title: gray-00298: s0191-onco

description: Array Type: E500

source_name: Cancer

tag: chemotherapy treatment

value: yes

tag: p53 positive (ihc)

tag: Sex

value: no

tag: family history

tag: followup time

tag: ethnicity

tag: tumor grading

tag: tumor staging

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment

source_name: normal female genomic DNA


title: FT2

status: Public on May 20 2015

type: RNA

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

description: total RNA

hyb_protocol: Standard Affymetix protocol.

scan_protocol: Standard Affymetix protocol.

data_processing: Raw data were normalized globally and processed with Microarray Suite, version 5.0 (Affymetrix) and Data Mining Tool (Affymetrix) software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Isolated and in vitro cultured placental trophoblasts

label_protocol: cDNA was labeled with the RNA Transcript Labeling Kit from Enzo diagnostics

growth_protocol: Prior to microarray analysis 800,000 trophoblasts w in flasks (25 cm²) using DMEM Medium with 5% FCS, or 800,000 placental endothelial cells were seeded in flasks (75 cm²) using EBM medium with 5% FCS. Cells were cultured for 48 h at 21% O2/5% CO2 environment at 37°C.

extract_protocol:
RNA isolation with TRI REAGENT according to manufacturer
cDNA was synthesized with SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen)

tag: tissue

value: placenta

tag: cell type

value: cytotrophoblasts


title: gray-00298: b0287-scan

type: genomic

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

description: Array Type: HA114

hyb_protocol: See mage-tab files linked to series entry for additional details

molecule: genomic DNA

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

value: African American

tag: dead of disease

tag: disease state

value: breast cancer

tag: hormonal therapy

tag: estrogen receptor status

value: negative

tag: alive at endpoint

value: alive

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender

value: female


title: EC2

description: total RNA

source_name: Isolated and in vitro cultured placental endothelial cells

value: endothelial cells


title: RWPE1-PMN rep1

city: singapore

first: Zhen Ning

last: Wee

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

description: Retroviral infection to insert vector

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genome Studio

source_name: RWPE1 (Benign prostate epithelial cell line)

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

growth_protocol: RWPE1 and all its derivative sub-lines were grown in K-SFM with 50mg/ml BPE, 5ng/ml EGF (Invitrogen). All media were supplemented with 5000U/mL penicillin/streptomycin (Invitrogen). All cells were maintained at 37 °C with 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: There is no treatment prior to harvesting of cells

tag: treatment

value: Empty vector

tag: cell line


title: RWPE1-PI3K rep1

description: Retroviral infection to insert vector

value: constitutive active PI3K (E545K)


title: EC1

description: total RNA

tag: tissue

tag: cell type


title: gray-00298: b0327-scan

description: Array Type: HA20

scan_protocol: See mage-tab files linked to series entry for additional details

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

value: mammary gland

tag: family history

tag: followup time

tag: ethnicity

value: Caucasian

tag: tumor grading

tag: tumor staging

tag: biosource type

tag: progesterone receptor status

value: dead

tag: recurrence

tag: radiation treatment


title: gray-00298: b0285-scan

description: Array Type: HA20

data_processing: See mage-tab files linked to series entry for additional details

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

value: positive

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0335-scan

description: Array Type: HA114

label_protocol: See mage-tab files linked to series entry for additional details

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: family history

tag: followup time

tag: ethnicity

value: Asian

tag: tumor grading

tag: tumor staging


title: gray-00298: s0190-onco

description: Array Type: E500

extract_protocol: See mage-tab files linked to series entry for additional details

value: yes

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0210-onco

description: Array Type: E500

tag: chemotherapy treatment

value: no

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: s0189-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state


title: gray-00298: s0188-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0265-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0255-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state


title: gray-00298: s0183-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0181-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0251-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state


title: gray-00298: s0177-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0176-onco

description: Array Type: D500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0252-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state


title: gray-00298: s0175-onco

description: Array Type: E950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0170-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: RWPE1-MYC rep1

description: Retroviral infection to insert vector

tag: treatment

value: MYC overexpression

tag: cell line


title: gray-00298: b0241-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status


title: gray-00298: b0246-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: s0158-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor size (mm)

tag: gender


title: gray-00298: b0248-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00298: b0200-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: b0243-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor size (mm)

tag: gender


title: gray-00298: s0151-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00298: s0162-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: b0165-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor size (mm)

tag: gender


title: gray-00298: s0163-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00298: s0154-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: b0239-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor size (mm)

tag: gender


title: gray-00298: b0202-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00298: s0168-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: b0277-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor size (mm)

tag: gender


title: gray-00298: s0146-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00298: s0138-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: NHDF2 miRNA

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: Normal Human dermal fibroblasts sample-2 for miRNA

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

label_protocol: Manufature's protocol

growth_protocol: For hPSCs, Primate ESC medium (ReproCELL) supplemented with 4 ng/ml bFGF at 37 ºC in a humidified incubator with 5% CO2. For cardiomyocytes, StemPro-34 supplemented with 2 mM L-glutamine, 4x10-4 M monothioglycerol (MTG), 50 mg/ml ascorbic acid (AA), 150 mg/ml transferrin, 0.5% penicillin/streptomycin, bFGF (10 ng/ml, final 5 ng/ml), activin A (12 ng/ml, final 6 ng/ml) and BMP4 (18 ng/ml, final 10 ng/ml)

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: hiPSCs were differentiated to cardiac lineage cells using ActivinA and BMP4.

tag: cell type

value: Normal Human dermal fibroblasts


title: gray-00298: s0133-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: tumor size (mm)

tag: gender


title: gray-00298: s0136-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

value: African American

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: gray-00298: s0129-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

value: breast cancer

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: primary Hepatocytes2 miRNA

description: Hepatocytes-2 for miRNA

source_name: primary Hepatocytes sample-2

tag: cell type

value: Hepatocytes


title: gray-00298: s0124-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

value: negative

tag: tumor size (mm)

tag: gender


title: gray-00298: s0119-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

value: alive

tag: node positive

value: female


title: gray-00298: s0115-onco

description: Array Type: E950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: HUVEC2 miRNA

description: Human Umbilical Vein Endothelial Cells-2 for miRNA

source_name: Human Umbilical Vein Endothelial Cells (HUVEC) sample-2

tag: cell type

value: Human Umbilical Vein Endothelial Cells


title: gray-00298: s0107-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: tumor size (mm)

tag: gender


title: gray-00298: s0106-onco

description: Array Type: D500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: gray-00298: s0116-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: s0110-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: tumor size (mm)

tag: gender


title: gray-00298: s0141-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor grading

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: HUVEC1 miRNA

description: Human Umbilical Vein Endothelial Cells-1 for miRNA

source_name: Human Umbilical Vein Endothelial Cells (HUVEC) sample-1

tag: cell type


title: gray-00298: s0109-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: AoSMC1 miRNA

description: Aortic Smooth Muscle Cells-1 for miRNA

source_name: Aortic Smooth Muscle Cells (AoSMC) sample-1

value: Aortic Smooth Muscle Cells


title: d20 EGFP- cells miRNA

description: day20 EGFP- cells differentiated from MYH6-EIP4 for miRNA

source_name: MYH6-EIP4 day20 differentiated cells (EGFP- cells)

value: Differentiated cells from human induced pluripotent stem cells


title: d8 EGFP- cells miRNA

description: day8 EGFP- cells differentiated from MYH6-EIP4 for miRNA

source_name: MYH6-EIP4 day8 differentiated cells (EGFP- cells)


title: NHDF1 miRNA

description: Normal Human dermal fibroblasts sample-1 for miRNA


title: d20 EGFP+ cells miRNA

description: day20 EGFP+ cells differentiated from MYH6-EIP4 for miRNA

source_name: MYH6-EIP4 day20 differentiated cells (EGFP+ cells)


title: gray-00298: s0103-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

value: mammary gland

value: Caucasian

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0104-onco

description: Array Type: F950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

value: positive

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: primary Hepatocytes1 miRNA

description: Hepatocytes-1 for miRNA

source_name: primary Hepatocytes sample-1

tag: cell type


title: d8 EGFP+ cells miRNA

description: day8 EGFP+ cells differentiated from MYH6-EIP4 for miRNA

source_name: MYH6-EIP4 day8 differentiated cells (EGFP+ cells)


title: gray-00298: s0101-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: s0098-onco

description: Array Type: D500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

value: dead

tag: tumor size (mm)

tag: gender


title: gray-00298: s0096-onco

description: Array Type: E950

tag: chemotherapy treatment

value: yes

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: gray-00298: s0100-onco

description: Array Type: D500

value: no

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: s0090-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

value: Asian

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0087-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: gray-00298: s0094-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: tumor staging

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: s0088-onco

description: Array Type: D500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: AoSMC2 miRNA

description: Aortic Smooth Muscle Cells-2 for miRNA

source_name: Aortic Smooth Muscle Cells (AoSMC) sample-2

tag: cell type


title: gray-00298: s0067-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: gray-00298: s0077-onco

description: Array Type: F950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: ethnicity

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: s0063-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: dead of disease

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: MDS 3

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)

source_name: Stromal cells from patients diagnosed with MDS

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: Bone marrow mononuclear cells (MNC) were isolated using ficoll-paque gradient separation (GE healthcare biosciences, Pittsburgh PA).

tag: restriction enzyme

value: MspI representation of genomic DNA

tag: sample type

value: HpaII representation of genomic DNA


title: gray-00298: s0053-onco

description: Array Type: D500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: ethnicity

tag: tumor grading

tag: tumor staging

tag: disease state

value: breast cancer

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: gray-00298: s0071-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: dead of disease

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: gray-00298: s0080-onco

description: Array Type: D500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: ethnicity

tag: tumor grading

tag: tumor staging

tag: disease state

tag: tumor size (mm)

tag: gender


title: gray-00298: s0086-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: dead of disease

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive


title: gray-00298: s0059-onco

description: Array Type: D500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: MDS 2

tag: restriction enzyme

tag: sample type

value: Stromal cells from patients diagnosed with MDS


title: gray-00298: s0060-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

value: negative

tag: tumor size (mm)

tag: gender


title: gray-00298: s0054-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

value: alive

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: MDS 6

tag: restriction enzyme

tag: sample type


title: gray-00298: s0084-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

value: female

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: recurrence

tag: radiation treatment


title: gray-00298: s0048-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: MDS 4

tag: restriction enzyme

tag: sample type


title: gray-00298: s0039-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0040-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: s0037-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor size (mm)

tag: gender


title: healthy control 1

source_name: Stromal cells from control bone marrow

tag: restriction enzyme

tag: sample type

value: Stromal cells from control bone marrow


title: gray-00298: s0050-onco

description: Array Type: G950

source_name: Cancer

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: MDS 1


title: MDS 5


title: healthy control 2


title: gray-00298: s0049-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment

source_name: normal female genomic DNA


title: gray-00298: s0019-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0018-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0025-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: s0021-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0035-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0530-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

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tag: tumor grading

tag: alive at endpoint

tag: node positive

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tag: radiation treatment


title: gray-00298: s0046-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0026-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0032-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0515-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0013-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0004-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: s0029-onco

description: Array Type: E950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

value: African American

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0047-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0006-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0551-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0566-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0512-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0502-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0042-onco

description: Array Type: D500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time


title: healthy control 3

tag: restriction enzyme

tag: sample type


title: gray-00298: b0468-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0494-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0434-onco

description: Array Type: F950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0447-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: s0031-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0428-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0521-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0427-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0433-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0421-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0394-onco

description: Array Type: F950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0414-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0370-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0383-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0387-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0404-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0372-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0382-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0371-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0359-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0365-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0499-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0358-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0374-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0357-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0348-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: b0346-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: GDF11_24hr_300_2

city: Basel

first: Sophie

last: Brachat

address: Novartis Campus

department: Muskuloskeletal

country: Switzerland

institute: Novartis Institutes For Biomedical Research

hyb_protocol: Affymetrix Hybridization control kit (including B2)

scan_protocol: Affymetrix standard protocol

data_processing: RMA normalization followed by 2% 150  trimmed mean scaling. Probesets with scaled RMA values below 50 in all groups were filtered out

source_name: hSKMCs

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2

growth_protocol: Human skeletal muscle derived cells (hSkMDC; Cook Myosite) were cultured in growth medium consisting of MyoTonic™ basal medium (Cook Myosite) supplemented with 20% FBS (Hyclone) and MyoTonic™ serum free growth supplement (Cook Myosite). Differentiation was initiated 24 h after seeding (day 0) by changing to serum-free differentiation medium consisting of MyoTonic™ differentiation medium (Cook Myosite) containing 2% horse serum (Hyclone) and 1% FBS, and altering the atmospheric conditions from 5 to 7.5% CO2.

extract_protocol: Total RNA was extracted from the snap-fozen tibialis anterior muscle using an RNeasy Fibrous Tissue Mini Kit (Qiagen), and eluted in 40μl RNase free water. RNA concentration and quality was measured by a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific). In case RNA quality was not acceptable (ratio 260/230<1.5), samples were cleaned using a RNeasy Plus Micro Kit (Qiagen), eluted in 15 μl and the new concentration and ratios measured again. RNA final quality was assessed on an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano kit, and processed for microarray when RIN>7

treatment_protocol: human primary muscle cells 24 hours after stimulation with 10, 30 or 300 ng/ml of Myostatin, GDF11 and control (vehicle alone)

tag: time

tag: dose

value: 300 ng/mL

tag: treatment


title: gray-00298: b0420-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

value: mammary gland

tag: followup time

tag: ethnicity

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: b0344-onco

description: Array Type: E950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

value: Caucasian

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: progesterone receptor status

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0341-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: hormonal therapy

tag: estrogen receptor status

value: positive

tag: biosource type

tag: alive at endpoint


title: GDF11_24hr_300_3

tag: time

tag: dose

tag: treatment


title: gray-00298: b0340-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: progesterone receptor status

tag: node positive

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0339-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0334-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: progesterone receptor status

value: dead

tag: node positive


title: gray-00298: b0338-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: hormonal therapy

value: yes

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0336-onco

description: Array Type: F950

value: no

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0327-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: progesterone receptor status

tag: node positive


title: gray-00298: b0335-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

value: Asian

tag: hormonal therapy

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: GDF11_24hr_30_2

tag: time

tag: dose

value: 30 ng/mL

tag: treatment


title: gray-00298: b0326-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: GDF11_24hr_300_1


title: Myostatin_24hr_300_3

value: Myostatin


title: GDF11_24hr_10_4

value: 10 ng/mL


title: GDF11_24hr_10_3


title: gray-00298: b0318-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

value: breast cancer

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0317-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint


title: gray-00298: b0337-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: GDF11_24hr_30_4

tag: time

tag: dose

tag: treatment


title: GDF11_24hr_10_1


title: GDF11_24hr_10_2


title: GDF11_24hr_30_1


title: Myostatin_24hr_300_1


title: GDF11_24hr_30_3


title: Myostatin_24hr_300_2


title: Myostatin_24hr_30_3


title: gray-00298: b0299-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0297-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

value: negative

tag: biosource type

tag: alive at endpoint

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0296-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive


title: Myostatin_24hr_30_2

tag: time

tag: dose

tag: treatment


title: Myostatin_24hr_30_4


title: Myostatin_24hr_300_4


title: GDF11_24hr_300_4


title: Myostatin_24hr_10_4


title: gray-00298: b0287-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

value: alive

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0285-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: recurrence time

tag: tumor size (mm)

tag: gender

value: female


title: Myostatin_24hr_10_3

tag: time

tag: dose

tag: treatment


title: Myostatin_24hr_30_1


title: gray-00298: b0277-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0265-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: Myostatin_24hr_10_1

tag: time

tag: dose

tag: treatment


title: Myostatin_24hr_10_2


title: gray-00298: b0255-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0305-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0252-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint


title: None_24hr_0_4

tag: time

tag: dose

tag: treatment


title: None_24hr_0_2


title: gray-00298: b0251-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: None_24hr_0_3


title: gray-00298: b0246-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: None_24hr_0_1

tag: time

tag: dose

tag: treatment


title: gray-00298: b0243-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0241-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: b0239-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive


title: GDF11_8hr_300_4

tag: time

tag: dose

tag: treatment


title: GDF11_8hr_300_3


title: gray-00298: b0202-onco

description: Array Type: G950

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: gray-00298: b0200-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: GDF11_8hr_300_1

tag: time

tag: dose

tag: treatment


title: GDF11_8hr_30_4


title: GDF11_8hr_300_2


title: gray-00298: b0248-onco

description: Array Type: E500

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: estrogen receptor status

tag: biosource type

tag: alive at endpoint

tag: age at diagnosis

tag: recurrence

tag: radiation treatment


title: GDF11_8hr_10_2


title: GDF11_8hr_10_4


title: GDF11_8hr_30_1


title: GDF11_8hr_10_1


title: Myostatin_8hr_300_4


title: gray-00298: b0165-onco

description: Array Type: E500

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: progesterone receptor status

tag: node positive

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: Myostatin_8hr_300_2

tag: time

tag: dose

tag: treatment


title: GDF11_8hr_10_3


title: Myostatin_8hr_300_1


title: GDF11_8hr_30_3


title: KO_treadmill_rep3

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

institute: CCHMC

hyb_protocol: The biotinylated cRNA was prepared and hybridized to the Mouse 430A_2.0 GeneChip in accordance with Affymetrix protocols.

scan_protocol: GeneChips were scanned by the Affymetrix GeneChip Scanner.

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF.

organism: Mus musculus

source_name: gastrocnemius muscle

label_protocol: Gene expression profiles were obtained from Affymetrics GeneChip Mouse Genome 430 2.0 Arrays. The microarray data was first preprocessed, including background correction and normalization, by Robust Multi-array Average (RMA) with custom CDF downloaded from BrainArray

growth_protocol: Mice were fed a high fat diet consisting of high-fat, high-sucrose diet (HFHSD, D12331 Research Diet) starting at 8-10 weeks of age for 14-18 weeks.

extract_protocol: Total RNA was isolated from flash-frozen mouse tissue samples by using Trizol (Invitrogen) isolation method and cleaned up with RNAEasy mini columns (Qiagen). cDNA was produced using a high capacity cDNA transcription kit.

treatment_protocol: Exercise endurance was determined using a Columbus Instruments modular treadmill.  Eight mice could be run at a time in this system.  Prior to the measurement, all mice were weighed and allowed to orient to the inclined treadmill (10o) surroundings for 3-5 minutes.  A ramping program was then begun at 4 m/min for 5 min to allow the animals to acclimate to the movement of the belt and orient them to the shock grid.  The speed was increased to 10 m/min for 10 min and then increased 2 m/min every 2 minutes (to a maximum speed of 40 m/min) until the animals run to exhaustion.

tag: tissue

value: gastrocnemius muscle

tag: genotype

value: CD38 KO

tag: exercise

value: treadmill


title: KO_treadmill_rep2


title: Myostatin_8hr_30_4


title: GDF11_8hr_30_2


title: Myostatin_8hr_30_2


title: Myostatin_8hr_30_1


title: Myostatin_8hr_30_3


title: Myostatin_8hr_10_4


title: Myostatin_8hr_10_3


title: Small Molecule Generated Stem Cells Replicate 1

city: beijing

first: chun

last: liu

state: beijing

address: beijing

country: China

institute: Peking University

description: Mouse Whole Genome OneArray® v2 (Phalanx Biotech Group, Taiwan)

hyb_protocol: Fragmented cDNA was hybridized at 42˚C overnight using the HybBag mixing system with 1× OneArray Hybridization Buffer (Phalanx Biotech, Belmont, CA, USA), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray protocol.

scan_protocol: Data extracton used GenePix 4100 scanner from molecular Devices, and measured using GenePixPro Software

data_processing: Normalized using matlab. Data selection by Flags and SNRs.

source_name: Small Molecule Generated Stem Cells

label_protocol: NHS ester dye.Ambion allyl MessageAmp IITM aRNA kit

growth_protocol: ES medium

extract_protocol: Total RNA extracted using Trizol and purified by QIAGEN Rneasy Kit following manufacturer's instructions

tag: development stage

value: embryo

tag: passage

tag: strain


title: KO_treadmill_rep1


title: Myostatin_8hr_10_2


title: WT_treadmill_rep4

value: WT


title: KO_sedentary_rep2

value: sedentary


title: WT_treadmill_rep3


title: None_8hr_0_4


title: WT_treadmill_rep1


title: WT_treadmill_rep2


title: Myostatin_8hr_10_1


title: KO_sedentary_rep4


title: KO_sedentary_rep3


title: None_8hr_0_2


title: WT_sedentary_rep4


title: WT_sedentary_rep3


title: Parental Cells Replicate 1

source_name: Parental Cells

growth_protocol: FBS medium


title: None_8hr_0_3


title: mid-Myc - Replicate 2

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf.  The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.

source_name: P493-6 cells expressing a moderate level of c-Myc

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 0 hours.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.

treatment_protocol: c-Myc expression released for 1 hours.

tag: cell line

tag: cell type

value: B-cell lymphoma


title: mid-Myc - Replicate 1


title: WT_sedentary_rep2


title: None_8hr_0_1


title: AOCS_112_ICGC_DBPC_20130205_133

status: Public on May 19 2015

city: Herston

first: Ann-Marie

last: Patch

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned  on iScan

data_processing: Data was extracted using  Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and LogR ratios.

source_name: PrimaryTumour

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA) (HumanOmni2.5-8 BeadChips).

extract_protocol: Nucleic acids were extracted from frozen tissue sections were incubated in Buffer AL and proteinase K at 56°C overnight, while ascites cells were only incubated in Buffer AL and proteinase K at 56°C for 10min. Ethanol was added to sample which was applied to a DNeasy Mini spin column. Captured DNA was washed and eluted in Buffer AE. DNA was quantitated using the NanoDrop1000 (Thermo Scientific) and the Qubit® dsDNA BR assay.

value: Female

value: Primary Tumour

value: high grade serous ovarian cancer


title: AOCS_134_ICGC_DBPC_20130205_134

source_name: Ascites

value: Ascites


title: AOCS_138_ICGC_DBPC_20130205_146


title: WT_sedentary_rep1


title: AOCS_111_ICGC_DBPC_20130205_131


title: AOCS_150_ICGC_DBPC_20130205_171


title: AOCS_147_ICGC_DBPC_20130205_166


title: AOCS_145_ICGC_DBPC_20130205_162


title: AOCS_148_ICGC_DBPC_20130205_168


title: AOCS_146_ICGC_DBPC_20130205_164


title: AOCS_135_ICGC_DBPC_20130205_137


title: AOCS_142_ICGC_DBPC_20130205_155


title: AOCS_144_ICGC_DBPC_20130205_160


title: AOCS_141_ICGC_DBPC_20130205_153


title: AOCS_149_ICGC_DBPC_20130205_170


title: AOCS_135_ICGC_DBPC_20130205_136


title: AOCS_137_ICGC_DBPC_20130205_143


title: AOCS_139_ICGC_DBPC_20130205_150


title: AOCS_137_ICGC_DBPC_20130205_145


title: AOCS_153_ICGC_DBPC_20130205_176


title: Exosomal_NATs_SW480_1

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

institute: Hirosaki University

description:
Exosomal RNA
Gene expression of exosomal NATs into culture medium of SW480 cells

hyb_protocol: Agilent 44 K × 4 human custom microarray slides (Agilent eArray Design ID = 19052, produced by Tsukuba GeneTech Laboratory, Ibaraki, Japan) were hybridized with Cy3-labeled cDNAs (5 µg) in hybridization solution and blocking Agent (Agilent Technologies) at 65°C for 24 h using a hybridization oven. Microarray slides were washed in wash Buffer 1 and 2 (Agilent Technologies) including 0.005% Triton X-102. Washed microarray slides were dried using nitrogen gas.

scan_protocol: Cy3 fluorescence images of array slides were obtained using a DNA microarray scanner (Agilent Technologies).

data_processing: Cy3 fluorescence images of array slides  were processed using Feature Extraction version 8.1 software based on instructions from Agilent Technologies.

source_name: Culture medium, SW480, replicate 1

label_protocol: Exosomal RNAs (1 ng) derived from SW480 cells were amplified using Ovation Pico WTA System V2 (NuGEN Technologies, San Carlos, CA). Amplified exosomal RNAs were purified using QIAquick Nucleotide Removal Kit (Qiagen, Valencia, CA). Cyanine 3 (Cy3)-labeled cDNAs were synthesized by Agilent Genomic DNA Enzymatic Labeling Kit (Agilent Technologies), according to the manufacturer’s instructions. Cy3-labeled cDNAs were purified using QIAquick Nucleotide Removal Kit (Qiagen). Measurement of the concentration and quality of Cy3-labeled cDNAs was performed using an Agilent 2100 Bioanalyzer.

growth_protocol: SW480 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Wako, Tokyo, Japan) supplemented with 10% fetal bovine serum (FBS) (Life Technologies, Carlsbad, CA), 100 U/ml of penicillin and 100 µg/ml of streptomycin. Cells were cultured at 37 °C in a humidified atmosphere of 95% air/5% CO2.

extract_protocol: Isogen II (NipponGene, Tokyo, Japan) was used to isolate exosomal RNAs from exosome pellets, respectively. Exosomal RNAs were stored at −80 °C until use. The concentrations of RNAs extracted were examined using a Quant-iT RiboGreen RNA Reagent and kit (ThermoFisher Scientific, DE, USA) according to the manufacturer’s instructions. In addition, the size of exosomal RNAs were confirmed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Pico kit (Agilent Technologies, Foster City, CA), according to the manufacturer’s instructions.

treatment_protocol: SW480 cells were plated on collagen-coated 10-cm dishes at 1 × 10^6 cells per dish with the culture media described above. After 72 h, culture medium was discarded and the cells were washed three times in serum-free culture medium. Serum-free culture medium was then added at 10 ml per dish, after which cells were cultured for 48 h. Cell culture media were collected and subjected to a sequence of centrifugation steps. Cell culture media were first centrifuged at 300 ×g at 4 °C for 3 min to remove floating cells. These supernatants were then centrifuged at 2,000 ×g at 4 °C for 15 min and collected in new tubes. In addition, culture supernatants were centrifuged at 12,000 ×g at 4 °C for 35 min to remove cellular debris and these supernatants were collected in new tubes. Supernatants were then filtered (0.22-µm filter). These filtrates were ultracentrifuged at 120,000 ×g at 4 °C for 70 min to collect exosomes using an Optima TLX Ultracentrifuge (Beckman Coulter, Brea, CA). Exosome pellets were washed in Dulbecco’s phosphate buffered saline (D-PBS) and further ultracentrifuged at 120,000 × g at 4 °C for 70 min. Finally, exosome pellets were re-suspended in D-PBS.

tag: medium


title: AOCS_152_ICGC_DBPC_20130205_174


title: AOCS_078_ICGC_DBPC_20130205_126


title: AOCS_125_ICGC_DBPC_20130205_108


title: Exosomal_NATs_SW480_2

source_name: Culture medium, SW480, replicate 2

value: Roswell Park Memorial Institute (RPMI) 1640


title: KO_sedentary_rep1


title: AOCS_143_ICGC_DBPC_20130205_158


title: AOCS_113_ICGC_DBPC_20130205_088


title: AOCS_114_ICGC_DBPC_20130205_090


title: AOCS_115_ICGC_DBPC_20130205_092


title: AOCS_122_ICGC_DBPC_20130205_102


title: AOCS_132_ICGC_DBPC_20130205_120


title: AOCS_116_ICGC_DBPC_20130205_094


title: AOCS_128_ICGC_DBPC_20130205_112


title: AOCS_095_ICGC_DBPC_20130205_068


title: AOCS_077_ICGC_DBPC_20130205_037


title: AOCS_109_ICGC_DBPC_20130205_086


title: AOCS_126_ICGC_DBPC_20130205_110


title: AOCS_124_ICGC_DBPC_20130205_106


title: AOCS_131_ICGC_DBPC_20130205_118


title: AOCS_091_ICGC_DBPC_20130205_056


title: AOCS_064_ICGC_DBPC_20130205_026


title: AOCS_086_ICGC_DBPC_20130205_050


title: AOCS_094_ICGC_DBPC_20130205_067


title: AOCS_093_ICGC_DBPC_20130205_062


title: AOCS_034_ICGC_DBPC_20130205_007


title: AOCS_119_ICGC_DBPC_20130205_097


title: AOCS_120_ICGC_DBPC_20130205_099


title: AOCS_085_ICGC_DBPC_20130205_049


title: AOCS_001_ICGC_DBPC_20130205_002


title: AOCS_081_ICGC_DBPC_20130205_043


title: AOCS_079_ICGC_DBPC_20130205_039


title: AOCS_130_ICGC_DBPC_20130205_116


title: AOCS_060_ICGC_DBPC_20130205_021


title: AOCS_059_ICGC_DBPC_20130205_019


title: AOCS_090_ICGC_DBPC_20130205_055


title: AOCS_034_ICGC_DBPC_20130205_009


title: AOCS_080_ICGC_DBPC_20130205_041


title: AOCS_092_ICGC_DBPC_20130205_059


title: AOCS_084_ICGC_DBPC_20130205_047


title: AOCS_105_ICGC_DBPC_20130205_078


title: AOCS_057_ICGC_DBPC_20130205_015


title: AOCS_005_ICGC_DBPC_20130205_006


title: AOCS_083_ICGC_DBPC_20130205_045


title: AOCS_104_ICGC_DBPC_20130205_076


title: AOCS_075_ICGC_DBPC_20130205_033


title: AOCS_093_ICGC_DBPC_20130205_064


title: AOCS_064_ICGC_DBPC_20130205_028


title: AOCS_076_ICGC_DBPC_20130205_035


title: AOCS_091_ICGC_DBPC_20130205_058


title: AOCS_058_ICGC_DBPC_20130205_017


title: AOCS_086_ICGC_DBPC_20130205_052


title: AOCS_056_ICGC_DBPC_20130205_013


title: AOCS_055_ICGC_DBPC_20130205_011


title: AOCS_004_ICGC_DBPC_20130205_004


title: AOCS_065_ICGC_DBPC_20130205_031


title: AOCS_094_ICGC_DBPC_20130205_066

source_name: TumourLocalRecurrence

value: Tumour Local Recurrence


title: AOCS_097_ICGC_DBPC_20130205_074


title: AOCS_092_ICGC_DBPC_20130205_061


title: AOCS_061_ICGC_DBPC_20130205_023


title: AOCS_096_ICGC_DBPC_20130205_072


title: AOCS_063_ICGC_DBPC_20130205_025


title: KO_treadmill_rep4


title: Myostatin_8hr_300_3

value: 300 ng/mL

value: Myostatin


title: GP_104

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Triple-negative breast cancer tumours

hyb_protocol: Double-stranded complementary DNA (cDNA) and labeled complementary RNA (cRNA) were synthesized from the total RNA and hybridized to the Affymetrix Human U133 Plus 2 gene chips (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were further processed and scanned according to the manufacturer’s protocol using the GeneChip Scanner 3000 7G.

data_processing: The arrays were normzalized using the MAS 5.0 Affymetrix software (Expression Console - Affymetrix).

label: Biotin

source_name: Breast tumor biospsie

label_protocol: According to manufacturer protocol

extract_protocol: Total RNA was prepared using the RNeasy® Mini kit (Qiagen, Valencia, CA). The integrity of the RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: diagnosis

value: triple negative breast cancer

tag: age at diag

tag: meta

tag: mfs (days)

tag: death

tag: os (days)

tag: er-ihc

tag: pr-ihc


title: GP_107

description: Triple-negative breast cancer tumours


title: GP_105

description: Triple-negative breast cancer tumours


title: GP_103

description: Triple-negative breast cancer tumours


title: GP_101

description: Triple-negative breast cancer tumours


title: GP_102

description: Triple-negative breast cancer tumours


title: GP_106

description: Triple-negative breast cancer tumours


title: group 1-wt-3

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Microarray: SurePrint G3 Human Gene Expression 8x60K v2 Microarray (Agilent microarray design ID 039494)

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent).

data_processing: Images were quantified using Agilent Feature Extraction Software (ver. 10.7). Date were processed using the RMA algorithm.

source_name: H157 Squamous Cell Lung Cancer Cell Line (SCC)

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis” v.6.6 kit by following manufacturer instructions. Agilent manual G4140-90040 of September 2012. Amplification: by RNA polymerases.

growth_protocol: Cells where growth on RPMI media with 10% FBS, 1% PS

extract_protocol: Total mRNA  where extrated using Trizol Reagent.

treatment_protocol: Induction with doxocyclyn (1 ng/ul)

tag: vector

value: tet repressor vector and a vector with the wt form of PARD3 gene (NM_001184785.1)


title: group 1-mutant-3

value: tet repressor vector and a vector with a mutant form of PARD3 gene, NM_001184785.1 without exon 2


title: group 1-mock-3

value: tet repressor vector and empty vector


title: group 1-mutant-2


title: GP_097

description: Triple-negative breast cancer tumours


title: GP_096

description: Triple-negative breast cancer tumours


title: GP_100

description: Triple-negative breast cancer tumours


title: GP_099

description: Triple-negative breast cancer tumours


title: GP_093

description: Triple-negative breast cancer tumours


title: group 1-mock-2


title: GP_094

description: Triple-negative breast cancer tumours


title: group 1-wt-2


title: group 1-mutant-1


title: GP_095

description: Triple-negative breast cancer tumours


title: group 1-wt-1


title: GP_092

description: Triple-negative breast cancer tumours


title: GP_090

description: Triple-negative breast cancer tumours


title: group 1-mock-1


title: GP_091

description: Triple-negative breast cancer tumours


title: GP_089

description: Triple-negative breast cancer tumours


title: GP_087

description: Triple-negative breast cancer tumours


title: GP_098

description: Triple-negative breast cancer tumours


title: GP_085

description: Triple-negative breast cancer tumours


title: GP_083

description: Triple-negative breast cancer tumours


title: GP_086

description: Triple-negative breast cancer tumours


title: gray-00215: SUM149PT

source_name: breast cancer


title: gray-00215: MDAMB134


title: gray-00215: BT20


title: GP_082

description: Triple-negative breast cancer tumours


title: gray-00215: SKBR3


title: GP_088

description: Triple-negative breast cancer tumours


title: GP_084

description: Triple-negative breast cancer tumours


title: gray-00215: MDAMB453


title: gray-00215: HCC1143


title: GP_080

description: Triple-negative breast cancer tumours


title: GP_081

description: Triple-negative breast cancer tumours


title: gray-00215: MDAMB157


title: GP_078

description: Triple-negative breast cancer tumours


title: gray-00215: HCC1954


title: GP_077

description: Triple-negative breast cancer tumours


title: gray-00215: CAMA1


title: GP_076

description: Triple-negative breast cancer tumours


title: GP_073

description: Triple-negative breast cancer tumours


title: GP_079

description: Triple-negative breast cancer tumours


title: gray-00215: HCC1937


title: gray-00215: BT549


title: GP_075

description: Triple-negative breast cancer tumours


title: gray-00215: SUM52PE


title: GP_074

description: Triple-negative breast cancer tumours


title: GP_072

description: Triple-negative breast cancer tumours


title: gray-00215: HS578T


title: gray-00215: MCF10A


title: GP_070

description: Triple-negative breast cancer tumours


title: GP_069

description: Triple-negative breast cancer tumours


title: GP_068

description: Triple-negative breast cancer tumours


title: gray-00215: LY2


title: gray-00215: MCF7


title: GP_067

description: Triple-negative breast cancer tumours


title: gray-00215: MDAMB175


title: GP_071

description: Triple-negative breast cancer tumours


title: gray-00215: HCC2157


title: GP_064

description: Triple-negative breast cancer tumours


title: GP_066

description: Triple-negative breast cancer tumours


title: GP_065

description: Triple-negative breast cancer tumours


title: gray-00215: SUM225CWN


title: GP_063

description: Triple-negative breast cancer tumours


title: GP_062

description: Triple-negative breast cancer tumours


title: gray-00215: MDAMB435


title: gray-00215: MDAMB468


title: gray-00215: SUM190PT


title: gray-00215: SUM44PE


title: gray-00215: AU565


title: GP_060

description: Triple-negative breast cancer tumours


title: GP_061

description: Triple-negative breast cancer tumours


title: GP_058

description: Triple-negative breast cancer tumours


title: gray-00215: HCC1007


title: GP_059

description: Triple-negative breast cancer tumours


title: GP_057

description: Triple-negative breast cancer tumours


title: gray-00215: HCC1428


title: gray-00215: ZR751


title: gray-00215: MDAMB436


title: gray-00215: HCC2185


title: gray-00215: HCC38


title: GP_055

description: Triple-negative breast cancer tumours


title: GP_054

description: Triple-negative breast cancer tumours


title: gray-00215: MDAMB415


title: gray-00215: SUM159PT


title: GP_056

description: Triple-negative breast cancer tumours


title: GP_053

description: Triple-negative breast cancer tumours


title: GP_051

description: Triple-negative breast cancer tumours


title: GP_052

description: Triple-negative breast cancer tumours


title: gray-00215: HCC202


title: GP_050

description: Triple-negative breast cancer tumours


title: gray-00215: HCC70


title: gray-00215: MCF12A


title: gray-00215: MDAMB361


title: GP_048

description: Triple-negative breast cancer tumours


title: gray-00215: BT483


title: GP_049

description: Triple-negative breast cancer tumours


title: gray-00215: HBL100


title: gray-00215: SUM185PE


title: gray-00215: ZR7530


title: gray-00215: MDAMB231


title: GP_047

description: Triple-negative breast cancer tumours


title: GP_046

description: Triple-negative breast cancer tumours


title: gray-00215: 600MPE


title: GP_043

description: Triple-negative breast cancer tumours


title: GP_044

description: Triple-negative breast cancer tumours


title: gray-00215: UACC812


title: gray-00215: SUM1315


title: gray-00215: T47D


title: GP_045

description: Triple-negative breast cancer tumours


title: gray-00215: HCC1569


title: gray-00215: HCC1187


title: GP_039

description: Triple-negative breast cancer tumours


title: gray-00215: HCC3153


title: GP_041

description: Triple-negative breast cancer tumours


title: GP_037

description: Triple-negative breast cancer tumours


title: GP_038

description: Triple-negative breast cancer tumours


title: GP_042

description: Triple-negative breast cancer tumours


title: gray-00215: HCC1500


title: gray-00215: BT474


title: GP_036

description: Triple-negative breast cancer tumours


title: gray-00215: ZR75B


title: GP_033

description: Triple-negative breast cancer tumours


title: Ppl_20_B_3_rep_1

city: Vancouver

first: Shawn

last: Mansfield

state: BC

address: 2424 Main Mall

department: Department of Wood Science

country: Canada

institute: University of British Columbia

description: This sample is of P. placenta incubated on substrate B for 30 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) following NimbleGen standard operating protocol.

scan_protocol: Scanningn was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) using Axon4000B Scanner( Molecular Dynamics)

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization , and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

organism: Rhodonia placenta

source_name: P. placenta on subsatrate B after 30 days

label_protocol: Labelling was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) following NimbleGen standard operating protocol.

growth_protocol: P. placenta was cultured on malt extract agar (MEA) (Oxoid, UK) for 10 days prior to inoculation with wood wafers.

extract_protocol: Frozen wood wafers with fungal mycelia were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. Total fungal RNA was purified as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).

treatment_protocol: Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days (time points: 10, 20 and 30, respectively). Following incubation, the wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. For substrates “A” and “B”, three(1) replicates were used for each substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed. (1)One of the tree replicates of substrate B after 10 days failes, therfore only 2 replicates were used .

tag: substrate

value: B:low lignin, high glucose

tag: incubation time(days)

tag: tissue

value: Mycelium


title: Ppl_18_A_3_rep_2

description: This sample is of P. placenta incubated on substrate A for 30 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: P. placenta on subsatrate A after 30 days

value: A:high lignin, low glucose


title: GP_029

description: Triple-negative breast cancer tumours


title: GP_026

description: Triple-negative breast cancer tumours


title: Ppl_17_A_3_rep_1

description: This sample is of P. placenta incubated on substrate A for 30 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: PpL_22_B_3_rep_3

description: This sample is of P. placenta incubated on substrate B for 30 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Ppl_21_B_3_rep_2

description: This sample is of P. placenta incubated on substrate B for 30 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Ppl_15_C_2_rep_1

description: This sample is of P. placenta incubated on substrate C for 20 days.  It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: P. placenta on subsatrate C after 20 days

value: C:average lignin, average glucose


title: GP_027

description: Triple-negative breast cancer tumours


title: Ppl_14_B_2_rep_3

description: This sample is of P. placenta incubated on substrate B for 20 days.  It is the second of two biological replicates used in this experiment, each from separate cultures. The third replicate failed.

source_name: P. placenta on subsatrate B after 20 days


title: GP_024

description: Triple-negative breast cancer tumours


title: GP_040

description: Triple-negative breast cancer tumours


title: GP_034

description: Triple-negative breast cancer tumours


title: GP_028

description: Triple-negative breast cancer tumours


title: Ppl_24_C_3_rep_2

description: This sample is of P. placenta incubated on substrate C for 30 days.  It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: P. placenta on subsatrate C after 30 days


title: GP_030

description: Triple-negative breast cancer tumours


title: GP_035

description: Triple-negative breast cancer tumours


title: Ppl_23_C_3_rep_1

description: This sample is of P. placenta incubated on substrate C for 30 days.  It is the first of two biological replicates used in this experiment, each from separate cultures.


title: Ppl_19_A_3_rep_3

description: This sample is of P. placenta incubated on substrate A for 30 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.


title: GP_032

description: Triple-negative breast cancer tumours


title: Ppl_16_C_2_rep_2

description: This sample is of P. placenta incubated on substrate C for 20 days.  It is the second of two biological replicates used in this experiment, each from separate cultures.


title: GP_031

description: Triple-negative breast cancer tumours


title: GP_023

description: Triple-negative breast cancer tumours


title: GP_025

description: Triple-negative breast cancer tumours


title: Ppl_13_B_2_rep_2

description: This sample is of P. placenta incubated on substrate B for 20 days.  It is the first of two biological replicates used in this experiment, each from separate cultures. The third replicate failed.


title: GP_020

description: Triple-negative breast cancer tumours


title: Ppl_9_A_2_rep_1

description: This sample is of P. placenta incubated on substrate A for 20 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: P. placenta on subsatrate A after 20 days


title: GP_021

description: Triple-negative breast cancer tumours


title: Ppl_7_C_1_rep_1

description: This sample is of P. placenta incubated on substrate C for 10 days.  It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: P. placenta on subsatrate C after 10 days


title: Ppl_3_A_1_rep_3

description: This sample is of P. placenta incubated on substrate A for 10 days.  It is the thrird of three biological replicates used in this experiment, each from separate cultures.

source_name: P. placenta on subsatrate A after 10 days


title: Ppl_10_A_2_rep_2

description: This sample is of P. placenta incubated on substrate A for 20 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Ppl_8_C_1_rep_2

description: This sample is of P. placenta incubated on substrate C for 10 days.  It is the second of two biological replicates used in this experiment, each from separate cultures.


title: GP_018

description: Triple-negative breast cancer tumours


title: Ppl_6_B_1_rep_3

description: This sample is of P. placenta incubated on substrate B for 10 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: P. placenta on subsatrate B after 10 days


title: GP_017

description: Triple-negative breast cancer tumours


title: Ppl_1_A_1_rep_1

description: This sample is of P. placenta incubated on substrate A for 10 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Ppl_2_A_1_rep_2

description: This sample is of P. placenta incubated on substrate A for 10 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Ppl_4_B_1_rep_1

description: This sample is of P. placenta incubated on substrate B for 10 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: GP_016

description: Triple-negative breast cancer tumours


title: EMT-6 tumor biological rep4

city: Bethesda

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

hyb_protocol: Labeled fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0ST array for 16 h at 45oC, 60 rpm.  GeneChips were washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip scanner 3000

data_processing:
Data were collected using Affymetrix AGCC software
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: EMT-6 primary mammary tumor

label_protocol: 100ng of RNA was reverse transcribed and amplified using Ambion WT expression kit following manufacturer's instructions.  Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Subconfluent cell suspensions were surgically implanted in the orthotopic site (#4 mammary fat pad) of fully immunocompetent syngeneic mice and primary tumors were allowed to grow to 0.5-1.0cm diameter before harvesting and snap-freezing for RNA preparation.

extract_protocol: 15-30mg of frozen tumor was homogenized in lysis buffer and total RNA was extracted using an RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Primary tumors were dissected free of surrounding non-malignant tissue and any necrotic tissue and snap frozen in liquid nitrogen for later RNA extraction

value: Balb/c

tag: cell line origin

value: Spontanteous tumor


title: GP_009

description: Triple-negative breast cancer tumours


title: Ppl_11_A_2_rep_3

description: This sample is of P. placenta incubated on substrate A for 10 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.

tag: strain


title: TS/A-E1 tumor biological rep1

source_name: TS/A-E1 primary mammary tumor


title: Ppl_5_B_1_rep_2

description: This sample is of P. placenta incubated on substrate B for 10 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: EMT-6 tumor biological rep3


title: EMT-6 tumor biological rep2


title: GP_019

description: Triple-negative breast cancer tumours


title: GP_011

description: Triple-negative breast cancer tumours


title: GP_014

description: Triple-negative breast cancer tumours


title: GP_015

description: Triple-negative breast cancer tumours


title: GP_012

description: Triple-negative breast cancer tumours


title: GP_013

description: Triple-negative breast cancer tumours


title: GP_008

description: Triple-negative breast cancer tumours


title: GP_010

description: Triple-negative breast cancer tumours


title: GP_006

description: Triple-negative breast cancer tumours


title: GP_007

description: Triple-negative breast cancer tumours


title: GP_004

description: Triple-negative breast cancer tumours


title: R3T tumor biological rep2

source_name: R3T primary mammary tumor

value: Genetically engineered mouse tumor


title: R3T tumor biological rep3


title: EMT-6 tumor biological rep1


title: E0771 tumor biological rep1

source_name: E0771 primary mammary tumor


title: 4T1 tumor biological rep4

source_name: 4T1 primary mammary tumor


title: GP_005

description: Triple-negative breast cancer tumours

source_name: Breast tumor biospsie


title: 73_C_3_rep_1

description: This sample is of P. chrysosporium incubated on substrate C for 30 days.  It is the first of two biological replicates used in this experiment, each from separate cultures.

organism: Phanerodontia chrysosporium

source_name: P. chrysosporium on subsatrate C after 30 days

growth_protocol: P. chrysosporium was cultured on malt extract agar (MEA) (Oxoid, UK) for 10 days prior to inoculation with wood wafers.


title: E0771 tumor biological rep2


title: HRM-1 tumor biological rep2

source_name: HRM-1 primary mammary tumor

value: FVB/N


title: HRM-1 tumor biological rep1


title: E0771 tumor biological rep4


title: R3T tumor biological rep1


title: GP_003

description: Triple-negative breast cancer tumours


title: 74_C_3_rep_2

description: This sample is of P. chrysosporium incubated on substrate C for 30 days.  It is the second of two biological replicates used in this experiment, each from separate cultures.


title: MVT-1 tumor biological rep2

source_name: MVT-1 primary mammary tumor


title: GP_002

description: Triple-negative breast cancer tumours


title: MVT-1 tumor biological rep1


title: GP_001

description: Triple-negative breast cancer tumours


title: HRM-1 tumor biological rep3


title: HRM-1 tumor biological rep4


title: 72_B_3_rep_3

description: This sample is of P. chrysosporium incubated on substrate B for 30 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: P. chrysosporium on subsatrate B after 30 days


title: MVT-1 tumor biological rep3


title: 4T1 tumor biological rep3


title: M6 tumor biological rep4

source_name: M6 primary mammary tumor


title: MVT-1 tumor biological rep4


title: 71_B_3_rep_2

description: This sample is of P. chrysosporium incubated on substrate B for 30 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: 69_A_3_rep_3

description: This sample is of P. chrysosporium incubated on substrate A for 30 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: P. chrysosporium on subsatrate A after 30 days


title: M6 tumor biological rep3


title: 4T1 tumor biological rep2


title: 68_A_3_rep_2

description: This sample is of P. chrysosporium incubated on substrate A for 30 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: M6 tumor biological rep2


title: M6 tumor biological rep1


title: 67_A_3_rep_1

description: This sample is of P. chrysosporium incubated on substrate A for 30 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 6DT1 tumor biological rep2

source_name: 6DT1 primary mammary tumor


title: Met-1 tumor biological rep2

source_name: Met-1 primary mammary tumor


title: 66_C_2_rep_2

description: This sample is of P. chrysosporium incubated on substrate C for 20 days.  It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: P. chrysosporium on subsatrate C after 20 days


title: 6DT1 tumor biological rep3


title: 65_C_2_rep_1

description: This sample is of P. chrysosporium incubated on substrate C for 20 days.  It is the first of two biological replicates used in this experiment, each from separate cultures.


title: Met-1 tumor biological rep3


title: D2A1 tumor biological rep3

source_name: D2A1 primary mammary tumor


title: 4T1 tumor biological rep1


title: 70_B_3_rep_1

description: This sample is of P. chrysosporium incubated on substrate B for 30 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 6DT1 tumor biological rep1