title: H9 [gene-level]

description:
H23 [gene-level]
H23_HuEx.CEL (see Series record)
H23_HuEx.rma-gene-core.chp


title: 833KE fe [gene-level]

status: Public on Jan 01 2015

type: RNA

city: Oslo

first: Sharmini

last: Alagaratnam

address: Radiumhospitalet, Montebello

department: Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
H27 [gene-level]
H27_HuEx.CEL (see Series record)
H27_HuEx.rma-gene-core.chp

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned in-house.

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

data_processing:
RMA expression value derived from Expression Console software; core-gene and core-exon analyses
CHP files were generated from raw CEL files by Expression Console software. Both CEL and CHP files were used as input for data analysis, specifically PCA in Qlucore (CHP), gene- and exon-level expression differences by XRAY (CEL files) and limma (CHP files), and two-class pair-wise Significance of Microarrays (CHP files).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: EC cell line

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

growth_protocol: All ES lines and the three EC lines marked 'fe' were grown on mitomycin C-inactivated mouse embryo fibroblasts in knock-out DMEM with 10% Serum Replacement and 4 ng/ml FGF. All EC cells were grown in plastic flasks in high-glucose DMEM with 10% FCS.

extract_protocol: Total RNA was isolated from the cell lines using the AllPrep DNA/RNA Mini kit (Qiagen).

treatment_protocol: All cells were FACS sorted for the surface marker SSEA3 before storage in RNAlater (Qiagen).

tag: cell line

value: EC cell line

tag: growth protocol

value: feeder-grown (fe)


title: UC_inactive_3 [mRNA]

city: Leuven

first: Jan

last: Van der Goten

address: Herestraat 49 bus 701

department: Clinical and Experimental Medicine

country: Belgium

institute: KU Leuven

description: colonic mucosal gene expression data from UC patient with inactive disease

hyb_protocol: Hybridization to GeneChip Human Gene 1.0ST arrays (Affymetrix) was performed at 45°C for 17 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).

data_processing: Quality assessment and outlier detection was performed before and after normalization using the Bioconductor package arrayQualityMetrics. Data were analyzed using the RMA algorithm with the aroma.affymetrix package (R version 2.15.0).

source_name: colonic mucosal biopsy from UC patient with inactive disease

label_protocol: Total RNA (150 ng) was reverse-transcribed into cDNA, followed by the generation of cRNA and ss DNA using the GeneChip WT Synthesis and Amplification kit (Ambion). Fragmented DNA is labeled with biotin (GeneChip WT terminal Labeling kit).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. RNA quality and quantity were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit.

tag: tissue

value: colon

tag: disease

value: UC

tag: disease activity

value: inactive


title: UC_active_7 [mRNA]

description: colonic mucosal gene expression data from UC patient with active disease

source_name: colonic mucosal biopsy from UC patient with active disease

value: active


title: control_8 [mRNA]

description: colonic mucosal gene expression data from control individual

source_name: colonic mucosal biopsy from control individual

value: control

value: not applicable


title: UC_inactive_6 [mRNA]


title: UC_inactive_5 [mRNA]


title: UC_inactive_2 [mRNA]


title: UC_active_6 [mRNA]


title: UC_active_3 [mRNA]


title: UC_inactive_4 [mRNA]


title: UC_active_4 [mRNA]


title: 833KE pl [gene-level]

description:
H21 [gene-level]
H21_HuEx.CEL (see Series record)
H21_HuEx.rma-gene-core.chp

value: plastic-grown


title: TERA1 [gene-level]

description:
H22 [gene-level]
H22_HuEx.CEL (see Series record)
H22_HuEx.rma-gene-core.chp


title: UC_active_9 [mRNA]


title: CLL049

type: SRA

city: New York

first: Dan

last: Landau

state: NY

address: 413 East 69th Street

country: USA

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
WGBS Alignment: bisulfite-convereted WGBS reads were aligned to the hg19 genome with bsMap using the following parameters -v 10 -f 40 -q 5 -S 1
RRBS Alignment: bisulfite-converted reads were aligned to a MspI-digested hg19 genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Genome_build: hg19
Supplementary_files_format_and_content: extended bed file. [Sample].hg.bed.txt contains counts of high-quality CG and TG at each sampled CpG in [Sample]. Format:<CpG chr hg19>  <CpG position hg19> < CpG strand hg19> <Unmethylated read count  is the number of TGs observed> <Concordantly unmethylated reads in the number of reads supporting the particular CpG that are fully unmethylated in all CpGs covered by the read> <Concordantly unmethylated reads in the number of reads supporting the particular CpG that are fully unmethylated in all CpGs covered by the read> <Discordant reads is the number of reads supporting the particular CpG that are neither fully methylated nor fully unmethylated in all CpGs covered by the read>

molecule: genomic DNA

source_name: CLL cells

extract_protocol:
Genomic DNA for RRBS library generation was isolated and quantified using previously described methods (Boyle et al., 2012)
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing. Each library was aligned to the HG19 (human genome version nineteen) and the original methylation sites were inferred based on cytosine-to-thymine conversion.  WGBS library generation was performed as previously described (Gifford et al., 2013)

tag: cell type

value: CLL cells

tag: disease status

value: CLL


title: UC_inactive_1 [mRNA]


title: control_7 [mRNA]


title: CLL040_TP1

source_name: CLL cells time point 1

value: CLL cells time point 1


title: UC_active_1 [mRNA]


title: control_10 [mRNA]


title: control_5 [mRNA]


title: 2102Ep pl [gene-level]

description:
H19 [gene-level]
H19_HuEx.CEL (see Series record)
H19_HuEx.rma-gene-core.chp


title: control_4 [mRNA]


title: control_3 [mRNA]


title: CLL038


title: Shef3 [gene-level]

description:
H20 [gene-level]
H20_HuEx.CEL (see Series record)
H20_HuEx.rma-gene-core.chp

source_name: ES cell line

value: ES cell line

value: feeder-grown


title: rci1a vs WT 20C rep3

city: Madrid

first: Rafa

last: Catalá

address: C/Ramiro de Maeztu n9

department: Biotechnology

country: Spain

institute: Centro de Investigaciones Biologicas

description: Biological replicate 3 of 3. 3-week-old Arabidopsis plants exposed.

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Arabidopsis

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Plants were sowed in pots containing a mixture of organic substrate and vermiculite (3:1 v/v). Plants were transferred to16h light/8 h dark at 22ºC under white fluorescent light.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Then, toral RNA was purified using the Rneasy MiniKit from QIAGEN following manufacturer's instructions.

tag: genotype/variation

tag: age

tag: time at 20ºc

value: 3 day

source_name: Col

value: Col


title: rci1a vs WT 20C rep2

description: Biological replicate 2 of 3. 3-week-old Arabidopsis plants exposed.


title: Shef 6 [gene-level]

description:
H17 [gene-level]
H17_HuEx.CEL (see Series record)
H17_HuEx.rma-gene-core.chp


title: HepG2_Senescent_3

city: Cambridge

first: Nicholas

middle: B

last: Shannon

address: Robinson Way

department: Oncology

country: United Kingdom

institute: Cambridge Research Institute

hyb_protocol: The libraries were hybridised to GeneChipR Human Gene ST 1.0 arrays (Affymetrix) for 18hrs using the GeneChipR Hybridisation wash and stain kit, according to Affymetrix standard protocol

scan_protocol: Scanning of the microarrays was carried out on a GeneScan 3000 (Affymetrix) according to Affymetrix standard protocols.

data_processing: R/Bioconductor: Normalised expression estimates were obtained from the raw intensity values using a probe level linear model pre-processing algorithm available in the Bioconductor library AffyPLM (fitPLM) using default parameters.  Differential expression of genes between cells treated with H2O2 and matched control cells was assessed using an empirical Bayes’ statistic and p-values were adjusted for multiple testing using the Bioconductor library limma (eBayes)

source_name: HepG2, 0.5mM H2O2, 60 minutes

label_protocol: The samples were reverse transcribed and cRNA generated using a AmbionR WT Expression kit (Ambion) then single stranded sense cDNA libraries were generated using a GeneChip WT HT Terminal Labelling kit (Affymetrix) according to Affymetrix standard protocols

growth_protocol: The human liver cell line HepG2 was grown in Dulbecco’s Modified Eagle Medium containing 10% foetal calf serum and standard antibiotics (100U/ml Penicillin, 100µg/ml Streptomycin).

extract_protocol: RNA extraction was performed using Qiagen RNeasy Plus Mini Kit with a standard protocol. RNA quality and quantity were measured using spectrophotometry at 260 and 280nm and on 2100 Bioanalyzer Eukaryote Total RNA Nano Series II chip (Agilent).

treatment_protocol: Hepatocytes were seeded in 6-well plates at a density of 5x105 per well and allowed to adhere overnight before treatment.  Senescence was induced by treating the cells for 60 minutes with a final concentration of 0.5mM H2O2 in culture media or, in culture media alone.  Hepatocytes were then washed three times with PBS and incubated at 37˚C, 5% CO2 for 5 days before observing cell morphology and testing for senescent phenotype.

tag: treatment

value: 0.5mM H2O2, 60 minutes


title: control_1 [mRNA]


title: rci1a vs WT rep3

organism: Arabidopsis thaliana

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Then, total RNA was purified using the Rneasy MiniKit from QIAGEN following manufacturer's instructions.

tag: time at 4ºc

source_name: WT

value: wild type


title: control_2 [mRNA]


title: rci1a vs WT 20C rep1

description: Biological replicate 1 of 3. 3-week-old Arabidopsis plants exposed.


title: HepG2_Senescent_4


title: HepG2_Normal_3

source_name: HepG2, untreated control

value: untreated control


title: Shef5 [gene-level]

description:
H7 [gene-level]
H7_HuEx.CEL (see Series record)
H7_HuEx.rma-gene-core.chp


title: HepG2_Senescent_1


title: H14 [gene-level]

description:
H4 [gene-level]
H4_HuEx.CEL (see Series record)
H4_HuEx.rma-gene-core.chp


title: NTERA2 fe [gene-level]

description:
H11 [gene-level]
H11_HuEx.CEL (see Series record)
H11_HuEx.rma-gene-core.chp

value: EC cell line

value: feeder-grown (fe)


title: 2102Ep fe [gene-level]

description:
H13 [gene-level]
H13_HuEx.CEL (see Series record)
H13_HuEx.rma-gene-core.chp


title: NCCIT [gene-level]

description:
H18 [gene-level]
H18_HuEx.CEL (see Series record)
H18_HuEx.rma-gene-core.chp


title: HepG2_Normal_4


title: HepG2_Normal_2


title: HepG2_Senescent_2


title: L1236_cell_8hr_control

city: Stockholm

first: Yongtao

last: Xue-Franzen

address: Solnavagen 9

country: Sweden

institute: Karolinska Insititutet

description:
Expression profile of Human HL cell line L1236, 8 hour control
L1236_8hr
L1236_control_8hr

hyb_protocol: According Affymetrix manufacture's manuel

data_processing: Gene expression profiling data analysis was processed with the RMA method using Affymetrix Expression Console software. Fold changes were obtained by comparing expression level to that of untreated samples or vehical methanol treated samples

source_name: Human Hodgkin  lymphoma cell line L1236

growth_protocol: The human HL cell lines L1236 (kind gifts from Prof. Volker Diehl, Cologne, Germany) were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum, L-glutamine (2 mM), penicillin (100 U/ml) and streptomycin (100 μg/ml) (Gibco, Paisley, Scotland, UK) at 37°C in an atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: L1236 cells were pelleted, resuspended in serum-free RPMI 1640 medium (Gibco, Paisley, Scotland, UK) (1 × 106 cells/ ml) supplemented with LTD4 (100nM) (Biomol, Rungsted Kyst, Denmark) or vehicle (methanol, 0.1%)

value: Hodgkin's Lymphoma Cell Line L1236

tag: agent

value: non-treated control

tag: time

value: 8 hours


title: L1236_cell_1hr_LTD4_treatment

description:
Expression profile of Human HL cell line L1236 treated with LTD4 for 1 hour
LTD 4_1hr
L1236_LTD4_1hr

scan_protocol: According Affymetrix manufacture's manuel

value: LTD4 treatment diliuted in vehicle methanol

value: 1 hour


title: L1236_cell_1hr_methanol_treatment

description:
Expression profile of Human HL cell line L1236 treated with methanol for 1 hour, vehicle control.
MeOH_1hr
L1236_methanol_1hr

label_protocol: According Affymetrix manufacture's manuel

value: methanol treatment as vehicle control


title: L1236_cell_8hr_LTD4_treatment

description:
Expression profile of Human HL cell line L1236 treated with LTD4 for 8 hour
LTD 4_8hr
L1236_LTD4_8hr


title: L1236_cell_1hr_control

description:
Expression profile of Human HL cell line L1236, 1 hour control
L1236_1hr
L1236_control_1hr

source_name: Human Hodgkin lymphoma cell line L1236


title: HepG2_Normal_1


title: rci1a vs WT rep 1


title: rci1a vs WT rep2


title: NOMO-1_ZFX-SH1

first: Stuart

last: Weisberg

address: 650 W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

hyb_protocol: Biotinylated DNA probe was made according to the standard Affymetrix protocol

scan_protocol: Arrays were scanned according to the Affymetrix protocol

data_processing: Affymetrix Expression Console (1.1) was used for RMA normalization of all microarray data.

source_name: NOMO-1 cells infected with ZFX shRNA SH1

label_protocol: Used the Ambion WT labelling kit as per manufacturer's instructions using 200ng of starting total RNA

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

treatment_protocol: NOMO-1 cells were infected with control and ZFX shRNA lentiviruses at an MOI of 1. RNA was collected for microarrays 48 hours after selection.

tag: genotype

value: ZFX knock-down


title: NOMO-1_SCR

source_name: NOMO-1 cells infected with scrambled shRNA control

value: ZFX wild type


title: V-ASCBottom, biological replicate 5

city: Bari

first: Ernesto

last: Picardi

address: Via Orabona

country: Italy

institute: University of Bari

description:
PET-TO-B
Gene expression data from V-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).

hyb_protocol: Labeled ssDNA were hybridized for 16 hr at 45C on Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The chips were scanned using the Affymetrix GeneChip Scanner 3000 7G according to the Affimetrix protocol.

data_processing: Partek Genomics Suite v6.4 by the GC-RMA algorithm.

source_name: ASCBottom isolated from visceral omental adipose tissue biopsies

label_protocol: 100ug of total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

extract_protocol: RNA from the experimental ASC populations was isolated by using an RNeasy Kit (Qiagen, Hamburg, Germany).

value: visceral omental (V) fat depots

value: adipose tissue-derived stem cells (ASCs)

tag: cell subpopulation

value: ASCBottom

tag: subject weight

value: lean


title: V-ASCSVF, biological replicate 4

description:
SCLP-TO-A
Gene expression data from V-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).

source_name: ASCSVF isolated from visceral omental adipose tissue biopsies

value: ASCSVF


title: Sc-ASCCeiling, biological replicate 4

description:
SCLP-TS-C
Gene expression data from Sc-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).

source_name: ASCCeiling isolated from abdominal subcutaneous adipose tissue biopsies

value: abdominal subcutaneous (Sc) fat depots

value: ASCCeiling


title: Sc-ASCBottom, biological replicate 5

description:
PET-TS-B
Gene expression data from Sc-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).

source_name: ASCBottom isolated from abdominal subcutaneous adipose tissue biopsies


title: Sc-ASCCeiling, biological replicate 3

description:
MZCC-TS-C
Gene expression data from Sc-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).


title: Sc-ASCSVF, biological replicate 4

description:
SCLP-TS-A
Gene expression data from Sc-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).

source_name: ASCSVF isolated from abdominal subcutaneous adipose tissue biopsies


title: V-ASCCeiling, biological replicate 4

description:
SCLP-TO-C
Gene expression data from V-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).

source_name: ASCCeiling isolated from visceral omental adipose tissue biopsies


title: Sc-ASCBottom, biological replicate 4

description:
MZCC-TS-B
Gene expression data from Sc-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).


title: NOMO-1_ZFX-SH3

source_name: NOMO-1 cells infected with ZFX shRNA SH3

tag: cell line


title: V-ASCBottom, biological replicate 4

description:
MZCC-TO-B
Gene expression data from V-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).


title: NOMO-1_LEN-GFP

source_name: NOMO-1 cells infected with GFP lentivirus


title: V-ASCCeiling, biological replicate 3

description:
MZCC-TO-C
Gene expression data from V-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).


title: UC_active_2 [mRNA]

description: colonic mucosal gene expression data from UC patient with active disease

source_name: colonic mucosal biopsy from UC patient with active disease

value: colon

value: UC

value: active


title: Sc-ASCBottom, biological replicate 3

description:
MANZ-TS-B
Gene expression data from Sc-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).


title: L1236_cell_8hr_methanol_treatment

description:
Expression profile of Human HL cell line L1236 treated with methanol for 8 hour, vehicle control.
MeOH_8hr
L1236_methanol_8hr

value: Hodgkin's Lymphoma Cell Line L1236


title: V-ASCBottom, biological replicate 3

description:
MANZ-TO-B
Gene expression data from V-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).


title: V-ASCSVF, biological replicate 2

description:
MANZ-TO-A
Gene expression data from V-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).


title: Smad3 ChIP, M4 cell, plus, biological rep2

type: genomic

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: Smad3 ChIPed DNA

hyb_protocol: Following fragmentation, 10ug biotinylated DNA was hybridized for 16 hr at 45oC on the GeneChip Human Promoter 1.0R Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using an Affymetrix GeneChip Scanner 3000 7G and data was collected using Affymetrix AGCC software.

data_processing:
Affymetrix Tiling Analysis Software (TAS, version 1.2.0) was used for data processing. Quantile normalization was performed within each comparison group; quadruplicate for M1 cells and M2 cells or duplicate for M3 cells and M4 cells.
The probe signals and p-values were computed using window size of 200 bp to generate BAR file (TAS Binary Analysis results).

label: Biotin

source_name: MCF10CA1a.cl1 ("M4"), TGF-beta treated

label_protocol: ChIPed DNA was biotinylated according to the standard Affymetrix protocol (Affymetrix Chromatin Immunoprecipitation Assay Protocol (Affymetrix).

growth_protocol: M1 and M2 cells were grown in DMEM/F12 medium supplemented with 10ug/ml insulin. 20ng/ml EGF, 0.5ug/ml hydrochortisone, and 100ng/ml cholera toxin and 5% horse serum. M3 and M4 cells were grown in DMEM/F12 medium supplemented with 5% Horse serum.

extract_protocol: Chromatin immunoprecipitation was performed using anti-Smad3 antibody (Abcam #28379) and ChIPed DNA was amplified through 2 rounds using a Whole Genome Reamplification kit (Sigma) followed by EtOH precipitation.

treatment_protocol: Cells were grown to 50-60% confluence and then serum-starved in DMEM/F12 supplemented with Serum Replacement 1 for 16 hours prior to treatment with TGF-beta (5ng/ml: "plus" condition) or vehicle ("minus condition) for 1 hour.

value: TGF-beta treated

tag: cell line origin

value: Breast epithelium

tag: tumor stage represented

value: Malignant, high grade, metastatic

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: V-ASCCeiling, biological replicate 2

description:
MANZ-TO-C
Gene expression data from V-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).

tag: tissue

tag: cell type


title: Smad3 ChIP, M4 cell, plus, biological rep1

description: Smad3 ChIPed DNA


title: Sc-ASCSVF, biological replicate 2

description:
MANZ-TS-A
Gene expression data from Sc-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).


title: Smad3 ChIP, M4 cell, minus, biological rep2

description: Smad3 ChIPed DNA

source_name: MCF10CA1a.cl1 ("M4"), vehicle treated

value: vehicle treated


title: Smad3 ChIP, M4 cell, minus, biological rep1

description: Smad3 ChIPed DNA


title: V-ASCSVF, biological replicate 3

description:
MZCC-TO-A
Gene expression data from V-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).


title: Smad3 ChIP, M3 cell, plus, biological rep2

description: Smad3 ChIPed DNA

source_name: MCF10CA1h ("M3"), TGF-beta treated

value: Malignant, low grade


title: Sc-ASCSVF, biological replicate 3

description:
MZCC-TS-A
Gene expression data from Sc-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).


title: Sc-ASCBottom, biological replicate 2

description:
DEM-TS-B
Gene expression data from Sc-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).


title: V-ASCBottom, biological replicate 2

description:
DEM-TO-B
Gene expression data from V-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).

value: visceral omental (V) fat depots


title: Sc-ASCCeiling, biological replicate 2

description:
DDN-TS-C
Gene expression data from Sc-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).

value: adipose tissue-derived stem cells (ASCs)


title: Sc-ASCBottom, biological replicate 1

description:
DDN-TS-B
Gene expression data from Sc-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).

value: ASCBottom


title: V-ASCCeiling, biological replicate 1

description:
CERV-TO-C
Gene expression data from V-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).

value: lean


title: Sc-ASCSVF, biological replicate 1

description:
CERV-TS-A
Gene expression data from Sc-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).

value: ASCSVF


title: V-ASCSVF, biological replicate 1

description:
CERV-TO-A
Gene expression data from V-ASCSVF cell culture.
Plastic-adherent cells isolated from adipose stromal-vascular fraction (SVF) of adipose tissue with self-renewal properties and able to regenerate adipocytes (ASCSVF).


title: Smad3 ChIP, M3 cell, plus, biological rep1

description: Smad3 ChIPed DNA


title: Smad3 ChIP, M3 cell, minus, biological rep2

description: Smad3 ChIPed DNA

source_name: MCF10CA1h ("M3"), vehicle treated


title: V-ASCBottom, biological replicate 1

description:
DDN-TO-B
Gene expression data from V-ASCBottom cell culture.
ASC populations isolated from the «fat cake» at the top of the supernatant, during the procedure of fat tissue enzymatic digestion and centrifugation (ASCBottom).


title: Smad3 ChIP, M2 cell, plus, biological rep4

description: Smad3 ChIPed DNA

source_name: MCF10AT1k.cl2 ("M2"), TGF-beta treated

value: Premalignant


title: MDA-MB231, GHSROS, rep3

city: Kelvin Grove

first: Inge

last: Seim

state: Queensland

address: 60 Musk Avenue

country: Australia

institute: Queensland University of Technology

description: Gene expression data from MDA-MB231 breast cancer cells transfected with the gene GHSROS in the pTargeT mammalian expression vector.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The raw data (.CEL files) from the Affymetrix Human Gene 1.0 ST (HuGene-1_0-st-v1) array run were normalised using the robust-multi-array analysis (RMA) algorithm via the Garvan Institute of Medical Research Institute in-house GenePattern module NormalizeAffymetrixST (v2.0, with default values).

source_name: MDA-MB231 cell line transfected with GHSROS-pTargeT vector

label_protocol: 500 ng total RNA was sent on dry ice to the Ramaciotti Centre for Gene Function Analysis, Sydney, Australia for processing and hybridization to Affymetrix Human Gene Arrays 1.0 as per the manufacterer’s instructions.

growth_protocol: MDA-MB231 cells were cultivated in DMEM/F12 (Invitrogen) at 37C in a humidified atmosphere containing 5% CO2 and 95% air. The complete medium contained 10% Cosmic calf serum (HyClone), 50 U/ml penicillin, and 50 µg/ml streptomycin (Invitrogen). Cells were tested to be free from Mycoplasma contamination.

extract_protocol: Total RNA was extracted from MDA-MB-231 cell pellets using the RNeasy plus mini kit (QIAGEN) according to the manufacturer’s instructions. Extracted RNA was stored at -80°C. RNA concentration and purity were measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). RNA quality was confirmed based on a RNA integrity number (RIN) higher than 8 by use of a 2100 BioAnalyzer (Agilent).

tag: cell line source

value: breast cancer

tag: transfection

value: GHSROS-pTargeT vector


title: Sc-ASCCeiling, biological replicate 1

description:
CERV-TS-C
Gene expression data from Sc-ASCCeiling cell culture.
ASC population developed from mature adipocytes of the fat cake adherent to the ceiling surface of the culture flask filled with growth medium (ASCCeiling).

value: abdominal subcutaneous (Sc) fat depots

value: ASCCeiling


title: MDA-MB231, vector-only, rep2

description: Gene expression data from MDA-MB231 breast cancer cells transfected with empty pTargeT mammalian expression vector.

source_name: MDA-MB231 cell line transfected with empty pTargeT vector

value: empty pTargeT vector


title: MDA-MB231, vector-only, rep3


title: Smad3 ChIP, M2 cell, plus, biological rep3

description: Smad3 ChIPed DNA

tag: treatment

value: TGF-beta treated


title: Smad3 ChIP, M2 cell, plus, biological rep2

description: Smad3 ChIPed DNA

value: Breast epithelium


title: Smad3 ChIP, M3 cell, minus, biological rep1

description: Smad3 ChIPed DNA


title: MDA-MB231, GHSROS, rep1


title: Smad3 ChIP, M2 cell, plus, biological rep1

description: Smad3 ChIPed DNA


title: MDA-MB231, GHSROS, rep2


title: MDA-MB231, vector-only, rep1


title: M4 cell, plus at 1h, biological rep1

description: RNA extracted by RNeasy

hyb_protocol: Three replicates of each group were hybridized to Affymetrix mouse (human) Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450

scan_protocol: Genechips were scanned using an Affymetrix GeneChip Scanner 3000 and data was collected using Affymetrix AGCC software.

data_processing:
Data were analyzed with Partek Genomics Suite (version 6.5) software using the RMA normalization algorithm with default format.
Original, Summarized, Difference, Filename, Chip Type, Attribute, cell, treatment, time, group, Scan Date, gene expression

source_name: MCF10CA1a.cl1 (M4), TGF-beta treated, 1h

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

growth_protocol: M1 and M2 cells were grown in DMEM/F12 medium supplemented with 10ug/ml, insulin, 20ng/ml EGF, 0.5ug/ml hydrocortisone, 100ng/ml cholera toxin and 5% horse serum. M3 and M4 cells were grown in DMEM/F12 medium supplemented with 5% Horse serum.

extract_protocol: Total RNA was extracted and purified by RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Cells were grown to 50-60% confluence and then serum-starved in DMEM/F12 supplemented with Serum Replacement 1 for 16 hours prior to TGF-beta treatment with 5ng/ml or vehicle for 1 hour or 6 hour.

value: MCF10Ca1a.cl1 (M4)

value: Malignant, high grade, metastatic


title: M4 cell, plus at 6h, biological rep2

description: RNA extracted by RNeasy

source_name: MCF10CA1a.cl1 (M4), TGF-beta treated, 6h


title: M4 cell, minus at 6h, biological rep2

description: RNA extracted by RNeasy

source_name: MCF10CA1a.cl1 (M4), vehicle treated, 6h

value: vehicle treated


title: M4 cell, plus at 1h, biological rep2

description: RNA extracted by RNeasy


title: M4 cell, minus at 1h, biological rep2

description: RNA extracted by RNeasy

source_name: MCF10CA1a.cl1 (M4), vehicle treated, 1h


title: M4 cell, plus at 6h, biological rep3

description: RNA extracted by RNeasy


title: M4 cell, minus at 1h, biological rep3

description: RNA extracted by RNeasy


title: M4 cell, minus at 6h, biological rep3

description: RNA extracted by RNeasy


title: M4 cell, plus at 6h, biological rep1

description: RNA extracted by RNeasy


title: Smad3 ChIP, M2 cell, minus, biological rep4

description: Smad3 ChIPed DNA

source_name: MCF10AT1k.cl2 ("M2"), vehicle treated

value: Abcam


title: M4 cell, plus at 1h, biological rep3

description: RNA extracted by RNeasy


title: Smad3 ChIP, M2 cell, minus, biological rep3

description: Smad3 ChIPed DNA


title: Smad3 ChIP, M2 cell, minus, biological rep2

description: Smad3 ChIPed DNA


title: Smad3 ChIP, M2 cell, minus, biological rep1

description: Smad3 ChIPed DNA


title: Smad3 ChIP, M1 cell, plus, biological rep4

description: Smad3 ChIPed DNA

source_name: MCF10A1 ("M1"), TGF-beta treated

value: Normal, immortalized


title: Smad3 ChIP, M1 cell, plus, biological rep2

description: Smad3 ChIPed DNA


title: M3 cell, plus at 6h, biological rep3

description: RNA extracted by RNeasy

source_name: MCF10CA1h (M3), TGF-beta treated, 6h

value: MCF10Ca1h (M3)

value: Malignant, low grade


title: M4 cell, minus at 1h, biological rep1

description: RNA extracted by RNeasy


title: M3 cell, plus at 6h, biological rep2

description: RNA extracted by RNeasy


title: M3 cell, minus at 6h, biological rep3

description: RNA extracted by RNeasy

source_name: MCF10CA1h (M3), vehicle treated, 6h


title: H37Rv 48h control vs. H37Rv 48h 100uM FS T7

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Features were extracted with an image analysis tool version A.9.5.3 using the GE2-V5_95_Feb07 protocol (Agilent Technologies).

hyb_protocol: Labeled samples was mixed and hybridized to 44K custom-made microarray according to the supplier`s protocol (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: The extracted MAGE-ML files was analyzed with the Rosetta Resolver Biosoftware, Build 7.1 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 2–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible. Additionally, data derived from the different labeling procedures (random FullSpectrum T7 labeling) and (WTA BioPrime indirect labeling) were combined. Only results derived from both labeling methods were considered as relevant for further verification.

organism: Mycobacterium tuberculosis H37Rv

source_name: H37Rv 48h unstimulated control

label_protocol: RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 10e8 cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer. The amount of RNA was determined by OD260/280 nm measurement using a NanoDrop 1000 spectrophotometer (Kisker, Steinfurt, Germany). The RNA size, integrity and the amount of total RNA were measured with a Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany) on a RNA Nano 6000 microfluidics kit.

tag: strain

source_name: H37Rv 48h 100uM compound 14


title: Smad3 ChIP, M1 cell, minus, biological rep4

description: Smad3 ChIPed DNA

source_name: MCF10A1 ("M1"), vehicle treated


title: M3 cell, minus at 1h, biological rep1

description: RNA extracted by RNeasy

source_name: MCF10CA1h (M3), vehicle treated, 1h


title: M3 cell, plus at 1h, biological rep3

description: RNA extracted by RNeasy

source_name: MCF10CA1h (M3), TGF-beta treated, 1h


title: Smad3 ChIP, M1 cell, plus, biological rep1

description: Smad3 ChIPed DNA


title: Smad3 ChIP, M1 cell, minus, biological rep3

description: Smad3 ChIPed DNA


title: M3 cell, minus at 1h, biological rep3

description: RNA extracted by RNeasy


title: M3 cell, plus at 1h, biological rep2

description: RNA extracted by RNeasy


title: M2 cell, minus at 6h, biological rep3

description: RNA extracted by RNeasy

source_name: MCF10AT1k.cl2 (M2), vehicle treated, 6h

value: MCF10AT1k.cl2 (M2)


title: M3 cell, minus at 1h, biological rep2

description: RNA extracted by RNeasy


title: M3 cell, plus at 1h, biological rep1

description: RNA extracted by RNeasy


title: H37Rv 48h 100uM vs. H37Rv 48h control WTA Bioprime indirect

label_protocol: RNA was amplified with the TransPlex Whole Transcriptome Amplification Kit (Sigma-Aldrich, Munich, Germany) and labeled with BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Karlsruhe, Germany) as WTA BioPrime indirect.


title: M2 cell, plus at 6h, biological rep2

description: RNA extracted by RNeasy

source_name: MCF10AT1k.cl2 (M2), TGF-beta treated, 6h


title: M3 cell, minus at 6h, biological rep1

description: RNA extracted by RNeasy


title: H37Rv 48h control vs. H37Rv 48h 50uM WTA Klenow indirect

source_name: H37Rv 48h 50uM compound 14


title: M2 cell, plus at 6h, biological rep3

description: RNA extracted by RNeasy


title: M2 cell, minus at 6h, biological rep2

description: RNA extracted by RNeasy


title: H37Rv 48h 50uM vs. H37Rv 48h control WTA Klenow indirect


title: M2 cell, plus at 6h, biological rep1

description: RNA extracted by RNeasy


title: M2 cell, minus at 6h, biological rep1

description: RNA extracted by RNeasy


title: H37Rv 48h 100uM vs. H37Rv 48h control FS T7


title: Smad3 ChIP, M1 cell, minus, biological rep2

description: Smad3 ChIPed DNA


title: H37Rv 48h control vs. H37Rv 48h 100uM WTA Bioprime indirect


title: Smad3 ChIP, M1 cell, minus, biological rep1

description: Smad3 ChIPed DNA


title: M2 cell, plus at 1h, biological rep2

description: RNA extracted by RNeasy

source_name: MCF10AT1k.cl2 (M2), TGF-beta treated, 1h


title: H37Rv 48h control vs. H37Rv 48h 50uM FS T7


title: M3 cell, plus at 6h, biological rep1

description: RNA extracted by RNeasy


title: M2 cell, plus at 1h, biological rep1

description: RNA extracted by RNeasy


title: Smad3 ChIP, M1 cell, plus, biological rep3

description: Smad3 ChIPed DNA


title: M2 cell, minus at 1h, biological rep2

description: RNA extracted by RNeasy

source_name: MCF10AT1k.cl2 (M2), vehicle treated, 1h


title: M2 cell, minus at 1h, biological rep3

description: RNA extracted by RNeasy


title: M1 cell, plus at 6h, biological rep3

description: RNA extracted by RNeasy

source_name: MCF10A1 (M1), TGF-beta treated, 6h


title: M2 cell, minus at 1h, biological rep1

description: RNA extracted by RNeasy


title: M1 cell, plus at 6h, biological rep2

description: RNA extracted by RNeasy


title: H37Rv 48h 50uM vs. H37Rv 48h control FS T7


title: M1 cell, minus at 6h, biological rep2

description: RNA extracted by RNeasy

source_name: MCF10A1 (M1), vehicle treated, 6h


title: M1 cell, plus at 6h, biological rep1

description: RNA extracted by RNeasy


title: M1 cell, minus at 6h, biological rep3

description: RNA extracted by RNeasy


title: LBL_mildly affected_rep4

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

hyb_protocol: Human HT-12v3 bead arrays (Illumina, San Diego, CA) were hybridized with 750ng cRNA for 18h at 58°C according to the Illumina® Whole-Genome Gene Expression with IntelliHyb Seal System Manual

scan_protocol: Arrays were washed three times with buffer E1BC, High-Temp Wash Buffer and 100% ethanol, respectively, stained with streptavidine-Cy3 and again washed with buffer E1BC

data_processing: Raw fluorescence intensities were recorded on a BeadArray Reader GX (Illumina). Average signal intensities without background correction (Dunning et al., 2008) were performed with BeadStudio 3.1 software (Illumina). Arrays were normalized with VSN (Bioconductor version 2.6.1) including a ln transformation step

source_name: Lymphoblastoid cell line

label_protocol: 400 ng of total RNA were linearly amplified and biotinylated using the Illumina® TotalPrepTM RNA Amplification Kits (Ambion) according to the manufacturer’s instructions

growth_protocol: lyphoblastoid cell lines grown in RPMI 1640 Medium without L.Glutamine

extract_protocol: RNA extraction with TRIzol (Invitrogen)

treatment_protocol: no treatment

tag: gender

value: female

tag: sma

value: SMAIII

tag: smn2 copies

tag: experiemental group

tag: sample


title: LBL_mildly affected_rep2


title: M1 cell, minus at 6h, biological rep1

description: RNA extracted by RNeasy

tag: time

tag: cell line


title: M1 cell, plus at 1h, biological rep3

description: RNA extracted by RNeasy

source_name: MCF10A1 (M1), TGF-beta treated, 1h

tag: cell line origin

tag: tumor stage represented


title: M1 cell, minus at 1h, biological rep1

description: RNA extracted by RNeasy

source_name: MCF10A1 (M1), vehicle treated, 1h


title: M1 cell, minus at 1h, biological rep3

description: RNA extracted by RNeasy


title: M1 cell, plus at 1h, biological rep1

description: RNA extracted by RNeasy


title: M1 cell, plus at 1h, biological rep2

description: RNA extracted by RNeasy


title: LBL_mildly affected_rep1

value: male


title: LBL_mildly affected_rep5


title: LBL_mildly affected_rep3


title: LBL_severly affected_rep2

value: SMAI


title: M1 cell, minus at 1h, biological rep2

description: RNA extracted by RNeasy


title: M3 cell, minus at 6h, biological rep2

description: RNA extracted by RNeasy


title: LBL_severly affected_rep1


title: RAW 264.7 macrophages, bilayer 2

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

institute: Max Planck-Institute for Molecular Genetics

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalized using cubic spline normalization and background subtraction implemented in Illumina GenomeStudio V2011.1.
Illumina GenomeStudio V2011.1 calculated intensity and detection P value.

organism: Mus musculus

source_name: RAW 264.7 macrophages, bilayer 2

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: 3T3-L1 preadipocytes were cultured in DMEM +10% fetal bovine serum at 37°C in humidified atmosphere. One to two days after post confluency, cell differentiation was started using 0.5 mM IBMX +1 µM dexamethasone +10 µg/mL insulin. Two days after differentiation start, 4/5 of the old media were renewed with fresh media containing 10 µg/mL insulin. On day 4 and 6 media was renewed without any additives. On day 8, differentiated 3T3-L1 adipocytes contained visible lipid droplets. The cells were detached using TrypLE™ Express and seeded at 50% confluency in 20 mL on the bottom of fifteen 75mm Transwell® dishes.  RAW 264.7 cells were cultured in DMEM +10% fetal bovine serum at 37°C in humidified atmosphere to a density of 70-80%. They were carefully detached using a scraper and seeded onto the polycarbonate membrane at a density of 1.3 x 106 cells/insert/20 mL. After 18 h settle- and attachment, insert containing macrophages and bottom dish containing adipocytes were combined in the bilayer system and 25 mL fresh media was added. A 0.4 μm polycarbonate membrane separates the two cell lines from each other while their secreted molecules are able to diffuse through the membrane and will be recognized by the other cell type and evoke a response. After 24 h of incubation the cells were harvested in ice cold PBS supplemented with protease and phosphatase inhibitor. Every five dish were pooled to triplicates and a proportion of 106 cells was taken for RNA purification and microarray analysis. The remaining cells were forwarded to protein enrichment and mass spectrometry analysis.

extract_protocol: Total RNA was purified and isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser or agarose gel electrophoresis.

value: bilayer

value: ascites

value: RAW 264.7 macrophages


title: M4 cell, minus at 6h, biological rep1

description: RNA extracted by RNeasy

source_name: MCF10CA1a.cl1 (M4), vehicle treated, 6h


title: RAW 264.7 macrophages, monolayer 2

description: replicate 2

source_name: RAW 264.7 macrophages, monolayer 2

value: monolayer


title: RAW 264.7 macrophages, bilayer 1

description: replicate 1

source_name: RAW 264.7 macrophages, bilayer 1


title: RAW 264.7 macrophages, monolayer 1

description: replicate 1

source_name: RAW 264.7 macrophages, monolayer 1


title: M2 cell, plus at 1h, biological rep3

description: RNA extracted by RNeasy

value: TGF-beta treated

value: Breast epithelium

value: Premalignant


title: L-GMP AMPKΔ/Δ, replicate 2

city: Houston

first: Yusuke

last: Saito

state: TX

address: One Baylor Olaza

institute: Baylor college of medicine

description: AMPK_delta L-GMP 2

hyb_protocol: 2.5μg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 2.0 microarrays.

scan_protocol: GeneChips were scanned using Affymetrics GeneChip Scanner 3000 and the GeneChip Command Console software v3.0.

data_processing: The data were analyzed with GeneSpring GX  using default analysis settings.

source_name: L-GMPs from AMPKΔ/Δ leukemia mice, replicate 2

label_protocol: Biotinylated cDNA were prepared using Nugen Ovation Pico WTA V2 system and the Encore Biotin Module (NuGEN Technologies, San Carlos, CA)

growth_protocol: Lethally irradiated (10Gy) recipients were injected with 50,000 WT or AMPKΔ/Δ MLL-AF9 expressing bone marrow progenitor/stem cells. Whole leukemia cells and L-GMP cells were purified from bone marrow of recipients at individual AML onset.

extract_protocol: 5000 whole leukemia cells (GFP+) or L-GMP  (GFP+,lin-,c-kit+, CD16/32+,CD34+) cells were sorted into Trizol reagent by cell sorter.

tag: genotype

value: AMPKΔ/Δl(KO)

value: bone marrow

value: L-GMP (gfp+,lin-,c-kit+, CD16/32+,CD34+) cells


title: L-GMP AMPKΔ/Δ, replicate 3

description: AMPK_delta L-GMP 3

source_name: L-GMPs from AMPKΔ/Δ leukemia mice, replicate 3


title: 3T3-L1 adipocytes, bilayer 2

description: replicate 2

source_name: 3T3-L1 adipocytes, bilayer 2

value: embryo, fibroblast

value: 3T3-L1 adipocytes


title: 3T3-L1 adipocytes, monolayer 3

description: replicate 3

source_name: 3T3-L1 adipocytes, monolayer 3


title: L-GMP AMPKΔ/Δ, replicate １

description: AMPK_delta L-GMP 1

source_name: L-GMPs from AMPKΔ/Δ leukemia mice, replicate 1


title: LBL_unaffected_rep5

value: no


title: L-GMP AMPKfl/fl, replicate 3

description: WT L-GMP 3

source_name: L-GMPs  from  AMPKfl/f leukemia mice, replicate 3

value: AMPKfl/fl(WT)


title: LBL_unaffected_rep2

value: female


title: LBL_unaffected_rep4

value: male


title: LBL_unaffected_rep3


title: Whole AMPKΔ/Δ, replicate 3

description: AMPK_delta whole 3

source_name: Whole leukemia cells from AMPKΔ/Δ leukemia mice, replicate 3

value: whole AML cells


title: Healthy volunteer, Control_11854

city: Indianapolis

first: Robert

middle: W

last: Hoffman

state: IN

address: Lilly Corporate Center

department: Lilly Bio-Medicines/Immunology

institute: Eli Lilly and Company

description: Gene expression data from healthy volunteer blood

hyb_protocol: The cDNA generated during the amplification step was used in a fragmentation and labeling reaction to generate target for hybridization to the Affymetrix Human GeneChip® HU133 Plus 2.0.

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

data_processing: The data were analyzed with Partek Genomics Suite using the Affymetrix default analysis settings. RMA background correction and quantile normalization were applied with the median polish approach for summarizing probe sets.

source_name: Healthy volunteer blood

label_protocol: Not provided

extract_protocol:
Extraction of total RNA was performed using the Qiagen RNeasy Plus kit according to the manufacturer's instructions.
A custom, automated version of the NuGEN Ovation v2.0 WB amplification system was used for RNA extracted from blood.

tag: diagnosis

value: healthy

value: blood


title: L-GMP AMPKfl/fl, replicate 1

description: WT L-GMP 1

source_name: L-GMPs  from  AMPKfl/f leukemia mice, replicate 1

tag: tissue


title: L-GMP AMPKfl/fl, replicate 2

description: WT L-GMP 2

source_name: L-GMPs from  AMPKfl/f leukemia mice, replicate 2

tag: cell type


title: Healthy volunteer, Control_11855


title: male WT, replicate 2 [gene]

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics and Deep-Sequencing Unit

institute: Max-Planck-Institute for Immunobiology and Epigenetics

hyb_protocol: according to manufacturer's instructions

data_processing: We performed exon- (probeset-) and gene-level analysis using the Affymetrix Power Tools (version=1.14.3.1). The rma-sketch algorithm was used to normalize the intensities in CEL files and detection p-values were generated for each probeset using the “detection above background” (DABG) method.

source_name: Male MEFs, CAGG-Cre-ER T/+

growth_protocol: DMEM supplemented with 10% FCS, pen/strep

extract_protocol: QIAGEN Rneasy

treatment_protocol: 200nM 4-Hydroxytamoxifen for 4 days. Ethanol represents vehicle control.

tag: genotype/variation

value: WT

value: vehicle control


title: 3T3-L1 adipocytes, bilayer 3

description: replicate 3

source_name: 3T3-L1 adipocytes, bilayer 3

value: bilayer


title: 3T3-L1 adipocytes, bilayer 1

description: replicate 1

source_name: 3T3-L1 adipocytes, bilayer 1


title: Whole AMPKΔ/Δ, replicate 2

description: AMPK_delta whole 2

source_name: Whole leukemia cells from AMPKΔ/Δ leukemia mice, replicate 2


title: male KO, replicate 1 [gene]

scan_protocol: according to manufacturer's instructions

source_name: Male MEFs, CAGG-Cre-ER T/+, 4OHT treated

value: KO

value: 200nM 4-Hydroxytamoxifen for 4 days


title: 3T3-L1 adipocytes, monolayer 1

description: replicate 1

source_name: 3T3-L1 adipocytes, monolayer 1

value: monolayer


title: male WT, replicate 1 [gene]

label_protocol: according to manufacturer's instructions


title: male KO, replicate 3 [gene]


title: male KO, replicate 2 [gene]


title: LBL_unaffected_rep1

source_name: Lymphoblastoid cell line


title: female KO, replicate 3 [gene]

source_name: Female MEFs, CAGG-Cre-ER T/+, 4OHT treated


title: male WT, replicate 3 [gene]


title: 3T3-L1 adipocytes, monolayer 2

description: replicate 2

source_name: 3T3-L1 adipocytes, monolayer 2


title: female KO, replicate 2 [gene]


title: female WT, replicate 3 [gene]

source_name: Female MEFs, CAGG-Cre-ER T/+


title: female KO, replicate 1 [gene]


title: Whole AMPKfl/fl, replicate 3

description: WT whole 3

source_name: Whole leukemia cells  from  AMPKfl/f leukemia mice, replicate 3

value: bone marrow


title: female WT, replicate 2 [gene]


title: Whole AMPKΔ/Δ, replicate １

description: AMPK_delta whole 1

source_name: Whole leukemia cells from AMPKΔ/Δ leukemia mice, replicate 1

value: AMPKΔ/Δl(KO)


title: Whole AMPKfl/fl, replicate 2

description: WT whole 2

source_name: Whole leukemia cells from  AMPKfl/f leukemia mice, replicate 2


title: Healthy volunteer, Control_11852


title: Healthy volunteer, Control_11849


title: knockout biological replicate 4

city: Cincinnati

first: Alexander

last: Lange

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Reseach Foundation

description: Mst1/2 CKO_10P

hyb_protocol: Based on Affymetrix protocols

scan_protocol: Based on Affymetrix protocols

data_processing: Quantile normalized gene level expression values from Gene Spring MoGene-1_0-st-v1.r4.pgf

source_name: Epcam(+) cells from E18.5 lungs

label_protocol: Based on Affymetrix protocols for biotin labeling

growth_protocol: Timed matings were established with the presence of a copulation plug representing day 0.5

extract_protocol: Total RNA was isolated from Epcam(+) cells using a RNeasy Micro Kit (Qiagen)

treatment_protocol: Lungs dissected from E18.5 embryos were mechanically/enzymatically dissociated to generate single cell suspension.  Epcam(+) cells were isolated using magnetic microbeads and an AutoMACS Pro Separator (Miltenyi Biotec)

tag: developmental stage

value: embryo

tag: age

value: lung

value: Epcam(+) epithelial cells

value: Mst1/2 CKO


title: Healthy volunteer, Control_11853

source_name: Healthy volunteer blood


title: knockout biological replicate 3

description: Mst1/2 CKO_7P


title: knockout biological replicate 1

description: Mst1/2 CKO_3P


title: knockout biological replicate 2

description: Mst1/2 CKO_4P


title: Healthy volunteer, Control_11850


title: control biological replicate 1

value: Control


title: Healthy volunteer, Control_11848


title: female WT, replicate 1 [gene]

value: female

tag: treatment


title: control biological replicate 3


title: Healthy volunteer, Control_11847


title: Healthy volunteer, Control_11851


title: IFNgR2KO_DC_T. gondii_rep3

city: La Jolla

first: Li-Fan

last: Lu

state: CA

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

description: CD11c+ MHC classII hi DCs from mixed BM chimeras (WT + IFNgR2KO) day 8 post T. gondii infection were sorted on FACSAria (Becton Dickinson).

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix) and scanned at the UCSD Microarray Core Facility.

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

data_processing:
Raw CEL data files were processed with R using the oligo and pd.mogene.2.0.st libraries for RMA normalization.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: IFNgR2KO DC

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

extract_protocol: RNA was isolated by using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: T. gondii


title: Healthy volunteer, Control_11846

value: healthy


title: IFNgR2KO_DC_T. gondii_rep1


title: control biological replicate 4


title: control biological replicate 2


title: IFNgR2KO_DC_T. gondii_rep2


title: liver at T2, biological rep1

city: San Francisco

first: Aras

middle: N

last: Mattis

state: California

address: 35 Medical Center Way

institute: UCSF

description: Gene expression data from mice injected with AAV8-Ttr-Cre 4 weeks prior

hyb_protocol: GeneChip Expression Analysis Technical Manual 702232 Rev. 3

data_processing: GCOS 1.4

source_name: Liver tissue

label_protocol: Affymetrix Genechip Whole Transcript Sense Target Labeling Assay

growth_protocol: Mice were fasted for 4 hours prior to harvesting of liver tissue.

extract_protocol: Trizol isolation of RNA was performed according to manufacterers instructions.

treatment_protocol: Flash frozen tissue was used for trizol isolation.

value: Liver

value: Dicer1 fl/fl after AAV8-Ttr-Cre

tag: genetic background

value: mixed 129S4 and C57BL/

value: 4 wk


title: liver at T2, biological rep2


title: Whole AMPKfl/fl, replicate 1

description: WT whole 1

source_name: Whole leukemia cells  from  AMPKfl/f leukemia mice, replicate 1

tag: strain

value: AMPKfl/fl(WT)

value: whole AML cells


title: liver at T1, biological rep1

description: Gene expression data from mice injected with AAV8-Ttr-Cre 2 weeks prior

value: 2 wk


title: WT_DC_T. gondii_rep3

source_name: WT DC


title: liver at T1, biological rep2


title: WT_DC_T. gondii_rep2


title: liver at T0, biological rep3

description: Gene expression data from control

value: Dicer1 fl/fl

value: 0 wk


title: Healthy volunteer, Control_11823

value: blood


title: liver at T0, biological rep2

description: Gene expression data from control


title: WT_DC_T. gondii_rep1


title: Healthy volunteer, Control_11824


title: Rip1Tag2 islets_Angiogenic_rep5

city: Strasbourg

last: Hussenet

address: 3 avenue Molière

country: France

institute: INSERM

description: from 8-week-old Rip1Tag2 mice

hyb_protocol: Following Affymetrix instructions.

scan_protocol: Following Affymetrix instructions

data_processing: The data were analyzed with the Expression Console software (Affymetrix) with default analysis settings and normalized using the RMA method.

source_name: Pool of Angiogenic islets

label_protocol: Using 200ng total RNA, following Affymetrix instructions.  Following Affymetrix instructions.  Description  affymetrix

growth_protocol: 8 week-old Rip1Tag2 mice

extract_protocol: Total RNA was extracted from pools of isolated islets by using NucleoSpin RNA XS kit, according to the manufacturer's instructions.

treatment_protocol: Pancreata were digested with collagenase (Liberase, Roche) and Langerhans islets purified by centrifugation with a density gradient (Histopaque 1077, Sigma).

tag: strain background

value: early tumor islets

tag: angiogenic status

value: Angiogenic


title: Rip1Tag2 islets_Angiogenic_rep2

description: from 8-week-old Rip1Tag2 mice


title: Healthy volunteer, Control_11822


title: IFNgR2KO_DC_rep3

description: CD11c+ MHC classII hi DCs from CD11cCre IFNgR2fl/fl mice or WT littermates were sorted on FACSAria (Becton Dickinson).


title: Rip1Tag2 islets_Angiogenic_rep6

description: from 8-week-old Rip1Tag2 mice


title: Healthy volunteer, Control_11821


title: Rip1Tag2 islets_Angiogenic_rep4

description: from 8-week-old Rip1Tag2 mice


title: Healthy volunteer, Control_11820


title: IFNgR2KO_DC_rep1


title: WT_DC_rep1


title: IFNgR2KO_DC_rep2


title: Rip1Tag2 islets_Angiogenic_rep1

description: from 8-week-old Rip1Tag2 mice


title: Rip1Tag2 islets_NonAngiogenic_rep6

description: from 8-week-old Rip1Tag2 mice

source_name: Pool of NonAngiogenic islets

value: Non Angiogenic


title: Healthy volunteer, Control_11818


title: liver at T0, biological rep1

description: Gene expression data from control


title: WT_DC_rep3


title: WT_DC_rep2


title: Healthy volunteer, Control_11819


title: Rip1Tag2 islets_Angiogenic_rep3

description: from 8-week-old Rip1Tag2 mice


title: Rip1Tag2 islets_NonAngiogenic_rep2

description: from 8-week-old Rip1Tag2 mice


title: Rip1Tag2 islets_NonAngiogenic_rep3

description: from 8-week-old Rip1Tag2 mice


title: Rip1Tag2 islets_NonAngiogenic_rep5

description: from 8-week-old Rip1Tag2 mice


title: Healthy volunteer, Control_11816


title: diestrus 3

city: Worcester

first: Keith

middle: a

last: Sutton

state: MA

address: 55 Lake Avenue North

department: Cell Biology

institute: UMASS Medical School

data_processing: Affymetric Expression Console. RMA algorithm.

source_name: diestrus CD1 oviduct

label_protocol: Affymetrix protocol

growth_protocol: each sample was comprised of pooled tissue from 5 animals

extract_protocol: RNAzol

treatment_protocol: Animals were not hormonally stimulated

value: oviduct

tag: Sex

value: sexually mature

tag: estrous cycle

value: diestrus


title: Rip1Tag2 islets_NonAngiogenic_rep4

description: from 8-week-old Rip1Tag2 mice


title: Healthy volunteer, Control_11815

value: healthy


title: diestrus 2

value: female


title: diestrus 1


title: Healthy volunteer, Control_11817


title: estrus 3

source_name: estrus CD1 oviduct

value: estrus


title: estrus 2


title: Rip1Tag2 islets_NonAngiogenic_rep1

description: from 8-week-old Rip1Tag2 mice


title: Healthy volunteer, Control_11698


title: Control 2

source_name: d21 CD1 female oviduct

value: sexually immature


title: Control 3


title: Healthy volunteer, Control_11696


title: Healthy volunteer, Control_11699


title: estrus 1


title: Healthy volunteer, Control_11697


title: 42946-1m -/- Liver Normal

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

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

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software.

source_name: Liver

label_protocol: Per RNA labeling, 300 nanograms  of total RNA was used in conjunction with the Affymetrix recommended protocol GeneChip WT Terminal Labeling and Controls Kit (Cat#901525) and Ambion WT Expression Kit (cat#4411973)

extract_protocol: Total RNAs from liver tissues (including small and long RNAs) was extracted using miRNeasy Mini kit (Qiagen). (cat. no. 217004)

treatment_protocol: All animals received a postnatal AAV-mediated insertional mutagenesis and adult liver was processed for whole genome expression analysis.

value: Adult

value: liver

tag: gender

value: Male

tag: disease status

value: Normal tissue

tag: disease causing mutation

value: AAV-mediated insertional mutagenesis

value: mixed strain of FVB/NJ, C57BL/6, and 129/Sv


title: 17240-1m +/- Liver Tumor

value: Tumor tissue


title: MS0906414C Normal Liver


title: Healthy volunteer, Control_11695

value: blood


title: TREM2-/- alveolar macrophages (replicate 2)

city: Vienna

first: Jacques

last: Colinge

address: Lazarettgasse 14, AKH BT-25.3

country: Austria

institute: CeMM

description: TREM2-/-  AM (pooled mice)

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit according to affymetrix guidelines • Transfered 80μl of hyb cocktail to each array, then septas were closed with tough spots  • Hybridized 17 hours +/- 1 hour at 45° at 60 rpm• Fluidics washing protocol FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 7G

data_processing:
Normalization with the Affy console (RMA), differential gene expression done with SAM
MoGene-1_0-st-v1.na27.1.mm9.probeset.csv

source_name: TREM2-/- alveolar macrophages

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Alveolar macrophages isolated from WT and TREM2-/- mice via bronchoalveolar lavage (BAL)

extract_protocol: Qiagen RNEasy kit

tag: background strain

value: Backcrossed 10 x C57/Blk6

value: alveolar macrophages


title: MS0907064E  Liver Normal


title: 19434-1m -/-  Liver Tumor


title: WT alveolar macrophages (replicate 1)

description: WT Ams (pooled mice)

source_name: WT alveolar macrophages

value: wild type


title: TREM2-/- alveolar macrophages (replicate 1)

description: TREM2-/-  AM (pooled mice)


title: Control 1

value: oviduct


title: WT alveolar macrophages (replicate 2)

description: WT Ams (pooled mice)


title: Healthy volunteer, Control_11694

tag: diagnosis


title: Endothelial cells (CD45- CD31+)_empty adenovirus

city: New York

first: Emmanuel

last: GAUTIER

address: 1425 Madison ave

institute: Mount Sinai School of Medecine

data_processing: Affymetrix protocol

extract_protocol: Sorted samples were pelleted and immediately resuspended in TRIzol (Invitrogen, Carlsbad, CA) and stored at -80˚C until RNA isolation. RNA was isolated with RNeasy Micro-RNA isolation kit (Qiagen).

tag: tissue

value: aorta

value: male

tag: genotype

value: apoE KO


title: 42946-1m +/- Liver Normal


title: Macrophages (CD45+ F4/80+ CD11b+)_empty adenovirus


title: MS0906414A 32856-2m Liver Tumor


title: MS0906531 32856-4f -/- Liver Tumor

value: Female


title: Healthy volunteer, Control_11691

value: healthy


title: Endothelial cells (CD45- CD31+)_PBS

source_name: Endothelial cells (CD45- CD31+)_PBS


title: MS0906531 32856-5f Liver Tumor

value: Adult


title: Healthy volunteer, Control_11692


title: Macrophages (CD45+ F4/80+ CD11b+)_apoE adenovirus


title: 543-1f-1 Liver Normal

value: liver


title: MS0905524 3814-3 -/- Tumor Liver


title: Healthy volunteer, Control_11693


title: Healthy volunteer, Control_11690


title: Endothelial cells (CD45- CD31+)_apoE adenovirus


title: Macrophages (CD45+ F4/80+ CD11b+)_PBS

source_name: Macrophages (CD45+ F4/80+ CD11b+)_PBS


title: SLE patient, 1127V1

description: Gene expression data from RNP autoantibody+ SLE patient blood

source_name: SLE patient blood

value: systemic lupus erythematosus (SLE)


title: Brassica napus MINELESS seedlings treated with Mamestra brassicae: replica 3

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

institute: Norwegian University of Science and Technology

description: Two color microarray. Biological replicas are dye-swaped between slides.

hyb_protocol: The cDNAs were hybridized to the microarray slides at 55°C in a Slide Booster Hybridization Station (Advalytix, Brunnthal, Germany) together with Cy3 and Cy5 labelled dendrimers from Genisphere. The slides were washed according to the manufacturers’ descriptions (Genisphere and Advalytix) with first wash at 55°C, and rest following the protocol (Genisphere, Hatfield, USA).

scan_protocol: The slides were scanned at 10 mm resolution on a G2505B Agilent DNA microarray scanner (Agilent Technologies,Palo Alto, CA, USA). The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).

data_processing: Spots identified as not found or which were manually flagged out as bad were filtered out during the data analysis. The statistical analysis was done using R (version 2.10.1) and the Linear Models for Microarray Data (LIMMA) package (Smyth, 2004), The data sets were log-transformed and normalized using the print tip-loess approach. Within-array replicated measurements for the same gene were merged by taking the average between the replicates. No background subtraction was performed. Probe specific dye-effects were identified and genes with strong dye-bias removed. Genes with an adjusted P-value less than 0.05 were considered as significantly differentially expressed. Reference: Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3 (2004)

organism: Brassica napus

source_name: 6-7 days old MINELESS seedlings, untreated: biological replica 3

label_protocol: First strand cDNA was made from total RNA (15 µg) with the Superscript III Reverse Transcriptase (Invitrogen, Carlsbad, USA) and using oligo dT primers with 3DNA capture sequence from the 3DNA Array 350TM kit (Genisphere, Hatfield, USA). RNA samples were labelled alternately with either the Cy5-capture primer or the Cy3-capture primers (sample dye-swapping). Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway).

growth_protocol: The Brassica napus wild-type and MINELESS plants were grown under greenhouse conditions at Department of Multitrophic Interactions, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands. Seeds were germinated on glass beads in water in 10x10 cm plastic containers with a clear plastic lid. The containers were placed on a table in a greenhouse (21°C/16°C; L16:D8 photoperiod). After 3-4 days the seedlings were transferred to unfertilized soil (peat-sand mixture, Lentse Potgrond no. 4, Horticoop, Bleiswijk, the Netherlands) (4 seedlings pot-1). The eggs of M. brassicae were kept in an incubator at 21°C/16°C; L16:D8. The eggs hatched after 4-5 days.

extract_protocol: Total RNA was extracted from 100 mg of seedlings using RNeasy Plant Minikit (Qiagen, Hilden, Germany), and eluted in 2 x 50 µl RNAse free water. To remove any traces of residual DNA, the RNA was treated on column with RNAse free DNase. The eluted RNA was concentrated to 10-20 µl using a 30kDa cut-off Microcon spin filter unit (Amicon, Bedford, USA). To protect RNA from degradation, RNasin Plus RNase inhibitor (Promega, Madison, USA) was added to a final concentration of 1 unit µl-1.  The purity and quantity of RNA concentration was determined using a Nanodrop ND 1000 (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: M. brassicae larvae were maintained and propagated on wild-type (Brassica napus) and MINELESS (Brassica napus) seedlings. 10-days old M. brassicae larvae were transferred to 6-7 days old seedlings of wild-type and MINELESS, respectively. In order to retain the larvae, pots (4 seedlings in each pot) were enclosed in cages. Controls were treated in the same way, without insects. Pots with control (non-infested) and M. brassicae infested seedlings were kept under the same conditions in greenhouse. Control and M. brassicae challenged seedlings were harvested after 24h of induction. Cages and larvae were removed and seedlings were harvested and flash frozen in liquid nitrogen. Each biological replica of untreated plants (controls) comprised 4 pots (4 seedlings in each pot), while for M. brassicae challenged seedlings, each biological replica comprised 6 pots (4 seedlings in each pot).

tag: genotype/variation

value: MINELESS

value: 6-7 days old

source_name: 6-7 days old MINELESS seedlings treated with Mamestra brassicae for 24h (biological replica 3)


title: Brassica napus MINELESS seedlings treated with Mamestra brassicae: replica 4

source_name: 6-7 days old MINELESS seedlings, untreated: biological replica 4

source_name: 6-7 days old MINELESS seedlings treated with Mamestra brassicae for 24h (biological replica 4)


title: Brassica napus seedlings treated with Mamestra brassicae: replica 4

description: Two color microarray. Biological replicas are dye-swaped between slides

source_name: 6-7 days old Brassica napus seedlings, untreated: biological replica 4

value: untreated

source_name: 6-7 days old Brassica napus seedlings treated with Mamestra brassicae for 24h (biological replica 4)


title: 543-2f-1  Liver Normal

tag: developmental stage

value: Normal tissue

value: AAV-mediated insertional mutagenesis

value: mixed strain of FVB/NJ, C57BL/6, and 129/Sv


title: Brassica napus MINELESS seedlings treated with Mamestra brassicae: replica 1

source_name: 6-7 days old MINELESS seedlings treated with Mamestra brassicae for 24h (biological replica 1)

tag: age

source_name: 6-7 days old MINELESS seedlings, untreated: biological replica 1


title: MS0906032B32814-6m Liver Normal

value: Male


title: Brassica napus MINELESS seedlings treated with Mamestra brassicae: replica 2

source_name: 6-7 days old MINELESS seedlings treated with Mamestra brassicae for 24h (biological replica 2)

tag: treatment

source_name: 6-7 days old MINELESS seedlings, untreated: biological replica 2


title: Brassica napus seedlings treated with Mamestra brassicae: replica 1

source_name: 6-7 days old Brassica napus seedlings treated with Mamestra brassicae for 24h (biological replica 1)

value: wild type

source_name: 6-7 days old Brassica napus seedlings, untreated: biological replica 1


title: SLE patient, 1125V1

value: blood


title: SLE patient, 1123V2


title: MS0906414B 32856-2m -/-

source_name: Liver

value: Tumor tissue


title: 19349-1m -/- Liver Normal


title: SLE patient, 1121V1


title: OPNM8-L5

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

institute: University of Alabama in Huntsville

description: Replicate 2

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

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

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

organism: Drosophila mojavensis sonorensis

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

growth_protocol: Flies were reared in opuntia/banana food in bottle at low density.

extract_protocol: Total RNA extraction was performed using Invitrogen’s PureLink Micro-to-Midi Total Purification System.  The suggested manufacturer’s instructions were followed, which included a DNase I digestion to remove any possible genomic DNA contamination.  The quality and concentration of the RNA was determined using a NanoDrop spectrophotometer (NanoDrop Technologies).  Following RNA extraction, mRNA was amplified using the MessageAmp™ II aRNA amplification kit (Applied Biosystems/Ambion, Austin, TX, USA)

treatment_protocol: A generation prior to the experiment five females and five males were placed in a banana-molasses 8-dram vial with granules of live yeast for 24 hours. After this period the ten adults were removed and placed in new vials for another 24 hours. A total of five of these replicate vials were established per each of the 22 isofemale lines used. All vials were maintained in a temperature controlled incubator at 25°C in a 12 hour light/dark cycle. Approximately eight days after oviposition third instar wandering larvae were collected and placed in groups of 20 in microcentrifuge tubes, frozen in liquid nitrogen and stored at -80°C until processing.

tag: subspecies

value: sonorensis

tag: isofemale line


title: OPNM10-L3

description: Replicate 1


title: Brassica napus seedlings treated with Mamestra brassicae: replica 3

source_name: 6-7 days old Brassica napus seedlings, untreated: biological replica 3

source_name: 6-7 days old Brassica napus seedlings treated with Mamestra brassicae for 24h (biological replica 3)


title: OPNM6-L4

description: Replicate 2


title: Brassica napus seedlings treated with Mamestra brassicae: replica 2

source_name: 6-7 days old Brassica napus seedlings treated with Mamestra brassicae for 24h (biological replica 2)

source_name: 6-7 days old Brassica napus seedlings, untreated: biological replica 2


title: OPNM8-L3

description: Replicate 1


title: 19349-2m Liver Tumor

tag: strain


title: OPNM10-L5

description: Replicate 2


title: SLE patient, 1120V1

source_name: SLE patient blood


title: OPNM5-L3

description: Replicate 2


title: 7064-F 45626-7m Liver Normal


title: MS0906032A 4m, -/- Liver Normal


title: OPNM3-L6

description: Replicate 2


title: OPNM6-L2

description: Replicate 1


title: OPNM5-L1

description: Replicate 1


title: OPNM2-L4

description: Replicate 2


title: SLE patient, 1117V1


title: SLE patient, 1116V1


title: OPNM3-L3

description: Replicate 1


title: SLE patient, 1118V3_2


title: SLE patient, 1115V2


title: OPNM2-L2

description: Replicate 1


title: MS0905556 51101-2f Liver Tumor


title: MJBC216-L4

description: Replicate 2

organism: Drosophila mojavensis

value: baja


title: 45626-2m Liver Tumor


title: MS0906531 32856-6F

value: Female


title: MS0905556 51101-2f Liver Normal


title: SLE patient, 1115V1


title: MJBC35-L5

description: Replicate 2


title: MJBC103-L3

description: Replicate 2


title: MJBC155-L3

description: Replicate 2


title: MJBC216-L1

description: Replicate 1


title: SLE patient, 1111V2


title: CI27-L3

description: Replicate 2

organism: Drosophila mojavensis wrigleyi

value: wrigleyi


title: SLE patient, 1114V4


title: MJBC155-L1

description: Replicate 1


title: 45626-2m -/- Liver Normal

value: Adult


title: 7064-B Liver Tumor

value: liver


title: MJBC103-L2

description: Replicate 1


title: 42946-1f -/- Liver Tumor


title: SLE patient, 1111V1

value: systemic lupus erythematosus (SLE)


title: MJBC35-L2

description: Replicate 1


title: CI23-L2

description: Replicate 2


title: SLE patient, 1113V1


title: 7064-A Liver Normal


title: CI27-L2

description: Replicate 1


title: CI9-L6

description: Replicate 2


title: CI23-L1

description: Replicate 1


title: 26558-2f Liver Tumor


title: CI8-L1

description: Replicate 1


title: 26558-2f Liver Normal


title: CI9-L4

description: Replicate 1


title: SLE patient, 1105V1


title: SLE patient, 1110V1


title: SLE patient, 1104V1


title: CI6-L5

description: Replicate 2


title: CI8-L6

description: Replicate 2


title: 26558-5m  +/- Liver Normal


title: 26558-5m +/-  Liver Tumor


title: CI3-L1

description: Replicate 1


title: CI3-L2

description: Replicate 2


title: CI6-L1

description: Replicate 1


title: 543-3m Liver Normal


title: ANZA10-L6

description: Replicate 2

organism: Drosophila mojavensis mojavensis

value: mojavensis


title: SLE patient, 1103V1


title: ANZA8-L5

description: Replicate 2


title: 543-3m Liver Tumor


title: ANZA10-L5

description: Replicate 1


title: SLE patient, 1103V2_2


title: ANZA17-L3

description: Replicate 1


title: SLE patient, 1102V2


title: 5740-3m +/- Liver Tumor


title: ANZA5-L6

description: Replicate 2


title: SLE patient, 1102V1


title: ANZA17-L6

description: Replicate 2


title: ANZA8-L2

description: Replicate 1


title: SLE patient, 1100V3


title: ANZA4-L6

description: Replicate 2


title: ANZA5-L2

description: Replicate 1


title: 12945-4f Liver Tumor


title: ANZA3-L5

description: Replicate 2


title: 5740-3m +/- Liver Normal


title: 12945-4f Liver Normal


title: SLE patient, 1101V3


title: shRNA-58335_LacZ

city: Sapporo

first: Masashi

last: Idogawa

country: Japan

institute: Sapporo Medical University

description:
Gene expression after Ad-LacZ infection in shRNA-58335-expressing cells
Huh-7_3

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: Huh-7 cells were cultured in DMEM with 10% FCS.

extract_protocol: 72h after infection, total RNA was extracted by RNeasy mini kit (QIAGEN) according to manufacturer's protocol. RNA was quantified using the NanoDrop spectrophotometer.

treatment_protocol: Huh-7 cells stably expressing shRNA-58335 or control shRNA were infected with adenovirus expressing p53 (Ad-p53) or LacZ (Ad-LacZ) as control at 200 moi.

tag: cell line

value: stably expressing shRNA-58335

tag: infected with

value: adenovirus expressing LacZ (Ad-LacZ)


title: SLE patient, 1097V3


title: SLE patient, 1099V2


title: ANZA4-L2

description: Replicate 1


title: shRNA-58335_p53

description:
Gene expression after Ad-p53 infection in shRNA-58335-expressing cells
Huh-7_4

value: adenovirus expressing p53 (Ad-p53)


title: shRNA-cont_LacZ

description:
Gene expression after Ad-LacZ infection in shRNA-control-expressing cells
Huh-7_1

value: stably expressing control shRNA


title: 5796-5f  Liver Tumor

value: AAV-mediated insertional mutagenesis

value: mixed strain of FVB/NJ, C57BL/6, and 129/Sv


title: 5796-5F Liver Normal

value: Normal tissue


title: shRNA-cont_p53

description:
Gene expression after Ad-p53 infection in shRNA-control-expressing cells
Huh-7_2


title: WM1361 - Interferon

first: Dana

last: Pe'er

address: 1212 Amsterdam Ave.

institute: Columbia University

hyb_protocol: Agilent's protocol, using 600ng labeled cRNA

scan_protocol: Agilent's protocol

data_processing: Probes were filtered based on their values. Probes with low or high levels in more than 20% of samples were removed. Then samples were normalized based on their 75% percentile

source_name: WM1361 - Interferon

label_protocol: Agilent's Quick Amp One Color labeling using 100ng total RNA

growth_protocol: All cell lines were plated in 60-80% confluency in RPMI1640, 10%FBS + PenStrep/Glut

extract_protocol: Rneasy protocol

treatment_protocol: Samples were treated with 50nM of PD901, 1000U/mL of interferon beta, or their combination

tag: cell type

value: melanoma

tag: phenotype

value: high interferon pathway basal activity


title: 12945-2m Liver Tumor

tag: gender

value: Male

tag: disease status

value: Tumor tissue


title: SLE patient, 1099V1

value: blood


title: SLE patient, 1096V1


title: WM1361 - PD901 + Interferon

source_name: WM1361 - PD901 + Interferon


title: WM1361 - Control

source_name: WM1361 - Control


title: WM1361 - PD901


title: 26558-6m Liver Tumor

tag: disease causing mutation


title: SkMel39 - PD901 + Interferon

source_name: SkMel39 - PD901 + Interferon


title: SLE patient, 1093V1

tag: diagnosis


title: SLE patient, 1097V1

tag: tissue


title: SLE patient, 1095V2


title: 12945-2m Liver Normal


title: 26558-6m  Liver Normal


title: SkMel2 - PD901

source_name: SkMel2 - PD901

value: low interferon pathway basal activity


title: SkMel2 - PD901 + Interferon

source_name: SkMel2 - PD901 + Interferon


title: ANZA3-L2

description: Replicate 1


title: SkMel39 - Interferon

source_name: SkMel39 - Interferon


title: SLE patient, 1097V2


title: SkMel133 - PD901 + Interferon

source_name: SkMel133 - PD901 + Interferon


title: SkMel2 - Control

source_name: SkMel2 - Control


title: SkMel2 - Interferon

source_name: SkMel2 - Interferon


title: SkMel133 - Control

source_name: SkMel133 - Control


title: 42955-1m  Liver Tumor

source_name: Liver

value: Adult


title: SkMel39 - PD901

source_name: SkMel39 - PD901


title: 42955-1m  Liver Normal

value: liver


title: SkMel39 - Control

source_name: SkMel39 - Control


title: 19849-4m +/- Liver Tumor


title: SkMel133 - PD901

source_name: SkMel133 - PD901


title: SkMel133 - Interferon

source_name: SkMel133 - Interferon


title: SLE patient, 1090V1

source_name: SLE patient blood

value: systemic lupus erythematosus (SLE)


title: SkMel105 - PD901 + Interferon

source_name: SkMel105 - PD901 + Interferon


title: SLE patient, 1092V1


title: SkMel105 - PD901

source_name: SkMel105 - PD901


title: 5755-2f  Liver Tumor

value: Female


title: SLE patient, 1088V3


title: SLE patient, 1091V1


title: 19849-4m +/- Liver Normal


title: SkMel105 - Control

source_name: SkMel105 - Control


title: SkMel105 - Interferon

source_name: SkMel105 - Interferon


title: A375 - PD901


title: MS0907119 5752-3m Tumor Liver


title: A375 - Control

source_name: A375 - Control


title: A375 - PD901 + Interferon

source_name: A375 - PD901 + Interferon


title: 5755-2f Liver Normal


title: MS0907119 5752-3m Liver Normal


title: SkMel39 - Control [Batch 2]

treatment_protocol: Samples were treated with 50nM of PD901


title: WM1361 - Control [Batch 2]

source_name: WM1361 - Control


title: 17420-1m +/- Liver Tumor


title: SkMel30 - PD901 8h [Batch 2]

source_name: SkMel30 - PD901 8h


title: SLE patient, 1088V2


title: SLE patient, 1087V1


title: SLE patient, 1083V2


title: SkMel39 - PD901 8h [Batch 2]

source_name: SkMel39 - PD901 8h


title: SkMel30 - Control [Batch 2]

source_name: SkMel30 - Control


title: WM1361 - PD901 8h [Batch 2]


title: A375 - Interferon

source_name: A375 - Interferon


title: SkMel28 - PD901 8h [Batch 2]

source_name: SkMel28 - PD901 8h


title: SLE patient, 1084V3


title: SkMel28 - Control [Batch 2]

source_name: SkMel28 - Control


title: SLE patient, 1083V1


title: SkMel207 - PD901 8h [Batch 2]

source_name: SkMel207 - PD901 8h


title: 19349-4f liver tumor

source_name: Liver


title: SLE patient, 1081V4


title: 5740-4m Liver Tumor


title: 19349-4f Liver Normal


title: SLE patient, 1082V2


title: SkMel2 - PD901 8h [Batch 2]

source_name: SkMel2 - PD901 8h


title: SkMel2 - Control [Batch 2]

source_name: SkMel2 - Control


title: 17420-1m +/- GFP Liver Normal


title: SLE patient, 1076V1

source_name: SLE patient blood


title: SkMel19 - Control [Batch 2]

source_name: SkMel19 - Control


title: SkMel207 - Control [Batch 2]

source_name: SkMel207 - Control


title: SkMel133 - PD901 8h [Batch 2]

source_name: SkMel133 - PD901 8h


title: SkMel19 - PD901 8h [Batch 2]

source_name: SkMel19 - PD901 8h


title: 5740-4m Liver Normal


title: SLE patient, 1075V1


title: SkMel190 - Control [Batch 2]

source_name: SkMel190 - Control


title: SkMel190 - PD901 8h [Batch 2]

source_name: SkMel190 - PD901 8h


title: MS0905965 26558-3F Liver Normal


title: SLE patient, 1072V1


title: Colo829 - PD901 8h [Batch 2]


title: Cortical astrocytes 7DIV, Mecp2 WT/y, biological rep 3

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description: Gene expression data

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were preprocessed and analyzing using Partek Genomic Suite.

source_name: P0 mouse cortical astrocytes 7DIV, Mecp2 WT/y

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: P0 newborns from pregnant Mecp2 308/+ heterozygous mice were used for the preparation of dissociated cortical astrocyte cultures. Astrocytes were kept 7 days in vitro in DMEM supplemented with 10% FBS and 1% Pen/Strep (GIBCO)

extract_protocol: Total RNA extraction with the Qiagen RNeasy kit (Qiagen) as described by the manufacturer

value: Primary culture of astrocytes from cortex

tag: genotype

value: Mecp2 WT/y

value: P0 pups, 7 days in vitro


title: SLE patient, 1066V1


title: Colo829 - Control [Batch 2]

source_name: Colo829 - Control


title: SkMel105 - Control [Batch 2]

source_name: SkMel105 - Control


title: MS0905965 26558-3F Liver Tumor


title: A375 - PD901 8h [Batch 2]


title: SLE patient, 1064V1


title: SLE patient, 1069V1


title: A2058 - Control [Batch 2]

source_name: A2058 - Control


title: A2058 - PD901 8h [Batch 2]


title: Cortical astrocytes 7DIV, Mecp2 WT/y, biological rep 2

description: Gene expression data


title: A375 - Control [Batch 2]

source_name: A375 - Control


title: SLE patient, 1060V1


title: MalMe3M - Control [Batch 2]

source_name: MalMe3M - Control


title: MalMe3M - PD901 8h [Batch 2]

source_name: MalMe3M - PD901 8h


title: SLE patient, 1056V1


title: SLE patient, 1065V1


title: Cortical astrocytes 7DIV, Mecp2 308/y, biological rep 3

description: Gene expression data

source_name: P0 mouse cortical astrocytes 7DIV, Mecp2 308/y

value: Mecp2 308/y


title: Cortical astrocytes 7DIV, Mecp2 308/y, biological rep 2

description: Gene expression data


title: Cortical astrocytes 7DIV, Mecp2 WT/y, biological rep 4

description: Gene expression data


title: SLE patient, 1054V1


title: Cortical astrocytes 7DIV, Mecp2 308/y, biological rep 4

description: Gene expression data


title: SkMel39 - Control [Batch 1]

source_name: SkMel39 - Control


title: WM1361 - PD901 8h [Batch 1]


title: SkMel30 - PD901 8h [Batch 1]

source_name: SkMel30 - PD901 8h


title: SkMel30 - Control [Batch 1]

source_name: SkMel30 - Control


title: Cortical astrocytes 7DIV, Mecp2 308/y, biological rep 1

description: Gene expression data


title: Cortical astrocytes 7DIV, Mecp2 WT/y, biological rep 1

description: Gene expression data


title: SkMel39 - PD901 8h [Batch 1]

source_name: SkMel39 - PD901 8h


title: SkMel207 - Control [Batch 1]

source_name: SkMel207 - Control


title: SkMel2 - Control [Batch 1]

source_name: SkMel2 - Control


title: Nkx2.5-Cre; R26R-miR302-367, 3

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

source_name: heart at postnatal day 14 heart

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

treatment_protocol: The mouse hearts were harvested at 14 days after birth

value: heart

value: Mixed  C57BL/6 x 129S6


title: SLE patient, 1050V1

source_name: SLE patient blood


title: SLE patient, 1049V2


title: SLE patient, 1052V1


title: WM1361 - Control [Batch 1]

source_name: WM1361 - Control


title: Nkx2.5-Cre; R26R-miR302-367, 2


title: SLE patient, 1049V4


title: SkMel190 - Control [Batch 1]

source_name: SkMel190 - Control


title: SkMel190 - PD901 8h [Batch 1]

source_name: SkMel190 - PD901 8h


title: SkMel2 - PD901 8h [Batch 1]

source_name: SkMel2 - PD901 8h


title: SkMel19 - PD901 8h [Batch 1]

source_name: SkMel19 - PD901 8h


title: SLE patient, 1051V1


title: SLE patient, 1053V1


title: Nkx2.5-Cre, 3


title: SkMel19 - Control [Batch 1]

source_name: SkMel19 - Control


title: SkMel207 - PD901 8h [Batch 1]

source_name: SkMel207 - PD901 8h


title: SLE patient, 1048V1


title: SkMel133 - Control [Batch 1]

source_name: SkMel133 - Control


title: SkMel133 - PD901 8h [Batch 1]

source_name: SkMel133 - PD901 8h


title: SLE patient, 1048V2


title: Nkx2.5-Cre, 2


title: Nkx2.5-Cre; R26R-miR302-367, 1


title: Nkx2.5-Cre, 1


title: SkMel105 - PD901 8h [Batch 1]

source_name: SkMel105 - PD901 8h


title: SkMel105 - Control [Batch 1]

source_name: SkMel105 - Control


title: SLE patient, 1047V1


title: A375 - PD901 8h [Batch 1]


title: SLE patient, 1046V1


title: A2058 - Control [Batch 1]

source_name: A2058 - Control


title: A375 - Control [Batch 1]

source_name: A375 - Control


title: A2058 - PD901 8h [Batch 1]


title: MalMe3M - PD901 8h [Batch 1]

source_name: MalMe3M - PD901 8h


title: SLE patient, 1044V1


title: MalMe3M - Control [Batch 1]

source_name: MalMe3M - Control


title: SLE patient, 1046V2


title: SLE patient, 1045V2


title: SLE patient, 1045V1


title: Dose_1/2 rep1

city: Nagpur

first: praveen

middle: Kumar

last: Naoghare

state: Maharashtra

address: CSIR Lab,Nehru Marg

department: Environmental Health Division

country: India

institute: Innovative Life Discoveries

description: Dose1_2 1

hyb_protocol: Complex probes were hybridized to each GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix)

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

data_processing: The data were analyzed with Expression Console and Gene springGX 12.0.  For the data normalization, Affymetrix default analysis settings and RMA+DABG All organism  was selected. The probe set  reprsents fonly or  the human from the normalized data had been included and imported  in GeneSpring for differnetiall miRNA analysis followed by intensities less than the 20.0 percentile in the normalized data were excluded.

source_name: HOS_MEM media treated with sodium fluoride

label_protocol: Complex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA)Affymetrix)

growth_protocol: HOS cells grown on MEM media

extract_protocol: Total RNA prepared using STRATAGENE ABSOLUTELY RNA KIT

treatment_protocol: Treated with 1/5th and 1/2 concentration of 24h LC50 of sodium fluoride.

value: HOS

value: Osetoblast cells

tag: treated with

value: 1/2 conc. of 24h LC50 of sodium fluoride

tag: time point

value: after 1 month of chronic exposure


title: SkMel105 - PD901 8h [Batch 2]

value: melanoma


title: Dose_1/5 rep2

description: Dose_1_5 2

value: 1/5th conc. of 24h LC50 of sodium fluoride


title: Dose_1/2 rep2

description: Dose1_2 2


title: Control rep1

source_name: HOS_MEM media

value: none (control)


title: SLE patient, 1041V1

last: Hoffman

institute: Eli Lilly and Company

data_processing: The data were analyzed with Partek Genomics Suite using the Affymetrix default analysis settings. RMA background correction and quantile normalization were applied with the median polish approach for summarizing probe sets.

source_name: SLE patient blood

extract_protocol:
Extraction of total RNA was performed using the Qiagen RNeasy Plus kit according to the manufacturer's instructions.
A custom, automated version of the NuGEN Ovation v2.0 WB amplification system was used for RNA extracted from blood.

value: blood


title: SLE patient, 1042V1


title: SLE patient, 1040V1


title: Control rep2


title: SLE patient, 1037V1


title: SLE patient, 1043V2


title: Infected_48h pi_Rep3

city: FARIDABAD

first: ARUP

last: BANERJEE

state: Haryana

address: THSTI, 3RD MILE STONE, FARIDABAD GURGAON EXPRESSWAY, NCR BIOTECH CLUSTER

department: VIDRC

institute: TRANSLATIONAL HEALTH SCIENCE & TECHNOLOGY INSTITUTE

description:
SAMPLE 6C
miRNA microarray data.

hyb_protocol: Complex probes were hybridized to each GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix).

data_processing: Scanned images of microarray chips were analyzed using Affymetrix Expression Console with the default RMA settings. Raw data were processed and normalized on basis of organism human using RMA algorithm. The normalized data (CHP files) processed for the differential miRNA analysis in Affymetrix TAC software.

source_name: CHME3 cells grown on transwells, infected with JEV, 48h pi

label_protocol: Complex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: CHME3 cells grown on 6-well plates.

extract_protocol: Total RNA prepared using Qiagen RNA extraction kit.

treatment_protocol: Infected with an MOI of 5 pfu/cell of Japanese encephalitis virus (P20778 strain).

value: microglial cell line

tag: cell state

value: polarized

value: Japanese encephalitis virus strain P20778 infection

value: 48h post infection


title: SkMel133 - Control [Batch 2]


title: Dose_1/5 rep1

description: Dose_1_5 1


title: SLE patient, 1036V1

city: Indianapolis

first: Robert

address: Lilly Corporate Center

label_protocol: Not provided

value: systemic lupus erythematosus (SLE)


title: SLE patient, 1035V1


title: SLE patient, 1034V3


title: SLE patient, 1032V3


title: SLE patient, 1031V2