title: Affy Clip Syn-T cells biological rep 1

value: T lymphocytes


title: Sample_09

status: Public on Jan 18 2013

type: RNA

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description:
Sample name: 5627224039_I
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224039_I.txt

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.
NOTE: At our institute we use the Bioconductor beadarray software to carry out spatial artefact removal(e.g. with tools such as BASH and HULK), and this can only be carried out on the bead-level data as is provided in the text files. This cannot be carried out on the bead-summarised data such as is provided in the non-normalised data matrices or the output of BeadStudio. As such we would prefer for Illumina microarray users to provide these text files on GEO so that artefact correction can be carried out.
Related to the bead-level .txt files are the two Metrics.txt files (linked as supplementary files on the Series record) which are generated by the scanner and contain metrics such as signal and noise levels which are useful for array QC.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF-7 human cell lines

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

growth_protocol: Cells were grown in charcoal dextran treated DMEM for three days prior to siRNA treatment

extract_protocol: Cells were extracted using Qiagen RNAeasy extraction kit

treatment_protocol: Cells were treated with 100nm siNT or siGREB1 by lipofectamine based transfection for 6 hours. 100nM of drug ICI182 was added the next day for 24hrs. Cells were then treated with 100nM of Estrogen or vehicle for 6 or 24 hrs

tag: cell line

value: MCF-7 cells (human breast adenocarcinoma cell line)

tag: sample group

tag: sitype

value: siNT

tag: treatment

tag: treatment time (hours)


title: Beas-2B parental cells [DEG.C]

status: Public on Jan 19 2013

city: Tuxedo

first: Lisa

last: Passantino

state: New York

address: 57 Old Forge Road

department: School of Medicine

country: USA

institute: New York University

description: culture dish only

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 1.0 ST Arrays and scanned at the NYU Cancer Institute Genomics Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Gene expression changes for transformed clones and parental cells versus control clones were analyzed using GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Significant genes were determined by a moderated T-test with p-values < 0.05. The p-values were subjected to FDR correction for multiple hypothesis testing. Control clones were used as the controls for all samples to be compared to.
probe group file: HuGene-1_0-st-v1_na31_hg19_2010-09-03.pgf
meta-probeset file: HuGene-1_0-st-v1_na31_hg19_2010-09-03.mps

source_name: Beas-2B unexposed parental

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Immortalized human bronchial epithelial cells (Beas-2B; #CRL-9609, ATCC, Manassas, VA) were cultured in 1X Dulbecco’s Modified Eagle Medium (DMEM; ordered in-house from NYU) supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals, Lawrenceville, GA) and 100ug/mL Pen Strep (GIBCO, Grand Island, NY) (“complete culture media”). The cells were maintained in 25 cm2 polystyrene tissue culture flasks in an incubator at 37oC with 5% CO2 and 100% humidity. The media was changed every 2 days, and the cells were passaged every 4 days using 0.05% trypsin-EDTA (GIBCO).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). The isolated T.RNA was subjected to a colum purification using Rneasy Plus Micro Kit (Qiagen)

treatment_protocol: Beas-2B cells were seeded at 3X105 into 25 cm2 polystyrene tissue culture flasks. The flasks then received media containing 10 µM NaVO3 and the cells were cultured for 4 weeks. Control cells received distilled water in place of NaVO3. Every 3-4 days, the cells were trypsinized, counted, and re-seeded into fresh 25 cm2 flasks at a density of 3X105 live cells/flask, and given fresh media with 10 µM NaVO3. A subset of cells were only treated for 24 hours (acute exposure). Soft Agar Assay: Warm (37oC, 2 mL/well) base agar solution (0.5% [w/v] agar [#214530, BD Biosciences, San Diego, CA] in 1X DMEM complete culture media) was poured into each well of 6-well untreated polystyrene plates. The base layer was allowed to solidify at 4oC for 2 hours. Then 2 mL of a warm (37oC) top agar solution consisting of 5,000 cells in 0.35% agar + 1X DMEM complete tissue culture media was added over the base layer. Duplicate wells were used for each treatment and control cells. The 6-well plates were then incubated at 37oC in the tissue culture incubator for 3 weeks; 0.5 mL of fresh media was added once per week without disturbing the cells. After 3 weeks, the colonies were either stained overnight with INT/BCIP solution (#11-681-460-001, Roche, New York, NY) in 0.1 M Tris/0.05 M MgCl2/0.1 M NaCl to visualize (and subsequently permit a count of) all colonies, or colonies were instead extracted from the agar. Each extracted colony was trypsinized in a 96-well plate in order to break up the colony, and then transferred into a 24-well plate to begin expansion of the individual transformed and control clones.

value: unexposed


title: Sample_15

description:
Sample name: 5627224057_C
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224057_C.txt

value: siGreb


title: Sample_17

description:
Sample name: 5627224039_J
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224039_J.txt


title: Sample_03

description:
Sample name: 5627224057_J
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224057_J.txt


title: Sample_08

description:
Sample name: 5627224057_B
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224057_B.txt


title: Sample_14

description:
Sample name: 5627224057_E
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224057_E.txt


title: Sample_01

description:
Sample name: 5627224039_K
MCF7 cells  48hrs of siNT transfection
Bead-level data: 5627224039_K.txt

value: vehicle

value: control


title: Sample_11

description:
Sample name: 5627224039_G
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224039_G.txt


title: Sample_16

description:
Sample name: 5627224039_H
MCF7 cells  48hrs of siGREB1 transfection
Bead-level data: 5627224039_H.txt


title: Affy Clip Syn-T cells biological rep 2

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

description: AGO-Clip Enriched transcripts from Syn-T cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.

data_processing: Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.

organism: Mus musculus

source_name: T cells co-cultured with syngeneic dendritic cells

label_protocol: Samples were processed using WT-Ovation™ Pico System  ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.

growth_protocol: Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).

extract_protocol: Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

treatment_protocol: Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2  from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.

tag: strain

tag: cell type

tag: clip antibody

value: AGO


title: Sample_07

description:
Sample name: 5627224039_C
MCF7 cells  48hrs of siNT transfection
Bead-level data: 5627224039_C.txt


title: Sample_23

description:
Sample name: 5627224039_D
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224039_D.txt


title: Sample_06

description:
Sample name: 5627224039_E
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224039_E.txt


title: Sample_24

description:
Sample name: 5627224039_B
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224039_B.txt


title: Sample_13

description:
Sample name: 5627224039_F
MCF7 cells  48hrs of siGREB1 transfection
Bead-level data: 5627224039_F.txt


title: Sample_02

description:
Sample name: 5627224039_A
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224039_A.txt


title: IRCR-GBM11-074

city: Seoul

first: Jinkuk

last: Kim

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: gene expression profile

hyb_protocol: Performed according to the manufacturer's (Affymetrix) recommendations.

data_processing: CEL files were normalized using Robust Multichip Averaging procedure.

source_name: patient 58

label_protocol: Biotinylated RNAs were prepared according to the manufacturer's recommendations.

extract_protocol: Total RNA was extracted according to the manufacturer’s recommendations.

tag: patient

tag: disease state

value: glioblastoma

tag: Stage

value: GBM (IV)

tag: location of lesion

value: Lt. Temporal

tag: gender

value: M

tag: age

tag: progression-free survival (weeks)

tag: overall survival (weeks)

tag: status (0=alive, 1=death, 2=follow-up loss)


title: IRCR-GBM10-011

description: gene expression profile

scan_protocol: Performed according to the manufacturer's (Affymetrix) recommendations.

source_name: patient 49

value: Rt. Parietal

value: F


title: IRCR-GBM10-016

description: gene expression profile

source_name: patient 50

value: Rt. Frontoparietal


title: HFF

city: Dallas

first: young-jae

last: Nam

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: SAMPLE 3

hyb_protocol: Standard affymetrix hybridization protocol

data_processing: The data was processed using RMA using GeneSpring Software (v.2).

label_protocol: Cy3-labeled cRNA were prepared with Ambion MessageAmp kit for affymetrix array

extract_protocol: RNA was extracted using Qiagen Rneasy kit as per manufacturer's protocol

value: human foreskin fibroblasts (HFF)


title: 5F

description: SAMPLE 1

scan_protocol: Standard affymetrix hybridization protocol

source_name: infant_HFF_5 TF

tag: tranduced with

value: 5 transcription factors (Gata4, Hand2, Mef2c, Tbx5, and Myocardin)


title: Adult heart

description: SAMPLE 2

source_name: adult human heart

tag: tissue

value: heart


title: PC-NS09-723

description: gene expression profile

source_name: patient 36

value: R-GBM (IV)

value: Lt. Occipital


title: PC-NS09-740

description: gene expression profile

source_name: patient 35


title: PC-NS09-690

description: gene expression profile

source_name: patient 38


title: PC-NS09-780

description: gene expression profile

source_name: patient 47

value: Lt. Frontal


title: IRCR-GBM10-047

description: gene expression profile

source_name: patient 56


title: PC-NS09-748

description: gene expression profile

source_name: patient 43

value: Rt. Parieto-Occipital


title: IRCR-GBM10-025

description: gene expression profile


title: PC-NS09-696

description: gene expression profile

source_name: patient 39


title: PC-NS09-751

description: gene expression profile

source_name: patient 44


title: IRCR-GBM10-022

description: gene expression profile

source_name: patient 51

value: Rt. Frontal


title: PC-NS09-671

description: gene expression profile


title: PC-NS09-745

description: gene expression profile

source_name: patient 42


title: PC-NS09-727

description: gene expression profile

source_name: patient 41


title: IRCR-GBM10-023

description: gene expression profile

source_name: patient 52


title: PC-NS08-608

description: gene expression profile

source_name: patient 29

value: Lt. Fronto-Parietal


title: PC-NS09-630

description: gene expression profile

source_name: patient 32


title: PC-NS08-592

description: gene expression profile

source_name: patient 28


title: PC-NS08-609

description: gene expression profile

source_name: patient 30

value: Lt. Parietal


title: PC-NS09-672

description: gene expression profile

value: glioblastoma


title: PC-NS09-631

description: gene expression profile

source_name: patient 33

value: GBM (IV)

value: Rt. Temporo-Parietal


title: PC-NS09-660

description: gene expression profile

value: Lt. Temporal

value: M


title: PC-NS09-663

description: gene expression profile

source_name: patient 26

value: Rt. Temporal


title: PC-NS08-577

description: gene expression profile

source_name: patient 23

value: F


title: PC-NS08-541

description: gene expression profile

source_name: patient 18


title: PC-NS08-496

description: gene expression profile

source_name: patient 12


title: PC-NS09-680

description: gene expression profile


title: PC-NS09-633

description: gene expression profile

source_name: patient 34


title: PC-NS08-585

description: gene expression profile


title: PC-NS09-773

description: gene expression profile

source_name: patient 17


title: PC-NS09-732

description: gene expression profile

source_name: patient 21


title: PC-NS08-538

description: gene expression profile


title: PC-NS08-503

description: gene expression profile

source_name: patient 14

value: Both Frontal


title: PC-NS08-567

description: gene expression profile


title: PC-NS08-543

description: gene expression profile

source_name: patient 19


title: PC-NS08-586

description: gene expression profile

source_name: patient 27

value: Rt. sylvian


title: PC-NS08-578

description: gene expression profile

source_name: patient 24

value: Rt thalamus


title: PC-NS08-531

description: gene expression profile

source_name: patient 15

value: GS (IV)

value: Corpus Callosal


title: PC-NS09-647

description: gene expression profile

value: R-GBM (IV)


title: PC-NS08-498

description: gene expression profile

source_name: patient 13

value: Rt. Fronto-Parietal


title: PC-NS07-466

description: gene expression profile

source_name: patient 9


title: PC-NS08-532

description: gene expression profile

source_name: patient 16


title: PC-NS08-568

description: gene expression profile

source_name: patient 7

value: Rt. Frontal


title: PC-NS08-493

description: gene expression profile

source_name: patient 11


title: BoneMarrow_6hr_PBS_rep2

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression after 6hr in PBS-treated bone marrow

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: The data were analyzed and normalized with GeneSpring software. After normalization, the data was baseline transformed to the median of all samples.

source_name: Bone marrow, 6hr, PBS, replicate 2

label_protocol: 500 ng of total RNA was amplified and labeled using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Bone marrow cells were collected from mouse femurs. Total RNA was extracted from bone marrow cells using ISOGEN (Nippon Gene). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Recombinant human erythropoietin (3,000 U/kg body weight) or PBS was injected into the intraperitoneal cavity of ISAM 6 hours before analysis.

tag: genotype

value: Mixed

value: Bone marrow cells

value: Male

value: 10 weeks

value: 6hr PBS


title: PC-NS08-492

description: gene expression profile

source_name: patient 10

value: glioblastoma

value: GBM (IV)

value: Lt. Parieto-Occipital


title: BoneMarrow_6hr_rHuEPO_rep2

description: Gene expression after 6hr in rHuEPO-treated bone marrow

source_name: Bone marrow, 6hr, rHuEPO, replicate 2

tag: treatment

value: 6hr rHuEPO


title: BoneMarrow_6hr_rHuEPO_rep3

source_name: Bone marrow, 6hr, rHuEPO, replicate 3


title: miR Clip Syn-T cells biological rep 2

description:
AGO-Clip Enriched miRNA from Syn-T cells
Hy3 is used as a slide marker

hyb_protocol: The denatured labeled samples were hybridized to microRNA Array slides at 56 ºC for 16 h using an Agilent Hybridization SureHyb chamber and gasket slide followed by stringency wash protocol.

scan_protocol: Stained slides were scanned using GenePix 4000 microarray scanner. Because the design for quality control has to be monitored with green (Hy3-F532) channel for demonstrating existing internal markers on Exiqon 6th generation miRCURY LNA microRNA Arrays, the scanning parameters were set as dual channels (Hy5-F635 for labeled samples with PMTGain 600 and Hy3-532 for internal markers with PMTGain 100 or 600).

data_processing: The images were captured and analyzed by GAL-file (Exiqon Inc, Woburn, MA) which covers 1032 miRNA IDs annotated by version 16.0 of miRBase (http://microrna.sanger.ac.uk). The median of the spot median signals after substraction of relative background signals was used as the expression value. The expression levels were calculated with signals above the background level.

source_name: T cells co-cultured with syngeneic dendritic cells

label_protocol: miRNA microarray experiments were conducted with single label Hy5 on Exiqon 6th generation miRCURY LNA microRNA Array.

growth_protocol: Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection (MACS).

extract_protocol: The total RNA, including miRNA and other small RNA molecules was purified from CLIP agarose beads using miRNeasy Mini Kit according to the manufacturer's instructions and the RNA was verified by an Agilent 2100 Bioanalyzer profile.

value: T lymphocytes

value: AGO


title: BoneMarrow_6hr_rHuEPO_rep1

source_name: Bone marrow, 6hr, rHuEPO, replicate 1


title: PC-NS07-460

description: gene expression profile

value: F


title: BoneMarrow_6hr_PBS_rep1

source_name: Bone marrow, 6hr, PBS, replicate 1


title: PC-NS08-594

description: gene expression profile

source_name: patient 6

value: Rt. Temporal

value: M


title: PC-NS07-464

description: gene expression profile

source_name: patient 8


title: PC-NS07-458

description: gene expression profile


title: PC-NS07-453

description: gene expression profile

source_name: patient 5

value: Lt. Temporal


title: tamox_fasted_rep3

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

hyb_protocol: Affymetrix Mouse Genome 430 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: Liver RNA from fasted/refed LG2KO (tamoxifen treated) mouse

label_protocol: The synthesis of cRNA was performed using the GeneChip® One-Cycle cDNA Synthesis according to the manufacturer' protocol (Affymetrix, Santa Clara, CA, USA). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

extract_protocol: Liver RNAs were extracted using Trifast reagent (Peqlab). For each group, 3 pools of RNA from 3 animals were prepared.

value: liver

tag: diet

value: fasted


title: control_fasted_rep3

source_name: Liver RNA from fasted control mouse

tag: strain

value: control


title: macrophage-MCSF-norep

city: Frederick

first: Richard

middle: A

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

description: treatment

hyb_protocol: Labeled cRNA was hybridized to the Affymetrix Exon 1.0 microarray according to the manufacturer's recommended standard protocol.

scan_protocol: Hybridized Affymetrix EXON human microarrays were scanned according to the manufacturer's recommended standard protocol.

data_processing:
Gene expression profiles were analyzed using Partek Genomic Sutie
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

source_name: monocyte-derived macrophage induced with MCSF

label_protocol: cRNA was labelled according  to the manufacturer's recommended standard protocol for the Affymetrix Exon 1.0 microarray .

growth_protocol: CD14+ monocytes were isolated from PBMC of healthy donors. Isolated CD14+ monocytes were plated in 24-well plates at 0.7× 106 cells/well. Monocytes were stimulated with 25 ng/ml M-CSF alone or in combination with 25-100 ng/ml IL-27 in macrophage serum-free medium (Invitrogen) for 7 days. MDMs were then maintained in DMEM (Invitrogen) containing 10% FBS (HyClone Laboratories), 25mM HEPES (Quality Biology) and 5 µg/ml Gentamicin (Invitrogen) prior to use in experiments.

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

tag: cell type

value: macrophage

value: untreated


title: tamox_fasted_rep2


title: PC-NS07-448

description: gene expression profile

source_name: patient 4


title: PC-NS08-559

description: gene expression profile

source_name: patient 3

value: R-GBM (IV)

value: Rt. Frontal


title: tamox_fasted_rep1


title: PC-NS07-437

description: gene expression profile

value: glioblastoma


title: control_fasted_rep1


title: tamox_refed_rep3

value: fasted/refed


title: Carcinoma_6

city: South San Francisco

first: Zhaoshi

last: Jiang

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Agilent Feature Extraction software version 10.7 was used to create feature extraction files. The normal exponential convolution model was applied for the background correction, Loess and quantile were applied for within array and cross-array normalization. Gene differential expression was analyzed by the package of limma.

source_name: breast cancer tissue

label_protocol: Samples listed under SPR784: total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. Samples listed under SPR799: all samples were labeled by two-rounds of amplification using Ambion's MessageAmpII aRNA Amplification kit and Agilent's QuickAmp Labeling kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

treatment_protocol: We treated early carcinomas (2 months post-transplant) with docetaxel + doxorubicin + cyclophosphamide, and the resulting tumors undergo 90% tumor shrinkage.

tag: sampleID

value: Carcinoma

tag: strain/background

value: FVB/n

tag: experimentid

tag: diagnosis

value: breast cancer

source_name: Universal mouse reference (UMR) from Stratagene

tag: reference

value: pooled mouse reference RNA


title: tamox_refed_rep1


title: BoneMarrow_Untreated_rep1

description: Gene expression in untreated bone marrow

source_name: Bone marrow, untreated, replicate 1

value: Mixed

value: Bone marrow cells

tag: gender

value: Male

value: 10 weeks


title: Disseminated cells_6

value: Disseminated cells


title: control_refed_rep3

source_name: Liver RNA from fasted/refed control mouse

value: liver


title: control_refed_rep2

value: control


title: control_fasted_rep2

value: fasted


title: Carcinoma_5


title: tamox_refed_rep2


title: Metastases_5

value: Metastases


title: Carcinoma_4


title: PC-NS07-436

description: gene expression profile

source_name: patient 2

tag: patient

tag: disease state

tag: Stage

value: GBM (IV)

tag: location of lesion

value: Lt. Frontal

value: F

tag: age


title: macrophage-MCSF-IL27-norep

description: treatment

source_name: monocyte-derived macrophage induced with MCSF and IL-27

treatment_protocol: Monocytes were stimulated with 25 ng/ml M-CSF alone or in combination with 25-100 ng/ml IL-27 in macrophage serum-free medium (Invitrogen) for 7 days.

value: macrophage


title: PC-NS07-428

description: gene expression profile

source_name: patient 1

value: glioblastoma

value: Rt. Frontal

value: M

tag: progression-free survival (weeks)

tag: overall survival (weeks)

tag: status (0=alive, 1=death, 2=follow-up loss)


title: Skin_hs_normal 2

city: Melbourne

first: Charbel

last: Darido

state: Vic

address: 99 Commercial road

department: Medicine

country: Australia

institute: Monash University

description:
afmi2944-2-2N-160810
miRNA expression

hyb_protocol: Hybridization was performed according to Affymetrix-recommended procedures

scan_protocol: Scanning was performed according to Affymetrix-recommended procedures. The fluorecence data is extracted at 1.4 micron pixel resolution using the Affymetrix 3000 7G scanner

data_processing: Data processing was performed using the Partek GS software

source_name: RNA from normal human skin

label_protocol: The 3’ ends of the RNA molecules were tailed and biotin-labeled using the mirVana™ miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit’s dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).

growth_protocol: Surgical specimens of SCC resected from patients (including tumour and adjacent normal tissue) were snap frozen and stored at -80 C.

extract_protocol: Differential microRNA expression in two normal skin and two squamous cell carcinoma (SCC) samples were analysed using Genechip miRNA array (Affymetrix, CA, USA) and the data were analysed using the Partek GS software.

treatment_protocol: Total RNA was isolated from two SCC primary tissue samples and their matched normal skin controls. RNA extraction was performed using Trizol (Invitrogen) according to the manufacturers instructions.

tag: tissue

value: normal skin


title: Skin_hs_tumor 2

description:
afmi2944-4-4T-160810
miRNA expression

source_name: RNA from human skin SCC

value: skin SCC


title: Skin_hs_tumor 1

description:
afmi2944-3-3T-160810
miRNA expression


title: Adenoma_4

value: Adenoma

value: FVB/n

value: breast cancer

value: pooled mouse reference RNA


title: Adenoma_3


title: Skin_hs_normal 1

description:
afmi2944-1-1N-160810
miRNA expression


title: Adenoma_5


title: Disseminated cells_5

value: Disseminated cells


title: Metastases_4


title: Wild-type GMP

city: Suita

first: Takashi

last: Satoh

state: Osaka

address: 3-1 Yamada-oka

department: RIMD

institute: Osaka university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Gene CHIP scanner 3000.

data_processing: The data were analyzed with RMA using R program

source_name: Wild-type GMP

label_protocol: Biotinylated cRNA were prepared by NuGEN Ovation system according to the manufactuerer's inscrution.

growth_protocol: Mouse progenitor cells were sorted.  No treatment

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

treatment_protocol: no treatment

tag: strain

value: mixed background C57BL6J/129SV

tag: genotype/ variation

value: wild-type unstimulated

value: granulocyte monocyte progenitor


title: Adenoma_2

tag: sampleID


title: Trib1-/- GMP

source_name: Trib1-/- GMP

value: Trib1-/- unstimulated

tag: cell type


title: Trib1-/- MDP

source_name: Trib1-/- MDP

value: macrophage dendritic cell


title: Wild-type MDP

source_name: Wild-type MDP


title: HCC827 100nM AUY 24h

city: Santa Monica

first: Habib

last: Hamidi

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

hyb_protocol: Equal amounts of labeled treated cell and untreated cell  RNA were mixed and hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K (G4112F) microarray slides at 65 C for 17 hr. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization;: (1) local background used, (2) special detrend OFF, (3) adjust background globally OFF, (4) red autoestimate OFF, and (5) green autoestimate OFF. Rosetta Resolver (v.7.2) was used for data analysis.

source_name: HCC827 100nM AUY 24h

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions.

growth_protocol: All 8 cell lines were obtained from ATCC.  A549 was cultured in HAM’s F12 (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin G-streptomycin-fungizone solution (PSF, Irvine Scientific, Santa Ana, CA).  H1155, and H1435  were grown in ACL-4. H1793 were grown in HITES supplemented with 5% heat-inactivated FBS and PSF. The remaining lines were cultured in RPMI 1640 (Cellgro, Manassas, VA) supplemented with 10% heat-inactivated FBS, 2 mmol/L glutamine (Invitrogen, Carlsbad, CA), and PSF.

extract_protocol: Total RNA  was extracted using the Rneasy Kit(Qiagen), treated with DNAse I (DNA-free, Ambion), and cDNA produced using SuperScript II Reverse Transcriptase (Invitrogen).

treatment_protocol: Cells were grown to log phase and treated with media alone or with media containing  50nM or 100nM of AUY for 24 hours.

tag: cell line

value: non-small cell lung cancer (NSCLC)

tag: treatment

value: Treated with 100nM of AUY for 24 hours

value: Control - Untreated


title: Metastases_3

value: Metastases

tag: strain/background

tag: experimentid

tag: diagnosis

tag: reference


title: Prdm14(+/+): Serum (day2), rep1

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

source_name: Prdm14(+/+) ESCs

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: mESCs and mESC-like cells are culured on MEF in the following medium. 2i: N2B27 medium with 2i (PD0325901, 0.4 uM: Stemgent, San Diego, CA; CHIR99021, 3 uM: Stemgent) and LIF (1000 u/ml) .

extract_protocol: Total RNA was isolated with Qianeg RNeasy Micro according to manufacture's instruction.

treatment_protocol: Cells were cultured 2 days on MEF under the following conditions. (2) Serum: GMEM containing 2 mM L-glutamine (cat#11710-035; Invitrogen) with 1xMEM non-essential amino acids (cat#11140-050; Invitrogen), 1 mM sodium pyruvate (cat#11360-070; Invitrogen), 100uM 2-mercaptoethanol (cat#21985-023; Invitrogen), 1x10^3 units/ml LIF (cat#ESG1107;  Chemicon), and 20% FBS (Stem Cell Science).  (3) Serum without LIF: The same as the Serum medium except for removal of LIF.  (4) Serum+MEK inhibitor: The same as Serum excepto for addition of 0.4 uM MEK inihibitor PD0325901)

tag: gender

value: male

value: ESCs

tag: genotype/variation

value: No genetic modification

tag: culture conditions

value: Serum (day2)


title: Prdm14(+/+): Serum+MEK inhibitor (day2), rep1

value: Serum+MEK inhibitor (day2)


title: Prdm14(-/-)+AGP14: Serum (day2), rep1

source_name: Prdm14(-/-)+AGP14 ESC-like cells

value: ESC-like cells

value: Prdm14 Knockout, pPyCAG-AGP14 transgene


title: Prdm14(-/-): Serum (day2), rep2

source_name: Prdm14(-/-) ESC-like cells

value: Prdm14 Knockout


title: HCC827 50nM AUY 24h

source_name: HCC827 50nM AUY 24h

value: Treated with 50nM of AUY for 24 hours


title: Prdm14(-/-): Serum+MEK inhibitor (day2), rep1


title: Prdm14(-/-): Serum+MEK inhibitor (day2), rep2


title: Prdm14(+/+): Serum+MEK inhibitor (day2), rep2


title: Metastases_2

source_name: breast cancer tissue

value: FVB/n

value: breast cancer

source_name: Universal mouse reference (UMR) from Stratagene

value: pooled mouse reference RNA


title: H23 50nM AUY 24h

source_name: H23 50nM AUY 24h


title: Prdm14(-/-)+AGP14: Serum (day2), rep2


title: Prdm14(-/-): Serum (day2), rep1


title: control_refed_rep1

source_name: Liver RNA from fasted/refed control mouse

value: liver

tag: genotype

value: control

tag: diet

value: fasted/refed


title: Prdm14(+/+): Serum (day2), rep2


title: Metastases_1


title: Disseminated cells_3

value: Disseminated cells


title: H23 100nM AUY 24h

source_name: H23 100nM AUY 24h

value: non-small cell lung cancer (NSCLC)

value: Treated with 100nM of AUY for 24 hours

value: Control - Untreated


title: Disseminated cells_4


title: Prdm14(-/-): Serum without LIF (day2), rep1

value: male

value: Serum without LIF (day2)


title: H2172 50nM AUY 24h


title: Prdm14(+/+): Serum without LIF (day2), rep1

value: ESCs

value: No genetic modification


title: Epiblast-like cells (day3), rep2

source_name: Prdm14 (+/+) Epiblast-like cells (day3)

value: epiblast like cells (EpiLCs)


title: Prdm14(-/-): Serum without LIF (day2), rep2

value: ESC-like cells

value: Prdm14 Knockout


title: Prdm14(-/-)+AGP14: Serum without LIF (day2), rep1

value: Prdm14 Knockout, pPyCAG-AGP14 transgene


title: Carcinoma_3

value: Carcinoma

value: FVB/n

value: breast cancer


title: Epiblast-like cells (day2), rep1

source_name: Prdm14 (+/+) Epiblast-like cells (day2)


title: H1793 100nM AUY 24h


title: Epiblast-like cells (day3), rep1


title: Prdm14(+/+): 2i, rep1


title: Prdm14(+/+): 2i, rep2


title: Prdm14(-/-)+AGP14: 2i, rep2


title: Prdm14(-/-)+AGP14: Serum without LIF (day2), rep2


title: Epiblast-like cells (day2), rep2


title: Disseminated cells_1

value: pooled mouse reference RNA


title: H1975 50nM AUY 24h

value: Treated with 50nM of AUY for 24 hours


title: Prdm14(-/-): 2i, rep1


title: H1975 100nM AUY 24h


title: Prdm14(-/-): 2i, rep2


title: Disseminated cells_2

value: Disseminated cells


title: Carcinoma_2


title: H1793 50nM AUY 24h

value: non-small cell lung cancer (NSCLC)


title: H2172 100nM AUY 24h

value: Treated with 100nM of AUY for 24 hours


title: Carcinoma_1


title: PC-NS09-626

description: gene expression profile

source_name: patient 31

tag: patient

tag: disease state

value: glioblastoma

tag: Stage

value: GBM (IV)

tag: location of lesion

value: Lt. Fronto-Temporal

value: M

tag: age

tag: progression-free survival (weeks)

tag: overall survival (weeks)

tag: status (0=alive, 1=death, 2=follow-up loss)


title: Adenoma_1

tag: sampleID

tag: tissue

value: Adenoma

tag: strain/background


title: H1435 100nM AUY 24h

tag: cell line

tag: treatment

value: Control - Untreated


title: Prdm14(-/-)+AGP14: 2i, rep1

tag: strain

tag: gender

value: male

tag: cell type

value: ESC-like cells

tag: genotype/variation


title: A549 50nM AUY 24h

source_name: A549 50nM AUY 24h


title: H1435 50nM AUY 24h


title: H2405

hyb_protocol: Equal amounts of labeled cell line specific and reference mix (consisting of equal amounts of RNA from 45 NSCLC cell lines) RNA were mixed and hybridized to Agilent 1A Oligo V.2 microarray slides at 65 C for 17 hr. After hybridization, slides were washed sequential.

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization;: (1) local background used, (2) special detrend OFF, (3) adjust background globally OFF, (4) red autoestimate OFF, and (5) green autoestimate OFF. Rosetta Resolver (v.7.2) was used for data analysis.

growth_protocol: All 34 cell lines were obtained from ATCC.  A549 was cultured in HAM’s F12 (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin G-streptomycin-fungizone solution (PSF, Irvine Scientific, Santa Ana, CA). Calu-3 was grown in EMEM (ATCC) supplemented with 10% heat-inactivated FBS and 1% PSF. H1155, H1435, H1581 (10% FBS), and H2286 and H2405 (2% BSA) were grown in ACL-4. H1793, H1836, H2342, and H810 were grown in HITES supplemented with 5% heat-inactivated FBS and PSF. The remaining lines were cultured in RPMI 1640 (Cellgro, Manassas, VA) supplemented with 10% heat-inactivated FBS, 2 mmol/L glutamine (Invitrogen, Carlsbad, CA), and PSF

treatment_protocol: Cell were grown to log phase.

source_name: in-house reference mix (consisting of equal amounts of RNA from 45 NSCLC cell lines)

tag: reference


title: Regressed tumor_3

value: Regressed tumor

value: chemo

tag: experimentid

tag: diagnosis


title: H2286

value: reference mix (consisting of equal amounts of RNA from 45 NSCLC cell lines)


title: Calu-1


title: H1155 100nM AUY 24h


title: Resistant tumor_2

value: Resistant tumor

value: FVB/n

value: breast cancer


title: MLL-AF9 LGMP N1-IC+ replicate 2

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

description: 6 days after tamoxifen last injection

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.

source_name: Lineage negative, cKit+, Sca1-, YFP+, CD34+, FcgRII/III+  bone marrow cells from MLL-AF9 EF1αwt/lsl-N1-IC ROSAwt/CreERT2 mouse

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

extract_protocol: Qiagen RNEasy Plus mini Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: 12 week old wt lethaly irradiated mice were transplanted with 50000 cKit+ MLL-AF9-IRES-YFP infected cells from MLL-AF9 EF1αwt/wt ROSAwt/CreERT2 or MLL-AF9 EF1αwt/lsl-N1-IC ROSAwt/CreERT2 mice + 250000 support wt total bone marrow cells. 4 weeks after transplant mice were injected 2 times with tamoxifen (0.2mg/g body weight) every other day. Mice were sacrificed and analyzed 6days after last injection. LGMP were flow purified for RNA extraction.

value: female

tag: genotype

value: MLL-AF9 EF1αwt/lsl-N1-IC ROSAwt/CreERT2


title: Resistant tumor_4

value: pooled mouse reference RNA


title: MLL-AF9 LGMP N1-IC+ replicate 3

description: 6 days after tamoxifen last injection

value: Lineage negative, cKit+, Sca1-, YFP+, CD34+, FcgRII/III+  bone marrow cells


title: Regressed tumor_5


title: H1435

value: non-small cell lung cancer (NSCLC)


title: H1155 50nM AUY 24h

value: Treated with 50nM of AUY for 24 hours


title: Regressed tumor_4


title: MLL-AF9 LGMP WT replicate3

description: 6 days after tamoxifen last injection

source_name: Lineage negative, cKit+, Sca1-, YFP+, CD34+, FcgRII/III+  bone marrow cells from MLL-AF9 EF1αwt/wt ROSAwt/CreERT2 mouse

value: MLL-AF9 EF1αwt/wt ROSAwt/CreERT2


title: Prdm14(+/+): Serum without LIF (day2), rep2

value: ESCs

value: No genetic modification

tag: culture conditions

value: Serum without LIF (day2)


title: A549 100nM AUY 24h

value: Treated with 100nM of AUY for 24 hours

value: Control - Untreated


title: Resistant tumor_1

value: chemo


title: Control_6

value: Control_breast cancer

value: control


title: HCC827

value: reference mix (consisting of equal amounts of RNA from 45 NSCLC cell lines)


title: MLL-AF9 LGMP N1-IC+ replicate 1

description: 6 days after tamoxifen last injection


title: MLL-AF9 LGMP WT replicate2

description: 6 days after tamoxifen last injection

value: male


title: Resistant tumor_3

value: Resistant tumor

value: FVB/n

value: breast cancer


title: Regressed tumor_6

value: Regressed tumor

value: pooled mouse reference RNA


title: H1581

value: non-small cell lung cancer (NSCLC)


title: Control_5


title: H810


title: MLL-AF9 LGMP WT replicate1

description: 6 days after tamoxifen last injection

value: Lineage negative, cKit+, Sca1-, YFP+, CD34+, FcgRII/III+  bone marrow cells

value: MLL-AF9 EF1αwt/wt ROSAwt/CreERT2


title: Control_3


title: H2342


title: H23


title: Calu-3


title: Control_4


title: H838


title: H520


title: H1944


title: Control_2


title: A427


title: Regressed tumor_2


title: H1568


title: H1651


title: 1021 grown in MMglutamate biological replicate 3

city: Pullman

first: Jennifer

last: Rice

state: WA

address: 100 Dairy Road

institute: WSU

description: Gene expression data from 1021 grown in MMglutamate

hyb_protocol: Following fragmentation, labeled cDNA was hybridized at 48C for 16 hr in the GeneChip Hybridization Oven 640 according to the manufacturer's recommendations.  Hybridized arrays were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: Processed arrays were scanned using a 121 GeneChip 3000 7G scanner.

data_processing: Array quality was assessed, and images were quantified using GeneChip Operating Software v1.2 (Affymetrix).  The data were viewed and analyzed using Partek Genomic Suite 6.5 beta software (Partek Incorporated).  The genes with absolute expression ratio ≥2 (p < 0.05) were considered induced or repressed.  The list of differentially expressed genes was created using analysis of variance (ANOVA).

organism: Sinorhizobium meliloti

source_name: 1021 grown in MMglutamate

label_protocol: Single-stranded cDNA was end labeled with biotin using the GeneChip DNA Labeling Reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega).

growth_protocol: Liquid cultures were grown at 30C with agitation at 250rpm to mid-log phase (0.5-0.6 OD600)

extract_protocol: Extraction of total RNA was performed using the Qiagen RNeasy Kit according to the protocol published by Barnett et al. (2004).

treatment_protocol: Cell processes were halted by addition of 1/9th sample volume of 5% buffer equilibrated phenol (pH 7.4) in ethanol, and cultures were harvested by centrifugation at 15000rpm for 1 minute. Total RNA was processed according to the Affymetrix User Guide, Prokaryotic Sample and Array Processing.

tag: phenotype in plant

value: Fix+Eff+


title: Botrytis cinerea _bmp1 mutant_3.5h_b

city: Kaiserslautern

first: Michaela

last: Leroch

department: Phytopathology

country: Germany

institute: University of Kaiserslautern

description: This sample is of bmp1 deletion mutant in wild-type B0510 genetic backgound in the germination stage. It is the second of three bmp1 biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (pair files) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Botrytis cinerea

source_name: Botrytis cinerea bmp1 deletion mutant in B05.10 background; 3.5h incubated

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Botrytis cinerea wild-type strain B05.10 and bmp1 deletion mutant were incubated in Gamborg minimal medium containg 10mM fructose on apple wax coated Petri dishes. After different time points the material was collected and used for total RNA extraction.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Hilden, Germany) and the RNAprotect reagent (Qiagen) by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

value: bmp1 deletion mutant

tag: phenotype

value: apathogenic, no appressoria

tag: developmental stage

value: germination stage


title: H460


title: GlnD mutation grown in MMglutamate biological replicate 3

description: Gene expression data from GlnD mutation grown in MMglutamate

source_name: GlnD mutation grown in MMglutamate

value: Fix+Eff-


title: H1299


title: GlnD mutation grown in MMglutamate biological replicate 2


title: Botrytis cinerea _bmp1 mutant_3.5h_a

description: This sample is of bmp1 deletion mutant in wild-type B0510 genetic backgound in the germination stage. It is the first of three bmp1 biological replicates used in this experiment, each from separate cultures.


title: Botrytis cinerea _bmp1 mutant_3.5h_c

description: This sample is of bmp1 deletion mutant in wild-type B0510 genetic backgound in the germination stage. It is the third of three bmp1 biological replicates used in this experiment, each from separate cultures.


title: 1021 grown in MMglutamate biological replicate 2


title: GlnD mutation grown in MMglutamate biological replicate 1


title: Regressed tumor_1

tag: sampleID

value: chemo


title: H2172

tag: tissue


title: Control_1

value: Control_breast cancer

value: control

tag: strain/background


title: 1021 grown in MMNH4 biological replicate 4

description: Gene expression data from 1021 grown in MMNH4

source_name: 1021 grown in MMNH4


title: H2110

tag: cell line

value: reference mix (consisting of equal amounts of RNA from 45 NSCLC cell lines)


title: SHP77


title: GlnBGlnK deletion grown in MMglutamate biological replicate 3

description: Gene expression data from GlnBGlnK deletion grown in MMglutamate

source_name: GlnBGlnK deletion grown in MMglutamate


title: 1021 grown in MMglutamate biological replicate 1


title: H596


title: Botrytis cinerea _B0510_15h_c

description: This sample is of wild-type B0510 in the mycelium stage. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea wild-type strain B05.10; 15h incubated

value: Wild-type

value: normal

value: mycelium stage


title: Botrytis cinerea _B0510_15h_b

description: This sample is of wild-type B0510 in the mycelium stage. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: H358


title: A549


title: GlnBGlnK deletion grown in MMglutamate biological replicate 2


title: Botrytis cinerea _B0510_4h_c

description: This sample is of wild-type B0510 in the appressorial stage. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea wild-type strain B05.10; 4h incubated

value: appressorial stage


title: Botrytis cinerea _B0510_4h_a

description: This sample is of wild-type B0510 in the appressorial stage. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Botrytis cinerea _B0510_15h_a

description: This sample is of wild-type B0510 in the mycelium stage. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: GlnBGlnK deletion grown in MMglutamate biological replicate 1


title: 1021 grown in MMNH4 biological replicate 3


title: 1021 grown in MMNH4 biological replicate 1


title: Botrytis cinerea _B0510_2.5h_c

description: This sample is of wild-type B0510 in the germination stage. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea wild-type strain B05.10; 2.5h incubated


title: 1021 grown in MMNH4 biological replicate 2


title: GlnD mutation grown in MMNH4 biological replicate 3

description: Gene expression data from GlnD mutation grown in MMNH4

source_name: GlnD mutation grown in MMNH4


title: H1793


title: H2135


title: Botrytis cinerea _B0510_4h_b

description: This sample is of wild-type B0510 in the appressorial stage. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Calu-6


title: Botrytis cinerea _B0510_2.5h_a

description: This sample is of wild-type B0510 in the germination stage. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Botrytis cinerea _B0510_1h_c

description: This sample is of wild-type B0510 in the swelling stage. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea wild-type strain B05.10; 1h incubated

value: conidia in the swelling stage


title: H522

value: non-small cell lung cancer (NSCLC)


title: GlnD mutation grown in MMNH4 biological replicate 1


title: Botrytis cinerea _B0510_2.5h_b

description: This sample is of wild-type B0510 in the germination stage. It is the secondof three wild-type biological replicates used in this experiment, each from separate cultures.


title: H1563


title: HCT116 3 days hypoxia exp A

first: Nicole

last: Fer

institute: Frederick National Laboratory for Cancer Research

description: HCT116 3 days hypoxia exp A.

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

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

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

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: Subconfluent HCT116 were washed with PBS once and media without serum was added for 24 hours.

extract_protocol: Total RNA was extracted using Qiagen extraction kits.

treatment_protocol: Serum starved HCT116 were placed under normoxia or hypoxia for 72 hours.

tag: disease state

value: colon cancer

value: HCT116 colon cancer cells

tag: treatment protocol

value: hypoxia


title: GlnD mutation grown in MMNH4 biological replicate 2

tag: strain


title: THP1 Dll4-Fc treated replicate 3

description: 60nM Dll4-Fc treated

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix)

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Genespring GX program. No further adjustments were made to the data in the table.

source_name: THP1 cell line

growth_protocol: Grown in RPMI + 10% FCS + 1% Glutamax + 1% Pen/Strep

treatment_protocol: cultured  on plate coated with 30 nM Dll4-Fc or vehicle for 48 hours prior to RNA extraction

tag: treatment

value: 60nM Dll4-Fc treated

tag: cell type

value: Acute Myeloid leukemia cell line


title: HCT116 3 days hypoxia exp B

description: HCT116 3 days hypoxia exp B.


title: GlnBGlnK deletion grown in MMNH4 biological replicate 2

description: Gene expression data from GlnBGlnK deletion grown in MMNH4

source_name: GlnBGlnK deletion grown in MMNH4

value: Fix+Eff+


title: GlnBGlnK deletion grown in MMNH4 biological replicate 3


title: HCT116 3 days normoxia exp B

description: HCT116 3 days normoxia exp B.

value: normoxia


title: HCT116 3 days normoxia exp A

description: HCT116 3 days normoxia exp A.


title: H1975

tag: reference


title: Botrytis cinerea _B0510_1h_a

description: This sample is of wild-type B0510 in the swelling stage. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: GlnBGlnK deletion grown in MMNH4 biological replicate 1


title: H1155


title: H1836


title: Botrytis cinerea _B0510_0h_c

description: This sample is of wild-type B0510 in the dormant stage. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea wild-type strain B05.10 dormant spores

value: dormant spore stage


title: H2073


title: Botrytis cinerea _B0510_1h_b

description: This sample is of wild-type B0510 in the swelling stage. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Botrytis cinerea _B0510_0h_b

description: This sample is of wild-type B0510 in the dormant stage. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Daphnia magna Zinc rep1

status: Public on Jan 17 2013

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

institute: University of Liverpool

description: Control-Media

hyb_protocol: Agilent 1 colour Quick-Amp Labelling Protocol

scan_protocol: The scanning and feature extraction were performed using GenePix 4000B (Axon, USA) and GenePix Pro 6.0 software (Axon, USA).

data_processing: Raw microarray data was read and normalized against their respective controls (listed in the description field) using loess within the statistical environment R using the marray and limma packages.

organism: Daphnia magna

source_name: Daphnia magna exposed for 24h

growth_protocol: D. Magna were obtained from Aquatic Research Organisms (Hampton, NH) and cultured at 20C in modified COMBO medium. Culturing medium was renewed three times a week, and Pseudokirchneriella subcapitata (formerly Selenastrum capricornutu) and YCT added for food.

extract_protocol: After 24 h exposure, total RNA was extracted with Trizol (Invitrogen, CA, USA) according to the standard method.

treatment_protocol: Twenty daphnids (Two-week old) were exposed to 1 L of COMBO medium containing 1/10 LC50 concentration of each chemical with four replicates

tag: chemical

value: Zinc

tag: age

value: 14 days

tag: exposure time

tag: dose


title: Daphnia magna Trichloroethylene rep4

description: Control-Ethanol

label_protocol: Agilent 1 colour Quick-Amp Labelling Protocol

value: Trichloroethylene


title: Daphnia magna Toxaphene rep1

description: Control-Ethanol

value: Toxaphene


title: Daphnia magna Toxaphene rep3

description: Control-Ethanol


title: Daphnia magna Zinc rep4

description: Control-Media


title: THP1 untreated replicate 1

description: Untreated

value: Untreated


title: Daphnia magna Trichloroethylene rep1

description: Control-Ethanol


title: Daphnia magna Zinc rep3

description: Control-Media


title: Daphnia magna Toxaphene rep2

description: Control-Ethanol


title: Daphnia magna Zinc rep2

description: Control-Media


title: Daphnia magna Trichloroethylene rep2

description: Control-Ethanol


title: Botrytis cinerea _B0510_0h_a

description: This sample is of wild-type B0510 in the dormant stage. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

tag: genotype

value: Wild-type

value: normal


title: THP1 Dll4-Fc treated replicate 1

description: 60nM Dll4-Fc treated


title: Daphnia magna Toxaphene rep4

description: Control-Ethanol


title: THP1 untreated replicate 3

description: Untreated


title: THP1 untreated replicate 2

description: Untreated


title: H1385

source_name: in-house reference mix (consisting of equal amounts of RNA from 45 NSCLC cell lines)


title: Daphnia magna Trichloroethylene rep3

description: Control-Ethanol


title: Daphnia magna Toluene rep2

description: Control-Ethanol

value: Toluene


title: 559-Prim

type: genomic

description: copy number profile

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

molecule: genomic DNA

source_name: Human glioblastoma tissue PC-NS08-559

label_protocol: Performed according to the manufacturer's (Agilent) recommendations. 500ng gDNA was used as input.

growth_protocol: For xenograft, acutely dissociated GBM cells were stereotactically (2mm left and 1mm anterior to the bregma, 2mm deep from the dura) injected into the brains of NOG mice (Ito et al., 2002) within 12 hours after surgery (2.5X104-1.0X105 cells in 10μl HBSS for each mice, n=4-9 for each sample).

extract_protocol: gDNA was extracted by using QIAmp DNA mini kit (QIAgen).

tag: gender

value: female

value: GBM

source_name: Control

value: male


title: Daphnia magna Toluene rep3

description: Control-Ethanol


title: Daphnia magna Selenium rep2

description: Control-Media

value: Selenium


title: Daphnia magna Pyripoxyfen rep2

description: Control-Ethanol

value: Pyripoxyfen


title: Daphnia magna Toluene rep1

description: Control-Ethanol


title: Daphnia magna Pyripoxyfen rep1

description: Control-Ethanol


title: Daphnia magna Silver rep2

description: Control-Media

value: Silver


title: 559-Xeno

description: copy number profile

hyb_protocol: Performed according to the manufacturer's (Agilent) recommendations.

source_name: Orthotopic xenograft tissue derived from PC-NS08-559


title: Daphnia magna Selenium rep3

description: Control-Media


title: Daphnia magna Pyripoxyfen rep3

description: Control-Ethanol


title: Daphnia magna Silver rep4

description: Control-Media


title: Daphnia magna Selenium rep4

description: Control-Media


title: Daphnia magna Silver rep1

description: Control-Media


title: Daphnia magna Phenanthrene rep4

description: Control-DMSO

value: Phenanthrene


title: Daphnia magna PonasteroneA rep1

description: Control-Ethanol

value: PonasteroneA


title: Daphnia magna Phenol rep2

description: Control-Media

value: Phenol


title: Daphnia magna Phenol rep3

description: Control-Media


title: Daphnia magna Phenol rep1

description: Control-Media


title: Daphnia magna PonasteroneA rep4

description: Control-Ethanol


title: Daphnia magna Phenol rep4

description: Control-Media


title: Daphnia magna Pyripoxyfen rep4

description: Control-Ethanol


title: Daphnia magna Silver rep3

description: Control-Media


title: Daphnia magna Selenium rep1

description: Control-Media


title: Daphnia magna PonasteroneA rep2

description: Control-Ethanol


title: Daphnia magna Phenanthrene rep3

description: Control-DMSO


title: Daphnia magna Toluene rep4

description: Control-Ethanol


title: Daphnia magna Phenanthrene rep2

description: Control-DMSO


title: Daphnia magna PonasteroneA rep3

description: Control-Ethanol


title: THP1 Dll4-Fc treated replicate 2

description: 60nM Dll4-Fc treated

value: 60nM Dll4-Fc treated

value: Acute Myeloid leukemia cell line


title: Daphnia magna Phenanthrene rep1

description: Control-DMSO

value: 14 days


title: Daphnia magna Permethrin rep3

description: Control-DMSO

value: Permethrin


title: Daphnia magna Parathion rep4

description: Control-Acetone

value: Parathion


title: Daphnia magna Permethrin rep4

description: Control-DMSO


title: Daphnia magna Parathion rep3

description: Control-Acetone


title: Daphnia magna Nonylphenol rep4

description: Control-Ethanol

value: Nonylphenol


title: Daphnia magna Parathion rep2

description: Control-Acetone


title: Daphnia magna Nonylphenol rep3

description: Control-Ethanol


title: Daphnia magna Parathion rep1

description: Control-Acetone


title: Daphnia magna MTBE rep3

description: Control-Media

value: MTBE


title: Daphnia magna Nonylphenol rep2

description: Control-Ethanol


title: Daphnia magna Nickel rep1

description: Control-Media

value: Nickel


title: Daphnia magna Nickel rep4

description: Control-Media


title: Daphnia magna Nickel rep2

description: Control-Media


title: Daphnia magna MTBE rep4

description: Control-Media


title: Daphnia magna Nonylphenol rep1

description: Control-Ethanol


title: Daphnia magna MTBE rep2

description: Control-Media


title: Daphnia magna Permethrin rep1

description: Control-DMSO


title: Daphnia magna MTBE rep1

description: Control-Media


title: Daphnia magna Methylfarnesoate rep1

description: Control-Methanol

value: Methylfarnesoate

value: 20 nM mg/L


title: Daphnia magna Methylfarnesoate rep3

description: Control-Methanol


title: Daphnia magna Methylfarnesoate rep2

description: Control-Methanol


title: Daphnia magna Methylfarnesoate rep4

description: Control-Methanol


title: Daphnia magna Methoxychlor rep4

description: Control-Ethanol

value: Methoxychlor


title: Daphnia magna Nickel rep3

description: Control-Media


title: Daphnia magna Methoxychlor rep3

description: Control-Ethanol


title: Daphnia magna Permethrin rep2

description: Control-DMSO


title: Daphnia magna Manganese rep4

description: Control-Media

value: Manganese


title: Daphnia magna Manganese rep3

description: Control-Media


title: Daphnia magna Methoxychlor rep2

description: Control-Ethanol


title: Daphnia magna Methoxychlor rep1

description: Control-Ethanol


title: Daphnia magna Manganese rep2

description: Control-Media


title: Daphnia magna Lamda Cyhalothrin rep1

description: Control-Ethanol

value: Lamda Cyhalothrin


title: Daphnia magna Diazinon rep1

description: Control-Acetone

value: Diazinon


title: Daphnia magna Dichlorobenzene rep1

description: Control-Ethanol

value: Dichlorobenzene


title: Daphnia magna Manganese rep1

description: Control-Media


title: Daphnia magna Lamda Cyhalothrin rep4

description: Control-Ethanol


title: Daphnia magna Dichlorobenzene rep3

description: Control-Ethanol


title: Daphnia magna Diazinon rep3

description: Control-Acetone


title: Daphnia magna Copper rep2

description: Control-Media

value: Copper


title: Daphnia magna Copper rep1

description: Control-Media


title: Daphnia magna Dichlorobenzene rep2

description: Control-Ethanol


title: Daphnia magna Lamda Cyhalothrin rep3

description: Control-Ethanol


title: Daphnia magna Copper rep4

description: Control-Media


title: Daphnia magna Dichlorobenzene rep4

description: Control-Ethanol


title: Daphnia magna Lamda Cyhalothrin rep2

description: Control-Ethanol


title: Daphnia magna Copper rep3

description: Control-Media


title: Daphnia magna Chlorpyrifos rep3

description: Control-Methanol

value: Chlorpyrifos


title: Daphnia magna Chromium rep3

description: Control-Media

value: Chromium


title: Daphnia magna Diazinon rep2

description: Control-Acetone


title: Daphnia magna Chlorpyrifos rep2

description: Control-Methanol


title: Daphnia magna Chromium rep4

description: Control-Media


title: Daphnia magna Chloroform rep3

description: Control-Ethanol

value: Chloroform


title: Daphnia magna Chromium rep1

description: Control-Media

value: 14 days


title: Daphnia magna Diazinon rep4

description: Control-Acetone


title: Daphnia magna Chloroform rep2

description: Control-Ethanol


title: Daphnia magna Chlorpyrifos rep4

description: Control-Methanol


title: Daphnia magna Chloroform rep4

description: Control-Ethanol


title: Daphnia magna Chlorpyrifos rep1

description: Control-Methanol


title: Daphnia magna Chloroform rep1

description: Control-Ethanol


title: Daphnia magna Chromium rep2

description: Control-Media


title: Daphnia magna Bifenthrin rep4

description: Control-Ethanol

value: Bifenthrin


title: Daphnia magna Cadmium rep2

description: Control-Media

value: Cadmium


title: Daphnia magna Cadmium rep3

description: Control-Media


title: Daphnia magna Bis2-ethylhexyl phthalate rep2

description: Control-Ethanol


title: Daphnia magna Bis2-ethylhexyl phthalate rep4

description: Control-Ethanol


title: Daphnia magna Bis2-ethylhexyl phthalate rep1

description: Control-Ethanol


title: Daphnia magna Bis2-ethylhexyl phthalate rep3

description: Control-Ethanol


title: Daphnia magna Beta-benzene hexachloride rep3

description: Control-Ethanol

value: Beta-benzene hexachloride


title: Daphnia magna Beta-estradiol rep2

description: Control-Ethanol

value: Beta-estradiol

value: 1 mg/L


title: Daphnia magna Beta-benzene hexachloride rep4

description: Control-Ethanol


title: Daphnia magna Beta-estradiol rep3

description: Control-Ethanol


title: Daphnia magna Beta-estradiol rep1

description: Control-Ethanol


title: Daphnia magna Bifenthrin rep3

description: Control-Ethanol


title: Daphnia magna Bifenthrin rep1

description: Control-Ethanol


title: Daphnia magna Beta-estradiol rep4

description: Control-Ethanol


title: Daphnia magna Cadmium rep4

description: Control-Media


title: Daphnia magna Atrazine rep3

description: Control-Acetone

value: Atrazine


title: Daphnia magna Bifenthrin rep2

description: Control-Ethanol


title: Daphnia magna Atrazine rep1

description: Control-Acetone


title: Daphnia magna Atrazine rep2

description: Control-Acetone


title: Daphnia magna Cadmium rep1

description: Control-Media


title: Daphnia magna Beta-benzene hexachloride rep2

description: Control-Ethanol


title: Daphnia magna Beta-benzene hexachloride rep1

description: Control-Ethanol


title: Daphnia magna Arsenic rep4

description: Control-Media

value: Arsenic


title: Daphnia magna Aroclor rep4

description: Control-Methanol

value: Aroclor


title: Daphnia magna Arsenic rep3

description: Control-Media


title: Daphnia magna Arsenic rep2

description: Control-Media


title: Daphnia magna Aroclor rep3

description: Control-Methanol


title: Daphnia magna Arsenic rep1

description: Control-Media


title: Daphnia magna Atrazine rep4

description: Control-Acetone


title: Daphnia magna Acrylonitrile rep3

description: Control-Media

value: Acrylonitrile


title: Daphnia magna Aroclor rep1

description: Control-Methanol


title: Daphnia magna Acrylonitrile rep4

description: Control-Media


title: Daphnia magna Acrylonitrile rep1

description: Control-Media


title: Daphnia magna 20 hydroxyecdysone rep1

description: Control-Media


title: Daphnia magna 2-chloro vinyl ether rep3

description: Control-Ethanol

value: 2-chloro vinyl ether


title: Daphnia magna 20 hydroxyecdysone rep2

description: Control-Media


title: Daphnia magna 2-chloro vinyl ether rep4

description: Control-Ethanol


title: Daphnia magna Acrylonitrile rep2

description: Control-Media


title: Daphnia magna 2-chloro vinyl ether rep2

description: Control-Ethanol


title: Daphnia magna 20 hydroxyecdysone rep4

description: Control-Media


title: Daphnia magna 2-chloro vinyl ether rep1

description: Control-Ethanol


title: infected leaf tissue, Biological Replicate 2 (BR2)

city: Braamfontein

first: Chrissie

last: Rey

state: Johannesburg, Gauteng

address: 1 Jan Smuts Avenue

department: School of Molecular and Cell Biology

country: South Africa

institute: University of the Witswatersrand

description:
N.benthamiana leaf tissue infected by SACMV.This is the 2nd of 3 biological replicates.
Biological Replicate 2 (BR2)

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Reykjavik, Iceland.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Reykjavik, Iceland.

data_processing: Data processing was performed by NimbleGen Systems Inc., Reykjavik, Iceland., using DNASTAR Arraystar Software.

organism: Nicotiana benthamiana

source_name: Nicotiana benthamiana wild-type

label_protocol: RNA extracted from the  SACMV-and mock-inoculated leaves from 21dpi leaf tissue  was converted to double-stranded cDNA by using the SuperScript Choice System for cDNA Synthesis (Invitrogen).  10 μg of total RNA was used for each sample. Double-stranded cDNA was purified by using phenol-chloroform extraction and precipitated with ethanol. This was washed with 80% ethanol, and resuspended in 30 μl of water.  Double-stranded cDNA was send off to NimbleGen Iceland where all hybridization and scanning was conducted. Labeling was performed by NimbleGen Systems Inc., Reykjavik, Iceland

growth_protocol: Nicotiana benthamiana plants were grown at 25 °C with a photoperiod of 16 h light/8 h dark for 6 weeks.

extract_protocol: Total RNA was extracted from 100mg of either SACMV-infected or mock-inoculated leaf tissue using TRI Reagent (Sigma). DNA was removed trating total RNA with  RNase-Free Dnase I (Promega).Thw quality and concentration of the total RNA extracted for each of the samples was measured by a NanoDrop ND-1000 spectrophotometer.Final purified RNA products were stored with RiboLock RNAse Inhibitor (Thermo Scientific)  at -80C until use.

treatment_protocol: Thirty plants, at the 3-4 leaf stage (6 week old), were agroinoculated with 100µl of Agrobacterium C58C1 harbouring infectious clones of SACMV-[ZA:99] DNA-A and DNA-B (OB600 - 0.8) (Berrie et al, 2001). Subsequently, 30 plants were mock-inoculate using Agrobacterium C58C1 harbouring an empty plasmid vector pBIN19. This represented the control experiment. All plants were screened for infection over a 35day period and subsequently only 18 plants each group (SACMV-infected and control) was used for downstream microarray analysis.

tag: genotype/variation

value: wild-type

tag: infection

value: SACMV

value: leaf


title: infected leaf tissue, Biological replicate 1 (BR1)

description:
N.benthamiana leaf tissue infected by SACMV.This is the 1st of 3 biological replicates.
Biological replicate 1 (BR1)

tag: tissue


title: pooled mock-inoculated leaf tissue, Reference (Ref)

description:
N.benthamiana leaf tissue  mock-inculated with Agrobacterium Agl1. (Experimental control). 3 independent biological replicates for mock-inoculated leaf-tissue was pooled together to form one reference sample.
Reference (Ref)

value: mock-inoculated (control)


title: Daphnia magna Aroclor rep2

description: Control-Methanol


title: Daphnia magna 20 hydroxyecdysone rep3

description: Control-Media


title: infected leaf tissue, Biological replicate 3 (BR3)

description:
N.benthamiana leaf tissue infected by SACMV.This is the 3rd of 3 biological replicates.
Biological replicate 3 (BR3)


title: Epcam(-), CD45(-) patient VIII

city: Barcelona

first: Alexandre

last: CALON

address: Dr. Aiguader, 88

country: Spain

institute: Hospital del Mar Medical Research Institute (IMIM)

description: expression data from stromal cells

hyb_protocol: Affymetrix HG-U133 plus 2.0 arrays arrays were hybridized with 8 ug of labeled, amplified dsDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual.

data_processing: We used RMA background correction, quantile normalization and RMA summarization(Gautier et al., 2004).

source_name: patient VIII

label_protocol: RNA was labeled (biotin) using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

extract_protocol: Total RNA was isolated with TRIZOL and washed with Qiagen kit following manufacturer's instructions.

tag: marker

value: human CRC

value: stromal cells

tag: individual

value: patient VIII


title: Epcam(-), CD45(+) patient VIII

description: expression data from leukocytes

tag: disease state

value: leukocytes


title: Epcam(-), CD45(-) patient VI

description: expression data from stromal cells

source_name: patient VI

value: patient VI


title: Epcam(+), CD45(-) patient VI

description: expression data from epithelial cells

value: epithelial cells


title: LC-3

city: Shanghai

first: Jun

last: Yang

address: 300 Fenglin Road

country: China

institute: SIPPE

description:
Cassava (Manihot esculenta Crantz)
9 h-2

hyb_protocol: Arrays were incubated at 65°C for 17 h in Agilent hybridization chambers (G2545A), and then washed according to the Agilent protocol at room temperature.

scan_protocol: Hybridized microarray slides were scanned at 5-μm resolution with an Agilent Technologies Scanner (G2505B), and images were saved in JPG format. Both 10% and 100% Photomultiplier tube (PMT) settings were selected, and combined images were exported.

data_processing: The signal intensities of all spots on each image were quantified by Agilent Feature Extraction software, and data were saved as .txt files for further analysis. Signal intensities were globally normalized with the GeneSpring GX Software (Agilent Technologies) following the work flow guide.

organism: Manihot esculenta

source_name: Cassava apical shoot, cold stress, 9h

label_protocol: RNA labeling was conducted by the Shanghai Biochip Corporation (Shanghai) following the manufacturer’s protocol of Agilent Technology.

growth_protocol: The cultivar TMS60444, which is frequently used for genetic engineering, was employed in the present study. The in vitro plants were transferred to pots for 3 months of growth in a greenhouse.

extract_protocol: Total RNA was extracted from apical shoots, including 0 h, 4 h, and 9 h, using the RNeasy Mini Kit (Qiagen). RNA quality was checked on a 1% agarose gel using an RNase-free electrophoresis system.

treatment_protocol: Apical shoots subjected to cold at 7℃ for 0 h, 4 h, and 9 h were collected from three independent healthy 3-month-old cassava plants in the greenhouse and submerged into liquid nitrogen immediately. All samples were maintained in liquid nitrogen during transportation, and they were stored in an ultra-freezer (-80°C) until RNA extraction.

tag: cultivar

value: 3 months

value: healthy

value: apical shoot

value: cold stress (7°C)

tag: treatment duration

value: 9 hrs

tag: biological replicate


title: EC-4

description:
Cassava (Manihot esculenta Crantz)
4 h-3

source_name: Cassava apical shoot, cold stress, 4h

tag: treatment

value: 4 hrs


title: LC-4

description:
Cassava (Manihot esculenta Crantz)
9 h-3


title: Epcam(-), CD45(+) patient VI

description: expression data from leukocytes

tag: cell type


title: Epcam(+), CD45(-) patient VII

description: expression data from epithelial cells

source_name: patient VII

value: patient VII


title: EC-3

description:
Cassava (Manihot esculenta Crantz)
4 h-2


title: Epcam(-), CD45(+) patient IV

description: expression data from leukocytes

source_name: patient IV

value: patient IV


title: Epcam(-), CD45(+) patient VII

description: expression data from leukocytes


title: Epcam(+), CD45(-) patient V

description: expression data from epithelial cells

source_name: patient V

value: patient V


title: Epcam(-), CD45(-) patient IV

description: expression data from stromal cells


title: Epcam(-), CD45(-) patient V

description: expression data from stromal cells


title: CK-3

description:
Cassava (Manihot esculenta Crantz)
0 h-2

source_name: Cassava apical shoot, cold stress, 0h

value: 0 hrs


title: LC-2

description:
Cassava (Manihot esculenta Crantz)
9 h-1


title: CK-2

description:
Cassava (Manihot esculenta Crantz)
0 h-1


title: Epcam(+), CD45(-) patient VIII

description: expression data from epithelial cells


title: Epcam(-), CD45(+) patient V

description: expression data from leukocytes


title: Epcam(-), CD45(+) patient III

description: expression data from leukocytes

source_name: patient III

value: patient III


title: Epcam(-), CD45(-) patient II

description: expression data from stromal cells

source_name: patient II

value: human CRC

value: patient II


title: Epcam(+), CD45(-) patient III

description: expression data from epithelial cells


title: Epcam(-), CD45(+) patient II

description: expression data from leukocytes


title: Epcam(+), CD45(-) patient II

description: expression data from epithelial cells


title: Epcam(-), CD45(-) patient I

description: expression data from stromal cells

source_name: patient I

value: stromal cells

value: patient I


title: Epcam(-), CD45(-) patient VII

description: expression data from stromal cells


title: CCD treated rep2

description: expression data from fibroblasts treated with TGF-Beta

hyb_protocol: Affymetrix HG-U133 plus 2.0 arrays were hybridized with 8 ug of labeled, amplified dsDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual.

source_name: cells treated for 8h

label_protocol: RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled (biotin) using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS at 37ºC and 5% CO2.

extract_protocol: RNA extraction was done with TRIZOL and washed with Qiagen kit following manufacturer's instructions.

treatment_protocol: CCD-Co-18 were seeded at 60% confluence and treated with TGF-β1 (Peprotech; 5 ng mL-1) for 8 hours.

value: primary normal colon mucosa-derived fibroblasts

value: TGB-beta1 for 8h

tag: pair

value: pair 2


title: Epcam(-), CD45(+) patient I

description: expression data from leukocytes

value: leukocytes


title: Epcam(+), CD45(-) patient I

description: expression data from epithelial cells

value: epithelial cells


title: CK-4

description:
Cassava (Manihot esculenta Crantz)
0 h-3

tag: age

value: 3 months

value: healthy

value: apical shoot

value: cold stress (7°C)


title: Epcam(+), CD45(-) patient IV

description: expression data from epithelial cells

value: patient IV


title: CCD treated rep1

value: pair 1


title: CCD non treated rep1

description: expression data from untreated fibroblasts

source_name: cells non treated

value: non-treated


title: Epcam(-), CD45(-) patient III

description: expression data from stromal cells

value: patient III


title: vif_6hrs_rep2

city: San Francisco

first: Nevan

last: Krogan

address: 1700 4th Street

department: Cellular & Molecular Pharmacology

institute: University of California, San Francisco

description: SAMPLE 11

hyb_protocol: hybridizations were performed according to Affymetrix standard protocols.

scan_protocol: scans were performed according to Affymetrix standard protocols.

data_processing:
data were analyzed using the MMBGX software platform.
expression level defined by MMBGX.  Note that the summaries (average) of the replicates are calculated after performing a loess curve.

source_name: Jurkat Trex expressing Vif_6hrs PMA/PHA

label_protocol: total RNA was amplified by SPRI.

growth_protocol: cells were grown in RPMI-1640 for two days, then exposed to 1 ug/ml doxycycline for 16 hrs

extract_protocol: TRIZOL was used according to the manufacturer's instructions

treatment_protocol: cells were treated with 50 ng/ml PMA and 1 ug/ul PHA for 4 or 6 hours as indicated

tag: cell line

value: Invitrogen Jurkat Trex (Invitrogen)

value: expressing stably integrated, tetracycline inducible HIV-1 Vif

tag: treated with

value: 50 ng/ml PMA and 1 ug/ul PHA for 6hrs


title: EC-2

description:
Cassava (Manihot esculenta Crantz)
4 h-1

value: 4 hrs


title: vif_6hrs_rep3

description: SAMPLE 12


title: CCD non treated rep2

value: primary normal colon mucosa-derived fibroblasts


title: FAP patient K

description: expression data from fibroblasts

hyb_protocol: Affymetrix HG-U133  +PM arrays were hybridized with 8 ug of labeled, amplified dsDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual.

source_name: patient K

extract_protocol: RNA was processed and amplified as previously described(Gonzalez-Roca et al., 2010).

value: patient K

value: FAP

value: human CRC

tag: cell population

value: fibroblasts


title: CD45 patient K

description: expression data from leukocytes

value: leukocytes


title: vif_6hrs_rep1

description: SAMPLE 10


title: PGC_E13_F3-Vinclozolin_biological rep2

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

description:
Male gonads  from embryonic day E13 rat
Gene expression data from embryonic day E13 male gonads of F3 vinclozolin lineage rat
For each mRNA microarray replica, PGC from 7-20 different male embryos were combined.

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 4500.

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

data_processing: The data were analyzed with Partek Genomic Suite 6.6 beta software  (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.  Cell preparation date batch effect was removed.

organism: Rattus norvegicus

source_name: Primordial germ cell from E13 days old F3 vinclozolin lineage rat embryo

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Primordial germ cell were isolated from male embryos age E13 and E16 of F3 generation of vinclozolin and control lineages rats as described before [. Kafri T, Ariel M, Brandeis M, Shemer R, Urven L, et al. (1992) Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev 6: 705-714.].  Male sex of gonads was confirmed by PCR for male specific SRY gene.

extract_protocol: RNA was isolated from primordial germ cells after lysis in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003].  Subsequent  F2 and F3 generations wee obtained from F1 rats.

value: F3 vinclozolin lineage

tag: cell preparation date batch

tag: genetic background

value: Sprague-Dawley rat

tag: gender

value: Male

value: Primordial germ cell

tag: developmental stage


title: PP_PP4

first: Minoti

last: Apte

state: NSW

address: Level 4, Ingham Institute

institute: University of New South Wales

description: RNA from rat PSC

hyb_protocol: Labeled, fragmented RNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalised using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

source_name: Rat PSC on plastic

label_protocol: RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

growth_protocol: Rat PSCs were isolated by density gradient centrifugation using Nycodenz

extract_protocol: Total RNA from stellate cells in 10 cm Petri dishes was isolated by Qiagen RNeasy Mini Plus kit as per manufacturer’s instructions

treatment_protocol: 1 million PSCs were seeded on either plastic, Matrigel or collagen I, in 10cm Petri-dishes. PSCs were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% foetal bovine serum (FBS) (Invitrogen) for 72 hours

tag: strain

value: Sprague Dawley

value: male

tag: protocol

value: Plastic


title: PGC_E13_F3-Vinclozolin_biological rep1


title: PP_AM2

description: RNA from rat PSC

source_name: Rat PSC on matrigel

value: Matrigel


title: vif_4hrs_rep3

description: SAMPLE 9

source_name: Jurkat Trex expressing Vif_4hrs PMA/PHA

value: Invitrogen Jurkat Trex (Invitrogen)

tag: genotype/variation

value: expressing stably integrated, tetracycline inducible HIV-1 Vif

value: 50 ng/ml PMA and 1 ug/ul PHA for 4hrs


title: PGC_E13_F3-Control_biological rep2

description:
Male gonads  from embryonic day E13 rat
Gene expression data from embryonic day E13 male gonads of F3 control lineage rat
For each mRNA microarray replica, PGC from 7-20 different male embryos were combined.

source_name: Primordial germ cell from E13 days old F3 control lineage rat embryo

value: F3 control lineage


title: vif_4hrs_rep2

description: SAMPLE 8


title: PP_SP6

description: RNA from rat PSC


title: PP_AP5

description: RNA from rat PSC


title: PGC_E16_F3-Control_biological rep1

description:
Male gonads  from embryonic day E16 rat
Gene expression data from embryonic day E16 male gonads of F3 control lineage rat
For each mRNA microarray replica, PGC from 7-20 different male embryos were combined.

source_name: Primordial germ cell from E16 days old F3 control lineage rat embryo


title: PGC_E16_F3-Vinclozolin_biological rep2

description:
Male gonads  from embryonic day E16 rat
Gene expression data from embryonic day E16 male gonads of F3 vinclozolin lineage rat
For each mRNA microarray replica, PGC from 7-20 different male embryos were combined.

source_name: Primordial germ cell from E16 days old F3 vinclozolin lineage rat embryo


title: PGC_E16_F3-Control_biological rep2


title: PP_PC8

description: RNA from rat PSC

source_name: Rat PSC on collagen

value: Collagen


title: PGC_E16_F3-Vinclozolin_biological rep1


title: PP_SM3

description: RNA from rat PSC


title: CD31 patient K

description: expression data from endothelial cells

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

tag: individual

value: patient K

tag: marker

tag: disease state

value: endothelial cells


title: PP_ZC10

description: RNA from rat PSC


title: PP_ZP7

description: RNA from rat PSC


title: vif_4hrs_rep1

description: SAMPLE 7


title: reference_6hrs_rep3

description: SAMPLE 6

source_name: Jurkat Trex_6hrs PMA/PHA

value: 50 ng/ml PMA and 1 ug/ul PHA for 6hrs


title: PGC_E13_F3-Control_biological rep1

tag: treatment


title: CD31 patient J

description: expression data from endothelial cells

source_name: patient J

value: patient J

value: human CRC


title: CD45 patient J

description: expression data from leukocytes

value: leukocytes


title: Epcam patient K

description: expression data from epithelial cells

value: Epcam

value: epithelial cells


title: FAP patient J

description: expression data from fibroblasts

value: FAP

value: fibroblasts


title: reference_4hrs_rep3

description: SAMPLE 3

source_name: Jurkat Trex_4hrs PMA/PHA


title: Duplication pre-frontal cortex DUP_pfc_1011MK0095-20110510

city: New York

first: Bin

last: XU

state: NY

address: 1051 Riverside Drive

institute: columbia university

hyb_protocol: According to Affymetrix Standard Protocols

data_processing: The CEL files were analyzed using Bioconductor of R project. The raw intensity data of all PFC samples or HPC samples were first RMA normalized and log2 transformed. differential expression analysis was conducted using limma package.

growth_protocol: Adult male mice were collected

extract_protocol: Total RNA were extracted and purified with the miRNeasy Mini-kit (Qiagen).

tag: genotype

value: 22q11.2 microduplication

tag: tissue

value: pre-frontal cortex

value: adult


title: PP_AC9

description: RNA from rat PSC

value: Sprague Dawley

value: male


title: reference_6hrs_rep2

description: SAMPLE 5

value: Invitrogen Jurkat Trex (Invitrogen)


title: Epcam patient J

description: expression data from epithelial cells


title: Deletion pre-frontal cortex DEL_pfc_1011MK0094-20110510

scan_protocol: According to Affymetrix Standard Protocols

value: 22q11.2 microdeletion

tag: age


title: reference_6hrs_rep1

description: SAMPLE 4

tag: cell line


title: Reference pre-frontal cortex REF_pfc_1011MK0096-20110510

label_protocol: According to Affymetrix Standard Protocols

value: heterozygous balanced copy number


title: Deletion pre-frontal cortex DEL_pfc_1011MK0093-20110510


title: reference_4hrs_rep2

description: SAMPLE 2

tag: treated with

value: 50 ng/ml PMA and 1 ug/ul PHA for 4hrs


title: Reference pre-frontal cortex REF_pfc_1011MK0092-20110510


title: Deletion pre-frontal cortex DEL_pfc_1011MK0089-20110510


title: Duplication pre-frontal cortex DUP_pfc_1011MK0084-20110510


title: CD45 patient E

description: expression data from leukocytes

source_name: patient E

value: patient E

tag: cell population


title: FAP patient D

description: expression data from fibroblasts

source_name: patient D

value: patient D


title: reference_4hrs_rep1

description: SAMPLE 1


title: Deletion pre-frontal cortex DEL_pfc_1011MK0085-20110510


title: Reference pre-frontal cortex REF_pfc_1011MK0090-20110510


title: CD31 patient D

description: expression data from endothelial cells

value: human CRC

value: endothelial cells


title: CD31 patient E

description: expression data from endothelial cells


title: Duplication pre-frontal cortex DUP_pfc_1011MK0091-20110510


title: Reference pre-frontal cortex REF_pfc_1011MK0087-20110510


title: FAP patient E

description: expression data from fibroblasts


title: Deletion pre-frontal cortex DEL_pfc_1011MK0088-20110510


title: Duplication pre-frontal cortex DUP_pfc_1011MK0086-20110510


title: Duplication pre-frontal cortex DUP_pfc_1011MK0081-20110510


title: Reference pre-frontal cortex REF_pfc_1011MK0083-20110510


title: Epcam patient D

description: expression data from epithelial cells

value: Epcam


title: Epcam patient E

description: expression data from epithelial cells

value: epithelial cells


title: Deletion pre-frontal cortex DEL_pfc_1011MK0079-20110510


title: Duplication pre-frontal cortex DUP_pfc_1011MK0080-20110510


title: CD45 patient D

description: expression data from leukocytes

value: leukocytes


title: CD45 patient C

description: expression data from leukocytes

source_name: patient C

value: patient C


title: FAP patient C

description: expression data from fibroblasts

value: FAP

value: fibroblasts


title: Duplication hippocampus DUP_HPC_1011MK0071-20110510

value: 22q11.2 microduplication

value: hippocampus

value: adult


title: Reference pre-frontal cortex REF_pfc_1011MK0075-20110510

value: pre-frontal cortex


title: Deletion pre-frontal cortex DEL_pfc_1011MK0073-20110510

value: 22q11.2 microdeletion


title: Duplication pre-frontal cortex DUP_pfc_1011MK0077-20110510


title: CD31 patient C

description: expression data from endothelial cells


title: Reference hippocampus REF_HPC_1011MK0072-20110510

value: heterozygous balanced copy number


title: CD31 patient A

description: expression data from endothelial cells

source_name: patient A

value: patient A


title: Reference pre-frontal cortex REF_pfc_1011MK0078-20110510


title: Duplication hippocampus DUP_HPC_1011MK0067-20110510


title: Epcam patient C

description: expression data from epithelial cells


title: Reference hippocampus REF_HPC_1011MK0068-20110510


title: Deletion hippocampus DEL_HPC_1011MK0070-20110510


title: Atm-/- MEFs at T8

city: Houston

first: Guohui

last: Wan

state: TX

address: 7777 Knight Road

department: Cancer Biology

institute: The University of Texas M.D. Anderson Cancer Center

description: Gene expression data from MEFs after DNA damage

hyb_protocol: Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. 1 ug of each labeled cRNA was  fragmented by adding 11 ul 10 x Blocking Agent and 2.2 ul of 25 x Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 ul 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 100 ul of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

scan_protocol: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 3 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Mouse embryonic fibroblast

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from 1 ug total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The MEFs were plated on multiple 100-mm dishes for each line in 15% fetal calf serum and Dulbecco's modified Eagle's medium (DMEM) in 37? with 5% CO2.

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

treatment_protocol: The MEFs were treated with or without DNA damaging reagent neocarzinostatin (NCS),  a radiomimetic drug that generates DSBs. Cells were harvested at varying time points (0-24h).

value: Mouse embryonic fibroblast

value: Atm-/-

value: DNA damaging agent neocarzinostatin (NCS)


title: Atm-/- MEFs at T24


title: Atm-/- MEFs at T4


title: CD45 patient A

description: expression data from leukocytes

value: human CRC