title: Prostate DU145(ATCC) 141690HUEX1A11

description: Derived from metastatic site: brain (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: Renal UO-31 141689HUEX1A11

status: Public on Jun 17 2011

type: RNA

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

country: USA

institute: HiThru Analytics

description: Renal cell carcinoma-very poorly differentiated

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Probes were normalized using GC-RMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Renal cell carcinoma

label_protocol: standard Affymetrix protocol

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0,5 x 10-6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 370C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10-6 cells into new T162’s w 30 ml media.  Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Growth schedule prior to harvest: Grow cells to ~80 confluencey. Re-feed cells the day prior to harvest. Draw off media from attached cells, or spin down suspended cells. Rinse cells with ~10 ml 1x PBS. Purify using Quiagen Midi Kit (Cat # 75144) per instructions.  In brief, lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml) per 4 T162s. Scrape (attached) cells. Pipet into a 50 ml tube.  Repeat with the next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a 20 guage needle 12x’s. Freeze lysate at -80 deg C. Use a maximum of 100 x 10-6 cells per column.

tag: cell line

tag: tissue of origin

value: Renal

tag: Sex

value: F

tag: prior treatment

tag: epithelial

value: yes

tag: ploidy

tag: p53 mutation

value: WT

tag: doubling time

tag: contributing institute

value: National Cancer Institute, NIH

tag: contributing person


title: Human breast biopsy V64

city: New York

first: Ilana

last: Belitskaya-Levy

address: 650 First Avenue, 5th Floor

department: Environmental Medicine

institute: New York University School of Medicine

description: Gene expression data from breast biopsies of healthy postmenopausal women

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G.

data_processing: Raw data from array scans were pre-processed using the Robust Multi-chip Analysis method (RMA) implemented in the Bioconductor package affy that includes background correction, quantile normalization and summarization of expression values.

source_name: Human breast biopsy, normal

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

extract_protocol: Allprep DNA/RNA Mini Kit was used for extraction of total RNA according to the manufacturer's instructions. Samples were treated with Dnase.

treatment_protocol: Breast biopsies were performed with BARD MONOPTY (C. R. BARD Inc, AZ, USA) automated core biopsy instruments (14 Gauge, 10 cm long, 22 mm penetration depth)

tag: full time pregancy

value: nulliparous


title: Human breast biopsy V67

value: parous


title: Human breast biopsy V61


title: Melanoma UACC-257 141671HUEX1A11

description: Melanotic melanoma

source_name: Melanotic melanoma

value: Melanoma

value: no

value: 3n+, Hypertriploid (70-80)

value: University of Arizona

value: A. Leibovitz, UACC


title: Melanoma MDA-N 141667HUEX1A11

description: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: MDA-N

tag: age

tag: source

value: Pleural effusion

value: MT


title: Melanoma SK-MEL-28 141669HUEX1A12

description: Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

value: M

value: 4n-, Hypotetraploid (81-91)

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi

tag: reference


title: Melanoma SK-MEL-2 141668HUEX1A11

description: Malignant melanotic melanoma

value: Metastasis

value: G. Trempe; L.J. Old

value: Human Tumor Cells in vitro, pp 115-159, 1975


title: Human breast biopsy V66


title: Human breast biopsy V57


title: Human breast biopsy V56


title: Human breast biopsy V5

value: nulliparous


title: Human breast biopsy V59

value: parous


title: Human breast biopsy V62


title: Human breast biopsy V58


title: Human breast biopsy V54


title: Human breast biopsy V55


title: Melanoma MDA-MB-435 141666HUEX1A11

source_name: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: Melanoma

value: F

value: 2n+, Hyperdiploid (47-57)

value: R. Cailleau


title: Human breast biopsy V51


title: Leukemia MOLT-4 141660HUEX1A21

description: ALL (cells were taken when patient was in relapse)

source_name: ALL

value: Leukemia

value: no

value: PB

value: 4n, Tetraploid (92)

value: WT

value: Roswell Park Memorial Institute

value: J. Minowada


title: Human breast biopsy V53


title: Leukemia SR 141662HUEX1A11

description: Lymphoma

source_name: Lymphoma

value: SR

value: M

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.


title: Leukemia RPMI-8226 141661HUEX1A11

description: Myeloma

source_name: Myeloma

value: 3n-, Hypotriploid (58-68)

value: G.E. Moore


title: Melanoma LOXIMVI 141663HUEX1A11

description: Malignant amelanotic melanoma

source_name: Malignant amelanotic melanoma

value: LOXIMVI

value: Melanoma

value: Norsk Hydro's Institut, Norway


title: Human breast biopsy V48

value: nulliparous


title: Human breast biopsy V49

value: parous


title: Human breast biopsy V47


title: Human breast biopsy V43


title: Human breast biopsy V45


title: Melanoma MALME-3M 141665HUEX1A11

description: Malignant melanotic melanoma

value: no

value: Metastasis

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh


title: Human breast biopsy V46


title: Melanoma M14 141664HUEX1A11

description: Melanotic melanoma

value: MT

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine


title: Leukemia K-562 141659HUEX1A11

description: CML

source_name: CML

value: Leukemia

value: F

value: Bisulfan/PiBr

value: Pleural effusion

value: University of Tennesse

value: H.T. Holden


title: Leukemia HL-60 141658HUEX1A11

description: Pro myelocytic leukemia

source_name: Pro myelocytic leukemia

value: M

value: PBL

value: National Cancer Institute, NIH

value: R.C. Gallo


title: Human breast biopsy V39

value: nulliparous


title: Non-Small Cell Lung NCI-H322M 141654HUEX1A11

description: Small cell Bronchioalveolar Carcinoma

source_name: Small cell Bronchioalveolar Carcinoma

value: Non-Small Cell Lung

value: yes


title: Human breast biopsy V42


title: Human breast biopsy V3

value: parous


title: Leukemia CCRF-CEM 141657HUEX1A11

description: ALL

value: CCRF-CEM

value: Rad/Mtx/Cyx

value: no

value: Children's Cancer research Foudation

value: G.E. Foley


title: Non-Small Cell Lung NCI-H460 141655HUEX1A11

description: Large Cell Carcinoma-undifferentiated

source_name: Large Cell Carcinoma

value: WT

value: J.D. Minna; A.F. Gazdar


title: Human breast biopsy V38


title: Non-Small Cell Lung NCI-H226 141652HUEX1A11

description: Squamous cell carcinoma-very poorly differentiated

source_name: Squamous cell carcinoma

value: None (non smoker)

value: 3n, Triploid (69)

value: MT


title: Non-Small Cell Lung NCI-H522 141656HUEX1A11

description: Adenocarcinoma-very poorly differentiated

source_name: Adenocarcinoma

value: M


title: Human breast biopsy V35


title: Human breast biopsy V36


title: Non-Small Cell Lung NCI-H23 141653HUEX1A11

description: Adenocarcinoma-undifferentiated

value: 2n+, Hyperdiploid (47-57)

value: National Cancer Institute, NIH


title: Human breast biopsy V33

value: nulliparous


title: Human breast biopsy V37


title: Non-Small Cell Lung A549 141648HUEX1A11

description: Adenocarcinoma-poor to moderate differentiation

value: Non-Small Cell Lung

value: Giard DJ


title: Human breast biopsy V29


title: Non-Small Cell Lung HOP-92 141651HUEX1A11

description: Large cell-undifferentiated

source_name: Large cell

value: yes

value: Johns Hopkins University


title: Human breast biopsy V30

value: parous


title: Human breast biopsy V31


title: Non-Small Cell Lung HOP-62 141650HUEX1A11

description: adenocarcinoma-undifferentiated

source_name: adenocarcinoma

value: F

value: 4n+, Hypertetraploid (93-103)


title: Colon HCC-2998 141642HUEX1A11

description: carcinoma

source_name: carcinoma

value: Colon

value: MD Anderson Hospital and Tumor Institute


title: Colon SW-620 141647HUEX1A11

description: Carcinoma-undifferentiated

source_name: Carcinoma

value: Scott White Clinic

value: A. Leibovitz


title: Human breast biopsy V23

source_name: Human breast biopsy, normal


title: Non-Small Cell Lung EKVX 141649HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: EKVX

value: Norsk Hydro's Institut, Norway


title: Colon HCT-15 141644HUEX1A11

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)


title: Colon KM12 141646HUEX1A11

description: Adenocarcinome-poor differentiation

source_name: Adenocarcinome

value: MT

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute


title: Colon HT29 141645HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: Primary

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975


title: Human breast biopsy V2

value: parous


title: Colon HCT-116 141643HUEX1A11

description: carcinoma-very poorly differentiated

value: M

value: yes

value: 2n-, Hypodiploid (35-45)

value: Baylor College


title: Colon COLO205 141641HUEX1A11

description: Adenocarcinoma

value: Colon

value: Ascites

value: 3n, Triploid (69)

value: Denver Medical Hospital

value: G.E. Moore


title: CNS SNB-75 141639HUEX1A11

description: Astrocytoma

source_name: Astrocytoma

value: CNS

value: F

value: no

value: 2n+, Hyperdiploid (47-57)

value: NINCDS

value: P.L. Kornblith


title: Breast MCF7 141633HUEX1A11

description: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: Breast

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath


title: CNS U251 141640HUEX1A11

description: Glioblastoma-undifferentiated

source_name: Glioblastoma

value: M

value: MT

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981


title: CNS SF-295 141637HUEX1A11

description: Glioblastoma-undifferentiated

value: Rad

value: University of California

value: M.L. Rosenblum

value: Acta Neuropathol 75:92-103, 1988


title: Human breast biopsy V1

value: parous


title: CNS SF-268 141636HUEX1A11

description: Glioblastoma-undifferentiated

value: CNS

value: F

value: no

value: 2n+, Hyperdiploid (47-57)

value: Acta Neuropathol 75:92-103, 1987


title: Human breast biopsy V27


title: CNS SNB-19 141638HUEX1A11

description: Glioblastoma-undifferentiated

value: NINCDS

value: P.L. Kornblith


title: Human breast biopsy V20


title: Human breast biopsy V25


title: Breast HS578T 141632HUEX1A11

description: Carcinosarcoma-mammary gland; breast

source_name: Carcinosarcoma-mammary gland; breast

value: Breast

value: yes

value: Primary

value: Naval Bioscience Laboratory

value: A.J. Hackett


title: Human breast biopsy V19


title: Human breast biopsy V21


title: Human breast biopsy V15


title: Breast MDA-MB-231 141634HUEX1A11

description: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: Pleural effusion

value: MT

value: MD Anderson Hospital and Tumor Institute

value: R. Cailleau


title: Breast BT-549 141631HUEX1A11

description: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: Metastasis

value: W. Coutinho; E.Y. Lasfargues


title: Human breast biopsy V13

value: nulliparous


title: Breast T47D 141635HUEX1A11

description: infiltrating ductal carcinoma

source_name: infiltrating ductal carcinoma

value: F

value: I. Keydar


title: Renal SN12C 141045HUEX1A11

description: Renal cell carcinoma-poor differentiation

source_name: Renal cell carcinoma

value: Renal

value: M

value: 3n, Triploid (69)


title: Renal TK-10 141046HUEX1A11

description: Renal Spindle cell carcinoma

source_name: Renal Spindle cell carcinoma

value: 4n, Tetraploid (92)

value: R.V.Clayman, Washington Univ.School of Medicine


title: Human breast biopsy V11

value: parous


title: Human breast biopsy s86


title: Human breast biopsy s85


title: Renal UO-31 141047HUEX1A11

value: yes

value: WT

value: National Cancer Institute, NIH


title: Human breast biopsy s83


title: Human breast biopsy s87


title: Human breast biopsy s84


title: Renal RXF-393 141044HUEX1A11

description: hypernephroma-poor differentiation

source_name: hypernephroma

value: MT

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992


title: Human breast biopsy s82


title: Human breast biopsy s80


title: Human breast biopsy V18


title: Human breast biopsy V22


title: Human breast biopsy s79


title: Human breast biopsy s81


title: Prostate RC01 141049HUEX1A11

description: Drug resistant variant of DU145(ATCC)

source_name: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: Human breast biopsy s78


title: Renal ACHN 141042HUEX1A11

description: Renal cell carcinoma-poor to moderate differentiation

value: ACHN

value: Renal

value: Rad/VB/CCNU/Mto/Pred

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)


title: Renal A498 141041HUEX1A11

description: Adenocarcinoma

value: F

value: 3n, Triploid (69)


title: Renal 786-0 141040HUEX1A11

description: Adenocarcinoma

value: M

value: yes

value: R.D.Williams, Univ. of Iowa


title: Ovarian NCI-ADR-RES 141036HUEX1A11

description: Adenocarcinoma

value: NCI-ADR-RES

value: Ovarian

value: MT

value: National Cancer Institute, NIH

value: K.Cowan, NCI


title: Renal CAKI-1 141043HUEX1A11

description: Clear cell carcinoma

source_name: Clear cell carcinoma

value: Metastasis

value: WT

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975


title: Prostate PC-3 141039HUEX1A11

description: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: 4n, Tetraploid (92)

value: Pasadena Center for Medical Research

value: M.E. Kaighn


title: Human breast biopsy s75

value: parous


title: Human breast biopsy s72


title: Prostate DU-145(DTP) 141038HUEX1A11

description: prostate; metastatic site: brain; carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma

value: M

value: Androgen independent and unresponsive to hormone therapy

value: yes

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: CD8+ cDC rep2

city: Parkville

first: Priyanka

last: Sathe

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Labeled RNA was prepared for hybridization to Illumina Sentrix Mouse-6 v2 Beadchips following standard Illumina protocol. The bead arrays were washed and blocked in E1 buffer 10 min in rocking incubator and 10 additional minutes with 2 ml of E1 buffer. They were then stained with streptavidin conjugated to Cy3 fluorescent dye. The fluorescent reagent was washed away with E1BC solution. The arrays were finally air dried.

scan_protocol: Arrays were sanned by an Illumina BeadArray Reader (Illumina California USA). Default setting was used.

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma packages of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normexp background corrected with offset 16, normalized by neqc function.

organism: Mus musculus

source_name: Spleen

label_protocol: 125 ng of RNA was labelled with biotin using the Total Prep RNA amplification kit (Ambion).

extract_protocol: RNA from splenic cells was prepared with an Qiagen RNeasy mini or micro kit . RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.

tag: strain

tag: cell type

value: CD8+ cDC


title: Human breast biopsy s73

value: nulliparous


title: Human breast biopsy s71


title: Ovarian SK-OV-3 141037HUEX1A11

source_name: Adenocarcinoma

value: Ovarian

value: F

value: Thiotepa

value: Ascites

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: CD8- cDC rep2

value: CD8- cDC


title: Ovarian OVCAR-5 141034HUEX1A11

description: Adenocarcinoma-well differentiated

value: 2n+, Hyperdiploid (47-57)

value: MT

value: National Cancer Institute, NIH

value: R. Ozols


title: Ovarian OVCAR-8 141035HUEX1A11

description: Carcinoma-undifferentiated

value: Ctx/Adr/CsPt/CyPh

value: T.C. Hamilton


title: Prostate DU145(ATCC) 141048HUEX1A11

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: yes

value: Metastasis


title: CD8- cDC rep1


title: Macrophages rep2

value: Macrophages


title: Ovarian OVCAR-3 141032HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: Ovarian

value: F

value: CyPh/CsPt/Adr


title: Human breast biopsy s70

value: parous


title: Human breast biopsy s68


title: Macrophages rep1


title: Ovarian OVCAR-4 141033HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: WT


title: CD8+ cDC rep1

value: CD8+ cDC


title: Human breast biopsy s67

value: nulliparous


title: AWR58 (D1-n) vs FL100 (wt-n) (1 of 2)

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

description: Biological replicate 1 of 2

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scanning

scan_protocol: Scanned on a genepix 4000B scanner (Axon)

data_processing:
Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method

organism: Saccharomyces cerevisiae

source_name: total RNA extracted from AWR58 (also known as D1-n) labeled with Cyanine5 (red)

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column

growth_protocol: cells growth at 30°C in YNB medium (yeast nitrogen base 6,7 g/L ; glucose 20 g/L ; Tryptophan 40 µg/mL) to an OD600 = 0.33-0.36

extract_protocol: Hot phenol extract procedure followed by RNeasy Mini Kit purification step (Qiagen)

value: AWR58 (also known as D1-n) MATa trp1delta63

tag: description

value: This strain carries a deletion of the chromosome X where loci from YJL130c to YJL128c are deleted.

source_name: total RNA extracted from FL100 (wt-n) labeled with Cyanine3 (green)

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column

value: FL100 (wt-n) MATa


title: FL100 (wt-n) vs B286 (SD1-n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from FL100 (wt-n) labeled with Cyanine5 (red)

source_name: total RNA extracted from B286 (also konwn as SD1-n) labeled with Cyanine3 (green)

value: B286 (also konwn as SD1-n) MATa trp1delta63

value: This strain carries a segmental duplication where loci from YJL130c to YJL133c-A of the chromosome X are tandemly duplicated.


title: FL100 (wt-n) vs AWR58 (D1-n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from AWR58 (also known as D1-n) labeled with Cyanine3 (green)


title: B286 (SD1-n) vs FL100 (wt-n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from B286 (also konwn as SD1-n) labeled with Cyanine5 (red)


title: Leukemia SR 141025HUEX1A11

description: Lymphoma

source_name: Lymphoma

tag: cell line

value: SR

value: Leukemia

value: M

value: no

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.


title: Human breast biopsy s76

source_name: Human breast biopsy, normal


title: Human breast biopsy s69


title: Melanoma LOXIMVI 141026HUEX1A11

description: Malignant amelanotic melanoma

source_name: Malignant amelanotic melanoma

value: LOXIMVI

tag: tissue of origin

value: Melanoma

value: Norsk Hydro's Institut, Norway


title: Melanoma SK-MEL-5 141028HUEX1A11

description: Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

tag: Sex

value: F

value: Metastasis

value: 4n+, Hypertetraploid (93-103)

value: WT

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi


title: Melanoma UACC-62 141030HUEX1A11

description: Melanotic melanoma

source_name: Melanotic melanoma

value: University of Arizona

value: A. Leibovitz, UACC


title: Melanoma UACC-257 141029HUEX1A11

description: Melanotic melanoma

value: 3n+, Hypertriploid (70-80)


title: Melanoma M14 141022HUEX1A12

description: Melanotic melanoma

value: MT

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine


title: Ovarian IGROV1 141031HUEX1A11

description: Cystoadenocarcinoma-poor differentiation

source_name: Cystoadenocarcinoma

value: Ovarian

tag: prior treatment

value: Rad

value: yes

value: Institute Gustave Roussy, France


title: Melanoma MALME-3M 141023HUEX1A11

description: Malignant melanotic melanoma

value: Melanoma

value: M

tag: epithelial

value: no

value: J. Fogh


title: Melanoma SK-MEL-28 141027HUEX1A11

description: Malignant melanotic melanoma

tag: ploidy

value: 4n-, Hypotetraploid (81-91)


title: Leukemia MOLT-4 141018HUEX1A11

source_name: ALL

value: Leukemia

value: PB

value: 4n, Tetraploid (92)

tag: p53 mutation

value: WT

value: Roswell Park Memorial Institute

value: J. Minowada


title: FL100 (wt-n) vs REV27 (SD2-n) (2 of 2)

description: Biological replicate 2 of 2

value: FL100 (wt-n) MATa

source_name: total RNA extracted from Rev27 (also known as SD2-n) labeled with Cyanine3 (green)

value: Rev27 (also known as SD2-n) MATa trp1delta63

value: This strain carries a segmental duplication where loci from YJL130c to YJL151c of the chromosome X are tandemly duplicated.


title: BR15-2-2n (D3-2n) vs wt-2n (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from BR15-2 (also known as D3-2n) labeled with Cyanine5 (red)

value: BR15-2 (also known as D3-2n) MATa/alpha trp1delta63

value: This strain carries a deletion of the chromosome X where loci from YJL130c to YJL123c are deleted.

source_name: total RNA extracted from 2nU+ (wt-2n) labeled with Cyanine3 (green)

value: 2nU+ (wt-2n) MATa/alpha


title: B284 (A4-n) vs FL100 (wt-n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from B284 (also known as A4-n) labeled with Cyanine5 (red)

value: B284 (also known as A4-n) MATa trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chromosome XII ranging from the left telomere to YLR249w including notably the chromosome XII centromere.


title: B038-n (A2-n) vs FL100 (wt-n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from B038 (also known as A2-n) labeled with Cyanine5 (red)

value: B038 (also known as A2-n) MATa trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chromosome XIV ranging from the right telomere to YNL064c including notably the chromosome XIV centromere.


title: Human breast biopsy s60

value: nulliparous


title: Human breast biopsy s59

value: parous


title: FL100 (wt-n) vs B038-n (A2-n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from B038 (also known as A2-n) labeled with Cyanine3 (green)


title: Human breast biopsy s57


title: Human breast biopsy s63


title: Human breast biopsy s65


title: REV27 (SD2-n) vs FL100 (wt-n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from Rev27 (also known as SD2-n) labeled with Cyanine5 (red)

source_name: total RNA extracted from FL100 (wt-n) labeled with Cyanine3 (green)


title: B259 (A3-n) vs FL100 (wt-n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from B259 (also known as A3-n) labeled with Cyanine5 (red)

value: B259 (also known as A3-n) MATa trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chromosome VII ranging from the right telomere to YGL008c including notably the chromosome VII centromere.


title: Human breast biopsy s64


title: Human breast biopsy s62


title: wt-2n vs AWR58-2n (D1-2n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from 2nU+ (wt-2n) labeled with Cyanine5 (red)

source_name: total RNA extracted from AWR58 (also known as D1-2n) labeled with Cyanine3 (green)

value: AWR58 (also known as D1-2n) MATa/alpha trp1delta63

value: This strain carries a deletion of the chromosome X where loci from YJL130c to YJL128c are deleted.


title: FL100 (wt-n) vs B259 (A3-n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from FL100 (wt-n) labeled with Cyanine5 (red)

source_name: total RNA extracted from B259 (also known as A3-n) labeled with Cyanine3 (green)


title: FL100 (wt-n) vs B284 (A4-n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from B284 (also known as A4-n) labeled with Cyanine3 (green)


title: Leukemia K-562 141017HUEX1A11

description: CML

source_name: CML

value: Leukemia

value: F

value: Bisulfan/PiBr

value: no

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: MT

tag: doubling time

value: University of Tennesse

value: H.T. Holden


title: Leukemia HL-60 141016HUEX1A11

description: Pro myelocytic leukemia

source_name: Pro myelocytic leukemia

value: M

value: PBL

tag: contributing institute

value: National Cancer Institute, NIH

value: R.C. Gallo


title: wt-2n vs B286-2n (SD1-2n) (2 of 2)

description: Biological replicate 2 of 2

value: 2nU+ (wt-2n) MATa/alpha

source_name: total RNA extracted from B286 (also known SD1-2n) labeled with Cyanine3 (green)

value: B286 (also known SD1-2n) MATa/alpha trp1delta63

value: This strain carries a segmental duplication where loci from YJL130c to YJL133c-A of the chromosome X are tandemly duplicated.


title: wt-2n vs BR15-2-2n (D3-2n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from BR15-2 (also known as D3-2n) labeled with Cyanine3 (green)

value: BR15-2 (also known as D3-2n) MATa/alpha trp1delta63

value: This strain carries a deletion of the chromosome X where loci from YJL130c to YJL123c are deleted.


title: wt-2n vs AWR58-2n (D1-2n) (2 of 2)

description: Biological replicate 2 of 2

value: AWR58 (also known as D1-2n) MATa/alpha trp1delta63

value: This strain carries a deletion of the chromosome X where loci from YJL130c to YJL128c are deleted.


title: Human breast biopsy s56

source_name: Human breast biopsy, normal

value: parous


title: wt-2n vs REV46-2n (SD3-2n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from REV46 (also known as SD3-2n) labeled with Cyanine3 (green)

value: REV46 (also known as SD3-2n) MATa/alpha trp1delta63

value: This strain carries a segmental duplication where loci from YJL130c to YJL190c of the chromosome X are tandemly duplicated.


title: Human breast biopsy s61


title: REV46-2n (SD3-2n) vs wt-2n (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from REV46 (also known as SD3-2n) labeled with Cyanine5 (red)

source_name: total RNA extracted from 2nU+ (wt-2n) labeled with Cyanine3 (green)


title: wt-2n vs B259-2n (A3-2n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from B259 (also known as A3-2n) labeled with Cyanine3 (green)

value: B259 (also known as A3-2n) MATa/alpha trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chr XIV ranging from the right telomere to YGL008c including notably the chromosome XIV centromere.


title: wt-2n vs B066-2n (A5-2n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from B066 (also known as A5-2n) labeled with Cyanine3 (green)

value: B066 (also known as A5-2n) MATa/alpha trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chr XIII ranging from the left telomere to YMR186w including notably the chromosome XIII centromere.


title: wt-2n vs B286-2n (SD1-2n) (1 of 2)

description: Biological replicate 1 of 2


title: Non-Small Cell Lung NCI-H23 141011HUEX1A11

description: Adenocarcinoma-undifferentiated

source_name: Adenocarcinoma

value: Non-Small Cell Lung

value: M

value: yes

value: 2n+, Hyperdiploid (47-57)

value: MT

tag: contributing person

value: J.D. Minna; A.F. Gazdar


title: wt-2n vs B259-2n (A3-2n) (1 of 2)

description: Biological replicate 1 of 2

value: 2nU+ (wt-2n) MATa/alpha


title: Non-Small Cell Lung NCI-H226 141010HUEX1A11

source_name: Squamous cell carcinoma

value: None (non smoker)

value: 3n, Triploid (69)

value: National Cancer Institute, NIH


title: Non-Small Cell Lung NCI-H322M 141012HUEX1A11

description: Small cell Bronchioalveolar Carcinoma

source_name: Small cell Bronchioalveolar Carcinoma


title: wt-2n vs B199-2n (A1-2n) (2 of 2)

description: Biological replicate 2 of 2

source_name: total RNA extracted from 2nU+ (wt-2n) labeled with Cyanine5 (red)

source_name: total RNA extracted from B199 (also known as A1-2n) labeled with Cyanine3 (green)

value: B199 (also known as A1-2n) MATa/alpha trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chr XII ranging from the left telomere to YLR109w including notably the chromosome XII centromere.


title: Non-Small Cell Lung NCI-H460 141013HUEX1A11

description: Large Cell Carcinoma-undifferentiated

source_name: Large Cell Carcinoma

value: Pleural effusion

value: WT


title: wt-2n vs B038-2n (A2-2n) (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from B038 (also known as A2-2n) labeled with Cyanine3 (green)

value: B038 (also known as A2-2n) MATa/alpha trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chr XII ranging from the right telomere to YNL064c including notably the chromosome XII centromere.


title: B066-2n (A5-2n) vs wt-2n (1 of 2)

description: Biological replicate 1 of 2

source_name: total RNA extracted from B066 (also known as A5-2n) labeled with Cyanine5 (red)

value: B066 (also known as A5-2n) MATa/alpha trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chr XIII ranging from the left telomere to YMR186w including notably the chromosome XIII centromere.


title: Leukemia CCRF-CEM 141015HUEX1A11

description: ALL

source_name: ALL

value: CCRF-CEM

value: Leukemia

value: F

value: Rad/Mtx/Cyx

value: no

value: Children's Cancer research Foudation

value: G.E. Foley


title: Female_rep10

city: Santa Clara

first: Radha

last: Duttagupta

state: CA

address: 3450 Central Expressway

department: Applied Research

institute: Affymetrix

description: miRNA expression data.

hyb_protocol: The total amount of RNA was hybridized to the arrays for 16 hours at 48C with rotation at 60rpm.

scan_protocol: Samples were scanned using the GCS 3000 7G Scanner and processed using miRNA_1-0_2xgain library files.

data_processing: The data was preprocessed using the Affymetrix miRNA QC tool where Individual feature intensities were flagged by detection calls, background subtracted, transformed through addition of a small constant (value equal to 16), and quantile normalized and median summarized.

source_name: S1 fraction of plasma, female

label_protocol: A total of 500ng of total RNA was labelled using the Genisphere HSR Labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html).

growth_protocol: Blood was drawn in sodium EDTA tubes and processed within 4 hours of draw.

extract_protocol: Total RNA was extracted using Trizol-LS, Phenol:Choloroform and purified through Ambion mirVANA columns.

treatment_protocol: All samples were initially spun at 1700g for 10 minutes to separate the plasma from the Buffy Coat and Red Blood Cells. The plasma was re-centrifuged at 2000g for 10 minutes to obtain the Supernatant 1 (S1)  fraction.

tag: tissue

value: plasma-derived

tag: subfraction

value: supernatant 1

tag: gender

value: female

tag: disease state

value: healthy


title: Female_rep9

description: miRNA expression data.


title: Non-Small Cell Lung HOP-92 141009HUEX1A11

description: Large cell-undifferentiated

source_name: Large cell

value: Non-Small Cell Lung

tag: age

value: M

value: yes

value: MT

value: Johns Hopkins University


title: Human breast biopsy s54

source_name: Human breast biopsy, normal

tag: full time pregancy

value: parous


title: wt-2n vs B199-2n (A1-2n) (1 of 2)

description: Biological replicate 1 of 2

tag: strain

value: 2nU+ (wt-2n) MATa/alpha

value: B199 (also known as A1-2n) MATa/alpha trp1delta63

tag: description

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chr XII ranging from the left telomere to YLR109w including notably the chromosome XII centromere.


title: Human breast biopsy s55


title: wt-2n vs B038-2n (A2-2n) (2 of 2)

description: Biological replicate 2 of 2

value: B038 (also known as A2-2n) MATa/alpha trp1delta63

value: This strain carries an aneuploidy n+1. The chimeric additional chromosome comes from the fusion of a part of chromosome X ranging from YJL130c to the left telomere with a part of the chr XII ranging from the right telomere to YNL064c including notably the chromosome XII centromere.


title: Human breast biopsy s53

value: nulliparous


title: Human breast biopsy s52


title: Female_rep8

description: miRNA expression data.


title: Human breast biopsy s51


title: Non-Small Cell Lung NCI-H522 141014HUEX1A11

tag: cell line

tag: tissue of origin

value: National Cancer Institute, NIH

tag: reference


title: Female_rep7

description: miRNA expression data.

value: plasma-derived


title: Human breast biopsy s50


title: Female_rep6

description: miRNA expression data.

value: supernatant 1


title: Female_rep4

description: miRNA expression data.

value: female


title: Female_rep2

description: miRNA expression data.

value: healthy


title: Human breast biopsy s49


title: Female_rep5

description: miRNA expression data.


title: Female_rep1

description: miRNA expression data.


title: Male_rep7

description: miRNA expression data.

source_name: S1 fraction of plasma, male

value: male


title: Male_rep8

description: miRNA expression data.


title: Male_rep6

description: miRNA expression data.


title: Female_rep3

description: miRNA expression data.


title: Human breast biopsy s48


title: Male_rep5

description: miRNA expression data.


title: Human breast biopsy s47


title: Male_rep4

description: miRNA expression data.


title: Male_rep3

description: miRNA expression data.


title: Human breast biopsy s46


title: Male_rep2

description: miRNA expression data.


title: Human breast biopsy s45


title: Colon HT29 141003HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: Colon

tag: Sex

value: F

tag: prior treatment

tag: epithelial

tag: source

value: Primary

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975


title: Male_rep1

description: miRNA expression data.


title: Human breast biopsy s44


title: Human breast biopsy s43

value: parous


title: Non-Small Cell Lung EKVX 141007HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: EKVX

value: Non-Small Cell Lung

value: M

value: yes

tag: ploidy

tag: p53 mutation

value: MT

tag: doubling time

tag: contributing institute

value: Norsk Hydro's Institut, Norway


title: Blood_red blood cells (RBC)_rep4

description:
R_4
miRNA expression data.

data_processing: The data was preprocessed using the Affymetrix miRNA QC tool where Individual feature intensities were flagged by detection calls, background subtracted, transformed through addition of a small constant (value equal to 16) and median summarized. Non-normalized data was analyzed to preserve the individual distributions for rank correlation analysis.

source_name: red blood cells (RBC)

label_protocol: A total of 500-1000ng of total RNA was labelled using the Genisphere HSR labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html).

extract_protocol: Total RNA was extracted using Trizol-LS, Phenol:Chloroform and purified through Ambion mirVANA columns.

treatment_protocol: All samples were initially spun at 1700g for 10 minutes to separate the plasma from the Buffy Coat and Red Blood Cells. Leukocytes were separately isolated from whole blood fractionated through Ficoll-Hypaque gradients. The plasma was re-centrifuged at 2000g for 10 minutes to obtain the Supernatant 1 (S1) and Pellet 1 (P1) fractions. The S1 fraction was additionally centrifuged at 12000g for 10 minutes to generate the Supernatant 2 (S2) and Pellet 2 (P2) fractions.

tag: tissue

value: blood-derived

tag: subfraction

value: red blood cells (RBC)

tag: population

value: Caucasian


title: Colon SW-620 141005HUEX1A11

description: Carcinoma-undifferentiated

source_name: Carcinoma

tag: age

value: Scott White Clinic

tag: contributing person

value: A. Leibovitz


title: Blood_red blood cells (RBC)_rep2

description:
R_2
miRNA expression data.

tag: disease state

value: healthy


title: Blood_red blood cells (RBC)_rep3

description:
R_3
miRNA expression data.


title: Human breast biopsy s42

tag: full time pregancy


title: Non-Small Cell Lung HOP-62 141008HUEX1A11

description: adenocarcinoma-undifferentiated

source_name: adenocarcinoma

tag: cell line

tag: tissue of origin

value: F

value: 4n+, Hypertetraploid (93-103)

value: Johns Hopkins University


title: Colon KM12 141004HUEX1A11

description: Adenocarcinome-poor differentiation

source_name: Adenocarcinome

value: Colon

value: MD Anderson Hospital and Tumor Institute

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute

tag: reference


title: Colon HCT-116 141001HUEX1A11

description: carcinoma-very poorly differentiated

source_name: carcinoma

tag: Sex

value: 2n-, Hypodiploid (35-45)

value: Baylor College


title: Human breast biopsy s38

value: parous


title: CNS U251 140998HUEX1A11

description: Glioblastoma-undifferentiated

source_name: Glioblastoma

value: CNS

value: M

tag: epithelial

value: no

value: 2n+, Hyperdiploid (47-57)

value: MT

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981


title: Non-Small Cell Lung A549 141006HUEX1A11

source_name: Adenocarcinoma

value: Non-Small Cell Lung

value: yes

value: WT

value: National Cancer Institute, NIH

value: Giard DJ


title: Colon HCT-15 141002HUEX1A11

value: Colon

tag: prior treatment

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)


title: Blood_WBC_rep3

description:
W_3
miRNA expression data.

source_name: white blood cells (WBC)/buffy coat

value: blood-derived

value: white blood cells (WBC)/buffy coat

value: healthy

value: Caucasian


title: Blood_leukocytes_rep4

description:
L_4
miRNA expression data.

source_name: leukocyte

value: leukocytes


title: Blood_red blood cells (RBC)_rep1

description:
R_1
miRNA expression data.

value: red blood cells (RBC)


title: Blood_leukocytes_rep3

description:
L_3
miRNA expression data.


title: Blood_leukocytes_rep2

description:
L_2
miRNA expression data.


title: Human breast biopsy s36

value: nulliparous


title: Blood_WBC_rep2

description:
W_2
miRNA expression data.


title: Human breast biopsy s35

value: parous


title: Colon HCC-2998 141000HUEX1A11

description: carcinoma

tag: ploidy

value: MT

value: MD Anderson Hospital and Tumor Institute


title: Blood_leukocytes_rep5

description:
L_5
miRNA expression data.


title: Colon COLO205 140999HUEX1A11

description: Adenocarcinoma

value: M

value: yes

tag: source

value: Ascites

value: 3n, Triploid (69)

tag: p53 mutation

value: Denver Medical Hospital

value: G.E. Moore


title: Human breast biopsy s37


title: CNS SNB-19 140996HUEX1A11

description: Glioblastoma-undifferentiated

value: CNS

value: no

tag: doubling time

tag: contributing institute

value: NINCDS

value: P.L. Kornblith


title: CNS SF-268 140993HUEX1A11

description: Glioblastoma-undifferentiated

value: F

value: Rad

value: 2n+, Hyperdiploid (47-57)

value: Acta Neuropathol 75:92-103, 1987


title: CNS SF-295 140994HUEX1A11

description: Glioblastoma-undifferentiated

value: University of California

value: M.L. Rosenblum

value: Acta Neuropathol 75:92-103, 1988


title: Blood_leukocytes_rep1

description:
L_1
miRNA expression data.

tag: tissue

value: blood-derived

tag: subfraction

value: leukocytes

value: healthy

value: Caucasian


title: Human breast biopsy s33

value: nulliparous


title: Plasma_Supernatant2_rep2

description:
S2_2
miRNA expression data.

source_name: Supernatant 2

value: plasma-derived

value: supernatant 2

tag: population


title: Plasma_Supernatant2_rep3

description:
S2_3
miRNA expression data.


title: Human breast biopsy s32

value: parous


title: Plasma_Supernatant1_rep8

description:
S1_8
miRNA expression data.

source_name: Supernatant 1

value: supernatant 1


title: Plasma_Supernatant1_rep9

description:
S1_9
miRNA expression data.


title: Plasma_Supernatant2_rep1

description:
S2_1
miRNA expression data.


title: Human breast biopsy s31


title: Breast MDA-MB-231 140991HUEX1A11

source_name: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: Breast

tag: age

value: yes

value: Pleural effusion

value: MT

value: MD Anderson Hospital and Tumor Institute

tag: contributing person

value: R. Cailleau


title: Blood_WBC_rep1

description:
W_1
miRNA expression data.

value: white blood cells (WBC)/buffy coat

tag: disease state


title: Plasma_Supernatant1_rep7

description:
S1_7
miRNA expression data.


title: Plasma_Supernatant1_rep6

description:
S1_6
miRNA expression data.


title: Human breast biopsy s26

tag: full time pregancy


title: Breast T47D 140992HUEX1A11

description: infiltrating ductal carcinoma

source_name: infiltrating ductal carcinoma

tag: cell line

tag: tissue of origin

value: F

value: 2n+, Hyperdiploid (47-57)

value: I. Keydar


title: Plasma_Supernatant1_rep4

description:
S1_4
miRNA expression data.

value: healthy


title: Plasma_Supernatant1_rep5

description:
S1_5
miRNA expression data.

value: Caucasian


title: Plasma_Supernatant1_rep3

description:
S1_3
miRNA expression data.


title: CNS SNB-75 140997HUEX1A11

description: Astrocytoma

source_name: Astrocytoma

value: CNS

tag: Sex

value: no

value: NINCDS

value: P.L. Kornblith


title: Plasma_Supernatant1_rep2

description:
S1_2
miRNA expression data.

value: plasma-derived

value: supernatant 1


title: Human breast biopsy s20

value: parous


title: Human breast biopsy s22


title: Breast BT-549 140988HUEX1A11

source_name: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: Breast

tag: epithelial

value: yes

value: Metastasis

value: W. Coutinho; E.Y. Lasfargues


title: Plasma_Supernatant1_rep1

description:
S1_1
miRNA expression data.


title: Breast HS578T 140989HUEX1A11

description: Carcinosarcoma-mammary gland; breast

source_name: Carcinosarcoma-mammary gland; breast

value: Primary

value: MT

value: Naval Bioscience Laboratory

value: A.J. Hackett

tag: reference


title: Breast MCF7 140990HUEX1A11

source_name: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: F

value: Pleural effusion

tag: ploidy

value: 3n-, Hypotriploid (58-68)

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath


title: Plasma_Pellet2_rep1

description:
P2_1
miRNA expression data.

source_name: Pellet 2

value: plasma-derived

value: pellet 2

value: healthy

value: Caucasian


title: Plasma_Pellet2_rep3

description:
P2_3
miRNA expression data.


title: Human breast biopsy s1

source_name: Human breast biopsy, normal

value: nulliparous


title: Plasma_Pellet2_rep2

description:
P2_2
miRNA expression data.


title: Plasma_Pellet1_rep8

description:
P1_8
miRNA expression data.

source_name: Pellet 1

value: pellet 1


title: Human breast biopsy s18


title: Plasma_Pellet1_rep7

description:
P1_7
miRNA expression data.


title: Plasma_Pellet1_rep9

description:
P1_9
miRNA expression data.


title: Plasma_Supernatant1_rep10

description:
S1_10
miRNA expression data.

value: supernatant 1


title: Human breast biopsy s10

value: parous


title: Plasma_Pellet1_rep10

description:
P1_10
miRNA expression data.


title: Plasma_Pellet1_rep3

description:
P1_3
miRNA expression data.


title: Plasma_CS_rep5

description:
CS_5
miRNA expression data.

source_name: Cloudy Supernatant

value: cloudy supernatant


title: Plasma_Pellet1_rep1

description:
P1_1
miRNA expression data.


title: Plasma_Pellet1_rep2

description:
P1_2
miRNA expression data.


title: Normal5_old_rep2

city: College Park

first: Kan

last: Cao

address: 2219 Bioscience Research building

department: CBMG

institute: University of Maryland

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cDNAs were hybridized to The Affymetrix GeneChip® Human Exon 1.0 ST Array. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA). Each sample was processed in technical duplicates or triplicates.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Affymetrix Expression Console software and the CEL files were generated.

data_processing:
RMA expression values were derived from Expression Console software, and all downstream exon array analyses were performed using XRAY microarray analysis software, Version 3.9. Full quantile normalization was performed to minimize technical variance within the data. Only ‘Core’ probe-sets (probe-sets corresponding to high quality genomic features like RefSeq or Ensembl transcripts) were considered for analysis. Probes with GC count less than 6 and greater than 17 were filtered from the analysis and the probe scores were transformed by taking natural logarithm of 0 plus the probe score. Background correction for each probe score was carried out by subtracting the median expression score of background probes with similar GC content. The expression score for a probe-set was calculated as the median of all probes within the set, and probe-sets with fewer than three probes were filtered from further analysis. Mixed Model, nested ANOVA, was used to identify genes with statistically significant group specific gene expression or alternative splicing. The FDR method was used to correct for multiple testing and FDR of 1.00E+00 or less was considered significant both for differential alternative splicing and gene expression tests.   A p-value threshold of 0.001 was used to reject the null hypothesis that the average of group expression is not above background. P-value filters were also applied to group expression levels for each gene to reduce false-positives for alternative splicing. Quality Control diagnostics produced for each array before and after normalization proved the good quality of arrays. GO enrichment analysis for the gene lists was carried out using MetaCore (MetaCoreTM, GeneGo, St. Joseph, MI). Categories with an FDR of 0.05 or below were considered statistically significant.

Core exon analysis.

source_name: healthy fibroblast

label_protocol: For RNA labeling, 1 microgram of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip® WT Sense Target Labeling kit.  The total RNA was first subjected to a ribosomal RNA reduction using the Invitrogen RiboMinus Transcriptome Isolation Kit. The remaining RNA was then reverse transcribed in the presence of dT7N6 primers to generate cDNA. An in vitro transcription was then performed and the resulting cRNA was purified. A first strand cDNA was generated form the cRNA in the presence of dUTPs. After RNA hydrolysis, the single stranded cDNA was fragmented and end labeled with Biotin.

growth_protocol: Cells were grown under 5% CO2 in MEM supplied by 15 % FBS.

extract_protocol: RNA was isolated from 1 million cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Total RNAs were prepared according to Affymetrix protocols (Affymetrix, Inc). RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc), respectively.

tag: cell type

value: fibroblast

tag: cell culture passage

value: late

tag: treated with tert

value: no

tag: individual

value: normal 5


title: Normal5_old_rep3


title: Plasma_Pellet1_rep6

description:
P1_6
miRNA expression data.

tag: tissue


title: glioma olig2 cells derived from the cell of origin, bilogical rep3

first: Elena

last: Fomchenko

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description: Polysomal profile of olig2 glioma cells derived from the cell of origin, obtained from an individual adult murine glioblastoma

hyb_protocol: Samples were hybridized to Affymetrix 430 mouse 2.0 chips as described in Doyle et al., 2008; Heiman et al., 2008 and as per manufacturer's instructions

scan_protocol: GeneChips were scanned at the Rockefeller University Genomics Resource Center.

data_processing: Data was analyzed using Genespring GX10 software, as described in the text and in Doyle et al., 2008; Heiman et al., 2008. Briefly, samples were normalized using RMA, baseline set to median of all samples, data filtered to remove probe sets with low intensity, and analyzed using ANOVA (p<0.05) with SNK post-hoc and Benjamini and Hochberg FDR multiple testing correction. Probe quality, Pearson’s correlation, hierarchical clustering, heatmaps, gene profile plots were generated using Genespring GX10 software. Pathway analysis was performed using Ingenuity as per manufacturer’s instructions [RMA_normalized data not provided. ANOVA results available on Series record].

molecule: polyA RNA

source_name: Murine glioma olig2 cells derived from the cell of origin

label_protocol: 15ng per sample were amplified and biotinylated using Affymetrix Two-Cycle Amplification kit as per manufacturer's instructions

growth_protocol: All animal experiments were conducted using protocols approved by the Institutional Animal Care and Use Committees of Memorial Sloan-Kettering Cancer Center. The approved protocols are: 00-11-189(MSKCC, last approved 3/15/2010). RCAS-hPDGFb-HA-SV40-eGFP (RCAS-PSG) containing human PDGFb with partially deleted 5’UTR, RCAS-hPDGFb-HA, RCAS-Cre and RCAS-mRFP-SV40-Ras (RCAS-RSR) vectors were transfected into DF-1 chicken cells (ATCC; Shi et al 2004; Xu et al 2005). DF1 cells transfected with RCAS-PSG were FACS-sorted to select 15% brightest eGFP-expressing cells and cultured in 10% FBS-DMEM media under standard conditions. For tumor induction, transfected DF1 cells were trypsinized, centrifuged and injected into the brain parenchyma of Ntv-a mice that transgenically express RCAS-binding tv-a receptor after the nestin promoter, at post-natal days 0-2. At 3 weeks post-injection, injected Ntv-a mice were weaned and observed daily for the appearance of brain tumor symptoms. Normal adult cortial olig2 samples were collected from uninjected littermates.

extract_protocol: Normal olig2 progenitors were collected from three replicates of pooled cortices of three olig2 RP-eGFP bacTRAP reporter mice. Mouse gliomas induced by injection of a non-fluorescent RCAS-hPDGFb (Shih et al 2004) or by transplantation of muring glioma cells derived from Ntv-a gliomas induced by the non-fluorescent RCAS-hPDGFb were collected from Ntv-a olig2 RP-eGFP bacTRAP reporter mice and immunoprecipitated; each tumor was processed as a separate sample. Briefly, upon the appearance of brain tumor symptoms (e.g. poor grooming, lethargy, macrocephaly, hydrocephaly, hemiparesis, weight loss), mice were anesthetized by an intraperitoneal injection of 1mg/kg Nembutal solution or ketamine (150mg/kg)/xylazine (15mg/kg) cocktail, their tumors excised based on gross glioblastoma characteristics, and placed into  ice-cold cyclohexamide-containing buffer. All samples were homogenized, cells were lysed in NP-40 and DHPC-containing buffer, centrifuged at 20,000g for 15 min, supernatant incubated with anti-eGFP-conjugated protein G beads 30 min at 4C, washed and RNA collected using Trizol reagent as per manufacturer’s instructions (Doyle et al., 2008; Heiman et al., 2008). RNA was purified, concentrated using Qiagen RNeasy kit, its quality confirmed by Agilent Bioanalyzer.

treatment_protocol: Normal adult olig2 progenitors were obtained from adult mice, at the age of 3 months. Mice injected with RCAS-producing cells or with glioma cells were housed as described above. Upon the appearance of brain tumor symptoms (e.g. poor grooming, lethargy, macrocephaly, hydrocephaly, hemiparesis, weight loss), recruited olig2 glioma cells or olig2 tumor cells derived from the cell of origin were collected from individual mice.

value: collected-adult ; injected-day 0-2 after birth

tag: genotype/variation

value: progeny of olig2 RP-eGFP bacTRAP reporters and Ntv-a ink4a/arf-/- pten fl/fl mice, injected with RCAS-hPDGFb-producing chicken cells

value: brain

value: olig2 tumor cells


title: glioma olig2 cells derived from the cell of origin, bilogical rep2


title: glioma olig2 cells derived from the cell of origin, bilogical rep1


title: Plasma_CS_rep3

description:
CS_3
miRNA expression data.

value: plasma-derived

tag: subfraction

tag: population


title: proliferating glioma olig2 cells not derived from the cell of origin, biological rep3

description: Polysomal profile of proliferating olig2 glioma cells not derived from the cell of origin, obtained from an individual adult murine glioblastoma

source_name: Murine glioma olig2 cells not derived from the cell of origin

tag: age

value: progeny of olig2 RP-eGFP bacTRAP reporters and Ntv-a ink4a/arf-/- pten fl/fl mice, transplanted with non-fluorescent tumor cells intracranially

value: recruited olig2 glioma cells


title: proliferating glioma olig2 cells not derived from the cell of origin, biological rep2


title: Plasma_CS_rep4

description:
CS_4
miRNA expression data.

tag: disease state

value: healthy

value: Caucasian


title: Normal5_old_rep1


title: Plasma_Pellet1_rep4

description:
P1_4
miRNA expression data.

value: pellet 1


title: Plasma_Pellet1_rep5

description:
P1_5
miRNA expression data.


title: Plasma_CS_rep2

description:
CS_2
miRNA expression data.


title: Plasma_CS_rep1

description:
CS_1
miRNA expression data.


title: proliferating glioma olig2 cells not derived from the cell of origin, biological rep1


title: Normal3_old_rep3

value: normal 3


title: adult olig2 cortical progenitors, biological rep3

description: Polysomal profile of olig2 adult murine cortical progenitors, derived from cells of 3 pooled adult murine cortexes

source_name: Adult murine cortexes, 3 pooled

value: adult (3 months)

value: progeny of olig2 RP-eGFP bacTRAP reporters and Ntv-a ink4a/arf-/- pten fl/fl mice, uninjected

value: Normal cortial olig2 cells


title: adult olig2 cortical progenitors, biological rep2


title: Normal5_young_rep2

value: fibroblast

value: early

value: yes


title: P5

type: genomic

city: Ansan

first: Kim

last: Seung Jun

state: Kyunggido

address: Sangrokgu, sadong, Hanyang Univ., HBI 628

department: Genome Business

country: South Korea

institute: GenoCheck

description: DNA methylation array human MSCs passage 5

hyb_protocol: The hybridization procedure was performed using the NimbleGen Hybrdization Kit according to the manufacturer’s instructions. For hybridization, Cy3-input and Cy5-IEF were loaded on a Human 2.1M Deluxe Promoter Array (NimbleGen) containing 28,266 CpG islands and 475 miRNA promoters, and then it was hybridized at 42°C for 20 h using the MAUI 12-Bay Hybridization System (BioMicro Systems). The hybridized array was washed with Wash I, II and III and then spin-dried.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for NimbleScan 2.5 (NimbleGen) software package.

molecule: genomic DNA

source_name: MeDIP DNA from passage 5 of MSCs

label_protocol: One μg of the amplified input and IEF DNA was separately labeled by Cy3-dCTP and Cy5-dCTP (GeneChem) using the BioPrime® Array CGH Genomic Labeling System (Invitrogen) according to the manufacturer’s instructions. Twenty-one μl (1 μg) of input (or IEF) and 20 μl of 2.5X random primer solution were mixed and denatured at 95°C for 5 min. For labeling input and IEF DNA, 3 μl of Cy3- (or Cy5-) dCTP, 5 μl of 10X dCTP nucleotide mixture and 1 μl of Klenow fragment (exo-) were added to the denatured mixture. The mixture was incubated at 37°C for 2 h and then stopped with 5 μl of stop buffer. The labeled probes (Cy3-input and Cy5-IEF) were purified using the QIAquick PCR Purification Kit.

extract_protocol: MeDIP assay: The purification of genomic DNA from MSCs at P5 and P15 was performed using the Wizard® Genomic DNA Purification Kit (Promega) as specified by the manufacturer. Before carrying out MeDIP, we sonicated genomic DNA to generate random fragments between 300 and 1,000 bp. Four µg of fragmented DNA was denatured for 10 min at 95°C and immunoprecipitated with 10 µl of monoclonal antibody against 5-methylcytidine (Calbiochem®) in a final volume of 500 µl IP buffer (10 mM sodium phosphate, pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4°C. After adding 40 µl of Dynabeads® M-280 Sheep anti-Mouse IgG (Dynal Biotech) to the mixture, it was incubated for 2 h at 4°C and washed with 700 µl of IP buffer. Then the beads were collected, incubated with proteinase K for 3 h at 50°C, and then the methylated DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Whole genome amplification of input and immunoaffinity-enriched DNA fragments (IEF): Whole genome amplification (WGA) of input and IP DNA from MSCs at P5 and P15 was performed using the GenomePlex WGA kit (Sigma) according to the manufacturer’s instructions. For OmniPlex library preparation, 10 μl of DNA solution (1 ng/μl of input or IEF) and 2 μl of 1X Library Stabilization Solution were mixed, incubated at 95°C for 2 min, and then added to 1 μl of Library Preparation Enzyme. The mixture was performed in a PCR iCycler (Bio-Rad) at 16°C for 20 min, 24°C for 20 min, 37°C for 20 min, and 75°C for 5 min, and then it was held at 4°C. For WGA, the mixture was added to 7.5 μl of 10X Amplification Master Mix, 47.5 μl of Nuclease-free water and 5 μl of WGA DNA polymerase. Then the mixture was denatured at 95°C for 3 min and then 40 cycles of 94°C for 15 sec and 65°C for 5 min. The mixture was finally purified using the QIAquick PCR Purification Kit (QIAGEN).

value: bone marrow

value: mesenchymal stem cells (MSCs)

tag: passage

tag: antibody

value: 5-methylcytidine (Calbiochem)

source_name: Input DNA from passage 5 of MSCs


title: Normal5_young_rep3

value: normal 5


title: Normal5_young_rep1


title: Normal3_old_rep2

value: late

value: no


title: Normal3_young_rep3


title: Normal3_old_rep1


title: P15

description: DNA methylation array human MSCs passage 15

source_name: MeDIP DNA from passage 15 of MSCs

source_name: Input DNA from passage 15 of MSCs


title: lung_BALB_3

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

description:
lung, normal
GC_Gene1.0St_GES09_0261_112009_1.CEL

hyb_protocol: 2.3µg of biotin-labeled and fragmented cDNA were hybridized onto GeneChip® Mouse Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA) for 16 hours at 45°C.   Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix, Santa Clara, CA).

scan_protocol: The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

data_processing: The R affy package was used to extract intensity data using a custom Entrez Gene CDF (version 14, http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.asp).  Differentially expressed genes were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components, from within the R/maanova package.

source_name: right lung

label_protocol: Labeling occurs by terminal deoxynucleotidyltransferase (TdT) where biotin is added by an Affymetrix Labeling Reagent.

extract_protocol: Total RNA was isolated using the TRIzol Plus RNA isolation kit (Invitrogen, Carlsbad, CA), purified using the RNeasy mini columns (Qiagen, Valencia, CA), and checked for quality on the 2100 Bioanalyzer (Agilent, Santa Clara, CA).  Only high-quality RNA (i.e., RNA integrity > 7.5) was used for microarray analysis.  Following reverse transcription with T7 primers (Affymetrix, Santa Clara, CA), double stranded cDNA was synthesized using the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, CA).  In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified to generate cRNA.  In the second cycle of cDNA synthesis, random primers are used to generate single-stranded DNA in the sense orientation.  Incorporation of dUTP in the cDNA synthesis step allows for the fragmentation of the cDNA strand utilizing uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the dUTP and allows for breakage at these residues.

tag: strain

value: BALB/cJ

value: 11 weeks

tag: gender

value: female

value: right lung

tag: spontaneous pulmonary adenoma severity

value: increased

tag: spontaneous pulmonary adenoma frequency

value: decreased


title: adult olig2 cortical progenitors, biological rep1

value: adult (3 months)

value: progeny of olig2 RP-eGFP bacTRAP reporters and Ntv-a ink4a/arf-/- pten fl/fl mice, uninjected

value: brain


title: lung_MRL_3

description:
lung, normal
GC_Gene1.0St_GES09_0275_112009_1.CEL

value: MRL/MpJ


title: lung_BALB_1

description:
lung, normal
GC_Gene1.0St_GES09_0259_112009_1.CEL


title: Normal3_young_rep2

value: fibroblast

value: healthy

value: early

value: yes

value: normal 3


title: lung_BALB_2

description:
lung, normal
GC_Gene1.0St_GES09_0260_112009_1.CEL


title: lung_MRL_2

description:
lung, normal
GC_Gene1.0St_GES09_0258_112009_1.CEL


title: lung_A_3

description:
lung, normal
GC_Gene1.0St_GES09_0255_112009_1.CEL

value: A/J


title: Normal2_old_rep3

value: late

value: no

value: normal 2


title: lung_MRL_1

description:
lung, normal
GC_Gene1.0St_GES09_0256_112009_1.CEL

value: 11 weeks

value: female


title: 112 liaR with RAM  rep. 2

city: Ithaca

first: John

middle: D.

last: Helmann

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

hyb_protocol: Labeled cDNA samples were combined plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 100oC and hybridized overnight at 42oC to DNA microarray slides (oligos from Sigma Genosys #BACLIB96; ultraGAPS coated slides Corning #40016) which had been prehybridized for at least 45 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 1X SSC + 0.2% SDS for 4 min at 42oC, 0.1X SSC + 0.2% SDS for 4 min at room temperature, 0.1X SSC for 4 min at room temperature, 0.1X SSC for 4 min at room temperature, and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.) Raw data files were produced from the scanned images using the GenePix Pro 3.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized  using the GenePix Pro 3.0 software package such that the ratio of medians of all features was equal to 1. Fold changes equal to average of ramoplanin treated/untreated samples  (635) / average of combined reference RNA (532). Ave represents the average of medians for duplicate spots (minus median of background).

organism: Bacillus subtilis

source_name: liaR/+RAM

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus (Invitrogen) as per the manufacturer’s instructions using 10 microgram of total RNA. Total cDNA was labeled for 1h Cy3/5 Dyes to amino-allyl cDNA.

extract_protocol: Cells were grown to mid-log phase (OD600 0.4) and split into 2 flasks. One flask was treated with 5 µg/ml ramoplanin for 10 minutes. Total RNA was isolated using the RNeasy Mini Kit (Qiagen Sciences, Maryland) and treated with TURBO DNA-freeTM (Ambion). RNA concentrations were quantified and cDNA was synthesized from 10 µg total RNA and differentially labeled according to manufacturer’s instructions with Cy3 (combined reference RNA) and Cy5 (sample) (Amersham). Before and after labeling for 1 h at room temperature) cDNA was purified using the Qiagen MinElute PCR Purification Kit (Qiagen, Maryland).

value: CU1065 liaR deletion

value: liaR deletion

source_name: WT+/-RAM, liaR +/-RAM (pooled reference RNA)

value: wild-type, liaR deletion (pooled)


title: Normal2_old_rep2


title: Normal3_young_rep1


title: 114 liaR with RAM  rep. 3


title: 113 liaR untreated rep. 3

source_name: liaR/-RAM


title: lung_A_2

description:
lung, normal
GC_Gene1.0St_GES09_0254_112009_1.CEL

value: right lung

value: increased


title: lung_C3H_3

description:
lung, normal
GC_Gene1.0St_GES09_0252_112009_1.CEL

value: decreased


title: Normal2_old_rep1

value: fibroblast


title: lung_C3H_1

description:
lung, normal
GC_Gene1.0St_GES09_0250_112009_1.CEL


title: lung_C3H_2

description:
lung, normal
GC_Gene1.0St_GES09_0251_112009_1.CEL


title: lung_A_1

description:
lung, normal
GC_Gene1.0St_GES09_0253_112009_1.CEL


title: 111 liaR untreated rep. 2


title: lung_129S1_3

description:
lung, normal
GC_Gene1.0St_GES09_0249_112009_1.CEL


title: lung_129S1_2

description:
lung, normal
GC_Gene1.0St_GES09_0248_112009_1.CEL


title: Normal2-rep2

value: healthy


title: Normal4-rep2

value: normal 4


title: Normal2_young_rep3

value: early


title: Normal4-rep1


title: 110 liaR with RAM  rep. 1


title: lung_129S1_1

description:
lung, normal
GC_Gene1.0St_GES09_0247_112009_1.CEL


title: 109 liaR untreated rep. 1


title: lung_D2_1

description:
lung, normal
GC_Gene1.0St_GES09_0244_112009_1.CEL


title: Normal2-rep1


title: Normal2_young_rep2


title: 108 wild-type with RAM  rep. 3

source_name: WT/+RAM

value: CU1065 wild-type

value: wild-type


title: 107 wild-type untreated rep. 3

source_name: WT/-RAM


title: lung_D2_3

description:
lung, normal
GC_Gene1.0St_GES09_0246_112009_1.CEL


title: Normal2_young_rep1


title: lung_C57L_2

description:
lung, normal
GC_Gene1.0St_GES09_0239_112009_1.CEL


title: Normal1_old_rep3

value: late

value: normal 1


title: lung_D2_2

description:
lung, normal
GC_Gene1.0St_GES09_0245_112009_1.CEL


title: 105 wild-type untreated rep. 2


title: 106 wild-type with RAM  rep. 2


title: lung_C57L_3

description:
lung, normal
GC_Gene1.0St_GES09_0240_112009_1.CEL


title: Normal1_old_rep2

value: no


title: Normal1_old_rep1


title: lung_B6_3

description:
lung, normal
GC_Gene1.0St_GES09_0237_112009_1.CEL

value: 11 weeks


title: lung_C57L_1

description:
lung, normal
GC_Gene1.0St_GES09_0238_112009_1.CEL

value: female


title: lung_KK_3

description:
lung, normal
GC_Gene1.0St_GES09_0234_112009_1.CEL

value: KK/HlJ


title: Normal1_young_rep3


title: lung_KK_2

description:
lung, normal
GC_Gene1.0St_GES09_0233_112009_1.CEL


title: lung_B6_2

description:
lung, normal
GC_Gene1.0St_GES09_0236_112009_1.CEL


title: 103 wild-type untreated rep. 1


title: lung_B6_1

description:
lung, normal
GC_Gene1.0St_GES09_0235_112009_1.CEL


title: 104 wild-type with RAM  rep. 1


title: lung_KK_1

description:
lung, normal
GC_Gene1.0St_GES09_0232_112009_1.CEL


title: Normal3-rep1

value: normal 3


title: HGPS2-rep1

source_name: HGPS fibroblast

value: Hutchinson-Gilford Progeria Syndrome (HGPS)

value: HGPS 2


title: Normal1_young_rep1


title: Normal1_young_rep2


title: HGPS1-rep2

value: HGPS 1


title: Fusarium graminearum grown on xylan 3

status: Public on Jun 16 2011

city: Illkirch

first: Raphael

last: Carapito

address: Bd Sébastien Brandt

institute: Ecole Supérieure de Biotechnologie de Strasbourg

hyb_protocol: Biotin-labeled cRNA was fragmented in 40 mM Tris (pH 8.1), 30 mM  magnesium acetate, 100 mM potassium acetate at 94 °C for 35 min. Prior to hybridization, free binding capacities were blocked with 100 mM 2-[N-morpholino] ethanesulfonic acid (MES), 0.9 M NaCl, 20 mM Na2EDTA, 0.01% (v/v) Tween 20, 1% BSA (Sigma Aldrich, Germany) at room temperature for 15 min. Then 0.5 g/l of fragmented biotin-labelled cRNA was hybridized to each array in the same buffer supplemented with 0.1 mg/ml herring sperm DNA (Promega, USA). Hybridization was carried out at 55 °C for 16 h, followed by a stringent washing step with 0.5 X SSPE (0.5 X 10 mM sodium phosphate buffer (pH 7.4), 150 mM NaCl, 1 mM EDTA) at 45 °C. Fluorescence-staining was performed with 5 g/ml streptavidin-R-phycoerythrin-conjugate (Invitrogen, USA) in 6 X SSPE at 25 °C for 15 min which was followed by a non-stringent wash with 6 X SSPE buffer at 25°C. Signal intensities were amplified by incubating the arrays with 3 g/ml biotinylated anti-streptavidin antibody (Vector Laboratories, USA) in 100 mM MES, 0.9 M NaCl, 0.05% Tween 20, 2 mg/ml BSA, and 0.1 mg/ml Goat IgG (Sigma Aldrich, Germany) at 25 °C for 15 min, followed by a non-stringent washing step, a SAPE incubation and a non-stringent washing step (conditions as described before).

scan_protocol: Detection and feature readout were performed using the CCD-based detection system of the Geniom device.

data_processing: Raw data were directly imported in the GeneSpring GX software (Agilent Technologies, USA), which was used for all post-processing steps. After background correction, the Robust Multi-Chip Average (RMA) algorithm was used to normalize and summarize probe-level intensities. The normalization used in RMA is quantile normalization (Bolstad et al., 2003). Intensities lower than 0.01 were set to 0.01. In order to be able to compare the expression values for each chip, per chip normalizations were performed by dividing each data set by the 50th percentile of all data sets. The intensities were further normalized per gene to the median of all replicates of both conditions tested to ensure that the expression value for one gene across the different conditions is centred on 1. Therefore, a gene that is constantly expressed in the tested conditions gets a normalized expression value of 1. A list of differentially expressed genes was created by applying a parametric Student's t-test with a p-value cut-off of 0.02 and a false discovery rate correction of 2% (Benjamini and Hochberg, 1995). The fold changes for the listed genes were then calculated and only those greater than +1.5 were analyzed.

label: Biotin

organism: Fusarium graminearum

source_name: Fusarium graminearum grown on xylan 3

label_protocol: One microgram of RNA was used for biotin labelled cRNA synthesis with the MessageAmp II-Biotin Enhanced Single Round aRNAAmplification Kit (Ambion, USA) according to manufacturer's instructions.

extract_protocol: Total RNA extraction was performed with the RNaqueous-4PCR kit (Ambion, USA) according to manufacturer's instructions.

tag: species

value: Fusarium graminearum

tag: teleomorph

value: Gibberella zeae


title: Fusarium graminearum grown on plant cell wall 4


title: Fusarium graminearum grown on xylan 1

source_name: Fusarium graminearum grown on xylan 1


title: Fusarium graminearum grown on glucose 3

source_name: Fusarium graminearum grown on glucose 3


title: Fusarium graminearum grown on cellulose 2


title: Fusarium graminearum grown on xylan 2

source_name: Fusarium graminearum grown on xylan 2


title: Fusarium graminearum grown on glucose 4

source_name: Fusarium graminearum grown on glucose 4


title: Fusarium graminearum grown on plant cell wall 3


title: Fusarium graminearum grown on cellulose 3


title: Fusarium graminearum grown on glucose 2

source_name: Fusarium graminearum grown on glucose 2


title: Fusarium graminearum grown on xylan 4

source_name: Fusarium graminearum grown on xylan 4


title: Fusarium graminearum grown on glucose 1

source_name: Fusarium graminearum grown on glucose 1


title: Fusarium graminearum grown on plant cell wall 1


title: Fusarium graminearum grown on cellulose 4


title: HGPS2-rep2

tag: cell type

value: fibroblast


title: Normal3-rep2

source_name: healthy fibroblast

value: healthy

tag: treated with tert


title: HGPS1-rep1

tag: individual


title: Fusarium graminearum grown on cellulose

source_name: Fusarium graminearum grown on cellulose


title: 80-2

city: Shanghai

first: Shuqing

last: Zhao

address: Fenglin 300

country: China

institute: SIPPE,CAS

description:
One-Cycle cDNA Synthesis Kit
Eukaryotic Poly-A RNA Controls Kit
MEGAscript○R T7 Kit（Ambion，Inc.）
GeneChip IVT Labeling Kit

hyb_protocol: As recommended by Affymetrix. Fifteen micrograms of biotin-labeled copy RNA was purified and fragmented into 35- to 300-nucleotide fragments and then hybridized with a Rice genome array (Affymetrix).

scan_protocol: Arrays were scanned using an Agilent GeneArray scanner (Affymetrix G2500A).

data_processing: Microarray data were normalized using the Affymetrix Microarray Suit program (version 5.0). The algorithm absolute call flag was set to indicate the reliability of the data points according to P (present), M (marginal), and A (absent). Significant differences for each gene between the WT and lc1 mutant plants were examined using the Wilcoxon rank test of the Affymetrix Microarray Suit program (P<0.01) and analysis of variance by fitting a mixed model in the MAANOVA package under R 1.8.0 for multiple testing (false discovery rate-corrected P<0.05). Genes with the consensus significant difference in two independent samples were selected and listed. Annotations for the selected probe set identification were rechecked at the Affymetrix website.

label: biotin-labeled

organism: Oryza sativa

source_name: lc1 mutant

label_protocol: Synthesis of biotin-labeled copy RNA as recommended by Affymetrix.

extract_protocol: As recommended by Affymetrix. The lamina joint (1-cm long) of the flag leaves of lc1 and WT plants were collected and frozen in liquid nitrogen, which were then used for RNAs extraction.

tag: tissue

value: collar of flag leaf

tag: genotype

value: lc1 mutant


title: TSA-treated HT1080

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description:
HT1080_TSA
Determining the hypermethylome of HT1080 through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

hyb_protocol: Agilent Gene Expression Hybridization Kit using the manufacturer's protocol.

scan_protocol: Microarrays are scanned with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Loess normalization as implemented in the Limma package from Bioconductor.

source_name: HT1080 fibrosarcoma line

label_protocol: Agilent low RNA input linear amplification kit.

growth_protocol: McCoy's 5A medium with 10% BCS and 1x PBS.

extract_protocol: Trizol extraction based on the manufacturer's instructions, followed by RNeasy cleanup as per the manufacturer's instructions.

tag: cell line

value: fibrosarcoma cells

tag: treatment

value: 1x PBS for 96 hours

source_name: TSA-treated HT1080 fibrosarcoma line

value: 300 nanomolar TSA for 18 hour


title: MP4 vs. H9

description:
MP4vsH9
Identifying differentially expressed genes between MP4 and H9.

source_name: H9 stem cell line

value: stem cells

source_name: MP4 iPS line

value: induced pluripotent stem cells (iPS)


title: AZA-treated HT1080

description:
HT1080_AZA
Determining the hypermethylome of HT1080 through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: AZA-treated HT1080 fibrosarcoma line

value: 5 micromolar 5-AZA for 96 hours


title: AZA-treated MR46

description:
MR46_AZA
Determining the hypermethylome of MR46 through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: MR46 iPS line

source_name: AZA-treated MR46 iPS line


title: IMR90 vs. MR46

description:
IMR90vsMR46
Identifying differentially expressed genes between IMR90 and MR46.

source_name: Cultured IMR90 fibroblasts

value: fibroblasts


title: 80-1


title: H9 vs. MR46

description:
H9vsMR46
Identifying differentially expressed genes between H9 and MR46.


title: wt-2

source_name: wild type

value: wild type


title: AZA-treated H9

description:
H9_AZA
Determining the hypermethylome of H9 through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: AZA-treated H9 stem cell line


title: wt-1

treatment_protocol: wild type


title: MSC vs. osteoblasts

description:
MSCvsO
Identifying differentially expressed genes between osteoblasts and MSC.

source_name: Cultured osteoblasts

value: osteoblasts

source_name: MSC mesenchymal stem cell line

value: mesenchymal stem cells


title: MP2 vs. H9

description:
MP2vsH9
Identifying differentially expressed genes between MP2 and H9.

source_name: MP2 iPS line


title: AZA-treated MR45

description:
MR45_AZA
Determining the hypermethylome of MR45 through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: MR45 iPS line

source_name: AZA-treated MR45 iPS line


title: H9 vs. MR45

description:
H9vsMR45
Identifying differentially expressed genes between H9 and MR45.


title: IMR90 vs. MR45

description:
IMR90vsMR45
Identifying differentially expressed genes between IMR90 and MR45.


title: MP4 vs. IMR90

description:
MP4vsIMR90
Identifying differentially expressed genes between MP4 and IMR90.


title: TSA-treated MR45

description:
MR45_TSA
Determining the hypermethylome of MR45 through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated MR45 iPS line


title: MP2 vs. IMR90

description:
MP2vsIMR90
Identifying differentially expressed genes between MP2 and IMR90.


title: TSA-treated MR46

description:
MR46_TSA
Determining the hypermethylome of MR46 through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated MR46 iPS line


title: TSA-treated H9

description:
H9_TSA
Determining the hypermethylome of H9 through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated H9 stem cell line


title: NFBD1a shRNA rep2

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description:
Replicate 2.
NFBD1_shRNA2_0_Gy_rep2

hyb_protocol: Hybridization was performed at the Yale Microarray Facility. After quality control assessment, 1.5 µg of cRNA was mixed with the hybridization controls and hybridized to the array. The array was hybridized for 16 hours in a hybridization oven with a rocking platform at 58°C. The array chip then was subjected to a series of washes before it was stained with streptavidin-Cy3. After the staining, it went through a final wash and drying.

scan_protocol: The standard Illumina scanning protocol was performed using an iScan system at the Yale Microarray Facility.

data_processing: Data were background corrected, variance stabilizing transformed and quantile normalized using the lumi software package (version 1.14.0) for the R programming environment (version 2.11.0).

source_name: U2OS cells, NFBD1, 0 Gy

label_protocol: Labeling was performed at the Yale Microarray Facility. Single-stranded cDNA was synthesized by reverse transcription using T7 oligo(dT) primers. The single-stranded cDNA was then converted into double-stranded cDNA and purified using the Ambion Illumina TotalPrep RNA Amplification Kit. An in vitro transcription (IVT) reaction was then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double-stranded cDNA. The cRNA from the IVT reaction was purified using the same Amplification Kit.

growth_protocol: U2OS cells (ATCC) were maintained in DMEM supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and L-glutamate.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit using the manufacturer's following the optional DNAse treatment steps.

treatment_protocol: U2OS cells were infected with NFBD1 and/or p53 shRNA-expressing retroviruses.  Two days later, cells were irradiated with a Shepherd Mark I 137Cs irradiator with a dose of 5 Gy or mock irradiated.  Four hours later RNA was isolated.

tag: array #

value: osteosarcoma

tag: shRNA-expressing retrovirus

value: pSIREN NFBD1a

tag: ionizing radiation

value: 0 Gy


title: TSA-treated MP4

description:
MP4_TSA
Determining the hypermethylome of MP4 through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated MP4 iPS line


title: NFBD1a shRNA rep3

description:
Replicate 3.
NFBD1_shRNA2_0_Gy_rep3


title: control shRNA rep2

description:
Replicate 2.
Control_shRNA_0_Gy_rep5

source_name: U2OS cells, neg, 0 Gy

value: pSIREN neg


title: control shRNA rep3

description:
Replicate 3.
Control_shRNA_0_Gy_rep6


title: NFBD1a shRNA rep1

description:
Replicate 1.
NFBD1_shRNA2_0_Gy_rep1


title: AZA-treated MP2

description:
MP2_AZA
Determining the hypermethylome of MP2 through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: AZA-treated MP2 iPS line


title: TSA-treated IMR90

description:
IMR90_TSA
Determining the hypermethylome of IMR90 through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated cultured IMR90 fibroblasts


title: AZA-treated MP4

description:
MP4_AZA
Determining the hypermethylome of MP4 through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: MP4 iPS line

source_name: AZA-treated MP4 iPS line


title: TSA-treated MP2

description:
MP2_TSA
Determining the hypermethylome of MP2 through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated MP2 iPS line


title: p53 shRNA 5 Gy rep3

description:
Replicate 3.
p53_shRNA_5_Gy_rep3

source_name: U2OS cells, p53, 5 Gy

value: pSIREN p53

value: 5 Gy


title: NFBD1/p53 shRNA 0 Gy rep3

description:
Replicate 3.
NFBD1+p53_shRNA_0_Gy_rep3

source_name: U2OS cells, NFBD1/p53, 0 Gy

value: pSIREN NFBD1sh b / pSIREN p53


title: NFBD1shRNA 0 Gy rep3

description:
Replicate 3.
NFBD1_shRNA_0_Gy_rep3

value: pSIREN NFBD1sh b


title: control shRNA rep1

description:
Replicate 1.
Control_shRNA_0_Gy_rep4


title: TSA-treated osteoblasts

description:
O_TSA
Determining the hypermethylome of osteoblasts through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: Cultured osteoblasts

value: 1x PBS for 96 hours

source_name: TSA-treated cultured osteoblasts


title: IMR904F-d12 DNA Methylome, rep2

description: DNA methylation profiling of the pool cells from which iPS cells are derived.

hyb_protocol: Bisulphite-converted (EZ DNA methylation kit) DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

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

data_processing: Background-subtracted beta values (M/(M+U)), corrected for presence through the detection p-value.

label: Cy5, Cy3

source_name: Pool cells of 4 factor iPS protocol at day 12

label_protocol: Standard Illumina protocol.

growth_protocol: As described in PMID 20841480.

extract_protocol: Phenol-chloroform extraction.

value: pool cells

tag: replicate type

value: biological


title: IMR901F-d12 DNA Methylome, rep2

value: technical


title: AZA-treated U2OS

description:
U2OS_AZA
Determining the hypermethylome of U2OS through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: U2OS osteosarcoma line

value: osteosarcoma cells

source_name: AZA-treated U2OS osteosarcoma line

value: 5 micromolar 5-AZA for 96 hours


title: MSC-B-4F-d16 DNA Methylome, rep2

source_name: Pool cells of 4 factor iPS protocol at day 16


title: TSA-treated U2OS

description:
U2OS_TSA
Determining the hypermethylome of U2OS through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated U2OS osteosarcoma line

value: 300 nanomolar TSA for 18 hour


title: AZA-treated IMR90

description:
IMR90_AZA
Determining the hypermethylome of IMR90 through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: Cultured IMR90 fibroblasts

value: fibroblasts

source_name: AZA-treated cultured IMR90 fibroblasts


title: MSC-B-4F-d16 DNA Methylome, rep1


title: NFBD1shRNA 5 Gy rep3

description:
Replicate 3.
NFBD1_shRNA_5_Gy_rep3

source_name: U2OS cells, NFBD1, 5 Gy


title: IMR901F-d12 DNA Methylome, rep1


title: IMR904F-d12 DNA Methylome, rep1


title: AZA-treated osteoblasts

description:
O_AZA
Determining the hypermethylome of osteoblasts through re-expression with the DNA demethylating agent 5-azacytidine.

value: osteoblasts

source_name: AZA-treated cultured osteoblasts


title: control shRNA 0 Gy rep3

description:
Replicate 3.
Control_shRNA_0_Gy_rep3

source_name: U2OS cells, neg, 0 Gy

value: osteosarcoma


title: control shRNA 5 Gy rep3

description:
Replicate 3.
Control_shRNA_5_Gy_rep3

source_name: U2OS cells, neg, 5 Gy


title: NFBD1/p53 shRNA 0 Gy rep2

description:
Replicate 2.
NFBD1+p53_shRNA_0_Gy_rep2


title: AZA-treated MSC

description:
MSC_AZA
Determining the hypermethylome of MSC through re-expression with the DNA demethylating agent 5-azacytidine.

source_name: MSC mesenchymal stem cell line

value: mesenchymal stem cells

source_name: AZA-treated MSC mesenchymal stem cell line


title: IMR904F-d6 DNA Methylome

source_name: Pool cells of 4 factor iPS protocol at day 6


title: TSA-treated MSC

description:
MSC_TSA
Determining the hypermethylome of MSC through lack of re-expression with trichostatin, an HDAC inhibitor that does not affect DNA methylation.

source_name: TSA-treated MSC mesenchymal stem cell line


title: p53 shRNA 5 Gy rep2

description:
Replicate 2.
p53_shRNA_5_Gy_rep2

source_name: U2OS cells, p53, 5 Gy


title: MSC-B-4F-d6 DNA Methylome


title: IMR90+GFP-RV DNA Methylome

description: DNA methylation profiling of IMR90 fibroblasts transfected with GFP.

source_name: Cultured IMR90 fibroblasts transfected with GFP

value: GFP-transfected fibroblasts (control)


title: U2OS vs. MSC

description:
U2OSvsMSC
Identifying differentially expressed genes between U2OS and MSC.


title: p53 shRNA 0 Gy rep2

description:
Replicate 2.
p53_shRNA_0_Gy_rep2

source_name: U2OS cells, p53, 0 Gy

value: 0 Gy


title: Fusarium graminearum grown on plant cell wall 2

value: Fusarium graminearum

value: Gibberella zeae


title: MR31 DNA Methylome

description: DNA methylation profiling of an iPS clone.

source_name: MR31 iPS

value: induced pluripotent stem cells (iPS)


title: NFBD1/p53 shRNA 5 Gy rep2

description:
Replicate 2.
NFBD1+p53_shRNA_5_Gy_rep2

source_name: U2OS cells, NFBD1/p53, 5 Gy

value: pSIREN NFBD1sh b / pSIREN p53

value: 5 Gy


title: SMC No Rx Donor 2 rep3

first: Amir

middle: Hossein

last: Lebastchi

address: 10 Amistad

department: Surgery

scan_protocol: The stained chips were read and analyzed with GeneChip Scanner 3000 (Affymetrix)

data_processing: Standard Protocols for Affymetrix Human Genechip 1.0 ST Array. Expressionintensities were quantified and compared using Partek Genomics Suite v6.4 with Robust Multi-Array Average for normalization and fold change calculations.

source_name: Smooth Muscle Cell No Treatment

growth_protocol: Smooth Muscle Cells were cultured from 4 different donors, deprived of serum in M199 medium for 48hr.

extract_protocol: Total human RNA was extracted from cultured smooth muscle cells using Rneasy Mini kits (Qiagen)

treatment_protocol: After culturing the cells in serum deprived medium for 48 hr the cells either remained untreated for 6 hr or were treated with 1ng/ml TGF-B for 6 hr.

value: male

value: smooth muscle cell from aorta


title: NFBD1shRNA 5 Gy rep2

description:
Replicate 2.
NFBD1_shRNA_5_Gy_rep2

value: pSIREN NFBD1sh b


title: SMC No Rx Donor 4 rep3

hyb_protocol: Standard Protocols for Affymetrix Human Genechip 1.0 ST Array


title: NFBD1shRNA 0 Gy rep2

description:
Replicate 2.
NFBD1sh_RNA_0_Gy_rep2

source_name: U2OS cells, NFBD1, 0 Gy


title: MR32 DNA Methylome

source_name: MR32 iPS


title: Osteoblasts vs. MSC

description:
OvsMSC
Identifying differentially expressed genes between osteoblasts and MSC.

value: 1x PBS for 96 hours

source_name: Cultured osteoblasts


title: 2102EP DNA Methylome

description: DNA methylation profiling of 2102EP nullipotent teratocarcinoma cell line.

source_name: Nullipotent teratocarcinoma line

value: nullipotent teratocarcinoma cancer cells


title: MMW2 DNA Methylome

source_name: MMW2 iPS


title: Tera2+EV DNA Methylome

description: DNA methylation profiling of Tera2 embryonic carcinoma cell line transfected with an empty vector.

source_name: Tera2 embryonal carcinoma cells transfected with an empty vector

value: embryonal carcinoma cancer cells


title: MR46 DNA Methylome

source_name: MR46 iPS


title: SMC No Rx Donor 3 rep2

label_protocol: Standard Protocols for Affymetrix Human Genechip 1.0 ST Array

value: female


title: SMC No Rx Donor 3 rep3


title: SMC No Rx Donor 2 rep2


title: SMC No Rx Donor 1 rep2


title: SMC No Rx Donor 1 rep3


title: MMW1 DNA Methylome

source_name: MMW1 iPS


title: control shRNA 0 Gy rep2

description:
Replicate 2.
Control_shRNA_0_Gy_rep2

source_name: U2OS cells, neg, 0 Gy

value: pSIREN neg


title: MR45 DNA Methylome

source_name: MR45 iPS


title: NFBD1/p53 shRNA 0 Gy rep1

description:
Replicate 1.
NFBD1+p53_shRNA_0_Gy_rep1

source_name: U2OS cells, NFBD1/p53, 0 Gy

value: osteosarcoma


title: p53 shRNA 0 Gy rep1

description:
Replicate 1.
p53_shRNA_0_Gy_rep1

value: pSIREN p53


title: Osteoblast DNA Methylome

description: DNA methylation profiling of differentiated osteoblasts.

value: differentiated osteoblast cells


title: SMC No Rx Donor 1 rep1


title: SMC No Rx Donor 2 rep1


title: NFBD1/p53 shRNA 5 Gy rep1

description:
Replicate 1.
NFBD1+p53_shRNA_5_Gy_rep1


title: IMR90T DNA Methylome

description: DNA methylation profiling of IMR90 fibroblasts transfected with T-antigen.

source_name: Cultured IMR90 fibroblasts transfected with T-antigen


title: SMC No Rx Donor 4 rep2


title: HT1080 DNA Methylome

description: DNA methylation profiling of HT1080 fibrosarcoma cell line.

source_name: HT1080 fibrosarcoma

value: fibrosarcoma cancer cells


title: p53 shRNA 5 Gy rep1

description:
Replicate 1.
p53_shRNA_5_Gy_rep1

source_name: U2OS cells, p53, 5 Gy


title: SMC No Rx Donor 4 rep1


title: SMC No Rx Donor 3 rep1


title: NFBD1shRNA 0 Gy rep1

description:
Replicate 1.
NFBD1_shRNA_0_Gy_rep1

value: 0 Gy


title: H1 DNA Methylome

description: DNA methylation profiling of an embryonic stem cell line.

source_name: Cultured H1 embryonic stem cells

value: embryonic stem cells


title: NFBD1/p53 shRNA 5 Gy rep3

description:
Replicate 3.
NFBD1+p53_shRNA_5_Gy_rep3

source_name: U2OS cells, NFBD1/p53, 5 Gy


title: control shRNA 0 Gy rep1

description:
Replicate 1.
Control_shRNA_0_Gy_rep1


title: NFBD1shRNA 5 Gy rep1

description:
Replicate 1.
NFBD1_shRNA_5_Gy_rep1

source_name: U2OS cells, NFBD1, 5 Gy


title: MB45 DNA Methylome

source_name: MB45 iPS

value: induced pluripotent stem cells (iPS)


title: control shRNA 5 Gy rep2

description:
Replicate 2.
Control_shRNA_5_Gy_rep2

source_name: U2OS cells, neg, 5 Gy


title: control shRNA 5 Gy rep1

description:
Replicate 1.
Control_shRNA_5_Gy_rep1


title: MB41 DNA Methylome

source_name: MB41 iPS


title: MSC-B DNA Methylome

description: DNA methylation profiling of a mesenchymal stem cell line.

source_name: Cultured MSC-B mesenchymal stem cells

value: MSC-B

value: mesenchymal stem cells


title: SMC TGF-B Rx Donor 2 rep3

source_name: Smooth Muscle Cell TGF-B Rx (1 ng/ml)

value: male

value: TGF-B Rx (1 ng/ml)


title: SMC TGF-B Rx Donor 3 rep2

value: smooth muscle cell from aorta


title: U2OS DNA Methylome

description: DNA methylation profiling of U2OS osteosarcoma cell line.

source_name: U2OS osteosarcoma

value: osteosarcoma cancer cells


title: MDA-MB-231 DNA Methylome

description: DNA methylation profiling of MDA-MB-231 breast cancer cell line.

source_name: MDA-MB-231 breast cancer cell line

value: breast cancer cells


title: SMC TGF-B Rx Donor 4 rep2


title: SMC TGF-B Rx Donor 4 rep3


title: MSC-A DNA Methylome

source_name: Cultured MSC-A mesenchymal stem cells

value: MSC-A


title: SMC TGF-B Rx Donor 1 rep2

value: female


title: IMR90 DNA Methylome

description: DNA methylation profiling of IMR90 fibroblasts.

source_name: Cultured IMR90 fibroblasts

value: fibroblasts


title: H9 DNA Methylome

source_name: Cultured H9 embryonic stem cells


title: SMC TGF-B Rx Donor 2 rep2


title: SMC TGF-B Rx Donor 1 rep3


title: SMC TGF-B Rx Donor 3 rep3