract_protocol: Total RNA from 3 dimensional tumor spheroids of MCF-7-Ctrl1, MCF-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells was isolated using TRIzol® reagent (Invitrogen/Life Technologies Grand Island, NY), and the quality of the RNA was determined using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Hanover Park, IL).

tag: cell line

value: ALK over-expressed clone


title: Human H1 ESC sample 2

description: Gene expression data from human H1 ESC


title: MCF-7 breast cancer cell line, Control clones, 3D, 2nd sample

description: Gene expression data from MCF-7 breast cancer cell line, control clones in three dimension

source_name: Human MCF-7 breast cancer cell line, control clones in three dimension

value: control


title: MCF-7 breast cancer cell line, Control clones, 3D


title: Twin_Pair_7_healthy

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.1
Average Beta, P-value, Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: Whole blood

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA samples from blood were extracted from thawed frozen whole blood collected in EDTA using the Nucleon Genomic DNA Extraction Kit BACC3

tag: tissue

value: Whole blood

tag: twin pair

tag: disease status

value: healthy sample


title: MCF-7 breast cancer cell line, ALK over-expressed clones, 3D, 2nd sample


title: LRRK2 (G2019S) heterozygous iPSC sample 2

description: Gene expression data from LRRK2 (G2019S) heterozygous iPSC

source_name: Human LRRK2 (G2019S) heterozygous induced pluripotent stem cells

value: GS / WT


title: 4GKD_10Gy_Total

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

hyb_protocol: Labeled and fragmented cRNA hybridized to HG_U133 Plus 2.0 Affymetrix GeneChips using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring GX11 program. No further adjustments were made to the data in the table.

source_name: cells were silenced for eIF4G1, irradiated then total RNA prepared from cells without polyribosome sorting

label_protocol: Labeled target cRNA population was generated with the Affymetrix 3’-IVT Express kit

growth_protocol: cells were grown cultivated under recommended guidelines by the ATCC

extract_protocol: Total RNA extracted using 0.5% NP40

treatment_protocol: Cells were irradiated with a Varian Linac 2300 linear accelerator at room temperature; silencing of target eIF4G1 expression was achieved by doxycycline inducible shRNA

value: eIF4G1 KD

tag: cell origin

value: breast cancer


title: Twin_Pair_5_affected

tag: gender

value: breast cancer sample


title: LRRK2 (G2019S) heterozygous iPSC sample 1


title: Wildtype H9 hESC derived NSC 3

description: H9 hESC derived NSC

source_name: Wildtype H9 hESC derived NSC 3


title: Control_KA4days_1

source_name: 4day _cultivated_in_KA_control_1


title: LRRK2 (G2019S) homozygous iPSC sample 2

description: Gene expression data from LRRK2 (G2019S) homozygous iPSC

source_name: Human LRRK2 (G2019S) homozygous induced pluripotent stem cells

value: GS / GS


title: 4GKD_mock_Total

source_name: cells were silenced for eIF4G1 then total RNA was prepared from cells without polyribosome sorting


title: LRRK2 (G2019S) homozygous iPSC sample 1


title: WT_10Gy_Total

source_name: total RNA was prepared from cells without polyribosome sorting after irradiation of cells

value: WT


title: Wildtype iPSC sample 2

description: Gene expression data from wildtype iPSC

source_name: Human wildtype induced pluripotent stem cells


title: Twin_Pair_14_affected

value: Female


title: Twin_Pair_15_affected


title: Twin_Pair_15_healthy


title: Twin_Pair_12_healthy


title: Twin_Pair_2_affected


title: Twin_Pair_13_affected


title: LRRK2 (G2019S) heterozygous fibroblast sample 2

description: Gene expression data from LRRK2 (G2019S) heterozygous fibroblasts

source_name: Human LRRK2 (G2019S) heterozygous patient fibroblast


title: Twin_Pair_14_healthy


title: LRRK2 (G2019S) heterozygous fibroblast sample 1


title: Wildtype iPSC sample 1

description: Gene expression data from wildtype iPSC


title: 4GKD_mock_HMW

source_name: eIF4G1 was silenced by shRNAs then heavy polyribosomes prepared and fractionated


title: 4GKD_mock_LMW

source_name: eIF4G1 was silenced by shRNAs then light polyribosomes prepared and fractionated


title: LRRK2 (G2019S) homozygous fibroblast sample 2

description: Gene expression data from LRRK2 (G2019S) homozygous fibroblasts

source_name: Human LRRK2 (G2019S) homozygous patient fibroblast


title: 4GKD_10Gy_LMW

source_name: cells were irradiated then light polyribosomes were prepared as described above


title: WT_mock_Total

source_name: total RNA was prepared from cells without polyribosome sorting


title: LRRK2 (G2019S) homozygous fibroblast sample 1


title: WT_10Gy_HMW

source_name: heavy polyribosomes were prepared as described following irradiation of cells


title: WT_10Gy_LMW

source_name: light polyribosomes were prepared as described following irradiation of cells


title: Wildtype fibroblast sample 2

description: Gene expression data from wildtype fibroblasts

source_name: Human wildtype fibroblast


title: 4GKD_10Gy_HMW

source_name: cells were irradiated then heavy polyribosomes were prepared as described above


title: Twin_Pair_10_healthy

source_name: Whole blood


title: WT_mock_HMW

source_name: polyribosomes were fractionated by sucrose gradient sedimentation and RNA extracted from pools of heavy polysomes corresponding to 4 or greater ribosomes


title: Twin_Pair_9_healthy


title: Twin_Pair_11_affected


title: Twin_Pair_8_healthy


title: Twin_Pair_10_affected


title: Wildtype fibroblast sample 1


title: Differentiated mouse podocyte Replicate 3

status: Public on Oct 16 2012

city: Rostock

first: Gregor

last: Warsow

address: Ernst-Heydemann-Str. 8

department: Medical Department

institute: University of Rostock

hyb_protocol: Biotinylated sense-strand DNA was then hybridized onto the Affymetrix GeneChip® Mouse Gene 1.0 ST arrays for 16h. Arrays were washed and stained using the Fluidics Station 450.

scan_protocol: Scanning was performed by Scanner 3000 7G (Affymetrix); raw CEL files were generated using the GCOS software.

data_processing: JMP Genomics 4.0, RMA background correction, quantile normalization

source_name: Conditionally immortalized mouse podocyte cell line SVI

label_protocol: Total RNA (200 ng) was reverse transcribed into cDNA, amplified, and in vitro transcribed to cRNA. Sense-strand cDNA was generated from 10 µg of purified cRNA using random primers, followed by fragmentation and labeling using 5.5 µg of purified sense-strand DNA.

growth_protocol: cultured for 1-2 weeks in RPMI + 10% FBS at 38°C; medium change 2-3 times weekly

extract_protocol: Three days after the last medium change, RNA was isolated using Trizol (Invitrogen) followed by purification using the RNA Clean-Up and Concentration Micro Kit (Norgen). RNA quantity and purity was measured at 260/280/230 nm with a Nanodrop photospectrometer (Thermo Scientific). RNA integrity was assessed by using the Bioanalyzer 2100 (Agilent).

value: kidney glomeruli

value: ImmortoMouse® mice (Charles River, St. Louis, MO), carrying a temperature-sensitive mutant of the immortalizing SV40 large T-antigen under control of the -interferon inducible H-2Kb promoter


title: Twin_Pair_9_affected


title: Tregs

city: Bellinzona

first: Silvia

last: Monticelli

address: Via Vincenzo Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

description:
Sample 5
common reference (Ch2) was made by pooling together a small amount of total CD4+ cells from all donors.
Cy3 : 1_Exiqon_13973336_S01_Cropped.txt
Cy5 : 0_Exiqon_13973336_S01_Cropped.txt

hyb_protocol: As by miRCURY™ LNA Array Power labeling kit  protocol

scan_protocol: Performed by Exiqon

data_processing: Performed by Exiqon. Normalisation means background subtraction and normalisation with a global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide is indicated by 'null'

source_name: FACS-sorted Tregs

label_protocol: Performed at Exiqon using a miRCURY™ LNA Array Power labeling kit

growth_protocol: Cells were nor cultured nor treated in any way, but immediately lysed in TRIzol upon purification from peripheral blood

extract_protocol: Cells recovered upon sorting were immediately lysed in TRIzol and total RNA was extracted following the manufacture's protocol

value: peripheral blood

value: CD4+ CD8- CD25hi

source_name: total CD4+ lymphocytes


title: Twin_Pair_13_healthy


title: Th17

description:
Sample 4
common reference (Ch2) was made by pooling together a small amount of total CD4+ cells from all donors.
Cy3 : 1_Exiqon_13973335_S01_Cropped.txt
Cy5 : 0_Exiqon_13973335_S01_Cropped.txt

source_name: FACS-sorted Th17

value: CD4+ CD8- CCR6+ CCR4+ CXCR4- CD45RA-


title: Differentiated mouse podocyte Replicate 1


title: Twin_Pair_12_affected


title: Twin_Pair_8_affected


title: Th2

description:
Sample 3
common reference (Ch2) was made by pooling together a small amount of total CD4+ cells from all donors.
Cy3 : 1_Exiqon_13973334_S01_Cropped.txt
Cy5 : 0_Exiqon_13973334_S01_Cropped.txt

source_name: FACS-sorted Th2

value: CD4+ CD8- CRTh2+ CCR5- CD45RA- CD25-


title: patient 97, non-cancerous tissue, homogenized (copy number analysis)

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

hyb_protocol: Using Genome-Wide Human SNP Sty assay kit (Affymetrix), DNA was prepared and was hybridized to each array according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Copy number analysis was performed using Genotyping Console software (Affymetrix).

source_name: surgically resected material

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from surgical materials using the QIAamp DNA Micro Kit (Qiagen) for tumor tissue or the QIAamp DNA Mini Kit (Qiagen) for non-cancerous tissue. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Tumor tissue was extracted using laser-capture microdissection. Whole tissue was used for analysis of non-tumor specimens.

value: non-cancerous tissue, homogenized


title: patient 98, non-cancerous tissue, homogenized (copy number analysis)


title: Naïve lymphocytes

description:
Sample 1
common reference (Ch2) was made by pooling together a small amount of total CD4+ cells from all donors.
Cy3 : 1_Exiqon_13973332_S01_Cropped.txt
Cy5 : 0_Exiqon_13973332_S01_Cropped.txt

source_name: FACS-sorted Naïve lymphocytes

value: CD4+ CCR7- CD25- CD45RO-


title: patient 95, non-cancerous tissue, homogenized (copy number analysis)


title: Differentiated mouse podocyte Replicate 2


title: patient 93, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_6_healthy

value: Whole blood


title: patient 94, non-cancerous tissue, homogenized (copy number analysis)


title: patient 89, non-cancerous tissue, homogenized (copy number analysis)


title: patient 86, non-cancerous tissue, homogenized (copy number analysis)


title: patient 83, non-cancerous tissue, homogenized (copy number analysis)


title: patient 99, non-cancerous tissue, homogenized (copy number analysis)


title: patient 88, non-cancerous tissue, homogenized (copy number analysis)


title: patient 84, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_6_affected


title: Twin_Pair_11_healthy

value: healthy sample


title: WT_mock_LMW

source_name: polyribosomes were fractionated by sucrose gradient sedimentation and RNA extracted from pools of light polysomes corresponding to 1-3 ribosomes


title: patient 90, non-cancerous tissue, homogenized (copy number analysis)


title: patient 85, non-cancerous tissue, homogenized (copy number analysis)


title: patient 82, non-cancerous tissue, homogenized (copy number analysis)


title: patient 81, non-cancerous tissue, homogenized (copy number analysis)


title: patient 79, non-cancerous tissue, homogenized (copy number analysis)


title: patient 78, non-cancerous tissue, homogenized (copy number analysis)


title: patient 77, non-cancerous tissue, homogenized (copy number analysis)


title: patient 72, non-cancerous tissue, homogenized (copy number analysis)


title: patient 70, non-cancerous tissue, homogenized (copy number analysis)


title: patient 73, non-cancerous tissue, homogenized (copy number analysis)


title: patient 65, non-cancerous tissue, homogenized (copy number analysis)


title: patient 64, non-cancerous tissue, homogenized (copy number analysis)


title: patient 63, non-cancerous tissue, homogenized (copy number analysis)


title: patient 41, non-cancerous tissue, homogenized (copy number analysis)


title: patient 38, non-cancerous tissue, homogenized (copy number analysis)


title: Th1

description:
Sample 2
common reference (Ch2) was made by pooling together a small amount of total CD4+ cells from all donors.
Cy3 : 1_Exiqon_13973333_S01_Cropped.txt
Cy5 : 0_Exiqon_13973333_S01_Cropped.txt

source_name: FACS-sorted Th1

value: CD4+ CD8- CCR5+ CD25- CD45RA-


title: patient 35, non-cancerous tissue, homogenized (copy number analysis)


title: patient 37, non-cancerous tissue, homogenized (copy number analysis)


title: patient 34, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_5_healthy


title: patient 32, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_7_affected


title: patient 96, non-cancerous tissue, homogenized (copy number analysis)


title: patient 30, non-cancerous tissue, homogenized (copy number analysis)


title: patient 26, non-cancerous tissue, homogenized (copy number analysis)


title: patient 33, non-cancerous tissue, homogenized (copy number analysis)


title: patient 61, non-cancerous tissue, homogenized (copy number analysis)


title: patient 36, non-cancerous tissue, homogenized (copy number analysis)


title: patient 28, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_4_affected


title: patient 25, non-cancerous tissue, homogenized (copy number analysis)


title: patient 23, non-cancerous tissue, homogenized (copy number analysis)


title: patient 24, non-cancerous tissue, homogenized (copy number analysis)


title: patient 31, non-cancerous tissue, homogenized (copy number analysis)


title: patient 27, non-cancerous tissue, homogenized (copy number analysis)


title: patient 155, non-cancerous tissue, homogenized (copy number analysis)


title: patient 20, non-cancerous tissue, homogenized (copy number analysis)


title: patient 17, non-cancerous tissue, homogenized (copy number analysis)


title: patient 22, non-cancerous tissue, homogenized (copy number analysis)


title: patient 133, non-cancerous tissue, homogenized (copy number analysis)


title: patient 145, non-cancerous tissue, homogenized (copy number analysis)


title: patient 127, non-cancerous tissue, homogenized (copy number analysis)


title: patient 130, non-cancerous tissue, homogenized (copy number analysis)


title: patient 134, non-cancerous tissue, homogenized (copy number analysis)


title: patient 129, non-cancerous tissue, homogenized (copy number analysis)


title: patient 124, non-cancerous tissue, homogenized (copy number analysis)


title: patient 125, non-cancerous tissue, homogenized (copy number analysis)


title: patient 128, non-cancerous tissue, homogenized (copy number analysis)


title: patient 68, non-cancerous tissue, homogenized (copy number analysis)


title: patient 131, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_4_healthy


title: Twin_Pair_3_healthy


title: Twin_Pair_3_affected


title: patient 118, non-cancerous tissue, homogenized (copy number analysis)


title: patient 119, non-cancerous tissue, homogenized (copy number analysis)


title: patient 121, non-cancerous tissue, homogenized (copy number analysis)


title: patient 123, non-cancerous tissue, homogenized (copy number analysis)


title: patient 117, non-cancerous tissue, homogenized (copy number analysis)


title: patient 113, non-cancerous tissue, homogenized (copy number analysis)


title: patient 110, non-cancerous tissue, homogenized (copy number analysis)


title: patient 111, non-cancerous tissue, homogenized (copy number analysis)


title: patient 115, non-cancerous tissue, homogenized (copy number analysis)


title: patient 108, non-cancerous tissue, homogenized (copy number analysis)


title: patient 109, non-cancerous tissue, homogenized (copy number analysis)


title: patient 106, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_2_healthy


title: Twin_Pair_1_affected


title: patient 104, non-cancerous tissue, homogenized (copy number analysis)


title: patient 102, non-cancerous tissue, homogenized (copy number analysis)


title: patient 103, non-cancerous tissue, homogenized (copy number analysis)


title: Twin_Pair_1_healthy


title: patient 101, non-cancerous tissue, homogenized (copy number analysis)


title: patient 100, non-cancerous tissue, homogenized (copy number analysis)


title: FO-I25

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

institute: Institute of Aquaculture Torre de la Sal (CSIC)

hyb_protocol: Labelled cDNA samples were mixed with sheared salmon sperm genomic DNA  as blocker. The cDNA mixture was concentrated by precipitation with 3M  NaOAC (pH 5.5) and absolute ethanol at -20 oC for 30 minutes followed by  centrifugation at 12500 x g  for 30 minutes. Following removal of  supernatant, the cDNA pellet was resuspended in 70 µl slide hyb buffer  #1 (Ambion) and was then denatured at 95 oC for 2 minutes. The  hybridisation mixture was then added to the microarray slide and sealed  using a coverslip (Erie Scientific). Hybridisations were performed in a  hybridisation chamber (Genetix) at 42 oC for 16 hours. Following  hybridisation the slides were washed (2 x 5 minute washes using 0.2 X  SSC/0.1 % SDS and 2 x 5 minute washes using 0.2 X SSC) using an Advawash  automatic washing station (Advalytix).

scan_protocol: Agilent G2565BA Microarray Scanner

data_processing: Data were extracted using the Agilent Feature Extraction Software 9.5.3, and was further analyzed, including percentile shift normalization, one-way ANOVA, principal components analysis and k-means clustering of differentially expressed genes, by means of GeneSpring GX 11.5.1 software (Agilent).

organism: Sparus aurata

source_name: intestine from late infected animal fed FO diet

label_protocol: 250 ng of total RNA was labeled using the Quick Amp Labeling Kit (Agilent) to produce Cyanine 3-CTP labeled cRNA.

extract_protocol: Total RNA from intestine tissue was extracted with the ABI PRISM 6100 Nucleic Acid Prepstation

tag: diet

value: fish oil

value: intestinal parasite Enteromyxum leei

tag: infective status

value: Late


title: FO-I26


title: patient 98, cancer, LCM (copy number analysis)

tag: metastasis

value: metastatic recurrence

tag: Stage

value: cancer, LCM


title: GBM_11-151

first: Dominik

last: Sturm

description:
dkfz_11-151
Methylation data from a glioblastoma tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Data analysis has been carried out using GenomeStudio 2011.1 (methylationmodule 1.9.0) and annotation 1.2. The methylation analysis has been performed as suggested by Illumina with no background subtraction and normalization to internal controls.

label: biotin/DNP

source_name: Primary brain tumor tissue

label_protocol: Illumina protocol.

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: primary glioblastoma

tag: brain location

value: temporal lobe

tag: age at diagnosis (years)

value: male

tag: h3f3a status

value: WT

tag: idh1 status

tag: dna methylation subgroup

value: mesenchymal


title: patient 99, cancer, LCM (copy number analysis)


title: patient 97, cancer, LCM (copy number analysis)


title: GBM_11-150

description:
dkfz_11-150
Methylation data from a glioblastoma tumor sample.


title: GBM_11-147

description:
dkfz_11-147
Methylation data from a glioblastoma tumor sample.

value: female


title: GBM_11-146

description:
dkfz_11-146
Methylation data from a glioblastoma tumor sample.

value: frontal lobe


title: GBM_11-148

description:
dkfz_11-148
Methylation data from a glioblastoma tumor sample.

value: DIPG


title: GBM_11-139

description:
dkfz_11-139
Methylation data from a glioblastoma tumor sample.

value: RTK I 'PDGFRA'


title: FO-I24

tag: infection


title: FO-I23


title: GBM_11-141

description:
dkfz_11-141
Methylation data from a glioblastoma tumor sample.

value: RTK II 'classic'


title: GBM_11-143

description:
dkfz_11-143
Methylation data from a glioblastoma tumor sample.

value: parietal lobe


title: GBM_11-144

description:
dkfz_11-144
Methylation data from a glioblastoma tumor sample.


title: GBM_11-142

description:
dkfz_11-142
Methylation data from a glioblastoma tumor sample.


title: FO-I22


title: GBM_11-145

description:
dkfz_11-145
Methylation data from a glioblastoma tumor sample.

value: thalamic


title: GBM_11-138

description:
dkfz_11-138
Methylation data from a glioblastoma tumor sample.


title: GBM_11-137

description:
dkfz_11-137
Methylation data from a glioblastoma tumor sample.

value: MUT

value: IDH


title: GBM_11-134

description:
dkfz_11-134
Methylation data from a glioblastoma tumor sample.

value: occipital lobe


title: patient 94, cancer, LCM (copy number analysis)


title: patient 95, cancer, LCM (copy number analysis)


title: patient 96, cancer, LCM (copy number analysis)

value: metastatic recurrence


title: FO-I21

value: fish oil

value: intestinal parasite Enteromyxum leei

value: Late


title: GBM_11-131

description:
dkfz_11-131
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: male


title: GBM_11-140

description:
dkfz_11-140
Methylation data from a glioblastoma tumor sample.

value: temporal lobe

value: WT


title: GBM_11-129

description:
dkfz_11-129
Methylation data from a glioblastoma tumor sample.


title: GBM_11-133

description:
dkfz_11-133
Methylation data from a glioblastoma tumor sample.

value: female


title: GBM_11-132

description:
dkfz_11-132
Methylation data from a glioblastoma tumor sample.


title: GBM_11-149

description:
dkfz_11-149
Methylation data from a glioblastoma tumor sample.


title: FO-I16

source_name: intestine from early infected animal fed FO diet

value: Early


title: GBM_11-136

description:
dkfz_11-136
Methylation data from a glioblastoma tumor sample.


title: patient 93, cancer, LCM (copy number analysis)

value: cancer, LCM


title: FO-C8

source_name: intestine from control animal fed FO diet

value: Control


title: FO-I11


title: patient 90, cancer, LCM (copy number analysis)


title: FO-I14


title: GBM_11-128

description:
dkfz_11-128
Methylation data from a glioblastoma tumor sample.

value: RTK II 'classic'


title: GBM_11-127

description:
dkfz_11-127
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: FO-I15


title: FO-I13


title: FO-I12


title: GBM_11-135

description:
dkfz_11-135
Methylation data from a glioblastoma tumor sample.

value: frontal lobe


title: FO-C6


title: GBM_11-130

description:
dkfz_11-130
Methylation data from a glioblastoma tumor sample.

value: parietal lobe


title: FO-C4


title: patient 89, cancer, LCM (copy number analysis)


title: FO-C3


title: FO-C2


title: FO-C5


title: FO-C7


title: 66VO-I24

source_name: intestine from late infected animal fed 66VO diet

value: vegetable oil


title: patient 86, cancer, LCM (copy number analysis)


title: 66VO-I23


title: patient 110, cancer, LCM (copy number analysis)


title: FO-C1


title: 66VO-I26


title: patient 84, cancer, LCM (copy number analysis)


title: 66VO-I25


title: GBM_11-125

description:
dkfz_11-125
Methylation data from a glioblastoma tumor sample.


title: 66VO-I22


title: 66VO-I21


title: patient 83, cancer, LCM (copy number analysis)

value: metastatic recurrence


title: patient 85, cancer, LCM (copy number analysis)

value: metastasis


title: patient 81, cancer, LCM (copy number analysis)


title: 66VO-I14

source_name: intestine from early infected animal fed 66VO diet

value: intestinal parasite Enteromyxum leei


title: GBM_11-123

description:
dkfz_11-123
Methylation data from a glioblastoma tumor sample.


title: patient 82, cancer, LCM (copy number analysis)


title: 66VO-I16


title: GBM_11-126

description:
dkfz_11-126
Methylation data from a glioblastoma tumor sample.


title: 66VO-C9

source_name: intestine from control animal fed 66VO diet


title: 66VO-I12


title: 66VO-I15


title: 66VO-I11


title: GBM_11-124

description:
dkfz_11-124
Methylation data from a glioblastoma tumor sample.

value: MUT

value: IDH


title: GBM_11-121

description:
dkfz_11-121
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: male


title: patient 108, cancer, LCM (copy number analysis)


title: GBM_11-122

description:
dkfz_11-122
Methylation data from a glioblastoma tumor sample.

value: WT


title: patient 78, cancer, LCM (copy number analysis)


title: GBM_11-120

description:
dkfz_11-120
Methylation data from a glioblastoma tumor sample.

value: female


title: 66VO-C8


title: patient 79, cancer, LCM (copy number analysis)


title: 66VO-C7


title: 66VO-C6


title: 66VO-C3


title: 66VO-C4


title: 66VO-C5


title: GBM_11-119

description:
dkfz_11-119
Methylation data from a glioblastoma tumor sample.


title: 66VO-C1


title: 66VO-I13

value: Early


title: patient 77, cancer, LCM (copy number analysis)

value: cancer, LCM


title: 66VO-C2

value: Control


title: GBM_11-118

description:
dkfz_11-118
Methylation data from a glioblastoma tumor sample.

value: RTK II 'classic'


title: patient 72, cancer, LCM (copy number analysis)


title: patient 68, cancer, LCM (copy number analysis)


title: GBM_11-117

description:
dkfz_11-117
Methylation data from a glioblastoma tumor sample.

value: RTK I 'PDGFRA'


title: patient 73, cancer, LCM (copy number analysis)


title: GBM_11-113

description:
dkfz_11-113
Methylation data from a glioblastoma tumor sample.


title: patient 70, cancer, LCM (copy number analysis)


title: KOPTK1_PD0332991_rep1

first: Takaomi

last: Sanda

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing: The data was normalized and analyzed by dChip software.

source_name: T-ALL cell line

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: KOPTK1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal calf serum (Hyclone) and Pen/Strep (100U/ml, Invitrogen).

extract_protocol: Total RNA was harvested by Trizol followed by a column purification using RNeasy Mini kit (Qiagen) following manufacturer's instruction.

treatment_protocol: KOPTK1 cells were treated with vehicle (VO) or 1 microM PD 0332991 (PD) for 48 hrs.

tag: agent

value: CDK4/6 inhibitor PD 0332991


title: GBM_11-116

description:
dkfz_11-116
Methylation data from a glioblastoma tumor sample.


title: patient 65, cancer, LCM (copy number analysis)


title: GBM_11-115

description:
dkfz_11-115
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: KOPTK1_PD0332991_rep3

tag: cell line


title: patient 64, cancer, LCM (copy number analysis)

tag: tissue


title: GBM_11-114

description:
dkfz_11-114
Methylation data from a glioblastoma tumor sample.


title: KOPTK1_PD0332991_rep2


title: GBM_11-112

description:
dkfz_11-112
Methylation data from a glioblastoma tumor sample.


title: GBM_11-157

first: Marcel

last: Kool

address: Im Neuenheimer Feld 580

department: Pediatric Neuro Oncology

description: Gene expression data from a glioblastoma tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: tumor location

value: temporal lobe

tag: subgroup


title: KOPTK1_vehicle_rep2

value: vehicle


title: GBM_11-158

value: frontal lobe


title: KOPTK1_vehicle_rep1


title: patient 63, cancer, LCM (copy number analysis)


title: GBM_11-156

value: parietal lobe


title: GBM_11-109

description:
dkfz_11-109
Methylation data from a glioblastoma tumor sample.


title: GBM_11-154


title: GBM_11-111

description:
dkfz_11-111
Methylation data from a glioblastoma tumor sample.


title: patient 59, cancer, LCM (copy number analysis)


title: GBM_11-153

value: central region


title: patient 61, cancer, LCM (copy number analysis)

value: metastatic recurrence


title: patient 57, cancer, LCM (copy number analysis)


title: GBM_11-148

value: pons


title: GBM_11-155


title: GBM_11-147


title: GBM_11-110

description:
dkfz_11-110
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: male


title: GBM_11-146

value: female

value: WT


title: GBM_11-152


title: GBM_11-145

value: thalamic


title: KOPTK1_vehicle_rep3


title: GBM_11-088


title: GBM_11-105

description:
dkfz_11-105
Methylation data from a glioblastoma tumor sample.


title: patient 53, cancer, LCM (copy number analysis)

value: cancer, LCM


title: patient 55, cancer, LCM (copy number analysis)


title: GBM_11-082


title: GBM_11-087

value: temporo-parietal


title: GBM_11-107

description:
dkfz_11-107
Methylation data from a glioblastoma tumor sample.


title: patient 52, cancer, LCM (copy number analysis)


title: GBM_11-084

value: parieto-occipital


title: GBM_11-081

value: hemispheric


title: GBM_11-080


title: GBM_11-083

value: MUT


title: GBM_11-104

description:
dkfz_11-104
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: GBM_11-108

description:
dkfz_11-108
Methylation data from a glioblastoma tumor sample.


title: GBM_11-102

description:
dkfz_11-102
Methylation data from a glioblastoma tumor sample.

value: RTK II 'classic'


title: patient 46, cancer, LCM (copy number analysis)


title: GBM_11-106

description:
dkfz_11-106
Methylation data from a glioblastoma tumor sample.


title: GBM_11-103

description:
dkfz_11-103
Methylation data from a glioblastoma tumor sample.

value: RTK I 'PDGFRA'


title: GBM_11-101

description:
dkfz_11-101
Methylation data from a glioblastoma tumor sample.


title: patient 48, cancer, LCM (copy number analysis)

value: metastasis


title: GBM_11-079


title: GBM_11-059

value: RTK II


title: patient 45, cancer, LCM (copy number analysis)

value: metastatic recurrence


title: GBM_11-058

value: frontal lobe

value: IDH


title: GBM_11-057

value: male


title: patient 47, cancer, LCM (copy number analysis)


title: GBM_11-099

description:
dkfz_11-099
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: female


title: GBM_11-055

value: WT


title: patient 44, cancer, LCM (copy number analysis)

value: cancer, LCM


title: GBM_11-053

value: temporal lobe


title: GBM_11-054

value: RTK I


title: GBM_11-052


title: GBM_11-050

value: cerebellar


title: GBM_11-097

description:
dkfz_11-097
Methylation data from a glioblastoma tumor sample.


title: GBM_11-051

value: Mesenchymal


title: GBM_11-049

value: MUT


title: patient 41, cancer, LCM (copy number analysis)


title: patient 38, cancer, LCM (copy number analysis)


title: patient 42, cancer, LCM (copy number analysis)


title: patient 37, cancer, LCM (copy number analysis)


title: patient 36, cancer, LCM (copy number analysis)


title: GBM_11-094

description:
dkfz_11-094
Methylation data from a glioblastoma tumor sample.


title: GBM_11-095

description:
dkfz_11-095
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: GBM_11-047


title: GBM_11-100

description:
dkfz_11-100
Methylation data from a glioblastoma tumor sample.


title: GBM_11-042

description: Gene expression data from a glioblastoma tumor sample


title: GBM_11-045

value: parietal lobe


title: GBM_11-044


title: GBM_11-043

value: frontal/temporal


title: GBM_11-041


title: GBM_11-056


title: GBM_11-078


title: patient 34, cancer, LCM (copy number analysis)