title: GREY_BI_14997_COMSTOCK_609


title: GREY_BI_0748_COMSTOCK_748

status: Public on Nov 12 2013

type: genomic

city: Cambridge

first: Elinor

last: Karlsson

state: MA

address: 7 Cambridge Center

country: USA

institute: Broad Institute

description: Genomic DNA extracted from blood was genotyped using the Illumina CanineHD Genotyping BeadChip

hyb_protocol: Standard Illumina protocol for Infinium HD Beadchip

scan_protocol: Illumina iScan with Dual-Scanner Autoloader

data_processing: Illumina GenomeStudio Version 2011.1 with Genotyping Module 1.9.4

label: biotin

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: blood

extract_protocol: Genomic DNA was isolated from whole blood (QIAamp DNA Midi kit).

tag: breed

value: greyhound

tag: gender

value: female

tag: tissue

value: blood

tag: disease state

value: osteosarcoma


title: GREY_BI_2933_BROAD_2933

label_protocol: Standard Illumina protocol for Infinium HD Beadchip

value: male


title: GREY_BI_14236_BROAD_14236


title: GREY_BI_14569_COMSTOCK_701


title: CellLine_untreated_SCRNA_1

type: RNA

city: Riverside

first: Eugene

middle: L

last: Bolotin

state: CA

address: 900 university ave

department: Cell Biology and Neuroscience

institute: UC Riverside

hyb_protocol: cRNA was randomized and hybridized in a single batch to Illumina HumanHT-12_V4 expression beadchips (Illumina, San Diego, CA) at Channing Laboratory (Division of Network Medicine, Brigham and Women's Hospital, Boston MA) according to the manufacturer’s protocols.

scan_protocol: Manufacturer standard.

data_processing: R lumi package was used for analysis,  log2 values were quantile normalized

molecule: total RNA

organism: Homo sapiens

label_protocol: All RNAs were converted to biotin-labeled cRNA using the Illumina TotalPrep-96 RNA amplification kit (Applied Biosystems, Foster City, CA) in a single batch.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from 10ml of blood using IsoPrep (Matrix Technologies) and transformed by EBV. Viable cells remaining after six weeks were considered to be LCLs. PBMCs were isolated from the remaining 50ml of blood using Lymphoprep (VWR), and B-lymphocytes were specifically isolated from PBMCs using the B-cell Negative Isolation kit (Invitrogen) according to the manufacturer's protocol. Aliquots of B-cells were incubated with FITC-conjugated CD19 fluorescent antibodies and the proportion of CD19 positive cells (B-cells only) was determined by FACS analysis (BD FACS Calibur) of 10,000 gated events. Only preparations with >90% B-lymphocyte purity were used for further analysis.

extract_protocol: RNA was isolated from all samples and stored at -80°C.

treatment_protocol: B-cells and LCLs were incubated with either 2 µM activated simvastatin or a sham buffer for 24 hours in RPMI media supplemented with 500 U/ml penicillin/streptomycin, 10% FBS and 2 nmol/L GlutaMAX, and all cultures were maintained at 37°C with 5% CO2.  The B-cells were statin or sham exposed at the time of isolation  while LCLs were frozen, thawed and exposed as a single batch. Simvastatin, obtained as a gift from Merck, was activated.

tag: tissue source

value: Peripheral blood mononuclear cells

tag: cell subtype

value: lymphoblastoid cell lines (LCLs)

tag: treated with

value: sham buffer for 24 h


title: FreshBs_Simvastatin_S_289

value: native B cells

value: 2 µM activated simvastatin for 24 h


title: FreshBs_Simvastatin_S_201


title: GREY_BI_0720_COMSTOCK_720


title: CellLine_Simvastatin_S_289


title: FreshBs_untreated_S_201


title: FreshBs_untreated_S_342


title: GREY_BI_0757_COMSTOCK_757


title: GREY_BI_15015_COMSTOCK_565

value: osteosarcoma-free


title: GREY_BI_0795_COMSTOCK_795


title: CellLine_Simvastatin_S_068


title: GREY_BI_0763_COMSTOCK_763


title: GREY_BI_0794_COMSTOCK_794


title: GREY_BI_0766_COMSTOCK_766


title: GREY_BI_0790_COMSTOCK_790


title: GREY_BI_0765_COMSTOCK_765


title: GREY_BI_0750_COMSTOCK_750


title: GREY_BI_0788_COMSTOCK_788


title: GREY_BI_019_COMSTOCK_19


title: GREY_BI_021_COMSTOCK_21


title: GREY_BI_6559_COMSTOCK_20


title: GREY_BI_0777_COMSTOCK_777


title: GREY_BI_Label_726_LABEL_726


title: GREY_BI_0785_COMSTOCK_785


title: GREY_BI_0746_COMSTOCK_746


title: GREY_BI_0688_COMSTOCK_688


title: GREY_BI_0775_COMSTOCK_775


title: GREY_BI_0744_COMSTOCK_744


title: GREY_BI_0687_COMSTOCK_687


title: GREY_BI_29688_BROAD_29688


title: GREY_BI_0784_COMSTOCK_784


title: GREY_BI_014_COMSTOCK_14


title: GREY_BI_0783_COMSTOCK_783


title: GREY_BI_015_COMSTOCK_15


title: GREY_BI_0690_COMSTOCK_690


title: GREY_BI_0731_COMSTOCK_731


title: GREY_BI_6226_COMSTOCK_115


title: GREY_BI_33638_BROAD_33638


title: BM miRNA KO

city: Chiba

first: Satoru

last: Miyagi

state: Chiba

department: Graduate school of Medicine

country: Japan

institute: Chiba university

description: miRNA expression in KO BM-derived KSL

hyb_protocol: The hybridization and washing were performed using a  miRNA Complete Labeling and Hyb Kit  (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: A n Agilent C Scanner (Agilent ) was used for array scanning.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent).

organism: Mus musculus

source_name: BM, KSL, KO, replicate 1

label_protocol: A total of 100 ng of total RNA were labeled with Cyanine 3 using a miRNA Complete Labeling and Hyb Kit (Agilent).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using  Qiagen miRNeasy Mini kit (QIAGEN).

treatment_protocol: HSCs (c-Kit+ Sca1+ Lineage- )  are sorted from  adult bone marrow and are subjected into RNA preparation.

tag: genetic background

tag: cell fraction

value: c-Kit+ Sca1+ Lineage-

value: Bone marrow

tag: genotype

value: CreERT, Tif1bf/f


title: BM miRNA WT

description: miRNA expression in WT BM-derived KSL

source_name: BM, KSL, WT, replicate 1

value: CreERT, Tif1bw/w


title: GREY_BI_36522_BROAD_36522


title: RO+ CXCR5hi D1

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
5826629023_K
RO+ CXCR5hi

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).

data_processing: Analysis of the iScan output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: RO+ CXCR5hi

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Gene expression was analyzed directly ex vivo

extract_protocol: totalRNA using Qiagen RNeasy Micro Kit  by the Genomics core at Collaborative Genomics Center (CGC) at http://www.vgtifl.org

tag: donor id

value: tonsil

tag: cell type

value: CD4+ T cell

tag: sorted population

value: RO+ CXCR5hi


title: RO+ CXCR5- D1

description:
5826629023_L
RO+ CXCR5-

source_name: RO+ CXCR5-

value: RO+ CXCR5-


title: GREY_BI_043_COMSTOCK_43

value: greyhound

value: blood


title: RO+ CXCR5hi D6.2

description:
5826629023_I
RO+ CXCR5hi


title: RO+ CXCR5- D5

description:
5826629023_H
RO+ CXCR5-


title: RO+ CXCR5hi D5

description:
5826629023_G
RO+ CXCR5hi


title: RO+ CXCR5hi D3

description:
5826629023_E
RO+ CXCR5hi


title: RO+ CXCR5hi D4

description:
5826629023_F
RO+ CXCR5hi


title: RO+ CXCR5- D2

description:
5826629032_L
RO+ CXCR5-


title: GREY_BI_0691_COMSTOCK_691

value: female

value: osteosarcoma


title: RO- CXCR5- D6.2

description:
5826611071_J
RO- CXCR5- Reference

source_name: RO- CXCR5-

value: RO- CXCR5-


title: GREY_BI_0682_COMSTOCK_682


title: GREY_BI_0680_COMSTOCK_680

value: male


title: GREY_BI_0796_COMSTOCK_796


title: RO+ CXCR5- D6

description:
5826629023_J
RO+ CXCR5-


title: GREY_BI_0728_COMSTOCK_728


title: RO+ CXCR5int D1

description:
5826611071_G
RO+ CXCR5int

source_name: RO+ CXCR5int

value: RO+ CXCR5int


title: Case 14.2

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: ID14.2US80203134_251469382252_S01_CGH_1010_Sep10

hyb_protocol: The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.

scan_protocol: Scanned on an Agilent G2565B scanner.

data_processing: Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and default settings of Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).  All alterations were analyzed by visual inspection of two different observers.

label_protocol: As per manufacturer (Agilent)

extract_protocol: Genomic DNA was extracted from 20 Follicular lymphoma samples using the phenol-chloroform extraction method according to previously published protocols with minor modification. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis. All extracted DNAs had at least a PCR control gene band of 200 bp.

value: Follicular lymphoma

source_name: Normal genomic DNA

tag: source type

value: DNA from a pool of 10 healthy donors (non-commercial)


title: GREY_BI_0678_COMSTOCK_678


title: RO- CXCR5- D2

description:
5826611071_I
RO- CXCR5- Reference


title: RO- CXCR5- D6

description:
5826611071_F
RO- CXCR5- Reference


title: GREY_BI_0773_COMSTOCK_773


title: RO- CXCR5- D5

description:
5826611071_D
RO- CXCR5- Reference


title: GREY_BI_0769_COMSTOCK_769


title: RO+ CXCR5int D6

description:
5826611071_E
RO+ CXCR5int


title: RO+ CXCR5int D5

description:
5826611071_C
RO+ CXCR5int


title: RO- CXCR5- D4

description:
5826611071_B
RO- CXCR5- Reference


title: GREY_BI_36610_BROAD_36610


title: GREY_BI_011_COMSTOCK_11


title: Case 13.2

description: ID13.2_US80203134_251469379334_S01_CGH-v4_95_Feb07


title: Case 12.1

description: ID12.1_US80203134_251469379338_S01_CGH-v4_95_Feb07

source_name: tumor_FL_in situ

value: Follicular lymphoma in situ


title: Case 13.1

description: ID13.1_US80203134_251469379339_S01_CGH-v4_95_Feb07


title: RO+ CXCR5int D4

description:
5826611071_A
RO+ CXCR5int


title: Case 10.2


title: Case 14.1

description: ID14.1_US80203134_251469382253_S01_CGH_1010_Sep10


title: Case 9.2


title: Case 11.1

description: ID11.1_US80203134_251469382266_S01_CGH_107_Sep09


title: Case 8

source_name: tumor_FL_partial infiltration

value: Follicular lymphoma partial infiltration


title: Case 12.2

description: ID12.2_US80203134_251469379319_S01_CGH-v4_95_Feb07


title: Case 11.2

description: ID11.2_US80203134_251469379316_S01_CGH-v4_95_Feb07


title: Case 10.1

description: ID10.1_US80203134_251469379317_S01_CGH-v4_95_Feb07


title: RO+ CXCR5int D2

description:
5826611071_H
RO+ CXCR5int


title: Case 9.1


title: staET7.3_con_2

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the Affymetrix GeneChip Command Console Software (AGCC).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm and the summarization method robust_weighted_average

source_name: Ewing's sarcoma cell line cell line grown under adherent culture condition, replica 2

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 500ng total RNA was processed to generate a biotinylated hybridization target using the Affymetrix GeneChip 3’ IVT Express kit and the Affymetrix GeneChip Hybridization, Wash, and Stain kit . All procedures were performed according to the manufacturer's protocols.

growth_protocol: adherent monolayers, maintained in RPMI 1640 (Invitrogen, Germany) supplemented with 10% fetal calf serum (PAA, Pasching, Austria) and 0,01% Penicillin/Streptomycin (PAA, Pasching, Austria). Cells were allowed to recover for 18 h before treatment.

extract_protocol: RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.

treatment_protocol: For treatments, cells were placed in a Thermo-CO2 incubator and grown in a humidified atmosphere containing 5% CO2 (Thermo Electron Corp., Asheville, NC) and treatment was applied for 24h.

value: Ewing's sarcoma cell line STA-ET-7.3, EWS-FLI1 fusion type 2

tag: p53 status

value: mutant


title: staET7.3_apr_2

description: Ewing's sarcoma cell line cell line grown under adherent culture condition


title: staET7.3_con_1

source_name: Ewing's sarcoma cell line cell line grown under adherent culture condition, replica 1


title: Case 7


title: RO+ CXCR5- D3

description:
5823049014_I
RO+ CXCR5-

value: tonsil


title: Case 6


title: RO- CXCR5- D1

description:
5823049022_E
RO- CXCR5- Reference

value: CD4+ T cell


title: staET7.3_apr_1


title: Case 4


title: RO+ CXCR5int D3

description:
5823049022_L
RO+ CXCR5int


title: Case 3


title: staET7.2_con_1

value: Ewing's sarcoma cell line STA-ET-7.2, EWS-FLI1 fusion type 2

value: mutated


title: Case 2


title: Case 5


title: Case 1


title: RO+ CXCR5hi D6

description:
5823049014_B
RO+ CXCR5hi

value: RO+ CXCR5hi


title: staET7.2_apr_2


title: CXCR5+ PD1+ CXCR3- D4

description:
6235783031_K
CXCR5+ PD1+ CXCR3-

data_processing: Analysis of the iScan probe level output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: CXCR5+ PD1+ CXCR3-

value: blood

value: CD4 T-cells

value: CXCR5+ PD1+ CXCR3-


title: staET7.1_apr_2

value: Ewing's sarcoma cell line STA-ET-7.1, EWS-FLI1 fusion type 2


title: staET7.1_apr_1


title: child-189

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from peripheral blood

hyb_protocol: Hybridization protocol following fragmentation. cRNA was hybridized on to the Affymetrix U133 2.0 Plus Human Array

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The normalization was a quantile normalization per the canonical Robust Multi-Chip method. Each sample was used as a stand alone expression value, but those values were normalized to provide a common distribution using the quantile normalization (at the probe level) and summarized using the median polish algorithm (to produce a single log2 transformed value per probe set).

source_name: peripheral blood sample

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

growth_protocol: Peripheral blood samples were collected in PAXgene blood RNA tubes (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was isolated using the Qiagen PAXgene Blood RNA Kit

tag: age (yr)

value: M

tag: disease status

value: non-asthmatic


title: staET7.1_con_1


title: child-195

value: asthmatic


title: child-194


title: CXCR5+ PD1- CXCR3+ D1

description:
6235783031_J
CXCR5+ PD1- CXCR3+

source_name: CXCR5+ PD1- CXCR3+

value: CXCR5+ PD1- CXCR3+


title: CXCR5+ PD1- CXCR3+ D4

description:
6235783031_H
CXCR5+ PD1- CXCR3+


title: child-191


title: child-188


title: child-187


title: CXCR5+ PD1+ CXCR3+ D3

description:
6235783031_F
CXCR5+ PD1+ CXCR3+

source_name: CXCR5+ PD1+ CXCR3+

value: CXCR5+ PD1+ CXCR3+


title: child-197


title: CXCR5- D4

description:
6235783031_E
CXCR5- Reference


title: child-196

value: F


title: child-186


title: CXCR5+ PD1- CXCR3+ D3

description:
6235783031_G
CXCR5+ PD1- CXCR3+


title: child-192


title: child-193


title: CXCR5+ PD1- CXCR3+ D2

description:
6235783031_L
CXCR5+ PD1- CXCR3+


title: CXCR5- D5

description:
6235783031_D
CXCR5- Reference


title: RO+ CXCR5- D7

description:
5823049014_J
RO+ CXCR5-

value: RO+ CXCR5-


title: CXCR5+ PD1- CXCR3- D1

description:
6235783031_I
CXCR5+ PD1- CXCR3-

source_name: CXCR5+ PD1- CXCR3-

value: CXCR5+ PD1- CXCR3-


title: child-179


title: child-182


title: staET7.1_con_2


title: CXCR5+ PD1- CXCR3- D4

description:
6235783031_A
CXCR5+ PD1- CXCR3-


title: child-178


title: CXCR5+ PD1+ CXCR3- D5

description:
6235783031_C
CXCR5+ PD1+ CXCR3-


title: CXCR5- D3

description:
6235783030_I
CXCR5- Reference


title: CXCR5+ PD1+ CXCR3- D2

description:
6235783030_K
CXCR5+ PD1+ CXCR3-


title: child-170


title: child-175


title: child-174


title: CXCR5+ PD1- CXCR3- D2

description:
6235783030_J
CXCR5+ PD1- CXCR3-


title: child-171


title: child-168


title: CXCR5+ PD1+ CXCR3+ D5

description:
6235783031_B
CXCR5+ PD1+ CXCR3+


title: child-169


title: child-166


title: child-176


title: child-160


title: child-164


title: child-159


title: child-163


title: CXCR5+ PD1- CXCR3+ D5

description:
6235783030_H
CXCR5+ PD1- CXCR3+


title: CXCR5- D1

description:
6235783030_G
CXCR5- Reference


title: staET7.2_apr_1


title: child-158


title: CXCR5+ PD1+ CXCR3+ D6

description:
6235783030_F
CXCR5+ PD1+ CXCR3+


title: child-173


title: child-157


title: CXCR5+ PD1+ CXCR3+ D2

description:
6235783030_E
CXCR5+ PD1+ CXCR3+


title: child-150


title: child-147


title: CXCR5- D2

description:
6235783030_D
CXCR5-  Reference


title: child-140


title: child-144


title: child-135


title: CXCR5+ PD1+ CXCR3- D1

description:
6235783030_C
CXCR5+ PD1+ CXCR3-


title: child-136


title: child-134


title: CXCR5+ PD1- CXCR3- D6

description:
6235783030_B
CXCR5+ PD1- CXCR3-


title: child-137


title: child-142


title: staET7.2_con_2


title: CXCR5+ PD1+ CXCR3+ D1

description:
6235783030_A
CXCR5+ PD1+ CXCR3+


title: TWIST2_KD-fibroblast-lot3

city: Yokohama

first: Yasuhiro

last: Tomaru

state: Kanagawa

address: 1-7-22 Suehicho

department: Omics Science Center

institute: RIKEN

description:
Replicate3
7509301138_I

hyb_protocol: Standard Illumina hybridyzation protocol

scan_protocol: BeadArray Reader

data_processing: Genomestudio V2011.1

source_name: Fibroblast

label_protocol: Biotinylated cRNA were prepared with TotalPrep™ RNA Amplification Kit for Illumina arrays

growth_protocol: Culturecondition of human deraml fibroblast was minimum essential medium (MEM-α) supplemented with 10% fetal bovine serum (FBS), 10ml of L-Glutamine and 0.5 ul of antibiotics (Takara Inc).

extract_protocol: Qiagen Rneasy

treatment_protocol: siRNA transfection; final 50nM of siRNA was transfected to fibroblast with lipofectamin RNAiMAX and OptiMEM according to manufacturer instruction. Medium was changed 48hr after transfection.

value: Fibroblast

tag: treatment

value: 72hr after TWIST2-siRNA transfection


title: child-128

tag: gender


title: child-141


title: child-122


title: child-133


title: child-131


title: child-125


title: child-124


title: child-119


title: child-121


title: child-123


title: TWIST2_KD-fibroblast-lot2

description:
Replicate2
7509301138_H


title: child-120


title: child-112


title: TBX3_KD-fibroblast-lot1

description:
Replicate1
7509301138_D

value: 72hr after TBX3-siRNA transfection


title: child-109


title: child-114


title: child-110


title: child-117


title: PRRX1_KD-fibroblast-lot2

description:
Replicate2
7509301129_K

value: 72hr after PRRX1-siRNA transfection


title: child-113


title: child-111


title: child-102


title: TBX3_KD-fibroblast-lot3

description:
Replicate3
7509301138_F


title: child-98


title: TBX3_KD-fibroblast-lot2

description:
Replicate2
7509301138_E


title: OSR1_KD-fibroblast-lot3

description:
Replicate3
7509301138_C

value: 72hr after OSR1-siRNA transfection


title: PRRX1_KD-fibroblast-lot1

description:
Replicate1
7509301129_J


title: TWIST2_KD-fibroblast-lot1

description:
Replicate1
7509301138_G


title: child-99


title: OSR1_KD-fibroblast-lot2

description:
Replicate2
7509301138_B


title: CXCR5+ PD1- CXCR3- D3

description:
6235783030_L
CXCR5+ PD1- CXCR3-

tag: tissue

value: blood


title: child-97


title: PRRX1_KD-fibroblast-lot3

description:
Replicate3
7509301129_L


title: child-96


title: child-93


title: child-172


title: child-95


title: child-94


title: child-103


title: child-92


title: child-86


title: child-89


title: child-87


title: OSR1_KD-fibroblast-lot1

description:
Replicate1
7509301138_A


title: child-88


title: child-77


title: HOXC4_KD-fibroblast-lot2

description:
Replicate2
7509301129_E

value: 72hr after HOXC4-siRNA transfection


title: child-79


title: child-76


title: child-74


title: FOXD1_KD-fibroblast-lot2

description:
Replicate2
7509301129_B

value: 72hr after FOXD1-siRNA transfection


title: child-83


title: child-84


title: child-85


title: child-75


title: child-80


title: LHX9_KD-fibroblast-lot1

description:
Replicate1
7509301129_G

value: 72hr after LHX9-siRNA transfection


title: HOXC4_KD-fibroblast-lot3

description:
Replicate3
7509301129_F


title: LHX9_KD-fibroblast-lot3

description:
Replicate3
7509301129_I


title: child-81

value: M


title: HOXC4_KD-fibroblast-lot1

description:
Replicate1
7509301129_D


title: child-73

value: non-asthmatic


title: LHX9_KD-fibroblast-lot2

description:
Replicate2
7509301129_H


title: FOXD1_KD-fibroblast-lot3

description:
Replicate3
7509301129_C


title: FOXD1_KD-fibroblast-lot1

description:
Replicate1
7509301129_A


title: child-71

value: asthmatic


title: child-82


title: child-70


title: NC-fibroblast-lot3

description:
Replicate3
7509301138_L

value: 72hr after NCsiRNA transfection


title: child-68


title: NC-fibroblast-lot1

description:
Replicate1
7509301138_J


title: child-67


title: child-69


title: child-72


title: NC-fibroblast-lot2

description:
Replicate2
7509301138_K


title: Fibroblast-4mixKDiADP-2week-lot3

description:
Replicate3
5713317020_G

growth_protocol: Culture condition and adipogenic condition of MSC and preadipocyte were archieved according to Lonza recommended protocol. Culturecondition of human deraml fibroblast was minimum essential medium (MEM-α) supplemented with 10% fetal bovine serum (FBS), 10ml of L-Glutamine and 0.5 ul of antibiotics (Takara Inc).

treatment_protocol: siRNA transfection; final 50nM of siRNA was transfected to fibroblast with lipofectamin RNAiMAX and OptiMEM according to manufacturer instruction. Medium was changed 48hr after transfection. Then adipogenic induction was started 24hr after medium change.

value: follow 2week adipogenic induction with 72hr after 4mix-siRNA transfection


title: child-63


title: child-64


title: child-49

value: F


title: child-51


title: child-53


title: child-58


title: child-52


title: Fibroblast-4mixKDiADP-2week-lot2

description:
Replicate2
5713317020_D


title: child-59


title: child-60


title: child-50


title: child-46


title: child-45


title: Fibroblast-NCiADP-2week-lot2

description:
Replicate2
5713317020_F

value: follow 2week adipogenic induction with 72hr after NC-siRNA transfection


title: Fibroblast-NCiADP-2week-lot1

description:
Replicate1
5713317020_C


title: Fibroblast-NCiADP-2week-lot3

description:
Replicate3
5713317020_I


title: Fibroblast-4mixKDiADP-2week-lot1

description:
Replicate1
5713317020_A


title: Fibroblast-4mixsiRNA-10day-lot3

description:
Replicate3
5713317037_C

value: 10days after 4mix-siRNA transfection


title: child-57


title: child-42


title: Fibroblast-4mixsiRNA-10day-lot2

description:
Replicate2
5713317037_B

value: Fibroblast


title: child-38


title: child-48


title: Fibroblast-4mixsiRNA-10day-lot1

description:
Replicate1
5713317037_A


title: child-35


title: Fibroblast-NCsiRNA-10day-lot3

description:
Replicate3
5713317037_F

value: 10days after NCsiRNA transfection


title: child-41


title: child-29


title: child-28


title: child-23


title: Fibroblast-NCsiRNA-10day-lot1

description:
Replicate1
5713317037_D


title: child-36


title: child-26


title: child-24


title: child-27


title: child-37


title: Fibroblast-NCsiRNA-10day-lot2

description:
Replicate2
5713317037_E


title: Fibroblast-4mixsiRNA-72hr-lot3

description:
Replicate3
5713317097_I

value: 72hr after 4mix-siRNA transfection


title: child-30


title: child-22


title: child-40


title: child-20


title: Fibroblast-4mixsiRNA-72hr-lot2

description:
Replicate2
5713317097_H


title: child-12


title: Fibroblast-NCsiRNA-72hr-lot3

description:
Replicate3
5713317097_L


title: child-13


title: Fibroblast-4mixsiRNA-72hr-lot1

description:
Replicate1
5713317097_G


title: child-21


title: child-10


title: Fibroblast-NCsiRNA-72hr-lot2

description:
Replicate2
5713317097_K


title: Fibroblast-NCsiRNA-72hr-lot1

description:
Replicate1
5713317097_J


title: child-7


title: child-8


title: child-15


title: child-9


title: child-11


title: child-2


title: child-5


title: MSC-ADP-14day-lot3

description:
Replicate3
5512751066_J

source_name: Mesenchymal Stem cell

value: Mesenchymal stem cell

value: 14days after adipogenic induction


title: child-1


title: MSC-ADP-14day-lot2

description:
Replicate2
5512751064_J


title: MSC-ADP-07day-lot3

description:
Replicate3
5512751066_I

value: 7days after adipogenic induction


title: MSC-ADP-07day-lot2

description:
Replicate2
5512751064_I


title: BreastTumor-S452-Rep1

city: Taipei

first: Chia-Hsien

last: Lee

address: No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan(R.O.C)

country: Taiwan

institute: National Taiwan University

description:
S452T1
Breast tumor sample obtained from patient

hyb_protocol: 2X hybridization buffer (Agilent Technologies, USA) was added to the labeled mixture to a final volume of 45ul. The mixture was heated for 5 min at 100°C and immediately cooled to 0°C. Each 45ul sample was hybridized onto an Agilent human miRNA Microarray Release 12.0, 8x15K (Agilent Technologies, USA) at 55°C for 20 hours.

scan_protocol: Slides were scanned on an Agilent microarray scanner (Agilent Technologies, model G2505C) at 100% and 5% sensitivity settings.

data_processing: Feature Extraction (Agilent Technologies) software version 10.7.3.1 was used for image analysis.

source_name: Tumor Breast tissue from patient 452

label_protocol: After RNA extraction, 100 ng of total RNAs were dephosphorylated and labeled with pCp-Cy3 by Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, USA, microRNA Spike- In Apply).

growth_protocol: The tissue are collected from patients directly.

extract_protocol: For RNA extraction, total RNA was extracted from tissues collected from the patients by Trizol® Reagent (Invitrogen, USA) according to the instruction mannual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

tag: patient id

value: patient 452

tag: tissue type

value: Tumor

tag: er

tag: pr

tag: tnm

tag: grade

tag: Stage

value: I


title: MSC-ADP-36hr-lot3

description:
Replicate3
5512751066_H

value: 36hr after adipogenic induction


title: MSC-ADP-14day-lot1

description:
Replicate1
5512751030_J


title: non-invading area, EcytodnTGFR epithelium, rep2

city: Nashville

first: Claudia

middle: D

last: Andl

state: TN

address: 1161 21St Ave S

department: Surgery

institute: Vanderbilt University

description: Gene expression

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 C for 5 min and hybridized for 16 h at 45 C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm.

data_processing: Affymetrix Expression Console 1.1.1 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. This Signal value, a relative measure of the expression level, was computed for each assayed gene. RMA-normalized.

source_name: human esophageal keratinocytes

label_protocol: First-strand cDNA was generated using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Organotypic cultures of wild-type E-cadherin, dominant-negative E-cadherin and dominant-negative TGF receptor type II expressing esophageal keratinocytes were harvested on day 15 and RNA isolated.

extract_protocol: RNA was isolated using laser-capture microdissection of frozen tissue sections using the PicoPure RNA isolation kit from Arcturus.

tag: cell culture

value: organotypic cultures

tag: cell line


title: BreastAdjacentNormal-S894-Rep1

description:
S894N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 894

value: patient 894

value: Adjacent Normal


title: invading area, Ecyto epithelium, rep2

description: Gene expression

value: invading area, Ecyto epithelium


title: BreastTumor-S464-Rep1

description:
S464T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 464

value: patient 464


title: MSC-ADP-36hr-lot2

description:
Replicate2
5512751064_H

tag: cell type


title: non-invading area, Ecyto epithelium, rep2

description: Gene expression

value: non-invading area, Ecyto epithelium


title: invading area, EcytodnTGFR epithelium, rep2

description: Gene expression

value: invading area, EcytodnTGFR epithelium


title: MSC-ADP-36hr-lot1

description:
Replicate1
5512751030_A


title: invading area, EcytodnTGFR epithelium, rep1

description: Gene expression


title: non-invading area, EcytodnTGFR epithelium, rep1

description: Gene expression


title: MSC-ADP-07day-lot1

description:
Replicate1
5512751030_I


title: non-invading area, Ecyto epithelium, rep1

description: Gene expression


title: non-invading area, wt Ecad epithelium, rep1

description: Gene expression

value: non-invading area, wt Ecad epithelium


title: MSC-ADP-24hr-lot3

description:
Replicate3
5512751066_G

value: 24hr after adipogenic induction


title: invading area, Ecyto epithelium, rep1

description: Gene expression


title: BreastTumor-S430-Rep1

description:
S430T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 430

value: patient 430

value: IIIC


title: BreastTumor-S437-Rep1

description:
S437T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 437

value: patient 437

value: IIIA


title: BreastTumor-S483-Rep1

description:
S483T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 483

value: patient 483


title: BreastTumor-S469-Rep1

description:
S469T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 469

value: patient 469

value: Tumor

value: IIA


title: BreastTumor-S917-Rep1

description:
S917T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 917

value: patient 917

value: Unknown


title: MSC-ADP-12hr-lot3

description:
Replicate3
5512751066_F

value: Mesenchymal stem cell

value: 12hr after adipogenic induction


title: MSC-ADP-24hr-lot2

description:
Replicate2
5512751064_G


title: BreastTumor-S454-Rep1

description:
S454T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 454

value: patient 454

value: I


title: MSC-ADP-12hr-lot1

description:
Replicate1
5512751030_C


title: BreastTumor-S445-Rep1

description:
S445T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 445

value: patient 445

value: IIB


title: BreastTumor-S453-Rep1

description:
S453T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 453

value: patient 453


title: BreastTumor-S887-Rep1

description:
S887T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 887

value: patient 887


title: non-invading area, wt Ecad epithelium, rep2

description: Gene expression

value: organotypic cultures

value: non-invading area, wt Ecad epithelium


title: MSC-ADP-24hr-lot1

description:
Replicate1
5512751030_B

value: 24hr after adipogenic induction


title: BreastTumor-S455-Rep1

description:
S455T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 455

value: patient 455

value: IV


title: BreastTumor-S698-Rep1

description:
S698T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 698

value: patient 698

value: Tumor


title: BreastTumor-S446-Rep1

description:
S446T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 446

value: patient 446

value: IIIA


title: BreastTumor-S446-Rep2

description:
S446T2
Breast tumor sample obtained from patient


title: BreastTumor-S417-Rep1

description:
S417T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 417

value: patient 417

value: IIA


title: MSC-ADP-12hr-lot2

description:
Replicate2
5512751064_F

source_name: Mesenchymal Stem cell

value: Mesenchymal stem cell

value: 12hr after adipogenic induction


title: BreastTumor-S375-Rep1

description:
S375T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 375

value: patient 375

value: I


title: BreastTumor-S427-Rep1

description:
S427T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 427

value: patient 427


title: MSC-ADP-06hr-lot2

description:
Replicate2
5512751064_E

value: 6hr after adipogenic induction


title: MSC-ADP-06hr-lot1

description:
Replicate1
5512751030_D


title: MSC-ADP-06hr-lot3

description:
Replicate3
5512751066_E


title: MSC-ADP-02hr-lot3

description:
Replicate3
5512751066_D

value: 2hr after adipogenic induction


title: BreastTumor-S180-Rep1

description:
S180T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 180

value: patient 180

value: IIIC


title: BreastTumor-S898-Rep1

description:
S898T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 898

value: patient 898

value: Unknown


title: BreastTumor-S941-Rep2

description:
S941T2
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 941

value: patient 941


title: BreastTumor-S474-Rep1

description:
S474T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 474

value: patient 474

value: Tumor


title: BreastTumor-S619-Rep1

description:
S619T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 619

value: patient 619


title: BreastAdjacentNormal-S622-Rep1

description:
S622N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 622

value: patient 622

value: Adjacent Normal


title: Wild type strain COL with diamide replicate 1

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: COL WT diamid

hyb_protocol: A mixture of RNA from WT or mutant strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

label: cyanine 3

organism: Staphylococcus aureus subsp. aureus COL

source_name: COL WT diamid

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grown in TSB

extract_protocol: Briefly, bacteria were lysed in 1 ml of Trizol reagent (Invitrogen Life Technologies, Karlsruhe, Germany) with 0.5 ml zirconia-silica beads (0.1 mm-diameter) in a high-speed homogenizer (Savant Instruments, Farmingdale, NY). RNA was pirified with RNeasy column (Qiagen). Then DNA digestion was performed as instructed by the RNA isolation kit.

treatment_protocol: Trizol

tag: sample type

value: S. aureus strains grown in TSB

tag: genotype

value: wild type

value: diamide

label: cyanine 5

source_name: gDNA pool

value: Staphylococcus aureus gDNA mixture


title: BreastTumor-S881-Rep1

description:
S881T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 881

value: patient 881

value: IIB


title: BreastTumor-S941-Rep1

description:
S941T1
Breast tumor sample obtained from patient

value: IIA


title: MSC-ADP-02hr-lot1

description:
Replicate1
5512751030_E

value: Mesenchymal stem cell

value: 2hr after adipogenic induction


title: Wild type strain COL with diamide replicate 2

description: COL WT diamid


title: MSC-ADP-01hr-lot2

description:
Replicate2
5512751064_C

value: 1hr after adipogenic induction


title: BreastTumor-S207-Rep1

description:
S207T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 207

value: patient 207


title: BreastTumor-S677-Rep1

description:
S677T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 677

value: patient 677


title: BreastTumor-S906-Rep1

description:
S906T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 906

value: patient 906

value: IIIC


title: bshA mutant of COL with diamide replicate 3

description: bshA mutant diamid

source_name: bshA mutant diamid

value: S. aureus strains grown in TSB enriched in diamide

value: bshA mutant


title: Wild type strain COL with diamide replicate 3

description: COL WT diamid


title: BreastTumor-S490-Rep1

description:
S490T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 490

value: patient 490

value: Tumor


title: MSC-ADP-01hr-lot1

description:
Replicate1
5512751030_F

source_name: Mesenchymal Stem cell


title: bshA mutant of COL with diamide replicate 1

description: bshA mutant diamid


title: bshA mutant of COL with diamide replicate 2

description: bshA mutant diamid


title: BreastTumor-S604-Rep1

description:
S604T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 604

value: patient 604


title: MSC-ADP-02hr-lot2

description:
Replicate2
5512751064_D


title: MSC-ADP-0.5hr-lot1

description:
Replicate1
5512751030_G

value: 0.5hr after adipogenic induction


title: BreastTumor-S602-Rep1

description:
S602T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 602

value: patient 602

value: I


title: MSC-ADP-0.5hr-lot2

description:
Replicate2
5512751064_B


title: bshA mutant of COL replicate 3

description: bshA mutant

source_name: bshA mutant

value: Staphylococcus aureus gDNA mixture


title: MSC-ADP-01hr-lot3

description:
Replicate3
5512751066_C


title: MSC-ADP-0.5hr-lot3

description:
Replicate3
5512751066_B


title: MSC-ADP-00hr-lot2

description:
Replicate2
5512751064_A

value: untreated


title: MSC-ADP-00hr-lot3

description:
Replicate3
5512751066_A

value: Mesenchymal stem cell


title: BreastTumor-S469-Rep2

description:
S469T2
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 469

value: patient 469

value: IIA


title: bshA mutant of COL replicate 2

description: bshA mutant


title: BreastTumor-S303-Rep1

description:
S303T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 303

value: patient 303


title: BreastTumor-S894-Rep1

description:
S894T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 894

value: patient 894


title: Wild type strain COL replicate 3

description: COL WT

source_name: COL WT

value: S. aureus strains grown in TSB

value: wild type


title: BreastTumor-S410-Rep1

description:
S410T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 410

value: patient 410


title: BreastTumor-S557-Rep1

description:
S557T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 557

value: patient 557


title: BreastTumor-S401-Rep1

description:
S401T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 401

value: patient 401


title: bshA mutant of COL replicate 1

description: bshA mutant

value: S. aureus strains grown in TSB enriched in diamide

value: bshA mutant

source_name: gDNA pool


title: BreastTumor-S929-Rep1

description:
S929T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 929

value: patient 929

value: Tumor


title: Wild type strain COL replicate 1

description: COL WT


title: BreastTumor-S448-Rep1

description:
S448T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 448

value: patient 448

value: I


title: BreastTumor-S673-Rep1

description:
S673T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 673

value: patient 673


title: MSC-ADP-00hr-lot1

description:
Replicate1
5512751030_H

value: untreated

value: Mesenchymal stem cell


title: BreastTumor-S367-Rep1

description:
S367T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 367

value: patient 367

value: IIIA


title: Mature-ADP-sub-lot3

description:
Replicate3
5713317099_I

source_name: Preadipocyte

value: Preadipocyte

value: after 2week adipogenic induction


title: Mature-ADP-sub-lot2

description:
Replicate2
5713317099_H


title: PreADP-sub-lot3

description:
Replicate3
5713317099_F

source_name: Preadipocyte (inducted)


title: Wild type strain COL replicate 2

description: COL WT

value: S. aureus strains grown in TSB

value: wild type

value: Staphylococcus aureus gDNA mixture


title: BreastAdjacentNormal-S562-Rep1

description:
S562N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 562

value: patient 562

value: Adjacent Normal


title: BreastTumor-S572-Rep1

description:
S572T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 572

value: patient 572

value: IIIC


title: BreastTumor-S574-Rep1

description:
S574T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 574

value: patient 574

value: Tumor

value: IIA


title: transfected with FoxP1 siRNA_2

city: Freiburg

first: Sebastian

last: Grundmann

address: Hugstetter Str. 55

country: Germany

institute: University Hospital Freiburg

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented according to the manufacturer´s instructions, and 1.5 µg of fragmented cRNA hybridized to an Agilent 4x44K array. Hybridization conditions: 65°C, 10 rpm, 17 h; in an Agilent hybridization oven

scan_protocol: Agilent arrays were washed using Agilent's gene expression wash buffer 1 and 2 according to Agilent's instructions. Scanning was performed using an Agilent DNA microarray Scanner and Agilent's Scan Control Software (version A.8.3.1).

data_processing: Primary data analysis was performed using Agilent's Feature Extraction Software (version 10.5.1.1).

source_name: HUVECs transfected with FoxP1 siRNA

label_protocol: Kit: Quick Amp Labeling Kit, One Color (#5190-0442), using 200 ng of total RNA as starting material, according to the manufacturer's instructions (Manual .One-color microarray-based gene expression analysis, version 5.5, February 2007). cRNA synthesis was regarded successful provided that .1.65 µg of cRNA with a Cy3-incorporation rate .8.0 pmol/µg cRNA were synthesized.

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were isolated from donated umbilical cords, pooled from two donors and cultivated up to passage 5.

extract_protocol: Total RNA was isolated from HUVECs 48h after transfection with TRIzol (Invitrogen) according to the manufacturers instructions.

treatment_protocol: For transfection with siRNA oligonucleotides (all invitrogen), cells were cultured to 70% confluence and transfected with a combination of three FoxP1-targeting siRNAs or an irrelevant control oligonucleotide (all from invitrogen) according to the manufacturers instructions.

value: umbilical cord endothelial cells (HUVEC)

tag: passage


title: Mature-ADP-sub-lot1

description:
Replicate1
5713317099_G


title: PreADP-sub-lot1

description:
Replicate1
5713317099_D

value: untreated


title: BreastTumor-S450-Rep1

description:
S450T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 450

value: patient 450

value: IIB


title: BreastTumor-S922-Rep1

description:
S922T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 922

value: patient 922

value: I


title: transfected with FoxP1 siRNA_3


title: BreastTumor-S433-Rep1

description:
S433T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 433

value: patient 433


title: BreastTumor-S896-Rep1

description:
S896T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 896

value: patient 896


title: BreastTumor-S328-Rep1

description:
S328T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 328

value: patient 328


title: transfected with control siRNA_5

source_name: HUVECs transfected with control siRNA


title: BreastAdjacentNormal-S420-Rep1

description:
S420N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 420

value: patient 420


title: transfected with FoxP1 siRNA_1


title: BreastTumor-S400-Rep1

description:
S400T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 400

value: patient 400


title: transfected with control siRNA_4


title: transfected with control siRNA_6


title: BreastTumor-S444-Rep1

description:
S444T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 444

value: patient 444

value: Unknown


title: PKh_55

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Data were processed using Affymetrix Expression Console software. Gene level expression were summarized using RMA quantile normalization method.

source_name: PHEO

label_protocol: The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin.

growth_protocol: Tissue samples collected on the day of surgery for each patient

extract_protocol: Extraction of RNA from normal and tumor tissue was performed following a protocol that combines separation of the RNA fraction of tissue homogenized in TRIZOL with subsequent column-based RNA purification.

tag: age(yrs)

value: male

value: pheochromocytoma (PHEO) tumor

tag: mutation

value: VHL


title: BreastTumor-S379-Rep1

description:
S379T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 379

value: patient 379

value: Tumor

value: IIIA


title: PKh_54

tag: gender


title: BreastTumor-S918-Rep1

description:
S918T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 918

value: patient 918

value: IIA


title: PKh_53


title: PKh_56


title: BreastTumor-S213-Rep1

description:
S213T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 213

value: patient 213


title: PKh_51


title: PKh_50


title: PreADP-sub-lot2

description:
Replicate2
5713317099_E

source_name: Preadipocyte (inducted)

tag: treatment

value: untreated

value: Preadipocyte


title: PKh_49


title: PKh_52


title: BreastAdjacentNormal-S906-Rep1

description:
S906N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 906

tag: patient id

value: patient 906

value: Adjacent Normal


title: BreastTumor-S891-Rep1

description:
S891T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 891

value: patient 891

tag: tissue type

value: IIA orIIB


title: BreastTumor-S403-Rep1

description:
S403T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 403

value: patient 403

tag: er

value: IIB


title: BreastTumor-S893-Rep1

description:
S893T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 893

value: patient 893

tag: pr


title: PKh_45

value: female

value: pheochromocytoma (PHEO) tumor


title: BreastTumor-S622-Rep1

description:
S622T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 622

value: patient 622

tag: tnm


title: PKh_46

value: male

value: VHL


title: PKh_47


title: PKh_48


title: BreastTumor-S434-Rep1

description:
S434T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 434

value: patient 434

value: Tumor

tag: grade


title: PKh_59

source_name: PGL

value: paraganglioma (PGL) tumor

value: SDHD

value: Head and neck


title: PKh_37


title: BreastTumor-S562-Rep1

description:
S562T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 562

value: patient 562

tag: Stage

value: I


title: PKh_58


title: BreastTumor-S380-Rep1

description:
S380T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 380

value: patient 380


title: PKh_57


title: BreastTumor-S961-Rep1

description:
S961T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 961

value: patient 961

value: IIIA


title: d-1

city: Wako

first: Makoto

last: Kimura

state: Saitama

address: 2-1 Hirosawa

description: SAMPLE 5

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 array in the GeneChip Hybridazation Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix default.  ExpressionStat 5.0

organism: Schizosaccharomyces pombe

source_name: opi10-_before heat shock

label_protocol: Biotinylated cRNA were prepared using GeneChip 3'IVT Expression Kit (Affymetrix).

growth_protocol: Cultured in liquid Edinburgh Minimal Medium at 30C to mid-log phase.

extract_protocol: phenol/chloroform

treatment_protocol: Shifted to 43C and cultured for 1 h, and then shifted back to 30C and cultured for 1 and 3 h.

tag: genotype/variation

tag: culture condition

value: cultured at 30C


title: BreastAdjacentNormal-S941-Rep1

description:
S941N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 941

value: patient 941

value: Adjacent Normal


title: PKh_60

value: female


title: d-2

description: SAMPLE 6

source_name: opi10-_during heat shock

value: treated for 1h at 43C


title: d-3

description: SAMPLE 7

source_name: opi10-_after heat shock

value: cultured for 1 h at 30C after the heat shock


title: d-4

description: SAMPLE 8

value: cultured for 3 h at 30C after the heat shock


title: PKh_25


title: BreastTumor-S422-Rep1

description:
S422T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 422

value: patient 422

value: IIA


title: PKh_01

value: paraganglioma (PGL) tumor


title: PKh_41

value: male

value: SDHD

value: extraadrenal


title: w-4

description: SAMPLE 4

source_name: opi10+_after heat shock


title: BreastTumor-S173-Rep1

description:
S173T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 173

value: patient 173

value: Tumor

value: IIIC


title: BreastTumor-S415-Rep1

description:
S415T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 415

value: patient 415

value: IIIA


title: BreastTumor-S475-Rep1

description:
S475T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 475

value: patient 475

value: I


title: w-3

description: SAMPLE 3


title: BreastTumor-S507-Rep1

description:
S507T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 507

value: patient 507


title: PKh_02

value: female

value: Head and neck


title: BreastTumor-S439-Rep1

description:
S439T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 439

value: patient 439


title: w-1

description: SAMPLE 1

source_name: opi10+_before heat shock

value: cultured at 30C


title: BreastTumor-S423-Rep1

description:
S423T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 423

value: patient 423


title: PKh_26

source_name: PHEO

value: pheochromocytoma (PHEO) tumor

value: adrenal


title: PKh_09

value: SDHD


title: BreastTumor-S586-Rep1

description:
S586T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 586

value: patient 586


title: PKh_29

source_name: PGL

value: paraganglioma (PGL) tumor


title: w-2

description: SAMPLE 2

source_name: opi10+_during heat shock

value: treated for 1h at 43C


title: PKh_40

value: SDHB


title: PKh_08

value: male


title: PKh_35


title: 011421_LCg

city: Dallas

first: jinyong

last: kim

state: tx

address: 5332 Harry Hines Blvd

department: Molecular Genetics

institute: UT southwestern medical Institute

description: Gene expression data from LPS CPN GGOH treatment data.

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

scan_protocol: GeneChips were scanned on the GeneArray® Scanner or the GeneChip® Scanner 3000.

data_processing: GeneSpring was used to perform data visualization, validation, normalization (MAS5.0), and analysis.

source_name: peritoneal macrophages, LPS+CPN+GGOH

label_protocol: First and second strand cDNA was prepared using Superscirpt Choice System (invitrogen). Biotinylated cRNA were prepared using RNA Transcript Labeling Kit (T7) (Enzo) according to the manufacturer's protocol.

growth_protocol: Collect peritoneal macrophage cells after 3 days of TG (thioglycolate) injection.

extract_protocol: RNeasy Mini Kit (Qiagen) was used to extract RNA according to the manufacturer's protocol.

treatment_protocol: LPS+CPN versus LPS+CPN+GGOH treatment.

tag: strain/background

tag: cell type

value: peritoneal macrophages

value: LPS+CPN+GGOH


title: PKh_24


title: BreastTumor-S418-Rep1

description:
S418T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 418

value: patient 418

value: Tumor

value: IIIC


title: BreastTumor-S629-Rep1

description:
S629T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 629

value: patient 629

value: I


title: 011421_LC

description: Gene expression data from LPS and CPN treatment data.

source_name: peritoneal macrophages, LPS+CPN

value: LPS+CPN


title: BreastTumor-S420-Rep1

description:
S420T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 420

value: patient 420


title: PKh_38

value: female


title: BreastTumor-S909-Rep1

description:
S909T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 909

value: patient 909

value: Unknown


title: PKh_39

value: pheochromocytoma (PHEO) tumor


title: PKh_34

value: paraganglioma (PGL) tumor


title: BreastTumor-S363-Rep1

description:
S363T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 363

value: patient 363

value: IIB


title: BreastTumor-S660-Rep1

description:
S660T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 660

value: patient 660


title: BreastAdjacentNormal-S358-Rep1

description:
S358N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 358

value: patient 358

value: Adjacent Normal


title: PKh_33

value: male

value: SDHB


title: YF-gh1

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: a mutation at STAT5 phosphorylation site (Y694F). YF-containing vector was introduced into Stat5-null MEFs by retroviral infection

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Expression values were determined with GeneChip Operating Software (GCOS) v1.1.1 software. RMA signals were summarized using GeneSpring GX 10.0.1 (Agilent) and normalized by quantile normalization. All data analysis was performed with GeneSpring software GX 10.01.

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

extract_protocol: Total cellular RNA from each group of the MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions

tag: genotype/varation

value: YF

value: mouse embryonic fibroblasts

tag: stimulation

value: growth hormone for 120 minutes

tag: strain


title: BreastAdjacentNormal-S593-Rep1

description:
S593N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 593

value: patient 593


title: EA1

description: a mutation of STAT5 binding domation (EE to AA). EA-containing vector was induced into Stat5-null MEFs by retroviral infection

value: EA


title: PKh_32

tag: age(yrs)

tag: mutation


title: EA-gh2


title: YF-gh2


title: BreastAdjacentNormal-S498-Rep1

description:
S498N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 498

value: patient 498


title: mia treat2 tumor.AVG_Signal

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: replicate 2

hyb_protocol: The single-stranded PCR product was hybridized to the Sentrix Array Matrix, where the labeled strand bound to the bead on the array containing the complementary address sequence.

scan_protocol: Arrays were imaged using an Illumina BeadArray Reader, and the fluorescent intensity of miRNA probes were analyzed using BeadStudio version 3.3.3 (Illumina San Diego, CA).

data_processing: quantile normalizationm of un-normalized data without background subtraction using gene data analyst version 5.1

source_name: Pancreatic Adenocarcinoa cells MIA PaCa-2

label_protocol: Cy3 labeling

extract_protocol: Total RNA (200 - 400 ng) was poly-adenylated and then converted to cDNA using a biotinylated oligo-dT primer with a universal PCR sequenced at its 5’-end. This was followed by annealing of a miRNA-specific oligonucleotide pool (MSO), which consisted of three parts: a universal PCR priming site at the 5’ end; an address sequence complementary to a capture sequence on the BeadArrayTM; and a microRNA-specific sequence at the 3’-end. Extension of MSO was facilitated by addition of a polymerase but only if their 3’ bases were complementary to the cognate sequence in the cDNA template. Common primers were used to amplify the cDNA templates; the primer complimentary to the BeadArrayTM was fluorescently labeled.

tag: cell line

tag: cultures

value: human xenograft tumor model in SCID mouse

tag: treatment

value: Minnelide (0.42 mg/kg for seven days i.p.)


title: mia treat3 tumor.AVG_Signal

description: replicate 3


title: mia ctl3 tumor.AVG_Signal

description: replicate 3

value: untreated


title: mia treat1 tumor.AVG_Signal

description: replicate 1


title: PKh_31

tag: gender

tag: tissue type

value: paraganglioma (PGL) tumor


title: mia ctl2 tumor.AVG_Signal

description: replicate 2


title: BreastTumor-S502-Rep1

description:
S502T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 502

tag: patient id

value: patient 502

value: Tumor

tag: er

tag: pr

tag: tnm


title: PKh_36


title: mia 48h n=3.AVG_Signal

description: replicate 3

value: RPMI containing 10% FBS

value: 100 nm triptolide


title: mia ctl1 tumor.AVG_Signal

description: replicate 1


title: BreastTumor-S536-Rep1

description:
S536T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 536

value: patient 536

tag: grade

tag: Stage

value: IIA


title: PKh_22

value: female

value: SDHB


title: EA-gh1

tag: cell type

value: mouse embryonic fibroblasts


title: EA-2

tag: genotype/varation


title: mia 12h n=3.AVG_Signal

description: replicate 3


title: PKh_21

value: male


title: PKh_28


title: PKh_20


title: mia 24h n=3.AVG_Signal

description: replicate 3


title: BreastTumor-S631-Rep1

description:
S631T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 631

value: patient 631

value: IV


title: BreastTumor-S628-Rep1

description:
S628T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 628

value: patient 628

value: I


title: PKh_19

source_name: PGL


title: YF2

value: YF

tag: stimulation


title: YF1

tag: strain


title: BreastTumor-S291-Rep1

description:
S291T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 291

value: patient 291

value: IIIA


title: BreastAdjacentNormal-S427-Rep1

description:
S427N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 427

value: patient 427

value: Adjacent Normal


title: BreastTumor-S201-Rep1

description:
S201T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 201

value: patient 201

value: Tumor


title: mia 6h n=3.AVG_Signal

description: replicate 3

value: RPMI containing 10% FBS

value: 100 nm triptolide


title: mia ctl n=3.AVG_Signal

description: replicate 3

value: untreated


title: BreastTumor-S645-Rep1

description:
S645T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 645

value: patient 645


title: PKh_27

tag: age(yrs)

value: female

value: paraganglioma (PGL) tumor

value: SDHB


title: PKh_13

source_name: PHEO

value: pheochromocytoma (PHEO) tumor

tag: mutation


title: mia 12h n=2.AVG_Signal

description: replicate 2

tag: cell line


title: mia 24h n=2.AVG_Signal

description: replicate 2

tag: cultures


title: PKh_18


title: PKh_10

value: male


title: BreastTumor-S477-Rep1

description:
S477T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 477

value: patient 477

value: I


title: BreastAdjacentNormal-S363-Rep1

description:
S363N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 363

value: patient 363


title: BreastTumor-S665-Rep1

description:
S665T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 665

value: patient 665

value: IIIC


title: PKh_11


title: PKh_44

source_name: Normal

value: Normal


title: BreastAdjacentNormal-S909-Rep1

description:
S909N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 909

value: patient 909

value: Adjacent Normal


title: mia 6h n=2.AVG_Signal

description: replicate 2

value: RPMI containing 10% FBS

tag: treatment


title: mia ctl n=2.AVG_Signal

description: replicate 2


title: mia 48h n=1.AVG_Signal

description: replicate 1

value: 100 nm triptolide


title: mia 24h n=1.AVG_Signal

description: replicate 1


title: mia 12h n=1.AVG_Signal

description: replicate 1


title: mia 48h n=2.AVG_Signal

description: replicate 2


title: BreastTumor-S462-Rep1

description:
S462T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 462

value: patient 462

value: Tumor


title: PKh_43

tag: gender


title: mia 6h n=1.AVG_Signal

description: replicate 1

source_name: Pancreatic Adenocarcinoa cells MIA PaCa-2


title: PKh_42

tag: tissue type


title: mia ctl n=1.AVG_Signal

description: replicate 1

value: untreated


title: BreastAdjacentNormal-S536-Rep1

description:
S536N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 536

tag: patient id

value: patient 536


title: BreastTumor-S614-Rep1

description:
S614T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 614

value: patient 614

tag: er

value: Unknown

value: IIIA


title: PKh_06

value: female


title: s2013 treat3 tumor.AVG_Signal

description: replicate 3

source_name: Pancreatic Adenocarcinoma cells S2-013

value: human xenograft tumor model in SCID mouse

value: Minnelide (0.42 mg/kg for seven days i.p.)


title: s2013 treat2 tumor.AVG_Signal

description: replicate 2


title: PKh_05


title: BreastTumor-S459-Rep1

description:
S459T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 459

value: patient 459

tag: pr

value: IV


title: BreastTumor-S389-Rep1

description:
S389T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 389

value: patient 389

tag: tnm

value: IIB


title: BreastTumor-S593-Rep1

description:
S593T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 593

value: patient 593

tag: grade

value: I


title: s2013 treat1 tumor.AVG_Signal

description: replicate 1


title: BreastTumor-S543-Rep1

description:
S543T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 543

value: patient 543

tag: Stage


title: PKh_07

value: Normal


title: s2013 ctl3 tumor.AVG_Signal

description: replicate 3


title: BreastTumor-S545-Rep1

description:
S545T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 545

value: patient 545

value: Tumor

value: IIA


title: PKh_03

value: male


title: BreastAdjacentNormal-S455-Rep1

description:
S455N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 455

value: patient 455

value: Adjacent Normal


title: BreastTumor-S498-Rep1

description:
S498T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 498

value: patient 498


title: s2013 24h n=3.AVG_Signal

description: replicate 3

value: DMEM containing 10% FBS

value: 100 nm triptolide

tag: timepoint


title: s2013 48h n=3.AVG_Signal

description: replicate 3


title: s2013 ctl2 tumor.AVG_Signal

description: replicate 2

value: human xenograft tumor model in SCID mouse

value: untreated


title: BreastTumor-S653-Rep1

description:
S653T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 653

value: patient 653

value: IIIC


title: spermatid_control_rep2

city: New York

first: Scott

last: Keeney

state: NY

address: 1275 York Ave

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA was hybridized to Illumina MouseWG-6v2 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner (Illumina iScan Control Software v.3.2.45).

data_processing: Scan data were analyzed with GenomeStudio (v2011.1) using Illumina default analysis settings and exported. Data were subjected to norm-exponential background correction using negative control beads, followed by quantile normalization (limma Bioconductor package v.3.12.1). All probes, all samples were used for normalization.

source_name: round spermatids_Baz1a+/-

label_protocol: Biotinylated cRNA was prepared according to the standard Illumina protocol from total RNA.

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

tag: strain background

value: mixed C57BL/6J and FVB/NJ

tag: genotype/variation

tag: cell type

value: round spermatids


title: spermatid_mutant_rep2

source_name: round spermatids_Baz1a-/-


title: spermatid_control_rep3


title: BreastTumor-S722-Rep1

description:
S722T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 722

value: patient 722

value: I


title: spermatocyte_control_rep3

value: spermatocytes


title: PKh_04

source_name: Normal

tag: age(yrs)

value: Normal


title: spermatid_mutant_rep3


title: spermatocyte_control_rep2


title: BreastTumor-S175-Rep1

description:
S175T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 175

value: patient 175

value: Tumor


title: spermatocyte_mutant_rep3


title: s2013 ctl1 tumor.AVG_Signal

description: replicate 1


title: spermatocyte_mutant_rep2


title: BreastTumor-S357-Rep1

description:
S357T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 357

value: patient 357


title: s2013 6h n=2.AVG_Signal

description: replicate 2


title: s2013 ctl n=2.AVG_Signal

description: replicate 2


title: s2013 6h n=3.AVG_Signal

description: replicate 3


title: s2013 ctl n=3.AVG_Signal

description: replicate 3


title: s2013 48h n=2.AVG_Signal

description: replicate 2


title: s2013 12h n=3.AVG_Signal

description: replicate 3


title: s2013 12h n=2.AVG_Signal

description: replicate 2


title: s2013 24h n=2.AVG_Signal

description: replicate 2


title: BreastTumor-S368-Rep1

description:
S368T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 368

value: patient 368


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_Cu0.5_strain_E_faecalis_OG1RF_copΔ_rep2

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  copper treatment (0.5 CuSO4), second of two technical microarray hybridization replicates.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com. Special support performe by ROCHE-Chile, Santiago, Chile. See www.roche.cl

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com. Special support performe by ROCHE-Chile, Santiago, Chile. See www.roche.cl

data_processing:
All data was processes automatically using DNASTAR software Array star 5.0. See www.dnastar.com.
Student's t-test statistics were used to identify significantly different gene expression levels with a p<0.05 of change between the average value of each gene and its corresponding reference, using the DNASTAR software Array star 5.0. See www.dnastar.com.

organism: Enterococcus faecalis OG1RF

source_name: Enterococcus faecalis  OG1RF copΔ 0.5 mM CuSO4

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com. Special support performe by ROCHE-Chile, Santiago, Chile. See www.roche.cl

growth_protocol: Enterococcus faecalis OG1RF wild-type and copΔ was grown to mid-log phase (O.D600nm 1.0), aerobically estandar condition at 37°C in N medium (Peptone 1 % (Difco), yeast extract 0.5 % (Difco), Na2HPO4 1 % (Merck) and glucose 1 % (Oxoid), Odermatt A, Solioz M. J Biol Chem 1995, 270(9).  In treatment cultures, strain was gowth at the same condition by adding copper (0.05 mM or 0.5 mM of CuSO4) to the control medium.

extract_protocol: The RNA was extracted using a Qiagen RNeasy mini kit (Qiagen). Residual contaminating genomic DNA was removed with RQ1 RNase-free DNase (Promega) treatment according to the manufacturer’s protocol. The integrity of the RNA was assessed by gel electrophoresis.

treatment_protocol: All copper-treated cells were exposed for 3 hours prior to harvesting (at mid-log phase, OD600nm 1.0); the untreated cells were collected simultaneously.

tag: genotype

value: operon cop deletion mutant (copΔ)

tag: phenotype

value: copper sensitive


title: spermatocyte_mutant_rep1_censored


title: BreastTumor-S358-Rep1

description:
S358T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 358

value: patient 358

value: IIIA


title: BreastTumor-S621-Rep1

description:
S621T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 621

value: patient 621


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_Cu0.05_strain_E_faecalis_OG1RF_copΔ_rep2

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  copper treatment (0.05 CuSO4), second of two technical microarray hybridization replicates.

source_name: Enterococcus faecalis  OG1RF copΔ 0.05 mM CuSO4


title: BreastAdjacentNormal-S173-Rep1

description:
S173N1
Adjacent breast normal sample obtained from patient

source_name: Adjacent Normal Breast tissue from patient 173

value: patient 173

value: Adjacent Normal


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_Cu0.05_strain_E_faecalis_OG1RF_copΔ_rep1

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  copper treatment (0.05 CuSO4), first of two technical microarray hybridization replicates.


title: BreastTumor-S594-Rep1

description:
S594T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 594

value: patient 594

value: IIIC


title: s2013 24h n=1.AVG_Signal

description: replicate 1

source_name: Pancreatic Adenocarcinoma cells S2-013

tag: cell line

tag: cultures

value: DMEM containing 10% FBS

value: 100 nm triptolide


title: s2013 48h n=1.AVG_Signal

description: replicate 1

tag: treatment


title: s2013 12h n=1.AVG_Signal

description: replicate 1


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_Cu0.5_strain_E_faecalis_OG1RF_copΔ_rep1

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  copper treatment (0.5 CuSO4), first of two technical microarray hybridization replicates.


title: IEC_GF-HDAC3FF -1

city: Cincinnati

first: Theresa

last: Alenghat

state: OH

address: 240 Albert Sabin Way, S5.409

department: Division of Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: cDNA was amplified with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania’s Microarray facility.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

source_name: Intestinal Epithelial Cells (IECs)

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

tag: tissue

value: large intestine

tag: strain


title: BreastTumor-S582-Rep1

description:
S582T1
Breast tumor sample obtained from patient

source_name: Tumor Breast tissue from patient 582

tag: patient id

value: patient 582

tag: tissue type

tag: er

value: IIA


title: Day 3 post-MRSA wild type infection, sample 4

city: Chicago

first: Jiwang

state: IL

address: 840 S Wood Street

institute: University of Illinois at Chicago

description: Day 3 post-MRSA wild type infection.

hyb_protocol: Standard protocol as recommended by Illumina.

scan_protocol: Standard protocol as recommended by Illumina using the Illumina iScan.

data_processing: Raw signal intensities of each probe were obtained using data analysis software (Illumina BeadStudio) and imported to the Lumi package of Bioconductor for data transformation and normalization (Du et al. 2008 [PMID 18467348], Lin et al. 2008 [PMID 18178591], Du et al. 2007 [PMID 17540033]). A/P call detection was performed based on detection p-value. The probes with less than 0.01 were considered as valid signals. The data for these probes were normalized by the quantile method. Differentially expressed genes were identified using an Analysis of Variance (ANOVA) model with empirical Bayesian variance estimation (Wettenhall et al. 2004 [PMID 15297296]). The problem of multiple comparisons was corrected using the false discovery rate (FDR). Initially, genes were identified as being differentially expressed on the basis of a statistically significant (raw p-value < 0.01 and fdr < 0.05 and 1.5-fold change (up or down) in expression level in different treatment samples.

source_name: male C57BL/6 mouse, day 3 post-MRSA infection

tag: gender

value: male

value: lung

value: methicillin-resistant Staphylococcus aureus (MRSA) infection

tag: time post-mrsa infection

value: 3 day


title: IEC_GF-HDAC3ΔIEC -3


title: spermatid_mutant_rep1

value: mixed C57BL/6J and FVB/NJ

value: round spermatids


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_wild-type_rep2

description: This sample correspond to wild-type Enterococcus faecalis OG1RF strain, second of two technical microarray hybridization replicates.

source_name: Enterococcus faecalis  OG1RF wild-type

value: Wild-type

value: normal


title: s2013 6h n=1.AVG_Signal

description: replicate 1

tag: timepoint


title: IEC_GF-HDAC3FF -3


title: spermatocyte_control_rep1

tag: strain background

value: spermatocytes


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_copΔ_rep1

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  first of two technical microarray hybridization replicates.

source_name: Enterococcus faecalis  OG1RF copΔ

value: operon cop deletion mutant (copΔ)

value: copper sensitive


title: IEC_GF-HDAC3ΔIEC -2


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_copΔ_rep2

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  second of two technical microarray hybridization replicates.


title: spermatid_control_rep1

source_name: round spermatids_Baz1a+/-

tag: genotype/variation


title: Day 3 post-MRSA wild type infection, sample 3

description: Day 3 post-MRSA wild type infection.

label_protocol: Standard protocol as recommended by Illumina.


title: GEO_MLATORRE2013_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_wild-type_rep1

description: This sample correspond to wild-type Enterococcus faecalis OG1RF strain, first of two technical microarray hybridization replicates.


title: IEC_GF-HDAC3ΔIEC -1


title: s2013 ctl n=1.AVG_Signal

description: replicate 1

value: untreated


title: IEC_GF-HDAC3FF -2


title: Day 1 post-MRSA wild type infection, sample 4

description: Day 1 post-MRSA wild type infection.

source_name: male C57BL/6 mouse, day 1 post-MRSA infection

extract_protocol: Standard protocol as recommended by Illumina.

value: 1 day


title: IEC_HDAC3ΔIEC -2


title: Day 3 post-MRSA wild type infection, sample 2

description: Day 3 post-MRSA wild type infection.


title: Day 3 post-MRSA wild type infection, sample 1

description: Day 3 post-MRSA wild type infection.


title: IEC_HDAC3ΔIEC -3


title: IEC_HDAC3ΔIEC -1


title: IEC_HDAC3FF -3


title: IEC_HDAC3FF -1


title: Case 11_adrenal metastasis_autopsy

status: Public on Nov 11 2013

city: Brisbane

first: Peter

last: Simpson

address: Royal Brisbane & Women's Hospital

department: UQ Centre for Clinical Research

country: Australia

institute: The University of Queensland

hyb_protocol: Labelled DNA was co-hybridised with Cy5 labelled normal female genomic DNA (Promega) to the SurePrint G3 Human CGH Microarray (Platform GPL10152; 8x60k AMDID design ID 0212924, Agilent Technologies)

scan_protocol: Slides were scanned on an Agilent C DNA scanner, with profile G3_CGH with a 3 μm resolution.

data_processing: Data was extracted from scanned images and processed using Feature Extraction software (v10.7; Agilent Technologies) and the default protocol CGH_107_Sep09.

source_name: Tumour genomic DNA

label_protocol: 250ng dsDNA was labelled with Cy3 using the ULS labelling system for formalin fixed paraffin embedded samples (Agilent Technologies).

extract_protocol: Tumour cores were punched from the FFPE blocks to enrich for tumour epithelial cells. Extraction of genomic DNA from these FFPE cores was performed using the DNeasy Blood and Tissue Kit (QIAGEN) according to the manufacturer’s instructions with the following exceptions (i)  tissue samples were pre-treated in 1M sodium thiocyanate overnight at 37oC to remove cross-links and (ii) an extended tissue digestion step was performed over three nights with supplementary Proteinase K added every 24 hours. Eluted DNA was further purified by ethanol precipitation and then assessed for purity using the Nanodrop-2000 and double stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer’s instructions.

value: female

tag: disease

value: breast cancer

tag: tumor type

value: adrenal metastasis

source_name: normal female genomic DNA (Promega)

tag: dna source

value: reference DNA (Promega)


title: Case 33_liver metastasis_autopsy

value: liver metastasis


title: Day 1 post-MRSA wild type infection, sample 2

description: Day 1 post-MRSA wild type infection.

value: male

value: lung


title: Case 11_lung metastasis_autopsy

value: lung metastasis


title: Case 11_lymph node (non axillar) metastasis_autopsy

value: lymph node (non axilla) metastasis


title: Case 11_breast primary_autopsy

value: breast primary


title: IEC_HDAC3FF -2

value: large intestine

tag: genotype


title: Case 33_breast primary_surgical

value: normal


title: Case 15_liver metastasis_autopsy


title: Day 1 post-MRSA wild type infection, sample 1

description: Day 1 post-MRSA wild type infection.

value: methicillin-resistant Staphylococcus aureus (MRSA) infection


title: Case 7_adrenal metastasis_autopsy


title: Day 1 post-MRSA wild type infection, sample 3

description: Day 1 post-MRSA wild type infection.


title: Case 7_lung metastasis_autopsy


title: Case 15_lymph node metastasis_surgical

value: lymph node metastasis


title: Case 13_lung metastasis_autopsy


title: Case 13_lymph node metastasis_autopsy


title: Case 7_liver metastasis_autopsy


title: Case 13_kidney metastasis_autopsy

value: kidney metastasis


title: Case 15_lung metastasis_autopsy


title: Case 1_breast primary_surgical


title: Case 1_ovary metastasis_autopsy

value: ovary metastasis


title: Case 15_breast primary_surgical


title: Case 33_lymph node metastasis_autopsy


title: Case 7_lymph node metastasis_autopsy


title: Case 7_lymph node metastasis_surgical


title: Case 15_adrenal metastasis_autopsy


title: Case 7_breast primary_surgical


title: Case 13_breast primary_surgical


title: Case 1_brain metastasis_autopsy

value: brain metastasis


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 10

city: Suita

first: Hiroshi

last: Takeyama

state: Osaka

address: Yamada-oka 2-2

department: Gastroenterological Surgery

institute: Graduate School of Medicine, Osaka University

hyb_protocol: Cy3-labeled samples were hybridized with the miRNA Complete Labeling and Hyb Kit(Agilent, Santa Clara,CA,USA) acording to the manufacture's procedure.

scan_protocol: Microarray slides were scanned with Agilent G2505C scanner. The sanned image files were analyzed using Agilent FeatureExtraction software ver 10.7.3.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1(Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid:021827_D_F_20100604) to obtain background subtracted and spatially detrended Processed Signal intensities.  The signal values were 90 percentile normalization with Agilent GeneSpring ver11.5.1

label_protocol: 100 ng totalRNA samples  were labeled and hybridized with the miRNA Complete Labeling and Hyb Kit(Agilent, Santa Clara,CA,USA) in accordance with the manufacture's procedure.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Applied Biosystems, Carlsbad, CA) following the manufacturer’s protocol. Total RNA concentration and purity were assessed with a spectrophotometer. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Colorectal cancer patients were administered anesthesia and 20 mL BM was taken from the right and left anterior iliac crests before surgery. Mononucleated cells were collected using a standard Ficoll-Hypaque gradient technique. To enrich for EpCAM+ cells, CD14+ cells were removed from the whole bone marrow using auto MACSTM pro (Milteny Biotec, Bergisch Gladbach, Germany) with anti-CD14 immunomagnetic beads (clone; TÜK4, Milteny Biotec). Next, CD45+ cells were removed by treatment with anti-CD45 immunomagnetic beads (clone; 5B1; Milteny Biotec). The residual CD14−CD45− cells were then incubated with FcR blocking reagent (Milteny Biotec), followed by incubation with anti-EpCAM immunomagnetic beads (clone; HEA-125, Milteny Biotec), and the CD14−CD45−EpCAM+ cells were taken up.

value: CD14-CD45-EpCAM+ cells

tag: group

value: non liver metastasis

tag: age


title: Case 1_lymph node metastasis_surgical

value: female

value: breast cancer


title: CD14-CD45-EpCAM+ cells In bone marrow, liver metastasis group, replicate 4

value: liver metastasis


title: CD14-CD45-EpCAM+ cells In bone marrow, liver metastasis group, replicate 7


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 12


title: CD14-CD45-EpCAM+ cells In bone marrow, liver metastasis group, replicate 6

value: male


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 9


title: CD14-CD45-EpCAM+ cells In bone marrow, liver metastasis group, replicate 1


title: Case 1_liver metastasis_autopsy

value: reference DNA (Promega)


title: CD14-CD45-EpCAM+ cells In bone marrow, liver metastasis group, replicate 5


title: LPC transplant day 8 (on dox), replicate2

first: Edward

middle: R.

last: Kastenhuber

department: Cancer Biology & Genetics

institute: Memorial Sloan-Kettering Cancer Center

description: gene expression data from liver tumors after p53 reconstitution

hyb_protocol: Samples were hybridized using the Affymetrix Hybridization, Wash and Scan kit (P/N 900720) according to Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2), using fluidics protocol FS450_0004 in a GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Command Console Software on a 3000 7G Affymetrix GeneChip Scanner (P/N GCS 3000)

data_processing: Raw data were RMA normalized using the limma package version 3.14.4 (Smyth, 2005) in R (http://cran.us.r-project.org/)

source_name: p53-deficient, liver progenitor cell-derived tumors after p53 reconstitution

label_protocol: Samples were Amplified by a Modified T7 IVT, with Ambion's Message Amp II Biotin Enhanced kit according to Manufacturer's instruction.

growth_protocol: LPCs were othotopical transplanted into recipient livers.

treatment_protocol: mice were treated with or without Doxycycline containing chow.

value: Liver Tumor


title: LPC transplant day 8 (on dox), replicate1


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 11


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 7


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 8


title: CD14-CD45-EpCAM+ cells In bone marrow, liver metastasis group, replicate 3


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 5


title: LPC transplant day 0 (off dox), replicate1

description: gene expression data from liver tumors expressing p53 shRNA

source_name: p53-deficient, liver progenitor cell-derived tumors


title: CD41+ HPC biological replicate 3

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

description: Gene expression data for CD41 hematopoietic cells isolated from pooled E8.5 mouse concepti

hyb_protocol: Hybridisation for 16 hr at 45C onto Affymetrix Mouse Genome 430 2.0 arrays by standard protocols at the Stanford Protein and Nucleic Acid facility

scan_protocol: Genechip Scanner 3000 7G

data_processing: CEL files were normalised using RMA normalisation in the affy package.

source_name: VE-Cad+ Ter119- CD45- CD41+ 23GFP+ cells from E8.5 conceptus

label_protocol: Labelled and fragmented using WT Ovation cDNA Biotin Module v2 (NuGEN)

growth_protocol: E8.5 embryos were genotyped and staged by counting somite pairs.

extract_protocol: Trizol extraction of total RNA according to manufacturers instructions and purified using RNeasy Micro kit. Samples were amplified using WT-Ovation Pico RNA amplification system (NuGEN).

treatment_protocol: Concepti were pooled and incubated for 20 mins at 37 degrees C in PBS with 10%FCS, 50U/ml penicillin and 50ug/ml streptomycin and 0.12% collagenase type I. A single cell suspension was generation by manual pipetting. Antibody staining was performed, and specific cell populations were isolated by FACS.

tag: genetic background

value: mixed (CBA x C57BL/6)

tag: cell type


title: 23GFP- EC biological replicate 2

description: Gene expression data for 23GFP- endothelial cells isolated from pooled E8.5 mouse concepti

source_name: VE-Cad+ Ter119- CD45- CD41- 23GFP- cells from E8.5 conceptus


title: CD14-CD45-EpCAM+ cells In bone marrow, liver metastasis group, replicate 2

tag: tissue


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 4


title: CD41+ HPC biological replicate 2

value: VE-Cad+ Ter119- CD45- CD41+ 23GFP+ cells from E8.5 conceptus


title: 23GFP+ EC biological replicate 3

description: Gene expression data for 23GFP+ endothelial cells isolated from pooled E8.5 mouse concepti

source_name: VE-Cad+ Ter119- CD45- CD41- 23GFP+ cells from E8.5 conceptus


title: 23GFP+ EC biological replicate 2

value: VE-Cad+ Ter119- CD45- CD41- 23GFP+ cells from E8.5 conceptus


title: 23GFP- EC biological replicate 3

value: VE-Cad+ Ter119- CD45- CD41- 23GFP- cells from E8.5 conceptus


title: CD41+ HPC biological replicate 1


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 1


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 2


title: G3ntES-2

city: Beijing

first: le

middle: rong

last: rong

state: Beijing

department: Gaoshaorong lab

country: China

institute: NIBS

description: G3 Terc-/- ntES-2

hyb_protocol: Hybridization, Wash and Stain Kit(Affymetrix, Inc.)

scan_protocol: GeneChip Scanner 3000 7G3000 (Affymetrix, Inc.)

data_processing: GCOS 1.4 software provided by Affymetrix

source_name: nuclear-transferred embryonic stem cell derived from G3 Terc-/- mice tail tip fibroblast

label_protocol: WT Terminal Labeling Kit (Affymetrix, Inc.)

growth_protocol: cultured on mitomycin C treated MEFs in ESM

extract_protocol: following manufacturer recommendation using Trizol reagent (Invitrogen)

value: nuclear-transferred embryonic stem cell

tag: strain

value: G3 Terc-/-


title: LPC transplant day 0 (off dox), replicate2


title: G3ntES-1

description: G3 Terc-/- ntES-1


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate3


title: G3iPS-3

description: G3 Terc-/- iPS-3

source_name: inducible pluripotent stem cell derived from G3 Terc-/- mice tail tip fibroblast

value: inducible pluripotent stem cell


title: 23GFP- EC biological replicate 1


title: G3iPS-1

description: G3 Terc-/- iPS-1


title: G3ntES-3

description: G3 Terc-/- ntES-3


title: HPSG-HLJ220-CGH

status: Public on Nov 10 2013

first: yuanhai

last: you

address: Changbai road 155,Changping district

institute: intitute of communicable disease control and prevention,China CDC

description: chronic superficial gastritis (HLJ220,HLJ215),atrophic gastritis (HLJ193,HLJ256), gastric ulcer (HLJ271,HLJ253), gastric cancer (HLJ038,HLJ005),reference strain (26695)

hyb_protocol: Microarrays were pre-hybridized with 6×SSPE containing 0.05% Tween-20, 5×Denhardt’s solution, and 100 ng salmon sperm DNA for 30 min at 50°C. TheCy5-ULS labeled DNA fragments were then hybridized in the hybridizing solution(6× SSPE and 0.05% SDS) by denaturing at 95°C for 3 min and then incubating for16 h at 50°C. Post-hybridization wash steps were 6× SSPET for 5 min at 50°C,3×SSPET for 1 min, 0.5× SSPET for 1 min, and PBST for 1 min at room temperature. After hybridization and imaging, the microarray was stripped using CustomArrayTM Stripping Solution.

scan_protocol: Hybridized microarrays were covered with imaging solution and scanned with an Axon GenePixTM 4000B.

data_processing: Data was extracted by using Microarray_Imager_5.9.3 software. The foreground median of each spot was taken into following analysis. Information of probe location and corresponding hybridization signals were extracted for further analysis. For ease of analysis, all genes were separated into two independent files, one including genes located in H.pylori P12 genome, another including strain specific genes in each of the other strains which are named chromosome 1~6 respectively (also including P12 strain specific genes). Isolates of gastric cancer were represented as GC, isolates of gastric ulcer were represented as GU, isolates of chronic superficial gastritis were represented as SG, and isolates of atrophic gastritis were represented as AG. Signal comparison were performed between the two strains in GC,GU,SG and AG group respectively.and by GC vs GU,GU vs AG,GC vs SG and AG vs SG. Signal ratios of two hybridized strains were log2 transformed and imported into a web tool ADaCGH, which was used for the analysis of microarray datasets to obtain gains and losses of genes between two genomes. The data was centered and segmented in ADaCGH by employing a position-dependent segmentation algorithm CBS (circular binary segmentation) to partition data points into absent, present and no change sequence segments

organism: Helicobacter pylori

label_protocol:
Four microgram of heated DNA from each H.pylor strain was labeled with
Cy5-ULS using the Kreatech ULS array CGH Labeling kit (EA-005, Kreatech,Netherlands) according to the manufacturer’s instructions and then hybridized to the microarray. Experiments were performed according to CombiMatrix protocol.

growth_protocol: H. pylori strains were routinely cultured for 24 h on Columbia agar plates (Oxoid) containing 5% goat blood under microaerophilic conditions at 37℃, following a wash in sterile PBS.

treatment_protocol:
Genomic DNA was extracted by using the Dneasy Blood & Tissue Kit (QIAGEN)according to the manufacturer’s instructions. The concentration of genomic DNA wasadjusted to 120ng/μl with nuclease-free water and to a volume of 40μl. DNA washeated in a PCR machine (Biorad, USA) at 95℃ for 10min to obtain DNA fragments
with sizes of 100bp to 600bp for genomic labeling. The results were visualized by 1% agarose gel electrophoresis.

value: HLJ220 (chronic superficial gastritis)


title: HPAG-HLJ256-CGH

extract_protocol: Genomic DNA was extracted by using the Dneasy Blood & Tissue Kit (QIAGEN)according to the manufacturer’s instructions

value: HLJ256 (atrophic gastritis)


title: HPSG-HLJ215-CGH

value: HLJ215 (chronic superficial gastritis)


title: HPGC-HLJ038-CGH

value: HLJ038 (gastric cancer)


title: G3iPS-2

description: G3 Terc-/- iPS-2