title: Xenograft HN014 Rep1

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: Gene expression data of PDAC-derived Xenograft from patient HN014 , Rep1

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation, using a Human Gene 2.0 ST Array (Genechip, Affymetrix). After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 according to the standard Affymetrix protocol (EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.

data_processing: GeneChip operating software version 1.4 (Affymetrix Inc., Santa Clara, CA) was used to obtain chip images and for quality control. Background subtraction and normalization of probe set intensities were performed using the method of Robust Multi-array Analysis (RMA) (Irizarry et al, 2003).

source_name: PDAC-derived Xenograft

label_protocol: For each sample, 400 ng of total RNA were labeled with the FlashTag Biotin HSR Labeling Kit (Affimetrix, Santa Clara, USA) and hybridized to the Affymetrix Human Gene 2.0 ST Array (Affymetrix).

growth_protocol: 30 primary tumors obtained from surgery and 25 biopsy samples taken by endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) were implanted subcutaneously into mice and preserved as Patient Derived Xenografts (PDX). Samples from EUS-FNA were mixed with 100 µl of MatrigelTM (BD Biosciences, Franklin Lakes, NJ) and injected in the upper right flank of a nude mouse (Swiss Nude Mouse Crl: NU(lco)-Foxn1nu; Charles River Laboratories, Wilmington, MA). Samples from surgery were fragmented, mixed with 100 µl of MatrigelTM, and implanted with a trocar (10 gauge; Innovative Research of America, Sarasota, FL) in the subcutaneous right upper flank of an anesthetized and disinfected mouse. When the tumors reached 1 cm3, the mice were sacrificed, and the tumors were removed.

extract_protocol: Total RNA was purified from xenograft using TRIzol® Reagent (Gibco, Life Technologies) according to the manufacturer. Briefly, 50 to 100 mg of fresh frozen tissue per ml of TRIzol® was disrupted using a homogenizer followed by a single step of phenol/chloroform purification. Total RNA was eluted in RNAse-free water and its concentration was quantified with a NanoDrop 1000 microvolume spectrophotometer (Thermo Scientific). RNA quality was assessed with the Agilent RNA 6000 pico and Agilent RNA nano kits on a 2100 Bioanalyzer(Agilent) from the transcriptomic Core facility of the CHUQ. The RNA integrity numbers were in the range of 8 to 10. Samples were stored at −80°C until use.

tag: sample type

value: xenograft


title: Xenograft HN014 Rep2

status: Public on Mar 17 2017

type: RNA

description: Gene expression data of PDAC-derived Xenograft from patient HN014 , Rep2

label: Biotin

molecule: total RNA

organism: Homo sapiens


title: PUMI_29697

type: genomic

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

country: USA

institute: NHGRI

description:
SKU_matrix.txt
SKU_signal.txt

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Pumi_whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: origin

value: North America

tag: breed

value: Pumi

tag: tissue

value: whole blood


title: Xenograft Foie_8b1 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient Foie_8b1 , Rep1


title: SCWT_23325

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Soft Coated Wheaten Terrier_whole blood

value: Soft Coated Wheaten Terrier


title: TIBS_5380

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Tibetan Spaniel_whole blood

value: Tibetan Spaniel


title: TIBS_5383

description:
SKU_matrix.txt
SKU_signal.txt


title: XIGO_24477

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Xigou_whole blood

value: China

value: Xigou


title: TIBS_5382

description:
SKU_matrix.txt
SKU_signal.txt


title: PUMI_29695

description:
SKU_matrix.txt
SKU_signal.txt


title: SCWT_22617

description:
SKU_matrix.txt
SKU_signal.txt


title: KERY_3174

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Kerry Blue Terrier_whole blood

value: Kerry Blue Terrier


title: Xenograft Foie_8b1 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient Foie_8b1 , Rep2


title: Xenograft AO-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient AO-IPC , Rep2


title: PUMI_29689

description:
SKU_matrix.txt
SKU_signal.txt


title: PUMI_29698

description:
SKU_matrix.txt
SKU_signal.txt


title: KERY_21525

description:
SKU_matrix.txt
SKU_signal.txt


title: KERY_27113

description:
SKU_matrix.txt
SKU_signal.txt


title: Xenograft 01-030 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01-030 , Rep2


title: KELP_9320

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Australian Kelpie_whole blood

value: Australian Kelpie


title: Xenograft 01-030 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01-030 , Rep1


title: Xenograft AO-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient AO-IPC , Rep1


title: Xenograft 01.054 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.054 , Rep2


title: KELP_9350

description:
SKU_matrix.txt
SKU_signal.txt


title: Xenograft 01.054 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.054 , Rep1


title: TURV_27484

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Belgian Tervuren_whole blood

value: Belgian Tervuren


title: AIRT_25288

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Airedale Terrier_whole blood

value: Airedale Terrier


title: AIRT_8388

description:
SKU_matrix.txt
SKU_signal.txt


title: PEKE_23356

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Pekingese_whole blood

value: Pekingese


title: Xenograft 02.087p Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.087p , Rep1


title: AUCD_9994

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Australian Cattle Dog_whole blood

value: Australian Cattle Dog


title: MAST_02299

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Mastiff_whole blood

value: Mastiff


title: Xenograft 03.096 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 03.096 , Rep1


title: IWOF_21534

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Irish Wolfhound_whole blood

value: Irish Wolfhound


title: TPOO_10442

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Toy Poodle_whole blood

value: Toy Poodle


title: ROTT_21895

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Rottweiler_whole blood

value: Rottweiler


title: HUSK 14529

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Siberian Husky_whole blood

value: North America

value: Siberian Husky


title: SCWT_20516

description:
SKU_matrix.txt
SKU_signal.txt

value: whole blood


title: SCOT_8542

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Scottish Terrier_whole blood

value: Scottish Terrier


title: AIRT_8387

description:
SKU_matrix.txt
SKU_signal.txt


title: MAST_21270

description:
PUL_matrix.txt
PUL_signal.txt


title: Xenograft 03.096 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 03.096 , Rep2

source_name: PDAC-derived Xenograft

value: xenograft


title: Xenograft 01.046 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.046 , Rep2


title: SSHP_11617

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Shetland Sheepdog_whole blood

value: Shetland Sheepdog


title: MAST_02297

description:
PUL_matrix.txt
PUL_signal.txt


title: Xenograft 02.087p Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.087p , Rep2


title: FCR_24743

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Flat Coated Retriever_whole blood

value: Flat Coated Retriever


title: CHOW_15630

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Chow Chow_whole blood

value: Chow Chow


title: AUCD_25269

description:
SKU_matrix.txt
SKU_signal.txt


title: FCR_20576

description:
PUL_matrix.txt
PUL_signal.txt


title: Xenograft 01.046 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.046 , Rep1


title: Xenograft 02.083f Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.083f , Rep2


title: CHOW_13802

description:
PUL_matrix.txt
PUL_signal.txt


title: BMD_4687

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Bernese Mountain Dog_whole blood

value: Bernese Mountain Dog


title: CHIH_13131

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Chihuahua_whole blood

value: Chihuahua


title: Xenograft 01.119 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.119 , Rep1


title: BMD_972

description:
PUL_matrix.txt
PUL_signal.txt


title: DANE_6610

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Great Dane_whole blood

value: Great Dane


title: Xenograft AP-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient AP-IPC , Rep2


title: BMD_4667

description:
PUL_matrix.txt
PUL_signal.txt


title: BLDH_25394

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Bloodhound_whole blood

value: Bloodhound


title: Xenograft 02.045 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.045 , Rep2


title: Xenograft AP-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient AP-IPC , Rep1


title: BMD_983

description:
PUL_matrix.txt
PUL_signal.txt


title: Xenograft 02.045 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.045 , Rep1


title: BMD_4679

description:
PUL_matrix.txt
PUL_signal.txt


title: BELS_27485

description:
PUL_matrix.txt
PUL_signal.txt

source_name: Belgian Sheepdog_whole blood

value: Belgian Sheepdog


title: HB9EBs_8.hunt

city: Seattle

first: G. Adam

last: Whitney

state: WA

address: 401 Terry Ave.

department: Bioinformatics

institute: PreCyte

description: Treated with plasma from a Huntington's disease mouse model

hyb_protocol: Total RNA samples were checked for quality (Agilent Bioanalyzer 2100) and quantity/concentration levels (NanoDrop ND-1000 spectrophotometer) and 0.1 μg of high quality RNA samples were processed for hybridization on GeneChip® Mouse Exon ST microarrays (Affymetrix) following manufacturers recommendations to generate amplified and biotinylated sense-strand (ss) DNA targets from the expressed genome using the Ambion® Whole Transcript (WT) Expression Kit. Samples were then labeled using the GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix).

scan_protocol: Affymetrix 7G GeneChip Scanner

data_processing: Microarray data from each batch of neurons were analyzed together using Affymetrix Expression Console™ software, and gene-level expression values were used to generate Pearson’s r scores for each array. Average Pearson’s r scores were evaluated using a Grubbs’ test (two-sided, alpha = 0.05) to identify outliers, which were removed from the data set. Gene expression data was derived from exon array data using the Robust Multi-array Averaging (RMA) [11] algorithm as implemented in the [R] Aroma Affymetrix package [12]. Gene expression was then estimated as the mean expression of all exons in each gene as annotated by release 33 of the Affymetrix MoEx-1_0-st-v1 annotation files.

label: biotin

organism: Mus musculus

source_name: Embryoid bodies containing motor neurons

label_protocol: The GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix) was used according to the manufactures recommendations.

extract_protocol: RNA was isolated using Trizol® according to the manufacturer’s recommendations.

tag: strain

tag: treatment


title: KEES_29631

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Keeshond_whole blood

value: Keeshond


title: Xenograft 01.119 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.119 , Rep2


title: BEDT_28915

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Bedlington Terrier_whole blood

value: Bedlington Terrier


title: Xenograft 01.101f Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.101f , Rep1


title: KEES_29630

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_6.hunt

value: plasma from a Huntington's disease mouse model


title: AMST_28499

description:
MPR_matrix.txt
MPR_signal.txt

source_name: American Staffordshire Bull Terrier_whole blood

value: American Staffordshire Bull Terrier


title: Xenograft 02.083f Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.083f , Rep1


title: NSDT_29586

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Nova Scotia Duck Tolling Retriever_whole blood

value: North America

value: Nova Scotia Duck Tolling Retriever


title: HB9EBs_7.hunt


title: HB9EBs_5.hunt


title: Xenograft 02.038 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.038 , Rep2


title: RATT_28509

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Rat Terrier_whole blood

value: Rat Terrier

value: whole blood


title: AMST_29567

description:
MPR_matrix.txt
MPR_signal.txt


title: RATT_28508

description:
MPR_matrix.txt
MPR_signal.txt


title: BEDT_28916

description:
MPR_matrix.txt
MPR_signal.txt


title: GORD_28456

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Gordon Setter_whole blood

value: Gordon Setter


title: KERY_12354

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Kerry Blue Terrier_whole blood

value: Kerry Blue Terrier


title: Xenograft 01.101f Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.101f , Rep2

source_name: PDAC-derived Xenograft

value: xenograft


title: HB9EBs_4.hunt


title: KEES_28498

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft I-NOR Rep2

description: Gene expression data of PDAC-derived Xenograft from patient I-NOR , Rep2


title: HB9EBs_2.hunt


title: Xenograft I-NOR Rep1

description: Gene expression data of PDAC-derived Xenograft from patient I-NOR , Rep1


title: NSDT_29588

description:
MPR_matrix.txt
MPR_signal.txt


title: NELK_28504

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Norwegian Elkhound_whole blood

value: Norwegian Elkhound


title: VIZS_28367

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Vizsla_whole blood

value: Vizsla


title: VIZS_28366

description:
MPR_matrix.txt
MPR_signal.txt


title: FIEL_28377

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Field Spaniel_whole blood

value: Field Spaniel


title: BEDT_28909

description:
MPR_matrix.txt
MPR_signal.txt


title: BORT_27568

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Border Terrier_whole blood

value: Border Terrier


title: ISET_27450

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Irish Setter_whole blood

value: Irish Setter


title: ACKR_11414

description:
PUL_matrix.txt
PUL_signal.txt

source_name: American Cocker Spaniel_whole blood

value: American Cocker Spaniel


title: VIZS_27571

description:
MPR_matrix.txt
MPR_signal.txt


title: FIEL_27554

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft 02.104 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.104 , Rep1


title: Xenograft L-NOR Rep2

description: Gene expression data of PDAC-derived Xenograft from patient L-NOR , Rep2


title: Xenograft 02.104 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.104 , Rep2


title: HB9EBs_HEMI2_10wk_24h

description: Serum from a hemizygous SOD1 mutant mouse

extract_protocol: Embryoid bodies were harvested by centrifugation and RNA was isolated using Trizol® according to the manufacturer’s recommendations.

value: F1 progeny of two different strains (C57BL/6 and SJL)

tag: time point

value: 10 weeks cultures


title: HB9EBs_HEMI3_10wk_24h


title: HB9EBs_HEMI1_10wk_24h


title: MALT_27447

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Maltese_whole blood

value: Maltese


title: HB9EBs_NCAR3_10wk_24h

description: Treated with serum from WT littermate of the mutant mice


title: MALT_27446

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft 02.042 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.042 , Rep2


title: HB9EBs_NCAR2_10wk_24h


title: DALM_27381

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Dalmatian_whole blood

value: Dalmatian


title: Xenograft X-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient X-IPC , Rep2


title: Xenograft 02.042 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.042 , Rep1


title: LMUN_27296

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Large Munsterlander_whole blood

value: North America

value: Large Munsterlander


title: CCRT_27336

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Curly Coated Retriever_whole blood

value: Curly Coated Retriever


title: Xenograft L-NOR Rep1

description: Gene expression data of PDAC-derived Xenograft from patient L-NOR , Rep1


title: HB9EBs_HEMI144_9wk_24h

source_name: Embryoid bodies containing motor neurons

value: 9 weeks cultures


title: HB9EBs_HEMI143_9wk_24h


title: LMUN_27295

description:
MPR_matrix.txt
MPR_signal.txt

value: whole blood


title: HB9EBs_NCAR1_10wk_24h


title: KEES_27433

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Keeshond_whole blood

value: Keeshond


title: Xenograft 01.069 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.069 , Rep1

value: xenograft


title: Xenograft X-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient X-IPC , Rep1


title: LMUN_27292

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_HEMI142_9wk_24h


title: Xenograft N-NOR Rep2

description: Gene expression data of PDAC-derived Xenograft from patient N-NOR , Rep2


title: IRTR_27176

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Irish Terrier_whole blood

value: Irish Terrier


title: HB9EBs_NCAR140_9wk_24h


title: FIEL_27194

description:
MPR_matrix.txt
MPR_signal.txt


title: CCRT_27282

description:
MPR_matrix.txt
MPR_signal.txt


title: BORT_27171

description:
MPR_matrix.txt
MPR_signal.txt


title: FIEL_27191

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft N-NOR Rep1

description: Gene expression data of PDAC-derived Xenograft from patient N-NOR , Rep1


title: HB9EBs_NCAR139_9wk_24h


title: Xenograft 01.069 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.069 , Rep2


title: HB9EBs_HEMI138_9wk_24h


title: Xenograft 01.077 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.077 , Rep2


title: IRTR_27166

description:
MPR_matrix.txt
MPR_signal.txt


title: IRTR_27175

description:
MPR_matrix.txt
MPR_signal.txt


title: IRTR_27163

description:
MPR_matrix.txt
MPR_signal.txt


title: IRTR_27164

description:
MPR_matrix.txt
MPR_signal.txt


title: PULI_27129

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Puli_whole blood

value: Puli


title: HB9EBs_HEMI137_9wk_24h


title: HB9EBs_HEMI136_9wk_24h


title: HB9EBs_NCAR141_9wk_24h


title: IRTR_27165

description:
MPR_matrix.txt
MPR_signal.txt


title: PULI_27429

description:
MPR_matrix.txt
MPR_signal.txt


title: BEDT_27105

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Bedlington Terrier_whole blood

value: Bedlington Terrier


title: Xenograft 01.077 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.077 , Rep1


title: Xenograft I-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient I-IPC , Rep2


title: Xenograft I-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient I-IPC , Rep1


title: IRTR_27162

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft 01.052 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.052 , Rep2


title: PRUS_27079

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Parson Russell_whole blood

value: Parson Russell


title: HB9EBs_NCAR134_9wk_24h


title: CCRT_27031

description:
MPR_matrix.txt
MPR_signal.txt


title: DALM_27075

description:
MPR_matrix.txt
MPR_signal.txt


title: DALM_27076

description:
MPR_matrix.txt
MPR_signal.txt


title: VIZS_27051

description:
MPR_matrix.txt
MPR_signal.txt

value: Vizsla


title: PRUS_27058

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_NCAR133_9wk_24h


title: HB9EBs_HEMI131_9wk_24h


title: WHPG_27039

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Wirehaired Pointing Griffon_whole blood

value: Wirehaired Pointing Griffon


title: VIZS_27073

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft 02.038 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.038 , Rep1

source_name: PDAC-derived Xenograft


title: Xenograft 01.052 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.052 , Rep1


title: ISET_27022

description:
MPR_matrix.txt
MPR_signal.txt

value: Irish Setter


title: HB9EBs_HEMI130_9wk_24h

description: Serum from a hemizygous SOD1 mutant mouse

value: F1 progeny of two different strains (C57BL/6 and SJL)


title: Xenograft 02.058 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.058 , Rep2


title: ISET_27002

description:
MPR_matrix.txt
MPR_signal.txt


title: VIZS_27015

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Vizsla_whole blood


title: Xenograft H-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient H-IPC , Rep2


title: WHPG_27017

description:
MPR_matrix.txt
MPR_signal.txt


title: WHPG_27013

description:
MPR_matrix.txt
MPR_signal.txt


title: WHPG_27012

description:
MPR_matrix.txt
MPR_signal.txt


title: WHPG_27016

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_NCAR127_9wk_24h

description: Treated with serum from WT littermate of the mutant mice


title: HB9EBs_NCAR128_9wk_24h


title: Xenograft H-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient H-IPC , Rep1


title: Xenograft AM-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient AM-IPC , Rep2


title: CCRT_27018

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_NCAR135_9wk_24h


title: Xenograft AM-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient AM-IPC , Rep1


title: WHPG_27001

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_NCAR126_9wk_24h


title: VIZS_26998

description:
MPR_matrix.txt
MPR_signal.txt


title: BORT_25438

description:
MPR_matrix.txt
MPR_signal.txt

value: Border Terrier


title: AHRT_24735

description:
MPR_matrix.txt
MPR_signal.txt

source_name: American Hairless Terrier_whole blood

value: American Hairless Terrier


title: Olfactory mucosa derived cell culture 2

city: schlieren

first: tamara

last: tanos

address: Wagistrasse 27

country: Switzerland

institute: InSphero

hyb_protocol: Hybridization was performed using the Affymetrix GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 10% and pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively

scan_protocol: GeneChip® cartridges were washed and stained in the Affymetrix Fluidics Station 450 following the FS450_0002 standard protocol. GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.

data_processing:
Expression profiles, preprocessed with MAS5 algorithm, were exported to GeneSpring GX software version 7.3 (Agilent Technologies). According to the GeneSpring normalization procedure, in each analysis the 50th percentile of all measurements was used as a positive control, within each hybridization array, and each measurement for each gene was divided by this control. The bottom 10th percentile was used for background subtraction. Among different hybridization arrays, each gene was divided by the median of its measurements in all samples. Data were then log transformed for subsequent analysis. Expression data were prefiltered by considering both MAS5 ‘Absolute Call’ flags and average expression measurements within each group analyzed. We selected probe sets called present or marginal (P or M) at least once across all samples. The prefiltering method removed those probe sets whose expression signal was constantly too close to the background throughout the entire set of samples.  In order to find genes whose expression levels significantly differed between OM cells and fibroblast, we adopted a supervised method of analysis, using the GeneSpring software. Mean values were calculated within the two classes for each probe set, and fold-change ratios between the OM and the fibroblast were derived. A difference of twofold cutoff was applied to select upregulated and downregulated genes. A further statistical analysis was performed using Welch’s approximate t-test and ANOVA, with P-value cutoff of 0.05, without the assumption of equality of variances. Benjamini and Hochberg false discovery rate (FDR) was used for multiple testing. By this analysis, 5759 probe sets were found to be significantly regulated between the two classes of samples.
A difference of twofold cutoff was applied to select upregulated and downregulated genes

source_name: Olfactory mucosa derived cell culture

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Affymetrix GeneChip® 3' IVT Plus Kit. With the same kit was synthesized the labeled aRNA before to be fragmented. Labeling was performed according to the manufacturer's protocol.

growth_protocol: In order to culture the OM, each sample was digested in Dispase II solution (2.4 U/ml) for 1h, 37ºC. The OE and lamina were thus dissociated brushing gently with a lancet. The remaining lamina was cut into 1 mm2 pieces and transferred into Collagenase I solution, 0,25 mg/ml (10 min, 37°C). The tissue was resuspended in epithelium/dispase 1:10 with PBS and centrifuged at 1500 rpm for 5 min. Red blood cells lysis buffer (Sigma) was added to remove contaminant cells and it was centrifuged again. The pellet was suspended and plated in OM medium. When adherent cells reached confluency, they were passaged using trypsin.

extract_protocol: Total RNA was extracted using commercial homogenization (QIAshredder) and purification (RNeasy Mini Kit) reagents (Qiagen). RNA quality was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: human adult olfactory mucosa


title: Olfactory mucosa derived cell culture 1


title: Olfactory mucosa derived cell culture 3


title: HB9EBs_HEMI124_9wk_24h


title: GORD_26995

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Gordon Setter_whole blood

value: North America

value: Gordon Setter


title: Xenograft 03.076 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 03.076 , Rep2


title: Xenograft 03.076 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 03.076 , Rep1


title: KEES_24629

description:
MPR_matrix.txt
MPR_signal.txt


title: KEES_24630

description:
MPR_matrix.txt
MPR_signal.txt


title: NSDT_26994

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Nova Scotia Duck Tolling Retriever_whole blood

value: Nova Scotia Duck Tolling Retriever


title: Xenograft 02.063 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.063 , Rep2


title: HB9EBs_HEMI123_9wk_24h

value: 9 weeks cultures


title: KEES_24631

description:
MPR_matrix.txt
MPR_signal.txt

value: Keeshond

value: whole blood


title: HB9EBs_NCAR125_9wk_24h


title: KEES_24633

description:
MPR_matrix.txt
MPR_signal.txt


title: ST2KO BMMCs IL33 stimulated 4hr rep3

city: Chicago

first: Paul

middle: J

last: Bryce

state: IL

address: 420 E Superior Street

institute: Northwestern University Feinberg School of Medicine

description: MC ST2KO3 IL33

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background correctted and quantile normalized aided by control probes using array analysis tools available via arrayanalysis.org

source_name: Bone marrow-derived mast cells

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted with QIAGEN RNeasy RNA isolation kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: cell type

value: Bone marrow-derived mast cells

tag: genotype

tag: age

value: 4-6 weeks


title: Xenograft 02.063 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.063 , Rep1

value: xenograft


title: FOXH_23110

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Foxhound_whole blood

value: Foxhound


title: HB9EBs_NCAR118_9wk_24h


title: FOXH_23089

description:
MPR_matrix.txt
MPR_signal.txt


title: KEES_24628

description:
MPR_matrix.txt
MPR_signal.txt


title: ST2KO BMMCs IL33 stimulated 4hr rep2

description: MC ST2KO2 IL33


title: Xenograft 01.037 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.037 , Rep1


title: HB9EBs_NCAR117_9wk_24h


title: HB9EBs_HEMI121_9wk_24h


title: HB9EBs_NCAR116_9wk_24h


title: ST2KO BMMCs IgE stimulated 4hr rep3

description: MC ST2KO3 IgE


title: Xenograft 01.048f Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.048f , Rep2


title: FOXH_23096

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_HEMI122_9wk_24h


title: ST2KO BMMCs IL33 stimulated 4hr rep1

description: MC ST2KO1 IL33


title: FOXH_23094

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_HEMI129_9wk_24h


title: ST2KO BMMCs IgE stimulated 4hr rep1

description: MC ST2KO1 IgE


title: Xenograft 01.048f Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.048f , Rep1


title: HB9EBs_HEMI120_9wk_24h


title: ST2KO BMMCs IgE stimulated 4hr rep2

description: MC ST2KO2 IgE


title: ST2KO BMMCs unstimulated rep3

description: MC ST2KO3 unstim


title: FOXH_23077

description:
MPR_matrix.txt
MPR_signal.txt


title: FOXH_23078

description:
MPR_matrix.txt
MPR_signal.txt


title: AHRT_25647

description:
MPR_matrix.txt
MPR_signal.txt


title: FOXH_23080

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_HEMI119_9wk_24h


title: Xenograft 02.029 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.029 , Rep2


title: HB9EBs_NCAR115_9wk_24h


title: FOXH_23074

description:
MPR_matrix.txt
MPR_signal.txt


title: FOXH_23075

description:
MPR_matrix.txt
MPR_signal.txt


title: ST2KO BMMCs unstimulated rep1

description: MC ST2KO1 unstim


title: FOXH_23056

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft 02.058 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.058 , Rep1


title: ST2KO BMMCs unstimulated rep2

description: MC ST2KO2 unstim


title: Xenograft 01.064 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.064 , Rep1


title: HB9EBs_HEMI112_9wk_24h

description: Serum from a hemizygous SOD1 mutant mouse


title: HB9EBs_NCAR114_9wk_24h


title: Xenograft 02.029 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.029 , Rep1


title: HB9EBs_HEMI111_9wk_24h


title: WT BMMCs IL33 stimulated 4hr rep2

description: MC WT2 IL33

value: wild type


title: WT BMMCs IL33 stimulated 4hr rep3

description: MC WT3 IL33


title: Xenograft 01.064 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.064 , Rep2


title: KEES_22830

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft S-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient S-IPC , Rep2


title: DALM_13301

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Dalmatian_whole blood

value: Dalmatian


title: SVAL_10600

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Swedish Vallhund_whole blood

value: Swedish Vallhund


title: Xenograft S-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient S-IPC , Rep1


title: WT BMMCs IL33 stimulated 4hr rep1

description: MC WT1 IL33


title: HB9EBs_NCAR109_9wk_24h

description: Treated with serum from WT littermate of the mutant mice

source_name: Embryoid bodies containing motor neurons

value: F1 progeny of two different strains (C57BL/6 and SJL)


title: HB9EBs_HEMI106_9wk_24h


title: HB9EBs_NCAR108_9wk_24h


title: Xenograft 01.033 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.033 , Rep2


title: HB9EBs_HEMI110_9wk_24h


title: WT BMMCs unstimulated rep3

description: MC WT3 unstim


title: Xenograft 01.037 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.037 , Rep2


title: Xenograft 01.053 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.053 , Rep1


title: Xenograft 01.053 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.053 , Rep2


title: HB9EBs_NCAR107_9wk_24h


title: WT BMMCs IgE stimulated 4hr rep1

description: MC WT1 IgE


title: WT BMMCs IgE stimulated 4hr rep2

description: MC WT2 IgE


title: WT BMMCs unstimulated rep2

description: MC WT2 unstim


title: WT BMMCs IgE stimulated 4hr rep3

description: MC WT3 IgE


title: SVAL_10447

description:
MPR_matrix.txt
MPR_signal.txt


title: SVAL_10043

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9EBs_HEMI105_9wk_24h


title: Xenograft 01.033 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.033 , Rep1


title: Xenograft 03.043 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 03.043 , Rep2


title: HB9EBs_HEMI104_9wk_24h


title: SVAL_10069

description:
MPR_matrix.txt
MPR_signal.txt


title: ST2KO BMBs IL33 stimulated 4hr rep2

description: Ba ST2KO2 IL33

source_name: Bone marrow-derived basophils

value: Bone marrow-derived basophils


title: Xenograft 03.043 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 03.043 , Rep1


title: HB9EBs_NCAR103_9wk_24h


title: ST2KO BMBs IL33 stimulated 4hr rep3

description: Ba ST2KO3 IL33


title: WT BMMCs unstimulated rep1

description: MC WT1 unstim


title: Xenograft 02.106 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.106 , Rep2


title: HB9EBs_NCAR102_9wk_24h


title: Xenograft 01.008 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.008 , Rep2


title: Xenograft 02.106 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.106 , Rep1


title: AHRT_1121

description:
MPR_matrix.txt
MPR_signal.txt

value: American Hairless Terrier


title: HB9EBs_NCAR101_9wk_24h


title: ST2KO BMBs IL33 stimulated 4hr rep1

description: Ba ST2KO1 IL33


title: HB9MNs_9wk_HEMI_24h_B


title: AHRT_1123

description:
MPR_matrix.txt
MPR_signal.txt


title: BORT_8386

description:
MPR_matrix.txt
MPR_signal.txt

source_name: Border Terrier_whole blood

value: Border Terrier


title: SVAL_8407

description:
MPR_matrix.txt
MPR_signal.txt

value: North America


title: SVAL_8343

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9MNs_9wk_HEMI_24h_A


title: AHRT_1122

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft AG-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient AG-IPC , Rep2


title: ST2KO BMBs IgE stimulated 4hr rep1

description: Ba ST2KO1 IgE


title: ST2KO BMBs IgE stimulated 4hr rep2

description: Ba ST2KO2 IgE


title: HB9MNs_9wk_NCAR_24h_B


title: ST2KO BMBs unstimulated rep3

description: Ba ST2KO3 unstim


title: motorneuron_HEMI_24h_rep3

description: Serum from a hemizygous SOD1 mutant mouse


title: ST2KO BMBs unstimulated rep2

description: Ba ST2KO2 unstim


title: motorneuron_NCAR_24h_rep4


title: AHRT_1117

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft AG-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient AG-IPC , Rep1


title: Xenograft 02.099 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 02.099 , Rep2


title: AHRT_1079

description:
MPR_matrix.txt
MPR_signal.txt


title: ST2KO BMBs unstimulated rep1

description: Ba ST2KO1 unstim


title: AHRT_1080

description:
MPR_matrix.txt
MPR_signal.txt


title: HB9MNs_9wk_NCAR_24h_A


title: Xenograft 01.080 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.080 , Rep1


title: motorneuron_HEMI_24h_rep2


title: motorneuron_NCAR_24h_rep3


title: Xenograft 01.080 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.080 , Rep2


title: Xenograft 02.099 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 02.099 , Rep1


title: Xenograft AR-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient AR-IPC , Rep1


title: Xenograft 01.008 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.008 , Rep1


title: AHRT_1120

description:
MPR_matrix.txt
MPR_signal.txt


title: AHRT_1081

description:
MPR_matrix.txt
MPR_signal.txt


title: Xenograft AR-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient AR-IPC , Rep2


title: WT BMBs IL33 stimulated 4hr rep3

description: Ba WT3 IL33


title: WT BMBs IL33 stimulated 4hr rep2

description: Ba WT2 IL33


title: motorneuron_HEMI_24h_rep1


title: motorneuron_NCAR_24h_rep2

description: Treated with serum from WT littermate of the mutant mice


title: Xenograft A-Nor Rep2

description: Gene expression data of PDAC-derived Xenograft from patient A-Nor , Rep2


title: WT BMBs IL33 stimulated 4hr rep1

description: Ba WT1 IL33


title: WT BMBs IgE stimulated 4hr rep3

description: Ba WT3 IgE


title: motorneuron_NCAR_24h_rep1


title: Xenograft A-Nor Rep1

description: Gene expression data of PDAC-derived Xenograft from patient A-Nor , Rep1


title: WT BMBs IgE stimulated 4hr rep2

description: Ba WT2 IgE


title: Xenograft H-Nor Rep2

description: Gene expression data of PDAC-derived Xenograft from patient H-Nor , Rep2


title: WT BMBs unstimulated rep2

description: Ba WT2 unstim


title: WT BMBs IgE stimulated 4hr rep1

description: Ba WT1 IgE


title: WT BMBs unstimulated rep3

description: Ba WT3 unstim


title: Xenograft H-Nor Rep1

description: Gene expression data of PDAC-derived Xenograft from patient H-Nor , Rep1


title: BQ0471

description: Treated with plasma from a control patient

hyb_protocol: Total RNA samples were checked for quality (Agilent Bioanalyzer 2100) and quantity/concentration levels (NanoDrop ND-1000 spectrophotometer) and 0.1 μg of high quality RNA samples were processed for hybridization on human exon arrays (ST 1.0) (Affymetrix) following manufacturers recommendations to generate amplified and biotinylated sense-strand (ss) DNA targets from the expressed genome using the Ambion® Whole Transcript (WT) Expression Kit. Samples were then labeled using the GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix).

data_processing: Microarray data from each batch of neurons were analyzed together using Affymetrix Expression Console™ software, and gene-level expression values were used to generate Pearson’s r scores for each array. Average Pearson’s r scores were evaluated using a Grubbs’ test (two-sided, alpha = 0.05) to identify outliers, which were removed from the data set. Gene expression data was derived from exon array data using the Robust Multi-array Averaging (RMA) [11] algorithm as implemented in the [R] Aroma Affymetrix package [12]. Gene expression was then estimated as the mean expression of all exons in each gene as annotated by release 33.1 of the Affymetrix human annotation files.

source_name: iCell Neurons from Cellular Dynamics International (CDI)

tag: plasma donor amyloid beta 42 level (pg/ml)


title: Xenograft HN-01 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient HN-01 , Rep2


title: BQ6163


title: #2BQ6110


title: WT BMBs unstimulated rep1

description: Ba WT1 unstim


title: AC903


title: ST2KO BMBs IgE stimulated 4hr rep3

description: Ba ST2KO3 IgE


title: BQ6165


title: BQ11002


title: Xenograft E-NOR Rep2

description: Gene expression data of PDAC-derived Xenograft from patient E-NOR , Rep2


title: BQ0474


title: Xenograft HN-01 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient HN-01 , Rep1


title: BQ/AC0486


title: Xenograft AH-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient AH-IPC , Rep2


title: AC637


title: AC524


title: Xenograft E-NOR Rep1

description: Gene expression data of PDAC-derived Xenograft from patient E-NOR , Rep1


title: BQ6127


title: Xenograft L-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient L-IPC , Rep2


title: Xenograft AH-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient AH-IPC , Rep1


title: Xenograft AD-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient AD-IPC , Rep2


title: BQ/AC0397


title: Xenograft AD-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient AD-IPC , Rep1


title: AC/BQ260


title: Xenograft L-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient L-IPC , Rep1


title: Xenograft J-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient J-IPC , Rep1


title: AC249


title: BQ024


title: Xenograft J-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient J-IPC , Rep2


title: Xenograft B-Tim Rep2

description: Gene expression data of PDAC-derived Xenograft from patient B-Tim , Rep2


title: Xenograft D-IPC Rep1

description: Gene expression data of PDAC-derived Xenograft from patient D-IPC , Rep1


title: AC094


title: Xenograft C-Nor Rep1

description: Gene expression data of PDAC-derived Xenograft from patient C-Nor , Rep1


title: Xenograft D-IPC Rep2

description: Gene expression data of PDAC-derived Xenograft from patient D-IPC , Rep2


title: BQ0246

description: Treated with plasma from a control patient


title: BQ6135

description: Treated with plasma from a pre-sympotmatic Alzheimer's patient


title: Xenograft B-Tim Rep1

description: Gene expression data of PDAC-derived Xenograft from patient B-Tim , Rep1


title: Xenograft 01.001 Rep2

description: Gene expression data of PDAC-derived Xenograft from patient 01.001 , Rep2


title: Xenograft C-Nor Rep2

description: Gene expression data of PDAC-derived Xenograft from patient C-Nor , Rep2


title: AC250


title: Xenograft 01.001 Rep1

description: Gene expression data of PDAC-derived Xenograft from patient 01.001 , Rep1


title: BQ339


title: AC643


title: 2BQ0168


title: #2AC/#2BQ0222


title: AC-070


title: #2AC1BQ199


title: #2BQ8107


title: #2AC126


title: AC119


title: AC024


title: AC127


title: ACBQHC324


title: Mesenchyme at 11WD, biological rep3

city: Paris

first: Raphael

last: Scharfmann

address: 123 bvd Port-Royal

country: France

institute: Institut Cochin - Bat. Cassini

description: Gene expression data from FACS sorted cells from human fetal pancreas at 11WD

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

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

data_processing: The data were analyzed with R Bioconductor packages using using RMA as normalization method

source_name: FACS sorted cells from mesenchyme of human fetal pancreas at 11WD

label_protocol: Total RNA is reverse transcribed following the Ovation Pico WTA System V2 (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3,6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).   After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.

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

tag: developmental stage

value: 11WD embryo

value: pancreas


title: Mesenchyme at 11WD, biological rep2


title: AC122


title: NA12878 Genomic DNA Replicate 1 (IlluminaCytoSNP850K)

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

department: Life Sciences

country: Trinidad and Tobago

institute: The University of the West Indies

description: Genomic DNA extracted from GM12878 cell lines. Genomic DNA obtained from Coriell

hyb_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

data_processing:
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Infinium human CytoSNP-850K array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package  (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary  material of the manuscript.
Processed data are final reports exported from GenomeStudio in the required format for downstream analysis in Nexus Copy Number. Columns include Sample Name (blank field - sample is NA12878), Sample ID (corresponding array barcode and sub-field on which sample was hybridized), SNP Name (equivalent to ID REF - unique identifier for each probe on the array), Chr (chromosome containing probe), Position (chromosomal coordinate of probe), Log R Ratio (the base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the cluster)), B Allele Freq (B allele theta value of this SNP for the sample, relative to the cluster positions),  GC Score (value between 0 and 1 indicating reliability of genotype call), SNP (Nucleotide substitution for the SNP on the Illumina top strand)

label: Cy5, Cy3

source_name: Blood, B Lymphocyte

extract_protocol: Genomic DNA was extracted from GM12878 cell lines by Coriell Cell Repositories

tag: gender

value: Female

tag: ethnicity

value: Caucasian

tag: cell line


title: BQ/2AC0048


title: #2AC/BQ071


title: NA12878 Genomic DNA Replicate 2 (IlluminaCytoSNP850K)

scan_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html


title: AC005


title: GP2 high at 11WD, biological rep2

source_name: FACS sorted cells from human fetal pancreas at 11WD expressing E-CADH and high level GP2


title: GP2 high at 11WD, biological rep1


title: GP2 high at 11WD, biological rep3


title: AC072


title: Mesenchyme at 11WD, biological rep1


title: AC097


title: GP2+ at 11WD, biological rep3

source_name: FACS sorted cells from human fetal pancreas at 11WD expressing E-CADH and GP2


title: ACBQ293


title: ACBQ323


title: GP2+ at 11WD, biological rep2


title: GP2+ at 11WD, biological rep1


title: GP2- at 11WD, biological rep2

source_name: FACS sorted cells from human fetal pancreas at 11WD expressing E-CADH but no GP2


title: E-CADHERIN low at 11WD, biological rep3

source_name: FACS sorted cells from human fetal pancreas at 11WD expressing low level of E-CADH and no GP2


title: GP2- at 11WD, biological rep1


title: BQ6150

description: Treated with plasma from a Alzheimer's patient


title: AX/BQ0402


title: Adipo cycled

city: Hannover

first: Denys

last: Pogozhykh

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V6.7’, except that 1000ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE2_107_Sep09.xml’, except that ‘Multiplicative detrending’ algorithm was inactivated.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) and of the red channel ,‘rProcessedSignal’ (rPS) to retrieve one resulting value per channel and  unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged PS values were normalized by Quantile normalization approach.   Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 5 normalized PS units. All measurements below this intensity cutoff were substituted by the respective surrogate value of 5.

source_name: amnion MSCs

label_protocol: Synthesis of Cy3- or Cy5-labeled cRNA was performed with the ‘Low Input Quick Amp Labeling kit, two color’ (#5190-2944, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: Amnion MSCs were cultured at 5% CO2 and 37ºC in humidified CO2 incubator (Thermo Fisher Scientific GmbH, Dreieich, Germany) under sterile conditions in Dulbecco’s modified Eagle’s medium high glucose (DMEM, Lonza, Basel, Switzerland) supplemented with 1% (v/v) 100 mM sodium pyruvate solution (Lonza, Basel, Switzerland), 10% (v/v) fetal bovine serum (FBS, Lonza, Basel, Switzerland), 1% (v/v) antibiotic-antimycotic solution (BioWest, Nuaillé, France), and 1% (v/v) ascorbic acid (Sigma-Aldrich, St. Louis, USA) in 10 cm tissue culture plates (CELLSTAR®, Greiner BioOne, Frickenhausen, Germany). Harvesting of the cells was performed with application of 0.25% trypsin solution.

extract_protocol: For RNA extraction Qiagen kit (QIAGEN, Hilden, Germany) according to manufacturer's protocol was used. Briefly, the samples were lysed in RLT buffer with beta-mercaptoethanol. Ethanol was added to the lysate to provide ideal binding conditions. The lysate was loaded onto the RNeasy silica membrane, and all contaminants were efficiently washed away. Pure, concentrated RNA was eluted in 30 µl water.

treatment_protocol: To assess the impact of temperature fluctuations on placental MSCs the method mimicking potential conditions of the practical biobanking was applied. In summary, the samples were removed from the cryo storage in standard cassette boxes and kept at +20°C on a styrofoam platform to achieve the required temperature with the following immersion of the cassette with probes in cryovials back to the liquid nitrogen. The temperature in cryovials was monitored with a dual-channel temperature controller OWEN TRM 200 (OWEN LLC, Moscow, Russia). Thermocouple sensors were immersed in the central position of identical cryovials with identical content. The software of the device manufacturer (OWEN Process Manager V. 1.2.) was applied for analysis. After cells were differentiated into 3 mesodermal lineges: adipocytes, chondrocytes and osteoblasts.

value: placental multipotent stromal cells


title: E-CADHERIN low at 11WD, biological rep2


title: Osteo cycled


title: Chondro cycled


title: Osteo -180


title: BQ8114


title: E-CADHERIN low at 11WD, biological rep1


title: Chondro -180


title: 2BQ0443


title: Osteo 37C


title: Mesenchyme at 9WD, biological rep3

description: Gene expression data from FACS sorted cells from human fetal pancreas at 9WD

source_name: FACS sorted cells from mesenchyme of human fetal pancreas at 9WD

value: 9WD embryo


title: Mesenchyme at 9WD, biological rep2


title: Adipo 37C


title: AC/BQ311


title: BQ6145


title: Chondro 37C


title: Adipo -180


title: 2BQ6147


title: AC222


title: AC207


title: Mesenchyme at 9WD, biological rep1


title: GP2+ at 9WD, biological rep3

source_name: FACS sorted cells from human fetal pancreas at 9WD expressing E-CADH and GP2


title: GP2+ at 9WD, biological rep1


title: 2BQ0043


title: BQ0362


title: GP2+ at 9WD, biological rep2


title: LY/AC/BQ/HC309


title: GP2- at 9WD, biological rep3

source_name: FACS sorted cells from human fetal pancreas at 9WD expressing E-CADH but no GP2


title: GP2- at 9WD, biological rep2


title: BQ206


title: GP2- at 9WD, biological rep1


title: E-CADHERIN low at 9WD, biological rep2

source_name: FACS sorted cells from human fetal pancreas at 9WD expressing low level of E-CADH and no GP2


title: AC202


title: ACBQ0440


title: BQ/AC0463


title: LP-151


title: E-CADHERIN low at 9WD, biological rep1


title: #2BQ8106


title: FBS_rep_3

status: Public on Mar 16 2017

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

description: normal rat kidney cells, 10% fetal bovine serum, replicate 3

hyb_protocol: Agilent one-color gene expression hybridization and wash protocol

scan_protocol: Microarrays were scanned at 5 um resolution on an Agilent Technologies G2505C Microarray Scanner. Images were processed using Agilent Feature Extraction software version 10.5.1.1.

data_processing: Control features and poor quality features were removed. Remaining spots were log scaled, and spots for each probe sequence were averaged, then quantile normalized.

organism: Rattus norvegicus

label_protocol: Agilent one-color quick amp labeling protocol

growth_protocol: NRK cells were seeded into 6 well plates at 2x105 cells per well, allowed to attach overnight in 10% FBS

extract_protocol: RNA was isolated using the Qiagen RNeasy mini kit with the use of DNase I

treatment_protocol: NRK cells were cultured in 10% SHAM or AKI serum for 48 hours.

value: Sprague Dawley

tag: Sex

value: male

tag: growth medium

value: 10% fetal bovine serum


title: sham_rep_2

description: normal rat kidney cells, 10% sham serum, replicate 2

source_name: normal rat kidney cells, 10% sham serum

value: 10% sham serum


title: AC-077


title: FBS_rep_2

description: normal rat kidney cells, 10% fetal bovine serum, replicate 2


title: sham_rep_3

description: normal rat kidney cells, 10% sham serum, replicate 3


title: AKI_rep_2

description: normal rat kidney cells, 10% AKI serum, replicate 2

source_name: normal rat kidney cells, 10% AKI serum

value: 10% AKI serum


title: AKI_rep_3

description: normal rat kidney cells, 10% AKI serum, replicate 3


title: SF_rep_3

description: normal rat kidney cells, serum free, replicate 3

source_name: normal rat kidney cells, serum free

value: serum free


title: sham_rep_1

description: normal rat kidney cells, 10% sham serum, replicate 1


title: AKI_rep_1

description: normal rat kidney cells, 10% AKI serum, replicate 1


title: SF_rep_1

description: normal rat kidney cells, serum free, replicate 1


title: SF_rep_2

description: normal rat kidney cells, serum free, replicate 2


title: 10 days mouse embryoid body NT, biological rep2

city: Madrid

first: Carlos

last: Martinez

state: Madrid

address: C/Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

hyb_protocol: The samples were loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Data processing was carried-out using the LIMMA package (Smyth, 2003) of Bioconductor project: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization). Linear model methods were then applied for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic.

source_name: 10 days mouse embryoid body

label_protocol: For each hybridization, 300 ng of Cy3 probes and 300 ng of Cy5 probes of amplified cRNA were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 ul reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer.

growth_protocol: All embryoid bodies were grown for 10 days in suspension in low attachment plates without LIF

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).1 ug of total RNA was amplified via the aRNA MessageAmp II kit (Ambion, 1751)

value: mouse embryoid bodies

tag: genotype/variation

value: Wildtype control

value: day 10

source_name: 10 days mouse embryoid body. Dido3deltaCT+HADidoNT


title: 10 days mouse embryoid body CT, biological rep2

source_name: 10 days mouse embryoid body. Dido3deltaCT+HADido3CT


title: 10 days mouse embryoid body NT, biological rep3


title: FBS_rep_1

description: normal rat kidney cells, 10% fetal bovine serum, replicate 1


title: 10 days mouse embryoid body, biological rep3

value: wildtype control

source_name: 10 days mouse embryoid body. Delta-CT mutant

value: Dido3deltaCT mutant


title: LNCaP oxBis RepB

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

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

scan_protocol: Standard Illumina Protocol

data_processing: Raw IDAT files were processed with minfi R package and background normalized using preprocessIllumina() function to generate methylation β-values which were used for all downstream analyses.

label: Cy5 and Cy3

source_name: LNCaP cells

label_protocol: Standard Illumina Protocol

growth_protocol: Adult Brain Frontal Lobe genomic DNA from a single donor was purchased from Banksia Scientific Company (Bulimba, Australia, cat no D1234035). LNCaP cells were cultured as desribed previously [Song JZ et al, Oncogene 2002, 21:1048-1061].

extract_protocol: Genomic DNA from LNCaP cells was exctracted using QIAamp DNA Mini kit (Qiagen, USA)

treatment_protocol: no treatment

value: oxBis

tag: tissue type

value: LNCaP clone FGC (ATCC® CRL-1740™). Androgen-sensitive human prostate adenocarcinoma cells derived from metastatic site:left supraclavicular lymph node


title: 10 days mouse embryoid body CT, biological rep1


title: 10 days mouse embryoid body, biological rep2


title: LNCaP oxBis RepA


title: mouse embryonic stem cell, wt, biological rep3

hyb_protocol: If the quality control was correct, then 10 µg of fragmented cRNA were hybridized to the mouse MOE 430 2.0 array (Affymetrix, Santa Clara, CA)  Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC.  Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix)

scan_protocol: Microarrays were scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Data analysis of raw intensity signal from scanned images was performed using the affylmaGUI R package.

source_name: mouse embryonic stem cell,wild type

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA. The cRNA preparation (10 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol: All mouse embryonic stem cells were grown in self-renewal conditions in stem cell media supplemented with leukemia inhibitory factor (LIF)

extract_protocol: Total RNA was extracted using the guanidinium isothiocynate method (TRIzol reagent; Invitrogen, Carlsbad, CA) followed by purification using an RNeasy column (Qiagen, Valencia, CA). Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA).

tag: source

value: cell culture

value: embryonic stem cell

value: wild type


title: mouse embryonic stem cell, wt, biological rep1

tag: tissue


title: LNCaP Bis RepB

value: Bis


title: mouse embryonic stem cell, exp, biological rep3

source_name: mouse embryonic stem cell,Truncated C-terminal Dido3deltaCT

value: truncated C-terminal Dido3deltaCT


title: Adult Brain oxBis RepA

source_name: Adult brain cells

value: Adult Brain Frontal Lobe


title: mouse embryonic stem cell, exp, biological rep2


title: 10 days mouse embryoid body NT, biological rep1


title: KPCZ_E_426+TGFb_2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

source_name: isolated tumor cells from KPCZ mice with a epithelial phenotype under TGFβ stimulation

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

growth_protocol: isolated primary tumour cells from tumors of KPC and KPCZ (Zeb1 Knockout)  mice are grown on 6-well plates in DMEM (Gibco, 31966)/ 10%FBS (Gibco, 10500)/ 1%P/S (Gibco, 15140) at 37°C/5% CO2 in a humidified incubator.

extract_protocol: Total RNA was isolated from isolated tumor cells using the RNeasy Plus Mini Kit (Qiagen, 74136)

treatment_protocol: two epithelial KPC cell lines and two KPCZ cell lines were treated wtih 5ng/ml TGFβ

value: ZEB1 knockout

tag: stimulus

value: TGFβ

tag: phenotype

value: epithelial

tag: replicate

value: Replicate 2


title: mouse embryonic stem cell, exp, biological rep1


title: KPCZ_E_346+TGFb_1

value: Replicate 1


title: KPCZ_E_346+TGFb_2


title: 10 days mouse embryoid body, biological rep1

tag: cell type

value: mouse embryoid bodies


title: LNCaP Bis RepA

tag: treatment


title: KPCZ_E_426+TGFb_1


title: HeLa.tet.eGFP+DOX_2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression of HeLa cells transformed with tet and tet-inducible eGFP, after treatment with doxycycline.

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

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

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

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

growth_protocol: The HeLa cell line stably expressing eGFP (HeLa/eGFP) was purchased from Cell Biolabs, Inc. (San Diego, CA) and grown in parallel with wild-type HeLa cells. HeLa.tet and HeLa.tet.eGFP were purchased from GenTarget Inc. (San Diego, CA). Cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium, supplemented with 10% heat-inactivated fetal bovine serum (v/v), 50 U/mL penicillin, 50 μg/mL streptomycin, 2 mM L-glutamine and 0.1 mM MEM nonessential amino acids (NEAA). Cells were maintained in a humidified atmosphere of 5% CO2 at 37°C and cultured in T-75 Falcon tissue culture flasks at an initial density of 1x10^6 cells/flask. The culture medium was replaced every 2 days and passaged when confluence was reached.

extract_protocol: Total RNA was isolated from three independent triplicates using the QIAshredder and RNeasy Midi® Kit (QIAGEN, Valencia, CA) with in-column DNAse treatment (QIAGEN, Valencia, CA).

treatment_protocol: Cultures of HeLa.tet and HeLa.tet.eGFP at 70% confluency were exposed to 1 ug/mL doxycycline for 48 h before collection. Confluent cells were collected for RNA isolation by trypsinization, washed with PBS and stored at -80°C.

value: HeLa


title: HeLa.tet.eGFP+DOX_3


title: HeLa.tet.eGFP+DOX_1


title: Control ( not diff)

source_name: amnion MSCs

value: placental multipotent stromal cells


title: mouse embryonic stem cell, wt, biological rep2


title: Adult Brain Bis RepA


title: KPC_E_661+TGFb_1

source_name: isolated tumor cells from KPC mice with a epithelial phenotype under TGFβ stimulation

value: wildtype


title: KPC_E_661+TGFb_2


title: Adult Brain Bis RepB


title: Adult Brain oxBis RepB

value: oxBis


title: HeLa.tet.eGFP_2

description: Gene expression of HeLa cells transformed with tet and tet-inducible eGFP.


title: HeLa.tet.eGFP_3


title: KPC_E_792+TGFb_2


title: HeLa.tet+DOX_1

description: Gene expression of HeLa cells transformed with tet, after treatment with doxycycline.


title: 10 days mouse embryoid body CT, biological rep3

value: Wildtype control

tag: age

value: day 10


title: HeLa.tet.eGFP_1

description: Gene expression of HeLa cells transformed with tet and tet-inducible eGFP


title: HeLa.tet+DOX_3


title: HeLa.tet_2

description: Gene expression of HeLa cells transformed with tet.


title: HeLa.tet+DOX_2


title: KPC_E_792_1

source_name: isolated tumor cells from KPC mice with a epithelial phenotype


title: KPC-E_792_3

value: Replicate 3


title: KPC_E_661_2


title: KPC_E_792+TGFb_1


title: KPC_E_792_2


title: HeLa.tet_3


title: KPC_E_661_1


title: HeLa.eGFP_3

description: Gene expression of HeLa cells stably expressing eGFP.


title: HeLa.eGFP_2


title: KPC_E_865_2


title: HeLa.tet_1


title: KPC_E_661_3


title: KPCZ_E_454_1

source_name: isolated tumor cells from KPCZ mice with a epithelial phenotype


title: HeLa_3

description: Gene expression of wildtype HeLa cells.

source_name: HeLa


title: KPCZ_E_346_3


title: KPCZ_E_454_2


title: HeLa_2

description: Gene expression of wildtype HeLa cells.


title: HeLa.eGFP_1


title: KPC_E_865_1


title: KPCZ_E_340_1


title: KPCZ_E_346_2


title: HeLa_1

description: Gene expression of wildtype HeLa cells.


title: KPCZ_E_426_3


title: KPCZ_E_346_1


title: KPCZ_E_340_2


title: KPCZ_E_426_1


title: KPCZ_E_426_2


title: KPCZ_E_387_1


title: KPCZ_E_387_2


title: KPCZ_E_398_2


title: KPCZ_E_398_1


title: KPC_M_550_1

source_name: isolated tumor cells from KPC mice with a mesenchmal phenotype

value: mesenchmal


title: D9 genomic DNA cell line

city: London

first: James

middle: M

last: Flanagan

state: London

address: Hammersmith Hospital, Du Cane Rd

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

description: normal blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

source_name: cell line DNA

extract_protocol: DNA samples were extracted fromcell lines using Qiagen QIA Amp DNA mini kit (Qiagen, Crawley, UK) according to standard instructions

value: Female

tag: disease state

value: ovarian cancer

tag: basename

tag: subjectid

tag: group

value: MLH1 plus mock treated


title: KPC_M_550_2


title: C7 genomic DNA cell line

description: normal blood sample

tag: gender

tag: cell line

value: MLH minus mock treated


title: A21 genomic DNA cell line

description: normal blood sample

value: MLH1 minus treated with 5uM Cisplatin


title: B1 genomic DNA cell line

description: normal blood sample

value: MLH1 plus treated with 5uM Cisplatin


title: D16 genomic DNA cell line

description: normal blood sample


title: A2 genomic DNA cell line

description: normal blood sample


title: C5 genomic DNA cell line

description: normal blood sample


title: C14 genomic DNA cell line

description: normal blood sample


title: KPC_M_827_2

value: Replicate 2


title: B2 genomic DNA cell line

description: normal blood sample


title: A6 genomic DNA cell line

description: normal blood sample


title: C2 genomic DNA cell line

description: normal blood sample


title: B22 genomic DNA cell line

description: normal blood sample


title: D15 genomic DNA cell line

description: normal blood sample


title: D24 genomic DNA cell line

description: normal blood sample


title: A24 genomic DNA cell line

description: normal blood sample


title: D13 genomic DNA cell line

description: normal blood sample


title: C16 genomic DNA cell line

description: normal blood sample


title: B21 genomic DNA cell line

description: normal blood sample


title: B15 genomic DNA cell line

description: normal blood sample


title: KPC_M_702_2


title: KPC_M_701_1

value: Replicate 1


title: B17 genomic DNA cell line

description: normal blood sample


title: A23 genomic DNA cell line

description: normal blood sample


title: B9 genomic DNA cell line

description: normal blood sample


title: A25 genomic DNA cell line

description: normal blood sample


title: SAM822643 Uncrushed.Cre-

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

institute: Genentech

description: SAM822643 Crushed.dlkPlus

hyb_protocol: 750 ng of labeled cRNA was fragmented and hybridized to Agilent’s Whole Mouse Genome 4x44Kv2 arrays as described in manufacturer’s hybridization kit, against an equal amount of Cy3-labeled universal mouse reference (Stratagene).

scan_protocol: Following hybridization, microarrays were washed, dried, and scanned on Agilent’s G2505C scanner. Agilent’s Feature Extraction 11.5 software was used to analyze acquired array images.

data_processing: Data were analyzed using the limma package from Bioconductor. ControlType weights were set to 0, spots with background signal more than 50 above the foreground signal were set to the median background intensity, background correction was performed with limma::backgroundCorrect() using the "normexp" method and an offset of 50, limma::normalizeWithinArrays() with the "loess" method,  and finally limma::normalizeBetweenArrays() with the "Aquantile" method. This gives the "test" and "reference" normalized probe intensities. Finally, for each probe an "expression ratio" was calculated, the ratio of the normalized signals in the test and reference channels.

source_name: RNA from whole retinas 3 days after optic nerve crush

label_protocol: The method for preparation of Cy-dye labeled cRNA and array hybridization was provided by Agilent. Briefly, 1 μg total RNA was converted to double-stranded cDNA and then to Cy5-labeled cRNA using Quick Amp Labeling Kit (Agilent). The labeled cRNA was purified using RNeasy mini kit (Qiagen). cRNA yield and Cy5 incorporation was determined using ND-1000 spectrophotometer.

extract_protocol: RNA was extracted from whole retina as described in Watkins et al. PNAS. (2013). RNA sample quantity and quality were determined using an ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent Technologies), respectively.

treatment_protocol: To investigate the role of DLK after optic nerve crush, we generated mice with a tamoxifen-inducible Cre recombinase-estrogen receptor (Cre-ERT) transgene driven by the chicken beta-actin-CMV hybrid (CAG) promoter, resulting in high levels of Cre-ERT in many tissues, including retina. CAG Cre-ERT:DLKlox/lox (referred to as DLKlox:Crepos) mice survive to adulthood with no evidence of the developmental abnormalities seen in DLK-null animals (8, 18). Dosing of DLKlox:Crepos mice at 10-12 wk of age with tamoxifen (Fig. S2A) results in elimination of the majority of DLK expression in retina (Fig. 1 C and L), with the small amount of remaining DLK protein varying slightly from animal to animal (Fig. 1C and Fig. S2B). No differences in health or behavior were observed between tamoxifen-treated DLKlox:Crepos mice and their tamoxifen-treated DLKlox:Creneg control littermates.

value: retina

tag: samid

value: Optic nerve uncrushed; Cre-

source_name: universal mouse reference (Stratagene)

label_protocol: Method for Cy-dye labeled cRNA preparation was provided by Agilent.

extract_protocol: By vendor


title: KPC_M_827_1

tag: genotype/variation


title: D18 genomic DNA cell line

description: normal blood sample


title: B4 genomic DNA cell line

description: normal blood sample


title: SAM822648 Uncrushed.Cre+

description: SAM822648 Uncrushed.dlkMinus

value: Optic nerve uncrushed; Cre+


title: C25 genomic DNA cell line

description: normal blood sample


title: D21 genomic DNA cell line

description: normal blood sample


title: SAM822635 Uncrushed.Cre-

description: SAM822635 Uncrushed.dlkPlus


title: C26 genomic DNA cell line

description: normal blood sample


title: SAM822651 Crushed.Cre+

description: SAM822651 Crushed.dlkMinus

value: Optic nerve crushed; Cre+


title: D25 genomic DNA cell line

description: normal blood sample


title: D6 genomic DNA cell line

description: normal blood sample


title: SAM822639 Crushed.Cre-

description: SAM822639 Crushed.dlkPlus

value: Optic nerve crushed; Cre-


title: A18 genomic DNA cell line

description: normal blood sample


title: SAM822649 Crushed.Cre+

description: SAM822649 Crushed.dlkMinus


title: SAM822650 Crushed.Cre+

description: SAM822650 Crushed.dlkMinus


title: SAM822637 Uncrushed.Cre-

description: SAM822637 Uncrushed.dlkPlus


title: C9 genomic DNA cell line

description: normal blood sample


title: SAM822653 Crushed.Cre+

description: SAM822653 Crushed.dlkMinus


title: SAM822634 Uncrushed.Cre-

description: SAM822634 Uncrushed.dlkPlus


title: SAM822645 Uncrushed.Cre+

description: SAM822645 Uncrushed.dlkMinus


title: SAM822640 Crushed.Cre-

description: SAM822640 Crushed.dlkPlus


title: C13 genomic DNA cell line

description: normal blood sample


title: SAM822642 Crushed.Cre-

description: SAM822642 Crushed.dlkPlus


title: B24 genomic DNA cell line

description: normal blood sample


title: B16 genomic DNA cell line

description: normal blood sample


title: SHX 567

city: Shanghai

first: Lingyan

last: Zhu

address: 2901 Caolang Road, Jin Shan District

country: China

institute: Shanghai Public Health Clinical Center, Fudan University

description:
SAMPLE 23
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.

data_processing: SDS software (Applied Biosystems) was used to collect data. Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems).

label: FAM

source_name: whole peripheral blood

label_protocol: 1-350 ng total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.

extract_protocol: PAXgene Blood miRNA Kit (QIAGEN, Hilden, Germany) was used for extraction and purification total RNA, including miRNA, from whole blood stabilized in PAXgene Blood RNA Tubes (PreAnalytix, BD, UK) per the manufacturer's protocol. RNA was eluted in 80 ul nuclease-free water.

tag: cd4+ t cell count (cells/µl)

tag: viral load (copies/ml)

value: female


title: SHX 566

description:
SAMPLE 22
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.

value: male


title: SAM822646 Uncrushed.Cre+

description: SAM822646 Uncrushed.dlkMinus

tag: tissue


title: D22 genomic DNA cell line

description: normal blood sample


title: SAM822636 Uncrushed.Cre-

description: SAM822636 Uncrushed.dlkPlus


title: SAM822647 Uncrushed.Cre+

description: SAM822647 Uncrushed.dlkMinus


title: SHX 564

description:
SAMPLE 21
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: A8 genomic DNA cell line

description: normal blood sample


title: B12 genomic DNA cell line

description: normal blood sample


title: SHX 558

description:
SAMPLE 18
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: A12 genomic DNA cell line

description: normal blood sample


title: D4 genomic DNA cell line

description: normal blood sample


title: SHX 553

description:
SAMPLE 15
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 556

description:
SAMPLE 17
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 554

description:
SAMPLE 16
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 552

description:
SAMPLE 14
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 551

description:
SAMPLE 13
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.

value: LDL


title: A7 genomic DNA cell line

description: normal blood sample


title: SHX 559

description:
SAMPLE 19
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: C24 genomic DNA cell line

description: normal blood sample


title: A11 genomic DNA cell line

description: normal blood sample


title: SHX 545

description:
SAMPLE 12
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 561

description:
SAMPLE 20
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-12 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: C17 genomic DNA cell line

description: normal blood sample


title: SHX 518

description:
SAMPLE 9
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-9 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 544

description:
SAMPLE 11
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-11 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 519

description:
SAMPLE 10
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-10 B’ with close genetic distances.ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 513

description:
SAMPLE 7
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-7 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 514

description:
SAMPLE 8
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-8 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 506

description:
SAMPLE 5
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-5 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: ExVivo liver_28

city: Toulouse

first: Matteo

last: Serino

address: Baylac place

institute: INSERM UMR1220-IRSD

description: Mice transplanted with obese microbiota

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library.

source_name: Mice transplanted with obese microbiota

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked with the Nanodrop ND2000 spectrophotometer (Thermo Scientific).

growth_protocol: 6-wk-old C57Bl/6 male mice were fed a normal chow (NC) for 4 weeks

extract_protocol: liver total RNAs has been prepared by the miRNeasy QIAGEN kit

treatment_protocol: Mice have been transplanted with the vehicle (reduced PBS), or lean or obese gut microbiota.

tag: background strain

value: liver

value: 10 weeks


title: SAM822652 Crushed.Cre+

description: SAM822652 Crushed.dlkMinus


title: ExVivo liver_29

description: Mice transplanted with obese microbiota


title: ExVivo liver_30

description: Mice transplanted with obese microbiota


title: ExVivo liver_26

description: Mice transplanted with obese microbiota


title: ExVivo liver_25

description: Mice transplanted with obese microbiota


title: ExVivo liver_17

description: Mice transplanted with lean microbiota

source_name: Mice transplanted with lean microbiota


title: SHX 503

description:
SAMPLE 3
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-3 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 504

description:
SAMPLE 4
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-4 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 502

description:
SAMPLE 2
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-2 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 501

description:
SAMPLE 1
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-1 B’ with close genetic distances. The participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: SHX 507

description:
SAMPLE 6
The participants of this study were former blood donors donated their plasma between 1995 and 1996 in Yuncheng city of China and were infected with HIV from common-source of contaminated blood. They were infected by HIV-6 B’ with close genetic distances..ଠe participants were screened and recruited at the beginning of 2009 from previously established cohort. The inclusion criteria were subjects with no symptoms of AIDS or related opportunity illnesses and naïve to ART.


title: P-4507993

city: Daejeon

first: Jei

last: Kim

address: 282 Moonhwa-ro, Joong-gu

country: South Korea

institute: Chungnam National University Hospital

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using  ExpressionSuite for QuantStudio™ 6 & 7 Flex Real Time PCR System
Matrix normalized worksheet reports normalized signal (against endogenous control genes, miR-197 and miR-374).

source_name: Serum

label_protocol: RT: Megaplex™ RT Human Pool A [part no. 4399966] for Panel A and Pool B [part no. 4399968] for Panel B, Applied Biosystems and TaqMan® MicroRNA Reverse Transcription Kit, Part No. 4366596 ; qPCR: TaqMan® Array Human microRNA Cards A and B, Part No. 4444913, Applied Biosystems

extract_protocol: TaqMan® miRNA ABC Purification Kit-Human-Panel A/B (part nos. 4473087 and 4473088, Applied Biosystems, Foster City, CA, USA)

value: Male

tag: disease

value: Atherosclerosis

value: Serum


title: P-4509250


title: P-4509748


title: P-4510020

value: Female


title: P-4457598


title: P-4164417


title: P-4060118


title: N-4507966

value: No-atherosclerosis


title: N-4605901


title: N-4507950


title: ExVivo liver_16

description: Mice transplanted with lean microbiota


title: SAM822644 Uncrushed.Cre+

description: SAM822644 Uncrushed.dlkMinus


title: ExVivo liver_13

description: Mice transplanted with lean microbiota


title: N-4507631


title: ExVivo liver_4

description: Ctrl mice not transplanted

source_name: Ctrl mice not transplanted


title: ExVivo liver_2

description: Ctrl mice not transplanted


title: ExVivo liver_15

description: Mice transplanted with lean microbiota


title: ExVivo liver_1

description: Ctrl mice not transplanted


title: ExVivo liver_14

description: Mice transplanted with lean microbiota


title: ExVivo liver_6

description: Ctrl mice not transplanted


title: ExVivo liver_5

description: Ctrl mice not transplanted


title: N-4100525


title: N-4019649


title: N-4504482


title: ExVivo liver_3

description: Ctrl mice not transplanted


title: N-4507906


title: 220 vs 220.2

city: Malaga

first: Eduardo

last: García-Fuentes

state: Malaga

address: Plaza del Hospital Civil s/n

institute: Instituto de Investigación Biomédica de Málaga (IBIMA)/Hospital Regional Universitario, Málaga, Spain.

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: Subcutaneous adipose tissue before bariatric surgery

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

extract_protocol:
Subcutaneous adipose tissue was immediately frozen at N2 after its removal from morbidly obese women.
Total RNA extracted using RNeasy Lipid Tissue Mini Kit (QIAGEN) following manufacturer's instructions

tag: type of patient

value: morbid obesity

source_name: Subcutaneous adipose tissue after bariatric surgery


title: 94.2 vs 94


title: 214 vs 214.2


title: 223 vs 223.2


title: 219 vs 219.2


title: 86.2 vs 86


title: 84.2 vs 84


title: 198.2 vs 198


title: NHK_rep1

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using Illumina's BeadStudio Data Analysis Software.

source_name: normal human keratinocytes

growth_protocol: Primary keratinocytes were isolated from skin of the patients and from a normal individual (NHK), and cultivated in serum-free keratinocyte growth medium supplemented with 2 ng/ml EGF and bovine pituitary extract (KGM, Invitrogen) using standard methods. Cell lines were derived from the primary keratinocytes by immortalization with the HPV18-E6E7 genes as described before, and designated as control (Co) and  A3- cells, respectively. The study was approved by the ethics committee of the University of Freiburg and was conducted in accordance to the Helsinki protocols.

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit from subconfluent cells in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Skin

tag: cell type

value: primary keratinocytes from healthy human donor

tag: transfected with

tag: mutation

tag: array id


title: NHK_rep2