title: 012_BMM_C57Bl6_IFNg_biorep3

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: E.-M.-Arndt-University Greifswald, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics

hyb_protocol: Labeled cDNA was hybridized to GeneChip® Mouse Gene 1.0 ST Arrays according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned using an Affymetrix Scanner 3000 under control of AGCC (Affymetrix GeneChip Command Console) version1.0. This software also performed the CEL-file generation from DAT-file raw data.

data_processing: Signal Intensity values were generated with RMA algorithm in Rosetta Resolver® System (Rosetta Biosoftware, Seattle, WA, USA). The software also generated a p-value to judge on presence (significant p-value) or absence (non-significant p-value) of expression.

source_name: C57Bl/6 BMM IFNgamma treated

label_protocol: Labeled cDNA for hybridization was prepared for each sample from 200 ng totalRNA using the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay  according to the manufacturer’s instructions version 4 (Affymetrix, Santa Clara, CA, USA).

growth_protocol: BMM were prepared as described in Eske et al. Journal of Immunological Methods 2009.

extract_protocol: Medium was carefully removed from the sample wells and BMM were lyzed in 1 ml TriReagent per sample (Sigma, Steinheim, Germany) by repetitive pipetting. After incubation at room temperature for 15 min the lysate was flash-frozen in liquid nitrogen and stored at -70°C till RNA-preparation.  RNA-preparation took place using a combined protocol of phenol-based preparation and column-based purification. Chloroform was added to TriReagent lysates, samples were vigorously shaken, and incubated at room temperature for 5 min. Organic and aqueous phase were separated by centrifugation for 15 min at 12000 x g and 4°C. Afterwards, the aqueous supernatant was mixed with 0.5 ml isopropanol and transferred to RNeasy Mini columns (Qiagen GmbH, Hilden, Germany). The following steps of RNA purification were carried out according to the manufacturer’s instructions including the optional DNase-treatment (RNase-free DNase Set, Qiagen GmbH, Hilden, Germany). After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: Mature BMM were seeded in 6-well-plates with 0.8E+06-1.5E+06 cells/well. BMM in half of the wells were activated for 24 hours by addition of 300 units/ml IFN¬γ (Roche, Mannheim, Germany) in serum-free BMM-medium, the other half was cultivated for the same time in the same medium without IFN¬γ. For transcriptome analysis 1.6E+06-4.5E+06 cells/sample were available.

value: IFNgamma

tag: biological replicate number


title: Case NC 1

status: Public on Apr 15 2014

type: RNA

city: Rockville

first: Paula

middle: Lisa

last: Hyland

state: MD

address: 6120 Executive Blvd

department: DCEG

country: USA

institute: NCI, NIH

description: Gene expression data

hyb_protocol: 20 ug fragmented cRNA were hybridized for 16 hr at 45C on GeneChip H133-A 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: Gene expression data were processed and normalized using Bioconductor Affy package, based on the Robust Multichip Average (RMA) for single-channel Affymetrix chips

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NC Tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Trizol extraction of total RNA and following clean-up with Qiagen Rneasy Mini Kit were performed according to the manufacturers instructions

tag: group

value: BE case

tag: cell type

value: NC


title: 168hr_CON_5

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Gene expression data from mouse lung tissue 168hr after sham control (CON) exposure

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

organism: Mus musculus

source_name: Lung tissue from mice 168hr after inhalation exposure with sham control (CON), biological rep5

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Male balb/c mice (N=5 per condition) were exposed to the SPIO nanoparticle aerosol (365 ug total mass), or a sham control (i.e. just humidified helium-oxygen-HEPA-filtered air atmosphere), for 4 hrs.  All mice were sacrificed with an overdose of sodium pe

tag: tissue

value: lung

tag: Sex

value: male

tag: strain

value: Balb/c

tag: treatment

value: control

tag: exposure time


title: Group3 neurophere  [mmm015-htmg430pm]

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled targets were hybridized on the HT_MG-430_PM plate array and processed using the GeneTitan system.

scan_protocol: Scanning uses the GeneTitan system.

data_processing: The data were analyzed with RMA, batch and assay corrected using Partek Genomics Suite 6.6 and STATA/MP 11

label: Biotin

source_name: Group3 neurophere

label_protocol: RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module.

extract_protocol: Total mRNA was extracted with Trizol

value: Medulloblastoma cells

tag: genotype

value: Trp53-/-, Cdkn2c-/- Myc


title: 010_BMM_Balbc_IFNg_biorep3

country: Germany

source_name: Balb/c BMM IFNgamma treated


title: Untreated multipotent progenitor (MPP) 3

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: Untreated multipotent progenitor (MPP)

label_protocol: biotin

growth_protocol: MPP and CDP were obtained from mouse bone marrow, followed by in vitro culture with a specific cytokine cocktail and FACS sorting (Felker et al., 2010; Seré et al., 2012).

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

treatment_protocol: Cells were treated with 10 ng/ml recombinant human TGF-β1 (R&D Systems, Minneapolis, USA) for 2, 4, 6, 12 and 24 h as described (Felker et al., 2010) or left untreated.

value: multipotent progenitor


title: 0hr_SPIO_4

description: Gene expression data from mouse lung tissue 0hr after SPIO nanparticle exposure

source_name: Lung tissue from mice 0hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep4

value: SPIO


title: Group3 neurophere  [mmm016-htmg430pm]


title: 0hr_SPIO_1

source_name: Lung tissue from mice 0hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep1


title: Group3 neurophere  [mmm014-htmg430pm]


title: 168hr_CON_4

source_name: Lung tissue from mice 168hr after inhalation exposure with sham control (CON), biological rep4


title: 168hr_CON_2

source_name: Lung tissue from mice 168hr after inhalation exposure with sham control (CON), biological rep2


title: Group3 tumor +pemetrexed+gemcitabine [mmm012-htmg430pm]

source_name: Group3 tumor +pemetrexed+gemcitabine

value: Medulloblastoma tumors


title: Group3 tumor +pemetrexed+gemcitabine [mmm011-htmg430pm]


title: 009_BMM_Balbc_Co_biorep3

source_name: Balb/c BMM medium control

value: medium control


title: 168hr_CON_1

source_name: Lung tissue from mice 168hr after inhalation exposure with sham control (CON), biological rep1


title: 011_BMM_C57Bl6_Co_biorep3

source_name: C57Bl/6 BMM medium control


title: 168hr_CON_3

source_name: Lung tissue from mice 168hr after inhalation exposure with sham control (CON), biological rep3


title: 96hr_CON_5

description: Gene expression data from mouse lung tissue 96hr after sham control (CON) exposure

source_name: Lung tissue from mice 96hr after inhalation exposure with sham control (CON), biological rep5


title: 006_BMM_Balbc_IFNg_biorep2


title: 008_BMM_C57Bl6_IFNg_biorep2


title: Group3 neurophere  [mmm013-htmg430pm]


title: 005_BMM_Balbc_Co_biorep2


title: Group3 tumor +pemetrexed+gemcitabine [mmm010-htmg430pm]


title: 96hr_CON_3

source_name: Lung tissue from mice 96hr after inhalation exposure with sham control (CON), biological rep3


title: Group3 tumor +gemcitabine [mmm007-htmg430pm]

source_name: Group3 tumor +gemcitabine


title: 96hr_CON_4

source_name: Lung tissue from mice 96hr after inhalation exposure with sham control (CON), biological rep4


title: 007_BMM_C57Bl6_Co_biorep2


title: Group3 tumor +gemcitabine [mmm008-htmg430pm]


title: 96hr_CON_2

source_name: Lung tissue from mice 96hr after inhalation exposure with sham control (CON), biological rep2


title: 002_BMM_Balbc_IFNg_biorep1


title: Group3 tumor +pemetrexed [mmm006-htmg430pm]

source_name: Group3 tumor +pemetrexed


title: 96hr_CON_1

source_name: Lung tissue from mice 96hr after inhalation exposure with sham control (CON), biological rep1


title: 004_BMM_C57Bl6_IFNg_biorep1

source_name: C57Bl/6 BMM IFNgamma treated


title: 003_BMM_C57Bl6_Co_biorep1


title: 48hr_CON_4

description: Gene expression data from mouse lung tissue 48hr after sham control (CON) exposure

source_name: Lung tissue from mice 48hr after inhalation exposure with sham control (CON), biological rep4


title: Group3 tumor +pemetrexed [mmm005-htmg430pm]


title: 48hr_CON_3

source_name: Lung tissue from mice 48hr after inhalation exposure with sham control (CON), biological rep3


title: Group3 tumor [mmm003-htmg430pm]

source_name: Group3 tumor


title: Group3 secondary tumor [dka224-htmg430pm]

source_name: Group3 secondary tumor


title: 48hr_CON_2

source_name: Lung tissue from mice 48hr after inhalation exposure with sham control (CON), biological rep2


title: 001_BMM_Balbc_Co_biorep1

source_name: Balb/c BMM medium control


title: Group3 secondary tumor [dka223-htmg430pm]


title: 48hr_CON_1

source_name: Lung tissue from mice 48hr after inhalation exposure with sham control (CON), biological rep1


title: Group3 tumor [mmm002-htmg430pm]


title: 24hr_CON_5

description: Gene expression data from mouse lung tissue 24hr after sham control (CON) exposure

source_name: Lung tissue from mice 24hr after inhalation exposure with sham control (CON), biological rep5


title: 48hr_CON_5

source_name: Lung tissue from mice 48hr after inhalation exposure with sham control (CON), biological rep5


title: Group3 neurophere  [dka215-htmg430pm]

source_name: Group3 neurophere


title: Group3 secondary tumor [dka225-htmg430pm]


title: 24hr_CON_4

source_name: Lung tissue from mice 24hr after inhalation exposure with sham control (CON), biological rep4


title: 24hr_CON_3

source_name: Lung tissue from mice 24hr after inhalation exposure with sham control (CON), biological rep3


title: Group3 neurophere  [dka213-htmg430pm]


title: Trp53 neurospheres [dka206-htmg430pm]

source_name: Trp53 neurospheres

value: granule neural progenitors


title: 24hr_CON_2

source_name: Lung tissue from mice 24hr after inhalation exposure with sham control (CON), biological rep2


title: Group3 tumor [dka203-htmg430pm]


title: 24hr_CON_1

source_name: Lung tissue from mice 24hr after inhalation exposure with sham control (CON), biological rep1


title: Trp53 neurospheres [dka204-htmg430pm]


title: 6hr_CON_4

description: Gene expression data from mouse lung tissue 6hr after sham control (CON) exposure

source_name: Lung tissue from mice 6hr after inhalation exposure with sham control (CON), biological rep4


title: 6hr_CON_5

source_name: Lung tissue from mice 6hr after inhalation exposure with sham control (CON), biological rep5


title: Trp53 neurospheres [dka205-htmg430pm]


title: Group3 neurophere  [dka214-htmg430pm]


title: Group3 tumor [dka201-htmg430pm]


title: Group3 tumor [dka202-htmg430pm]


title: 6hr_CON_2

source_name: Lung tissue from mice 6hr after inhalation exposure with sham control (CON), biological rep2


title: 6hr_CON_3

source_name: Lung tissue from mice 6hr after inhalation exposure with sham control (CON), biological rep3


title: 6hr_CON_1

source_name: Lung tissue from mice 6hr after inhalation exposure with sham control (CON), biological rep1


title: Pex19_reconstituted_16 hr_rep1

city: Boston

first: Jonathan

last: Kagan

state: MA

address: 300 Longwood Ave, Enders 649

institute: Children's Hospital Boston

description: replicate 1

hyb_protocol: Standard Illumina Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: Illumina Bead Array Reader BSGX Version 3.4.0 at Directhyb Gene Expression setting with BeadScan Software

data_processing: The data were normalised using average normalisation with Illumina Genome Studio

source_name: skin fibroblasts

label_protocol: Biotinylated cRNA was prepared with the Illumina® TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit in combination with QIAshredder and the RNase-free DNase Set (all QIAgen) according to the manufacturer's instructions.

value: Pex19 wild type

tag: time

value: 16 hr

tag: infection

value: reovirus

value: skin fibroblast


title: 0hr_CON_2

description: Gene expression data from mouse lung tissue 0hr after sham control (CON) exposure

source_name: Lung tissue from mice 0hr after inhalation exposure with sham control (CON), biological rep2


title: 0hr_CON_1

source_name: Lung tissue from mice 0hr after inhalation exposure with sham control (CON), biological rep1


title: Pex19_deficient_9 hr_rep1

description: replicate 1

value: Pex19 deficient

value: 9 hr


title: 0hr_CON_5

source_name: Lung tissue from mice 0hr after inhalation exposure with sham control (CON), biological rep5

value: lung


title: Pex19_deficient_16 hr_rep1

description: replicate 1


title: 0hr_CON_4

source_name: Lung tissue from mice 0hr after inhalation exposure with sham control (CON), biological rep4

value: male


title: Pex19_reconstituted_9 hr_rep1

description: replicate 1


title: Pex19_deficient_control_rep1

description: replicate 1


title: 0hr_CON_3

source_name: Lung tissue from mice 0hr after inhalation exposure with sham control (CON), biological rep3

value: Balb/c


title: Rb-1-1

status: Public on Apr 14 2014

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

country: Canada

institute: Western University

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files were converted to RMA expression values using BRB-Array Tools software (http://linus.nci.nih.gov/BRB-ArrayTools.html). BRB-Array Tools uses the affy package in R to calculate RMA values.

source_name: Mouse Embryonic Fibroblasts

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: MEFs were plated at low density 3 million cells per 15 cm culture dish. 24h later media was replaced with media cotaining 0.1%FBS to induce quiescence

extract_protocol: RNA was extracted according to Trizol user manual followed by purification by reprecititation with sodium acetate and 100% ethanol

tag: growth condition

value: Serum Deprived

value: Mouse Embryonic Fibroblasts


title: WT-3


title: G-3

value: Rb ∆G/∆G


title: WT-2


title: Rb-1-3


title: G-2


title: Rb-1-2


title: WT-1


title: G-1


title: CD8 T cell clone_unconventional _anti-CD3/CSA_rep2

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

hyb_protocol: Standar hybridization cocktail, hybed 17 hours at 45C.

scan_protocol: Standard wash and stain controlled by GCOS

data_processing: Cel Files generated by GCOS, imported into Partek (ver. 6.2) and RMA signals were generated for only the core probe sets (28,853).   RMA signals were generated for the core probe sets using the RMA background correction, quantile normalization and summarization by Median Polish.  Summarized signals for each probe set were log2 transformed.

label_protocol: Standard Affymetrix WT labeling and control kit.

growth_protocol: RPMI 1640 medium supplemented with 10 mM Hepes, 10% characterized FBS, 5x10-5M 2-ME, 25 uM gentamicin) supplemented with 500 ρg/ml IL-1a, 500 ρg/ml IL-6, 1 ηg/ml IL-7, 4 ηg/ml IL-15, 250 ρg/ml TNF-α, 3 ηM IFN4-α and 3 ηM IFN-g

extract_protocol: RNAeasy Kit with optional RNAse-free DNAse step (Qiagen)

treatment_protocol: Activated with immobilized anti-CD3 (145-2c11) monoclonal antibody in RPMI media without recombinant cytokines, in the absence and presence of 1 ug/ml cyclosporine A

value: cyclosporine-resistant CD8 T cell


title: CD8 T cell clone_unconventional _anti-CD3_rep4


title: CD8 T cell clone_unconventional _anti-CD3_rep2


title: Group3 tumor +gemcitabine [mmm009-htmg430pm]

source_name: Group3 tumor +gemcitabine

value: Trp53-/-, Cdkn2c-/- Myc


title: CD8 T cell clone_unconventional _anti-CD3/CSA_rep3


title: CD8 T cell clone_conventional_anti-CD3/CSA_rep2

value: cyclosporine-sensitive CD8 T cell


title: CD8 T cell clone_unconventional _anti-CD3/CSA_rep1


title: Pex19_reconstituted_control_rep1

description: replicate 1

value: control


title: CD8 T cell clone_unconventional _anti-CD3_rep1


title: CD8 T cell clone_conventional_anti-CD3/CSA_rep4


title: CD8 T cell clone_unconventional _anti-CD3/CSA_rep4


title: CD8 T cell clone_conventional_anti-CD3/CSA_rep3


title: CD8 T cell clone_conventional_anti-CD3_rep4

source_name: CD8 T cell clone_conventional_anti-CD3


title: CD8 T cell clone_conventional_anti-CD3_rep2


title: Embryoid Bodies (EB) Derived from TKO#29 mESCs, rep1

city: Cambridge

first: Inmaculada

last: Barrasa

address: Nine Cambridge Center

institute: Whitehead Institute

description:
TKO_29_1
Gene expression of TKO embryoid bodies cultured for 10 days.

hyb_protocol: Agilent-028005 mouse GE 8x60K expression array was hybridized and washed according to manufacturer's instructions.

scan_protocol: Agilent DNA microarray scanner was used following manufacturer's instructions.

data_processing: Data were normalized by quantile normalization using Bioconductor. Probes with the same probe_ID were summarized by mean.

source_name: Embryoid bodies, Tet TKO

label_protocol: Cy3-labeled cRNA was prepared using the Low Input Quick Amp labeling kit (Agilent).

growth_protocol: Mouse embryonic stem cells were differentiated to embryoid bodies by culturing them in suspension hanging drops for 2 days in the absence of LIF. Drops were washed into nonadherent plates and cultured in the absence of LIF for an additional 8 days. Media was refreshed every other day.

extract_protocol: RNA was extracted from EBs using Qiagen RNeasy Protocol.

treatment_protocol: Not applicable.

tag: strain/background

value: mixed 129/C57BL6

value: Tet1/2/3 triple knockout

value: embryoid bodies


title: CD8 T cell clone_conventional_anti-CD3/CSA_rep1


title: Embryoid Bodies (EB) Derived from TKO#26 mESCs, rep1

description:
TKO_26_1
Gene expression of TKO embryoid bodies cultured for 10 days.


title: MGG8DGC_3

type: SRA

first: Esther

last: Rheinbay

address: 7 Cambridge Center

institute: Broad Institute

description: MGG8 DGC

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome assembly hg19 with TopHat version 1.4.1.
Briefly, to calculate expression values for each gene we scanned 500 basepair window within 10 kb of the annotated 3’ end of all genes, and counted reads that fell in the highest 500 basepair window across all libraries. To normalize across libraries we fit each individual libraries distribution of gene expression values into the same negative binomial distribution.
For comparative analyses, we used the edgeR R package with general linear model (GLM) to identify expressed genes, annotate and collapse multiple values for each gene and identify differentially expressed genes between the three matched TPC/DGC pairs, and the MGG8 DGC empty (two replicates) and MGG8 POU3F2+SOX2+SALL2+OLIG2 iTPCs.
Density maps were generated with IGVTools
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG, density maps, value of gene expression values

source_name: MGG8 human glioblastoma serum-grown cell line

growth_protocol: MGG4 TPC and iTPC, MGG8 TPC and iTPC were cultured and passaged using standard neural stem cell conditions as described in Wakimoto et al, 2009 (PMID: 19351838) and Conti et al, 2005 (PMID: 16086633) MGG 4 FCS and MGG8 FCS were cultured in DMEM + 10% FCS and 1X P/S

extract_protocol:
Total RNA was isolated from cells using RNeasy Kit (Qiagen). 2 ug of total RNA were used to fragment and polyA isolate the 3’ends of mRNA transcripts.
Illumina sequencing libraries were constructed as described in Yoon and Brem, 2010.

value: glioblastoma


title: Embryoid Bodies (EB) Derived from TKO#26 mESCs, rep2

description:
TKO_26_2
Gene expression of TKO embryoid bodies cultured for 10 days.


title: Embryoid Bodies (EB) Derived from Wild Type mESCs, rep2

description:
WT_2
Gene expression of WT embryoid bodies cultured for 10 days.

source_name: Embryoid bodies, WT

value: WT


title: CD8 T cell clone_conventional_anti-CD3_rep1


title: Embryoid Bodies (EB) Derived from TKO#29 mESCs, rep2

description:
TKO_29_2
Gene expression of TKO embryoid bodies cultured for 10 days.


title: MGG8DGC_2

description: MGG8 DGC


title: C-33-1E2 FLAG-1E2-8

type: genomic

city: Bethesda

first: Kui

last: Shen

address: Room 3B62, 31 Center Drive

institute: National Institute of Allergy and Infectious Diseases, NIH

description: ChIP-chip C-33-1E2 with anti-FLAG

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

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

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: FLAG ChIP DNA from C-33-1E2

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: C-33 cells (Auersperg, 1964) were cultured in DMEM, 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: 2 mg of chromatin was incubated overnight with anti-FLAG M2 antibody prebound to Dynabeads conjugated to Protein G. Further processing for ChIP-chip was as described by Jang et al. (Jang et al., 2009). DNA isolated from immunoprecipitated chromatin was amplified using the whole genome amplification system (WGA, Sigma).

treatment_protocol: For mitotic cells, C-33 cells were blocked by 2 mM thymidine overnight and released into medium without thymidine for 9 h. Four hours before harvesting, E2 expression was induced with 3 μM CdSO4 and mitotic cells were collected by mitotic shake off

value: C-33-1E2, mitotic

tag: chip antibody

value: FLAG

source_name: Input DNA from C-33-1E2

value: None, input DNA


title: Gene expression comparison between malignant ascites OVC346 versus control peritoneal fluid OV370

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

description: Cy3 label sample being the reference

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

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

source_name: peritoneal fluid OV370

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: The three malignant ascites used in this study (OVC346, OVC508, OVC509) were obtained at the time of initial cytoreductive surgery from three ovarian cancer patients at the Centre hospitalier universitaire de Sherbrooke. Peritoneal fluids were obtained from three patients operated for conditions other than cancer. Fluids were centrifuged at 1000 rpm for 15 min and the cell-free fractions were stored at -20°C until assayed. HPMCs were isolated from peritoneal lavages of two women operated for conditions other than cancer. After centrifugation, the cell pellet is placed on T25 culture plates. HPMCs were grown in DMEM/F12 supplemented with 0.4 µg/ml of hydrocortisone and 10 ng/ml EGF (Sigma, Oakville, Canada), 10% FBS and antibiotics. The media was changed every 3 days while the cells were maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: Microarrays were performed on HPMCs exposed to 3 malignant ascites from women with advanced (stage III/IV) serous OC and two benign peritoneal fluids. First, we generated lists of significantly up-regulated and down-regulated genes that were differentially expressed between OC ascites (OVC346, OVC508 and OVC509) and control OV370 peritoneal fluid. Then, the set of genes that were commonly expressed between control peritoneal fluids (OV370 and OV401) were subtracted from the first list of genes to generate a dataset of differentially expressed genes between malignant ascites and benign peritoneal fluids.

value: peritoneal fluid

source_name: ascites OVC346

value: malignant ascites


title: Gene expression comparison between malignant ascites OVC509 versus control peritoneal fluid OV370

description: Cy3 label sample being the reference

source_name: ascites OVC509


title: Embryoid Bodies (EB) Derived from Wild Type mESCs, rep1

description:
WT_1
Gene expression of WT embryoid bodies cultured for 10 days.


title: MGG8DGC_1

description: MGG8 DGC


title: Gene expression comparison between malignant ascites OVC508 versus control peritoneal fluid OV370

description: Cy3 label sample being the reference

source_name: ascites OVC508


title: C-33-1E2 FLAG-1E2-37

description: ChIP-chip C-33-1E2 with anti-FLAG


title: MGG6DGC_1

description: MGG6 DGC

source_name: MGG6 human glioblastoma serum-grown cell line


title: C-33-1E2 FLAG-1E2-9

description: ChIP-chip C-33-1E2 with anti-FLAG


title: C-33-1E2 FLAG-1E2-10

description: ChIP-chip C-33-1E2 with anti-FLAG


title: MGG6DGC_3

description: MGG6 DGC


title: MGG4DGC_3

description: MGG4 DGC

source_name: MGG4 human glioblastoma serum-grown cell line


title: CD8 T cell clone_unconventional _anti-CD3_rep3


title: MGG6DGC_2

description: MGG6 DGC


title: MGG8TPC_3

description: MGG8 TPC

source_name: MGG8 human glioblastoma stem cell line


title: MGG8TPC_2

description: MGG8 TPC


title: MGG6TPC_1

description: MGG6 TPC

source_name: MGG6 human glioblastoma stem cell line


title: MGG6TPC_3

description: MGG6 TPC


title: MGG8iTPC_2

description: MGG8 iTPC induced with POU3F2, SOX2, SALL2, OLIG2


title: C-33-1E2 FLAG-1E2-35

description: ChIP-chip C-33-1E2 with anti-FLAG


title: C-33-16E1E2 HPV16 E1-3

description: ChIP-chip C-33-1E2 with anti-FLAG M2

source_name: 16E1 ChIP DNA from C-33-16E1E2

growth_protocol: C-33 cells were cultured in DMEM, 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

treatment_protocol: For transient HPV16 E1/E2 expression, C-33 cells were cotransfected with pMEP9/EE-HPV16 E1 and pMEP4/FLAG-HPV16 E2. E2 expression was induced with 3 μM CdSO4 induction for 4 h before harvest at 24 h post-transfection.

value: C-33-16E1E2, asynchronous

value: EE (Glu-Glu)

source_name: Input DNA from C-33-16E1E2


title: MGG6TPC_2

description: MGG6 TPC


title: MGG8DGC_emtpy_1

description: MGG8 DGC transfected with empty control vector


title: MGG8DGC_emtpy_2


title: MGG8iTPC_1


title: MGG8iTPC_3


title: CD8 T cell clone_conventional_anti-CD3_rep3


title: MGG4TPC_3

description: MGG4 TPC

source_name: MGG4 human glioblastoma stem cell line


title: C-33-1E2 FLAG-1E2-12

description: ChIP-chip C-33-1E2 with anti-FLAG


title: C-33 Brd4-3

description: ChIP-chip C-33 with anti-Brd4

source_name: Brd4 ChIP DNA from C-33

treatment_protocol: For mitotic cells, C-33 cells were blocked by 2 mM thymidine overnight and released into medium without thymidine for 9 h. Four hours before harvesting, the cells were treated with 3 μM CdSO4 and mitotic cells were collected by mitotic shake off

value: C-33, mitotic

source_name: Input DNA from C-33


title: MGG4TPC_1

description: MGG4 TPC


title: MGG4TPC_2

description: MGG4 TPC


title: MGG4DGC_2

description: MGG4 DGC


title: Gene expression comparison between control peritoneal fluid OV401 versus control peritoneal fluid OV370

description: Cy3 label sample being the reference

source_name: peritoneal fluid OV401


title: MGG4DGC_1

description: MGG4 DGC


title: MGG8TPC_1

description: MGG8 TPC


title: C-33-APH FancD2-3

description: ChIP-chip C-33-1E2 with anti-Brd4

source_name: FancD2 ChIP DNA from C-33-APH

treatment_protocol: C-33 cells were treated with 0.2 μM aphidicolin for 24 h before harvesting for ChIP-chip experiments.

value: C-33-APH, asynchronous

source_name: Input DNA from C-33-APH


title: PRMT5 shRNA expression A549 rep2

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

description: PRMT5 shRNA

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

label_protocol: 200 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: A549 cells were grown in DMEM medium plus 10 fetal bovine serum; LNCaP cells were grown in RPM1640 medium plus 10% fetal bovine serum.

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

treatment_protocol: Cells were infected with lentivirus expressing NT, p44/wdr77, or PRMT5 shRNA.  Cells were harvest for total RNA preparation six days post viral infection.

tag: cell line

value: lung cancer cell line

value: PRMT5 shRNA


title: PRMT5 shRNA expression A549 rep1

description: PRMT5 shRNA


title: C-33-1E2 FLAG-1E2-14

description: ChIP-chip C-33-1E2 with anti-FLAG

source_name: FLAG ChIP DNA from C-33-1E2

source_name: Input DNA from C-33-1E2


title: NT shRNA expression A549 rep4

description: NT shRNA

value: NT shRNA


title: NT shRNA expression A549 rep2

description: NT shRNA


title: C-33-1E2 FLAG-1E2-11

description: ChIP-chip C-33-1E2 with anti-FLAG


title: p44/wdr77 shRNA expression A549 rep1

description: p44 shRNA

value: p44 shRNA


title: PANC-1Tet/ZIC2 before the DOX withdrawal (mRNA)

city: Nagakute

first: Shingo

last: Inaguma

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Pathology

country: Japan

institute: Aichi Medical University School of Medicine

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.3.1

source_name: PANC-1Tet/Empty 48 hours after the DOX withdrawal.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Cells were maintained in DMEM containing 10% of DOX-free FBS with one microgram/ml of DOX.

extract_protocol: QIAGEN miRNeasy Mini Kit was used.

treatment_protocol: One microgram/ml of DOX was withdrawn from the medium.

value: Pancreatic Cancer Cell Line

tag: vector

value: Control clone

tag: tranfection

value: 48 hours after the DOX withdrawal


title: PANC-1Tet/Empty before the DOX withdrawal (mRNA)

source_name: PANC-1Tet/ZIC2 48 hours after the DOX withdrawal.

value: ZIC2 inducible clone


title: NT shRNA expression LNCaP rep2

description: NT shRNA

source_name: LNCaP

value: LNCaP

value: prostate cancer cell line


title: NT shRNA expression A549 rep1

description: NT shRNA


title: PRMT5 shRNA expression LNCaP rep2

description: PRMT5 shRNA


title: ZIC2-knockdown PANC-1 cells (mRNA)

source_name: Control-knockdown PANC-1 cells

value: Control

value: Control-knockdown


title: PRMT5 shRNA expression LNCaP rep1

description: PRMT5 shRNA


title: PANC-1Tet/ZIC2 48 hours after the DOX withdrawal (mRNA)

source_name: PANC-1Tet/ZIC2 before the DOX withdrawal.

value: before the DOX withdrawal


title: PANC-1Tet/Empty 48 hours after the DOX withdrawal (mRNA)

source_name: PANC-1Tet/Empty before the DOX withdrawal.


title: NT shRNA expression LNCaP rep1

description: NT shRNA


title: Control-knockdown PANC-1 cells (mRNA)

source_name: ZIC2-knockdown PANC-1 cells

value: ZIC2 knock-down


title: C-33-1E2 Brd4-3

description: ChIP-chip C-33-1E2 with anti-Brd4

source_name: Brd4 ChIP DNA from C-33-1E2

treatment_protocol: For mitotic cells, C-33-1E2 cells were blocked by 2 mM thymidine overnight and released into medium without thymidine for 9 h. Four hours before harvesting, E2 expression was induced with 3 μM CdSO4 and mitotic cells were collected by mitotic shake off

value: C-33-1E2, mitotic

value: None, input DNA


title: HBC5 Neg siRNA

status: Public on Apr 13 2014

city: Tokyo

first: Toshiro

last: Migita

address: 2-1-6 Kami-kitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

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

growth_protocol: The cell line was cultured in vitro in 10cm dishes until 80-90% confluency and then total RNA was isolated.

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

value: Human breast cancer


title: NT shRNA expression A549 rep3

description: NT shRNA

value: lung cancer cell line


title: LNC

city: St. Louis

first: ravindra

last: uppaluri

address: 660 South Euclid Avenue

institute: Washington University

description:
6958 -  LNC
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
GSGX Version: 1.8.0
Analysis: Individual_cubic_spline_bkgd
The data were normalized using cubic spline normalization

source_name: mouse oral cancer cell line

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

growth_protocol: Standard mouse oral cancer cell line media

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

treatment_protocol: No treatments

tag: genotype/variation

value: WT

value: mouse oral cancer cell line (a lymph node metastasis of the MOC2 tumor)

tag: gender

value: female

tag: growth

value: not done

tag: metastatic


title: LNCaP Neg siRNA

tag: cell type

value: Human prostate cancer


title: LNB

description:
6957 -  LNB
Replicate 2

tag: strain


title: OKB

description:
6963 - OKB
Replicate 2

source_name: normal oral keratinocytes

value: normal oral keratinocytes

value: normal

value: NO


title: HBC5 ACLY siRNA

source_name: HBC5_ACLY knockdown

tag: treated with

value: ACLY siRNA


title: p44/wdr77 shRNA expression A549 rep2

description: p44 shRNA

tag: treatment

value: p44 shRNA


title: OKA

description:
6962 - OKA
Replicate 1


title: LNA

description:
6956 -  LNA
Replicate 1


title: MOC23C

description:
6961 - MOC23C
Replicate 3

value: mouse oral cancer cell line MOC23

value: indolent


title: MOC22C

description:
6960 - MOC22C
Replicate 3

value: mouse oral cancer cell line MOC22


title: C-33-APH FancD2-2

description: ChIP-chip C-33-1E2 with anti-Brd4

value: C-33-APH, asynchronous


title: C-33 Brd4-2

description: ChIP-chip C-33 with anti-Brd4

source_name: Brd4 ChIP DNA from C-33

value: C-33, mitotic

source_name: Input DNA from C-33

value: C-33-1E2, mitotic

value: None, input DNA


title: MOC22B

description:
6953 -  MOC22B
Replicate 2

value: WT


title: MOC23B

description:
6955 -  MOC23B
Replicate 2


title: LNCaP ACLY siRNA

source_name: LNCaP_ACLY knockdown

value: LNCaP


title: C-33-1E2 Brd4-2

description: ChIP-chip C-33-1E2 with anti-Brd4


title: C-33-16E1E2 HPV16 E1-2

description: ChIP-chip C-33-1E2 with anti-FLAG M2

source_name: 16E1 ChIP DNA from C-33-16E1E2

value: C-33-16E1E2, asynchronous

value: EE (Glu-Glu)

source_name: Input DNA from C-33-16E1E2


title: MOC2-10C

description:
6951 -  MOC10C
Replicate 3

value: mouse oral cancer cell line MOC10

value: female

value: aggressive

value: lymph node/lung


title: MOC22A

description:
6952 -  MOC22A
Replicate 1

value: NO


title: MOC2-10A

description:
6949 -  MOC10A
Replicate 1


title: C-33-16E1E2 HPV16 E1-4

description: ChIP-chip C-33-1E2 with anti-FLAG M2


title: C-33 Brd4-4

description: ChIP-chip C-33 with anti-Brd4


title: MOC2-10B

description:
6950 -  MOC10B
Replicate 2


title: MOC2-7D

description:
6948 -  MOC7D
Replicate 3

value: mouse oral cancer cell line MOC7

value: lymph node


title: MOC2D

description:
6945 -  MOC2D
Replicate 3

value: mouse oral cancer cell line MOC2


title: MOC2A

description:
6943 -  MOC2A
Replicate 1


title: MOC2-7B

description:
6947 -  MOC7B
Replicate 2


title: MOC2-7A

description:
6946 -  MOC7A
Replicate 1


title: MOC1D

description:
6942 -  MOC1D
Replicate 3

value: mouse oral cancer cell line MOC1

value: indolent


title: Saliva from healthy human female card A 3

status: Public on Apr 12 2014

first: Hyun Min

last: Jung

address: 6 Center Drive

department: Division of Developmental Biology

institute: National Institutes of Health

data_processing: The analysis of expression of the >700 miRNAs was performed by the DNA Core at the Interdisciplinary Center for Biotechnology Research Center at the University of Florida, according to the manufacturer’s protocol except the pre-amplification step was omitted. The NormFinder algorithm was used to identify the optimal normalization of miRNA among the 25 most abundantly expressed miRNAs detected.

label: FAM

source_name: healthy human female

extract_protocol: Total RNA was extracted using a protocol combining the Oragene®•RNA Self-Collection Kit (DNA Genotek) and the mirVanaTM miRNA isolation kit (Ambion, Austin, TX). In brief, 300 µl of whole saliva mixed with 300 µl of Oragene®•RNA was incubated for 1 hour at 50ºC, then heated at 90ºC for 15 minutes and allowed to cool to room temperature. Afterwards, 48 µl of the Oragene®•RNA Neutralizer solution was added. Samples were mixed, incubated on ice for 10 minutes, and then centrifuged at 10 000 x g for 3 minutes at room temperature. The supernatant was collected and the isolation of total RNA was completed using the mirVanaTM miRNA isolation kit with modifications to the manufacturer’s protocol. First, for the lysis step, the addition of the Lysis/Binding buffer and the miRNA Homogenate Additive were bypassed and instead an equal volume of acid-phenol:chloroform was added directly to the collected supernatant. Second, only 50 µl of 95ºC elution solution was used to elute RNA. RNA was quantified using a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). An Agilent 2100 Bioanalyzer (Santa Clara, CA) was used to detect the size distribution of total RNA, as well as determine the quality of the RNA.

tag: sample type

value: saliva


title: Saliva from healthy human female card A 4


title: Saliva from healthy human female card A 6


title: MOC1E

description:
6959 - MOC1E
Replicate 4


title: MOC1C

description:
6941 -  MOC1C
Replicate 2


title: C-33-1E2 FLAG-1E2-36

description: ChIP-chip C-33-1E2 with anti-FLAG

source_name: FLAG ChIP DNA from C-33-1E2

value: C-33-1E2, mitotic

value: FLAG

source_name: Input DNA from C-33-1E2


title: C-33-1E2 Brd4-4

description: ChIP-chip C-33-1E2 with anti-Brd4

value: None, input DNA


title: Saliva from healthy human female card A 2


title: MOC2C

description:
6944 -  MOC2C
Replicate 2


title: Saliva from healthy human male card A 2

source_name: healthy human male

value: male


title: Saliva from healthy human male card A 5


title: Saliva from healthy human male card A 6


title: Saliva from healthy human male card A 1


title: Saliva from healthy human male card A 4


title: C-33-1E2 FLAG-1E2-34

description: ChIP-chip C-33-1E2 with anti-FLAG


title: MOC1A

description:
6940 -  MOC1A
Replicate 1

value: WT


title: Saliva from healthy human male card A 3


title: C-33-APH FancD2-4

description: ChIP-chip C-33-1E2 with anti-Brd4

source_name: FancD2 ChIP DNA from C-33-APH

value: C-33-APH, asynchronous

source_name: Input DNA from C-33-APH


title: C-33-1E2 H3K4me1

description: ChIP-chip C-33-1E2 with anti-H3K4me1

source_name: H3K4me1 ChIP DNA from C-33-1E2

treatment_protocol: Four hours before harvesting, C-33-1E2 cells were treated with 3 μM CdSO4 to produce HPV1 E2.

value: C-33-1E2, asynchronous


title: C-33-1E2 Brd4-1

description: ChIP-chip C-33-1E2 with anti-Brd4


title: Saliva from healthy human female card A 1

value: female


title: MOC23A

description:
6954 -  MOC23A
Replicate 1

value: mouse oral cancer cell line MOC23


title: Teff_rep4

city: New York

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Expression arrays were normalized in Bioconductor, using RMA and median polish settings in the expresso package.

source_name: Spl and LN sorted cells

label_protocol: Affymetrix protocol

growth_protocol: Cells were harvested from 6-8wk old mice.  T cells were purified by Dynal CD4 T cell positive selection kit and double sorted on GFP, etc.

extract_protocol: RNA was extracted using Trizol according to manufacturer's instructions.

tag: t cell type

value: Teff

value: Foxp3-negative CD4+ T cells from DT-treated Foxp3DTR mice


title: thymus-rep2

city: Albany

first: Dorina

last: Avram

address: 43 New Scotland Avenue

department: Center for Immunology and Microbial Disease

institute: Albany Medical Center

description: biological replicate 2 of 2

hyb_protocol: Agilent GeneExpression protocol

scan_protocol: Scanned on an Agilent C scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear LOWESS normalization.

source_name: Bcl11bF/FCD4Cre/Tcra-/- DP thymocytes

label_protocol: aRNA was generated using Agilent linear amplication kit then labeled using Kreatech ULS kit

growth_protocol: thymocytes isolated from mice with no treatment

extract_protocol: trizol and columns

value: DP thymocytes

source_name: TCRa-/- DP thymocytes

value: TCRa-/-


title: peripheral CD8+ T cells purified from infected mice repeat 1

description: biological replicate 1 of 2

source_name: CD8+ T cells purified from Bcl11bF/F/dLck-iCre mice infected with Listeria monocytogenes-OVA, day 6 postinfection

label_protocol: amplified RNA was generated using Agilent linear amplication kit then labeled using Kreatech ULS kit

treatment_protocol: CD8+ T cells purified by negative selection from Bcl11bF/F/dLck-iCre or wild type mice infected with Listeria monocytogenes-OVA, day 6 postinfection; purity of the cells - over 90%

value: CD8+ T cells

tag: infection

source_name: CD8+ T cells purified from wild type mice infected with Listeria monocytogenes-OVA, day 6 postinfection

value: wild type


title: human cd10+ cd19+ cells from tonsil rep4

city: Madrid

first: Lorena

last: Di Lisio

address: C/ Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description: GC 4

hyb_protocol: 100 ng of total RNA were hybridized on an Agilent Human miRNA one-color microarray, following the manufacturer’s instructions (Agilent Technologies)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Between-array median normalization was carried out to render miRNA expression datasets comparable using Genespring GX9 software.

source_name: human cd10+ cd19+ cells from tonsil

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

extract_protocol: total RNA was isolated by Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA quality was checked using total RNA (small fraction chip) with the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) and by 1% agarose electrophoresis, following the standard procedure.

tag: tissue

value: tonsil

value: germinal center B cells (CD10+ CD19+)


title: Teff_rep3


title: Teff_rep5


title: human cd10+ cd19+ cells from tonsil rep3

description: GC 3


title: human cd10+ cd19+ cells from tonsil rep1

description: GC 1


title: human cd10+ cd19+ cells from tonsil rep2

description: GC 2


title: human CD19+ IgD+ CD27- cells from tonsil rep3

description: naive 3

value: naive B cells (CD19+ IgD+ CD27-)


title: thymus-rep1

description: biological replicate 1 of 2


title: Teff_rep1


title: aTreg_rep4

value: Treg

value: Foxp3-positive CD4+ T cells from DT-treated Foxp3DTR mice


title: aTreg_rep3


title: C-33-16E1E2 HPV16 E1-1

description: ChIP-chip C-33-1E2 with anti-FLAG M2

value: C-33-16E1E2, asynchronous

value: EE (Glu-Glu)

value: None, input DNA


title: aTreg_rep5


title: peripheral CD8+ T cells purified from infected mice repeat 2

description: biological replicate 2 of 2

value: Listeria monocytogenes-OVA, day 6 postinfection


title: aTreg_rep2


title: aTreg_rep1


title: Saliva from healthy human female card A 5

value: female

value: saliva


title: human CD19+ IgD+ CD27- cells from tonsil rep1

description: naive 1


title: C-33-1E2 H3K4me2

description: ChIP-chip C-33-1E2 with anti-H3K4me2

source_name: H3K4me2 ChIP DNA from C-33-1E2

value: C-33-1E2, asynchronous


title: human CD19+ IgD+ CD27- cells from tonsil rep2

description: naive 2


title: C-33-APH FancD2-1

description: ChIP-chip C-33-1E2 with anti-Brd4

value: C-33-APH, asynchronous


title: C-33 Brd4-1

description: ChIP-chip C-33 with anti-Brd4

source_name: Brd4 ChIP DNA from C-33

value: C-33, mitotic

source_name: Input DNA from C-33

value: C-33-1E2, mitotic


title: C-33-1E2 Brd4

description: ChIP-chip C-33-1E2 with anti-Brd4

source_name: Brd4 ChIP DNA from C-33-1E2

value: FLAG


title: C-33-1E2 HPV1 E2

description: ChIP-chip C-33-1E2 with anti-FLAG M2

source_name: 1E2 ChIP DNA from C-33-1E2


title: B-cell lymphoma 146

description: US22502553_251643612275_S01_miRNA-v1_95_May07_2_2_CLL-G

hyb_protocol: Hybridization settings: 20 hours, at 55ºC, at 20rpm. Blocking agent, hybridization and washing buffers was performed according to agilent recomandation.

scan_protocol: Scan resolution 5um on an Agilent scanner

data_processing: Data are normalized to the median of the series (between arrays) by R program version 2.4, (available at http://www.r-project.org/). For normalization was used the "Processed Signal" of the feature extraction files (already includes background subtraction) was used. Average of miRs replicates was then applied using the following web page: http://prep.bioinfo.cnio.es/. Significance Analysis of Microarray excel macro (SAM) was used.

source_name: Tumoral sample

label_protocol: 100ng of total RNA were dephosphorilated, denaturalizated, treated with ligase T4 and labelled with Cy3 for 2 hours at 16ºC

extract_protocol: total RNA was extraxted by trizol reagent (Invitrogen, Carlsbad, CA, USA).

value: B-cell lymphoma

tag: tumor type

value: Small Lymphocytic Lymphoma / Chronic Lymphocytic Leukemia


title: B-cell lymphoma 141

description: US22502553_251643612275_S01_miRNA-v1_95_May07_1_1_CLL-G


title: B-cell lymphoma 144

description: US22502553_251643612275_S01_miRNA-v1_95_May07_1_4_CLL-G


title: B-cell lymphoma 143

description: US22502553_251643612275_S01_miRNA-v1_95_May07_1_3_CLL-G


title: B-cell lymphoma 142

description: US22502553_251643612275_S01_miRNA-v1_95_May07_1_2_CLL-G


title: B-cell lymphoma 145

description: US22502553_251643612275_S01_miRNA-v1_95_May07_2_1_CLL-G


title: B-cell lymphoma 147

description: US22502553_251643612276_S01_miRNA-v1_95_May07_2_4_CLL-G


title: B-cell lymphoma 137

description: US22502553_251643612274_S01_miRNA-v1_95_May07_2_1_CLL-G


title: B-cell lymphoma 139

description: US22502553_251643612274_S01_miRNA-v1_95_May07_2_3_CLL-G


title: B-cell lymphoma 140

description: US22502553_251643612274_S01_miRNA-v1_95_May07_2_4_CLL-G


title: B-cell lymphoma 138

description: US22502553_251643612274_S01_miRNA-v1_95_May07_2_2_CLL-G


title: CD4 D

city: Padova

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

country: Italy

institute: Università degli Studi di Padova

description: miRNA expression in control cells

hyb_protocol: Agilent kit G4470A according to protocol

scan_protocol: Agilent Microarray Scanner and Feature Extraction Software according to manual

data_processing: quantile-quantile normalization, after having substituted negative values with the lowest positive value obtained for the individual miRNA. Viral miRNA were excluded from results but reported in the raw data.

source_name: CD4 cells isolated from normal PBMC

label_protocol: 100 ng RNA was labelled with pCp-Cy3 using Agilent kit 5190-0408 according to protocol

extract_protocol: Total RNA was isolated using standard phenol-acid guanidine isothiocyanate procedure (TRIzol, Invitrogen)

treatment_protocol: ATLL samples represent freshly isolated PBMC from patients. CD4 controls were islolated from PBMC of normal donors using MACS isolation kits (Miltenyi). Cells were harvested immediately or after stimulation in vitro with PHA and IL-2

tag: disease state

value: normal

value: peripheral blood mononuclear cell (PBMC)


title: CD4 A stim

description: miRNA expression in control cells

source_name: CD4 cells isolated from normal PBMC; stimulated in vitro


title: CD4 D stim

description: miRNA expression in control cells


title: ATLL 3

description: miRNA expression in tumor cells

source_name: PBMC from ATLL patient

value: ATLL patient (leukemia)


title: CD4 A

description: miRNA expression in control cells


title: ATLL 12

description: miRNA expression in tumor cells


title: ATLL 24

description: miRNA expression in tumor cells

value: ATLL patient (lymphoma)


title: ATLL 32

description: miRNA expression in tumor cells


title: CD4 P

description: miRNA expression in control cells


title: CD4 P stim

description: miRNA expression in control cells


title: ATLL 5a

description: miRNA expression in tumor cells


title: ATLL 1

description: miRNA expression in tumor cells


title: ATLL 14

description: miRNA expression in tumor cells


title: CD4 B

description: miRNA expression in control cells


title: B-cell lymphoma 135

description: US22502553_251643612274_S01_miRNA-v1_95_May07_1_3_CLL-G


title: B-cell lymphoma 136

description: US22502553_251643612274_S01_miRNA-v1_95_May07_1_4_CLL-G


title: B-cell lymphoma 134

description: US22502553_251643612274_S01_miRNA-v1_95_May07_1_2_CLL-G


title: CD4 B stim

description: miRNA expression in control cells


title: B-cell lymphoma 133

description: US22502553_251643612274_S01_miRNA-v1_95_May07_1_1_CLL-G


title: B-cell lymphoma 131

description: US22502553_251643612265_S01_miRNA-v1_95_May07_1_3_CLL-G


title: B-cell lymphoma 130

description: US22502553_251643612265_S01_miRNA-v1_95_May07_1_2_CLL-G


title: B-cell lymphoma 132

description: US22502553_251643612265_S01_miRNA-v1_95_May07_2_3_CLL-G


title: B-cell lymphoma 128

description: US22502553_251643612181_S01_miRNA-v1_95_May07_2_3_SMZL

value: Splenic Marginal Zone Lymphoma


title: B-cell lymphoma 118

description: US22502553_251643612180_S01_miRNA-v1_95_May07_1_1_SMZL


title: B-cell lymphoma 121

description: US22502553_251643612180_S01_miRNA-v1_95_May07_1_4_SMZL


title: B-cell lymphoma 120

description: US22502553_251643612180_S01_miRNA-v1_95_May07_1_3_SMZL


title: B-cell lymphoma 117

description: US22502553_251643612179_S01_miRNA-v1_95_May07_2_4_SMZL


title: B-cell lymphoma 124

description: US22502553_251643612181_S01_miRNA-v1_95_May07_1_1_SMZL


title: B-cell lymphoma 126

description: US22502553_251643612181_S01_miRNA-v1_95_May07_1_3_SMZL


title: B-cell lymphoma 116

description: US22502553_251643612178_S01_miRNA-v1_95_May07_2_2_FL

value: Follicular Lymphoma


title: B-cell lymphoma 112

description: US22502553_251643611979_S01_miRNA-v1_95_May07_2_2_FL


title: B-cell lymphoma 122

description: US22502553_251643612180_S01_miRNA-v1_95_May07_2_1_SMZL


title: B-cell lymphoma 125

description: US22502553_251643612181_S01_miRNA-v1_95_May07_1_2_SMZL


title: B-cell lymphoma 123

description: US22502553_251643612180_S01_miRNA-v1_95_May07_2_2_SMZL


title: B-cell lymphoma 127

description: US22502553_251643612181_S01_miRNA-v1_95_May07_2_2_SMZL


title: B-cell lymphoma 113

description: US22502553_251643611979_S01_miRNA-v1_95_May07_2_3_FL


title: B-cell lymphoma 114

description: US22502553_251643611979_S01_miRNA-v1_95_May07_2_4_FL


title: B-cell lymphoma 115

description: US22502553_251643612178_S01_miRNA-v1_95_May07_2_1_FL


title: B-cell lymphoma 109

description: US22502553_251643611979_S01_miRNA-v1_95_May07_1_2_FL


title: B-cell lymphoma 106

description: US22502553_251643611978_S01_miRNA-v1_95_May07_2_2_FL


title: B-cell lymphoma 108

description: US22502553_251643611978_S01_miRNA-v1_95_May07_2_4_FL


title: B-cell lymphoma 110

description: US22502553_251643611979_S01_miRNA-v1_95_May07_1_4_FL


title: B-cell lymphoma 111

description: US22502553_251643611979_S01_miRNA-v1_95_May07_2_1_FL


title: B-cell lymphoma 105

description: US22502553_251643611978_S01_miRNA-v1_95_May07_2_1_FL


title: B-cell lymphoma 129

description: US22502553_251643612181_S01_miRNA-v1_95_May07_2_4_SMZL


title: Teff_rep2

value: Teff

value: Foxp3-negative CD4+ T cells from DT-treated Foxp3DTR mice


title: B-cell lymphoma 107

description: US22502553_251643611978_S01_miRNA-v1_95_May07_2_3_FL


title: B-cell lymphoma 104

description: US22502553_251643611978_S01_miRNA-v1_95_May07_1_4_FL


title: B-cell lymphoma 87

description: US22502553_251643611740_S01_miRNA-v1_95_May07_2_4_MALT

value: Mucosa-Associated Lymphatic Tissue Lymphoma


title: B-cell lymphoma 89

description: US22502553_251643611779_S01_miRNA-v1_95_May07_1_3_MALT


title: B-cell lymphoma 86

description: US22502553_251643611740_S01_miRNA-v1_95_May07_2_3_MALT


title: B-cell lymphoma 88

description: US22502553_251643611779_S01_miRNA-v1_95_May07_1_1_MALT


title: B-cell lymphoma 92

description: US22502553_251643611779_S01_miRNA-v1_95_May07_2_2_MALT


title: B-cell lymphoma 97

description: US22502553_251643611780_S01_miRNA-v1_95_May07_2_4_FL


title: B-cell lymphoma 100

description: US22502553_251643611977_S01_miRNA-v1_95_May07_1_2_FL


title: B-cell lymphoma 93

description: US22502553_251643611779_S01_miRNA-v1_95_May07_2_3_MALT


title: B-cell lymphoma 103

description: US22502553_251643611978_S01_miRNA-v1_95_May07_1_3_FL


title: B-cell lymphoma 98

description: US22502553_251643611781_S01_miRNA-v1_95_May07_2_4_FL


title: B-cell lymphoma 95

description: US22502553_251643611780_S01_miRNA-v1_95_May07_2_2_FL


title: B-cell lymphoma 101

description: US22502553_251643611978_S01_miRNA-v1_95_May07_1_1_FL


title: B-cell lymphoma 102

description: US22502553_251643611978_S01_miRNA-v1_95_May07_1_2_FL


title: B-cell lymphoma 82

description: US22502553_251643611740_S01_miRNA-v1_95_May07_1_3_MALT


title: B-cell lymphoma 80

description: US22502553_251643611739_S01_miRNA-v1_95_May07_2_4_MALT


title: B-cell lymphoma 79

description: US22502553_251643611739_S01_miRNA-v1_95_May07_2_3_MALT


title: B-cell lymphoma 83

description: US22502553_251643611740_S01_miRNA-v1_95_May07_1_4_MALT


title: B-cell lymphoma 85

description: US22502553_251643611740_S01_miRNA-v1_95_May07_2_2_MALT


title: B-cell lymphoma 94

description: US22502553_251643611780_S01_miRNA-v1_95_May07_2_1_FL


title: B-cell lymphoma 96

description: US22502553_251643611780_S01_miRNA-v1_95_May07_2_3_FL


title: B-cell lymphoma 84

description: US22502553_251643611740_S01_miRNA-v1_95_May07_2_1_MALT


title: B-cell lymphoma 77

description: US22502553_251643611739_S01_miRNA-v1_95_May07_2_1_DLBCL

value: Diffuse Large B Cell Lymphoma


title: B-cell lymphoma 90

description: US22502553_251643611779_S01_miRNA-v1_95_May07_1_4_MALT


title: B-cell lymphoma 78

description: US22502553_251643611739_S01_miRNA-v1_95_May07_2_2_DLBCL


title: B-cell lymphoma 99

description: US22502553_251643611977_S01_miRNA-v1_95_May07_1_1_FL


title: B-cell lymphoma 81

description: US22502553_251643611740_S01_miRNA-v1_95_May07_1_1_MALT


title: B-cell lymphoma 91

description: US22502553_251643611779_S01_miRNA-v1_95_May07_2_1_MALT


title: B-cell lymphoma 76

description: US22502553_251643611739_S01_miRNA-v1_95_May07_1_4_DLBCL


title: B-cell lymphoma 75

description: US22502553_251643611739_S01_miRNA-v1_95_May07_1_3_DLBCL


title: B-cell lymphoma 74

description: US22502553_251643611739_S01_miRNA-v1_95_May07_1_2_DLBCL


title: B-cell lymphoma 72

description: US22502553_251643611738_S01_miRNA-v1_95_May07_2_2_DLBCL


title: B-cell lymphoma 73

description: US22502553_251643611738_S01_miRNA-v1_95_May07_2_3_DLBCL


title: B-cell lymphoma 66

description: US22502553_251643611602_S01_miRNA-v1_95_May07_2_1_DLBCL


title: B-cell lymphoma 69

description: US22502553_251643611738_S01_miRNA-v1_95_May07_1_3_DLBCL


title: B-cell lymphoma 64

description: US22502553_251643611602_S01_miRNA-v1_95_May07_1_3_DLBCL


title: B-cell lymphoma 71

description: US22502553_251643611738_S01_miRNA-v1_95_May07_2_1_DLBCL


title: B-cell lymphoma 65

description: US22502553_251643611602_S01_miRNA-v1_95_May07_1_4_DLBCL


title: B-cell lymphoma 67

description: US22502553_251643611602_S01_miRNA-v1_95_May07_2_3_DLBCL


title: B-cell lymphoma 68

description: US22502553_251643611738_S01_miRNA-v1_95_May07_1_2_DLBCL


title: B-cell lymphoma 63

description: US22502553_251643611602_S01_miRNA-v1_95_May07_1_1_DLBCL


title: B-cell lymphoma 52

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_3_DLBCL


title: B-cell lymphoma 49

description: US22502553_251643611592_S01_miRNA-v1_95_May07_2_1_NMZL

value: Nodal Marginal Zone Lymphoma


title: B-cell lymphoma 51

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_2_DLBCL


title: B-cell lymphoma 56

description: US22502553_251643611593_S01_miRNA-v1_95_May07_2_4_DLBCL


title: B-cell lymphoma 50

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_1_DLBCL


title: B-cell lymphoma 57

description: US22502553_251643611600_S01_miRNA-v1_95_May07_1_3_DLBCL


title: B-cell lymphoma 55

description: US22502553_251643611593_S01_miRNA-v1_95_May07_2_3_DLBCL


title: B-cell lymphoma 48

description: US22502553_251643611592_S01_miRNA-v1_95_May07_1_4_NMZL


title: B-cell lymphoma 53

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_4_DLBCL


title: B-cell lymphoma 54

description: US22502553_251643611593_S01_miRNA-v1_95_May07_2_1_DLBCL


title: B-cell lymphoma 58

description: US22502553_251643611600_S01_miRNA-v1_95_May07_1_4_DLBCL


title: B-cell lymphoma 60

description: US22502553_251643611600_S01_miRNA-v1_95_May07_2_2_DLBCL


title: B-cell lymphoma 59

description: US22502553_251643611600_S01_miRNA-v1_95_May07_2_1_DLBCL


title: B-cell lymphoma 62

description: US22502553_251643611601_S01_miRNA-v1_95_May07_2_4_DLBCL


title: B-cell lymphoma 61

description: US22502553_251643611600_S01_miRNA-v1_95_May07_2_3_DLBCL


title: B-cell lymphoma 47

description: US22502553_251643611592_S01_miRNA-v1_95_May07_1_3_NMZL


title: B-cell lymphoma 70

description: US22502553_251643611738_S01_miRNA-v1_95_May07_1_4_DLBCL


title: B-cell lymphoma 46

description: US22502553_251643611592_S01_miRNA-v1_95_May07_1_2_NMZL


title: B-cell lymphoma 45

description: US22502553_251643611592_S01_miRNA-v1_95_May07_1_1_NMZL


title: B-cell lymphoma 41

description: US22502553_251643611591_S01_miRNA-v1_95_May07_1_3_NMZL


title: B-cell lymphoma 39

description: US22502553_251643611591_S01_miRNA-v1_95_May07_1_1_NMZL


title: B-cell lymphoma 40

description: US22502553_251643611591_S01_miRNA-v1_95_May07_1_2_NMZL


title: B-cell lymphoma 44

description: US22502553_251643611591_S01_miRNA-v1_95_May07_2_3_NMZL


title: B-cell lymphoma 42

description: US22502553_251643611591_S01_miRNA-v1_95_May07_1_4_NMZL


title: B-cell lymphoma 43

description: US22502553_251643611591_S01_miRNA-v1_95_May07_2_2_NMZL


title: B-cell lymphoma 37

description: US22502553_251643611462_S01_miRNA-v1_95_May07_1_3_MCL

value: Mantle Cell Lymphoma


title: B-cell lymphoma 36

description: US22502553_251643611462_S01_miRNA-v1_95_May07_1_2_MCL


title: B-cell lymphoma 34

description: US22502553_251643610354_S01_miRNA-v1_95_May07_2_4_MCL


title: B-cell lymphoma 35

description: US22502553_251643611462_S01_miRNA-v1_95_May07_1_1_MCL


title: Saliva from healthy human female card B 6

source_name: healthy human female

value: female

value: saliva


title: Saliva from healthy human female card B 2


title: Saliva from healthy human female card B 3


title: Saliva from healthy human female card B 5


title: B-cell lymphoma 33

description: US22502553_251643610354_S01_miRNA-v1_95_May07_2_3_MCL


title: Saliva from healthy human female card B 1


title: B-cell lymphoma 32

description: US22502553_251643610354_S01_miRNA-v1_95_May07_2_1_MCL


title: B-cell lymphoma 28

description: US22502553_251643610353_S01_miRNA-v1_95_May07_2_4_MCL


title: Saliva from healthy human female card B 4


title: B-cell lymphoma 31

description: US22502553_251643610354_S01_miRNA-v1_95_May07_1_3_MCL


title: B-cell lymphoma 27

description: US22502553_251643610353_S01_miRNA-v1_95_May07_2_3_MCL


title: B-cell lymphoma 30

description: US22502553_251643610354_S01_miRNA-v1_95_May07_1_2_MCL


title: B-cell lymphoma 24

description: US22502553_251643610353_S01_miRNA-v1_95_May07_1_1_MCL


title: B-cell lymphoma 26

description: US22502553_251643610353_S01_miRNA-v1_95_May07_1_4_MCL


title: B-cell lymphoma 25

description: US22502553_251643610353_S01_miRNA-v1_95_May07_1_2_MCL


title: B-cell lymphoma 22

description: US22502553_251643610352_S01_miRNA-v1_95_May07_2_3_MCL


title: B-cell lymphoma 23

description: US22502553_251643610352_S01_miRNA-v1_95_May07_2_4_MCL


title: B-cell lymphoma 38

description: US22502553_251643611462_S01_miRNA-v1_95_May07_1_4_MCL


title: B-cell lymphoma 29

description: US22502553_251643610354_S01_miRNA-v1_95_May07_1_1_MCL


title: B-cell lymphoma 119

description: US22502553_251643612180_S01_miRNA-v1_95_May07_1_2_SMZL


title: B-cell lymphoma 21

description: US22502553_251643610352_S01_miRNA-v1_95_May07_2_2_MCL


title: B-cell lymphoma 19

description: US22502553_251643610352_S01_miRNA-v1_95_May07_1_3_MCL


title: B-cell lymphoma 18

description: US22502553_251643610352_S01_miRNA-v1_95_May07_1_2_MCL


title: B-cell lymphoma 20

description: US22502553_251643610352_S01_miRNA-v1_95_May07_1_4_MCL


title: Saliva from healthy human male card B 6

source_name: healthy human male

value: male


title: Saliva from healthy human male card B 4


title: Saliva from healthy human male card B 5


title: B-cell lymphoma 16

description: US22502553_251643612182_S01_miRNA-v1_95_May07_2_3_BL

value: B-cell lymphoma

value: Burkitt Lymphoma


title: B-cell lymphoma 17

description: US22502553_251643610352_S01_miRNA-v1_95_May07_1_1_MCL


title: B-cell lymphoma 14

description: US22502553_251643611655_S01_miRNA-v1_95_May07_1_1_BL


title: B-cell lymphoma 15

description: US22502553_251643612182_S01_miRNA-v1_95_May07_2_2_BL


title: B-cell lymphoma 13

description: US22502553_251643611654_S01_miRNA-v1_95_May07_2_4_BL


title: B-cell lymphoma 10

description: US22502553_251643611654_S01_miRNA-v1_95_May07_1_4_BL


title: B-cell lymphoma 12

description: US22502553_251643611654_S01_miRNA-v1_95_May07_2_3_BL


title: B-cell lymphoma 8

description: US22502553_251643611654_S01_miRNA-v1_95_May07_1_2_BL


title: B-cell lymphoma 9

description: US22502553_251643611654_S01_miRNA-v1_95_May07_1_3_BL


title: B-cell lymphoma 11

description: US22502553_251643611654_S01_miRNA-v1_95_May07_2_1_BL


title: Saliva from healthy human male card B 1


title: Saliva from healthy human male card B 3


title: Saliva from healthy human male card B 2


title: B-cell lymphoma 7

description: US22502553_251643611653_S01_miRNA-v1_95_May07_2_4_BL


title: tPTEN-/- Premalignant DP Thymocytes Replicate 3

city: Berkeley

first: Megan

middle: L

last: Burger

state: CA

address: UC Berkeley, 465 Life Sciences Addition

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Biological replicate 3 of 3, premalignant tPTEN-/- DP thymocytes

hyb_protocol: Performed by Exiqon. Array = Exiqon miRCURY LNA array v11.0 miRBase 13.0 + miRPlus (Product Number 208202-A)

scan_protocol: Performed by Exiqon.

data_processing:
Performed by Exiqon.
The supplementary file normalized_data.txt contains the log2(Hy3/Hy5) ratios

source_name: tPTEN-/- DP thymocytes

label_protocol: Performed by Exiqon.

extract_protocol: Total RNA was extracted from 20 million DP thymocytes using a Qiagen miRNeasy Mini Kit per the manufacturer's protocol.

tag: genotype

value: Lck-Cre Pten fl/fl (tPTEN-/-)

tag: age

value: 9 weeks

tag: organ

value: Thymus

value: CD4+ CD8+ (DP) thymocytes collected by fluorescence-activated cell sorting

source_name: Total RNA pooled from equal amounts of Ctrl and tPTEN samples

value: mixture of Pten fl/fl (tPTEN-/-) and Lck-Cre Pten fl/fl (tPTEN-/-)


title: Layer 4 Visual Cortex Star Pyramid Non-Deprived, 3l

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

hyb_protocol: Following fragmentation, 15 or 20 ug of cRNA were hybridized for 18 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

data_processing:
The data were processed with Affymetrix Powertool with rma-sketch algorithm.
Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: Layer 4 visual cortex star pyramid neurons, non-deprived

label_protocol: Biotinylated cRNA was prepared using two rounds of T7 in vitro transcription based aRNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.3 to 1ng of total RNA.

growth_protocol: m-Citrin-labeled Star Pyramid neurons manually sorted from acutely dissociated mouse layer 4 visual cortex at postnatal day 14.

extract_protocol: Brain tissue was acutely dissociated and fluorescently labeled neurons were manually sorted using a glass pipette, then PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Monocular deprivation by TTX-injection at P12-P13 and again at P13-P14.

value: postnatal day 14 (P14)

value: monocular deprivation

tag: brain hemisphere

value: non-deprived

value: star pyramid neurons from layer 4 visual cortex


title: Layer 4 Visual Cortex Star Pyramid Non-Deprived, 1l


title: B-cell lymphoma 6

description: US22502553_251643611653_S01_miRNA-v1_95_May07_2_3_BL


title: Layer 4 Visual Cortex Star Pyramid Non-Deprived, 2l


title: B-cell lymphoma 5

description: US22502553_251643611653_S01_miRNA-v1_95_May07_2_1_BL


title: Layer 4 Visual Cortex Star Pyramid Deprived, 1r

source_name: Layer 4 visual cortex star pyramid neurons, deprived

value: deprived


title: Layer 4 Visual Cortex Star Pyramid Deprived, 2r


title: Layer 4 Visual Cortex Star Pyramid Deprived, 3r


title: tPTEN-/- Premalignant DP Thymocytes Replicate 2

description: Biological replicate 2 of 3, premalignant tPTEN-/- DP thymocytes


title: tPTEN-/- Premalignant DP Thymocytes Replicate 1

description: Biological replicate 1 of 3, premalignant tPTEN-/- DP thymocytes


title: Wild-type Control DP Thymocytes Replicate 3

description: Biological replicate 3 of 3, littermate wild-type control DP thymocytes

source_name: Wild-type DP thymocytes

value: Pten fl/fl (tPTEN-/-)


title: B-cell lymphoma 4

description: US22502553_251643611653_S01_miRNA-v1_95_May07_1_4_SMZL

value: Splenic Marginal Zone Lymphoma


title: AR7

city: Fukuoka

first: Sung Ouk

last: Nam

state: Fukuoka

address: 7-45-1 Nanakuma, Jonan-ku

department: Department of Obstetrics and Gynecology

institute: Faculty of Medicine, Fukuoka University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Human Genome Microarray Kit v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: HCT116, two dimensional culture for 72 hours

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Two CRC cell lines, HT29 and HCT116, were used in this study. For the 2DC, 2×10^5 cells were seeded in 6-well plates and incubated for 72 hours. For the 3DC, 1×10^5 cells were plated in 6-well plates precoated with Matrigel (Biocoat Cellware; Becton Dickinson, Franklin Lakes, NJ). Cells were incubated overnight and medium was removed and replaced with fresh medium. After incubation for 48 hours, cells from 3DC were retrieved from colonies using BD Cell Recovery Solution (Biocoat Cellware). For the tumor xenograft models, 5×10^6 cells were subcutaneously inoculated into 4-week old non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice (Charles River Laboratories Japan Inc., Yokohama, Japan). Tumors were resected when individual tumor volumes reached approximately 100 mm^3, and were frozen and fractured with liquid nitrogen.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: gender

value: colon

tag: cell line

value: CRC cell line HCT116

value: colorectal carcinoma

tag: growth condition

value: control two-dimensional cultures


title: Spl_Treg_rep2

source_name: Spl and LN sorted cells

value: Treg

tag: cell type

value: Foxp3-positive CD4+ T cells from Foxp3GFP mice


title: Spl_Teff_rep2

value: Teff

value: Foxp3-negative CD4+ T cells from Foxp3GFP mice


title: Spl_Teff_rep1


title: AR5

source_name: HT29, two dimensional culture for 72 hours

value: female

value: CRC cell line HT29

value: colorectal adenocarcinoma


title: AR6

source_name: HT29, three dimensional culture for 48 hours

value: three-dimensional cultures


title: AR8

source_name: HCT116, three dimensional culture for 48 hours

value: male


title: B-cell lymphoma 3

description: US22502553_251643611653_S01_miRNA-v1_95_May07_1_3_SMZL

value: B-cell lymphoma


title: B-cell lymphoma 2

description: US22502553_251643611653_S01_miRNA-v1_95_May07_1_2_SMZL


title: B-cell lymphoma 1

description: US22502553_251643611653_S01_miRNA-v1_95_May07_1_1_SMZL


title: Wild-type Control DP Thymocytes Replicate 2

description: Biological replicate 2 of 3, littermate wild-type control DP thymocytes

tag: strain

value: 9 weeks

value: Thymus

value: CD4+ CD8+ (DP) thymocytes collected by fluorescence-activated cell sorting

value: mixture of Pten fl/fl (tPTEN-/-) and Lck-Cre Pten fl/fl (tPTEN-/-)


title: B16_Treg_rep2

source_name: Tumor sorted cells


title: B16_Teff_rep2


title: B16_Treg_rep1


title: Spl_Treg_rep1


title: Wild-type Control DP Thymocytes Replicate 1

description: Biological replicate 1 of 3, littermate wild-type control DP thymocytes

value: Pten fl/fl (tPTEN-/-)


title: Hyperoxia control

status: Public on Apr 11 2014

city: Salt Lake City

first: Jesse

middle: Worth

last: Rowley

state: Ut

department: Medicine

institute: University of Utah

description: 80% oxygen for 48h - GM-CSF

data_processing: Matrix non-normalized are raw cT values. Matrix normalized are normalized to the average of P17:P20. Fold changes are calculated by dividing Matrix normalized values.

label: SYBR Green

source_name: alveolar epithelial cell

label_protocol: RT2 miRNA PCR array

growth_protocol: AEC culterd of fibronection in BEGM (Lonza) growth medium

extract_protocol: Qiagen miRNeasy (#217004)

treatment_protocol: Cells were grown in room air or 80% oxygen (in a sealed self-contained chamber (BillpsRothenberg) in the presence and absence of 20 ng/ml murine GM-CSF (R&D systems)

value: alveolar epithelial cell

value: Hyperoxia control


title: Hyperoxia + GM-CSF

description: 80% oxygen for 48h + GM-CSF

value: Hyperoxia + GM-CSF


title: Normoxia  + GM-CSF

description: +GM-CSF

value: Normoxia  + GM-CSF


title: Normoxia control

description: no treatment

value: Normoxia control


title: Bs_abrBS86D_rep2

city: Jouy-en-Josas

first: Olivier

last: Delumeau

address: Domaine de Vilvert

country: France

institute: INRA

description: abrB-S86D rep2

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

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

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region as described in (Nicolas et al., 2012 PMID: 22383849).
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).           10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).           10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: B. subtilis strains (wild-type and mutants) were grown in LB medium and harvested by centrifigution during the exponential phase of growth.

extract_protocol: Total RNA was extracted as described in Nicolas et al (2012) (PMID:22383849)

tag: genotype/variation

value: abrB-S86D mutant


title: Bs_abrB_rep1

description: abrB WT rep1

value: wild type


title: Bs_abrB_rep2

description: abrB WT rep2


title: B16_Teff_rep1

value: Teff

value: Foxp3-negative CD4+ T cells from Foxp3GFP mice


title: Bs_abrBS86A_rep2

description: abrB-S86A rep2

value: abrB-S86A mutant


title: Bs_abrBS86D_rep1

description: abrB-S86D rep1


title: Bs_abrBS86A_rep1

description: abrB-S86A rep1


title: Bsubtilis_KAcetate_t50min_combined_2_replicates

city: Amsterdam

first: Alexander

last: Ter Beek

address: Science Park 904

department: Molecular Biology & Microbial Food Safety

country: Netherlands

institute: University of Amsterdam - Swammerdam Institute for Life Sciences

description: 50 min treatment (potassium acetate) vs. control (average of 2 biological replicates)

hyb_protocol: Hybridization was performed in an automated slide processor (GE Healthcare) for 16 h at 37°C

scan_protocol: Microarrays were scanned in an Agilent DNA MicroArray Scanner (Agilent Technologies, Palo Alto, CA,USA) at 100 % PMT and 100% laser power

data_processing: Data supplied is log2 ratio of normalized and filtered 2 biological replicates, each containing 2 technical replicates (duplicate spots on the microarray and duplicate hybridization). Raw data and required information is supplied as supplementary file. The data was normalized in J-Express Pro 2.7 software (MolMine AS) using a global LOWESS (locally weighted scatterspot smoothing) algorithm. To avoid extreme intensity ratios, low intensity fluorescence data was floored at a value corresponding to a signal-to-noise ratio of 2.0. The data was averaged, log2 transformed and missing values were replaced by the average of the closest values. Genes with more than one missing value in the time-series were omitted. Since the variation in differential expression measurements depends on the fluorescent signal intensity (smaller variation at higher- and larger variation at lower fluorescence intensity levels), we applied an intensity-dependent method to identify differentially expressed genes. A sliding window of 50 genes was selected to calculate a Z-score from the local mean and standard deviation using the data in the R-I plot (log10(Cy5*Cy3) vs. log10(Cy5/Cy3). Genes more than 1.96 standard deviations away from the local average (|Z| > 1.96) were considered differentially expressed. This corresponds to a confidence level of 95 %. Genes that showed significant expression at t = 0 min were excluded from further analysis, unless the gene showed opposite significant expression in at least one of the other time-points. After the processing of the microarray data 3909 genes remained for each time-point, of which 459 were found to be significantly expressed. After the processing of the microarray data 3746 and 3685 genes of the total number of 4100 genes present on the array remained for each time-point, of which 503 and 582 were found to be significantly expressed in the potassium acetate and CCCP treatments, respectively.

organism: Bacillus subtilis

label_protocol: Direct incorporation: Random priming of SSII RT to incorporate Cy5- or Cy3-labeled dUTP, followed by NaOH hydrolysis of RNA

growth_protocol: An exponentially growing culture of B. subtilis WT strain 168 was inoculated in a well-controlled batch-fermentor (500 ml working volume) to an OD600 of 0.05. The culture was grown at 37 °C in defined medium at pH 6.4 with an aeration rate of 0.5 liters/min and vigorous stirring (200 rpm). At an OD600 of 0.2 (t_00min) the first sample of the time-series was taken.

extract_protocol: Total RNA was extracted using the Fast RNA pro Blue kit (Qbiogene) following manufacturer's instructions

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 50 min after t_00min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

tag: time

value: 50 minutes of exponential growth at an OD600 of 0.2 in defined minimal medium; sample is part of time series

growth_protocol: An exponentially growing culture of B. subtilis WT strain 168 was inoculated in a well-controlled batch-fermentor (500 ml working volume) to an OD600 of 0.05. The culture was grown at 37 °C in defined medium at pH 6.4 with an aeration rate of 0.5 liters/min and vigorous stirring (200 rpm). At an OD600 of 0.2 (t_00min), the culture was stressed with 25 mM potassium acetate.

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 50 min after addition of 25 mM potassium acetate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 50 minutes of growth in defined minimal medium after addition of 25 mM potassium acetate at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_KAcetate_t40min_combined_2_replicates

description: 40 min treatment (potassium acetate) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 40 min after t_00min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 40 minutes of exponential growth at an OD600 of 0.2 in defined minimal medium; sample is part of time series

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 40 min after addition of 25 mM potassium acetate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 40 minutes of growth in defined minimal medium after addition of 25 mM potassium acetate at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_CCCP_t50min_combined_2_replicates

description: 50 min treatment (CCCP) vs. control (average of 2 biological replicates)

growth_protocol: An exponentially growing culture of B. subtilis WT strain 168 was inoculated in a well-controlled batch-fermentor (500 ml working volume) to an OD600 of 0.05. The culture was grown at 37 °C in defined medium at pH 6.4 with an aeration rate of 0.5 liters/min and vigorous stirring (200 rpm). At an OD600 of 0.2 (t_00min), the culture was stressed with 0.85 µM CCCP.

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 50 min after addition of 0.85 µM CCCP. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 50 minutes of growth in defined minimal medium after addition of 0.85 µM CCCP  at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_CCCP_t10min_combined_2_replicates

description: 10 min treatment (CCCP) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 10 min after t_00min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 10 minutes of exponential growth at an OD600 of 0.2 in defined minimal medium; sample is part of time series

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 10 min after addition of 0.85 µM CCCP. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 10 minutes of growth in defined minimal medium after addition of 0.85 µM CCCP  at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_CCCP_t40min_combined_2_replicates

description: 40 min treatment (CCCP) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 40 min after addition of 0.85 µM CCCP. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 40 minutes of growth in defined minimal medium after addition of 0.85 µM CCCP  at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_KAcetate_t30min_combined_2_replicates

description: 30 min treatment (potassium acetate) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 30 min after t_00min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 30 minutes of exponential growth at an OD600 of 0.2 in defined minimal medium; sample is part of time series

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 30 min after addition of 25 mM potassium acetate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 30 minutes of growth in defined minimal medium after addition of 25 mM potassium acetate at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_CCCP_t00min_combined_2_replicates

description: 00 min treatment (CCCP) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture (OD600 = 0.2) at 00 min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 00 minutes of exponential growth at an OD600 of 0.2 in defined minimal medium; sample is part of time series

growth_protocol: An exponentially growing culture of B. subtilis WT strain 168 was inoculated in a well-controlled batch-fermentor (500 ml working volume) to an OD600 of 0.05. The culture was grown at 37 °C in defined medium at pH 6.4 with an aeration rate of 0.5 liters/min and vigorous stirring (200 rpm). At an OD600 of 0.2 (t_00min) the sample was taken.

value: 00 minutes of growth in defined minimal medium after addition of 0.85 µM CCCP  at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_CCCP_t20min_combined_2_replicates

description: 20 min treatment (CCCP) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 20 min after t_00min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 20 minutes of exponential growth at an OD600 of 0.2 in defined minimal medium; sample is part of time series

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 20 min after addition of 0.85 µM CCCP. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 20 minutes of growth in defined minimal medium after addition of 0.85 µM CCCP  at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_CCCP_t30min_combined_2_replicates

description: 30 min treatment (CCCP) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 30 min after addition of 0.85 µM CCCP. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 30 minutes of growth in defined minimal medium after addition of 0.85 µM CCCP  at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_KAcetate_t20min_combined_2_replicates

description: 20 min treatment (potassium acetate) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 20 min after addition of 25 mM potassium acetate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 20 minutes of growth in defined minimal medium after addition of 25 mM potassium acetate at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_KAcetate_t10min_combined_2_replicates

description: 10 min treatment (potassium acetate) vs. control (average of 2 biological replicates)

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 10 min after addition of 25 mM potassium acetate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 10 minutes of growth in defined minimal medium after addition of 25 mM potassium acetate at an OD600 of 0.2; sample is part of time series


title: Bsubtilis_KAcetate_t00min_combined_2_replicates

description: 00 min treatment (potassium acetate) vs. control (average of 2 biological replicates)

value: 00 minutes of growth in defined minimal medium after addition of 25 mM potassium acetate at an OD600 of 0.2; sample is part of time series


title: Nox vs. Hox.3h repl. 6

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Competitive hybridizations (hypoxia/normoxia) were performed for 18 hours in UltraHyb buffer (Ambion, Austin, TX) at 42 °C on 60mer oligonucleotide microarrays (MWG 30K mouse) using the GeneTAC hybridization station (PerkinElmer, Waltham, MA).

scan_protocol: Slides were scanned using the GenePix 4100A scanner (Axon Instruments, Downingtown, PA) at 10 µm resolution.

data_processing: Data were evaluated using the R software and the limma package from BioConductor. MA data was loess normalized.

source_name: lung homogenate, Hox, 3h

label_protocol: Labeled cDNA was generated using Superscript IIto reverse-transcribe 50 µg of RNA incorporating of Cy3- and Cy5-dCTP (all reagents from Invitrogen, Karlsruhe, Germany). The labeled cDNA was purified using a PCR purification kit (Qiagen). The volume of elute was reduced from 50 µl to 10 µL using a centrifugal vacuum concentrator.

extract_protocol: RNA was purified using RNeasy Mini Kit following the company’s instructions (Qiagen). Total RNA from 6 mice was pooled.

treatment_protocol: BALB/c mice were exposed for 3 hours to normobaric normoxia (FiO2of 0.21) or to normobaric hypoxia (FiO2of 0.10) (PMID:23161571)

value: BALB/c

tag: tissue type

value: lung

source_name: lung homogenate, Nox, 3h


title: Nox vs. Hox.3h repl. 5


title: Nox vs. Hox.3h repl. 4


title: Nox vs. Hox.3h repl. 1


title: Nox vs. Hox.3h repl. 2


title: Nox vs. Hox.3h repl. 3


title: CA1-transformed subiculum and retrosplenial cortex of D6/Zbtb20S mice, rep3

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

data_processing: RMA and loess normalization using the limma package in R.

source_name: CA1-transformed subiculum and retrosplenial cortex, D6/Zbtb20S

label_protocol: Ambion MessageAmp3.

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. Each RNA sample represents a pool of RNA obtained from dissected tissues of seven animals.

tag: strain/background

value: D6/Zbtb20S transgenic

value: postnatal day 1


title: CA1-transformed subiculum and retrosplenial cortex of D6/Zbtb20S mice, rep1


title: Wildtype subiculum and retrosplenial cortex, rep1

source_name: subiculum and retrosplenial cortex, wildtype

value: wildtype

value: subiculum and retrosplenial cortex


title: Wildtype subiculum and retrosplenial cortex, rep3