title: PBMC patient with alloimmune lesion in renal biopsy:ALLOIM_6

source_name: PBMC from patients with alloimmune lesion

value: alloimmune lesions (ALLOIM)

value: Peripheral blood mononuclear cells (PBMC)


title: I13_rep1

status: Public on Dec 24 2015

type: RNA

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

description: raw data: 253432110001-4_2: Cy5

hyb_protocol: Co-hybridization of Cy5- and Cy3-labeled cDNA probes was performed on these oligonucleotide arrays at 65°C and 10 rpm for 17 h using GEX HI-RPM buffer (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: The raw expression data were Lowess normalized and scaled to normalized probe expression levels using MicroPreP (van Hijum, 2003). As in general multiple probes were designed for each ORF, the ORF expression level was calculated from the median of its probe signals.

molecule: total RNA

organism: Lactococcus lactis subsp. lactis Il1403

source_name: IL1403 fermentation 13

label_protocol: 5 µg of total RNA was used for cDNA synthesis and indirect labeling with cyanine 5 or cyanine 3

growth_protocol: Lactococcus lactis strain IL1403 was grown in chemically defined medium

extract_protocol: Cultures were lysed by bead-beating and total RNA was isolated by subsequent phenol/chloroform extraction.

treatment_protocol: Harvested cells were resuspended in cold TE buffer with phenol/chloroform, SDS, sodium acetate and zirconia beads, frozen in liquid nitrogen and stored at -80°C.

tag: fermentation conditions

value: 100 mM NaCl, pH 6.5, 30°C, static


title: K13_rep2

description: raw data: 253432310002-3_2: Cy5

organism: Lactococcus lactis subsp. lactis KF147

source_name: KF147 fermentation 13

growth_protocol: Lactococcus lactis strain KF147 was grown in chemically defined medium


title: PBMC from patient showing IFTA in renal biopsy:IFTA_1

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.13) 'rma' in R.3.0.1

label: biotin

organism: Homo sapiens

source_name: PBMC from patients with signs of tubular atrophy and interstitial fibrosis (IFTA)

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: renal biopsy group

tag: cell type


title: single culture_ 96h_biological rep3

city: Vila Real

first: Ana

last: Mendes-Ferreira

address: Quinta de Prados

country: Portugal

institute: Universidade de Trás-os-Montes e Alto Douro

description: Gene expression data from cells in single culture at 96h

hyb_protocol: 5 µg of fragmented aRNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0003; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae in single culture at 96h

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Yeast Genome 2.0 Arrays, according to the manufacturer's GeneChip 3' IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3' IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3' IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Exponential cell populations of both yeast strains  were used to inoculate natural grape juice (10^6 cel/ml). Paralell fermentations were conducted with S. cerevisiae pure-culture and S. cerevisiae in mxed-culture with H. guilliermondii strain

extract_protocol: Total RNA isolation was performed using the hot-phenol method (Koher & Domdey, 1991, Methods in Enzimology 194:398-405).

treatment_protocol: Natural grape juice fermentations were conducted by inoculation with with S. cerevisiae (UCD522) either in single (Control) or in mixed culture with a strain of Hanseniaspora guilliermondii (Treatment)

tag: strain

tag: treatment

value: single culture

tag: time


title: I6_rep4

description: raw data: 253432110001-4_2: Cy3

source_name: IL1403 fermentation 6


title: K12_rep1

description: raw data: 253432310002-3_1: Cy5

source_name: KF147 fermentation 12

value: 100 mM NaCl, pH 6.0, 35°C, static


title: K12_rep2

description: raw data: 253432310002-3_2: Cy3


title: I6_rep3

description: raw data: 253432110001-4_1: Cy5


title: I3_rep3

description: raw data: 253432110001-4_1: Cy3

source_name: IL1403 fermentation 3

value: 0 mM NaCl, pH 6.5, 27°C, static


title: single culture_ 96h_biological rep2


title: single culture_ 96h_biological rep1


title: K11_rep2

description: raw data: 253432310002-3_1: Cy3

source_name: KF147 fermentation 11

value: 0 mM NaCl, pH 6.5, 35°C, static


title: I1_rep2

description: raw data: 253432110001-3_2: Cy5

source_name: IL1403 fermentation 1

value: 0 mM NaCl, pH 6.0, 27°C, shaken


title: PBMC patient with alloimmune lesion in renal biopsy:ALLOIM_5


title: K11_rep1

description: raw data: 253432310002-2_2: Cy5


title: I6_rep2

description: raw data: 253432110001-3_2: Cy3


title: I6_rep1

description: raw data: 253432110001-3_1: Cy5


title: K10_rep1

description: raw data: 253432310002-2_1: Cy5

source_name: KF147 fermentation 10

value: 100 mM NaCl, pH 6.5, 35°C, shaken


title: I5_rep2

description: raw data: 253432110001-3_1: Cy3

source_name: IL1403 fermentation 5

value: 0 mM NaCl, pH 6.0, 30°C, static


title: mixed culture_ 48h_biological rep2

description: Gene expression data from cells in mixed culture at 48h

source_name: S. cerevisiae in mixed culture at 48h

value: mixed culture


title: K9_rep2

description: raw data: 253432310002-2_1: Cy3

source_name: KF147 fermentation 9

value: 0 mM NaCl, pH 6.0, 35°C, shaken


title: I5_rep1

description: raw data: 253432110001-2_2: Cy5


title: K9_rep1

description: raw data: 253432310002-1_2: Cy5


title: mixed culture_ 48h_biological rep3


title: PBMC patient with alloimmune lesion in renal biopsy:ALLOIM_4


title: PBMC patient with alloimmune lesion in renal biopsy:ALLOIM_3


title: K8_rep2

description: raw data: 253432310002-1_2: Cy3

source_name: KF147 fermentation 8

value: 100 mM NaCl, pH 6.0, 30°C, shaken


title: 23_ccpA-R304W_NOgluc_347257

city: Groningen

first: Ruud

last: Detert Oude Weme

state: Groningen

address: Nijenborgh 7

institute: University of Groningen

description:
CcpA-R304W versus CcpA-wt. LB. Exp.phase.
Sample 23

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing:
Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with PrePreP, Prep, PostPrep as previously described (Marciniak BC BMC genomics 2012 PMID: 22900538). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.
Please note that Net{A} (in each raw data file)  is the raw signal of channel A minus the local corner background signal of channel A, and Net{B} is the raw signal of channel B minus the local corner background signal of channel B.

organism: Bacillus subtilis

source_name: CcpA-R304W_LB without 1% glucose

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using NucleoSpin Extract II columns

growth_protocol: Bacillus subtilis strain ccpA::spec carrying pHT304 (empty plasmid), pWH_ccpA_M17R, pWH_ccpA_T62H, or pWH_ccpA_R304W were grown in LB with or without 1% glucose. The control in the microarray study was the strain Bacillus subtilis ccpA::spec carrying pWH_ccpA-wt. All Bacillus subtilis cultures were harvested in the early exponential growth phase at an OD600 of 0.3 from 100 ml culture. Two independent cultures of each strain per growth condition (+/- glucose) and a technical replicate (dye-swap) were used.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Marciniak BC BMC genomics 2012 PMID: 22900538). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: no treatment

tag: genotype/variation

tag: growth media

value: LB without 1% glucose

source_name: wild type_LB without 1% glucose

value: wild type


title: 24_ccpA-R304W_NOgluc_346937

description:
CcpA-wt versus CcpA-R304W. LB. Exp.phase.
Sample 24


title: I4_rep2

description: raw data: 253432110001-2_2: Cy3

source_name: IL1403 fermentation 4

value: 100 mM NaCl, pH 6.0, 27°C, static


title: I4_rep1

description: raw data: 253432110001-2_1: Cy5


title: PBMC patient with alloimmune lesion in renal biopsy:ALLOIM_2

source_name: PBMC from patients with alloimmune lesion


title: mixed culture_ 48h_biological rep1


title: PBMC patient with alloimmune lesion in renal biopsy:ALLOIM_1


title: 22_ccpA-R304W_NOgluc_347256

description:
CcpA-wt versus CcpA-R304W. LB. Exp.phase.
Sample 22


title: 21_ccpA-T62H_NOgluc_347060

description:
CcpA-wt versus CcpA-T62H. LB. Exp.phase.
Sample 21

source_name: CcpA-T62H_LB without 1% glucose


title: single culture_ 48h_biological rep2

description: Gene expression data from cells in single culture at 48h

source_name: S. cerevisiae in single culture at 48h


title: K10_rep2

description: raw data: 253432310002-2_2: Cy3


title: single culture_ 48h_biological rep1


title: K8_rep1

description: raw data: 253432310002-1_1: Cy5


title: I3_rep2

description: raw data: 253432110001-2_1: Cy3


title: mixed culture_ 24h_biological rep2

description: Gene expression data from cells in mixed culture at 24h

source_name: S. cerevisiae in mixed culture at 24h


title: I3_rep1

description: raw data: 253432110001-1_2: Cy5


title: 19_ccpA-T62H_NOgluc_347236

description:
CcpA-T62H versus CcpA-wt. LB. Exp.phase.
Sample 19


title: single culture_ 48h_biological rep3


title: K13_rep1

description: raw data: 253432310001-4_2: Cy5

source_name: KF147 fermentation 13


title: I2_rep2

description: raw data: 253432110001-1_2: Cy3

source_name: IL1403 fermentation 2

value: 100 mM NaCl, pH 6.5, 27°C, shaken


title: K6_rep4

description: raw data: 253432310001-4_2: Cy3

source_name: KF147 fermentation 6


title: mixed culture_ 24h_biological rep1


title: single culture_ 24h_biological rep2

description: Gene expression data from cells in single culture at 24h

source_name: S. cerevisiae in single culture at 24h


title: 20_ccpA-T62H_NOgluc_347059

description:
CcpA-T62H versus CcpA-wt. LB. Exp.phase.
Sample 20


title: 18_ccpA-M17R_NOgluc_347237

description:
CcpA-wt versus CcpA-M17R. LB. Exp.phase.
Sample 18

source_name: CcpA-M17R_LB without 1% glucose


title: K6_rep3

description: raw data: 253432310001-4_1: Cy5


title: I2_rep1

description: raw data: 253432110001-1_1: Cy5


title: single culture_ 24h_biological rep1


title: K3_rep3

description: raw data: 253432310001-4_1: Cy3

source_name: KF147 fermentation 3


title: I1_rep1

description: raw data: 253432110001-1_1: Cy3

source_name: IL1403 fermentation 1


title: 17_ccpA-M17R_NOgluc_347240

description:
CcpA-M17R versus CcpA-wt. LB. Exp.phase.
Sample 17


title: 16_ccpA-M17R_NOgluc_347238

description:
CcpA-M17R versus CcpA-wt. LB. Exp.phase.
Sample 16


title: K7_rep1

description: raw data: 253432310002-1_1: Cy3

source_name: KF147 fermentation 7

value: 0 mM NaCl, pH 6.5, 30°C, shaken


title: K1_rep2

description: raw data: 253432310001-3_2: Cy5

source_name: KF147 fermentation 1


title: 15_DELTAccpA_NOgluc_346945

description:
CcpA-wt versus DELTAccpA. LB. Exp.phase.
Sample 15

source_name: DELTAccpA_LB without 1% glucose

value: DELTAccpA


title: 14_DELTAccpA_NOgluc_347239

description:
DELTAccpA versus CcpA-wt. LB. Exp.phase.
Sample 14


title: K6_rep2

description: raw data: 253432310001-3_2: Cy3

value: 100 mM NaCl, pH 6.5, 30°C, static


title: 13_DELTAccpA_NOgluc_346944

description:
DELTAccpA versus CcpA-wt. LB. Exp.phase.
Sample 13


title: 12_ccpA-R304W_gluc_347249

description:
CcpA-wt versus CcpA-R304W. LB+1%gluc. Exp.phase.
Sample 12

source_name: wild type_LB with 1% glucose

value: LB with 1% glucose

source_name: CcpA-R304W_LB with 1% glucose


title: mouse SKPs prepared from wounded skin treated with vehicle, biological replicate 2

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

country: Canada

institute: Hospital for Sick Children

description: Gene expression of mouse SKPs prepared from injured skin treated with vehicle

hyb_protocol: Affymetrix Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the Fluidics Protocol FS450_0002 using 5.5 ug of cDNA

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using the oligo package of Bioconductor in R. The data were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) method.

organism: Mus musculus

source_name: SKPs prepared from injured skin treated with Vehicle

label_protocol: cDNA was prepared using the Ambion WT Expression Kit using 400 ng of total RNA

growth_protocol: Cells were cultured at 50,000 cells/ml in SKPs basal growth medium (DMEM-F12, 3:1 and 40 ng/ml FGF2, 20 ng/ml EGF,  2% B27, and 1 μg/ml fungizone) and allowed to form spheres

extract_protocol: RNA was extracted using the Ambion Ribopure kit as described by the manufacturer

treatment_protocol: Secondary SKPs spheres were generated for each condition

tag: treatment group

value: Wound Vehicle


title: K6_rep1

description: raw data: 253432310001-3_1: Cy5


title: mouse SKPs prepared from wounded skin treated with trimebutine maleate, biological replicate 3

description: Gene expression of mouse SKPs prepared from injured skin treated with trimebutine maleate

value: Wound trimebutine maleate


title: neonatal rat skps treated with trimebutine maleate and trametinib, biological replicate 3

description: Gene expression of neonatal rat SKPs treated with trimebutine maleate and trametinib for 24 hours.

hyb_protocol: Affymetrix Rat Gene 2.0 ST arrays were washed, stained and scanned according to the Fluidics Protocol FS450_0002 using 5.5 ug of cDNA

organism: Rattus norvegicus

treatment_protocol: Secondary SKPs spheres were dissociated, treated with 100 nM of alprostadil, trimebutine maleate or 100 nM of both trimebutine maleate and trametinib for 24 hour

value: Sprague-Dawley

value: Trimebutine maleate and trametinib


title: mouse SKPs prepared from wounded skin treated with vehicle, biological replicate 3


title: mouse SKPs prepared from wounded skin treated with trimebutine maleate, biological replicate 2

source_name: SKPs prepared from injured skin treated with trimebutine maleate


title: S2_rep2

description: raw data: 253432210001-1_2: Cy3

organism: Lactococcus cremoris subsp. cremoris SK11

source_name: SK11 fermentation 2

growth_protocol: Lactococcus lactis strain SK11 was grown in chemically defined medium


title: K5_rep1

description: raw data: 253432310001-2_2: Cy5

source_name: KF147 fermentation 5


title: K4_rep2

description: raw data: 253432310001-2_2: Cy3

source_name: KF147 fermentation 4


title: 11_ccpA-R304W_gluc_346943

description:
CcpA-R304W verus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 11


title: 10_ccpA-R304W_gluc_346950

description:
CcpA-R304W verus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 10


title: 9_ccpA-T62H_gluc_347247

description:
CcpA-wt versus CcpA-T62H. LB+1%gluc. Exp.phase.
Sample 9

source_name: CcpA-T62H_LB with 1% glucose


title: K5_rep2

description: raw data: 253432310001-3_1: Cy3


title: K4_rep1

description: raw data: 253432310001-2_1: Cy5


title: mouse SKPs prepared from wounded skin treated with vehicle, biological replicate 1


title: 7_ccpA-T62H_gluc_346953

description:
CcpA-T62H versus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 7


title: mouse SKPs prepared from wounded skin treated with alprostadil, biological replicate 1

description: Gene expression of mouse SKPs prepared from injured skin treated with alprostadil

value: Wound alprostadil


title: neonatal rat skps treated with trimebutine maleate, biological replicate 2

description: Gene expression of neonatal rat SKPs treated with trimebutine maleate for 24 hours.

value: Trimebutine maleate


title: neonatal rat skps treated with trimebutine maleate and trametinib, biological replicate 2


title: K3_rep2

description: raw data: 253432310001-2_1: Cy3

value: 0 mM NaCl, pH 6.5, 27°C, static


title: neonatal rat skps treated with trimebutine maleate and trametinib, biological replicate 1


title: mouse SKPs prepared from wounded skin treated with alprostadil, biological replicate 3

source_name: SKPs prepared from injured skin treated with alprostadil


title: mouse SKPs prepared from wounded skin treated with alprostadil, biological replicate 2


title: neonatal rat skps treated with trimebutine maleate, biological replicate 1


title: mouse SKPs prepared from uninjured skin treated with vehicle, biological replicate 3

description: Gene expression of mouse SKPs prepared from uninjured skin treated with vehicle

value: Uninjured Vehicle


title: neonatal rat skps treated with alprostadil, biological replicate 3

description: Gene expression of neonatal rat SKPs treated with alprostadil for 24 hours.

value: Alprostadil


title: mouse SKPs prepared from uninjured skin treated with vehicle, biological replicate 2


title: K3_rep1

description: raw data: 253432310001-1_2: Cy5


title: mouse SKPs prepared from wounded skin treated with trimebutine maleate, biological replicate 1


title: mouse SKPs prepared from uninjured skin treated with vehicle, biological replicate 1


title: 6_ccpA-M17R_gluc_347246

description:
CcpA-wt versus CcpA-M17R. LB+1%gluc. Exp.phase.
Sample 6

source_name: CcpA-M17R_LB with 1% glucose


title: 8_ccpA-T62H_gluc_346947

description:
CcpA-T62H versus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 8


title: 4_ccpA-M17R_gluc_346939

description:
CcpA-M17R versus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 4


title: K2_rep1

description: raw data: 253432310001-1_1: Cy5

source_name: KF147 fermentation 2


title: neonatal rat skps treated with trimebutine maleate, biological replicate 3


title: neonatal rat skps treated with alprostadil, biological replicate 2


title: K1_rep1

description: raw data: 253432310001-1_1: Cy3

value: 0 mM NaCl, pH 6.0, 27°C, shaken


title: neonatal rat skps treated with alprostadil, biological replicate 1


title: 5_ccpA-M17R_gluc_346946

description:
CcpA-M17R versus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 5

value: wild type


title: neonatal rat skps treated with vehicle, biological replicate 1

description: Gene expression of neonatal rat SKPs treated with vehicle for 24 hours.

source_name: neonatal rat skps treated with vehicle

value: Vehicle


title: AA19m CTCF

status: Public on Dec 23 2015

type: SRA

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
Reads were aligned to hg19 using BWA.
Resulting alignment files were filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq density tracks were generated with ‘igvtools count’.
Genome_build: hg19
Supplementary_files_format_and_content: TDF density files were generate by igvtools

molecule: genomic DNA

source_name: BT19m CTCF

growth_protocol: Neurosphere cultures were maintained in Neurobasal media supplemented with 20 ng/mL recombinant EGF (R and D Systems), 20ng/mL FGF2 (R and D Systems), 1X B27 supplement (Invitrogen), 0.5X N2 supplement (Invitrogen), 3mM L-glutamine,  and penicillin/ streptomycin.

extract_protocol:
Cultured cells or minced tissue was fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of tumor specimens and gliomaspheres was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418).  H3K27ac was immunoprecipitated with an antibody from Active Motif (cat 39133).
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

tag: material type

value: Frozen Anaplastic Astrocytoma Surgical Resection

tag: chip antibody

value: CTCF (D31H2), Cell Signaling #3418

tag: idh1 status

value: Mutant (R132H)


title: AA19m Input

source_name: BT19m Input


title: neonatal rat skps treated with vehicle, biological replicate 2


title: 2_DELTAccpA_gluc_347250

description:
DELTAccpA versus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 2

source_name: DELTAccpA_LB with 1% glucose

value: DELTAccpA


title: AA17m Input

source_name: BT17m Input

value: Anaplastic Astrocytoma Surgical Resection


title: OD18m Input

source_name: BT18m Input

value: Oligodendroglioma Surgical Resection


title: K2_rep2

description: raw data: 253432310001-1_2: Cy3

value: 100 mM NaCl, pH 6.5, 27°C, shaken


title: GBM6w CTCF

source_name: BT6w CTCF

value: GBM Surgical Resection

value: Wild Type


title: GBM7w CTCF

source_name: BT7w CTCF


title: GBM3w Input

source_name: BT3w Input


title: GBM5w Input

source_name: BT5w Input


title: OD18m CTCF

source_name: BT18m CTCF


title: neonatal rat skps treated with vehicle, biological replicate 3

value: Sprague-Dawley


title: 1_DELTAccpA_gluc_346938

description:
DELTAccpA versus CcpA-wt. LB+1%gluc. Exp.phase.
Sample 1

value: LB with 1% glucose

source_name: wild type_LB with 1% glucose


title: GBM5w CTCF

source_name: BT5w CTCF


title: GBM6w Input

source_name: BT6w Input


title: GBM3w CTCF

source_name: BT3w CTCF


title: GBM2w Input

source_name: BT2w Input

value: Frozen GBM Surgical Resection


title: AA15m Input

source_name: MGH15m Input


title: GBM7w Input

source_name: BT7w Input


title: AA15m H3K27ac

source_name: MGH15m H3K27ac

value: H3K27ac (cat 39133), Active Motif


title: GBM1w Input

source_name: BT1w Input

value: Frozen GBM Autopsy Specimen


title: GBM1w CTCF

source_name: MGH1w CTCF


title: AA15m CTCF

source_name: MGH15m CTCF


title: GBM1w H3K27ac

source_name: MGH1w H3K27ac


title: GSC6 CTCF

source_name: GSC6 CTCF

tag: cell line


title: AA16m CTCF

source_name: MGH16m CTCF


title: BT142 Input

source_name: BT142 Input


title: GSC4 H3K27ac

source_name: GSC4 H3K27ac


title: Healthy donor HD3_RT-PCR

city: Ghent

first: Hetty

middle: Hilde

last: Helsmoortel

address: De Pintelaan 185

department: Department of Pediatric Hematology-Oncology and Stem Cell Transplantation

country: Belgium

institute: Ghent University

data_processing: Cq-values were determined based on a threshold of 0.1 and filtered using a detection cut-off of 32 cycles (ViiATM 7 Real-Time PCR System, Life technologies). In order to assess data quality, two quality control parameters were calculated: the number of detected miRNAs per sample and the mean miRNA expression per sample. Expression data were subsequently normalized by Biogazelle using the modified global mean according to D’haene et al.23

label: TaqMan probes

source_name: Bone marrow

label_protocol: miRNA expression profiles were generated by Biogazelle on a qPCR-based platform (Zwijnaarde, Belgium). RNA was reverse transcribed using the stem-loop RT Megaplex pools A and B (Life Technologies). MiRNA cDNA was then pre-amplified and quantified using miRNA specific Taqman probes.

extract_protocol: Mononuclear cells and RNA were isolated with slightly different methods in distinct labs. Overall, RNA was extracted from stored, frozen cells using Trizol. A detailed overview of the method per sample can be found in Supplementary Table 1 of the article.

tag: group

value: LIN28B low


title: BT142 CTCF

source_name: BT142 CTCF


title: Healthy donor HD11_RT-PCR


title: GSC4 CTCF

source_name: GSC4 CTCF


title: AA16m Input

source_name: MGH16m Input


title: GBM2w CTCF

source_name: MGH2w CTCF


title: Healthy donor HD2_RT-PCR


title: GSC6 Input

source_name: GSC6 Input


title: Patient F33_RT-PCR

value: LIN28B high


title: Patient F25_RT-PCR


title: Healthy donor HD1_RT-PCR


title: Patient F27_RT-PCR

source_name: Peripheral blood


title: Patient F13_RT-PCR


title: Patient F14_RT-PCR


title: Patient F10_RT-PCR


title: Patient F16_RT-PCR


title: Patient F15_RT-PCR


title: GBM2w H3K27ac

source_name: MGH2w H3K27ac


title: Patient F9_RT-PCR


title: Patient F11_RT-PCR


title: Patient F17_RT-PCR


title: Patient F5_RT-PCR


title: Patient F12_RT-PCR


title: Patient F34_RT-PCR


title: Patient B011_RT-PCR


title: Patient F4_RT-PCR


title: Patient B034_RT-PCR


title: Patient CZ067_RT-PCR


title: Patient B014_RT-PCR


title: Patient F3_RT-PCR


title: Patient F1_RT-PCR


title: Tonsil Tissue SCC (HN43-05T-2)

type: mixed

city: Sydney

first: Nham

last: Tran

state: NSW

address: Jones

department: CHT/FEIT

country: Australia

institute: UTS

description:
Sample name: HN43-05T-2
microRNAs

hyb_protocol: Pre-hybridization of array slide was performed in 3x SSC, 0.1% SDS, 0.2% BSA at 60oC for 1 h. Each slide was then rinsed with in full DEPC-treated water, followed by 100% ethanol. Hybridization was then performed in disposable reaction chambers (ABGene, USA). The combined hybridization mixture of 330 µl was injected into the chamber, and then incubated in a hybridization oven with constant rotation at 5 rpm for 3 h at 52°C. Slides were then washed briefly in 4x SSC, twice in 2x SSC plus 0.1% SDS, twice in 0.2% SSC and twice in 0.1% SSC.

scan_protocol: GenePix 4000B Scanner (Axon Instruments, USA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed green signal/processed red signal. MEV software.

label: 3'-end P-CU-C3-Cy3 RNA linker

source_name: Tonsil tissue, SCC

label_protocol: MicroRNAs were labeled at 3'-end with a P-CU-C3-Cy3 RNA linker by RNA ligation. A reference mixture of 371 synthetic DNA reference oligonucleotides (IDT) containing complementary sequences to all LNA probes was randomly labeled using the ULYSIS labeling kit.

extract_protocol: Approximately 100 mg of fresh frozen tissue was diced, homogenized and then rinsed with 1 ml of Trizol reagent.

tag: tissue

value: tonsil SCC

tag: patient identifier

label: Ulysis™ Alexa Fluor® 647

molecule: other

organism: synthetic construct

source_name: Synthetic oligo library

extract_protocol: Synthetic oligonucleotides made by IDT.

tag: sample type

value: reference


title: Tonsil Tissue Normal (HN37-02Nr-2)

description:
Sample name: HN37-02Nr-2
microRNAs

source_name: Tonsil tissue, normal

value: normal tonsil


title: Tonsil Tissue Normal (HN43-05N-2)

description:
Sample name: HN43-05N-2
microRNAs


title: Tonsil Tissue SCC (HN33-03T-2)

description:
Sample name: HN33-03T-2
microRNAs


title: Tonsil Tissue SCC (HN39-05T-1)

description:
Sample name: HN39-05T-1
microRNAs


title: Tonsil Tissue Normal (HN43-05N-1)

description:
Sample name: HN43-05N-1
microRNAs


title: Tonsil Tissue Normal (HN39-05N-1)

description:
Sample name: HN39-05N-1
microRNAs


title: Tonsil Tissue Normal (HN32-05N-2)

description:
Sample name: HN32-05N-2
microRNAs


title: Tonsil Tissue Normal (HN39-05N-2)

description:
Sample name: HN39-05N-2
microRNAs


title: Tonsil Tissue SCC (HN37-02T-1)

description:
Sample name: HN37-02T-1
microRNAs


title: Tonsil Tissue Normal (HN37-02Nr-1)

description:
Sample name: HN37-02Nr-1
microRNAs


title: Tonsil Tissue Normal (HN32-05N-1)

description:
Sample name: HN32-05N-1
microRNAs


title: Tonsil Tissue SCC (HN31-05T-2)

description:
Sample name: HN31-05T-2
microRNAs


title: Tonsil Tissue SCC (HN39-05T-2)

description:
Sample name: HN39-05T-2
microRNAs


title: Tonsil Tissue SCC (HN32-05T-2)

description:
Sample name: HN32-05T-2
microRNAs


title: Tonsil Tissue SCC (HN33-03T-1)

description:
Sample name: HN33-03T-1
microRNAs


title: Tonsil Tissue SCC (HN43-05T-1)

description:
Sample name: HN43-05T-1
microRNAs


title: Tonsil Tissue Normal (HN33-03Nr-1)

description:
Sample name: HN33-03Nr-1
microRNAs


title: Tonsil Tissue Normal (HN33-03Nr-2)

description:
Sample name: HN33-03Nr-2
microRNAs


title: Tonsil Tissue SCC (HN37-02T-2)

description:
Sample name: HN37-02T-2
microRNAs


title: Tonsil Tissue Normal (HN31-05N-2)

description:
Sample name: HN31-05N-2
microRNAs


title: Tonsil Tissue SCC (HN31-05T-1)

description:
Sample name: HN31-05T-1
microRNAs


title: Tonsil Tissue SCC (HN29-02T-2)

description:
Sample name: HN29-02T-2
microRNAs


title: Tonsil Tissue SCC (HN32-05T-1)

description:
Sample name: HN32-05T-1
microRNAs


title: Tonsil Tissue SCC (HN29-02T-1)

description:
Sample name: HN29-02T-1
microRNAs


title: Tonsil Tissue Normal (HN31-05N-1)

description:
Sample name: HN31-05N-1
microRNAs


title: Tonsil Tissue SCC (HN27-02T-2)

description:
Sample name: HN27-02T-2
microRNAs


title: Tonsil Tissue Normal (HN27-02N-1)

description:
Sample name: HN27-02N-1
microRNAs


title: Tonsil Tissue SCC (HN27-02T-1)

description:
Sample name: HN27-02T-1
microRNAs


title: Tonsil Tissue SCC (HN25-02T-2)

description:
Sample name: HN25-02T-2
microRNAs


title: Tonsil Tissue Normal (HN27-02N-2)

description:
Sample name: HN27-02N-2
microRNAs


title: Tonsil Tissue SCC (HN23-02T-1)

description:
Sample name: HN23-02T-1
microRNAs


title: Tonsil Tissue SCC (HN03-05T-1)

description:
Sample name: HN03-05T-1
microRNAs


title: Tonsil Tissue SCC (HN22-04T-1)

description:
Sample name: HN22-04T-1
microRNAs


title: Tonsil Tissue SCC (HN23-03T-1)

description:
Sample name: HN23-03T-1
microRNAs


title: Tonsil Tissue SCC (HN23-02T-2)

description:
Sample name: HN23-02T-2
microRNAs


title: Tonsil Tissue SCC (HN23-03T-2)

description:
Sample name: HN23-03T-2
microRNAs


title: Tonsil Tissue SCC (HN06-03T-2)

description:
Sample name: HN06-03T-2
microRNAs


title: Tonsil Tissue SCC (HN06-03T-1)

description:
Sample name: HN06-03T-1
microRNAs


title: Tonsil Tissue Normal (HN22-02N-2)

description:
Sample name: HN22-02N-2
microRNAs


title: Tonsil Tissue Normal (HN06-03Nr-2)

description:
Sample name: HN06-03Nr-2
microRNAs


title: Tonsil Tissue SCC (HN03-05T-2)

description:
Sample name: HN03-05T-2
microRNAs


title: Tonsil Tissue SCC (HN22-04T-2)

description:
Sample name: HN22-04T-2
microRNAs


title: Tonsil Tissue Normal (HN06-03Nr-1)

description:
Sample name: HN06-03Nr-1
microRNAs


title: Tonsil Tissue SCC (HN25-02T-1)

description:
Sample name: HN25-02T-1
microRNAs


title: Tonsil Tissue Normal (HN22-02N-1)

description:
Sample name: HN22-02N-1
microRNAs


title: Healthy donor HD10

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed with the VSN-package (Limma).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.


title: Healthy donor HD1


title: Healthy donor HD4


title: Healthy donor HD3


title: Healthy donor HD9


title: Patient NL072


title: Healthy donor HD2


title: Healthy donor HD11


title: AA17m CTCF

source_name: BT17m CTCF

value: CTCF (D31H2), Cell Signaling #3418

value: Mutant (R132H)


title: Patient NL043


title: Patient NL079


title: Patient NL105


title: Patient NL109


title: Patient F34


title: Patient NL118


title: Patient F11


title: Patient F16


title: Patient F25


title: Patient F17


title: Patient NL162


title: Patient F35


title: Patient F27


title: Patient F12


title: Patient F15


title: 3_DELTAccpA_gluc_347245

description:
CcpA-wt versus DELTAccpA. LB+1%gluc. Exp.phase.
Sample 3

source_name: wild type_LB with 1% glucose

value: wild type

source_name: DELTAccpA_LB with 1% glucose

value: DELTAccpA


title: Patient F26


title: Patient NL094


title: Patient F10


title: GSC119 H3K27ac

source_name: GSC119 H3K27ac


title: Patient F13


title: Patient F9


title: Patient F14


title: Patient F3


title: Patient D127


title: Patient D003


title: Patient D311


title: Patient F1


title: Patient D397


title: PAO1 ∆sbrR pSbrR, biological rep 2

city: Boston

first: Bryan

last: McGuffie

state: MA

address: 300 Longwood Ave

department: Infectious Diseases

country: USA

institute: Boston Children's Hospital

description: Gene expression data from cells grown to mid-log

hyb_protocol: Microarrays were hybridized, washed, and stained according to the manufacturer's recommendations.

scan_protocol: Microarrays were scanned with an Affymetrix Genechip Scanner 3000 7G according to the manufacturer's recommendations.

data_processing: The data were analyzed with the Genespring software suite. Robust multi-array averaging (RMA) was used for normalization. Cutoffs for significant differential expression levels were p ≤ 0.05 and ≥2-fold change in expression level.

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 ∆sbrR pSbrR

label_protocol: Biotinylated cDNA was produced as described previously (Wolfgang et al., Dev Cell 2003) and end labeled with ddUTP-biotin according to the Affymetrix Expression Analysis Protocol.

growth_protocol: Grown to mid-log in 200 ml of lysogeny broth supplemented with 30 ug/ml gentamicin at 37ºC

extract_protocol: The Qiagen RNeasy kit was used for the extraction of total RNA according to the manufacturer's recommendations.

value: deltasbrR

tag: plasmid

value: pSbrR


title: Patient F4


title: Patient F5


title: Patient D123


title: Patient D360


title: Patient B014


title: Patient B009


title: Patient D102


title: Patient D368


title: Patient B041


title: Patient F33


title: Patient B034


title: Patient CZ022


title: Patient B011


title: PAO1 ∆sbrIR pPSV38, biological rep 2

source_name: PAO1 ∆sbrIR pPSV38

value: deltasbrIR


title: Patient CZ067

source_name: Bone marrow


title: PAO1 ∆sbrR pSbrR, biological rep 1


title: PAO1 ∆sbrR pPSV38, biological rep 2

source_name: PAO1 ∆sbrR pPSV38


title: Patient B013


title: Patient CZ076


title: PAO1 pPSV38, biological rep 1

source_name: PAO1 pPSV38

value: WT


title: PAO1 pPSV38, biological rep 2


title: PAO1 ∆sbrR pPSV38, biological rep 1


title: normal tissue patient p46

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol for Illumina BeadArray reader

data_processing: Raw data were obtained from scanned images using Illumina BeadStudio v3.3.8 and pre-processed in R using the Bioconductor package lumi. Raw expression data were log2-transformed and normalized using the robust spline normalization method. After quality control a batch effect was observed and removed using the ComBat method implemented in the Bioconductor package sva.

source_name: non_neoplastic prostate tissue

label_protocol: Biotinylated cRNA were prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

extract_protocol: Total RNA with miRNA fraction was extracted from cell lines with miRNeasy mini kit (Qiagen) according to manufacturer’s instructions.

tag: tissue type

value: normal

tag: patient

tag: batch


title: normal tissue patient p47


title: S4-H278

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing: The data were analyzed with  Affy package in R, RMA method

source_name: Human breast cancer

label_protocol: 3' IVT express

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

treatment_protocol: breast tumor samples, flash frozen

value: Breast cancer

tag: triple-negative status

value: not TN

tag: age (years)

tag: gender

value: Female

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

value: Menopausal

tag: histology

value: Infiltrating ductal carcinoma of the breast

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation not TN

tag: er

value: Positive

tag: pr

value: Negative

tag: tumor grade

value: Moderately Differentiated


title: S4-H274

tag: tissue


title: S4-H266

value: Pre-menopausal

value: Poorly Differentiated


title: S4-H272


title: S4-H269


title: S4-H265

value: Post-menopausal


title: S4-H276


title: S4-H280


title: S4-H267

value: Post-Menopausal


title: S4-H270

value: Unknown

value: Well Differentiated


title: S4-H279


title: S4-H263

value: Infiltrating papillary carcinoma of the bre


title: S4-H273

value: Breast cancer


title: S4-H275

value: not TN


title: S4-H264

value: Female


title: S4-H271

value: Caucasian


title: S4-H268

value: Medullary carcinoma of the breast


title: S4-H262

value: Infiltrating ductal carcinoma of the breast


title: S4-H261

value: Validation not TN


title: normal tissue patient p43

value: normal


title: PAO1 ∆sbrIR pPSV38, biological rep 1

tag: genotype/variation

value: deltasbrIR

tag: plasmid


title: normal tissue patient p42

tag: tissue type

tag: patient


title: normal tissue patient p45

tag: batch


title: tumor tissue patient p46

source_name: prostate cancer tissue

value: tumor


title: tumor tissue patient p47


title: tumor tissue patient p19


title: normal tissue patient p39


title: tumor tissue patient p42


title: S4-H258

tag: triple-negative status

tag: age (years)

value: Pre-menopausal

value: Positive

value: Negative


title: S4-H256

tag: gender

tag: race


title: S4-H255

tag: body mass index


title: S4-H259

tag: menopausal status

value: Post-menopausal

tag: histology

value: Poorly Differentiated


title: normal tissue patient p34


title: S4-H252

tag: ajcc stage (7th edition, 2010)

tag: set


title: normal tissue patient p33


title: tumor tissue patient p39


title: tumor tissue patient p32


title: S4-H257

tag: er

tag: pr

value: Moderately Differentiated


title: tumor tissue patient p43


title: tumor tissue patient p11


title: normal tissue patient p31


title: normal tissue patient p30


title: normal tissue patient p29


title: S4-H245

tag: tissue

tag: tumor grade


title: normal tissue patient p35


title: S4-H249


title: tumor tissue patient p36


title: S4-H254


title: tumor tissue patient p35


title: S4-H248


title: S4-H253


title: tumor tissue patient p34


title: tumor tissue patient p28


title: tumor tissue patient p29


title: S4-H244


title: normal tissue patient p27


title: normal tissue patient p26


title: S4-H246


title: S4-H237


title: S4-H247


title: S4-H251


title: S4-H250


title: S4-H238


title: S4-H243


title: S4-H242


title: normal tissue patient p28


title: S4-H239


title: tumor tissue patient p33


title: tumor tissue patient p25


title: S4-H241


title: S4-H240


title: normal tissue patient p25


title: tumor tissue patient p26


title: S1-H5


title: normal tissue patient p24


title: normal tissue patient p23


title: normal tissue patient p22


title: S3-H223


title: S4-H235


title: S4-H236


title: tumor tissue patient p17


title: normal tissue patient p21


title: tumor tissue patient p22


title: S4-H231

value: Lobular carcinoma of breast


title: S1-H37

value: Breast cancer

value: Ductal carcinoma in situ of breast


title: S3-H195

value: not TN

value: Female


title: S1-H32

value: Caucasian


title: S4-H232

value: Infiltrating ductal carcinoma of the breast


title: S1-H42

value: Validation not TN


title: S4-H234

value: Infiltrating lobular carcinoma of the breas


title: S4-H233

value: Lobular carcinoma of the breast


title: normal tissue patient p14

value: normal


title: tumor tissue patient p21

value: tumor


title: S1-H39

value: Positive


title: S1-H25

value: Menopausal

value: Negative


title: S1-H1B

value: Post-menopausal

value: Poorly Differentiated


title: normal tissue patient p17


title: S1-H18

value: Pre-menopausal

value: Moderately Differentiated


title: normal tissue patient p12


title: normal tissue patient p15


title: S1-H16

value: Breast cancer


title: S1-H30

value: not TN


title: tumor tissue patient p20


title: 17211-BL6-normal

city: Philadelphia

first: Michael

middle: K.

last: Parente

state: PA

address: 3615 Civic Center Blvd.

department: Neurology

institute: Children's Hospital of Philadelphia

description:
File descriptor - Animal number-genotype.cel
17211-N

hyb_protocol: Hybridization to GPL8321  [Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array, staining and washing were performed on an Affymetrix Fluidics Station 400 according to Affymetrix protocols.

scan_protocol: Affymetrix Gene Chip Scanner 3000 controlled by a GeneChip Operating software 1.4

data_processing: Raw microarray image files were processed using  Affymetrix GCOS 1.4 software to calculate individual probe cell intensity data and generate CEL data files. CEL files were normalized by RMA. Significance and false discovery evaluated by Significant Analysis of Microarray (SAM).

label: biotin-aRNA

source_name: hippocampus from normal bl6 mouse

label_protocol: 1 µg RNA from each brain region was used to prepare biotinylated aRNA using MessageAMP II-biotin Enhanced Signal Round aRNA Amplification Kit

growth_protocol: Animals maintained in breeding colony through carrier-carrier brother-sister mating. Normals and mutants housed together

extract_protocol: Total RNA was isolated separately from the hippocampus of the right hemisphere which were placed into TRIzol (Invitrogen)  purified using the RNeasy Lipid Tissue mini kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Diseased and normal mice were housed together until brain harvest

tag: strain background

tag: genoytype/variation

value: normal; B6.C-H2-Kbm1/ByBir-Gusb mps/+/J

tag: Sex

value: male

tag: age

value: hippocampus


title: tumor tissue patient p14

tag: tissue type

tag: patient

tag: batch


title: tumor tissue patient p13


title: S1-H23

tag: triple-negative status

tag: age (years)

tag: gender

value: Female

tag: race

value: Caucasian

value: Infiltrating ductal carcinoma of the breast

value: Validation not TN


title: tumor tissue patient p15

value: tumor


title: 17039-BL6-mutant

description:
File descriptor - Animal number-genotype.cel
17039-M

source_name: hippocampus from mutant bl6 mouse

value: mutant; B6.C-H2-Kbm1/ByBir-Gusb mps/mps /J

value: female


title: 17216-BL6-mutant

description:
File descriptor - Animal number-genotype.cel
17216-M


title: normal tissue patient p13

value: normal


title: S1-H21

tag: body mass index

tag: menopausal status

value: Post-menopausal

tag: histology

tag: ajcc stage (7th edition, 2010)

value: Negative

value: Positive


title: 17209-BL6-mutant

description:
File descriptor - Animal number-genotype.cel
17209-M

tag: tissue


title: 17214-BL6-normal

description:
File descriptor - Animal number-genotype.cel
17214-N


title: tumor tissue patient p12


title: S1-H17

value: Pre-menopausal

tag: set

tag: er

tag: pr

tag: tumor grade

value: Moderately Differentiated


title: AIM-KO (HFD 20 W), biological rep1

city: Kisarazu

first: Osamu

last: Ohara

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Technology Development

country: Japan

institute: Kazusa DNA Research Institute

description: AIM-KO_HFD 20w

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction Software v9.5 using default parameters (protocol GE1-v5_95_Feb07). The dataset was normalized using the 75 percentile median shift method.

source_name: AIM-KO_HFD 20 W

label_protocol: 500 ng of total RNA was amplified and labeled using the One-Color Agilent Quick Amp Labeling kit

extract_protocol: Total RNA was isolated with Trizol reagent.

tag: strain background

tag: genotype/variation

value: AIM KO; AIM-/-

tag: diet

value: high-fat diet (HFD) for 20 wks

value: liver


title: tumor tissue patient p9

tag: tissue type

tag: patient

tag: batch


title: normal tissue patient p10


title: tumor tissue patient p8


title: 17097-BL6-normal

description:
File descriptor - Animal number-genotype.cel
17097-N

tag: genoytype/variation

value: normal; B6.C-H2-Kbm1/ByBir-Gusb mps/+/J

tag: Sex

value: male

tag: age

value: hippocampus


title: 17098-BL6-mutant

description:
File descriptor - Animal number-genotype.cel
17098-M


title: S1-H15

value: Breast cancer

tag: triple-negative status

value: not TN

tag: age (years)

tag: gender

value: Female

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

value: Menopausal

value: Infiltrating ductal carcinoma of the breast

value: Poorly Differentiated


title: tumor tissue patient p10

value: tumor


title: tumor tissue patient p7


title: normal tissue patient p6

value: normal


title: 17040-BL6-normal

description:
File descriptor - Animal number-genotype.cel
17040-N

value: female

tag: tissue


title: S1-H13

value: Post-menopausal

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation not TN

tag: er

value: Negative

tag: pr

value: Positive

tag: tumor grade


title: normal tissue patient p7

tag: tissue type

tag: patient

tag: batch


title: S1-H12

value: Moderately Differentiated


title: S1-H11


title: Healthy donor HD_I7

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

description: Gene expression data from healthy bone marrow sample

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA and removal batch effect were applied using ComBat in the sva package

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

growth_protocol: No growth protocol

extract_protocol: Mononuclear cells and RNA were isolated with slightly different methods in distinct labs. Overall, RNA was extracted from stored, frozen cells using Trizol.

treatment_protocol: No treatment protocol

tag: diagnosis

value: healthy

value: low


title: WT (HFD 12 W), biological rep1

description: WT_HFD 12w

source_name: WT_HFD 12 W

tag: strain background

tag: genotype/variation

value: wild type; AIM+/+

tag: diet

value: high-fat diet (HFD) for 12 wks

value: liver


title: Healthy donor HD_I9


title: WT (HFD 6 W), biological rep1

description: WT_HFD 6w

source_name: WT_HFD 6 W

value: high-fat diet (HFD) for 6 wks


title: AIM-KO (HFD 12 W), biological rep1

description: AIM-KO_HFD 12w

source_name: AIM-KO_HFD 12 W

value: AIM KO; AIM-/-


title: tumor tissue patient p6


title: WT (HFD 20 W), biological rep1

description: WT_HFD 20w

source_name: WT_HFD 20 W

value: high-fat diet (HFD) for 20 wks


title: Healthy donor HD_I8


title: normal tissue patient p5


title: AIM-KO (HFD 6 W), biological rep1

description: AIM-KO_HFD 6w

source_name: AIM-KO_HFD 6 W


title: tumor tissue patient p5


title: WT (normal chow), biological rep1

description: WT_HFD 0w

source_name: WT_normal chow

value: normal chow


title: AIM-KO (normal chow), biological rep1

description: AIM-KO_HFD 0w

source_name: AIM-KO_normal chow


title: Healthy donor HD_I6


title: Healthy donor HD_I5


title: Healthy donor HD_I3


title: Healthy donor HD_I4


title: transgenic Replicate 4

city: bethesda

first: yan

last: cai

state: maryland

address: 9000 rockville pike

department: NCI

institute: NIH

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

scan_protocol: Scanned on an Agilent G26000 scanner. Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and LOWESS normalization.

source_name: over-expressing secretoglobin 3A2

label_protocol: MonoReactive Dye Pack

extract_protocol: Total RNAs were extracted using miRNeasy Mini Kit following the manufacturer's instruction, and antisense RNAs were amplified with Amino Allyl MessageAmp™ II aRNA Kit and labelled with MonoReactive Dye Pack

treatment_protocol: 8-10 weeks old male mice were used in this study with no-treatment.

tag: strain

value: whole lung

source_name: pooled whole mouse lung


title: transgenic Replicate 1


title: tumor tissue patient p2

value: tumor


title: Healthy donor HD_I1

source_name: Bone marrow


title: Healthy donor HD_I2


title: transgenic Replicate 3


title: normal tissue patient p2

value: normal


title: normal tissue patient p3


title: tumor tissue patient p3


title: wild type NSC cells rep2

city: London

first: Axel

last: Behrens

state: London

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick institute

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Protocol (Illumina) as per manufacturers instructions

scan_protocol: Scanning using the Illumina iScan with default settings

data_processing: Bioconductor lumi package V 2.20.2, with lumiT (vst) and lumi.N for transformation and normalization with default settings.  Data filtered so that at least one sample detected at p<0.05

label: bitoin

source_name: wild type NSC cells

label_protocol: Illumina® TotalPrep™-96 RNA Amplification Protocol (Ambion) as per manufacturers instructions

growth_protocol: Adherent NSC cultures were cultures in Neurobasal Medium (Invitrogen) supplemented with 1% Penicillin/Streptomycin (Invitrogen), 1% L-glutamine (Invitrogen), 2% B27 supplement (Invitrogen), 1% N-2  supplement (Invitrogen), 20 ng/ml EGF (PeproTech), 20 ng/ml FGF-basic (PeproTech) and 1 μg/ml laminin (Sigma). All experiments were performed using undifferentiated adherent neural stem cells. Adherent NSC cultures were cultures in Neurobasal Medium (Invitrogen) supplemented with 1% Penicillin/Streptomycin (Invitrogen), 1% L-glutamine (Invitrogen), 2% B27 supplement (Invitrogen), 1% N-2 supplement (Invitrogen), 20 ng/ml EGF (PeproTech), 20 ng/ml FGF-basic  (PeproTech) and 1 μg/ml laminin (Sigma).

extract_protocol: Qiagen RNeasy Mini Kit as per manufacturers instructions

tag: cell type

value: primary neural stem cells

value: wild type


title: transgenic Replicate 2


title: Patient D155

description: Gene expression data from juvenile myelomonocytic leukemia samples at diagnosis

source_name: Peripheral blood

value: Juvenile myelomonocytic leukemia (JMML)


title: Patient SC077

value: high


title: Patient D117


title: GSC119 CTCF

source_name: GSC119 CTCF

tag: cell line

tag: chip antibody

value: CTCF (D31H2), Cell Signaling #3418

tag: idh1 status

value: Mutant (R132H)


title: wildtype Replicate 4

source_name: wildtype

tag: tissue


title: wildtype Replicate 3


title: Patient I233

value: low


title: p53 mutant NSC cells rep2

source_name: p53 mutant NSC cells

value: p53 mutant


title: wildtype Replicate 2


title: Patient D098


title: ATMIN/p53 double mutant NSC cells rep1

source_name: ATMIN/p53 double mutant NSC cells

value: ATMIN/p53 double mutant


title: Patient D097


title: Patient I232


title: ATMIN/p53 double mutant NSC cells rep2


title: wildtype Replicate 1


title: Patient I226


title: Patient I217


title: Patient I214


title: wild type NSC cells rep1


title: Patient I213


title: normal tissue patient p20

source_name: non_neoplastic prostate tissue


title: p53 mutant NSC cells rep1


title: Patient I203


title: ATMIN mutant NSC cells rep1

source_name: ATMIN mutant NSC cells

value: ATMIN mutant


title: Patient I228


title: Patient I211


title: rRBr root tip 10d, biological rep3

city: Wageningen

first: Gabino

last: Sanchez-Perez

address: Droevendaalsesteeg 1

department: Bioscience

institute: Wageningen University

description: Gene expression data from rRBr-0 root tips from 10 das.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: GeneChip intensities were background-corrected, normalized and summarized by RMA method (Irizarry et al., 2003), using the Affy package from Bioconductor.

organism: Arabidopsis thaliana

source_name: rRBr tip roots from 10 das

label_protocol: One Cycle Affymetrix Labeling kit

growth_protocol: Seeds were sterilized in a sealed container with 100 ml bleach supplemented by 3 ml of 37% hydrochloric acid for 2 to 5 h, and then suspended in 0.1% agarose and plated on a growth medium consisting of Murashige and Skoog salts, 1% Suc, 1.2% plant agar, MES, pH 5.8 and 50 μg/ml ampicilin, stratified for 2 d in a 4°C, and grown vertically in long-day conditions (16 h light followed by 8 h of dark).

extract_protocol: Qiagen Rneasy plant minikit

treatment_protocol: Germination of seeds, Col0 and rRBr, for the different time points started at the same time under the same conditions and were repeated three times. The phenotypic changes were followed in each experiment via Lugol staining. As the changes occur mainly in the stem cell niche we have dissected the root tips carefully under the microscope and collected material between 20-40mg.

tag: genetic background

tag: genotype

value: rRBr

tag: developmental stage

value: 10 days after stratification

value: Root tips


title: ATMIN mutant NSC cells rep2


title: NZW.SP.Treg#1

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: RNA was prepared from cells sorted into Trizol

tag: age

value: 9 Weeks Old

tag: exclusion markers

value: CD19, CD8α, TCRγδ, CD11b, CD11c, NK1.1, Gr-1, Ter-119, DAPI

value: NZW/LacJ

tag: phenotype markers

value: TCRb+ CD4+ CD25hi

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Male

tag: source prep description

value: Mechanical cell dissociation


title: Patient I193

tag: diagnosis

value: Juvenile myelomonocytic leukemia (JMML)

value: high


title: rRBr root tip 6d, biological rep2

description: Gene expression data from rRBr-0 root tips from 6 das.

source_name: rRBr tip roots from 6 das

value: 6 days after stratification


title: rRBr root tip 4d, biological rep1

description: Gene expression data from rRBr-0 root tips from 4 das.

source_name: rRBr tip roots from 4 das

value: 4 days after stratification


title: Patient I187


title: Patient I186

value: low


title: rRBr root tip 10d, biological rep2


title: rRBr root tip 10d, biological rep1


title: NZW.BM.Treg#2

value: 8 Weeks Old


title: NOD.Treg.SP#2

value: NOD/LtJ


title: rRBr root tip 4d, biological rep2

value: rRBr


title: NZW.Treg.SP#2


title: NZW.BM.Treg#1


title: rRBr root tip 6d, biological rep1


title: Col root tip 10d, biological rep3

description: Gene expression data from Col-0 root tips from 10 das.

source_name: Col-0 tip roots from 10 das

value: wild type

value: 10 days after stratification


title: NZW.Treg.SP#1

value: 9 Weeks Old


title: Patient I149


title: CBA.Treg.SP#1

value: CD19, CD8α, TCRγδ, CD11b, CD11c, NK1.1, Gr-1, Ter-119, DAPI

value: CBA/J


title: Patient I110


title: Col root tip 10d, biological rep1

value: Root tips


title: Col root tip 10d, biological rep2


title: Balb.Treg.SP#2

value: Balb/c

value: TCRb+ CD4+ CD25hi

value: MoFlo Sorter


title: Patient I143

value: Juvenile myelomonocytic leukemia (JMML)


title: Patient I133


title: Patient I107


title: Patient I061


title: Col root tip 6d, biological rep1

description: Gene expression data from Col-0 root tips from 6 das.

source_name: Col-0 tip roots from 6 das


title: Patient I055


title: NZW.SP.Treg#2

value: NZW/LacJ

value: Male

value: Mechanical cell dissociation


title: B6.BM.Treg#1

extract_protocol: TriZol

value: TCRb+ CD4+ GFP+


title: Balb.Treg.SP#1


title: B6.SP.Treg#2


title: B6.SP.Treg#1


title: Patient I303

value: low


title: Patient I255


title: Col root tip 4d, biological rep2

description: Gene expression data from Col-0 root tips from 4 das.

source_name: Col-0 tip roots from 4 das

value: 4 days after stratification


title: Patient I046

value: high


title: Patient I304


title: NOD.Treg.SP#1

value: NOD/LtJ


title: Patient I283


title: B6.BM.Treg#2


title: Patient I244


title: Patient I241


title: HeLa_PNA

city: Bangkok

first: jirattha

last: siriluksana

address: Rama 4

country: Thailand

institute: Chulalongkorn university

description:
replicate 1
replicate 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: HeLa cells treated with PNAs-A15

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: HeLa and C33A cells were maintained in DMEM medium (Gibco,USA) supplemented with 10% fetal bovine serum (Gibco,USA) and cultured in a humidified incubator at 37 °C under 5% CO2.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen, USA), followed by clean-up and DNase I treatment with QIAGEN RNeasy (Qiagen, Valencia, USA) according to the manufacturers’ protocol.Quality control was performed with Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Cells were treated with PNAs-A15 in 6-well microplates for 6h.

value: HeLa

value: cervical cancer


title: B6.BM.Treg#3

source_name: Bone marrow

value: 9 Weeks Old

value: CD19, CD8α, TCRγδ, CD11b, CD11c, NK1.1, Gr-1, Ter-119, DAPI


title: Patient I247


title: C33A_PNA

description:
replicate 1
replicate 2

source_name: C33A cells treated with PNAs-A15


title: Patient I173


title: Patient I248


title: B6.Treg.SP#2


title: Patient I334


title: Patient I160


title: Col root tip 4d, biological rep1

value: wild type

value: Root tips


title: Patient I242


title: C33A SC

description:
replicate 1
replicate 2

source_name: C33A cells treated with Scramble


title: HeLa_SC

description:
replicate 1
replicate 2

source_name: HeLa cells treated with Scramble


title: B6.Treg.SP#1

value: TCRb+ CD4+ CD25hi


title: wild-type mouse intestine, segment 4, biological rep3

status: Public on Dec 22 2015

city: University of Oulu

first: Kaija

middle: J

last: Autio

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

description: wild-type 3, segment 4

hyb_protocol: Hydridizations and washing of the chips were carried out at the Microarray Facility in Leuven (MAF, Leuven, Belgium).

scan_protocol: Scanning of the chips was carried out at the Microarray Facility in Leuven (MAF, Leuven, Belgium).

data_processing: The data were collected using the Affymetrix standard protocol and processed and normalized using Chipster Software Suite version 2.0 using Affymetrix default analysis settings and RMA as normalization method. Variances were not stabilized.

source_name: mouse intestine, segment 4, wild-type

label_protocol: Labelling of the samples was carried out at the Microarray Facility in Leuven (MAF, Leuven, Belgium).

extract_protocol: The intestine endothelial layer was collected by scraping and homogenized into TRIzol reagent (Invitrogen). Total RNA was isolated with the MagMAX-96 for Microarrays Total RNA isolation kit (Ambion).

treatment_protocol: The intestine was rinsed with 0.85% NaCl and cut into four equal size segments, and the segments were opened with scissors.

value: wild-type

value: intestine, segment 4

value: endothelial

tag: gender

value: male

value: 3-3.5 months


title: Amacr-/- mouse intestine, segment 4, biological rep3

description: knock-out 3, segment 4

source_name: mouse intestine, segment 4, Amacr-/-

tag: strain

value: Amacr-/-


title: wild-type mouse intestine, segment 4, biological rep1

description: wild-type 1, segment 4

tag: cell type


title: Amacr-/- mouse intestine, segment 4, biological rep2

description: knock-out 2, segment 4


title: Amacr-/- mouse intestine, segment 2, biological rep1

description: knock-out 1, segment 2

source_name: mouse intestine, segment 2, Amacr-/-

value: intestine, segment 2


title: wild-type mouse intestine, segment 3, biological rep1

description: wild-type 1, segment 3

source_name: mouse intestine, segment 3, wild-type

value: intestine, segment 3


title: Amacr-/- mouse intestine, segment 4, biological rep1

description: knock-out 1, segment 4


title: Amacr-/- mouse intestine, segment 3, biological rep1

description: knock-out 1, segment 3

source_name: mouse intestine, segment 3, Amacr-/-


title: Amacr-/- mouse intestine, segment 2, biological rep3

description: knock-out 3, segment 2


title: wild-type mouse intestine, segment 3, biological rep2

description: wild-type 2, segment 3


title: Amacr-/- mouse intestine, segment 3, biological rep3

description: knock-out 3, segment 3


title: Amacr-/- mouse intestine, segment 2, biological rep2

description: knock-out 2, segment 2


title: Amacr-/- mouse intestine, segment 3, biological rep2

description: knock-out 2, segment 3


title: Amacr-/- mouse intestine, segment 1, biological rep3

description: knock-out 3, segment 1

source_name: mouse intestine, segment 1, Amacr-/-

value: intestine, segment 1


title: wild-type mouse intestine, segment 2, biological rep3

description: wild-type 3, segment 2

source_name: mouse intestine, segment 2, wild-type


title: Amacr-/- mouse intestine, segment 1, biological rep2

description: knock-out 2, segment 1


title: Amacr-/- mouse intestine, segment 1, biological rep1

description: knock-out 1, segment 1


title: wild-type mouse intestine, segment 4, biological rep2

description: wild-type 2, segment 4


title: wild-type mouse intestine, segment 3, biological rep3

description: wild-type 3, segment 3


title: wild-type mouse intestine, segment 2, biological rep2

description: wild-type 2, segment 2


title: wild-type mouse intestine, segment 2, biological rep1

description: wild-type 1, segment 2


title: Patient I108

value: Juvenile myelomonocytic leukemia (JMML)

value: low


title: wild-type mouse intestine, segment 1, biological rep3

description: wild-type 3, segment 1

source_name: mouse intestine, segment 1, wild-type


title: Amacr-/- mouse liver, biological rep1

description: knock-out 1

source_name: mouse liver, Amacr-/-

extract_protocol: Total RNA was isolated from liver samples by using TRIzol reagent (Invitrogen, Merelbeke, Belgium) according to manufacturer's instructions.

value: liver


title: Amacr-/- mouse liver, biological rep3

description: knock-out 3


title: wild-type mouse intestine, segment 1, biological rep2

description: wild-type 2, segment 1


title: Amacr-/- mouse liver, biological rep4

description: knock-out 4


title: wild-type mouse intestine, segment 1, biological rep1

description: wild-type 1, segment 1


title: Amacr-/- mouse liver, biological rep2

description: knock-out 2


title: wild-type mouse liver, biological rep3

description: wild-type 3

source_name: mouse liver, wild-type


title: wild-type mouse liver, biological rep4

description: wildtype 4


title: wild-type mouse liver, biological rep2

description: wild-type 2


title: Normal nasal activated_rep2

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

institute: University of Leicester

description:
9423249074_K
Activated

hyb_protocol: Standard Illumina hybridization protocol except hyb performed at 48 degrees C

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization within Genome Studio without background correction. Data was submitted using Illumina's GEO Data Submission Report Plug-in for Gene Expression

source_name: Normal nasal

label_protocol: cDNA synthesis and amplification was performed with the Ovation PicoSL WTA system V2 kit (NuGEN, Leek, Netherlands) as per the manufacturer’s instructions. Purity and yield was then analyzed using the Bioanalyzer platform (Agilent, Stockport, UK) and NanoDrop 2000 spectrophotometer (Thermo Scientific, Loughborough, UK) respectively before amplified cDNA was biotin-labeled with the NuGEN Encore BiotinIL module according to the manufacturer’s instructions

growth_protocol: Nasal mucosal tissue was dissected and resuspended in complete medium. Peripheral blood mononuclear cells were isolated using Lymphoprep.  Samples were cultured at 37°C, 5% CO2 in the presence of rIL-2 (50 U/ml). After 2-3 days, cells were passed through a 0.2 μm cell strainer to obtain single cell suspensions and restimulated by culturing on anti-CD3/28 antibody coated plates. Cells were cultured for a further 7 days with removal from stimulation after 3-4 days.

extract_protocol: RNA was isolated from cell pellets using the miRNeasy mini kit and RNeasy MinElute cleanup kit (Qiagen, Manchester, UK) according to the manufacturer’s instructions.

treatment_protocol: T-helper cells were sorted based upon expression of CD4 using flow cytometric sorting. Cells were then activated with PMA/Ionomycin for 4hrs or left in a resting state.

tag: disease state

value: healthy control

value: nasal mucosa

value: T-helper cells

tag: cell subtype

value: activated


title: Normal nasal resting_rep1

description:
9423249074_G
Resting

value: resting


title: Blood resting_rep2

description:
9423249074_B
Resting

source_name: Blood

value: peripheral blood


title: Blood activated_rep3

description:
9423249074_F
Activated


title: wild-type mouse liver, biological rep1

description: wild-type 1

value: wild-type


title: IL17RB+ Activated_rep2

source_name: IL17RB+ Activated

growth_protocol: Nasal polyp tissue was dissected and resuspended in complete medium. Tissues were cultured at 37°C, 5% CO2 in the presence of rIL-2 (50 U/ml). After 2-3 days, cells were passed through a 0.2 μm cell strainer to obtain single cell suspensions and restimulated by culturing on anti-CD3/28 antibody coated plates. Cells were cultured for a further 7 days with removal from stimulation after 3-4 days.

extract_protocol: RNA was isolated from cell pellets using the miRNeasy mini kit and RNeasy MinElute cleanup kit (Qiagen, Manchester, UK) according to the manufacturer’s instructions

treatment_protocol: T-helper cells were sorted based upon expression of IL17RB using flow cytometric sorting. Cells were then activated with PMA/Ionomycin for 4hrs or left in a resting state.

value: chronic rhinosinusitis

value: Nasal polyp tissue

value: IL17RB+ Activated


title: Normal nasal activated_rep3

description:
9423249074_L
Activated


title: IL17RB- Activated_rep2

source_name: IL17RB- Activated

value: IL17RB- Activated


title: Blood activated_rep2

description:
9423249074_E
Activated


title: Normal nasal resting_rep2

description:
9423249074_H
Resting


title: IL17RB+ Activated_rep1


title: Normal nasal resting_rep3

description:
9423249074_I
Resting


title: Blood resting_rep3

description:
9423249074_C
Resting


title: IL17RB+ Activated_rep3


title: IL17RB- Resting_rep3

source_name: IL17RB- Resting

value: IL17RB- Resting


title: Normal nasal activated_rep1

description:
9423249074_J
Activated


title: Blood resting_rep1

description:
9423249074_A
Resting


title: IL17RB+ Resting_rep3

source_name: IL17RB+ Resting

value: IL17RB+ Resting


title: Blood activated_rep1

description:
9423249074_D
Activated


title: IL17RB+ Resting_rep2


title: IL17RB- Activated_rep3


title: Subject 24238, lung, 122 dpc

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.  Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: All 316 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output in base 2 logarithmic scale.

source_name: whole lung human fetus

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: For each experimental sample, total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) and quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

tag: subject id

tag: age (days post conception)

value: 122 dpc

value: female

value: lung

tag: cotinine (ng/g placenta)

tag: hybridization batch id


title: IL17RB- Resting_rep2

tag: tissue


title: IL17RB+ Resting_rep1


title: IL17RB- Resting_rep1


title: Subject 24206, lung, 63 dpc

value: 63 dpc

value: male


title: Subject 24205, lung, 85 dpc

value: 85 dpc


title: Subject 24201, lung, 113 dpc

value: 113 dpc


title: IL17RB- Activated_rep1

value: T-helper cells


title: Subject 21885, lung, 115 dpc

value: 115 dpc


title: Subject 24199, lung, 94 dpc

value: 94 dpc


title: Subject 21900, lung, 57 dpc

value: 57 dpc


title: Subject 21893, lung, 76 dpc

value: 76 dpc


title: Subject 21892, lung, 101 dpc

value: 101 dpc


title: Subject 21884, lung, 89 dpc

value: 89 dpc


title: Subject 21785, lung, 72 dpc

value: 72 dpc


title: Subject 21880, lung, 57 dpc


title: Subject 21901, lung, 94 dpc


title: Subject 21790, lung, 98 dpc

value: 98 dpc


title: Subject 21745, lung, 82 dpc

value: 82 dpc


title: Subject 21744, lung, 76 dpc


title: Subject 21883, lung, 115 dpc


title: Subject 21798, lung, 87 dpc

value: 87 dpc


title: Subject 21656, lung, 59 dpc

value: 59 dpc


title: Subject 21666, lung, 59 dpc

value: female

value: lung


title: Subject 21649, lung, 63 dpc

value: 63 dpc


title: Subject 21696, lung, 72 dpc


title: Subject 21646, lung, 94 dpc

value: male


title: Subject 21698, lung, 80 dpc

value: 80 dpc


title: Subject 21632, lung, 91 dpc

value: 91 dpc


title: Subject 21633, lung, 91 dpc


title: Subject 21640, lung, 57 dpc


title: Subject 21628, lung, 74 dpc

value: 74 dpc


title: Subject 21572, lung, 101 dpc


title: Subject 21603, lung, 94 dpc

value: 94 dpc


title: Subject 21594, lung, 101 dpc


title: Subject 21602, lung, 105 dpc

value: 105 dpc


title: Subject 21563, lung, 82 dpc


title: Subject 21781, lung, 87 dpc


title: Subject 21605, lung, 103 dpc

value: 103 dpc


title: Subject 21575, lung, 63 dpc


title: Subject 21634, lung, 96 dpc

value: 96 dpc


title: Subject 21544, lung, 96 dpc


title: Subject 21532, lung, 67 dpc

value: 67 dpc


title: Subject 21564, lung, 74 dpc


title: Subject 21589, lung, 74 dpc


title: Subject 21598, lung, 76 dpc

value: 76 dpc


title: Subject 21527, lung, 59 dpc


title: Subject 21648, lung, 59 dpc


title: Subject 21627, lung, 91 dpc


title: Subject 24190, lung, 105 dpc


title: Subject 24186, lung, 137 dpc

value: 137 dpc


title: Subject 24191, lung, 91 dpc


title: Subject 24183, lung, 74 dpc


title: Subject 24174, lung, 120 dpc

value: 120 dpc


title: Subject 21530, lung, 85 dpc

value: 85 dpc


title: Subject 24173, lung, 78 dpc

value: 78 dpc


title: Subject 24181, lung, 74 dpc


title: Subject 24108, lung, 74 dpc

value: female


title: Subject 24103, lung, 103 dpc

value: lung


title: Subject 23987, lung, 91 dpc


title: Subject 24155, lung, 101 dpc

value: 101 dpc


title: Subject 24082, lung, 67 dpc


title: Subject 24172, lung, 74 dpc


title: Subject 24071, lung, 67 dpc

value: male


title: Subject 24153, lung, 87 dpc

value: 87 dpc


title: Subject 24159, lung, 96 dpc


title: Subject 24145, lung, 74 dpc


title: Subject 21653, lung, 91 dpc

value: 91 dpc


title: Subject 24085, lung, 103 dpc


title: Subject 24040, lung, 74 dpc

value: 74 dpc


title: Subject 24132, lung, 108 dpc

value: 108 dpc


title: Subject 24117, lung, 101 dpc


title: Subject 23985, lung, 110 dpc

value: 110 dpc


title: Subject 24093, lung, 78 dpc


title: Subject 24094, lung, 72 dpc

value: 72 dpc


title: Subject 24096, lung, 76 dpc


title: Subject 24070, lung, 59 dpc

value: 59 dpc


title: Subject 21985, lung, 74 dpc


title: Subject 21977, lung, 80 dpc

value: 80 dpc


title: Subject 21971, lung, 96 dpc

value: 96 dpc


title: Subject 21961, lung, 89 dpc

value: 89 dpc


title: Subject 21978, lung, 109 dpc

value: 109 dpc


title: Subject 21941, lung, 76 dpc

value: 76 dpc


title: Subject 21964, lung, 59 dpc


title: Subject 21968, lung, 82 dpc

value: 82 dpc


title: Subject 21939, lung, 96 dpc


title: Subject 21520, lung, 89 dpc

value: female


title: Subject 21938, lung, 78 dpc

value: 78 dpc

value: lung


title: Subject 21349, lung, 101 dpc

value: 101 dpc


title: Subject 21175, lung, 91 dpc

value: male


title: Subject 21926, lung, 94 dpc

value: 94 dpc


title: Subject 21516, lung, 74 dpc

value: 74 dpc


title: Subject 21927, lung, 80 dpc


title: Subject 20902, lung, 89 dpc


title: Subject 21525, lung, 87 dpc

value: 87 dpc


title: Subject 21518, lung, 105 dpc

value: 105 dpc


title: Subject 20900, lung, 108 dpc

value: 108 dpc


title: Subject 21334, lung, 76 dpc


title: Subject 21353, lung, 103 dpc

value: 103 dpc


title: Subject 21092, lung, 74 dpc


title: Subject 20848, lung, 59 dpc

value: 59 dpc


title: Subject 20718, lung, 78 dpc


title: Subject 20885, lung, 91 dpc

value: 91 dpc


title: Subject 21049, lung, 91 dpc


title: Subject 20473, lung, 72 dpc

value: 72 dpc


title: Subject 20469, lung, 76 dpc


title: Subject 20679, lung, 57 dpc

value: 57 dpc


title: Subject 20676, lung, 74 dpc


title: Subject 21432, lung, 113 dpc

value: 113 dpc


title: Subject 20435, lung, 63 dpc

value: 63 dpc


title: Subject 20422, lung, 87 dpc

value: female


title: Subject 20683, lung, 78 dpc

value: 78 dpc


title: Subject 20149 replicate 2, lung, 80 dpc

value: 80 dpc

value: lung


title: Subject 20189, lung, 54 dpc

value: 54 dpc


title: Subject 20302, lung, 89 dpc

value: 89 dpc

value: male


title: Subject 20148, lung, 74 dpc

value: 74 dpc


title: Subject 20043, lung, 67 dpc

value: 67 dpc


title: Subject 20181, lung, 80 dpc


title: Subject 18452, lung, 87 dpc

value: 87 dpc


title: Subject 19023, lung, 89 dpc


title: Subject 18056, lung, 83 dpc

value: 83 dpc


title: Subject 18354, lung, 96 dpc

value: 96 dpc


title: Subject 24119, lung, 84 dpc

value: 84 dpc


title: Subject 21173, lung, 91 dpc

value: 91 dpc


title: Subject 21335, lung, 87 dpc


title: Subject 21802, lung, 74 dpc


title: Subject 20156, lung, 127 dpc

value: 127 dpc


title: Subject 21923, lung, 101 dpc

value: 101 dpc


title: Subject 21800, lung, 85 dpc

value: 85 dpc


title: Subject 18508, lung, 76 dpc

value: 76 dpc


title: Subject 20000, lung, 91 dpc


title: Subject 21055, lung, 80 dpc


title: Subject 21663, lung, 85 dpc


title: Subject 21862, lung, 87 dpc


title: Subject 24227, lung, 108 dpc

value: 108 dpc

value: female


title: Subject 21803, lung, 78 dpc

value: 78 dpc

value: lung


title: Subject 20225, lung, 82 dpc

value: 82 dpc


title: Subject 21541, lung, 91 dpc


title: Subject 21720, lung, 58 dpc

value: 58 dpc

value: male


title: Subject 21973, lung, 75 dpc

value: 75 dpc


title: Subject 21664, lung, 74 dpc

value: 74 dpc


title: Subject 21461, lung, 90 dpc

value: 90 dpc


title: Subject 21483, lung, 54 dpc

value: 54 dpc


title: Subject 21499, lung, 82 dpc


title: Subject 21601, lung, 115 dpc

value: 115 dpc


title: Subject 20296, lung, 72 dpc

value: 72 dpc


title: Subject 21460, lung, 87 dpc

value: 87 dpc


title: Subject 21368, lung, 96 dpc

value: 96 dpc


title: Subject 21364, lung, 105 dpc

value: 105 dpc


title: Subject 21366, lung, 82 dpc


title: Subject 21402, lung, 91 dpc

value: 91 dpc


title: Subject 21464, lung, 78 dpc


title: Subject 21604, lung, 98 dpc

value: 98 dpc


title: Subject 21740, lung, 105 dpc

value: female


title: Subject 21451, lung, 72 dpc


title: Subject 21355, lung, 91 dpc


title: Subject 21442, lung, 67 dpc

value: 67 dpc


title: Subject 21359, lung, 89 dpc

value: 89 dpc

value: lung


title: Subject 21365, lung, 85 dpc

value: 85 dpc


title: Subject 20313, lung, 67 dpc


title: Subject 21345, lung, 98 dpc

value: male


title: Subject 21340, lung, 80 dpc

value: 80 dpc


title: Subject 21339, lung, 57 dpc

value: 57 dpc


title: Subject 21281, lung, 87 dpc


title: Subject 21338, lung, 77 dpc

value: 77 dpc


title: Subject 21341, lung, 72 dpc


title: Subject 21292, lung, 127 dpc

value: 127 dpc


title: Subject 21284, lung, 98 dpc


title: Subject 21257, lung, 87 dpc


title: Subject 21239, lung, 91 dpc


title: Subject 21251, lung, 103 dpc

value: 103 dpc


title: Subject 21287, lung, 94 dpc

value: 94 dpc


title: Subject 21238, lung, 89 dpc


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.1H-1, rep2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description:
TV39 - 0.1B
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

hyb_protocol: Hybridization of labelled fragmented aRNA to the microarrays, and staining and washing of the microarrays, were performed according to Affymetrix instructions (EukGE_WS2v5).

scan_protocol: Scanning of the microarrays was performed according to Affymetrix instructions (EukGE_WS2v5).

data_processing: .CEL files were converted to .CHP files and hybridization intensities were scaled to 240 with global array intensity methods using GCOS 1.4.

source_name: CEN.PK113-7D, glucose-limited chemostat culture, -0.1H-1

label_protocol: cDNA synthesis, cRNA synthesis, labelling and array hybridization were performed as described previously [Mendes et al., Appl Environ Microbiol 2013, 79:5949-5961].

growth_protocol: Aerobic chemostat cultivation was performed in 2 litre bioreactors (Applikon, Delft, the Netherlands) equipped with a level sensor to maintain a constant working volume of 1 litre. The culture temperature was controlled at 30°C and dilution rates between 0.025 h-1 and 0.15 h-1 were set by controlling the flow rate. Chemostat cultures were grown on synthetic medium, supplemented with 7.5 g•l-1 D-glucose, 0.3 g•l-1 Struktol J673 antifoam (Schill and Scheilacher AG, Hamburg, Germany), and 0.015 g•l-1 copper sulfate pentahydrate (copper concentrations in the medium required for induction of CUP1p controlled PAL2 were optimized for specific resveratrol production rate in batch to a concentration of 0.015 g.l-1, without affecting the µmax of FS09322). The pH was kept constant at 6.5 by automatic addition of 2M KOH. Cultures were sparged with air (0.5 l•min 1) and stirred at 800 rpm. Chemostat cultures were assumed to be in steady state when, after at least 6 volume changes, the culture dry weight and specific carbon-dioxide production rate changed by less than 3% over 2 consecutive volume changes. Steady-state samples were taken between 10 and 16 volume changes after inoculation to minimize the impact of evolutionary adaptation. Carbon recoveries for independent chemostats were >95%.

extract_protocol: Prior to RNA extraction, samples were stored in a mixture of phenol/chloroform and TEA buffer at -80°C. Total RNA extraction and isolation of mRNA were performed as described previously [Mendes et al., Appl Environ Microbiol 2013, 79:5949-5961], with the following modifications. To chelate the copper present at 4 mg/L in the culture medium and thereby prevent copper-induced mRNA degradation, EDTA was added to defrosting samples at a final concentration of 80 mM.

treatment_protocol: Microarray analysis was performed with samples from independent duplicate steady-state chemostat cultures of S. cerevisiae strains FS09322 and CEN.PK113-7D grown at four different dilution rates, comprising a total dataset of 16 microarrays. Sampling from chemostat cultures for transcriptome analysis was carried out by using liquid nitrogen for rapid quenching of mRNA turnover (Piper et al., J Biol Chem. 277:37001-8).

tag: genetic background

value: CEN.PK113-7D (MATa MAL2-8C SUC2 )

tag: genotype/variation

value: MATa MAL2-8C SUC2

tag: c-source

value: glucose

tag: dilution rate


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.1H-1, rep1

description:
TV35 - 0.1A
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.


title: Subject 21221, lung, 85 dpc


title: Subject 20995, lung, 96 dpc

value: 96 dpc


title: Subject 21098, lung, 89 dpc


title: Subject 21003, lung, 75 dpc

value: 75 dpc


title: Subject 21150, lung, 96 dpc


title: Subject 21172, lung, 94 dpc

value: female


title: Subject 21064, lung, 89 dpc


title: Subject 21223, lung, 91 dpc

value: 91 dpc


title: Subject 21147, lung, 76 dpc

value: 76 dpc


title: Subject 21006, lung, 96 dpc

value: lung


title: Subject 21048, lung, 94 dpc


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.15H-1, rep1

description:
TV36 - 0.15A
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.15h-1.

source_name: CEN.PK113-7D, glucose-limited chemostat culture, -0.15H-1


title: Subject 20569, lung, 89 dpc

value: 89 dpc


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.15H-1, rep2

description:
TV40 - 0.15B
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.15h-1.


title: Subject 20989, lung, 76 dpc

value: male


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.05H-1, rep2

description:
TV27 - 0.05B
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.05h-1.

source_name: CEN.PK113-7D, glucose-limited chemostat culture, -0.05H-1


title: FS09322 -Glucose-limited chemostat culture -0.15H-1, rep2

description:
TV14 - 0.15D
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.15h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.

source_name: FS09322, glucose-limited chemostat culture, -0.15H-1

value: resveratrol producer based on CEN.PK family


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.025H-1, rep1

description:
TV28 - 0.025A
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.025h-1.

source_name: CEN.PK113-7D, glucose-limited chemostat culture, -0.025H-1


title: Subject 20968, lung, 87 dpc

value: 87 dpc


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.05H-1, rep1

description:
TV26 - 0.05A
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.05h-1.


title: FS09322 -Glucose-limited chemostat culture -0.1H-1, rep2

description:
TV02 - 0.1B
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.

source_name: FS09322, glucose-limited chemostat culture, -0.1H-1


title: FS09322 -Glucose-limited chemostat culture -0.15H-1, rep1

description:
TV13 - 0.15C
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.15h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.


title: Subject 20973, lung, 80 dpc

value: 80 dpc


title: CEN.PK113-7D -Glucose-limited chemostat culture -0.025H-1, rep2

description:
TV25 - 0.025B
S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.025h-1.


title: FS09322 -Glucose-limited chemostat culture -0.05H-1, rep2

description:
TV11 - 0.05B
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.05h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.

source_name: FS09322, glucose-limited chemostat culture, -0.05H-1


title: FS09322 -Glucose-limited chemostat culture -0.025H-1, rep1

description:
TV04 -0.025A
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.025h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.

source_name: FS09322, glucose-limited chemostat culture, -0.025H-1


title: Subject 20882, lung, 87 dpc


title: Subject 20906, lung, 85 dpc

value: 85 dpc


title: FS09322 -Glucose-limited chemostat culture -0.025H-1, rep2

description:
TV12 - 0.025B
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.025h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.


title: Subject 20903, lung, 80 dpc


title: Subject 20880, lung, 98 dpc

value: 98 dpc


title: Subject 20846, lung, 76 dpc


title: Subject 20905, lung, 76 dpc


title: Subject 20899, lung, 59 dpc

value: 59 dpc


title: Subject 20879, lung, 113 dpc

value: 113 dpc


title: FS09322 -Glucose-limited chemostat culture -0.05H-1, rep1

description:
TV03 - 0.05A
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.05h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.


title: Subject 20847, lung, 87 dpc


title: Subject 20836, lung, 76 dpc


title: FS09322 -Glucose-limited chemostat culture -0.1H-1, rep1

description:
TV01 - 0.1A
S. cerevisiae FS09322 aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.
Resveratrol producer based on CEN.PK family, (Katz M, Durhuus T, Smits HP, Forster J. Production of metabolites. US patent 13/700,011(US20130209613 A1). 24-5-2011.


title: Subject 20877, lung, 78 dpc

value: 78 dpc


title: Subject 20777, lung, 87 dpc


title: Subject 20775, lung, 74 dpc

value: 74 dpc


title: Subject 20401, lung, 87 dpc


title: Subject 21797, lung, 67 dpc

value: 67 dpc


title: Berberine (BER) only

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description:
2-BER
MC/9 cells were treated with BER at 37°C for 24 h followed by culturing at 37°C for 6 h

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing:
GeneChip Analysis Suite
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: Mouse mast cell line MC/9

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: The MC/9 murine mast cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 50 microM 2-mercaptoethanol, 10% Rat T-STIM (Becton Dickenson) and 10% fetal bovine serum (Summit Biotechnology) at 37°C in humidified air with 5% CO2.

extract_protocol: Total RNA was isolated from cells using a NucleoSpin RNA II kit (TaKaRa Bio) according to the manufacturer’s protocol. RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: The cells were treated with BER (10 microM), DNP (500 microg/ml) or a combination of BER and DNP at 37°C for 24 h. After then, the cells were cultured at 37°C for 6 h.

tag: strain background

value: (B6 X A/J)F1

tag: cell line

value: mouse mast cell line

tag: age

value: 13 days

tag: tissue origin

value: liver

tag: life span

value: infinite

tag: morphology

value: lymphoblast

tag: treated with

value: BER (10 microM) at 37°C for 24 h


title: Control

description:
1-Ctr
MC/9 cells (nontreated)

tag: cell type

value: none (control)


title: BER + DNP

description:
4-BER+DNP
MC/9 cells were treated with a combination of BER and DNP at 37°C for 24 h followed by culturing at 37°C for 6 h


title: DNP (anti-DNP IgE) only

description:
3-DNP
MC/9 cells were treated with DNP at 37°C for 24 h followed by culturing at 37°C for 6 h

value: DNP (500 microg/ml) at 37°C for 24 h


title: heart of wildtype littermate, biological replicate 4

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

country: Germany

institute: Institute of Pharmacology

hyb_protocol: 10 µg of fragmented cRNA were hybridized (16h) to the array. Staining and washing was conducted according to the Affymetrix protocol.

scan_protocol: The processed array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data was analyzed using ArrayAssist 5.0 software (Stratagene). Probe levels were calculated using the GCRMA algorithm.

source_name: heart

label_protocol: Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).

growth_protocol: 2-3 week old mice

extract_protocol: Total RNA (5 µg) from hearts was extracted using the RNeasy fibrous tissue kit (Qiagen, Hilden, Germany).

treatment_protocol: No additional treatment was applied.

tag: genotype

value: WT

value: heart


title: Subject 20164, lung, 87 dpc

tag: subject id

tag: age (days post conception)

value: 87 dpc

tag: gender

value: male

value: lung


title: Subject 20767, lung, 72 dpc

value: 72 dpc

value: female

tag: tissue

tag: cotinine (ng/g placenta)

tag: hybridization batch id


title: Subject 20733, lung, 103 dpc

value: 103 dpc


title: Subject 20731, lung, 87 dpc


title: Subject 20730, lung, 76 dpc

value: 76 dpc


title: heart of wildtype littermate, biological replicate 3


title: Subject 20732, lung, 87 dpc


title: Subject 20729, lung, 67 dpc

value: 67 dpc


title: Subject 20728, lung, 59 dpc

value: 59 dpc


title: Subject 20723, lung, 74 dpc

value: 74 dpc


title: heart of Myh6-MeCP2TG, biological replicate 1


title: Subject 20721, lung, 110 dpc

value: 110 dpc


title: heart of wildtype littermate, biological replicate 1


title: Subject 20717, lung, 89 dpc

value: 89 dpc


title: heart of wildtype littermate, biological replicate 2


title: IgM Il1-202

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: IgM Il1-202

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);  Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization);

source_name: chondrocytes_neg vehicle control + IL1

label_protocol: NuGen Applause WT-Amp Plus ST System M01199v2-1, (Cat No. 5510); Encore Biotin Module, M01111v6 (Cat No. 4200);

growth_protocol: Monolayer culture PMID 22150225

extract_protocol: Extraction with Trizol

treatment_protocol: Treatment with interleukin-1 and anti-LAMA4-Antibody ( 2A3) as decribed before, PMID 22150225

tag: patient id

value: Knee joint

value: chondrocytes

tag: treatment group

value: neg vehicle control + IL1


title: heart of Myh6-MeCP2TG, biological replicate 2


title: L4 Il1-202

description: L4 Il1-202

source_name: chondrocytes_Lama4 + IL1

value: Lama4 + IL1


title: U-202

value: untreated


title: L4 Il1-192

description: L4 Il1-192


title: Subject 20678, lung, 59 dpc

institute: Boston Children's Hospital


title: Subject 20685, lung, 96 dpc

value: 96 dpc


title: Subject 20677, lung, 67 dpc

value: male


title: U Il1-202

description: U Il1-202

source_name: chondrocytes_untreated + IL1

value: untreated + IL1


title: U-192


title: Subject 20684, lung, 89 dpc

value: lung


title: IgM Il1-192

description: IgM Il1-192


title: U Il1-192

description: U Il1-192


title: Subject 20562, lung, 80 dpc

value: 80 dpc


title: Subject 20630, lung, 87 dpc

value: 87 dpc


title: Subject 20636, lung, 103 dpc

value: 103 dpc


title: Subject 20716, lung, 59 dpc