description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-Low    ;Rep.5 (M36F005.0X.5)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: genomic DNA concentration-0X


status: Public on Nov 06 2014

type: RNA

city: Pittsburgh

first: Victoria

last: Plamadeala

state: Pennsylvania

address: 2516 Jane St

country: USA

institute: Precision Therapeutics

description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-Low    ;Rep.4 (M36F005.0X.4)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

hyb_protocol: Fragmented and labelled cDNA was hybridized to HG-U133 Plus 2.0 microarray (Affymetrix) at 45C for 18 hours at a rotation speed of 60rpm. Arrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash & Stain kit in the Affymetrix FS450Dx2 Fluidics Station.

scan_protocol: Arrays were scanned on the GeneChip System 3000Dx v.2 (Affymetrix) using the HG-U133+2.0 protocol.

data_processing: RefRMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lung

label_protocol: Extracted total RNA was amplified using the Ovation Pico WTA System V2 (NuGEN Technologies, Inc.) and then fragmented and labelled with the Encore Biotin Module (NuGEN Technologies, Inc.).

growth_protocol: Immediately upon surgical extraction, specimens were either flash frozen and stored at -80C or placed in RNAL. Specimens were not subjected to any type of growth environment between surgical extraction and total RNA extraction.

extract_protocol: Total RNA was extracted from each specimen via a phenol-chloroform protocol.

treatment_protocol: Specimens were treated in 2 different ways to ensure stabilization of genomic material, notably total RNA.  Specimens were either flash frozen and then stored at -80C or placed immediately in RNAL.

tag: study

value: SPECIFICITY STUDY

tag: tissue

value: non-small-cell lung carcinoma

tag: agent

tag: risk

value: low


title: RNA_24hours_subjectF

city: Cambridge

first: Emma

middle: Elisabeth

last: Davenport

state: Cambridgeshire

address: Hinxton

country: United Kingdom

institute: Wellcome Sanger Institute

hyb_protocol: The amplified biotin-labeled cRNA were used for hybridisation with the Illumina HumanHT-12 V4.0 Expression Beadchip.

scan_protocol: The hybridised Illumina arrays were scanned using Illumina iScan scanner.

data_processing: Background signals were subtracted. Two samples were identified as outliers and removed (F_t12 and U_t24).  11,158 low expression probes (detection value < 0.95) were removed. The raw data were transformed and normalised using the Variance Stabilization and Normalization method in R.

label: Biotin

source_name: Peripheral blood RNA, 24 hours post influenza challenge

label_protocol: Biotin-labeled cRNA were generated using the Illumina TotalPrep-96 Amplification Kit.

extract_protocol: Total RNA was extracted from whole blood using the PAXgene Blood RNA Kit. Globin depletion was carried out using the GLOBINclear Human kit.

tag: timepoint

value: 24 hours post-challenge

tag: vaccination status

value: Vaccinee

tag: symptom severity

value: Mild

tag: seroconversion

value: Negative

tag: viral shedding


title: DNA_29_pRCC2

type: genomic

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridizated with the Perkin Elmer hybridization Kit according its recommendations

scan_protocol: Slide was scaned on an Innopsys 700 scanner

data_processing: Data were analysed with SpectralWare software supplied by Perkin Elmer (unknown default parameters)

molecule: genomic DNA

source_name: Renal Cells Tumor

label_protocol: DNA was labeled with the Perkin Elmer labeling Kit according its recommendations

extract_protocol: Dna was extcracted from fresh or frozen fragment with the QIAmp DNA Mini Kit

tag: cell type

value: Papillary renal cell carcinoma (pRCC)

tag: rcc type

value: type 2

source_name: Promega Human Genommic DNA (G1471/G1521)

tag: sample type

value: reference


title: RNA_12hours_subjectF

source_name: Peripheral blood RNA, 12 hours post influenza challenge

value: 12 hours post-challenge


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-Low    ;Rep.2 (M36F005.0.5X.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: genomic DNA concentration-1/2X


title: DNA_27_pRCC2


title: DNA_21_pRCC2


title: DNA_16_pRCC2


title: DNA_24_pRCC2


title: DNA_3_pRCC1

value: type 1


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-Low    ;Rep.3 (M36F005.0X.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_0hours_subjectF

source_name: Peripheral blood RNA, pre influenza challenge

value: Pre-challenge


title: Metastatic_rep4

city: South San Francisco

first: Josh

last: Kaminker

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

description:
Sample name: BIO116264
Gene expression of lung, Metastatic_rep4

hyb_protocol: The method for hybridization of the arrays was provided by Affymetrix. Fifteen micrograms of cRNA was fragmented and hybridized to Mouse430v2 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained in the Affymetrix Fluidics station and scanned on GeneChip scanner 3000.

data_processing: Data analysis was performed using the Affymetrix GeneChip operating system and analysis software.

organism: Mus musculus

source_name: Lung, Metastatic_rep4

label_protocol: The method for prepartation of cRNA was provided by Affymetrix. Briefly, 3 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice (Invitrogen) and a T7-(dT) primer (Biosearch Technologies, Inc.). cDNA was purified using Sample Cleanup Module Kit (Affymetrix) and used to generate biotin labeled cRNA using an in vitro transcription kit (Enzo Diagnostics, Inc.,).  The labeled cRNA was purified using Sample Cleanup Module Kit (Affymterix).

growth_protocol: BALB/c mice were injected with nonmetastatic 67NR or metastatic 4T1 cells. Control (naïve) mice received PBS only.

extract_protocol: Total DNA-free RNA was prepared from PBS-perfused lungs with the RNeasy kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: Six days after tumor cell inoculation (or when tumors reached about 50 mm3), mice were euthanized, and lungs were perfused with PBS to completely remove blood from the lung vasculature. Cleaned lung lobes were immersed in RNAlater (Qiagen) to stabilize RNA.

tag: strain

value: BALB/c

tag: treatment

value: 4T1 mouse breast carcinoma cell line injected into fourth mammary fat pad of BALB/c mouse

value: Lung, Metastatic


title: RNA_48hours_subjectE

source_name: Peripheral blood RNA, 48 hours post influenza challenge

value: 48 hours post-challenge

value: Positive


title: RNA_12hours_subjectE


title: RNA_48hours_subjectD

value: Moderate/severe


title: RNA_24hours_subjectD

value: 24 hours post-challenge


title: RNA_24hours_subjectE

value: Vaccinee


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-Low    ;Rep.1 (M36F005.0X.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SPECIFICITY STUDY

value: non-small-cell lung carcinoma

value: genomic DNA concentration-0X

value: low


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-High   ;Rep.2 (M36F004.1X.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: genomic DNA concentration-1X

value: high


title: RNA_0hours_subjectD


title: RNA_12hours_subjectD

value: 12 hours post-challenge


title: RNA_0hours_subjectE

value: Negative


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-Low    ;Rep.2 (M36F005.0X.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-High   ;Rep.1 (M36F004.1X.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-High   ;Rep.4 (M36F004.0.5X.4)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: genomic DNA concentration-1/2X


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-High   ;Rep.5 (M36F004.1X.5)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-High   ;Rep.2 (M36F004.0.5X.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-High   ;Rep.3 (M36F004.0.5X.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-High   ;Rep.3 (M36F004.1X.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_24hours_subjectC

value: Mild


title: RNA_48hours_subjectB


title: RNA_12hours_subjectC


title: RNA_48hours_subjectC


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-High   ;Rep.1 (M36F004.0.5X.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-High   ;Rep.5 (M36F004.0X.5)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-High   ;Rep.4 (M36F004.0X.4)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-High   ;Rep.4 (M36F004.1X.4)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_12hours_subjectB


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-High   ;Rep.3 (M36F004.0X.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-High   ;Rep.5 (M36F004.0.5X.5)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_24hours_subjectB


title: RNA_0hours_subjectC

value: Pre-challenge


title: RNA_0hours_subjectB


title: Risedronate, biological rep 3

city: New York

first: Tony

last: Yuen

state: NY

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from human osteoclasts treated with 100 nM risedronate

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Differentiating peripheral blood mononuclear cells_Risedronate

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

growth_protocol: Peripheral blood mononuclear cells (PBMC) were collected and pooled from 3 human donors using Ficoll gradients (Histopaque 1077).  Cells were seeded at a density of 1.5 million/cm^2 and grown for 4 days in the presence of 50 ng/mL M-CSF.

extract_protocol: Total RNA was isolated using Qiagen RNeasy according to the manufacturer's instructions.

treatment_protocol: After 4 days, cells were grown in a culture medium containing 30 ng/mL M-CSF and 50 ng/mL RANKL, and were treated with either vehicle, 100 nM alendronate, or 100 nM risedronate.  The cells were then grown for another 8 days, with a change of the medium every 4 days.


title: RNA_0hours_subjectA


title: RNA_48hours_subjectA


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-High   ;Rep.1 (M36F004.0X.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_12hours_subjectA


title: Risedronate, biological rep 2

value: Differentiating peripheral blood mononuclear cells


title: RNA_24hours_subjectA


description:
SPECIFICITY STUDY::Concentration-0X   ;Risk-High   ;Rep.2 (M36F004.0X.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: Alendronate, biological rep 2

description: Gene expression data from human osteoclasts treated with 100 nM alendronate

source_name: Differentiating peripheral blood mononuclear cells_Alendronate


title: Risedronate, biological rep 1


title: Alendronate, biological rep 1


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-Low    ;Rep.5 (M36F005.0.5X.5)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: Vehicle, biological rep 1

description: Gene expression data from human osteoclasts treated with vehicle

source_name: Differentiating peripheral blood mononuclear cells_vehicle


title: KO MEF 3

city: Richmond

first: Joseph

middle: William

last: Landry

state: Virginia

address: 401 College Street

department: Human and Molecular Genetics

institute: Virginia Commonwealth University

description:
5935260027_F_KO MEF 3
KO Replicate 3

hyb_protocol: Labeled RNA was hybridized to BeadChip arrays, washed and detected using standard Illumina protocols.

scan_protocol: BeadChips were scanned using default setting on BeadChip work station.

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R.

source_name: Mouse embryonic fibroblasts, Bptf KO

label_protocol: Total RNA was amplified and labeled with biotinylated nucleotides using Ambion Message Map kit cRNA kit according to standard protocols.

growth_protocol: Mouse embryonic fibroblasts were prepared from 12.5 dpc embryos according to standard protocols. Cells were maintained in DMEM supplemented with 10% FBS, 1x Pen/Strep, 1 mM glutamine, 1X NEAA. Cells were grown at 37 C in 5% CO2 and passaged prior to confluence.

extract_protocol: At day 10, total RNA was harvested from cells using Trizol, and further purified using a Qiagen RNeasy minikit.

treatment_protocol: Mouse embryonic fibroblasts with an inducible knockout genotype (TetO-Cre, rtTA, Bptf Floxed/Floxed), and control mouse embryonic fibroblasts (rtTA, Bptf Floxed/Floxed) were induced with 10ug/ml doxycycline for 48 hours. Following 48 hour doxycycline induction, the cells were passaged for 8 days to deplete the fibroblasts of residual Bptf protein.

tag: strain/background

value: C57/B6x129 mixed background

tag: genotype/variation

value: Bptf KO

tag: age

value: mouse embryonic fibroblasts


title: EC-6-INVASIVE

status: Public on Nov 05 2014

city: Santiago de Compostela

first: Miguel

last: Abal

state: A Coruña

address: Trav Choupana s/n

department: Medical Oncology

country: Spain

institute: University Clinical Hospital

hyb_protocol: Samples were prepared and hybridized to GeneChip Human Tiling 1.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 TGPLUS according to manufacturer's instruction.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. CEL files were imported Partek Genomic Suite 6.5 software, pre-normalized using the Robust MultichIp algorithm and converted to log2. With the purpose of detecting genes that ETV5 binds differently at the invasive front, the mean signal from each probe corresponding to the superficial zone was substracted to that of the invasion front across all probes.  Statistical parameters were set as p<0.005 (paired t test).

label_protocol: Samples were labelled using the GeneChip Wtdouble-Stranded DNA Terminal Labeling Kit according to Affymetrix specifications.

extract_protocol: Upon chromatin cross-linking in 1% formaldehyde, tissue from paired samples corresponding to the superficial zone and invasive front from 6 endometrial carcinomas (30mg) was disaggregated in 600μl of ChIP lysis buffer (PIC, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After sonication (Branson sonifier 150; Biogen), chromatin fragments (200-1000bp) were pre-cleared with 100 μl of Protein G Agarose/Salmon Sperm DNA beads (Millipore, California, USA). Immunocomplexes of chromatin fragments and ETV5 antibodies (10 µg; Santa Cruz Biotechnologies) were recovered with G protein beads and de-cross-linked (5M NaCl at 65 °C overnight). Resulting DNA was purified using the QIAquick PCR purification kit (Qiagen, Hilden, Germany),

tag: antibody

tag: antibody source

value: ETV5 (H-100)X; sc-22807X; lot#B1904; Rabbit polyclonal IgG; Santa Cruz Biotech, CA, USA

value: endometrial carcinoma

tag: tumor region

value: invasive front


title: KO MEF 1

description:
5935260027_A_KO MEF 1
KO Replicate 1


title: EC-5-INVASIVE


title: EC-6-SUPERFICIAL

value: superficial zone


title: Control MEF 3

description:
5935260027_E_Control MEF 3
Control Replicate 3

source_name: Mouse embryonic fibroblasts, control

value: control


title: Alendronate, biological rep 3


title: EC-5-SUPERFICIAL


title: EC-4-SUPERFICIAL


title: EC-3-INVASIVE


title: EC-4-INVASIVE


title: Control MEF 1

description:
5935260027_B_Control MEF 1
Control Replicate 1


title: KO MEF 2

description:
5935260027_C_KO MEF 2
KO Replicate 2


title: EC-3-SUPERFICIAL


title: Vehicle, biological rep 3


title: Control MEF 2

description:
5935260027_D_Control MEF 2
Control Replicate 2


title: EC-2-SUPERFICIAL


title: EC-1-INVASIVE


title: EC-2-INVASIVE


title: Vehicle, biological rep 2


title: EC-1-SUPERFICIAL


title: 021N01_130925

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

country: Germany

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

description: Genomic profiling of single white blood cells (WBCs). WBCs were used as control samples to validate the assay and to select the most optimal settings to process single-cells extracted from the CellSearch System

hyb_protocol: Array CGH was performed on oligonucleotide-based SurePrint G3 Human CGH 4x180K microarray slides (design code: 022060) according the protocol provided by the manufacturer (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.1, December 2011) with slight modifications. The hybridization mix consisted of 5.0 µg of Cot1-DNA (Roche Diagnostics), 12 µl of 10x Blocking Reagent (Agilent Technologies), 60 µl of 2x Hi RPM Hybridization Buffer, 1% (v/v) of both Tween20 and Igepal and 19 µl of test and reference DNA. For each hybridization 100 µl of the hybridization mix was applied on the array and hybridized at 65◦C for 24 h. Following the hybridization, the slides were washed sequentially: twice for 2:30 min in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technologies) at room temperature and twice for 30 sec min in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technologies) at 37◦C. Washed slides were immersed in acetonitrile to remove all remaining traces of the wash buffers.

scan_protocol: Scanned on an Agilent G2565CA scanner (Dye channel: R+G; Scan resolution: 2.5µm, double pass; Tiff file dynamic range: 16 Bit; Red PMT gain: 100%; Green PMT gain: 100%; No XDR)

data_processing:
Microarray TIFF image files were processed with the Agilent Genomic Feature Extraction Software (version 10.7.3.1). The resulting text files were imported and analyzed with Agilent Genomic Workbench Software (version 6.5.0.18 Lite). Aberrant regions were recognized using ADM-2 algorithm with threshold set to 7.0. Centralization algorithm was set to a threshold of 6.0 and bin size of 10. To avoid false positive aberration calls, aberration filters were applied to define the minimum log2 ratio (minAvgAbsLogRatio = 0.25) and the minimum number of probes in an aberrant interval (minimum number of probes in an interval = 50).
The normalization algorithm is an integral part of the standard data extraction/normalization algorithm (CGH_107_Sep09) protocol implemented in the Agilent Feature Extraction Software v10.7. Exactly this version of software in combination with extraction/normalization algorithm stated above were used to process the data generated for my submission.

source_name: Circulating tumor cells collected from peripheral blood of breast cancer patients

label_protocol: Single-cell WGA samples were labeled using a previously published PCR-based approach. Prior to labeling, the primary WGA products were reamplified by PCR. Reamplification of the WGA products and the subsequent labeling were conducted as decribed by Czyz ZT et al., PLoS One. 2014 Jan 21;9(1):e85907.

growth_protocol: Not applicable. Samples for the analysis were collected from peripheral blood. No cell culture protocols were applied on the blood cells prior to sample processing.

extract_protocol: Cancer patients: following the enrichment with the CellSearch System single cells and cell pools were extracted using the DEPArray System. Subsequently, DNA from single-cell and cell pools were amplified using the Ampli1 WGA Kit. Healthy donors: single-cell were collected in non-automatized manner using an inverted microscope equipped with a micromanipulator. Single-cell specimens were processed using the Ampli1 WGA Kit.

treatment_protocol: Cancer patients: 7.5 mL of peripheral blood was collected into a CellSave preservative tube. Following enrichment and enumeration of circulating tumor cells (CTCs) by use of the CellSearch System, single CTCs, single white blood cells (WBCs) and CTC cell pools were collected using the DEPArray System. Single-cell specimens and cell pools were subjected to Ampli1 WGA protocol. The quality of the resulting WGA products was assessed using the Ampli1 QC Kit. Healthy donor: 10 mL of peripheral blood was collected from a healthy female donor. Mononuclear cell fraction was enriched using centrifugation in density gradient of Percoll. Single-cell were picked in a manual fashion using the micromanipulator and subjected to whole genome amplification using the Ampli1 WGA Kit. The quality of the resulting WGA products was assessed using the Ampli1 QC Kit. Four high quality single-cell WGA products were pooled and used as reference sample for array CGH.

tag: patient id

tag: origin

value: Clinical Sample

tag: breast cancer patient/heathy donor

value: breast cancer patient

tag: gender

value: female

tag: enrichemnt/isolation procedure

value: CellSearch® System/DEPArray™ System

value: White Blood Cell (WBC)

tag: expressed markers

value: Cytokeratin (+); CD45(+); DAPI(+)

tag: product

value: Single-cell WGA product

tag: method of whole genome amplification (wga)

value: Ampli1™ WGA Kit (Silicon Biosystems)

value: Reference Female

value: Percoll density centrifugation/Manual isolation of single cells

source_name: White blood cells (WBCs) collected from peripheral blood of ahealthy female individual

value: healthy donor

value: Mix of 4 single-cell WGA products


title: S0088202

city: Austin

first: Christopher

last: Daige

address: 2150 Woodward street, suite 100

institute: Mirna Therapeutics

description:
Sample name: MRX34 1 mg/kg 3-4
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft

hyb_protocol: cRNA were hybridized at Asuragen Inc following their established SOP's

scan_protocol: GENEChips were scanned at Asuragen Inc following their established SOP's

data_processing: Data were globally normalized using RMAExpress software

source_name: Tumor

label_protocol: cRNA were labeled at Asuragen Inc following their established SOP's

growth_protocol: Nod/Scid mice were surgically implanted with 1 x 106 cultured HuH7 cells and tumors were allowed to grow for ~ 5 weeks

extract_protocol: RNA was isolated from whole tumors using the mirVana PARIS RNA isolation Kit (Lifetech; cat# AM1556, or equivalent)

treatment_protocol: Animals received a single IV injection of test or control articles 24 hours prior to sacrifice

tag: cell line

tag: surgically implanted into

value: livers of Nod/Scid mice

tag: tissue

value: HuH7 orthotopic liver tumors


title: S0088201

description:
Sample name: MRX34 1 mg/kg 3-3
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft

tag: treatment


title: 108T10_130725

description: Genomic profiling of single circulating tumor cells (CTCs) from advanced breast cancer patients.

tag: cell type

value: Circulating Tumor Cell (CTC)

value: Cytokeratin (+); CD45(-); DAPI(+)


title: 108P1_140509

value: Cell pool WGA product


title: S0088199

description:
Sample name: MRX34 1 mg/kg 3-1
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft


title: 070N01_130925

value: Clinical Sample


title: S0088198

description:
Sample name: Empty Liposomes 2-4
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft

value: control (Empty Liposomes)


title: 108N02_130925

value: breast cancer patient

value: female


title: S0088683

description:
Sample name: MRX34 1 mg/kg 4-2
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft


title: 082P1_140509

value: CellSearch® System/DEPArray™ System

value: White Blood Cell (WBC)


title: 069P1_140509


title: S0088197

description:
Sample name: Empty Liposomes 2-3
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft


title: 071P1_140509


title: 108T03_130725

value: Single-cell WGA product


title: 108T07_130725

value: Ampli1™ WGA Kit (Silicon Biosystems)


title: 064N02_130925

value: Cytokeratin (+); CD45(+); DAPI(+)

value: Reference Female


title: 106T01_130129

value: Percoll density centrifugation/Manual isolation of single cells

value: healthy donor


title: 108T08_130827

value: Mix of 4 single-cell WGA products


title: 106T02_130226


title: S0088196

description:
Sample name: Empty Liposomes 2-2
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft

value: livers of Nod/Scid mice

value: HuH7 orthotopic liver tumors


title: 106T04_130211

value: Circulating Tumor Cell (CTC)

value: Cytokeratin (+); CD45(-); DAPI(+)


title: 108T06_130725

value: Clinical Sample


title: 108T02_130725


title: 082T09_130606


title: 106T03_130211


title: 090T02_130606


title: 082T13_130606


title: 082T06_130606


title: 082T02_130606


title: S0088192

description:
Sample name: Dilution Buffer 1-2
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft

value: control (Dilution Buffer)


title: S0088191

description:
Sample name: Dilution Buffer 1-1
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft


title: Blood_HV25

city: Lyon

first: Marie-Angélique

last: Cazalis

address: Pl, Arsonval

institute: LCR HCL-bioMérieux

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

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000.

data_processing: The data were normalized using RMA methods.

source_name: Temoin HV25

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

extract_protocol: Whole blood Paxgene tubes extraction

tag: age

value: FEMALE

tag: sapsii


title: 078T04_130717

value: breast cancer patient

value: female


title: Blood_HV23

source_name: Temoin HV23


title: 075T04_130717

value: CellSearch® System/DEPArray™ System

value: White Blood Cell (WBC)


title: Blood_HV24

source_name: Temoin HV24


title: Blood_HV22

source_name: Temoin HV22


title: Blood_HV21

source_name: Temoin HV21


title: S0088194

description:
Sample name: Dilution Buffer 1-4
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft


title: Blood_HV19

source_name: Temoin HV19


title: 071T05_130416

value: Single-cell WGA product

value: Ampli1™ WGA Kit (Silicon Biosystems)


title: Blood_HV20

source_name: Temoin HV20


title: 070T02_130717

value: Reference Female


title: 075T01_130717

value: Percoll density centrifugation/Manual isolation of single cells


title: 078T07_130717

value: healthy donor


title: Blood_HV16

source_name: Temoin HV16


title: Blood_HV18

source_name: Temoin HV18


title: treatment1: Asti soil - treatment2: 1103-P rootstock - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description:
germplasm name: Pinot noir
organism part: leaf ('PO:0009025')
development stage: A vegetative growth ('PO:0007134')
age: 2-years
growth media: garden soil
Leaves of Pinot noir grafted on Paulsen 1103 rootstock. Plants were grown in 18.5 liter pots with soil from Asti, a North Italy region. (May still include original submitter created erros/discrepancies)

hyb_protocol: Affymetrix vitis vinifera Genechips

scan_protocol: Affymetrix (AGRF)

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Vitis vinifera

source_name: leaf (treatment1: Asti soil - treatment2: 1103-P rootstock)

label_protocol: Affy- Whole transcript target preparation

growth_protocol: Environmental Conditions:  Greenhouse

extract_protocol: RNA Isolation Using Trizol And Qiagen RNAeasy Columns

value: Asti soil + 1103-P rootstock

value: leaf

tag: cultivar

value: Pinot Noir


title: 069T02_130822

value: Circulating Tumor Cell (CTC)

value: Mix of 4 single-cell WGA products


title: treatment1: Asti soil - treatment2: 1103-P rootstock - rep1


title: 069T01_130822

value: Clinical Sample

value: Cytokeratin (+); CD45(-); DAPI(+)


title: treatment1: Asti soil - treatment2: 1103-P rootstock - rep2


title: Blood_HV15

source_name: Temoin HV15

value: FEMALE


title: S0088193

description:
Sample name: Dilution Buffer 1-3
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft

value: livers of Nod/Scid mice

value: control (Dilution Buffer)

value: HuH7 orthotopic liver tumors


title: Blood_HV17

source_name: Temoin HV17


title: 064T07_130822

value: breast cancer patient

value: female

value: CellSearch® System/DEPArray™ System

value: White Blood Cell (WBC)


title: treatment1: Asti soil - treatment2: 101-14 rootstock - rep2

description:
germplasm name: Pinot noir
organism part: leaf ('PO:0009025')
development stage: A vegetative growth ('PO:0007134')
age: 2-years
growth media: garden soil
Leaves of Pinot noir grafted on 101-14 rootstock. Plants were grown in 18.5 liter pots with soil from Asti, a North Italy region. (May still include original submitter created erros/discrepancies)

source_name: leaf (treatment1: Asti soil - treatment2: 101-14 rootstock)

value: Asti soil + 101-14 rootstock


title: S0088195

description:
Sample name: Empty Liposomes 2-1
gene expression data from HuH7 tumors growing in the livers of Nod/Scid mice
liver xenograft

value: control (Empty Liposomes)


title: treatment1: Asti soil - treatment2: 101-14 rootstock - rep3


title: 064T02_130822

value: Single-cell WGA product

value: Ampli1™ WGA Kit (Silicon Biosystems)

value: Reference Female

value: Percoll density centrifugation/Manual isolation of single cells

value: healthy donor


title: 064T03_130822

value: Clinical Sample

value: Circulating Tumor Cell (CTC)

value: Mix of 4 single-cell WGA products


title: 070T01_130717

value: Cytokeratin (+); CD45(-); DAPI(+)


title: Blood_HV13

source_name: Temoin HV13

value: FEMALE


title: treatment1: Sand - treatment2: 1103-P rootstock - rep2

description:
germplasm name: Pinot noir
organism part: leaf ('PO:0009025')
development stage: A vegetative growth ('PO:0007134')
age: 2-years
growth media: garden soil
Leaves of Pinot noir grafted on Paulsen 1103 rootstock. Plants were grown in 18.5 liter pots with sand. (May still include original submitter created erros/discrepancies)

source_name: leaf (treatment1: Sand - treatment2: 1103-P rootstock)

value: sand + 1103-P rootstock

value: leaf

value: Pinot Noir


title: treatment1: Sand - treatment2: 1103-P rootstock - rep1


title: Blood_HV14

source_name: Temoin HV14


title: Blood_HV12

source_name: Temoin HV12


title: treatment1: Asti soil - treatment2: 101-14 rootstock - rep1


title: 061T03_130725

source_name: Circulating tumor cells collected from peripheral blood of breast cancer patients

value: breast cancer patient

value: female

value: CellSearch® System/DEPArray™ System

source_name: White blood cells (WBCs) collected from peripheral blood of ahealthy female individual


title: 061T02_130725

value: White Blood Cell (WBC)


title: 071T06_130416

value: Single-cell WGA product


title: 043T02_130717

value: Ampli1™ WGA Kit (Silicon Biosystems)


title: treatment1: Sand - treatment2: 1103-P rootstock - rep3


title: treatment1: Sand - treatment2: 101-14 rootstock - rep2

description:
germplasm name: Pinot noir
organism part: leaf ('PO:0009025')
development stage: A vegetative growth ('PO:0007134')
age: 2-years
growth media: garden soil
Leaves of Pinot noir grafted on 101-14 rootstock. Plants were grown in 18.5 liter pots with sand. (May still include original submitter created erros/discrepancies)

source_name: leaf (treatment1: Sand - treatment2: 101-14 rootstock)

value: sand + 101-14 rootstock


title: treatment1: Sand - treatment2: 101-14 rootstock - rep1


title: treatment1: Turf - treatment2: 1103-P rootstock - rep3

description:
germplasm name: Pinot noir
organism part: leaf ('PO:0009025')
development stage: A vegetative growth ('PO:0007134')
age: 2-years
growth media: garden soil
Leaves of Pinot noir grafted on Paulsen 1103 rootstock. Plants were grown in 18.5 liter pots with garden soil. (May still include original submitter created erros/discrepancies)

source_name: leaf (treatment1: Turf - treatment2: 1103-P rootstock)

value: turf + 1103-P rootstock


title: Blood_HV11

source_name: Temoin HV11


title: treatment1: Turf - treatment2: 1103-P rootstock - rep2


title: Blood_HV10

source_name: Temoin HV10

value: MALE


title: treatment1: Turf - treatment2: 1103-P rootstock - rep1


title: Blood_HV08

source_name: Temoin HV08


title: treatment1: Turf - treatment2: 101-14 rootstock - rep1

description:
germplasm name: Pinot noir
organism part: leaf ('PO:0009025')
development stage: A vegetative growth ('PO:0007134')
age: 2-years
growth media: garden soil
Leaves of Pinot noir grafted on 101-14 rootstock. Plants were grown in 18.5 liter pots with garden soil. (May still include original submitter created erros/discrepancies)

source_name: leaf (treatment1: Turf - treatment2: 101-14 rootstock)

value: turf + 101-14 rootstock


title: Blood_HV09

source_name: Temoin HV09


title: treatment1: Turf - treatment2: 101-14 rootstock - rep3


title: treatment1: Turf - treatment2: 101-14 rootstock - rep2


title: treatment1: Sand - treatment2: 101-14 rootstock - rep3


title: Experimental group  individual 20

city: London

last: Segal

address: 5 University Street

department: Medicine

institute: UCL

hyb_protocol: Labelled cRNA was hybridised to Illumina Human-WG6 v3.0 Expression BeadChips (Illumina) for 16 h at 58°C

scan_protocol: Scanned using the Beadarray reader

data_processing: Image data was processed using Genome Studio software. The processed data contains 22K due to our in-house filter which only includes probes which have been identified as present in 1 or more sample with a detection cut off p<0.01.

source_name: Monocyte derived macrophage

label_protocol: Biotin-Labelled cRNA

growth_protocol: Peripheral venous blood was collected into syringes containing 5 U/ml heparin. Mononuclear cells were isolated by differential centrifugation (800 g, 30 min, 20ºC) over Lymphoprep. Cells were resuspended in 10 ml RPMI-1640 medium supplemented with 100U/ml of penicillin, 100 μg/ml streptomycin and 20 mM HEPES pH 7.4, and plated at a density of approximately 5x10(6) cells/ml in 8cm2 NunclonTM Surface tissue culture dishes at 37ºC, 5% CO2. After 2h, non-adherent cells were discarded and 10 ml of fresh RPMI supplemented with 10% foetal bovine serum added. Cells were then cultured for 5 days at 37oC, 5% CO2, with the addition of a further 10ml of fresh 10% FBS/RPMI after 24 h. Cells were then washed twice in PBS, scrapped and spun down at 500 g. Cells were resuspended into X-vivo-15 medium and plated at a density of 10(6) cells per 8 cm(2) NunclonTM dish for a further 25 h at 37oC, 5% CO2.

extract_protocol: total RNA extracted using Quiagen RNeasy Mini Kit with RNase–free DNase treatment

treatment_protocol: Macrophages were untreated

tag: assigned group

value: experimental


title: Blood_HV07

source_name: Temoin HV07


title: 038T03_130226

description: Genomic profiling of single circulating tumor cells (CTCs) from advanced breast cancer patients.

tag: patient id

value: Clinical Sample

value: Circulating Tumor Cell (CTC)

value: Reference Female

value: Percoll density centrifugation/Manual isolation of single cells

value: healthy donor

value: Mix of 4 single-cell WGA products


title: 035T05_130211

tag: origin

value: breast cancer patient

value: Cytokeratin (+); CD45(-); DAPI(+)


title: 035T07_130211

tag: breast cancer patient/heathy donor

value: female

value: CellSearch® System/DEPArray™ System


title: Experimental group  individual 17


title: Experimental group  individual 19


title: Blood_HV06

source_name: Temoin HV06

tag: gender


title: 021T03_130822

tag: disease state

tag: enrichemnt/isolation procedure

value: Single-cell WGA product

value: White Blood Cell (WBC)


title: Blood_HV05

source_name: Temoin HV05

value: FEMALE


title: Experimental group  individual 15


title: 035T10_130129

tag: expressed markers

tag: product

value: Ampli1™ WGA Kit (Silicon Biosystems)


title: Experimental group  individual 16


title: Experimental group  individual 18


title: 021T01_130725

tag: method of whole genome amplification (wga)


title: Blood_HV04

source_name: Temoin HV04


title: 023T02_130226


title: Experimental group  individual 14


title: 071N01_130416

description: Genomic profiling of single white blood cells (WBCs). WBCs were used as control samples to validate the assay and to select the most optimal settings to process single-cells extracted from the CellSearch System

value: Cytokeratin (+); CD45(+); DAPI(+)


title: Experimental group  individual 13


title: Blood_HV03

source_name: Temoin HV03

value: MALE


title: 106N01_130129


title: Experimental group  individual 10

value: experimental


title: Blood_HV02

source_name: Temoin HV02


title: Experimental group  individual 11


title: Experimental group  individual 9


title: 061N01_130822

value: Clinical Sample


title: Experimental group  individual 8


title: Experimental group  individual 6


title: Blood_P111_H48

source_name: patient 111, H48

value: SAPSII-High

tag: collection time

value: 48 hr


title: Blood_HV01

source_name: Temoin HV01


title: 038N02_130226

source_name: Circulating tumor cells collected from peripheral blood of breast cancer patients

value: Reference Female

value: Percoll density centrifugation/Manual isolation of single cells

source_name: White blood cells (WBCs) collected from peripheral blood of ahealthy female individual


title: Blood_P111_H24

source_name: patient 111, H24

value: 24 hr


title: Experimental group  individual 5


title: Experimental group  individual 7


title: liver_SM+MSTF_24hr_rep1

city: ShangHai

first: Jian-Zhong

last: Li

address: Guo He Road 325#

country: China

institute: Second Military Medical University

description:
Sample name: S21
Gene expression after 24hr in MSTF administration  3.5 mg/kg SM-treated rat liver

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4×44K Whole Rat Genome Oligo Microarrays  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: Raw data were obtained by Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) and normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: liver,SM+MSTF,24hr,replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the liver tissue of rat using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

value: male

value: SM+MSTF

tag: tissue

value: liver


title: Experimental group  individual 3


title: Experimental group  individual 1


title: control group  individual 20

value: control


title: 035N01_130129

value: breast cancer patient

value: female

value: CellSearch® System/DEPArray™ System

value: Single-cell WGA product

value: healthy donor

value: Mix of 4 single-cell WGA products


title: liver_SM+MSTF_24hr_rep2

description:
Sample name: S22
Gene expression after 24hr in MSTF administration  3.5 mg/kg SM-treated rat liver

source_name: liver,SM+MSTF,24hr,replicate 2

tag: treatment


title: Experimental group  individual 4

value: experimental


title: control group  individual 19


title: Blood_P109_H48

source_name: patient 109, H48

value: FEMALE

value: SAPSII-Low


title: Experimental group  individual 2


title: liver_SM+MSTF_24hr_rep3

description:
Sample name: S23
Gene expression after 24hr in MSTF administration  3.5 mg/kg SM-treated rat liver

source_name: liver,SM+MSTF,24hr,replicate 3


title: liver_SM_24hr_rep4

description:
Sample name: Z4
Gene expression after 24hr in  3.5 mg/kg SM-treated rat liver

source_name: liver,SM,24hr,replicate 4

value: SM


title: liver_SM_24hr_rep3

description:
Sample name: Z3
Gene expression after 24hr in  3.5 mg/kg SM-treated rat liver

source_name: liver,SM,24hr,replicate 3


title: control group  individual 18

source_name: Monocyte derived macrophage


title: control group  individual 17


title: liver_SM_24hr_rep2

description:
Sample name: Z2
Gene expression after 24hr in  3.5 mg/kg SM-treated rat liver

source_name: liver,SM,24hr,replicate 2


title: Blood_P109_H24

source_name: patient 109, H24


title: 035N02_130226

value: Clinical Sample

tag: cell type

value: White Blood Cell (WBC)

value: Cytokeratin (+); CD45(+); DAPI(+)

value: Ampli1™ WGA Kit (Silicon Biosystems)

value: Reference Female


title: Blood_P109_H00

source_name: patient 109, H0

tag: age

value: 0 hr


title: Blood_P108_H48

source_name: patient 108, H48

value: MALE

tag: sapsii

value: SAPSII-High

value: 48 hr


title: liver_24hr_rep3

description:
Sample name: C33
Gene expression after 24hr in 0 SM-treated rat liver

source_name: liver,24hr,replicate 3

value: male

value: control

value: liver


title: control group  individual 14


title: Blood_P111_H00

source_name: patient 111, H0


title: control group  individual 15


title: Blood_P108_H24

source_name: patient 108, H24

value: 24 hr


title: control group  individual 16


title: control group  individual 13


title: liver_SM_24hr_rep1

description:
Sample name: Z1
Gene expression after 24hr in  3.5 mg/kg SM-treated rat liver

source_name: liver,SM,24hr,replicate 1


title: control group  individual 11


title: control group  individual 12


title: Blood_P107_H48

source_name: patient 107, H48


title: liver_24hr_rep2

description:
Sample name: C32
Gene expression after 24hr in 0 SM-treated rat liver

source_name: liver,24hr,replicate 2


title: Blood_P108_H00

source_name: patient 108, H0


title: control group  individual 9


title: liver_24hr_rep1

description:
Sample name: C31
Gene expression after 24hr in 0 SM-treated rat liver

source_name: liver,24hr,replicate 1


title: control group  individual 8


title: control group  individual 5


title: control group  individual 10


title: Blood_P107_H24

source_name: patient 107, H24


title: control group  individual 6


title: Blood_P107_H00

source_name: patient 107, H0


title: control group  individual 7


title: control group  individual 2


title: Experimental group  individual 12

value: experimental


title: Blood_P106_H24

source_name: patient 106, H24


title: control group  individual 3


title: Gene expression in DNR Spelnic CD4+Foxp3+ Treg

city: Hefei

first: Yin-Hu

last: Wang

state: Anhui

address: Huangshan Road 443, Western Campus of USTC

department: School of Life Sciences and Institution of Immunology

institute: University of Science and Technology of China

description:
Gene expression in DNR splenic CD4+Foxp3+ Tregs
DNR_Treg

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data were normalized by MAS 5.0 algorithm,GCOS1.4.

source_name: DNR-mice derived Treg cells

label_protocol: cRNA were labeled by using One-Cycle Target Labeling and Control Reagents, Affymetrix, P/N 900493,and then purified by using QIAGEN RNeasy Total RNA Isolation kit.

extract_protocol: Total RNA was extracted from each sample using Trizol Plus (TAKARA) according to the manufacturer's protocol. RNA was then further purified using RNeasy Kit (Qiagen).

treatment_protocol: CD4+Foxp3+ Treg cells were sorted from the spleen of naive B6 DNR mice by FACS Aria.

tag: strain background

tag: genotype/variation

value: Dominant negative TGF-beta receptor II (DNR) mice

value: Spleen

value: 10 weeks

value: CD4+Foxp3+ Tregs


title: Blood_P106_H48

source_name: patient 106, H48

value: SAPSII-Low


title: p53 Transfection 1

city: Iowa City

first: Daniel

last: Fox

address: 4400 PBDB, 500 Newton Rd.

department: Internal Medicine

institute: University of Iowa

description: skeletal muscle RNA

hyb_protocol: Amplified and labeled cRNA was quantified (Ribogreen assay) and hybridized to Mouse Ref-8 version 2.0 BeadChip Arrays (Illumina) overnight at 58°C. Following hybridization, arrays were washed, blocked, stained, and dried (Little Dipper Processor).

scan_protocol: Arrays were scanned with an iScan reader, and data were extracted and analyzed with BeadStudio Software (Illumina).

data_processing: Data was processed using Bioconductor Software with VST transformation and RSN normalization.

source_name: tibialis anterior

label_protocol: RNA was then amplified and labeled (Ambion TotalPrep Kit), and cDNA was synthesized using robotic-assisted magnetic capture. Using the cDNA template, biotinylated cRNA was produced via an in vitro transcription reaction.

extract_protocol: Skeletal muscle RNA was extracted using TRIzol solution (Invitrogen) and then purified using the RNeasy kit and RNase Free DNase Set (Qiagen).

treatment_protocol: Bilateral tibialis anterior muscles were harvested at three days for the following conditions: 1) hindlimb immobilization of C57BL/6 mice; 2) hindlimb immobilization of p53 mKO and control mice; 3) transfection of wild type mice with p53 plasmid or control plasmid

value: 8 weeks

tag: Sex

tag: condition

value: transfection with p53 plasmid

tag: strain


title: Gene expression in WT Spelnic CD4+Foxp3+ Treg

description:
Gene expression in WT splenic CD4+Foxp3+ Tregs
WT_Treg

source_name: WT mice derived Treg cells

value: wild type (WT)


title: Blood_P105_H24

source_name: patient 105, H24

tag: gender


title: p53 Transfection 4

description: skeletal muscle RNA


title: control group  individual 4

source_name: Monocyte derived macrophage

tag: assigned group


title: Blood_P106_H00

source_name: patient 106, H0

value: 0 hr


title: control group  individual 1


title: Control Transfection 3

description: skeletal muscle RNA

value: transfection with control plasmid


title: p53 Transfection 2

description: skeletal muscle RNA


title: Control Transfection 4

description: skeletal muscle RNA


title: p53 Transfection 3

description: skeletal muscle RNA


title: Blood_P104_H48

source_name: patient 104, H48

value: MALE


title: Control Transfection 2

description: skeletal muscle RNA


title: Blood_P105_H00

source_name: patient 105, H0

value: SAPSII-High


title: p53 mKO Immobile 3

description: skeletal muscle RNA

value: male

value: hindlimb immobilization of p53 mKO mice


title: Control Transfection 1

description: skeletal muscle RNA


title: B10-3

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: SAMPLE 13

hyb_protocol: Used Human Expression Array U133 plus 2.0 (Affymetrix, Santa Clara, CA) for hybridization and stain kit following the manufacturer’s instructions

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF (Entrez Gene, version 13)

source_name: human PPrEC prostaspheres_10 nM BPA_7 days

label_protocol: Ovation Pico WTA System (NuGEN, San Carlos, CA) following the manufacturer’s instructions

growth_protocol: human primary prostate epithelial cell derived prostaspheres cultured in matrigel/PrEGM matrices in vitro

extract_protocol: Prostaspheres were homogenized and lyzed with TRIzol reagent. Total RNA was extracted according to the manufacturer's instructions. Purified total RNA was DNase treated and quality was checked by an Agilent Bioanalyser. Samples with a RIN number >9 were used for microarray experiments.

treatment_protocol: 7 days

tag: donor status

value: disease-free Caucasian donor

tag: donor id

value: donor #3

value: Primary prostate epithelial cells (PPrEC)

tag: treated with

value: 10 nM BPA for 7 days


title: Blood_P104_H24

source_name: patient 104, H24

value: 24 hr


title: B1000-3

description: SAMPLE 15

source_name: human PPrEC prostaspheres_1000 nM BPA_7 days

value: 1000 nM BPA for 7 days


title: B200-3

description: SAMPLE 14

source_name: human PPrEC prostaspheres_200 nM BPA_7 days

value: 200 nM BPA for 7 days


title: p53 mKO Immobile 1

description: skeletal muscle RNA


title: p53 mKO Immobile 2

description: skeletal muscle RNA


title: E0.1-3

description: SAMPLE 12

source_name: human PPrEC prostaspheres_0.1 nM E2_7 days

value: 0.1 nM estradiol-17β for 7 days


title: Control Immobile 3

description: skeletal muscle RNA

value: 8 weeks

value: hindlimb immobilization of littermate control mice


title: Control Immobile 2

description: skeletal muscle RNA


title: Control Immobile 1

description: skeletal muscle RNA


title: Control Mobile 3

description: skeletal muscle RNA

value: mobile hindlimb of littermate control mice


title: Blood_P104_H00

source_name: patient 104, H0

value: SAPSII-Low

value: 0 hr


title: Blood_P102_H48

source_name: patient 102, H48

value: MALE

value: 48 hr


title: Control Mobile 2

description: skeletal muscle RNA

value: male


title: C-3

description: SAMPLE 11

source_name: human PPrEC prostaspheres_vehicle_7 days

value: vehicle (control) for 7 days


title: Blood_P101_H48

source_name: patient 101, H48


title: Blood_P102_H00

source_name: patient 102, H0


title: B10-2

description: SAMPLE 8

value: disease-free Caucasian donor

value: donor #2


title: GE1_107_5R3

city: STRASBOURG

first: Nicolas

last: MATT

address: 15 rue René Descarte

department: IBMC

institute: CNRS

description: Gene expression of S2 cells knocked down for Akirin and immune-challenged by over-expressing PGRP-LC vector

hyb_protocol: The resulting Cy3 labeled cRNA was then hybridized onto the 4x44k Drosophila V2 microarray using Agilent GeneExpression Hyb Kit (5188-5242) for 20 hours at 65oC

scan_protocol: The microarray was scanned using Agilent Microarray Scanner (G2565CA) and data extracted with Feature Extraction Software v10.7.2

data_processing: Median raw expression values where further normalized by quantile method

organism: Drosophila melanogaster

source_name: dsAkirin stimulated

label_protocol: Samples were normalized to 100ng in 1.5ul working volume for the labeling reaction and was labeled one-color (Cy3) using Agilent LowInput QuickAmp Labeling Kit (5190-2331)

growth_protocol: S2 cells were cultured at 25 °C in Schneider's medium (Biowest) supplemented with 10% fetal calf serum (FCS), penicillin/streptomycin (50 μg/ml of each) and 2 mM glutamax.

extract_protocol: RNA was extracted and treated with DNAse, using RNA Spin kit (Macherey Nagel). RNA quality was checked by Eukaryote Total RNA Pico assay (Agilent) and validated with a RIN > 6,5. 200 ng of RNA were used to perform micro-array (Agilent DNA microarrays Drosophila) thanks to GeneCore Genomics facility at European Molecular Biology Lab (Heidelberg, Germany; http://genecore3.genecore.embl.de/genecore3/).

treatment_protocol: To perform micro-array, 2x10^6 S2 cells (10^6/mL) were transfected in 6-wells plates by calcium phosphate precipitation with 1 μg of p-actin5C-tomato, 1 μg of p-actin5C-PGRP-LCa or empty p-actin5C vector and 5 μg of dsRNAs against GFP, Relish or Akirin. After 12–16 h, the cells were washed with PBS and incubated in fresh complete Schneider’s medium for 48 h.Cells were washed with PBS and resuspended in serum-free Schneider’s Drosophila Medium (Biowest) before sorting. 105 to 5x105 transfected Tomato-positive S2 cells were sorted in serum-free medium with the help of to the flow cytometry facility at Institut de Génétique et de Biologie Molécuaire et Cellulaire (Illkirch, France; http://www.igbmc.fr/technologies/6/team/64/).

tag: dsrna

value: Akirin

tag: vector

value: PGRP-LC

tag: slide number

tag: replicat


title: B1000-2

description: SAMPLE 10

tag: cell type

value: Primary prostate epithelial cells (PPrEC)


title: GE1_107_6R3

description: Gene expression of S2 cells knocked down for Akirin and non immune-challenged

source_name: dsAkirin

value: Empty vector


title: GE1_107_6R2


title: Blood_P102_H24

source_name: patient 102, H24

tag: age

tag: collection time

value: 24 hr


title: GE1_107_6R1


title: GE1_107_4R3

description: Gene expression of S2 cells knocked down for Relish and immune-challenged by over-expressing PGRP-LC vector

source_name: dsRelish stimulated

value: Relish


title: Control Mobile 1

description: skeletal muscle RNA

source_name: tibialis anterior

value: 8 weeks


title: Blood_P101_H24

source_name: patient 101, H24

tag: sapsii


title: B200-2

description: SAMPLE 9

value: 200 nM BPA for 7 days


title: E0.1-2

description: SAMPLE 7

value: 0.1 nM estradiol-17β for 7 days


title: GE1_107_2R3

description: Gene expression of S2 cells knocked down for GFP and immune-challenged by over-expressing PGRP-LC vector

source_name: dsGFP stimulated

value: GFP


title: GE1_107_3R3

description: Gene expression of S2 cells knocked down for Relish and non immune-challenged

source_name: dsRelish


title: GE1_107_1R3

description: Gene expression of S2 cells knocked down for GFP and non immune-challenged

source_name: dsGFP


title: B1000-1

description: SAMPLE 5

source_name: human PPrEC prostaspheres_1000 nM BPA_7 days

value: donor #1

value: 1000 nM BPA for 7 days


title: Blood_P101_H00

source_name: patient 101, H0

value: MALE

value: SAPSII-Low

value: 0 hr


title: Blood_P021_H48

source_name: patient 021, H48

value: SAPSII-High

value: 48 hr


title: C-2

description: SAMPLE 6

value: disease-free Caucasian donor

value: donor #2

value: vehicle (control) for 7 days


title: GE1_107_2R2

value: PGRP-LC


title: B200-1

description: SAMPLE 4

source_name: human PPrEC prostaspheres_200 nM BPA_7 days

value: Primary prostate epithelial cells (PPrEC)


title: GE1_107_4R2

value: Relish


title: Blood_P021_H24

source_name: patient 021, H24

value: 24 hr


title: GE1_107_1R2

value: Empty vector


title: B10-1

description: SAMPLE 3

source_name: human PPrEC prostaspheres_10 nM BPA_7 days

value: 10 nM BPA for 7 days


title: GE1_107_5R2

value: Akirin


title: Blood_P021_H00

source_name: patient 021, H0


title: E0.1-1

description: SAMPLE 2

source_name: human PPrEC prostaspheres_0.1 nM E2_7 days

value: donor #1

value: 0.1 nM estradiol-17β for 7 days


title: GE1_107_3R1


title: GE1_107_4R1


title: GE1_107_3R2


title: GE1_107_1R1

value: GFP


title: C-1

description: SAMPLE 1

source_name: human PPrEC prostaspheres_vehicle_7 days


title: Blood_P020_H00

source_name: patient 020, H0

value: MALE


title: Blood_P019_H48

source_name: patient 019, H48

value: SAPSII-Low


title: GE1_107_2R1


title: GE1_107_5R1

source_name: dsAkirin stimulated


title: Blood_P019_H00

source_name: patient 019, H0

value: 0 hr


title: Blood_P020_H24

source_name: patient 020, H24

value: SAPSII-High


title: Blood_P019_H24

source_name: patient 019, H24


title: Id1KO_Zrf1KD_replicate3

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

description:
Id1KO_Zrf1KD_3
KO of Id1 and KD of Zrf1

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized to Agilent-028005 array in an in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing:
Raw data was corrected for background noise using the normexp method [Ritchie et al., 1007] method. To assure comparability across samples we use quantile normalization [Bolstad, 2001].
-Ritchie ME, Silver J, Oshlack A, Silver J, Holmes M, Diyagama D, Holloway A, Smyth GK. (2007). A comparison of background correction methods for two‐colour microarrays. Bioinformatics, 23, 2700‐2707.
-Bolstad, B. (2001). Probe Level Quantile Normalization of High Density Oligonucleotide Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf

source_name: Wild type ESCs and ID1KO ESCs were a kind gift of Dr. Benezra (Memorial Sloan Kettering Cancer Center, New York, USA) (Romero-Lanman et al., Stem Cell Dev. 2012)

label_protocol: 100 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Low Input Quick Amp Labeling kit (Agilent) and purified using RNeasy columns (Qiagen, Hilden, Germany).

growth_protocol: mESCs were grown in GMEM supplemented with 15% FBS and LIF.

extract_protocol: Total RNAs were prepared with Qiagen RNeasy Mini Kit according to manufacturer's protocol.

treatment_protocol: Zrf1 knock-down was obtained by lentiviral infection of mID1KO ESC with vectors encoding for Zrf1 shRNAs (pLKO Sigma). Stable mESC depleted for Zrf1 expression (Id1KO_Zrf1KD cells) were generated after selection with puromycin.

value: embryonic stem cells

tag: genotype/variation

value: Id1 knockout, Zrf1 knockdown


title: Blood_P018_H24

source_name: patient 018, H24


title: Id1KO_Zrf1KD_replicate2

description:
Id1KO_Zrf1KD_2
KO of Id1 and KD of Zrf1

data_processing:
Raw data was corrected for background noise using the normexp method [Ritchie et al., 1007]. To assure comparability across samples we use quantile normalization [Bolstad, 2001].
-Ritchie ME, Silver J, Oshlack A, Silver J, Holmes M, Diyagama D, Holloway A, Smyth GK. (2007). A comparison of background correction methods for two‐colour microarrays. Bioinformatics, 23, 2700‐2707.
-Bolstad, B. (2001). Probe Level Quantile Normalization of High Density Oligonucleotide Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf


title: Id1KO_Zrf1KD_replicate1

description:
Id1KO_Zrf1KD_1
KO of Id1 and KD of Zrf1


title: Blood_P018_H48

source_name: patient 018, H48

value: 48 hr


title: Id1KO_Zrf1KD_replicate4

description:
Id1KO_Zrf1KD_4
KO of Id1 and KD of Zrf1


title: Id1KO_replicate3

description:
Id1KO_3
KO of Id1

value: Id1 knockout


title: Id1KO_replicate4

description:
Id1KO_4
KO of Id1


title: genomic DNA from whole blood_6057825027_R01C01

city: Druham

first: Weiwei

last: Zhang

address: 101 Research Drive

department: Biostatistics and Bioinformatics

institute: Duke University

description:
Sample name: X100
normal whole blood sample

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

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

data_processing: BeadStudio softwarewas used to process the raw signal. After the beta values are calculated (Beta value=methylated signal/(methylated signal+unmethylated signal), data quality control was implemented using R (http://www.r-project.org/) (version 2.15.3). We removed 17,764 CpG sites for which probes mapped to multiple loci in the human genome reference sequence. CpG sites that are SNPs, that had missing values, or that had detection p-values >0.01 were excluded. Methylation data from probes mapping to the X and Y chromosomes were excluded. We were left with 394,354 CpG sites from 100 individuals in downstream analyses.

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from whole blood samples

tag: 450k chip

tag: order on 450k chip

value: Female

tag: tissue

value: whole blood

tag: disease state

value: normal

tag: date born


title: Id1KO_replicate2

description:
Id1KO_2
KO of Id1


title: Blood_P017_H48

source_name: patient 017, H48

tag: gender


title: genomic DNA from whole blood_6057825005_R02C01

description:
Sample name: X99
normal whole blood sample


title: genomic DNA from whole blood_6055432084_R06C02

description:
Sample name: X98
normal whole blood sample


title: genomic DNA from whole blood_6057825025_R02C01

description:
Sample name: X97
normal whole blood sample


title: Blood_P018_H00

source_name: patient 018, H0


title: genomic DNA from whole blood_6055432168_R02C02

description:
Sample name: X95
normal whole blood sample


title: Blood_P017_H24

source_name: patient 017, H24

value: 24 hr


title: genomic DNA from whole blood_6042308121_R03C01

description:
Sample name: X96
normal whole blood sample


title: Id1KO_replicate1

description:
Id1KO_1
KO of Id1


title: genomic DNA from whole blood_6057825040_R01C01

description:
Sample name: X94
normal whole blood sample


title: Blood_P017_H00

source_name: patient 017, H0


title: Blood_P015_H48

source_name: patient 015, H48


title: WT_replicate4

description:
WT_4
WT

value: wild type


title: Blood_P015_H24

source_name: patient 015, H24


title: WT_replicate2

description:
WT_2
WT


title: WT_replicate3

description:
WT_3
WT


title: genomic DNA from whole blood_6055432118_R06C01

description:
Sample name: X93
normal whole blood sample


title: WT_replicate1

description:
WT_1
WT

source_name: Wild type ESCs  and ID1KO ESCs were a kind gift of Dr. Benezra (Memorial Sloan Kettering Cancer Center, New York, USA) (Romero-Lanman et al., Stem Cell Dev. 2012)


title: genomic DNA from whole blood_6057825005_R02C02

description:
Sample name: X92
normal whole blood sample


title: Blood_P014_H48

source_name: patient 014, H48


title: genomic DNA from whole blood_6057825042_R03C01

description:
Sample name: X90
normal whole blood sample


title: genomic DNA from whole blood_6055432144_R03C02

description:
Sample name: X86
normal whole blood sample


title: Blood_P015_H00

source_name: patient 015, H0


title: Blood_P014_H24

source_name: patient 014, H24


title: genomic DNA from whole blood_6057825036_R06C01

description:
Sample name: X91
normal whole blood sample


title: genomic DNA from whole blood_6929726097_R03C01

description:
Sample name: X87
normal whole blood sample


title: Immortalized murine embryonic fibroblasts, knock out for TIA1, rep1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

hyb_protocol: Briefly, for each hybridization, 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease-free water in a 25 ul reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with 25 ul of 2x Hybridization Buffer. The samples were placed on ice and quickly loaded onto Agilent SurePrint G3 Mouse 8x60 arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute).

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots were quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Raw intensities were background-corrected by the normexp method with an offset of 50. Background-corrected signals were log2 transformed and normalized by quantile adjustment as described in the limma package of Bioconductor.

source_name: Immortalized murine embryonic fibroblasts, TIA1 knock out

label_protocol: Total RNA (200 ng) was amplified using the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with the RNeasy Mini Kit (Qiagen). Preparation of probes and hybridization were performed as described in the One-Color Microarray-Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies.

growth_protocol: Immortalized murine embryonic fibroblast (MEF) wild type and knock-out for either TIA1 or TIAR were maintained as described previously [Izquierdo, J. M. and Valcárcel, J. (2007) Two isoforms of the T-cell intracellular antigen 1 (TIA1) splicing factors display distinct splicing regulation activities. Control of TIA1 isoform ratio by TIA1 related protein. J. Biol. Chem. 282, 19410-19417].

extract_protocol: Total RNA isolation and semiquantitative and quantitative RT-PCR analysis were carried out as described previously [Reyes, R., Alcalde, J. and Izquierdo, J. M. (2009) Depletion of T-cell intracellular antigen (TIA)-proteins promotes cell proliferation. Genome Biol. 10, R87].

tag: strain/background

value: BALB/c

value: TIA1 knock out

value: immortalized murine embryonic fibroblasts


title: genomic DNA from whole blood_6057825042_R06C02

description:
Sample name: X85
normal whole blood sample


title: genomic DNA from whole blood_6042308075_R05C01

description:
Sample name: X83
normal whole blood sample


title: genomic DNA from whole blood_6057825036_R02C02

description:
Sample name: X84
normal whole blood sample


title: Blood_P014_H00

source_name: patient 014, H0


title: Immortalized murine embryonic fibroblasts, knock out for TIAR, rep2

source_name: Immortalized murine embryonic fibroblasts, TIAR knock out

value: TIAR knock out


title: genomic DNA from whole blood_6055432155_R01C02

description:
Sample name: X82
normal whole blood sample


title: genomic DNA from whole blood_6042316146_R05C01

description:
Sample name: X80
normal whole blood sample


title: Blood_P013_H48

source_name: patient 013, H48

value: MALE


title: genomic DNA from whole blood_6057825036_R03C02

description:
Sample name: X89
normal whole blood sample


title: genomic DNA from whole blood_6042308108_R04C02

description:
Sample name: X88
normal whole blood sample


title: genomic DNA from whole blood_6057825042_R02C02

description:
Sample name: X79
normal whole blood sample


title: genomic DNA from whole blood_6057825040_R06C02

description:
Sample name: X76
normal whole blood sample


title: genomic DNA from whole blood_6042316028_R05C01

description:
Sample name: X77
normal whole blood sample


title: Blood_P013_H24

source_name: patient 013, H24

value: SAPSII-Low


title: Immortalized murine embryonic fibroblasts, wild type, rep2


title: genomic DNA from whole blood_6057825006_R06C01

description:
Sample name: X78
normal whole blood sample


title: genomic DNA from whole blood_6042316146_R03C01

description:
Sample name: X75
normal whole blood sample


title: Jag1+/-Rfng+/-_portal tract Rep 5

city: Philadelphia

first: Matthew

middle: Joseph

last: Ryan

state: PA

address: 34th and Civic Center Blvd

department: Pediatrics

institute: The Children's Hospital of Philadelphia

description:
Sample name: dbl_2304-2 excl
portal tracts were laser capture-microdissected

hyb_protocol: Folllowing fragmentation, 3.4ug of labeled products were hybridized for 16hr at 45C on GeneChip Mouse Gene 2.0 ST Arrays.Chips were washed and stained according to Affymetrix guidelines.

scan_protocol: GeneChips were scanned using a GeneChip 3000 7G scanner.

data_processing: Raw data was converted to average intensities using Affymetrix Command Console software. Robust Multi-array Average normalization was applied using Partek Genomics Suite software (v6.6).Significance Analysis of Microarrays was applied yielding q-values and fold changes to identify differentially expressed genes .

source_name: 1 week old mut

label_protocol: Biotinylated cDNA were prepared using 5ug of template according to the manufacturer's instructions.

extract_protocol: RNA was extracted from 12-20 portal tracts per replicate from frozen sections using the PicoPure RNA isolation kit. Samples were Dnased during purification protocol.

value: 1 week

value: portal tract


title: Blood_P011_H48

source_name: patient 011, H48

value: SAPSII-High


title: genomic DNA from whole blood_6042316146_R03C02

description:
Sample name: X72
normal whole blood sample

source_name: whole blood


title: Immortalized murine embryonic fibroblasts, wild type, rep1


title: Jag1+/-Rfng+/-_portal tract Rep 4

description:
Sample name: dbl_2304-8
portal tracts were laser capture-microdissected


title: genomic DNA from whole blood_6057825006_R03C02

description:
Sample name: X73
normal whole blood sample


title: Blood_P013_H00

source_name: patient 013, H0

value: 0 hr


title: genomic DNA from whole blood_6057825046_R04C01

description:
Sample name: X74
normal whole blood sample


title: Blood_P011_H24

source_name: patient 011, H24


title: genomic DNA from whole blood_6057825033_R05C01

description:
Sample name: X70
normal whole blood sample


title: genomic DNA from whole blood_6055432122_R05C01

description:
Sample name: X71
normal whole blood sample


title: Immortalized murine embryonic fibroblasts, knock out for TIA1, rep2


title: Blood_P011_H00

source_name: patient 011, H0


title: Jag1+/-Rfng+/-_portal tract Rep 3

description:
Sample name: dbl_2304-6
portal tracts were laser capture-microdissected


title: Jag1+/-Rfng+/-_portal tract Rep 2

description:
Sample name: dbl_2304-11
portal tracts were laser capture-microdissected


title: genomic DNA from whole blood_6057825019_R01C01

description:
Sample name: X67
normal whole blood sample


title: Blood_P010_H48

source_name: patient 010, H48

value: FEMALE

value: 48 hr


title: genomic DNA from whole blood_6042308121_R06C02

description:
Sample name: X81
normal whole blood sample

value: Female


title: genomic DNA from whole blood_6042316028_R03C01

description:
Sample name: X68
normal whole blood sample

value: whole blood


title: genomic DNA from whole blood_6055432118_R03C02

description:
Sample name: X63
normal whole blood sample

value: normal


title: genomic DNA from whole blood_6042316073_R02C02

description:
Sample name: X65
normal whole blood sample


title: Jag1+/-Rfng+/-_portal tract Rep 1

description:
Sample name: dbl_2285-10
portal tracts were laser capture-microdissected


title: Immortalized murine embryonic fibroblasts, knock out for TIAR, rep1


title: genomic DNA from whole blood_6057825006_R05C01

description:
Sample name: X64
normal whole blood sample


title: Blood_P010_H00

source_name: patient 010, H0


title: genomic DNA from whole blood_6055432168_R03C02

description:
Sample name: X66
normal whole blood sample


title: Control_portal tract Rep 5

description:
Sample name: cont_2365-2
portal tracts were laser capture-microdissected

source_name: 1 week old ctrl

tag: strain

value: control


title: Blood_P010_H24

source_name: patient 010, H24

value: 24 hr


title: Blood_P009_H48

source_name: patient 009, H48


title: Control_portal tract Rep 4

description:
Sample name: cont_2304-9
portal tracts were laser capture-microdissected


title: Control_portal tract Rep 3

description:
Sample name: cont_2304-12
portal tracts were laser capture-microdissected


title: genomic DNA from whole blood_6042316073_R06C01

description:
Sample name: X60
normal whole blood sample


title: Control_portal tract Rep 2

description:
Sample name: cont_2304-10
portal tracts were laser capture-microdissected


title: Blood_P009_H00

source_name: patient 009, H0


title: Blood_P009_H24

source_name: patient 009, H24


title: genomic DNA from whole blood_6042316145_R06C02

description:
Sample name: X61
normal whole blood sample


title: Blood_P008_H48

source_name: patient 008, H48


title: Control_portal tract Rep 1

description:
Sample name: cont_2303-1
portal tracts were laser capture-microdissected


title: genomic DNA from whole blood_6042316021_R01C01

description:
Sample name: X58
normal whole blood sample


title: genomic DNA from whole blood_6055432118_R04C01

description:
Sample name: X55
normal whole blood sample


title: Blood_P008_H24

source_name: patient 008, H24


title: genomic DNA from whole blood_6055432118_R06C02

description:
Sample name: X59
normal whole blood sample


title: genomic DNA from whole blood_6057825025_R03C02

description:
Sample name: X62
normal whole blood sample


title: genomic DNA from whole blood_6057825036_R05C02

description:
Sample name: X57
normal whole blood sample


title: genomic DNA from whole blood_6057825019_R02C01

description:
Sample name: X53
normal whole blood sample


title: Blood_P008_H00

source_name: patient 008, H0


title: genomic DNA from whole blood_6055432109_R05C01

description:
Sample name: X69
normal whole blood sample


title: genomic DNA from whole blood_6057825025_R04C01

description:
Sample name: X52
normal whole blood sample


title: genomic DNA from whole blood_6055432155_R03C02

description:
Sample name: X56
normal whole blood sample


title: genomic DNA from whole blood_6057825027_R03C01

description:
Sample name: X54
normal whole blood sample


title: Blood_P007_H24

source_name: patient 007, H24


title: Blood_P006_H48

source_name: patient 006, H48


title: genomic DNA from whole blood_6055432118_R01C02

description:
Sample name: X46
normal whole blood sample


title: genomic DNA from whole blood_6057825027_R06C01

description:
Sample name: X47
normal whole blood sample


title: genomic DNA from whole blood_6057825027_R05C01

description:
Sample name: X51
normal whole blood sample


title: genomic DNA from whole blood_6042316074_R02C02

description:
Sample name: X49
normal whole blood sample


title: Blood_P007_H00

source_name: patient 007, H0


title: genomic DNA from whole blood_6042316074_R06C01

description:
Sample name: X50
normal whole blood sample

source_name: whole blood


title: genomic DNA from whole blood_6055432122_R03C01

description:
Sample name: X43
normal whole blood sample


title: Blood_P006_H00

source_name: patient 006, H0


title: genomic DNA from whole blood_6055432084_R02C01

description:
Sample name: X41
normal whole blood sample


title: genomic DNA from whole blood_6057825040_R02C02

description:
Sample name: X40
normal whole blood sample


title: Blood_P005_H48

source_name: patient 005, H48


title: genomic DNA from whole blood_6042316098_R02C01

description:
Sample name: X45
normal whole blood sample


title: Blood_P005_H24

source_name: patient 005, H24


title: Blood_P004_H48

source_name: patient 004, H48


title: Blood_P005_H00

source_name: patient 005, H0


title: genomic DNA from whole blood_6042316074_R06C02

description:
Sample name: X38
normal whole blood sample


title: genomic DNA from whole blood_6057825027_R02C02

description:
Sample name: X48
normal whole blood sample


title: Blood_P007_H48

source_name: patient 007, H48


title: genomic DNA from whole blood_6042316074_R04C01

description:
Sample name: X37
normal whole blood sample


title: genomic DNA from whole blood_6055432155_R06C02

description:
Sample name: X44
normal whole blood sample


title: genomic DNA from whole blood_6057825027_R06C02

description:
Sample name: X29
normal whole blood sample


title: Blood_P006_H24

source_name: patient 006, H24


title: genomic DNA from whole blood_6042308005_R03C01

description:
Sample name: X32
normal whole blood sample


title: genomic DNA from whole blood_6055432120_R06C01

description:
Sample name: X33
normal whole blood sample


title: genomic DNA from whole blood_6055432144_R04C01

description:
Sample name: X35
normal whole blood sample


title: Blood_P003_H48

source_name: patient 003, H48


title: Blood_P004_H24

source_name: patient 004, H24


title: Blood_P004_H00

source_name: patient 004, H0


title: genomic DNA from whole blood_6042308108_R01C01

description:
Sample name: X36
normal whole blood sample


title: genomic DNA from whole blood_6042308121_R05C01

description:
Sample name: X31
normal whole blood sample


title: genomic DNA from whole blood_6055432144_R03C01

description:
Sample name: X39
normal whole blood sample


title: genomic DNA from whole blood_6055432092_R04C01

description:
Sample name: X34
normal whole blood sample


title: Blood_P003_H24

source_name: patient 003, H24


title: genomic DNA from whole blood_6055432139_R04C01

description:
Sample name: X42
normal whole blood sample


title: genomic DNA from whole blood_6055432139_R02C01

description:
Sample name: X26
normal whole blood sample


title: genomic DNA from whole blood_6055432120_R05C02

description:
Sample name: X28
normal whole blood sample


title: genomic DNA from whole blood_6042308068_R05C01

description:
Sample name: X27
normal whole blood sample


title: genomic DNA from whole blood_6042316028_R01C02

description:
Sample name: X30
normal whole blood sample


title: genomic DNA from whole blood_6055432140_R02C02

description:
Sample name: X25
normal whole blood sample


title: Blood_P002_H48

source_name: patient 002, H48


title: Blood_P003_H00

source_name: patient 003, H0


title: Blood_P002_H24

source_name: patient 002, H24


title: genomic DNA from whole blood_6057825027_R05C02

description:
Sample name: X23
normal whole blood sample


title: genomic DNA from whole blood_6055432139_R01C02

description:
Sample name: X24
normal whole blood sample


title: S0058195

description:
Sample name: MRX34 3-3
Test 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard can protocol

data_processing: Data processed by CRO Asuragen Inc who performed arrays

source_name: tumor

label_protocol: Standard Illumina label protocol

growth_protocol: Nod/Scid mice were surgically implanted with 1 x 106 cultured Hep3B cells and tumors were allowed to grow for ~ 5 weeks

tag: cell line

tag: surgically implanted into

value: livers of Nod/Scid mice

tag: treatment

value: Hep3B orthotopic liver tumors


title: S0058194

description:
Sample name: MRX34 3-2
Test 2


title: Blood_P001_H24

source_name: patient 001, H24


title: Blood_P002_H00

source_name: patient 002, H0


title: S0058193

description:
Sample name: MRX34 3-1
Test 1


title: genomic DNA from whole blood_6042308154_R05C01

description:
Sample name: X22
normal whole blood sample

source_name: whole blood