title: Hylobiu_ infection_3

city: Helsinki

first: Tommaso

last: Raffaello

address: Latokartanonkaari 7 PO Box 27

department: Forest Sciences

country: Finland

institute: University of Helsinki

hyb_protocol: Hybridization by NimbleGen Company.

scan_protocol: Scanning by NimbleGen Company.

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264.

organism: Pinus sylvestris

source_name: Tree stem, Hylobius infection

label_protocol: Labelling by NimbleGen Company.

growth_protocol: Scots pine seedlings, Pinus sylvestris L. (Pinaceae) (with their sixth growing season in summer 2011) were obtained from a commercial nursery (Taimityllilä Oy, Mäntyharju, Finland). The seedlings were individually planted in 7.5 L plastic pots in a 2:1 (v/v) quartz sand (0.5-1.2 mm diameter, SP Minerals, Partek, Finland) and fertilized Sphagnum peat (Kekkilä PP6, Finland) mix. The seedlings were fertilised with Taimiston kestolannos (N 9%, P 5%, K 5%, Mg 5%, S 4% and micronutrients, Kemira Oy, Finland). The potted plants were grown in a field site at the UEF Research Garden, Kuopio Campus (62o53´N, 27o37´E, and 80 m above sea level) with natural rainfall and supplementary watering (if required).

extract_protocol: Reference:  Chang SJ, Puryear J, Cairney J: A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 1993, 11(2):113-116.  Isolation of RNA from plant tissue    1. Grind plant tissue in liquid nitrogen with mortar and pestle. Transfer the ground sample to a sterile tube. Add 5 ml of Extraction buffer (preheated at 65ºC) and 50 μl DTT (1mol/L). Incubate for 15 min at 65ºC.   2. Add equal volume of chloroform:isoamyl alcohol (24:1). Shake well and centrifuge at 8000rpm for 30 min at 25ºC. Repeat this step.  3. Transfer aqueous phase to a new sterile tube. Add 1/4 volume of 10M LiCl and mix well. Precipitate RNA overnight at 4ºC. Centrifuge at 8000rpm for 40 min.  4. Pour out the supernatant carefully and dry the pellet briefly. Dissolve the pellet in 2 ml SSTE and transfer each 500 μl into a sterile 1.5 ml tube.  5. Add an equal volume of chloroform:isoamyl alcohol. Shake well and centrifuge at 13000rpm for 30 min at 25ºC.  6. Transfer aqueous phase to a new tube. Add 2 volume of cold absolute ethanol. Precipitate at -20ºC for at least 2 hours. Centrifuge at 13000rpm for 30 minutes.   7. Pour out the supernatant carefully. Wash the pellet by adding approximately 100 μl cold 70% ethanol at room temperature. Centrifuge at half speed for 5 min.  8. Pour out the supernatant and dry the pellet in the sterile hood. Re-suspend the pellet in DEPC-treated water.    Extraction buffer: 50 ml  2% CTAB CTAB 1 g  100 mM Tris-HCl 1 M Tris-HCl 5 ml  25 mM EDTA 0.5 M EDTA 2.5 ml  2 M NaCl 4 M NaCl 25 ml  DEPC-treated water  17.5 ml (up to 50 ml)          SSTE: 2 ml  1 M NaCl 4 M NaCl 0.5 ml  0.5% SDS 5% SDS (pre-heated at 65ºC) 0.2 ml  10 mM Tris-HCl 1 M Tris-HCl 20 μl  1 mM EDTA 0.5 M EDTA 4 μl  DEPC-treated water  1.276 ml (up to 2 ml)

treatment_protocol: We randomly selected three Scots pine seedlings for damaged treatment group (H-plants) and the same number of seedlings for control treatment group (C-plants). Six Hylobius abietis beetles were kept in two lowest whorl branches (three beetles per branch were enclosed  inside a 12 cm x 12 cm mesh cloth cage with plastic foam frames) of all H-plants. Hylobius weevils were kept on the plants (enclosed into cage) until September 2, 2011. Same sized empty cages were also attached to the stem of C- plants to create similar environmental conditions.  For micro array analyses stem and lowest whorl branch base samples from H-damaged and C plants were collected and used for total RNA extraction.

value: stem

tag: infection

value: Hylobius


title: M-2D04-DMSO-EGF 4h

status: Public on Apr 01 2015

type: RNA

city: San Francisco

first: Wolfgang

middle: Michael

last: Korn

state: CA

address: 2340 Sutter Street

department: Medicine

country: USA

institute: UCSF

description: gene expression data in MDAMB231 cells treated with EGF and the MEK inhibitor U0126 or controls

hyb_protocol: automated GeneChip® HT System (Affymetrix)

data_processing: probe set based gene expression measurements were generated from quantitated Affymetrix image files (“.CEL” files) with the RMA algorithm from the BioConductor tools suite.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 4h, repeat 2

growth_protocol: Cells were grown to 80% confluence in full serum containing medium. 24 hours prior to treatment, cells were transferred to low serum conditions

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen)

treatment_protocol: Cells were pre-treated the cells with U0126 (10uM) or DMSO (vehicle control) for 30 minutes (time -0.5h).  At time 0h, the cells were stimulated with EGF (10ng/ml).

tag: cell line

tag: cell type

value: Breast cancer

tag: culture

value: 2D culture

tag: treatment

value: DMSO-EGF


title: Child's neonatal blood: 001-095-001-2009-A

type: genomic

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

hyb_protocol: Standard protocol defined by Illumina for HM450K

data_processing: Data normalization was performed using ChAMP in R (>3.0.3). Data was filtered for all possible SNPs from dbSNP database. Differential methylation analysis was done using A-clustering algorithm followed by estimation of methylation difference by Generalized estimation equation (GEE) from Sofer et al, 2012.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Dried blood spots

extract_protocol: DNA was isolated from dried blood spots with Qiagen EZ1 Advanced® using the DNA Investigator® reagents and protocol card. The “Stains on Fabric” preprocessing and Trace® (tip-dance) instrument protocol was used for isolation. The Quantifiler Human DNA Quantification Kit® (Applied Biosystems, Inc.) was used to determine the amount of amplifiable DNA.Approximately 3µg genomic DNA was diluted in 130µl of buffer TE (10mM Tris (pH 8.0), and 1mM EDTA (pH 8.0)) and sheared into ~200-600bp fragment using microcavitation (Covaris, Inc, setting: Duty Cycle = 5%, Intensity = 3, Cycles/burst = 200, Time = 75 seconds run at 6-8°C). 125µl of the sheared DNA samples were mixed with 330µl of buffer TE. The sheared DNA was denatured by boiling it in the Thermomixer at 95°C and 700rpm for ten minutes and left on ice for 10min.

tag: sample blood lead level

tag: mother's blood lead level

tag: gender

value: M

tag: age (months)

tag: mother's age (months)

tag: gestational age (months)

tag: smoking

value: No


title: p53KO_ctrl_C

city: Galway

first: Sharon

last: Glynn

address: Biosciences, NUI Galway

country: Ireland

institute: National University of Ireland Galway

description: Gene expression data from HCT116p53KO

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

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

data_processing: The data was collated and analyzed with BRBarraytools version 4.4 (MAS 5.0),

label: Biotin

source_name: p53KO ctrl

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

growth_protocol: Cells were grown in 10% Serum for 24 hours prior to treatment

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

treatment_protocol: HCT116 cells were treated with 0.5 mg/ml of BFA or 2 mg/ml of Tm for 24 h.

tag: genotype/variation

value: Control


title: Child's neonatal blood: 001-095-003-2011-A

scan_protocol: Standard protocol defined by Illumina for HM450K


title: Child's neonatal blood: 001-045-001-2008-A

label_protocol: Standard protocol defined by Illumina for HM450K


title: M-2D04-EGF 4h

scan_protocol: automated GeneChip® HT System (Affymetrix)

source_name: MDA-MB-231 cells, 2D culture, EGF, 4h, repeat 2

value: EGF


title: Hylobiu_ infection_2

tag: tissue


title: M-2D04-control 4h

source_name: MDA-MB-231 cells, 2D culture, control, 4h, repeat 2

label_protocol: automated GeneChip® HT System (Affymetrix)


title: Hylobiu_ infection_1


title: Wt_BrefA_C

description: Gene expression data from HCT116wt treated with BrefA

source_name: Wt , BrefA, 24hr

value: wildtype

value: BREFELDIN A


title: Child's neonatal blood: 001-113-002-2012-A

value: F


title: Child's neonatal blood: 001-001-001-2012-A


title: Child's neonatal blood: 001-025-001-2007-A


title: Child's neonatal blood: 001-130-001-2007-A


title: Wt_Tm_C

description: Gene expression data from HCT116wt, treated with Tm

source_name: Wt , Tm, 24hr

value: Tunicamycin


title: M-2D04-EGF 1h

source_name: MDA-MB-231 cells, 2D culture, EGF, 1h, repeat 2


title: M-2D04-DMSO-EGF 1h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 1h, repeat 2


title: Child's neonatal blood: 001-130-003-2012-A


title: M-2D04-U0126 1h

source_name: MDA-MB-231 cells, 2D culture, U0126, 1h, repeat 2


title: Wt_BrefA_A


title: p53KO_ctrl_A

description: Gene expression data from HCT116p53KO


title: p53KO_ctrl_B

description: Gene expression data from HCT116p53KO


title: Child's neonatal blood: 001-130-002-2007-A


title: Child's neonatal blood: 001-087-002-2010-A

value: Yes


title: Wt_BrefA_B


title: Control_3

source_name: Tree stem, control

value: control


title: Control_1


title: Child's neonatal blood: 001-051-001-2011-A


title: M-2D04-control 1h

source_name: MDA-MB-231 cells, 2D culture, control, 1h, repeat 2


title: Control_2


title: M-2D04-EGF 8h

source_name: MDA-MB-231 cells, 2D culture, EGF, 8h, repeat 2


title: Wt_Tm_B


title: Child's neonatal blood: 001-118-002-2009-A


title: Wt_Tm_A


title: M-2D04-DMSO-EGF 05h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 05h, repeat 2


title: M-2D04-U0126 05h

source_name: MDA-MB-231 cells, 2D culture, U0126, 05h, repeat 2


title: Child's neonatal blood: 001-079-002-2010-A


title: Wt_ctrl_C

description: Gene expression data from HCT116wt

source_name: Wt ctrl


title: Child's neonatal blood: 001-033-002-2010-A


title: MEFE4F1_H12_RasV12KOE4F1_RepC_Cy3

city: Montpellier

first: Claude

last: Sardet

address: 208 rue des Apothicaires

department: Inserm U1194 - Université de Montpellier - Institut Régional du Cancer de Montpellier (ICM)

country: France

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

description:
Sample 24
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.

hyb_protocol: The two labelled aRNA were mixed, fragmented and hybridized on one array of a NimbleGen 12-plex microarray according to the manufacturer's instructions.

scan_protocol: Scanned on an Innopsys Innoscan900 scanner.

data_processing: Images were quantified using NimbleScan V2.5. The raw data were normalized by Loess (Limma Package). Analyses of the differentially expressed genes have been performed with LIMMA packages (limma*.txt) and SAM packages (sam*.txt) with an FDR of 1% or 5%.

organism: Mus musculus

label_protocol: For the preparation of the Cy3- and Cy5-labelled aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according to the manufacturer's instructions.

growth_protocol: Cells were grown at 37°C in Dulbecco's modified medium supplemented with 10% Fetal Bovine Serum, glutamax, pyruvate and 4.5g/l D-glucose under 5% CO2, 100% saturated H2O incubator.

extract_protocol: Total RNA has been recovered with kits RNeasy® Mini from Qiagen.

treatment_protocol: E4F1 depletion is achieved three days after MEFs infection with a self-excising CRE-recombinase-encoding retrovirus.

tag: strain/background

value: mixed (C57BL/6; 129Sv/J)

value: 13.5-day embryo

value: mouse embryonic fibroblasts


title: Wt_ctrl_B

description: Gene expression data from HCT116wt


title: M-2D04-EGF 05h

source_name: MDA-MB-231 cells, 2D culture, EGF, 05h, repeat 2


title: MEFE4F1_H12_RasV12WTE4F1_RepC_Cy5

description:
Sample 23
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: Wt_ctrl_A

description: Gene expression data from HCT116wt


title: M-2D04-control 05h

source_name: MDA-MB-231 cells, 2D culture, control, 05h, repeat 2


title: Child's neonatal blood: 001-084-001-2011-A

source_name: Dried blood spots


title: 76N Ecd siRNA, biological rep3

city: Omaha

first: Vimla

last: Band

state: NE

address: Room 6011, DRC, 985805 Nebraska Medical Center

department: Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Ecd siRNA treated 76N hMECs

label_protocol: standard Affymetrix protocol

growth_protocol: 76N cells cultured in DFCI-1 media at 37C and 5%CO2

treatment_protocol: siRNA transfection

value: Normal mammary epithelial cells


title: Child's neonatal blood: 001-033-001-2012-A


title: M-2D04-DMSO 0h

source_name: MDA-MB-231 cells, 2D culture, DMSO, 0h, repeat 2

value: Breast cancer

value: DMSO


title: Child's neonatal blood: 001-082-001-2009-A


title: 76N control siRNA, biological rep3

source_name: Control siRNA treated 76N hMECs


title: M-2D04-U0126 0h

source_name: MDA-MB-231 cells, 2D culture, U0126, 0h, repeat 2

value: 2D culture


title: MEFE4F1_H11_RasV12KOE4F1_RepC_Cy5

description:
Sample 22
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: M-2D04-control 0h-1

source_name: MDA-MB-231 cells, 2D culture, control, 0h, repeat 4


title: 76N Ecd siRNA, biological rep2


title: MEFE4F1_H11_RasV12WTE4F1_RepC_Cy3

description:
Sample 21
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: MEFE4F1_H10_RasV12KOE4F1_RepB_Cy3

description:
Sample 20
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: Child's current blood: 001-010-002-2009-B


title: Child's current blood: 001-079-002-2010-B


title: 76N Ecd siRNA, biological rep1


title: 76N control siRNA, biological rep2


title: M-2D03-U0126 48h

source_name: MDA-MB-231 cells, 2D culture, U0126, 48h, repeat 1


title: M-2D03-DMSO-EGF 48h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 48h, repeat 1

value: DMSO-EGF


title: MEFE4F1_H09_RasV12KOE4F1_RepB_Cy5

description:
Sample 18
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: M-2D03-EGF 48h

source_name: MDA-MB-231 cells, 2D culture, EGF, 48h, repeat 1


title: Child's current blood: 001-019-003-2007-B

value: M


title: M-2D04-control 0h

source_name: MDA-MB-231 cells, 2D culture, control, 0h, repeat 2


title: MEFE4F1_H09_RasV12WTE4F1_RepB_Cy3

description:
Sample 17
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: M-2D03-U0126 24h

source_name: MDA-MB-231 cells, 2D culture, U0126, 24h, repeat 1


title: lip tissue, biological rep1

city: Fuzhou

first: Zhen

last: Huang

address: Fujian Key Laboratory of Developmental and Neuro Biology, College of Life Science, Fujian Normal University, Fuzhou, Fujian, P.R. China.

country: China

institute: Fujian Normal University

description: Gene expression data from the lip tissue of human embryos at week 11 of gestation

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: The lip tissue of human embryos at week 11 of gestation

extract_protocol: RNA purification was performed according to the protocol of QIAGEN RNAeasy Mini Kit  provided by the manufacturer (QIAGEN).

value: lip tissue

tag: embryo age

value: week 11 of gestation


title: 76N control siRNA, biological rep1


title: lip tissue, biological rep3


title: Child's current blood: 001-033-002-2010-B

value: No


title: M-2D03-control 48h

source_name: MDA-MB-231 cells, 2D culture, control, 48h, repeat 1


title: MEFE4F1_H08_RasV12KOE4F1_RepA_Cy3

description:
Sample 16
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: Child's current blood: 001-118-002-2009-B


title: MEFE4F1_H07_RasV12KOE4F1_RepA_Cy5

description:
Sample 14
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: canine germ, biological rep3

description: Gene expression data from the canine germ of human embryos at week 11 of gestation

source_name: The canine germ of human embryos at week 11 of gestation

value: canine germ


title: MEFE4F1_H08_RasV12WTE4F1_RepA_Cy5

description:
Sample 15
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: lip tissue, biological rep2


title: Child's current blood: 001-130-002-2007-B

value: F


title: Child's current blood: 001-095-003-2011-B


title: MEFE4F1_H07_RasV12WTE4F1_RepA_Cy3

description:
Sample 13
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: M-2D03-DMSO-EGF 24h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 24h, repeat 1


title: M-2D03-EGF 24h

source_name: MDA-MB-231 cells, 2D culture, EGF, 24h, repeat 1

value: EGF


title: Child's current blood: 001-015-002-2010-B


title: Child's current blood: 001-036-003-2008-B

value: Yes


title: Child's current blood: 001-019-001-2006-B


title: incisor germ, biological rep3

description: Gene expression data from the incisor germ of human embryos at week 11 of gestation

source_name: The incisor germ of human embryos at week 11 of gestation

value: incisor germ


title: MEFE4F1_H06_KOE4F1_RepC_Cy3

description:
Sample 12
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.

value: mixed (C57BL/6; 129Sv/J)


title: M-2D03-DMSO-EGF 12h

description: gene expression data in MDAMB231 cells treated with EGF and the MEK inhibitor U0126 or controls

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 12h, repeat 1


title: M-2D03-U0126 12h

source_name: MDA-MB-231 cells, 2D culture, U0126, 12h, repeat 1


title: canine germ, biological rep2


title: MEFE4F1_H05_KOE4F1_RepC_Cy5

description:
Sample 10
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.

value: 13.5-day embryo


title: Child's current blood: 001-015-004-2008-B

source_name: Dried blood spots


title: canine germ, biological rep1


title: MEFE4F1_H06_WTE4F1_RepC_Cy5

description:
Sample 11
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.

value: mouse embryonic fibroblasts


title: MEFE4F1_H10_RasV12WTE4F1_RepB_Cy5

description:
Sample 19
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: incisor germ, biological rep2


title: MEFE4F1_H04_KOE4F1_RepB_Cy3

description:
Sample 8
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: M-2D03-control 24h

source_name: MDA-MB-231 cells, 2D culture, control, 24h, repeat 1


title: incisor germ, biological rep1


title: M-2D03-EGF 12h

source_name: MDA-MB-231 cells, 2D culture, EGF, 12h, repeat 1


title: molar germ, biological rep3

description: Gene expression data from the molar germ of human embryos at week 11 of gestation

source_name: The molar germ of human embryos at week 11 of gestation

value: molar germ


title: MEFE4F1_H04_WTE4F1_RepB_Cy5

description:
Sample 7
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: MEFE4F1_H03_KOE4F1_RepB_Cy5

description:
Sample 6
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: Child's current blood: 001-099-001-2011-B


title: M-2D03-U0126 8h

source_name: MDA-MB-231 cells, 2D culture, U0126, 8h, repeat 1

value: Breast cancer


title: Child's current blood: 001-095-001-2009-B


title: molar germ, biological rep2


title: M-2D03-DMSO-EGF 8h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 8h, repeat 1


title: M-2D03-EGF 8h

source_name: MDA-MB-231 cells, 2D culture, EGF, 8h, repeat 1


title: M-2D03-U0126 4h

source_name: MDA-MB-231 cells, 2D culture, U0126, 4h, repeat 1


title: Child's current blood: 001-099-003-2007-B


title: MEFE4F1_H05_WTE4F1_RepC_Cy3

description:
Sample 9
Replicate C
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: MEFE4F1_H03_WTE4F1_RepB_Cy3

description:
Sample 5
Replicate B
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: M-2D03-control 8h

source_name: MDA-MB-231 cells, 2D culture, control, 8h, repeat 1


title: molar germ, biological rep1


title: MEFE4F1_H02_KOE4F1_RepA_Cy3

description:
Sample 4
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: Child's current blood: 001-045-001-2008-B


title: Child's current blood: 001-121-002-2007-B


title: Child's current blood: 001-130-001-2007-B


title: Child's current blood: 001-036-002-2011-B


title: MEFE4F1_H02_WTE4F1_RepA_Cy5

description:
Sample 3
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: MEFE4F1_H01_WTE4F1_RepA_Cy3

description:
Sample 1
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: Child's current blood: 001-025-001-2007-B


title: Child's current blood: 001-036-005-2009-B


title: MEFE4F1_H01_KOE4F1_RepA_Cy5

description:
Sample 2
Replicate A
J3 post infection with a self-excising CRE-recombinase-encoding retrovirus.


title: Child's current blood: 001-033-001-2012-B


title: LS174dnTCF4, doxycycline, rep 2

city: Amsterdam

first: Jarom

last: Heijmans

address: Meibergdreef 69-71

department: Tytgat Institute for liver and intestinal research

country: Netherlands

institute: Academic Medical Center

description: Replicate 2 of 3.

hyb_protocol: According to Illumina instructions.

scan_protocol: According to Illumina instructions on the BeadArray 500GX scanner.

data_processing: Data was extracted in GenomeStudio. No normalization was performed.

source_name: colon cancer cell line LS174dnTCF4, doxycycline

label_protocol: Ambion cRNA synthesis for Illumina.

growth_protocol: DMEM 10% FCS penicillin/streptomycin.

extract_protocol: Trizol, subsequently Qiagen Rneasy cleanup.

treatment_protocol: 1 microgram ml-1 doxycycline for 20 hours.

tag: phenotype

value: doxycycline-inducible expression of dominant-negative TCF4

value: colon cancer cells

value: doxycycline (Dox)


title: LS174dnTCF4, doxycycline, rep 3

description: Replicate 3 of 3.


title: Child's current blood: 001-015-006-2009-B


title: LS174dnTCF4, vehicle, rep 3

description: Replicate 3 of 3.

source_name: colon cancer cell line LS174dnTCF4, control

value: vehicle


title: Child's current blood: 001-084-001-2011-B

value: M


title: Child's current blood: 001-036-001-2007-B


title: M-2D03-DMSO-EGF 4h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 4h, repeat 1

value: 2D culture

value: DMSO-EGF


title: LS174dnTCF4, doxycycline, rep 1

description: Replicate 1 of 3.


title: hypoxia serum minus

city: Yokohama

first: Shiro

last: Koizume

state: Please Select

address: 2-3-2 Nakao Asahi-ku

country: Japan

institute: Kanagawa Cancer Center Research Institute

description: OVSAYO cells were cultured under 1%O2 without FCS for 16h.

hyb_protocol: Hybridization to 2006-08-03_HG18_60mer_expr array (Euk expr 385K catalog Arr Del (NimbleGen, Roche, Madison, WI, USA)) was performed using NimbleGen Hybridization kit (Roche, Madison, WI, USA) according to recommended standard operating protocol provided with gene expression microarray.

scan_protocol: Scanning was performed by NimbleScan v2.6 software using GenePix Personal 4100A instrument (Axon Instruments, Sunyvale, CA, USA).

data_processing: Scanned TIFF images were processed by NimbleScan v2.6 software (Roche NimbleGen, Inc.) to obtain raw data (pair) files. Data were further processed by same software to obtain normalized data (norm_RMA.pair and RMA.Calls files). These data were analyzed by contract research service at Subio Inc. (Kagoshima, Japan, www.subio.jp/) using Subio platform v 1.14 software.

source_name: hypoxia serum minus

label_protocol: Labeling (Cy3) was performed using NimbleGen one-colour DNA labeling kit (Roche, Indianapolis, IN, USA) according to recommended standard operating protocol provided with gene expression microarray.

growth_protocol: An ovarian cancer cell line, OVSAYO was cultured under four culture conditions (normoxia and fetal calf serum (FCS) plus, normoxia and FCS minus, hypoxia and FCS plus, and hypoxia and FCS minus conditions) in RPMI1640 medium for 16 hours.

extract_protocol: Total RNA was isolated using SV total RNA isolation kit (Promega, Madison, WI, USA) according to recommended standard protocol.

value: OVSAYO

value: human ovarian cancer cells

tag: culture condition

value: hypoxia serum minus

tag: culture duration

value: 16 hours


title: M-2D03-control 4h

source_name: MDA-MB-231 cells, 2D culture, control, 4h, repeat 1

tag: cell line

tag: cell type


title: hypoxia serum plus

description: OVSAYO cells were cultured under 1%O2 with 10%FCS for 16h.

source_name: hypoxia serum plus

value: hypoxia serum plus


title: M-2D03-DMSO-EGF 1h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 1h, repeat 1

tag: culture

tag: treatment


title: M-2D03-U0126 1h

source_name: MDA-MB-231 cells, 2D culture, U0126, 1h, repeat 1


title: LS174dnTCF4, vehicle, rep 2

description: Replicate 2 of 3.


title: normoxia serum minus

description: OVSAYO cells were cultured under normoxia without FCS for 16h.

source_name: normoxia serum minus

value: normoxia serum minus


title: normoia serum plus

description: OVSAYO cells were cultured under normoxia with 10%FCS for 16h.

source_name: normoia serum plus

value: normoia serum plus


title: fur_mutant_rep6 vs. 33277_rep6

city: Carlton

first: Catherine

last: Butler

state: VIC

address: 720 Swanston St

department: The Melbourne Dental School

country: Australia

institute: The University of Melbourne

hyb_protocol: Slides were hybridised using either heme-excess or heme-limited samples labelled with Cy3, combined with a universal genomic reference labelled with Cy5. Prior to hybridisation, microarray slides were immersed for 1 h in blocking solution (35% formamide, 1% BSA, 0.1% SDS, 5X SSPE [1X SSPE is 150 mM NaCl, 10 mM NaH2PO4, 1 mM EDTA]) at 42ºC. After blocking, slides were briefly washed in H2O followed by 99% ethanol and then dried by centrifugation. Labelled cDNAs were resuspended in 55 µL of hybridization buffer (35% formamide, 5X SSPE, 0.1% SDS, 0.1 mg/mL Salmon Sperm DNA) and denatured at 95ºC for 5 min, and then applied to slides and covered with LifterSlips (Erie Scientific). Hybridisation was performed at 42ºC for 16 h. Following hybridisation, slides were successively washed in 0.1% SDS plus 2X SSC [1X SSC is 150 mM NaCl 15 mM sodium citrate] (5 min at 42 ºC, all further washes performed at room temperature), 0.1% SDS plus 0.1X SSC (10 min), 0.1X SSC (4 washes, 1 min each), and then quickly immersed in 0.01X SSC, then 99% ethanol and using centrifugation to dry the slides.

scan_protocol: GenePix 4000B microarray scanner (Molecular Devices) at 532 nm (Cy3) and 635 nm (Cy5) with a 10 µm resolution and laser power at 10 %. PMT setting adjusted to obtain a 1:1 ratio of Cy3:Cy5. Pictures of both channels saved as 16-bit tiff files.

data_processing: Image analysis was performed using the GenePix Pro 6.0 software (Molecular Devices), and “morph” background values were used as the background estimates in further analysis. The LIMMA software package (Smyth, 2005) was used to normalize the within-array data by subtracting the morph background and using the loess method to fit a global loess curve. Between-array normalization was also carried out for all arrays in the series using the VSN method.

organism: Porphyromonas gingivalis ATCC 33277

source_name: 33277 wild-type

label_protocol: cDNA was synthesized from 5 µg total RNA using the SuperScript Plus Indirect cDNA labelling system (Invitrogen) primed with 5 µg random hexamers. cDNA was labelled using the Cy5 post-labelling reactive dye pack (GE) and purified using the purification module of the Invitrogen labelling system.

growth_protocol: Porphyromonas gingivalis 33277 wild-type grown in continuous culture under conditions of heme-excess (BHI with 5 µg/mL hemin and 5 µg/mL Vitamin K).

extract_protocol: Samples were stabilized with 0.2 volumes of 5% phenol in absolute ethanol, then pelleted by centrifugation and frozen in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's instructions but enhanced with mechanical lysis (Precellys 24 homogenizer - Bertin Technologies, Lysing Matrix B Glass Beads - MP Biomedicals). RNA was further purified using the Illustra RNAspin Mini RNA Isolation kit (GE) according to the manufacturer's instructions including on-column DNase treatment.

value: wild-type

tag: chemostat

value: B

tag: biological replicate

source_name: Fur mutant

label_protocol: cDNA was synthesized from 5 µg total RNA using the SuperScript Plus Indirect cDNA labelling system (Invitrogen) primed with 5 µg random hexamers. cDNA was labelled using the Cy3 post-labelling reactive dye pack (GE) and purified using the purification module of the Invitrogen labelling system.

growth_protocol: Porphyromonas gingivalis Fur mutant of 33277 grown in continuous culture under conditions of heme-excess (BHI with 5 µg/mL hemin and 5 µg/mL Vitamin K).

value: Fur mutant


title: fur_mutant_rep4 vs. 33277_rep4


title: LS174dnTCF4, vehicle, rep 1

description: Replicate 1 of 3.

value: doxycycline-inducible expression of dominant-negative TCF4


title: fur_mutant_rep5 vs. 33277_rep5


title: Child's current blood: 001-010-001-2012-B

source_name: Dried blood spots

tag: sample blood lead level

tag: mother's blood lead level

tag: gender

tag: age (months)

value: No


title: M-2D03-control 1h

description: gene expression data in MDAMB231 cells treated with EGF and the MEK inhibitor U0126 or controls

source_name: MDA-MB-231 cells, 2D culture, control, 1h, repeat 1

value: Breast cancer


title: Child's current blood: 001-113-002-2012-B

value: F

tag: mother's age (months)

tag: gestational age (months)

tag: smoking


title: M-2D03-EGF 1h

source_name: MDA-MB-231 cells, 2D culture, EGF, 1h, repeat 1

value: EGF


title: M-2D03-EGF 4h

source_name: MDA-MB-231 cells, 2D culture, EGF, 4h, repeat 1

value: 2D culture


title: M-2D03-U0126 05h

source_name: MDA-MB-231 cells, 2D culture, U0126, 05h, repeat 1


title: Child's current blood: 001-130-003-2012-B

value: M


title: Child's current blood: 001-060-002-2010-B

value: Yes


title: Child's current blood: 001-087-002-2010-B


title: fur_mutant_rep1 vs. 33277_rep1

tag: strain/background

tag: genotype/variation

value: A

growth_protocol: Porphyromonas gingivalis 33277 grown in continuous culture under conditions of heme-excess (BHI with 5 µg/mL hemin and 5 µg/mL Vitamin K).


title: M-2D03-DMSO-EGF 05h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 05h, repeat 1

value: DMSO-EGF


title: Child's current blood: 001-122-002-2011-B


title: Child's current blood: 001-051-001-2011-B


title: M-2D03-EGF 05h

source_name: MDA-MB-231 cells, 2D culture, EGF, 05h, repeat 1


title: fur_mutant_rep2 vs. 33277_rep2


title: M-2D03-U0126 0h

source_name: MDA-MB-231 cells, 2D culture, U0126, 0h, repeat 1


title: Merit40-/- HSCs, biological replicate 2

city: Philadelphia

first: Wei

last: Tong

state: PA

address: 316A Abramson Bldg., 3615 Civic Center Blvd.

department: Pediatrics

institute: Children's Hospital of Philadelphia, and University of Pennsylvania School of Medicine

description: Gene expression data from Merit40-/- BM HSCs, biological replicate 2

hyb_protocol: Following fragmentation, cRNA were hybridized on Mouse Gene 2.0ST Array. GeneChips were washed and stained in the Tecan HS400 Hyb Station.

scan_protocol: GeneChips were scanned using the Axon GenePix 4000B scanner.

data_processing: The data were analyzed with the RMA method implemented by the affy package of R/Bioconductor

source_name: CD150+CD48-LSK bone marrow HSCs

label_protocol: Biotinylated cRNA were prepared according to NuGEN Pico protocol from 50 ng total RNA.

growth_protocol: None. Freshly isolated bone marrow hematopoietic stem cells.

extract_protocol: Trizol extraction of total RNA was performed according to QIAGEN miRNeasy instructions

tag: tissue

value: Adult bone marrow cells

tag: genotype

tag: age

value: Young


title: Primary human brain tumor sample_MDT-AP-2305_methylation

city: Toronto

first: Xin

last: Wang

state: Ontario

address: 686 Bay Street

department: Laboratory Medicine and Pathobiology

country: Canada

institute: Hospital for Sick Children

description: bisulfite-converted DNA

hyb_protocol: As directed by Illumina.

scan_protocol: As directed by Illumina.

data_processing: Normalization of raw values using Subset-quantile Within Array Normalization (SWAN) from the R/Bioconductor package minfi

source_name: Primary human brain tumor sample

label_protocol: As directed by Illumina.

extract_protocol: Total DNA was extracted from primary and metastases medulloblastoma samples using standard phenol-chloroform extraction bisulfite converted using EZ DNA Methylation Kit (Zymo Research) and hybridized to Illumina Infinium HumanMethylation450 BeadChip according to the manufacturer's instructions.

tag: sample

tag: sample id

tag: patient id

value: brain

tag: cell type

value: medulloblastoma

tag: tumor type

value: primary

tag: histology

tag: Sex

tag: death

tag: subgroup


title: M-2D03-control 0h-1

source_name: MDA-MB-231 cells, 2D culture, control, 0h, repeat 3

tag: cell line

tag: culture

tag: treatment


title: WT HSCs, biological replicate 2

description: Gene expression data from WT BM HSCs, biological replicate 2

treatment_protocol: None. Freshly isolated bone marrow hematopoietic stem cells.

value: WT


title: Merit40-/- HSCs, biological replicate 3

description: Gene expression data from Merit40-/- BM HSCs, biological replicate 3


title: M-2D03-DMSO 0h

source_name: MDA-MB-231 cells, 2D culture, DMSO, 0h, repeat 1

value: DMSO


title: Metastasis human brain tumor sample_MDT-AP-2123_methylation

description: bisulfite-converted DNA

source_name: Metastasis human brain tumor sample

value: metastasis

value: Classic


title: Child's current blood: 001-082-001-2009-B

tag: sample blood lead level

tag: mother's blood lead level

tag: gender

tag: age (months)

tag: mother's age (months)

tag: gestational age (months)

tag: smoking

value: No


title: M-2D03-control 12h

source_name: MDA-MB-231 cells, 2D culture, control, 12h, repeat 1

value: Breast cancer


title: M-2D03-control 05h

source_name: MDA-MB-231 cells, 2D culture, control, 05h, repeat 1


title: M-2D03-control 0h

source_name: MDA-MB-231 cells, 2D culture, control, 0h, repeat 1


title: Metastasis human brain tumor sample_MDT-AP-2305_methylation

description: bisulfite-converted DNA

tag: sample

tag: sample id

tag: patient id

tag: tissue

tag: age


title: WT HSCs, biological replicate 3

description: Gene expression data from WT BM HSCs, biological replicate 3

tag: genotype


title: Head kidney_Vaccine-virus_72h_rep4

city: Vigo

first: Patricia

last: Pereiro

state: Pontevedra

address: C/Eduardo Cabello, 6

department: Immunology and Genomics

country: Spain

institute: IIM-CSIC

hyb_protocol: Each amplified and labelled sample was briefly hybridized at 65 °C for 17 hours following manufacturer instructions.

scan_protocol: Microarray slides were scanned with Agilent Technologies Scanner model G2505B.

data_processing: Spot intensities and other quality control features were extracted with the Feature Extraction software version 10.4.0.0 (Agilent). The results for the fluorescence intensity data and quality annotations were imported into GeneSpring GX version 12.6 (Agilent Technologies). All of the control features (including the positive and negative controls and the landing lights) were excluded from subsequent analyses. Normalization was then carried out by a percentile shift at the 75th percentile. Entities with an expression between the 20 and 95th percentile in the raw data were retained and used in subsequent analyses.

organism: Scophthalmus maximus

source_name: Head kidney, DNA vaccine and VHSV-injected, 72hpi, juvenile turbot

label_protocol: Total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit according to manufacturer's instructions.

extract_protocol: RNA was extracted from 68 samples using TRIzol® (Invitrogen) in accordance with instructions provided by the manufacturer in combination with the RNeasy mini kit (Qiagen) for RNA purification after DNase treatment (RNase-free DNase set, Qiagen). RNA concentration was quantified using the spectrophotometer Nanodrop ND-1000 (Thermo Scientific). RNA integrity and quality were also assessed (Bioanalyzer 2100, Agilent Technologies)

treatment_protocol: A total number of 204 juvenile turbot were divided into 3 groups, two of them containing 72 fish and the last one 60 fish. Turbot were anaesthetized by immersion in 50 mg/ml buffered tricaine methanesulfonate (MS-222; Sigma) and then, fish from the first two groups were intramuscularly (i.m.) injected with 50 µl of PBS containing 2 µg of pMCV1.4 or pMCV1.4-G860. Turbot from the last batch were i.m. inoculated with 50 µl of PBS. At 8, 24 and 72 h after injection, 12 fish were removed from the first two tanks and, at 8 h after PBS inoculation, other 12 fish were taken from the last tank. These turbot were sacrificed by anaesthetic overdose and the head kidney was removed.  Equal amounts of tissue from three fish belonging to the same tank and sampling point were pooled, obtaining 4 biological replicates for each treatment and time point (3 turbot/replicate). The remaining fish (36 in the plasmid-injected groups and 48 in the PBS-inoculated tank) were maintained during one month and then, 12 fish from the PBS injected group were separated to another tank. This new group of fish was intraperitoneally (i.p.) injected with 50 µl of MEM + penicillin and streptomycin + 2% FBS (PBS - MEM group), whereas the other turbot were i.p. infected with a dose of VHSV860 of 5 x 105 TCID50/fish (pMCV1.4 - VHSV and pMCV1.4-G860 - VHSV groups). At 8, 24 and 72 hours after infection, 12 fish were removed from the VHSV-infected tanks, and at 8 h after MEM injection the 12 fish were taken from the non-infected tank. The fish were sacrificed by anaesthetic overdose and the head kidney was removed. Equal amounts of tissue from three fish belonging to the same tank and sampling point were pooled, obtaining 4 biological replicates for treatment and time point (3 turbot/replicate)

value: pMCV 1.4-G860 and VHSV

tag: sampling timepoint

value: Head kidney


title: WT HSCs, biological replicate 1

description: Gene expression data from WT BM HSCs, biological replicate 1


title: sp1 C

hyb_protocol: Experiments were performed by contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan). Cy3 labeled cRNA was fragmented  and hybridized to Agilent 018450 Whole Human Gene Genome microarray (4x44K v2, G4112F) at 65°C for 17 h with rotation and then, washed. Experiments were performed using Gene Expression Hybridization Kit (Agilent) and Gene expression Wash Pack (Agilent) according to manufacturer's recommendation.

scan_protocol: Slides were scanned by contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan) using Agilent DNA Microarray Scanner .

data_processing: Data were processed by contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan) using Agilent Feature Extraction 7 software. To obtain processed signal intensities, feature and background regions were determined by CookieCutter Method and then, signal intensities of feature and background was calculated. Background was subtracted (Spatial Detrending) and then, signal intensity of total array was corrected (Multiplicative Detrending).

source_name: Sp1 siRNA CoCl2 treatment

label_protocol: Experiments were performed by contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan). Cy3 labeled cRNA was prepared with 500 ng RNA using Quick Amp labeling Kit, one-colour (Agilent) according to manufacturer's recommendation.

extract_protocol: Total RNA was isolated using SV total RNA isolation kit (Promega, Madison, WI, USA). Quality of RNA was verified using Agilent 2100 bioanalyzer (Santa Clara, CA, USA).

treatment_protocol: OVSAYO cells were transfected with non-specific (Silencer negative control siRNA (Ambion)) or Sp1 (SMRT pool (Dharmacon)) siRNA using lipofectamine 2000 (Life technologies, Carlsbad, CA,USA) in RPMI1640 medium and cultured for 40 h. Medium was replaced and cells were further cultured in the presence of 0.5 mM CoCl2 for 4 h.

tag: cell line

value: OVSAYO

tag: cell type

value: human ovarian cancer cells

tag: transfected with

value: Sp1 siRNA

tag: exposed to

value: 0.5 mM CoCl2 for 4hrs


title: Primary human brain tumor sample_MDT-AP-2123_methylation

description: bisulfite-converted DNA

tag: tumor type

tag: histology

tag: Sex

value: F

tag: death

tag: subgroup


title: Metastasis human brain tumor sample_MDT-AP-2014_methylation

description: bisulfite-converted DNA


title: Child's current blood: 001-001-001-2012-B

source_name: Dried blood spots

tag: sample blood lead level

tag: mother's blood lead level

tag: gender

value: M

tag: age (months)

tag: mother's age (months)

tag: gestational age (months)

tag: smoking


title: neg C

source_name: scramble siRNA CoCl2 treatment

value: scramble siRNA


title: 787 MCL patient/AM6000

city: Copenhagen

first: Ulrik

last: Ralfkiaer

address: Blegdamsvej 9

department: Hematology

country: Denmark

institute: Copenhagen University Hospital

hyb_protocol: The hybridization was performed overnight at 56°C according to the manufacturer’s specifications using an HS4800 hybridization station (Tecan, Männendorf, Switzerland). Since it was not possible to hybridize all arrays at the same time point, samples were randomly split into six batches to minimize day-to-day variation in the hybridization process, and analyzed over six consecutive days. After hybridization, the microarray slides were scanned in an ozone free environment in order to prevent potential bleaching of the fluorescent Hy5 dye.

scan_protocol: Scanning was done using a G2565BA Microarray Scanner system (Agilent Technologies, Santa Clara, CA, USA) at 10-µm resolution

data_processing: Resulting TIFF images were analyzed using the GenePix 6.1 software on standard settings. Due to a confounding batch effect in the background (Hy5) intensities, we ended up only using the Hy3 signal and as such we treat the array data as single channel.

source_name: MCL patient

label_protocol: For miRNA microarray profiling, 500 ng of total RNA from samples or reference (AM6000; common RNA pool for identifying a maximum number of expressed miRNAs in patient samples, Ambion, Carlsbad, CA, USA) was labeled with Hy3 and Hy5 fluorescent dyes, respectively, using the miRCURY LNA array power labeling kit (Exiqon A/S, Vedbæk, Denmark). Samples with RNA concentrations lower than 160 ng/µl were vacuum-centrifuged (speedvac) to obtain higher concentrations. All samples were labeled the same day with the same master mix to minimize technical variation

extract_protocol: Total RNA from all samples was isolated from four 10μm tumor tissue sections using the RecoverAll total nucleic acid isolation kit (Ambion, Carlsbad, CA, USA) according to the manufacturer’s guidelines. The samples were incubated in Xylene at 50°C to remove paraffin, followed by ethanol wash. Proteins were degraded by digestion buffer and protease at 50/80°C. Subsequently, isolation buffer and ethanol were added, samples were bound to a spin-column, and DNA was degraded by DNAse treatment. The filter was washed and total RNA was eluted in a 60 μL elution solution. Total RNA quantity (OD 260 nm) and quality (260/280 ratio) were measured by an ND-1000 spectrophotometer (Thermo Scientific, Delaware, USA).

treatment_protocol: Tumor samples were taken prior to treatment of patients. All patients subsequently underwent treatment with the 'Nordic Regimen': R-maxiCHOP, alternating Rituximab and cytarabine. Responders were treated with BEAM/BEAC followed by autologous stem cell support.

tag: disease state

value: mantle cell lymphoma


title: 786 MCL patient/AM6000


title: neg

source_name: scramble siRNA

tag: cell line

value: none (control)


title: Head kidney_Vaccine-virus_24h_rep3

source_name: Head kidney, DNA vaccine and VHSV-injected, 24hpi, juvenile turbot

tag: treatment

tag: sampling timepoint

tag: tissue


title: Child's current blood: 001-122-001-2010-B

value: Yes


title: Head kidney_Vaccine-virus_24h_rep4


title: Head kidney_Vaccine-virus_72h_rep3


title: Head kidney_Vaccine-virus_72h_rep1


title: Head kidney_Vaccine-virus_24h_rep2


title: Head kidney_Vaccine-virus_24h_rep1


title: Head kidney_Vaccine-virus_72h_rep2


title: RcECF-L 7D #1

city: Kobe

first: Kenji

last: Yoshida

address: 2-2-2, Minatojima Minamimachim Chuo-ku

department: Regenerative & Cellular Medicine

institute: Sumitomo Dainippon Pharma Co.,Ltd.

description: Gene expression data

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Genome 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450-0001.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Data analysis was carried out by Expression Console 1.1 (Affymetrix). Detection and signal were obtained by MAS5 algorithm with default settings. Global normalization was performed to make average signal intensity of all probesets equal to 100.

source_name: NSC culture with ECF-L at day7 sample 1

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

growth_protocol: Neurospheres were cultured in MHM with or withour recombinant ECF-L.

treatment_protocol: Neurospheres were cultured in different condition.

tag: cell type

value: Neural stem cells (NSC)


title: shLrrfip1a differentiated C2C12

city: Shanghai

first: Ning

last: Wei

address: 320 Yueyang RD.

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Case

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: differentiated C2C12 depleting Lrrfip1a

growth_protocol: C2C12 myoblasts proliferated in DMEM + 10% FBS medium, then change to DMEM + 2% horse serum medium for differentiation. Differentiated time is 5 days.

treatment_protocol: Remove the medium, and wash cells three times by PBS. Then lysis these cells by using Trizol.

value: differenticated myoblasts

tag: genotype/variation


title: Metastasis human brain tumor sample_MDT-AP-1398_methylation

description: bisulfite-converted DNA

tag: sample

tag: sample id

tag: patient id

value: brain

value: medulloblastoma

tag: tumor type

value: metastasis

tag: age

tag: histology

tag: Sex


title: Metastasis human brain tumor sample_MDT-AP-1323_methylation

description: bisulfite-converted DNA

value: Classic

tag: death

tag: subgroup


title: Metastasis human brain tumor sample_MDT-AP-2001_methylation

description: bisulfite-converted DNA


title: Metastasis human brain tumor sample_MDT-AP-2004_methylation

description: bisulfite-converted DNA


title: sp1

source_name: Sp1 siRNA

tag: transfected with

tag: exposed to


title: Primary human brain tumor sample_MDT-AP-1398_methylation

description: bisulfite-converted DNA

source_name: Primary human brain tumor sample

value: primary


title: RcECF-L 7D #2

description: Gene expression data

source_name: NSC culture with ECF-L at day7 sample 2


title: Primary human brain tumor sample_MDT-AP-2014_methylation

description: bisulfite-converted DNA


title: 785 MCL patient/AM6000

tag: disease state


title: Child's current blood: 001-027-002-2010-B

tag: sample blood lead level

tag: mother's blood lead level

tag: gender

tag: age (months)

tag: mother's age (months)

tag: gestational age (months)

tag: smoking

value: No


title: Primary human brain tumor sample_MDT-AP-2004_methylation

description: bisulfite-converted DNA

tag: sample

tag: sample id

tag: patient id

tag: tissue

tag: cell type


title: Head kidney_Vaccine-virus_8h_rep3

source_name: Head kidney, DNA vaccine and VHSV-injected, 8hpi, juvenile turbot

tag: treatment

value: pMCV 1.4-G860 and VHSV

tag: sampling timepoint

value: 8 h

value: Head kidney


title: Merit40-/- HSCs, biological replicate 1

description: Gene expression data from Merit40-/- BM HSCs, biological replicate 1

source_name: CD150+CD48-LSK bone marrow HSCs

value: Adult bone marrow cells

tag: genotype

tag: age

value: Young


title: Primary human brain tumor sample_MDT-AP-2001_methylation

description: bisulfite-converted DNA

tag: tumor type

tag: histology

tag: Sex

value: F

tag: death

tag: subgroup


title: Head kidney_Vaccine-virus_8h_rep4


title: 783 MCL patient/AM6000

tag: disease state

value: mantle cell lymphoma


title: 782 MCL patient/AM6000


title: RcECF-L 3D #1

description: Gene expression data

source_name: NSC culture with ECF-L at day3 sample 1


title: RcECF-L 3D #2

description: Gene expression data

source_name: NSC culture with ECF-L at day3 sample 2


title: 780 MCL patient/AM6000


title: 784 MCL patient/AM6000


title: 781 MCL patient/AM6000


title: 779 MCL patient/AM6000


title: MHM 7D #1

description: Gene expression data

source_name: NSC culture without ECF-L at day7 sample 1


title: Head kidney_Empty plasmid-virus_72h_rep4

source_name: Head kidney, empty plasmid and VHSV-injected, 72hpi, juvenile turbot

value: pMCV 1.4 and VHSV


title: Metastasis human brain tumor sample_MDT-AP-0586_C_methylation

description: bisulfite-converted DNA

source_name: Metastasis human brain tumor sample

value: LCA

value: M


title: 778 MCL patient/AM6000


title: Primary human brain tumor sample_MDT-AP-1323_methylation

description: bisulfite-converted DNA


title: MHM 7D #2

description: Gene expression data

source_name: NSC culture without ECF-L at day7 sample 2

value: Neural stem cells (NSC)


title: Metastasis human brain tumor sample_MDT-AP-0586_A_methylation

description: bisulfite-converted DNA

value: brain


title: Head kidney_Vaccine-virus_8h_rep1


title: Head kidney_Vaccine-virus_8h_rep2


title: Metastasis human brain tumor sample_MDT-AP-0586_B_methylation

description: bisulfite-converted DNA

value: medulloblastoma


title: Head kidney_Empty plasmid-virus_72h_rep3


title: MHM 3D #1

description: Gene expression data

source_name: NSC culture without ECF-L at day3 sample 1


title: 753 MCL patient/AM6000

source_name: MCL patient


title: Head kidney_Empty plasmid-virus_72h_rep2


title: 752 MCL patient/AM6000


title: mOCp

city: Obu

first: Sunao

last: Takeshita

state: Aichi

address: 35 Gengo, Morioka

department: Department of Bone and Joint Disease

institute: National Center for Geriatrics and Gerontology

description: mature osteoclasts on plate

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: mature osteoclasts on plate

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Mouse bone marrow macrophages (BMMs) were cultured in the presence of M-CSF (100 ng/ml) and RANKL (100ng/ml) for 2 days.  TRAP positive mononuclear cells were harvested and used as pre-osteoclasts (pOC).  These pOC cells were further cultured in the presence of M-CSF and RANKL for 2 days in normal plastic plate or on dentin slices.  After 2 days, multinucleated TRAP positive mature osteoclasts were generated as mature osteoclasts on plate (mOCp) and mature resorbing osteoclasts on dentin (mOCd), respectively.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

tag: strain

value: mature osteoclasts on plate


title: Head kidney_Empty plasmid-virus_72h_rep1


title: mOCd

description: mature resorbing osteoclasts on dentin

source_name: mature resorbing osteoclasts on dentin

value: mature resorbing osteoclasts on dentin


title: 751 MCL patient/AM6000


title: 750 MCL patient/AM6000


title: MHM 3D #2

description: Gene expression data

source_name: NSC culture without ECF-L at day3 sample 2


title: Metastasis human brain tumor sample_MDT-AP-0527_B_methylation

description: bisulfite-converted DNA

value: metastasis


title: 749 MCL patient/AM6000


title: Primary human brain tumor sample_MDT-AP-0586_methylation

description: bisulfite-converted DNA

value: primary


title: 748 MCL patient/AM6000


title: Metastasis human brain tumor sample_MDT-AP-0527_A_methylation

description: bisulfite-converted DNA


title: Head kidney_Empty plasmid-virus_24h_rep4

source_name: Head kidney, empty plasmid and VHSV-injected, 24hpi, juvenile turbot


title: Metastasis human brain tumor sample_MDT-AP-0522_C_methylation

description: bisulfite-converted DNA


title: Primary human brain tumor sample_MDT-AP-0527_methylation

description: bisulfite-converted DNA


title: Head kidney_Empty plasmid-virus_24h_rep3


title: BMM

description: Mouse bone marrow macrophage

source_name: Mouse bone marrow macrophage

value: Mouse bone marrow macrophage


title: 747 MCL patient/AM6000


title: Head kidney_Empty plasmid-virus_24h_rep1


title: Head kidney_Empty plasmid-virus_8h_rep4

source_name: Head kidney, empty plasmid and VHSV-injected, 8hpi, juvenile turbot

value: 8 h


title: Head kidney_Empty plasmid-virus_8h_rep3

value: Head kidney


title: Metastasis human brain tumor sample_MDT-AP-0522_A_methylation

description: bisulfite-converted DNA


title: Primary human brain tumor sample_MDT-AP-0522_methylation

description: bisulfite-converted DNA

source_name: Primary human brain tumor sample


title: Head kidney_Empty plasmid-virus_24h_rep2


title: pOC

description: pre-osteoclasts

source_name: pre-osteoclasts

value: pre-osteoclasts


title: 746 MCL patient/AM6000


title: 745 MCL patient/AM6000


title: Head kidney_Empty plasmid-virus_8h_rep2


title: shLCUI differentiated C2C12

description: Control

source_name: differentiated C2C12 control

tag: cell line

value: differenticated myoblasts

tag: genotype/variation

value: shLCUI (control)


title: Head kidney_Empty plasmid-virus_8h_rep1


title: 744 MCL patient/AM6000

value: mantle cell lymphoma


title: Metastasis human brain tumor sample_MDT-AP-0321_methylation

description: bisulfite-converted DNA

tag: sample

tag: sample id

value: Classic

value: F


title: 743 MCL patient/AM6000


title: 742 MCL patient/AM6000


title: 740 MCL patient/AM6000


title: 739 MCL patient/AM6000


title: 736 MCL patient/AM6000


title: 733 MCL patient/AM6000


title: Head kidney_PBS-virus_72h_rep3

source_name: Head kidney, PBS and VHSV-injected, 72hpi, juvenile turbot

value: PBS and VHSV

tag: tissue


title: 732 MCL patient/AM6000


title: Head kidney_PBS-virus_72h_rep2


title: Head kidney_PBS-virus_72h_rep4


title: Head kidney_PBS-virus_72h_rep1


title: Primary human brain tumor sample_MDT-AP-0321_methylation

description: bisulfite-converted DNA

tag: patient id

tag: cell type


title: Head kidney_PBS-virus_24h_rep3

source_name: Head kidney, PBS and VHSV-injected, 24hpi, juvenile turbot

tag: treatment

tag: sampling timepoint


title: Head kidney_PBS-virus_24h_rep1


title: 731 MCL patient/AM6000


title: Head kidney_PBS-virus_24h_rep2


title: Head kidney_PBS-virus_8h_rep2

source_name: Head kidney, PBS and VHSV-injected, 8hpi, juvenile turbot


title: Head kidney_PBS-virus_24h_rep4


title: 729 MCL patient/AM6000


title: Head kidney_PBS-virus_8h_rep3


title: 725 MCL patient/AM6000


title: Head kidney_PBS-virus_8h_rep1


title: Head kidney_PBS-virus_8h_rep4


title: 724 MCL patient/AM6000


title: 722 MCL patient/AM6000


title: 730 MCL patient/AM6000


title: 615 MCL patient/AM6000


title: Head kidney_Control Exp2_8h_rep4

source_name: Head kidney, PBS and MEM-injected, 8hpi, juvenile turbot

value: PBS and MEM


title: Head kidney_Control Exp2_8h_rep3


title: Head kidney_Control Exp2_8h_rep2


title: Girl10_month36

city: Huddinge

first: Lovisa

middle: E

last: Reinius

address: Novum, Halsovagen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description:
Girl_10
SAMPLE 58

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation540 Beadchip using standard Illumina protocol

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

data_processing: Image analysis and signal detection were done using the Genome Studio Software. The first step of quality checks was conducted to evaluate detection p values, staining, extension, hybridization, bisulfite conversion and specificity. The lumi package was then used for pre-processing and normalization of the data. The quality control (QC) included unsupervised hierarchical clustering and principal component analysis (PCA) on sample relationships based on CpG sites; evaluation of the signal in the green and red channel, type I vs. type II probes and background correction. The data was QC verified as raw data and also after normalization by the quantile method. Unmethylated and methylated signals are available on the series record in the file: signal_intenstities_DIPP.txt

label: Cy5 and Cy3

source_name: peripheral leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from peripheral leukocytes was extracted from buffy coats using the FlexiGene kit (QIAGEN, Cat # 51204).

tag: age (months)

tag: gender

value: female


title: Head kidney_Control Exp2_8h_rep1


title: fur_mutant_rep3 vs. 33277_rep3

source_name: Fur mutant

tag: strain/background

value: Fur mutant

tag: chemostat

value: A

tag: biological replicate

source_name: 33277 wild-type

value: wild-type


title: Girl10_month6

description:
Girl_10
SAMPLE 55


title: Girl10_month12

description:
Girl_10
SAMPLE 56


title: 614 MCL patient/AM6000

source_name: MCL patient


title: Girl9_month12

description:
Girl_9
SAMPLE 49


title: Girl10_month48

description:
Girl_10
SAMPLE 59


title: Head kidney_Vaccine_72h_rep3

source_name: Head kidney, vaccinated, 72hpi, juvenile turbot


title: Girl10_month60

description:
Girl_10
SAMPLE 60


title: Head kidney_Vaccine_72h_rep4


title: 613 MCL patient/AM6000


title: Girl10_month24

description:
Girl_10
SAMPLE 57


title: 611 MCL patient/AM6000


title: Girl10_month3

description:
Girl_10
SAMPLE 54


title: 610 MCL patient/AM6000


title: 609 MCL patient/AM6000


title: Girl9_month36

description:
Girl_9
SAMPLE 51


title: Girl9_month60

description:
Girl_9
SAMPLE 53


title: Girl9_month48

description:
Girl_9
SAMPLE 52


title: 608 MCL patient/AM6000


title: 606 MCL patient/AM6000


title: Head kidney_Vaccine_24h_rep3

source_name: Head kidney, vaccinated, 24hpi, juvenile turbot


title: Head kidney_Vaccine_72h_rep2


title: Head kidney_Vaccine_72h_rep1


title: Girl9_month3

description:
Girl_9
SAMPLE 47


title: 605 MCL patient/AM6000


title: 604 MCL patient/AM6000


title: Head kidney_Vaccine_24h_rep2


title: Metastasis human brain tumor sample_MDT-AP-0522_B_methylation

description: bisulfite-converted DNA

source_name: Metastasis human brain tumor sample

value: brain

value: medulloblastoma

tag: tumor type

value: metastasis

tag: age

tag: histology

tag: Sex

tag: death

tag: subgroup


title: Head kidney_Vaccine_24h_rep1


title: Head kidney_Vaccine_8h_rep4

source_name: Head kidney, vaccinated, 8hpi, juvenile turbot

value: 8 h


title: Mtb_NH4+_biol. repl. 3

city: Hanover

first: Annegret

last: Hampel

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

hyb_protocol: After cDNA fragmentation and terminal labeling with  biotinylated GeneChip®DNA Labeling Reagent  labeled cDNA were hybridized for 16 hr at 50°C on GeneChip MTbH37Rva520456F (Custom Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to manufactures recommendations.

data_processing: Image analysis was done by GCOS 3.1 Software (Affymetrix). Probeset summarization and microarray normalization was performed by RMA algorithm.

organism: Mycobacterium tuberculosis

source_name: growth with ammonium chloride

label_protocol: cDNA was labeled using the terminal deoxynucleotidyl transferase (Promega) together with the GeneChip DNA Labeling Reagent (Affymetrix) according to the protocol of the manufacturer.

growth_protocol: M.tuberculosis was grown in basal medium with 5mM of arginine or ammonium chloride as sole nitrogen source. RNA was extracted at OD=0.8

extract_protocol: Sixty ml of bacterial culture were mixed with the same volume of GTC buffer (5.1 M guanidine thiocyanate, 17 mM n-lauroylsarcosine, 28.3 mM sodium citrate, 0.7 % ß-mercaptoethanol) and incubated for 15 min at room temperature. Cell pellets were resuspended in trizol reagent, disrupted mechanically by beat beating, and subjected to centrifugation (16,000 × g for 10 min). RNA was isolated using the RNeasy Kit from Qiagen. Remaining DNA was removed by an off-column DNase digestion (NEB). RNA integrity was determined using an Agilent Bioanalyzer 2100. 10 µg of RNA was transcribed into cDNA using the SuperScript® II reverse transcriptase (Invitrogen) and fragmented with Pierce DNaseI (Thermo Scientific).

tag: nitrogen source

value: ammonium chloride


title: Girl8_month12

description:
Girl_8
SAMPLE 42


title: 603 MCL patient/AM6000

tag: disease state


title: Girl9_month6

description:
Girl_9
SAMPLE 48


title: Girl9_month24

description:
Girl_9
SAMPLE 50


title: Mtb_arg_biol. repl. 3

source_name: growth with arginine

value: arginine


title: Head kidney_Vaccine_8h_rep3

tag: tissue

value: Head kidney


title: 602 MCL patient/AM6000


title: Girl8_month24

description:
Girl_8
SAMPLE 43


title: Girl8_month60

description:
Girl_8
SAMPLE 46


title: Head kidney_Vaccine_8h_rep2


title: Girl8_month3

description:
Girl_8
SAMPLE 40


title: 600 MCL patient/AM6000


title: Mtb_NH4+_biol. repl. 2, sample 2


title: 599 MCL patient/AM6000


title: Mtb_arg_biol. repl. 2, sample 2


title: Girl8_month6

description:
Girl_8
SAMPLE 41


title: Mtb_NH4+_biol. repl. 2, sample 1


title: Mtb_arg_biol. repl. 2, sample 1


title: Head kidney_Vaccine_24h_rep4


title: Head kidney_Vaccine_8h_rep1


title: Head kidney_Empty plasmid_72h_rep4

source_name: Head kidney, empty plasmid-injected, 72hpi, juvenile turbot

value: pMCV 1.4


title: Girl7_month36

description:
Girl_7
SAMPLE 37


title: Mtb_NH4+_biol. repl. 1


title: 597 MCL patient/AM6000

value: mantle cell lymphoma


title: Head kidney_Empty plasmid_72h_rep3


title: Girl8_month36

description:
Girl_8
SAMPLE 44


title: 595 MCL patient/AM6000


title: Girl7_month24

description:
Girl_7
SAMPLE 36


title: Girl7_month6

description:
Girl_7
SAMPLE 34


title: 594 MCL patient/AM6000


title: 593 MCL patient/AM6000


title: Mtb_arg_biol. repl. 1


title: 592 MCL patient/AM6000


title: Girl7_month48

description:
Girl_7
SAMPLE 38


title: Head kidney_Empty plasmid_72h_rep2


title: Head kidney_Empty plasmid_24h_rep3

source_name: Head kidney, empty plasmid-injected, 24hpi, juvenile turbot


title: Head kidney_Empty plasmid_24h_rep4


title: Girl8_month48

description:
Girl_8
SAMPLE 45


title: Head kidney_Empty plasmid_24h_rep1


title: Girl7_month60

description:
Girl_7
SAMPLE 39


title: 589 MCL patient/AM6000


title: 590 MCL patient/AM6000


title: Head kidney_Empty plasmid_24h_rep2


title: Head kidney_Empty plasmid_8h_rep4

source_name: Head kidney, empty plasmid-injected, 8hpi, juvenile turbot


title: Girl7_month12

description:
Girl_7
SAMPLE 35


title: 564009A12 - sup62-mips1_BR2 vs col0_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description:
Channel 1: arabidopsis thaliana (columbia) - dev.stage (boyes et al. plant cell 2001): boyes: 3.20
Channel 2: arabidopsis thaliana (columbia) mutant (col0) - dev.stage (boyes et al. plant cell 2001): boyes: 3.20
Transcriptome analysis of the mutant sup62, cpsf30, two suppressors of programmed cell death in A. thaliana

hyb_protocol: col0_BR2 Cy5 / sup62-mips1_BR2 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial,rosette - Media=Soil hygrometry=60% Temperature=20°C Light=180 µmol of photon/m2/s

extract_protocol: col0_BR2:3ug. (NucleoSpinRNAPlant.pdf)

treatment_protocol: no treatment

tag: ecotype

value: Columbia

tag: developmental stage (boyes et al. plant cell 2001)

value: boyes 3.20

tag: genotype/variation

value: wild type

value: rosette


title: 564009A10 - sup62-mips1_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / sup62-mips1_BR1 Cy3 : 30pmol.

extract_protocol: col0_BR1:3ug. (NucleoSpinRNAPlant.pdf)


title: Girl6_month48

description:
Girl_6
SAMPLE 31

tag: age (months)

value: female


title: 564009A11 - col0_BR2 vs sup62-mips1_BR2

description:
Channel 1: arabidopsis thaliana (columbia) mutant (col0) - dev.stage (boyes et al. plant cell 2001): boyes: 3.20
Channel 2: arabidopsis thaliana (columbia) - dev.stage (boyes et al. plant cell 2001): boyes: 3.20
Transcriptome analysis of the mutant sup62, cpsf30, two suppressors of programmed cell death in A. thaliana

hyb_protocol: sup62-mips1_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.


title: Girl6_month24

description:
Girl_6
SAMPLE 30

tag: gender


title: 601 MCL patient/AM6000


title: 586 MCL patient/AM6000


title: 564009A09 - col0_BR1 vs sup62-mips1_BR1

hyb_protocol: sup62-mips1_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.


title: 585 MCL patient/AM6000


title: Girl7_month3

description:
Girl_7
SAMPLE 33


title: Girl6_month60

description:
Girl_6
SAMPLE 32


title: 581 MCL patient/AM6000


title: Head kidney_Empty plasmid_8h_rep1

tag: treatment

tag: sampling timepoint


title: 579 MCL patient/AM6000


title: Head kidney_Empty plasmid_8h_rep2


title: 564009A07 - col0_BR2 vs sup62_BR2

hyb_protocol: sup62_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.

extract_protocol: sup62_BR2:3ug. (NucleoSpinRNAPlant.pdf)


title: Head kidney_Empty plasmid_8h_rep3


title: Head kidney_Control Exp1_8h_rep3

source_name: Head kidney, PBS-injected, 8hpi, juvenile turbot

value: PBS


title: Girl5_month36

description:
Girl_5
SAMPLE 25


title: Girl5_month24

description:
Girl_5
SAMPLE 24


title: Girl5_month60

description:
Girl_5
SAMPLE 27


title: Girl5_month48

description:
Girl_5
SAMPLE 26


title: Head kidney_Control Exp1_8h_rep2


title: Head kidney_Control Exp1_8h_rep4


title: 577 MCL patient/AM6000


title: 578 MCL patient/AM6000


title: Girl6_month3

description:
Girl_6
SAMPLE 28


title: 564009A05 - col0_BR1 vs sup62_BR1

hyb_protocol: sup62_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.

extract_protocol: sup62_BR1:3ug. (NucleoSpinRNAPlant.pdf)


title: Girl6_month12

description:
Girl_6
SAMPLE 29


title: Head kidney_Empty plasmid_72h_rep1


title: 564009A06 - sup62_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / sup62_BR1 Cy3 : 30pmol.


title: Head kidney_Control Exp1_8h_rep1


title: 588 MCL patient/AM6000


title: 576 MCL patient/AM6000


title: 575 MCL patient/AM6000


title: Girl5_month3

description:
Girl_5
SAMPLE 21


title: Patient SU453 cultured blasts, CD14 sorted

city: Stanford

first: Christopher

last: Dove

address: Room 3005, 265 Campus Drive, 3rd Floor

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: Performed according to manufacturer's instructions

data_processing: MAS5; quantile normalization

source_name: B cell acute lymphoblastic leukemia, pre-rx, myeloid cytokine culture

growth_protocol: After sorting, input blasts were cultured in suspension at 5 x 10^5 cells/mL in Iscove’s modified Dulbecco’s medium (IMDM, Life Technologies, Grand Island, NY) with 20% fetal calf serum, 2mM GlutaMAX (Life Tech.), penicillin/streptomycin, 25mM HEPES, 55 µM β-mercaptoethanol, and 1mM sodium pyruvate.

extract_protocol: Used Allprep DNA/RNA Micro Kit according to manufacturer's instructions

treatment_protocol: The following recombinant human cytokines were added to cultures: 100ng/mL Fms-like tyrosine kinase ligand (FLT3L), 10ng/mL interleukin 7 (IL-7), 20ng/mL IL-3, 20ng/mL granulocyte-macrophage colony-stimulating factor (GM-CSF), and 25 ng/mL macrophage colony-stimulating factor (M-CSF); all cytokines were obtained from Peprotech (Rocky Hill, NJ).  Cultures were incubated at 37˚C in a 5% CO2 and 5% O2 humidified atmosphere with weekly half-media changes and replenishment of cytokines.

tag: morphology

value: macrophage-like cell


title: Girl5_month6

description:
Girl_5
SAMPLE 22


title: Girl4_month60

description:
Girl_4
SAMPLE 20


title: 573 MCL patient/AM6000


title: Girl5_month12

description:
Girl_5
SAMPLE 23


title: Patient SU453 cultured blasts, CD19 sorted

scan_protocol: Performed according to manufacturer's instructions

value: residual blast


title: 564009A02 - mips1_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / mips1_BR1 Cy3 : 30pmol.

extract_protocol: mips1_BR1:3ug. (NucleoSpinRNAPlant.pdf)


title: 574 MCL patient/AM6000


title: Patient SU453 input blasts

source_name: B cell acute lymphoblastic leukemia, pre-rx, no culture

label_protocol: Performed according to manufacturer's instructions

value: input blast


title: 564009A01 - col0_BR1 vs mips1_BR1

hyb_protocol: mips1_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.


title: Patient SU401 cultured blasts, CD14 sorted


title: Girl4_month24

description:
Girl_4
SAMPLE 18


title: Girl4_month48

description:
Girl_4
SAMPLE 19


title: 564009A04 - mips1_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / mips1_BR2 Cy3 : 30pmol.

extract_protocol: mips1_BR2:3ug. (NucleoSpinRNAPlant.pdf)


title: 560415A02 - cpsf30-mpk4_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / cpsf30-mpk4_BR1 Cy3 : 30pmol.


title: 560415A03 - col0_BR2 vs cpsf30-mpk4_BR2

hyb_protocol: cpsf30-mpk4_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.


title: 560415A04 - cpsf30-mpk4_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / cpsf30-mpk4_BR2 Cy3 : 30pmol.


title: 571 MCL patient/AM6000

hyb_protocol: The hybridization was performed overnight at 56°C according to the manufacturer’s specifications using an HS4800 hybridization station (Tecan, Männendorf, Switzerland). Since it was not possible to hybridize all arrays at the same time point, samples were randomly split into six batches to minimize day-to-day variation in the hybridization process, and analyzed over six consecutive days. After hybridization, the microarray slides were scanned in an ozone free environment in order to prevent potential bleaching of the fluorescent Hy5 dye.


title: 572 MCL patient/AM6000


title: Patient SU401 input blasts


title: 569 MCL patient/AM6000


title: 560415A01 - col0_BR1 vs cpsf30-mpk4_BR1

hyb_protocol: cpsf30-mpk4_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.


title: Girl3_month24

description:
Girl_3
SAMPLE 12

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation540 Beadchip using standard Illumina protocol


title: 570 MCL patient/AM6000


title: Girl4_month6

description:
Girl_4
SAMPLE 16


title: 45 min_rep3

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

country: Switzerland

institute: University of Lausanne and University Hospital Center

description: 45 min drug-exposed cells

hyb_protocol: Agilent gene expression hybridization kit protocol

scan_protocol: Agilent Scanning protocol on an Agilent DNA Microarray Scanner G2565BA  Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR

data_processing: Data were extracted from the images with Feature Extraction (FE) software. Data were normalized using a combined rank consistency filtering with LOWESS intensity normalization. The gene expression values obtained from FE software were imported into GeneSpring 10.0.2 software (Agilent technologies) for preprocessing and data analysis.

organism: Candida albicans

source_name: Clinical isolate

label_protocol: Agilent one-color quick amp labeling kit protocol

growth_protocol: log-pase culture grown in YPD

extract_protocol: total RNA extraction using glass beads

treatment_protocol: 3µM FR59 given to log phase cells  and cells harvested after 15 min and 45 min treatment

tag: time

value: 45 min


title: Patient SU312 cultured blasts, CD14 sorted


title: 566 MCL patient/AM6000


title: 45 min_rep1

description: 45 min drug-exposed cells


title: Girl3_month48

description:
Girl_3
SAMPLE 13

source_name: peripheral leukocytes


title: Patient SU401 cultured blasts, CD19 sorted


title: Patient SU312 cultured blasts, CD19 sorted


title: 15 min_rep3

description: 15 min drug-exposed cells

value: 15 min


title: 568 MCL patient/AM6000


title: Girl3_month60

description:
Girl_3
SAMPLE 14


title: Patient SU312 input blasts


title: 15 min_rep2

description: 15 min drug-exposed cells


title: 564 MCL patient/AM6000


title: 564009A08 - sup62_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / sup62_BR2 Cy3 : 30pmol.


title: 565 MCL patient/AM6000


title: Patient SU215 cultured blasts, CD14 sorted


title: Patient SU215 cultured blasts, CD19 sorted


title: 15 min_rep1

description: 15 min drug-exposed cells


title: Patient SU215 input blasts


title: 561 MCL patient/AM6000


title: Patient SU079 cultured blasts, CD14 sorted


title: Girl4_month3

description:
Girl_4
SAMPLE 15


title: control_rep3

description: control conditions

value: control


title: 560 MCL patient/AM6000


title: Girl3_month12

description:
Girl_3
SAMPLE 11


title: siNF90-3-treated Huh7 cells

status: Public on Mar 31 2015

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

hyb_protocol: Each array was hybridized with 100 ng Cy3-labeled RNA using miRNA Complete Labeling Reagent and Hyb kit (Agilent Technologies) according to the manufacture's instructions.

scan_protocol: The array was scanned using Agilent Microarray Scanner (Agilent Technologies).

data_processing: RAW data were normalized using 90 percentile shift normalization by GeneSpring GX (Agilent Technologies).

source_name: siNF90-3-treated Huh7 cells

label_protocol: Total RNA was labeled with Cy3 by miRNA Complete Labeling Reagent and Hyb kit (Agilent Technologies) according to the manufacture's instructions.

extract_protocol: Total RNA was isolated from siNTC- or siNF90-treated Huh7 cells using miRNeasy kit (QIAGEN).

tag: cell line

tag: treated with


title: Girl4_month12

description:
Girl_4
SAMPLE 17


title: Patient SU079 cultured blasts, CD19 sorted


title: control_rep2

description: control conditions


title: 564009A03 - col0_BR2 vs mips1_BR2

hyb_protocol: mips1_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.


title: control_rep1

description: control conditions


title: siNF90-2-treated Huh7 cells

source_name: siNF90-2-treated Huh7 cells


title: siNTC-treated Huh7 cells

description: siNTC

source_name: siNTC-treated Huh7 cells

value: non-targeting control siRNA (siNTC)


title: Girl2_month60

description:
Girl_2
SAMPLE 8


title: ASid82

status: Public on Mar 09 2015

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix Expression Console

source_name: ID8 cells

label_protocol: Affymetrix standard protocol

extract_protocol: Rneasy Mini Kit with lysis by QIAshredder

treatment_protocol: ID8 cells were cultured in DMEM with 10% ascites developed by ID8 bearing mice.

tag: diagnosis

value: ovarian cancer


title: Girl1_month60

description:
Girl_1
SAMPLE 6


title: id83

source_name: parental ID8 cells

treatment_protocol: ID8 cells were cultured in DMEM with 10% FBS.


title: Patient SU079 input blasts


title: Girl2_month24

description:
Girl_2
SAMPLE 7


title: Girl3_month6

description:
Girl_3
SAMPLE 10


title: id82


title: 45 min_rep2

description: 45 min drug-exposed cells


title: ASid83


title: PLS1-A

status: Public on Feb 11 2015

city: Beijing

first: Jun

last: Zhu

address: No.52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital & Institute

description: GEP data from 1 uM PLS-123 treatment

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized with RMA.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: OCI-Ly7 cells were grown in DMEM supplemented with 10% FBS.

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

treatment_protocol: OCI-Ly7 cells were treated with indicated concentrations of ibrutinib, PLS-123 or vehicle for 24 hours.

tag: cell type

value: B-NHL cell line


title: PLS1-B

description: GEP data from 1 uM PLS-123 treatment


title: Ibru10-C

description: GEP data from 10 uM Ibrutinib treatment


title: Ibru10-B

description: GEP data from 10 uM Ibrutinib treatment


title: Girl1_month48

description:
Girl_1
SAMPLE 5


title: Girl3_month3

description:
Girl_3
SAMPLE 9


title: CT-B

description: GEP data from vehicle treatment


title: Ibru1-C

description: GEP data from 1 uM Ibrutinib treatment


title: EM_A1AT_pat1

status: Public on Jan 15 2015

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description: Sample 18

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Organoids cultured in expansion medium. Derived from A1AT patient 1. Early passage

label_protocol: 0.5µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

growth_protocol: Human liver derived organoid cultures were grown from a 1cm3 human liver biopsy from donor (Sample1-2 and 7-17) or Alpha1-antytrypsin patient (Samples 18-20) as described in Material and Methods (See accompaning material and methods section in manuscript).

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Sample 1 was grown in mouse liver medium. Sample 2 was treated with A83015uM. Samples 7-13 were cultured in complete Expansion medium containing A8301 and Forskolin or in differentiation medium (sample 14-17 and 20) as described in Methods.

tag: tissue type

value: liver

source_name: human reference RNA (Stratagene)

tag: sample type

value: common reference


title: id81


title: Girl1_month36

description:
Girl_1
SAMPLE 4


title: DM_A1AT_pat1

description: Sample 19

source_name: Organoids cultured in differentiation medium. Derived from A1AT patient 1. Early passage


title: Ibru1-B

description: GEP data from 1 uM Ibrutinib treatment


title: Ibru1-A

description: GEP data from 1 uM Ibrutinib treatment


title: CT-A

description: GEP data from vehicle treatment


title: Ibru10-A

description: GEP data from 10 uM Ibrutinib treatment


title: CT-C

description: GEP data from vehicle treatment


title: DM_2

description:
Sample 14
Sample 14-16 are biological replicates

source_name: Organoids cultured in Differentiation medium. Derived from Donor 3. Early passage


title: DM_4

description:
Sample 16
Sample 14-16 are biological replicates

source_name: Organoids cultured in Differentiation medium. Derived from Donor 7. Early passage


title: Girl1_month12

description:
Girl_1
SAMPLE 2


title: DM_3

description:
Sample 15
Sample 13-16 are biological replicates


title: EM_4

description:
Sample 10
Sample 7-12 are biological replicates

source_name: Organoids cultured in complete expansion medium. Donor 5. Early passage


title: EM_5

description:
Sample 11
Sample 7-12 are biological replicates

source_name: Organoids cultured in complete expansion medium. Donor 6. Early passage


title: Tissue 4

description:
Sample 6
Sample 3-6 are biological replicates

source_name: Human liver tissue lysate donor 4


title: Girl1_month3

description:
Girl_1
SAMPLE 1


title: DM_1

description:
Sample 13
Sample 13-16 are biological replicates

source_name: Organoids cultured in Differentiation medium. Derived from Donor 5. Late Passage


title: EM_6

description:
Sample 12
Sample 7-12 are biological replicates

source_name: Organoids cultured in complete expansion medium. Derived from Donor 7. Early passage


title: EM_2

description:
Sample 8
Sample 7-12 are biological replicates

source_name: Organoids cultured in complete expansion medium. Derived from Donor 3. Early passage


title: EM_3

description:
Sample 9
Sample 7-12 are biological replicates

source_name: Organoids cultured in complete expansion medium. Donor 6. Late passage


title: Girl1_month24

description:
Girl_1
SAMPLE 3

source_name: peripheral leukocytes


title: Tissue 2

description:
Sample 4
Sample 3-6 are biological replicates

source_name: Human liver tissue lysate donor 2


title: EM_1

description:
Sample 7
Sample 7-12 are biological replicates

source_name: Organoids cultured in complete expansion medium. Donor 5. Late Passage


title: Tissue 1

description:
Sample 3
Sample 3-6 are biological replicates

source_name: Human liver tissue lysate donor 1


title: ERFHNic+A sample

description: Sample 2

source_name: organoids cultured in mouse medium only. Donor 1


title: Tissue 3

description:
Sample 5
Sample 3-6 are biological replicates

source_name: Human liver tissue lysate donor 3


title: ERFHNic sample

description: Sample 1

source_name: human reference RNA (Stratagene)


title: Tissue A1AT_pat1

description: Sample 17

source_name: Human liver tissue lysate derived from A1AT patient 1


title: US 187

status: Public on Aug 01 2014

city: Milano

first: Elena

last: Landoni

address: Via Vanzetti 5

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: miRNA profile of archival plasma sample

hyb_protocol: Hybridization for 20 h at 55 °C on SurePrint G3 Human v16 miRNA 8x60K microarrays (G4870A) designed on miRBase 16.0 from Agilent Technologies. The arrays were washed in Agilent GE Wash Buffers, following the manufacturer’s instructions

scan_protocol: All slides were immediately scanned at 2 mm resolution using an Agilent DNA microarray scanner

data_processing: The resulting images were analyzed using Agilent’s Feature Extraction software v10.7. In the employed platform, each miRNA is targeted by one to 4 different probes and each probe is spotted 10 to 40 times on the array. Then, the total gene signal for each miRNA was obtained by summing the probe signals derived using the Agilent Feature Extraction software. Using this software, each probe is defined detected if its value is greater than 3 times its standard error, and each miRNA is defined as detected if at least one of the probes is detected. Summarized data were log2 transformed

source_name: plasma

label_protocol: 2.5 µl of total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured using 100% DMSO at 100°C for  5 min, labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 1 hour

growth_protocol: Plasma samples used in this study belong to the human plasma collection of the Fenretinide Breast Cancer Prevention Trial and RNA was extracted from 350 µl of sample.

extract_protocol: Total RNA was extracted from plasma using the commercial column-based system Qiagen miRNeasy® Mini Kit (Qiagen, Valencia, CA, USA), slightly modified by Exiqon (Vedbaek, Denmark. The eluate was digested using 1 u/µl heparinase I (Sigma-Aldrich, St. Luis, MO, USA), in the presence of an RNase inhibitor, (RNAsin; Promega, Madison, WI, USA) for 1 hour at room temperature, and RNA was stored at −80 °C.

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: hs class

value: hemolyzed


title: Nucleus pulposus_control_2

status: Public on Nov 17 2014

city: Xi'an

first: Hai-Qiang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

description: Derived from the lumbar disc of cadaveric donor with no significat degenerative signs on magnetic resonance imaging

hyb_protocol: The labeled cRNAs were purified with RNeasy mini column and subsequently hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1 (Agilent Technologies), and low intensity LncRNAs and mRNA (at most 4 out of 10 samples have flags in Present or Marginal ) were filtered.
GeneSpring GX v11.5.1 (Agilent Technologies) computed normalized signal intensity. Log2 value of normalized Intensity of each sample were presented in matrix table.

source_name: Nucleus pulposus tissue,normal

label_protocol: 1ug of total RNA was reverse transcripted into cDNA with T7 Promoter Primer and MMLV-Rtase, and then was labled with T7 polymerase and Cyanine-3-CTP.

extract_protocol: Control and degenerated samples were prefrozen with liquid nitrogen, ground into powder with mortar, extracted with Trizol reagent according its protocol.

treatment_protocol: All the specimens were collected from intervertebral discs of cadaveric donors or patients within 3 hours after anatomy or surgery respectively, following rinsed with phosphate-buffered saline, the nucleus pulposus tissue was carefully collected under stereoscopic microscope.

tag: tissue

value: Nucleus pulposus

tag: condition

value: Control

tag: idd related diseases

value: No

tag: gender

value: Male

tag: age

value: 35 years

tag: degeneration grading

value: Grading I

tag: disc level


title: US 110

description: miRNA profile of archival plasma sample

value: no hemolysis


title: Nucleus pulposus_degenerated_4

description: Derived from the lumbar disc of patient with intervertebral disc degeneration

source_name: Nucleus pulposus tissue,degenerated

value: Degenerated

value: Intervertebral disc herniation

value: 45 years

value: Grading Ⅴ


title: US 118

description: miRNA profile of archival plasma sample


title: Nucleus pulposus_degenerated_5

value: Female

value: 27 years

value: Grading Ⅳ


title: US 90

description: miRNA profile of archival plasma sample


title: US 114

description: miRNA profile of archival plasma sample


title: US 117

description: miRNA profile of archival plasma sample


title: Nucleus pulposus_control_5

value: 52 years


title: Nucleus pulposus_degenerated_2

value: 38 years


title: Nucleus pulposus_degenerated_1

value: 32 years


title: Nucleus pulposus_degenerated_3

value: Nucleus pulposus

value: 42 years


title: US 109

description: miRNA profile of archival plasma sample

value: plasma


title: Nucleus pulposus_control_3

value: Control

value: No

value: Male

value: 41 years


title: Nucleus pulposus_control_4

value: 43 years

value: Grading I


title: US 82

description: miRNA profile of archival plasma sample

value: no hemolysis


title: US 72

description: miRNA profile of archival plasma sample


title: OVCAR-3/H1.3(H), biological rep1

status: Public on Oct 31 2014

city: Atlanta

first: Yuhong

last: Fan

state: Georgia

address: IBB 2313, 315 Ferst Drive

department: School of Biology and the Petit Institute for Bioengineering and Bioscience

institute: Georgia Institute of Technology

description: Gene expression data from cells.

hyb_protocol: Following fragmentation, cRNA was hybridized to human Affymetrix ST1.0 arrays by standard Affymetrix hybridization protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Gene ChIP Scanner.

data_processing: Data were analyzed using RMA normalization in Expression Console (Affymetrix)

source_name: OVCAR-3 cells overexpressing human H1.3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: OVCAR-3 cells were cultured in RPMI-1640 (Fisher) media supplemented with 20% fetal bovine serum (Gemini), 100 U/ml penicillin and 100 mg/ml streptomycin (Life Technologies).

extract_protocol: Total RNA was isolated with TRIzol reagent (Life Technologies) and further purified using RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were lysed and total RNA was isolated with TRIzol reagent (Life Technologies) according to the manufacturer's protocol.

tag: cell line

value: OVCAR-3 ovarian epithelial cancer cells


title: US 78

description: miRNA profile of archival plasma sample


title: US 194

description: miRNA profile of archival plasma sample


title: OVCAR-3/VO, biological rep2

description: Gene expression data from cells.

source_name: OVCAR-3 cells transfected with vectors without H1.3

tag: cell type


title: US 66

description: miRNA profile of archival plasma sample

value: hemolyzed


title: PLS1-C

description: GEP data from 1 uM PLS-123 treatment

value: B-NHL cell line


title: US 177

description: miRNA profile of archival plasma sample


title: US 56

description: miRNA profile of archival plasma sample


title: OVCAR-3/H1.3(H), biological rep2

description: Gene expression data from cells.


title: OVCAR-3/VO, biological rep1

description: Gene expression data from cells.


title: Nucleus pulposus_control_1

last: Wang

value: 33 years


title: US 48

description: miRNA profile of archival plasma sample


title: US 43

description: miRNA profile of archival plasma sample


title: US 27

description: miRNA profile of archival plasma sample


title: US 14

description: miRNA profile of archival plasma sample


title: US 23

description: miRNA profile of archival plasma sample


title: WT_3wkleaves_mRNAseq

status: Public on Dec 24 2013

type: SRA

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: mRNA-Seq

library_source: transcriptomic

data_processing:
mRNA-seq: Reads were mapped using Bowtie (Langmead et al., 2009) allowing up to 2 mismatches, and uniquely mapping reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files format and content (mRNA-seq): Wiggle format files with normalized read densities calculated in 25 bp bins. Normalized reads were calculated by # reads/0.1kb/uniquely mapping readsx10^6.

molecule: polyA RNA

source_name: 3 wk leaves

growth_protocol: Plants were grown under continuous light

extract_protocol:
0.1 g of tissue was ground in Trizol (Invitrogen). Total RNA was treated with DNaseI (Roche) and cleaned up with phenol-chlorophorm    and precipitated with ethanol. Poly(A) puriﬁcations were performed by using mRNA puriﬁcation dynabeads (Invitrogen) following    manufacture instructions.
RNA-seq libraries were generated following manufacturer instructions (Illumina) and sequenced on    a Genome Analyzer. RNA-seq reads were uniquely mapped to the TAIR10 version of theArabidopsis genome with Bowtie (Langmead    et al., 2009) allowing 2 mismatches.

tag: genotype

value: wild type

tag: ecotype


title: US 13

description: miRNA profile of archival plasma sample

tag: plasmaid


title: EPN_943_1

status: Public on Aug 30 2013

city: Aurora

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

institute: University of Colorado Denver

description:
included_in_corresponding_manuscript:yes
Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 17,664 genes.

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: Primary

value: brain tumor (ependymoma)


title: EPN_871_1