title: keratinocytes_8h mature IL36B replicate 2

city: Dublin

first: Seamus

last: Martin

address: Linclon Place

country: Ireland

institute: Trinity College Dublin

hyb_protocol: Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v1 Microarrays (AMADID 039494). Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies)

data_processing: The software tools Feature Extraction 10.7.3.1, GeneSpring GX 12.6 (both Agilent Technologies) Excel 2010 (Microsoft) and the IMGM-internal tool marfin v1.9 were used for quality control, statistical data analysis and filtering of differentially expressed RNAs.

source_name: neonatal keratinocytes single donor

label_protocol: 100 ng total RNA per sample were introduced into a reverse transcription with subsequent in vitro transcription (RT-IVT) reaction. Prior to RT-IVT, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into Cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies). All steps were carried out according to the manufacturer’s instructions.

growth_protocol: Keratinocytes were cultures in Der,maLife K serum free media

extract_protocol: total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions, including an on-column DNase digestion step. Total RNA was eluted in 30 μl RNase-free water.

treatment_protocol: Keratinocytes were stimulated with mature IL-36B cytokine for 8 and 24 h timepoints.

value: Primary human neonatal keratinocytes (passage 3)


title: keratinocytes_8h control (untreated) replicate 1

status: Public on Dec 15 2015

type: RNA

middle: J

department: Genetics

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: keratinocytes_8h control (untreated) replicate 2


title: keratinocytes_8h mature IL36B replicate 1


title: B3-Hr28-1

type: genomic

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N. Lake Shore Drive, Suite 1400

country: USA

institute: Northwestern University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing:
GenomeStudio
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: iCell Neurons 3

label_protocol: Standard Illumina Protocol

extract_protocol: At each timepoint, DNA was extracted by adding 50 ul per well of tissue digestion buffer (100 mM NaCl, 50 mM Tris 8.0, 100 mM EDTA, 1% SDS) along with 2 mg/ml Proteinase K (Denville Scientific; South Plainfield, NJ). The plate was sealed with parafilm and agitated overnight at 55°C using 200 RPM in an Innova orbital shaker (Eppendorf; Enfield, CT). The digested cells from each well was combined and DNA extracted with equal volume of phenol:chloroform (Invitrogen), vortexing for 10 minutes (Lab Vortex-setting of 4) and the samples were centrifuged for 5 minutes at 14000 g.   The aqueous phase was collected, extracted with equal volume of chloroform and repeated two times. The DNA was precipitated with equal volume 100% ethanol and centrifuged for 10 minutes as 14000 g. Two washes with 70% ethanol produced a pellet that was air dried for 10 minutes at room temperature and finally dissolved in 50 µl of 10 mM Tris (8.0) for 3 days at 4°C then stored at -70°C.

tag: time point

value: 28 hrs

value: iCell Neurons

tag: disease state

value: normal


title: Lupus Nephritis Cprobe_29

status: Public on Dec 14 2015

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

description: Gene Expression data from the tubulointerstitial compartment of human Lupus Nephritis kidney

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing:
The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization
Each of the hybridization was normalized seperately and the last sheet contains the batchcorrected data using Combat

label: biotin

source_name: Kidney Biopsy from Human Lupus Nephritis

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

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol

tag: tissue

value: Tubulointerstitium from kidney biopsy


title: Lupus Nephritis Cprobe_19


title: Lupus Nephritis Cprobe_26


title: B1-Hr4-1

source_name: iCell Neurons 1

value: 4 hrs


title: RPTEC clone 3

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using Shift to 75 percentile with Genespring 11.0 (baseline transformation: median of all samples)
Please note that the data in the sample data table just normalized values without additional processing/normalization. However, additional processing/normalization procedure were performed to filter statistical significant probes.

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

extract_protocol: Total RNA was isolated with RNA easy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions and quantified by NanoDrop ND-1000 Spectrophotometer  (NanoDrop Technologies, Inc.) and its quality was assessed by  Agilent 2100 Bioanalyzer (Agilent Technologies), and only samples with RNA integrity number >8.5 were used.

value: kidney

value: human renal proximal tubular epithelial cells (RPTECs)

tag: stimulated with

value: none (unstimulated control)


title: Lupus Nephritis Cprobe_2


title: Lupus Nephritis Cprobe_4


title: B1-Hr76-1

value: 76 hrs


title: Lupus Nephritis Cprobe_41


title: Lupus Nephritis Cprobe_15


title: Lupus Nephritis Cprobe_43


title: CKD Cprobe_44

description: Gene Expression data from the tubulointerstitial compartment of human CKD

source_name: Kidney Biopsy from Human CKD


title: B2-Hr4-2

source_name: iCell Neurons 2


title: B2-Hr76-2


title: CKD Cprobe_24


title: CKD Cprobe_3


title: CKD Cprobe_11


title: CKD Cprobe_32


title: B3-Hr76-1


title: B2-Hr4-1


title: CKD Cprobe_10


title: B3-Hr0-1

value: 0 hr


title: Membranous Glomerulonephritis Cprobe_14

description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis kidney

source_name: Kidney Biopsy from Human Membranous Glomerulonephritis


title: Membranous Glomerulonephritis Cprobe_12


title: Membranous Glomerulonephritis Cprobe_6


title: Hypertensive nephropathy Cprobe_42

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive nephropathy kidney

source_name: Kidney Biopsy from Human Hypertensive nephropathy


title: B1-Hr28-1


title: IgA Nephropathy Cprobe_8

description: Gene Expression data from the tubulointerstitial compartment of human IgA Nephropathy kidney

source_name: Kidney Biopsy from Human IgA Nephropathy


title: B2-Hr76-1


title: BL2 LM-PCR IRF4 2

city: New Haven

first: Yasuhiro

last: Nakayama

state: CT

address: 1 Gilbert St

institute: Yale University

hyb_protocol: Probes were hybridized according to the manufacture's protocol

scan_protocol: Arrays were scanned according to the manufacture's protocol

data_processing: Data analysis was carried out by Tilescope [Lian Z, et al.,Genome Res. 18: 1224, 2008] and Integrated Genome Browser (IGB). Nimblegen ChIP-chip data were processed by automated Tilescope analysis [Zhang ZD, et al., Genome Biol. 8: R81, 2007]. The program normalizes Cy3 and Cy5 files of the tiling array results and identifies regions with statistically significant binding enrichment.

source_name: IRF4 ChIP DNA from BL21

label_protocol: ChIP DNA samples were randomly primed with Cy3 and Cy5 random nonomers or septamers and the labeled fragments were hybridized to the promoter arrays.

growth_protocol: The cell line was grown in RPMI1640 medium (Gibco/BRL, Gaithersburg, MD) supplemented with10% FCS and was maintained in a 5% CO2 incubator at 37C.

treatment_protocol: Briefly, 3X10^8 BL2 cells were cross-linked in 1% formaldehyde for 10 mins at room temperature and then the cells were lysed in RIPA buffer(0.1% SDS) containing protease inhibitors(Roche Inc) . Cell suspensions were sonicated under ice-cold conditions using a Branson 250 Sonifier (Branson, Danbury, CT) with a power setting 60%, fifteen 30-sec pulses on ice to shear the chromatin to a size of approximately 300-500b. Anti-IRF4 antibody (sc6059 Santa Cruz Biotechnology, Santa Cruz, CA) or normal pre-immune mouse serum IgG as a control were added to the suspensions. The suspension was incubated at 4C rotating overnight to allow the antibodies to bind to DNA fragments. Protein G beads were added next day and incubated at 4C with gentle agitation for 1 hr.  The antibody–DNA complexes were eluted from the beads by 1% SDS in TE incubated at 65°C. The beads were sedemented by centrifugation, and the supernatants were incubated overnight at 65°C to reverse the cross-linking in the chromatin-protein complex. RNA contamination was eliminated by incubating the samples with 200 mg of Rnase for 1 hour at 37°C. Finally, proteinase K (400 μg of proteinase K/mL, 1X TE) was added, and the samples were incubated for 2 h at 45°C, followed by a phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation to recover the DNA. Immunoprecipitated DNA was analyzed by PCR for the enriched factor binding at target sequences. In some cases we did LM-PCR, about 20-100ng of the ChIP-DNA was blunt-ended by T4 DNA polymerase (New England Biolabs, Boston MA), then ligated with pre-annealed oligonucleotide linkers (oligo-1: GCGGTGACCCGGGAGATCTGAATTC, oligo-2: GAATTCAGATC) using T4 DNA ligase (New England Biolabs) at 16°C overnight.  The ligated DNA was further amplified by PCR with oligo-1 as a PCR primer, followed by purification using the Qiaquick PCR purification kit (Qiagen).   We used Nimblegen high density promoter arrays based on human genome HG17 (Nimblegen System INC. Reykjavik Iceland).

tag: cell line

tag: cell typ

value: Burkitt's lymphoma-derived B cell line

tag: chip antibody

value: Anti-IRF4 antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #

source_name: Control IgG ChIP DNA from BL21

tag: cell type Burkitt's lymphoma-derived B cell line

value: normal pre-immune mouse serum IgG


title: Minimal Change Disease Cprobe_39

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease kidney

source_name: Kidney Biopsy from Human Minimal Change Disease


title: BL2 IRF4

treatment_protocol: Briefly, 3X10^8 BL2 cells were cross-linked in 1% formaldehyde for 10 mins at room temperature and then the cells were lysed in RIPA buffer(0.1% SDS) containing protease inhibitors(Roche Inc) . Cell suspensions were sonicated under ice-cold conditions using a Branson 250 Sonifier (Branson, Danbury, CT) with a power setting 60%, fifteen 30-sec pulses on ice to shear the chromatin to a size of approximately 300-500b. Anti-IRF4 antibody (sc6059 Santa Cruz Biotechnology, Santa Cruz, CA) or normal pre-immune mouse serum IgG as a control were added to the suspensions. The suspension was incubated at 4C rotating overnight to allow the antibodies to bind to DNA fragments. Protein G beads were added next day and incubated at 4C with gentle agitation for 1 hr.  The antibody–DNA complexes were eluted from the beads by 1% SDS in TE incubated at 65°C. The beads were sedemented by centrifugation, and the supernatants were incubated overnight at 65°C to reverse the cross-linking in the chromatin-protein complex. RNA contamination was eliminated by incubating the samples with 200 mg of Rnase for 1 hour at 37°C. Finally, proteinase K (400 μg of proteinase K/mL, 1X TE) was added, and the samples were incubated for 2 h at 45°C, followed by a phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation to recover the DNA. Immunoprecipitated DNA was analyzed by PCR for the enriched factor binding at target sequences. In some cases we did LM-PCR, about 20-100ng of the ChIP-DNA was blunt-ended by T4 DNA polymerase (New England Biolabs, Boston MA), then ligated with pre-annealed oligonucleotide linkers (oligo-1: GCGGTGACCCGGGAGATCTGAATTC, oligo-2: GAATTCAGATC) using T4 DNA ligase (New England Biolabs) at 16°C overnight.  The ligated DNA was further amplified by PCR with oligo-1 as a PCR primer, followed by purification using the Qiaquick PCR purification kit (Qiagen).  We used Nimblegen high density promoter arrays based on human genome HG17 (Nimblegen System INC. Reykjavik Iceland).


title: B3-Hr4-1


title: BL2 LM-PCR IRF4 1

extract_protocol: Briefly, 3X10^8 BL2 cells were cross-linked in 1% formaldehyde for 10 mins at room temperature and then the cells were lysed in RIPA buffer(0.1% SDS) containing protease inhibitors(Roche Inc) . Cell suspensions were sonicated under ice-cold conditions using a Branson 250 Sonifier (Branson, Danbury, CT) with a power setting 60%, fifteen 30-sec pulses on ice to shear the chromatin to a size of approximately 300-500b. Anti-IRF4 antibody (sc6059 Santa Cruz Biotechnology, Santa Cruz, CA) or normal pre-immune mouse serum IgG as a control were added to the suspensions. The suspension was incubated at 4C rotating overnight to allow the antibodies to bind to DNA fragments. Protein G beads were added next day and incubated at 4C with gentle agitation for 1 hr.  The antibody–DNA complexes were eluted from the beads by 1% SDS in TE incubated at 65°C. The beads were sedemented by centrifugation, and the supernatants were incubated overnight at 65°C to reverse the cross-linking in the chromatin-protein complex. RNA contamination was eliminated by incubating the samples with 200 mg of Rnase for 1 hour at 37°C. Finally, proteinase K (400 μg of proteinase K/mL, 1X TE) was added, and the samples were incubated for 2 h at 45°C, followed by a phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation to recover the DNA. Immunoprecipitated DNA was analyzed by PCR for the enriched factor binding at target sequences. In some cases we did LM-PCR, about 20-100ng of the ChIP-DNA was blunt-ended by T4 DNA polymerase (New England Biolabs, Boston MA), then ligated with pre-annealed oligonucleotide linkers (oligo-1: GCGGTGACCCGGGAGATCTGAATTC, oligo-2: GAATTCAGATC) using T4 DNA ligase (New England Biolabs) at 16°C overnight.  The ligated DNA was further amplified by PCR with oligo-1 as a PCR primer, followed by purification using the Qiaquick PCR purification kit (Qiagen).


title: IgA Nephropathy Cprobe_7


title: Focal and Segmental Glomerulosclerosis Cprobe_23

description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis kidney

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis


title: Membranous Glomerulonephritis Cprobe_35


title: Focal and Segmental Glomerulosclerosis Cprobe_1


title: Focal and Segmental Glomerulosclerosis Cprobe_28


title: Focal and Segmental Glomerulosclerosis Cprobe_13


title: Focal and Segmental Glomerulosclerosis Cprobe_25


title: Focal and Segmental Glomerulosclerosis Cprobe_30


title: Lupus Nephritis Cprobe_20


title: Focal and Segmental Glomerulosclerosis Cprobe_38


title: Focal and Segmental Glomerulosclerosis Cprobe_36


title: Diabetic Nephropathy Cprobe_17

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy kidney

source_name: Kidney Biopsy from Human Diabetic Nephropathy


title: Focal and Segmental Glomerulosclerosis Cprobe_40


title: Lupus Nephritis Cprobe_18


title: Focal and Segmental Glomerulosclerosis Cprobe_31


title: Lupus Nephritis Cprobe_9


title: Lupus Nephritis Cprobe_5


title: Focal and Segmental Glomerulosclerosis Cprobe_33


title: Lupus Nephritis Cprobe_27


title: Lupus Nephritis Cprobe_16


title: Lupus Nephritis Cprobe_22


title: Lupus Nephritis Cprobe_21


title: sample collected from patient P11 80 days post DLI

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

description: RNA was extracted using the PAXgene Blood RNA Kit (QIAgen)

hyb_protocol: The hybridization procedure was performed after control of RNA quality and integrity and according to the “One-Colour Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to RISET 1.0 microarrays using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37°C) Agilent Gene Expression Wash Buffer 2 containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Inc.). The Agilent Feature Extraction Software (FES v. 10.2.1.3/10.5.1.1) was used to read out and process the microarray image files.

data_processing: In order to determine differential gene expression, FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (v. 7.2.2.0.0., Rosetta Inpharmatics LLC). Quantile normalized log2 signal intensities in the data table. Platforms GPL10370 and GPL8136 can easily be compared after removing the "_riset1" and "riset2" tags in the ID_REF column in GPL8136.

source_name: peripheral vein blood

label_protocol: Sample labeling was performed as detailed in the “One-Colour Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040). Briefly, 0.5 µg of each total RNA sample was used for the amplification and labelling step using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.).

extract_protocol: Peripheral vein blood was drawn directly into PAXgene Blood RNA tubes (QIAgen, Crawley UK). Whole-blood RNA was extracted using the PAXgene Blood RNA Kit including DNAse I treatment (QIAgen). Quality and integrity of PAXgene purified RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Transplanted patients received myeloablative conditioning regimen, followed by infusion of highly purified G-CSF mobilized CD34+ cells from haploidentical donors, containing 1x104/kg CD3+ T cells. For IL-10-DLI cell therapy product, peripheral blood mononuclear cells (PBMC) were collected by leukapheresis from the donors before G-CSF mobilisation, and from the patients before the conditioning regimen. Cell manipulation was performed in GMP-validated conditions and the cell product manufacturing was approved by Italian Ministery of Health. The donor-derived cell product was obtained after mixed lymphocyte reaction towards host-derived cells, in the presence of IL-10, for 10 days. IL-10 anergized T cells were infused, either fresh or frozen, at the dose of 105 CD3+ cells/Kg one month post-transplant after sustained neutrophils engraftment and in the absence of immunosuppressive therapy. The primary endpoints of the cell therapy were safety defined as no acute adverse reactions, bone marrow aplasia and lack of GvHD > grade II. Secondary endpoints included immune-reconstitution (defined as circulating CD3+ T cells ≥100/µl), infectious episodes and restored in vitro immunological functions. Gene expression analysis was obtained from patient samples collected at different time-points (from 2 weeks up to 1 year, 2.7 and 3.5 years) in 3 long-term tolerant patients, fully immune-reconstituted and in the absence of immune-suppression.

value: 80 days post DLI

tag: patient


title: sample collected from patient P11 100 days post DLI

value: 100 days post DLI


title: sample collected from patient P11 150 days post DLI

value: 150 days post DLI


title: sample collected from patient P11 1 year post DLI

value: 1 year post DLI


title: sample collected from patient P09 150 days post DLI


title: sample collected from patient P11 2.0 years post DLI

value: 2.0 years post DLI


title: sample collected from patient P11 0.75 years post DLI

value: 0.75 years post DLI


title: sample collected from patient P11 4 days pre DLI

value: 4 days pre DLI


title: sample collected from patient P09 120 days post DLI

value: 120 days post DLI


title: sample collected from patient P09 90 days post DLI

value: 90 days post DLI


title: sample collected from patient P09 43 days post DLI

value: 43 days post DLI


title: sample collected from patient P09 2.0 years post DLI


title: sample collected from patient P09 60 days post DLI

value: 60 days post DLI


title: sample collected from patient P11 30 days post DLI

value: 30 days post DLI


title: sample collected from patient P11 1.5 years post DLI

value: 1.5 years post DLI


title: sample collected from patient P11 2.5 days post DLI

value: 2.5 days post DLI


title: sample collected from patient P09 2.7 years post DLI

value: 2.7 years post DLI


title: sample collected from patient P09 1.5 years post DLI


title: sample collected from patient P11 51 days post DLI

value: 51 days post DLI


title: sample collected from patient P09 180 days post DLI

value: 180 days post DLI


title: sample collected from patient P09 1 year post DLI


title: sample collected from patient P07 2.5 years post DLI

value: 2.5 years post DLI


title: sample collected from patient P07 3 years post DLI

value: 3 years post DLI


title: sample collected from patient P07 1 year post DLI


title: sample collected from patient P09 14 days post DLI

value: 14 days post DLI


title: sample collected from patient P07 1.5 years post DLI


title: sample collected from patient P07 3.5 years post DLI

value: 3.5 years post DLI


title: sample collected from patient P09 60 days before first and 4 days before second DLI


title: sample collected from patient P07 142 days post DLI

value: 142 days post DLI


title: sample collected from patient P07 0.75 years post DLI

value: 0.75 years post DLI


title: sample collected from patient P07 120 days post DLI


title: sample collected from patient P07 180 days post DLI


title: cardiomyocyte_P2_CD49fhigh_sample5

description: gene expression analysis of T7-amplified polyA RNA

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1) was used to read out and process the microarray image files.

molecule: polyA RNA

organism: Mus musculus

source_name: flow-sorted (CD49fhigh) neonatal (P2) cardiomyocytes

label_protocol: 10 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Mouse embryos were removed from pregnant females (CD1, wild-type) at 15.5 days after coitus, and the hearts were isolated from the embryos. Neonatal hearts were removed from newborn mice (CD1, wild-type) two days after birth.

extract_protocol: Total RNA was isolated using the NucleoSpin® RNA kit (Macherey-Nagel) following manufacturer's instructions

treatment_protocol: For each experiment pools of 20 – 30 embryonic or 15 neonatal hearts were dissociated with the MACS® Neonatal Heart Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s instructions. The single cells obtained from E15.5 hearts were co-labeled with the PE rat anti-mouse ErbB2/Her2 (R&D Systems, 1:10) and the FITC rat anti-human and mouse CD49f antibody (Miltenyi Biotec, 1:11).  Cells were resuspended in 0.5 % BSA and 2 mM EDTA in PBS and sorted on a FACSVantage SETM cell sorter. Dead cells were excluded by propidium iodide (PI) staining. Sorting gates were set on PI negative, ErbB-2-positive, CD49flow and CD49fhigh cells. Single cells obtained from neonatal mouse hearts (P2) were first depleted from non-myocytes using the Neonatal Cardiomyocyte Isolation Kit, mouse (Miltenyi Biotec) according to the manufacturer’s instructions. Purified cardiomyocytes were then labeled with the PE rat anti-human and mouse CD49f antibody (Miltenyi Biotec, 1:11). Cells were resuspended in 0.5 % BSA in PBS and sorted on a FACSVantage SETM cell sorter. Sorting gates were set on PI negative, CD49flow and CD49fhigh cells. A minimum of 50,000 cells per fraction was collected and taken up in RA1 lysis buffer (Macherey-Nagel) directly after sorting.

tag: tissue type

value: enriched cardiomyocytes

tag: developmental stage

value: neonatal (P2)

tag: sorting parameter

tag: strain

value: CD1, wild-type


title: cardiomyocyte_P2_CD49flow_sample5

source_name: flow-sorted (CD49flow) neonatal (P2) cardiomyocytes


title: wildtype control - FLAG IP WholeWormInput - replicate 1

city: Madison

first: Daniel

last: Noble

state: wi

address: 433 Babcock Dr

institute: University of Wisconsin-Madison

description: mRNA from whole worm lysate of late L3/early L4 whole worm extract

hyb_protocol: aRNA was Hybridized according to protocols and procedures in the AFX Expression Analysis Technical Manual with Specific Protocols for Using the GeneChip Hybridization, Wash and Stain kit.

scan_protocol: Arrays were scanned using GC3000 G7 Scanner (Affymetrix)

data_processing: Unscaled intensities were extracted and exported to Bioconductor software. Array data were background corrected by Robust Multi-array Average (RMA), and normalized by Variance Stabilization (VSN), both available in Bioconductor package Affy (affy 1.42.2).

organism: Caenorhabditis elegans

label_protocol: Labeled aRNA samples were prepared using Ambion MessageAmp Premier IVT kit according to manufacturer's instructions

growth_protocol: Synchronized worms were grown to the late L3/early L4 stage at 25C

extract_protocol: Trizol followed by RNeasy Micro kit following manufacturers instructions.  Antibodies include: Sigma anti-c-Myc agarose affinity gel (catalog number A7470-1ML, lot number 112M4822) and Sigma Anti-FLAG M2 affinity gel (catalog number A2220-1ML, lot number 054K6047).

treatment_protocol: Worms were washed and UV irradiated followed by flash freezing in liquid nitrogen to prepare extracts.

tag: strain background

tag: genotype/variation

value: wildtype (N2)

value: late L3/early L4

value: whole worm


title: wildtype control - FLAG IP WholeWormInput - replicate 3


title: cardiomyocyte_P2_CD49fhigh_sample3

tag: cell type

value: flow-sorted (CD49fhigh) neonatal (P2) cardiomyocytes


title: wildtype control - FLAG IP WholeWormInput - replicate 2


title: FOG-3::FLAG - FLAG IP WholeWormInput - replicate 3

source_name: FOG-3::FLAG - FLAG IP WholeWormInput


title: cardiomyocyte_E15.5_ErbB-2+/CD49fhigh_sample8

source_name: flow-sorted (ErbB-2+/CD49fhigh) embryonic (E15.5) cardiomyocytes

value: heart

value: embryonic (E15.5)


title: FOG-3::FLAG - FLAG IP WholeWormInput - replicate 2


title: wildtype control - Myc IP WholeWormInput - replicate 3


title: cardiomyocyte_P2_CD49flow_sample4

value: flow-sorted (CD49flow) neonatal (P2) cardiomyocytes


title: cardiomyocyte_P2_CD49fhigh_sample2


title: cardiomyocyte_E15.5_ErbB-2+/CD49fhigh_sample6

value: flow-sorted (ErbB-2+/CD49fhigh) embryonic (E15.5) cardiomyocytes


title: cardiomyocyte_P2_CD49flow_sample2


title: cardiomyocyte_P2_CD49flow_sample3


title: FOG-3::FLAG - FLAG IP WholeWormInput - replicate 1


title: cardiomyocyte_P2_CD49fhigh_sample4


title: wildtype control - Myc IP WholeWormInput - replicate 2


title: wildtype control - Myc IP WholeWormInput - replicate 1


title: cardiomyocyte_E15.5_ErbB-2+/CD49fhigh_sample2


title: Nicd vs Input replicate 2

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

hyb_protocol: 34 µg labeled sample DNA and 34 µg labeled control DNA were combined, dried in a speed vac with medium heat and resuspended in 12.3 µl water.  For each hybridization 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) were combined and 31.7µl added to each hybridization sample. Samples were incubated at +95°C for 5 minutes, 42°C for 5 minutes and 41 µl loaded onto the array. The hybridization was performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridization station at 42°C (mix mode B) for 18 hours. Post hybridization washes were performed according to the NimbleGen Wash Buffer Kit instructions.

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

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Quantile normalization was applied across the 3 arrays.
The three normalized replicates were processed with TAMALPAIS webserver (Bieda et al., 2006 Genome Research 16:595). The nicd_brain_quant_tamalpais_3files_t02p005.sgr file (linked as a supplementary file on the Series record) contains the log2 ratio profiles of the identified enriched regions.

organism: Drosophila melanogaster

source_name: Nicd replicate 2

label_protocol: In duplicate reactions: 1 μg of amplified DNA with 30 µl 2.5X Random Primers Solution (BioPrime DNA labelling kit, Life Technologies) was incubated at 100°C for 5 minutes and then cooled on ice. The samples were labelled as technical dye-swap replicates using the BioPrime DNA labelling kit (Life Technologies) in the presence of 4.5nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 72 U of Klenow at 37°C. After 2 hours the reactions were stopped with 7.5 µl Stop Buffer (BioPrime DNA labelling kit, Life Technologies). Duplicate reactions were pooled into single tubes and then precipitated with 165 µl Isopropanol and 0.2M sodium chloride and washed with cold 80% ethanol. The DNA was resuspened in 50 µl water and quantified on a Nanodrop spectrophotometer (Thermo Scientific).

growth_protocol: animals were raised at 18C for 10 days in standard fly food

extract_protocol: 50 CNSs, from animals where Notch (UAS-NΔecd transgene) is hyperactivated in neuroblasts (via grhGal4, tubGal80ts system) for 24 hours, were dissected out in cold PBS and fixed with 1% formaldehyde in PBS for 20 min at RT followed by quenching with 0.2 M glycine for 5 min. The CNSs were washed three times with ice-cold PBS (with Roche Complete Inhibitor) and homogenized (plastic pestle) and lysed in 50ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 20 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 5 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 150mM NaCl, Roche Complete inhibitor) and pre-cleared with 40 µl protein G agarose beads and 2ug goat IgG for 3 h at 4C. 10% of pre-cleared chromatin supernatant was kept as Total Input. The rest of the chromatin supernatant was then incubated overnight with 2.4 µg of Su(H) antibody [Santa Cruz: sc15813] at 4C. After incubation with protein G agarose beads (50 µl) ON at 4C, the immune complexes were collected by centrifugation and washed for 5min at 4C with the following buffers: dilution buffer, IP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 50mM NaCl) (two washes), IP wash buffer 2 (1% NP-40 substitute, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.0, 250mM LiCl) (two washes) and TE (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted from the beads (twice) in 250 µl of fresh elution buffer (1% SDS, 100 mM NaHCO3) at 65C for 10min followed by 10 min vortex and de-crosslinked by overnight incubation at 65C with addition of 27 ul 5M NaCl. Following the treatment with 5 ul RNase A (20mg/ml) for 30 min at 37C and 9 ul proteinase K (10mg/ml) ON at 45C, genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by Phenol/Chloroform and precipitated by 0.15 M Sodium acetate [accompanied by 5ng of Glucogen and 1ul of tRNA 95mg/ml stock)] and 1ml of 100% Ethanol ON at -20C. Genomic DNA pellet was washed with 70% of Ethanol and resuspended in 30 ul of ddH2O.

treatment_protocol: larvae were shifted to 30C for 24h and then CNSs were dissected out

value: L3 larval stage

value: Central Nervous System (CNS)

tag: antibody

value: goat-anti-Su(H) [Santa Cruz:sc15813]

source_name: Input replicate 2

value: none, input DNA


title: Nicd vs Input replicate 1

source_name: Nicd replicate 1

tag: tissue

source_name: Input replicate 1


title: Myc::FOG-1 - Myc IP WholeWormInput - replicate 2

source_name: Myc::FOG-1 - Myc IP WholeWormInput


title: cardiomyocyte_E15.5_ErbB-2+/CD49flow_sample8

source_name: flow-sorted (ErbB-2+/CD49flow) embryonic (E15.5) cardiomyocytes


title: cardiomyocyte_E15.5_ErbB-2+/CD49flow_sample3

value: flow-sorted (ErbB-2+/CD49flow) embryonic (E15.5) cardiomyocytes


title: wildtype control - FLAG IP - replicate 5

description: mRNA from anti-FLAG immunoprecipitation of late L3/early L4 whole worm extract

source_name: C. elegans late L3/early L4 whole worm extracts


title: cardiomyocyte_E15.5_ErbB-2+/CD49flow_sample6


title: wildtype control - FLAG IP - replicate 6


title: wildtype control - FLAG IP - replicate 1


title: cardiomyocyte_E15.5_ErbB-2+/CD49fhigh_sample3


title: FOG-3::FLAG - FLAG IP - replicate 6


title: wildtype control - FLAG IP - replicate 7


title: FOG-3::FLAG - FLAG IP - replicate 7


title: Full-blown adenocarcinoma. Biological replicate 6

city: Madrid

first: Chiara

last: Ambrogio

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

description:
Tumoral sample. Biological replicate 6
Gene expression data from K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression

hyb_protocol: cRNA was hybridized on GeneChip Mouse Genome Array (Affymetrix)

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

data_processing: The data were processed using affy package available in Bioconductor. RMA was employed for normalization.

source_name: K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression (T2 subtype)

label_protocol: RNA was amplified and labelled the RNA with the WT-Ovation™ One-Direct RNA Amplification System

growth_protocol: Tumors were isolate from K-RasG12V knock-in mice

extract_protocol: RNA was extracted with Arcturus® PicoPure® Frozen RNA Isolation Kit

treatment_protocol: Tumors were isolated manually 10 months after adeno-CRE infection in vivo

value: Lung


title: Myc::FOG-1 - Myc IP WholeWormInput - replicate 1


title: cardiomyocyte_E15.5_ErbB-2+/CD49flow_sample2


title: wildtype control - FLAG IP - replicate 4


title: FOG-3::FLAG - FLAG IP - replicate 5


title: wildtype control - FLAG IP - replicate 2


title: Full-blown adenocarcinoma. Biological replicate 5

description:
Tumoral sample. Biological replicate 5
Gene expression data from K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression


title: wildtype control - FLAG IP - replicate 3


title: Myc::FOG-1 - Myc IP WholeWormInput - replicate 3


title: FOG-3::FLAG - FLAG IP - replicate 4


title: Full-blown adenocarcinoma. Biological replicate 7

description:
Tumoral sample. Biological replicate 7
Gene expression data from K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression


title: CEP-2

city: Philadelphia

first: Sandra

middle: Viviana

last: Fernandez

state: PA

address: 233 South 10th Street

department: Medical Oncology

institute: Thomas Jefferson University

hyb_protocol: Affymetrix gene chips, Human gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 110 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h. Arrays were then washed and stained using Gene chip Fluidic Station 450, using  Affymetrix GeneChip hybridization wash & stain kit.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Data analyses were performed using GeneSpring software 13.1 (Agilent Technologies, Inc., Santa Clara, CA). The probe set signals were calculated with the Iterative Plier 16 summarization algorithm; baseline to median of all samples was used as baseline option. Data was filtered by percentile and lower cut off was set at 25. The criteria for differentially expressed genes were set at ≥ 2.0-fold changes. Statistical analysis was performed to compare 2 groups using TTest unpaired with p-value less than equal to 0.05.

source_name: Human breast epithelial cells

label_protocol: 2.5 ug ST-cDNAs were fragmented and chemically labeled with biotin to generate biotinylated ST-cDNA using FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

growth_protocol: The human inflammatory breast cancer cells FC-IBC02 were grow in vitro as described elsewhere (Fernandez et al, 20013, Breast cancer research and treatment 140 (1):23-33)

extract_protocol: RNA was isolated from the cells using RiboPureTM kit (Life Technologies, NY) and the RNA quality was analyzed using the Agilent 2100 Bioanalyzer.

treatment_protocol: To study the effect of CEP-37440, FC-IBC02 cells were treated for 48 h with 1,000 nM CEP-37440 (Teva Pharmaceuticals).

tag: agent

value: Tumor breast

value: FC-IBC02 cells


title: Full-blown adenocarcinoma. Biological replicate 3

description:
Tumoral sample. Biological replicate 3
Gene expression data from K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression


title: CEP-1


title: Control-2


title: Full-blown adenocarcinoma. Biological replicate 4

description:
Tumoral sample. Biological replicate 4
Gene expression data from K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression


title: sample collected from patient P09 0.75 years post DLI

tag: time point

value: 0.75 years post DLI


title: Full-blown adenocarcinoma. Biological replicate 2

description:
Tumoral sample. Biological replicate 2
Gene expression data from K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression


title: FOG-3::FLAG - FLAG IP - replicate 2


title: FOG-3::FLAG - FLAG IP - replicate 3


title: Control-1


title: Normal sample. Biological replicate 8

description:
Normal sample. Biological replicate 8
Gene expression data from Normal lung cells

source_name: Normal murine lung cells


title: FOG-3::FLAG - FLAG IP - replicate 1


title: Normal sample. Biological replicate 5

description:
Normal sample. Biological replicate 5
Gene expression data from Normal lung cells


title: Full-blown adenocarcinoma. Biological replicate 1

description:
Tumoral sample. Biological replicate 1
Gene expression data from K-RasG12V full-blown adenocarcinomas 10 months after oncogene expression


title: BMDC_UBC9WT_6hrLPS_rep2

city: Paris

first: Adrien

last: Decque

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

description: UBC9WT BMDCs were stimulated with 10ng/ml for 6 hours

hyb_protocol: Two hundred ng of total RNA per sample were processed, labelled and hybridized to Affymetrix Mouse Gene ST 1.0 arrays, following Affymetrix Protocol (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

scan_protocol: Following hybridization, the arrays were stained and scanned at 532 nm using an Affymetrix GeneChip Scanner 3000 which generates individual CEL files for each array.

data_processing: Gene-level expression values were derived from the CEL file probe-level hybridization intensities using the model-based Robust Multichip Average algorithm (RMA) (Bolstad et al., 2003). RMA performs normalization, background correction and data summarization. An analysis is performed using the LPE test (Jain, 2003) to identify significant differences in gene expression between UBC9 Knock-Out and UBC9 WT BMDCs, and a p-value threshold of p < 0.05 is used as the criterion for significant differential expression.

source_name: BMDC, UBC9WT, 6 hours LPS

growth_protocol: RPMI + 10% FBS + pen/strep + GM-CSF(20ng/ml) for 10 days at 37°C

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

treatment_protocol: At day 6 of culture, 4-hydroxytamoxifen (100nM) was added to the culture. Samples were stimulated for indicated times with 10 ng/ml LPS.

tag: genotype

value: Bone marrow derived dendritic cells

tag: stimulation

value: 6 hours LPS 10 ng/ml


title: wildtype control - Myc IP - replicate 7

description: mRNA from anti-Myc immunoprecipitation of late L3/early L4 whole worm extract

value: wildtype (N2)

value: late L3/early L4

value: whole worm


title: Normal sample. Biological replicate 1

description:
Normal sample. Biological replicate 1
Gene expression data from Normal lung cells


title: BMDC_UBC9WT_6hrLPS_rep3

label_protocol: Two hundred ng of total RNA per sample were processed, labelled and hybridized to Affymetrix Mouse Gene ST 1.0 arrays, following Affymetrix Protocol (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).


title: Hyperplastic lesion. Biological replicate 7

description:
Tumoral sample. Biological replicate 7
Gene expression data from K-RasG12V hyperplastic lesion 3 months after oncogene expression

label: bioitin

source_name: K-RasG12V murine hyperplastic lesion 3 months after oncogene expression (H2 subtype)

growth_protocol: Cells were isolated from lung frozen sections obtained from K-RasG12V knock-in mice

treatment_protocol: Cells were isolated by Laser Capture Microdissection (LCM) 3 months after adeno-CRE infection in vivo


title: Normal sample. Biological replicate 7

description:
Normal sample. Biological replicate 7
Gene expression data from Normal lung cells


title: Normal sample. Biological replicate 3

description:
Normal sample. Biological replicate 3
Gene expression data from Normal lung cells


title: wildtype control - Myc IP - replicate 6


title: Normal sample. Biological replicate 4

description:
Normal sample. Biological replicate 4
Gene expression data from Normal lung cells


title: Nicd vs Input replicate 3

source_name: Nicd replicate 3

source_name: Input replicate 3


title: Normal sample. Biological replicate 2

description:
Normal sample. Biological replicate 2
Gene expression data from Normal lung cells


title: BMDC_UBC9WT_1hrLPS_rep2

description: UBC9WT BMDCs were stimulated with 10ng/ml for 1 hour

source_name: BMDC, UBC9WT, 1 hour LPS

value: 1 hours LPS 10 ng/ml


title: BMDC_UBC9WT_6hrLPS_rep1


title: BMDC_UBC9WT_1hrLPS_rep3


title: wildtype control - Myc IP - replicate 3


title: wildtype control - Myc IP - replicate 5


title: BMDC_UBC9WT_1hrLPS_rep1


title: wildtype control - Myc IP - replicate 4


title: Hyperplastic lesion. Biological replicate 6

description:
Tumoral sample. Biological replicate 6
Gene expression data from K-RasG12V hyperplastic lesion 3 months after oncogene expression


title: Hyperplastic lesion. Biological replicate 4

description:
Tumoral sample. Biological replicate 4
Gene expression data from K-RasG12V hyperplastic lesion 3 months after oncogene expression

source_name: K-RasG12V murine hyperplastic lesion 3 months after oncogene expression (H1 subtype)


title: Hyperplastic lesion. Biological replicate 5

description:
Tumoral sample. Biological replicate 5
Gene expression data from K-RasG12V hyperplastic lesion 3 months after oncogene expression


title: Hyperplastic lesion. Biological replicate 2

description:
Tumoral sample. Biological replicate 2
Gene expression data from K-RasG12V hyperplastic lesion 3 months after oncogene expression


title: BMDC_UBC9WT_unstim_rep3

description: UBC9WT BMDCs were left unstimulated

source_name: BMDC, UBC9WT, unstimulated


title: Normal sample. Biological replicate 8


title: Hyperplastic lesion. Biological replicate 1

description:
Tumoral sample. Biological replicate 1
Gene expression data from K-RasG12V hyperplastic lesion 3 months after oncogene expression


title: Normal sample. Biological replicate 7


title: wildtype control - Myc IP - replicate 2


title: Normal sample. Biological replicate 5


title: Normal sample. Biological replicate 4


title: wildtype control - Myc IP - replicate 1


title: BMDC_UBC9WT_unstim_rep2

description: UBC9WT BMDCs were left unstimulated


title: BMDC_UBC9WT_unstim_rep1

description: UBC9WT BMDCs were left unstimulated


title: Normal sample. Biological replicate 3


title: BMDC_UBC9KO_6hrLPS_rep2

description: UBC9KO BMDCs were stimulated with 10ng/ml for 6 hours

source_name: BMDC, UBC9KO, 6 hours LPS


title: Normal sample. Biological replicate 6

description:
Normal sample. Biological replicate 6
Gene expression data from Normal lung cells


title: Myc::FOG-1 - Myc IP - replicate 4


title: Normal sample. Biological replicate 2


title: BMDC_UBC9KO_6hrLPS_rep3


title: BMDC_UBC9KO_1hrLPS_rep3

description: UBC9KO BMDCs were stimulated with 10ng/ml for 1 hour

source_name: BMDC, UBC9KO, 1 hour LPS


title: Myc::FOG-1 - Myc IP - replicate 2


title: sample of healthy donor HC3

description: RNA was extracted using the PAXgene Blood RNA Kit (QIAgen)

source_name: peripheral vein blood


title: Normal sample. Biological replicate 1


title: BMDC_UBC9KO_6hrLPS_rep1


title: BP1-2-unstressed2

city: Honolulu

first: Kazue

last: Ishihara

state: HI

address: 1955 East-West Rd AgSci 218

department: Molecular Biosciences and Bioengineering

institute: University of Hawaii at Manoa

hyb_protocol: Hybridization was performed by Roy J. Carver Center for Genomics (the University of Iowa, Iowa). Labeled cDNAs were prepared using the Hybridization Kit (Roche NimbleGen cat# 05583934001) and loaded on a 4x72K gene expression microarray from Roche NimbleGen. The Microarray slide was hybridized overnight on a Hybridization System 4 (NimbleGen System, Inc.).

scan_protocol: Scanning was peformed by Roy J. Carver Center for Genomics (the University of Iowa, Iowa) using a NimbleGen MS 200 Microarray Scanner (Roche NimbleGen, Inc.).

data_processing: The 4 tiff images generated by the scanner were imported into the NimbleScan software v.2.6 (Roche NimbleGen, Inc.). A grid containing probe information was laid over each of the arrays and aligned. Raw intensities were extracted from the images and then subjected to a Robust Multichip Average (RMA) algorithm included in the NimbleScan software using the default settings. During the RMA analyses, the probe raw intensities where corrected for background noise, quantile normalized between arrays and normalized probe intensity values were averaged to give a single intensity value per transcript and per sample.

organism: Acacia koa

source_name: Acacia koa

label_protocol: Labelling was performed by Roy J. Carver Center for Genomics (the University of Iowa, Iowa).Double-stranded cDNAs were treated with RNase A followed by phenol:chloroform:isoamyl alcohol extraction in conjunction with Phase Lock tube clean up, and ethanol precipitation. cDNAs were labeled with the Cy3 Cyanine dye using the One-Color DNA Labeling Kit (Roche NimbleGen cat# 06370438001).

extract_protocol: A. koa seedlings were frozen in liquid nitrogen and grounded into powder.  Qiagen Plant Rneasy Minikit and Takara Fruit-Mate was combined to extract total RNA.

treatment_protocol: For mechanical stress, the stems of A. koa seedlings were manually bent (without wounding) in four cardinal directions.

tag: treatment

value: Unstressed

value: seedling


title: Myc::FOG-1 - Myc IP - replicate 3

description: mRNA from anti-Myc immunoprecipitation of late L3/early L4 whole worm extract


title: BP1-1-unstressed1


title: BP1-4-stressed2

value: Stressed


title: BP1-3-stressed1


title: BMDC_UBC9KO_1hrLPS_rep2


title: BMDC_UBC9KO_1hrLPS_rep1


title: sample of healthy donor HC1


title: BMDC_UBC9KO_unstim_rep2

description: UBC9KO BMDCs were left unstimulated

source_name: BMDC, UBC9KO, unstimulated


title: Myc::FOG-1 - Myc IP - replicate 1


title: sample of healthy donor HC2


title: BMDC_UBC9KO_unstim_rep3

description: UBC9KO BMDCs were left unstimulated


title: BMDC_UBC9KO_unstim_rep1

description: UBC9KO BMDCs were left unstimulated


title: Brain_inattentive_to_noninteracting_30min_rep2

status: Public on Dec 13 2015

city: Oeiras

first: Joao

middle: Sollari

last: Lopes

address: Rua da Quinta Grande N6

country: Portugal

institute: IGC

description: Gene expression data from brain of adult male wild-type (AB) zebrafish (11 months old)

hyb_protocol: 3.5 µg of end-labeled, fragmented cDNA was used in a 150-µl hybridization cocktail containing added hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix), of which 120 ul were hybridized on array strips for 20 h at 48°C. Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system, followed by scanning of the array strips.

scan_protocol: GeneChips were scanned with GeneChip® Scanner 3000

data_processing: All ZebGene 1.1 ST arrays were processed using the BioConductor package oligo. Arrays were assessed for quality using R core and oligo package functions and normalized using the Robust Multichip Average (RMA) method at the probe level, collapsing probes into core transcripts based on the pd.zebgene.1.1.db annotation package. Probes were assigned to genes using Netaffx annotations (ZebGene-1_1-st-v1.na33.3.zv9.transcript.csv). Differential expression using isolated fish as reference were generated by linear model for microarray data analysis (limma) using empirical Bayes shinkage methods. Differentially expressed genes were assessed as those with at least a log fold expression change of 0.1 and an FDR based adjusted pvalue of less than 0.05.

organism: Danio rerio

source_name: whole brain, inattentive to non-interacting conspecifics, 30min

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) Zebrafish Gene 1.1 ST Array by using the Ambion WT Expression Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal Labeling Kit, according to the manufacturer’s protocols. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Ambion WT Expression Kit) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (Ambion WT Expression Kit). 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis (Ambion WT Expression Kit). 5.5 ug of single stranded cDNA was fragmented and end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Fish were kept in mixed sex groups in environmentally enriched stock tanks (gravel substrate, artificial plants and rocks) at Instituto Gulbenkian de Ciencia (IGC, Oeiras, Portugal).

extract_protocol: Immediately after the test, each focal fish was euthanized with an overdose of tricaine solution (MS222, Pharmaq; 500–1000 mg/L) and its spinal cord was sectioned. The brain was immediately removed and stored at -80◦C in qiasol for posterior analysis. RNA was extracted from the brains using the RNeasy Lipid Tissue Mini kit (Qiagen) with some procedural modifications. In brief, samples were homogenized by vortex and added 20μl of chloroform. Incubation times were increased in order to maximize RNA recovery and in the end samples were diluted in 25μl of RNase-free water. Concentration and purity was determined by spectrophotometry and integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Fish were subjected to one of 3 treatments for 30 minutes: bystander to an interacting male conspecific dyad; bystander to two non-interacting male conspecifics; and socially isolated. Each focal fish was subjected to a single test after an overnight baseline period of isolation in the corresponding test tank. Bystanders could visually observe through a one-way mirror the corresponding stimuli fish without being observed and no chemical communication was possible.

tag: gender

value: male

value: AB

value: brain

value: adult


title: Brain_attentive_to_noninteracting_30min_rep3

source_name: whole brain, attentive to non-interacting conspecifics, 30min


title: Brain_inattentive_to_noninteracting_30min_rep1

value: inattentive to non-interacting conspecifics, 30min


title: Brain_attentive_to_noninteracting_30min_rep1

value: attentive to non-interacting conspecifics, 30min


title: Brain_attentive_to_noninteracting_30min_rep2


title: Brain_attentive_to_fight_30min_rep3

source_name: whole brain, attentive to fighting conspecifics, 30min


title: Brain_isolated_30min_rep2

source_name: whole brain, isolated, 30min

value: isolated, 30min


title: Brain_isolated_30min_rep3


city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description:
Hippocampus, Neuronal Culture, WT, Untreated, Mouse ID: 3569
Hippo_Culture_WT_Untr_3569

hyb_protocol: Fragmented aRNA was hybridized onto Affymetrix Mouse Genome 430 2.0 arrays using the manufacturer's standard protocols.

scan_protocol: Scanned using Affymetrix GeneChip scanner 3000 at 2.5 um resolution.

data_processing: All 42 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output in base 2 logarithmic scale.

label: Biotin

source_name: Hippocampus_Neuronal Culture_WT_pooled from littermates

label_protocol: Total RNA was reverse-transcribed to synthesize double-stranded cDNA using T7 oligo (dT) primers and then transcribed in vitro into biotin-modified aRNA with IVT Labeling Master Mix. The aRNA was purified, quantified and fragmented.

growth_protocol: Hippocampal and cortical neuron cultures were prepared from C57BL/6 congenic WT and Fmr1 KO embryos at 17-18 days post conception in parallel and allowed to mature for 14 days in vitro following PMID: 12351721

extract_protocol: RNA was extracted using the miRNeasy Mini Kit (Qiagen). Eluted RNA was analyzed on a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer (OD260/280 ratio: 1.8-2.2; RNA Integrity Number >8). A total of 100ng of RNA was processed using Affymetrix (Affymetrix Inc, Santa Clara, CA) protocols and kits, which were used to generate biotinylated aRNA, and for hybridization, staining and scanning of arrays (GeneChip 3’IVT Express Kit and GeneChip Expression Wash, Stain and Scan protocol).

tag: gentoype/variation

value: wild type

tag: mouse id

tag: age

value: embryos (at 17-18 days post conception; pooled littermate)

tag: tissue/cell type

value: Hippocampus, Neuronal Culture


title: Brain_attentive_to_fight_30min_rep2

tag: developmental stage

value: attentive to fighting conspecifics, 30min


description:
Hippocampus, Neuronal Culture, WT, Untreated, Mouse ID: NT
Hippo_Culture_WT_Untr_NT

value: NT


description:
Hippocampus, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 4236
Hippo_Culture_KO_Untr_4236

source_name: Hippocampus_Neuronal Culture_Fmr1-KO_pooled from littermates


description:
Hippocampus, Neuronal Culture, WT, Untreated, Mouse ID: 2644
Hippo_Culture_WT_Untr_2644


description:
Hippocampus, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2038
Hippo_Culture_KO_Untr_2038


description:
Hippocampus, Neuronal Culture, WT, Untreated, Mouse ID: 2643
Hippo_Culture_WT_Untr_2643


title: Brain_attentive_to_fight_30min_rep1

tag: strain


title: Brain_isolated_30min_rep1


description:
Hippocampus, Brain, WT, Untreated, Mouse ID: NT
Hippo_Brain_WT_Untr_NT

tag: strain background

value: Hippocampus, Brain


description:
Hippocampus, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2037
Hippo_Culture_KO_Untr_2037


description:
Hippocampus, Neuronal Culture, WT, Untreated, Mouse ID: 2236
Hippo_Culture_WT_Untr_2236


description:
Hippocampus, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2620
Hippo_Culture_KO_Untr_2620


description:
Hippocampus, Brain, WT, Untreated, Mouse ID: 3569
Hippo_Brain_WT_Untr_3569


description:
Hippocampus, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2221
Hippo_Culture_KO_Untr_2221


title: Myc::FOG-1 - Myc IP - replicate 7

source_name: C. elegans late L3/early L4 whole worm extracts

value: late L3/early L4

value: whole worm


description:
Hippocampus, Brain, WT, Untreated, Mouse ID: 3104
Hippo_Brain_WT_Untr_3104


description:
Hippocampus, Brain, WT, Untreated, Mouse ID: 2644
Hippo_Brain_WT_Untr_2644


description:
Hippocampus, Brain, Fmr1-KO, Untreated, Mouse ID: 4237
Hippo_Brain_KO_Untr_4237


description:
Hippocampus, Brain, Fmr1-KO, Untreated, Mouse ID: 2221
Hippo_Brain_KO_Untr_2221


description:
Hippocampus, Brain, Fmr1-KO, Untreated, Mouse ID: 4236
Hippo_Brain_KO_Untr_4236


description:
Hippocampus, Brain, Fmr1-KO, Untreated, Mouse ID: 2620
Hippo_Brain_KO_Untr_2620


title: Normal sample. Biological replicate 6

description:
Normal sample. Biological replicate 6
Gene expression data from Normal lung cells

source_name: Normal murine lung cells

value: Lung


description:
Hippocampus, Brain, Fmr1-KO, Untreated, Mouse ID: 2037
Hippo_Brain_KO_Untr_2037


description:
Hippocampus, Brain, Fmr1-KO, Untreated, Mouse ID: 2038
Hippo_Brain_KO_Untr_2038


title: E39

first: Jesús

last: Sánchez Ruiz

address: Calle Melchor Fdez Almagro 3

hyb_protocol: Human Exon 1.0 ST arrays.

scan_protocol: All liquid handling steps were performed using a GeneChip Fluidics Station 450, and GeneChips were scanned with the GeneChip Scanner 3000 (Affymetrix) using GCOS 1.2.

data_processing:
Both at the exon and gene levels, data were analyzed using the Partek Genomics Suite. CEL files were imported using the Partek defaults (adjusted for GC content, RNA background correction and mean probe set summarization). Partek’s ANOVA was run, using cell type (Wt/COGDR-5 cells) and condition (Normo/Hypoxia) as categorical factors. Differentially expressed genes were selected based on p-value for either cell type or condition. Alternatively spliced exons were selected based on p-value for the interaction of type and condition. MIAME guidelines were followed and data were deposited in GEO database.
core meta probeset

source_name: MDA-MB-231 WT

label_protocol: Single-stranded complementary DNA (cDNA) was prepared from 1.0μg total RNA as per the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix). First, an rRNA reduction step was performed, followed by cDNA synthesis and in vitro transcription.

growth_protocol: Quadruplicate samples of Wt or COGDR-5 cells cells (107) were allowed to attach overnight in 10-cm dishes in normoxia/high glucose.

extract_protocol: Total RNA was extracted using RNA-mini columns (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) and the RNA 6000 Nano kit (Caliper Life Sciences).

treatment_protocol: The next morning, the cells were either left untreated or incubated for 8hr in 0.2%O2

value: MDA-MB-231 WT

tag: growth condition

value: Hypoxia


title: E28

description: C4 stands for COGDR-5

source_name: MDA-MB-231 C4

tag: cell type

value: MDA-MB-231 COGDR-5


description:
Cortex, Neuronal Culture, WT, Untreated, Mouse ID: 3569
Cortex_Culture_WT_Untr_3569

source_name: Cortex_Neuronal Culture_WT_pooled from littermates

value: Cortex, Neuronal Culture


title: E40

description: C4 stands for COGDR-5


title: E36

description: C4 stands for COGDR-5


title: E32

description: C4 stands for COGDR-5


description:
Cortex, Neuronal Culture, WT, Untreated, Mouse ID: 2644
Cortex_Culture_WT_Untr_2644


description:
Cortex, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 4236
Cortex_Culture_KO_Untr_4236

source_name: Cortex_Neuronal Culture_Fmr1-KO_pooled from littermates


description:
Cortex, Neuronal Culture, WT, Untreated, Mouse ID: 2643
Cortex_Culture_WT_Untr_2643


description:
Cortex, Neuronal Culture, WT, Untreated, Mouse ID: NT
Cortex_Culture_WT_Untr_NT


description:
Hippocampus, Brain, WT, Untreated, Mouse ID: 2643
Hippo_Brain_WT_Untr_2643


description:
Hippocampus, Brain, WT, Untreated, Mouse ID: 2236
Hippo_Brain_WT_Untr_2236


title: E35


description:
Cortex, Neuronal Culture, WT, Untreated, Mouse ID: 2236
Cortex_Culture_WT_Untr_2236


title: Myc::FOG-1 - Myc IP - replicate 6

description: mRNA from anti-Myc immunoprecipitation of late L3/early L4 whole worm extract


description:
Cortex, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2221
Cortex_Culture_KO_Untr_2221


title: E38

description: C4 stands for COGDR-5

value: Normoxia


title: Hyperplastic lesion. Biological replicate 3

description:
Tumoral sample. Biological replicate 3
Gene expression data from K-RasG12V hyperplastic lesion 3 months after oncogene expression

source_name: K-RasG12V murine hyperplastic lesion 3 months after oncogene expression (H1 subtype)


title: E27


description:
Cortex, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2620
Cortex_Culture_KO_Untr_2620


title: E30

description: C4 stands for COGDR-5


title: E26

description: C4 stands for COGDR-5


description:
Cortex, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2038
Cortex_Culture_KO_Untr_2038


description:
Cortex, Brain, WT, Untreated, Mouse ID: NT
Cortex_Brain_WT_Untr_NT

source_name: Cortex_Brain_WT_pooled from littermates

value: Cortex, Brain


title: E34

description: C4 stands for COGDR-5


title: Myc::FOG-1 - Myc IP - replicate 5


description:
Cortex, Brain, WT, Untreated, Mouse ID: 3569
Cortex_Brain_WT_Untr_3569


description:
Cortex, Neuronal Culture, Fmr1-KO, Untreated, Mouse ID: 2037
Cortex_Culture_KO_Untr_2037


title: E29


title: E37


description:
Cortex, Brain, Fmr1-KO, Untreated, Mouse ID: 2620
Cortex_Brain_KO_Untr_2620


description:
Cortex, Brain, WT, Untreated, Mouse ID: 2644
Cortex_Brain_WT_Untr_2644


title: E33


description:
Cortex, Brain, WT, Untreated, Mouse ID: 2643
Cortex_Brain_WT_Untr_2643


description:
Cortex, Brain, Fmr1-KO, Untreated, Mouse ID: 2038
Cortex_Brain_KO_Untr_2038


description:
Cortex, Brain, Fmr1-KO, Untreated, Mouse ID: 4236
Cortex_Brain_KO_Untr_4236


description:
Cortex, Brain, Fmr1-KO, Untreated, Mouse ID: 2221
Cortex_Brain_KO_Untr_2221


title: SW480 HOXA5 overexpressing (OE) rep1

city: Lausanne

first: Paloma

last: Ordóñez

address: Station 19

department: Swiss Experimental Cancer Research Institute

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

hyb_protocol: Following Affymetrix protocols, labeled RNAs were hybridized to [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array.

scan_protocol: Scanning was performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The final processed data are represented by the RMA  signals in Matrix Template.

source_name: SW480 HOXA5 overexpressing (OE)

label_protocol: RNA samples were labeled using the MessageAmp II-Biotin Enhanced kit (Ambion 1791)

growth_protocol: SW480 cells were cultured in Dulbecco´s modified Eagle´s medium plus 10% fetal bovine serum.

extract_protocol: Extraction of total RNA was performed using the microRNA Kit qiagen RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA)

tag: tumor stage

value: Duke's type B

tag: cell line

value: colon cancer cell line SW480

value: HOXA5 overexpression


description:
Cortex, Brain, WT, Untreated, Mouse ID: 2236
Cortex_Brain_WT_Untr_2236

value: wild type

value: embryos (at 17-18 days post conception; pooled littermate)


title: Brain_inattentive_to_noninteracting_30min_rep3

description: Gene expression data from brain of adult male wild-type (AB) zebrafish (11 months old)

value: male

value: AB

tag: tissue

value: brain

value: adult

value: inattentive to non-interacting conspecifics, 30min


title: E25


description:
Cortex, Brain, Fmr1-KO, Untreated, Mouse ID: 2037
Cortex_Brain_KO_Untr_2037


title: SW480 HOXA5 knock down (KD) rep2

source_name: SW480 HOXA5 knock down (KD)

value: HOXA5 knockdown


title: SW480 HOXA5 overexpressing (OE) rep2


title: Surgically removed parathyroid gland from patient Pc

status: Public on Dec 12 2015

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: For all samples a total of 750 ng of labeled cRNA was hybridized at 58°C for 16 hours to the Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) and subsequently washed.

scan_protocol: Fluorescence signals of the hybridized IlLumina Microarrays were detected using BeadStation 500 instrument (Illumina Inc). The raw data were extracted with the BeadStudio Data Analysis Software (Illumina).

data_processing: Bead level data were summarized by Illumina BeadStudio Software v3, imported into R and normalized using the quantile method in the Lumi package. All probes with no signal in any samples were removed from data tables and non-normalized matrix.

source_name: parathyroid gland

label_protocol: RNA was amplified and biotinylated  for hybridization using Ambion® Illumina® TotalPrep™ RNA Amplification Kit according to manufacturer´s instructions. For all samples 200 ng of total RNA was used for amplification. Yields of labeled cRNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was isolated from parathyroid gland using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany).Quality and integrity of  RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Based on morphology and uniform diagnosis of parathyroid glands 29 candidate samples from different patients were selected. Five clinically homogenous subgroups were formed for transcriptome expression screening using Illumina Microarrays technology

tag: patient id

value: Pc

tag: patient type

value: patients with primary hyperparathyroidism


title: Surgically removed parathyroid gland from patient Pb

value: Pb


title: Surgically removed parathyroid gland from patient Pg

value: Pg


title: Surgically removed parathyroid gland from patient DTXa

value: DTXa

value: kidney transplant patients with diffuse hyperplasia


title: Surgically removed parathyroid gland from patient Pa

value: Pa


title: Surgically removed parathyroid gland from patient DTXc

value: DTXc


title: Surgically removed parathyroid gland from patient Pf

value: Pf


title: Surgically removed parathyroid gland from patient DTXb

value: DTXb


title: Surgically removed parathyroid gland from patient Pe

value: Pe


title: Surgically removed parathyroid gland from patient Pd

value: Pd


title: Surgically removed parathyroid gland from patient DHDd

value: DHDd

value: hemodialysis patients with diffuse hyperplasia


title: Surgically removed parathyroid gland from patient DHDe

value: DHDe


title: Surgically removed parathyroid gland from patient DHDc

value: DHDc


title: Surgically removed parathyroid gland from patient DHDa

value: DHDa


title: Surgically removed parathyroid gland from patient DTXd

value: DTXd


title: Surgically removed parathyroid gland from patient NTXd

value: NTXd

value: kidney transplant patients with nodular hyperplasia


title: Surgically removed parathyroid gland from patient NTXa

value: NTXa


title: Surgically removed parathyroid gland from patient NHDg

value: NHDg

value: hemodialysis patients with nodular hyperplasia


title: Surgically removed parathyroid gland from patient NHDd

value: NHDd


title: SW480 HOXA5 knock down (KD) rep1

value: Duke's type B

value: colon cancer cell line SW480

value: HOXA5 knockdown


title: Surgically removed parathyroid gland from patient NHDe

value: NHDe


title: Surgically removed parathyroid gland from patient NHDb

value: NHDb


title: Surgically removed parathyroid gland from patient NHDf

value: NHDf


title: Surgically removed parathyroid gland from patient NHDh

value: NHDh


title: Surgically removed parathyroid gland from patient DHDb

value: DHDb

value: hemodialysis patients with diffuse hyperplasia


title: Surgically removed parathyroid gland from patient NHDa

value: NHDa


title: Surgically removed parathyroid gland from patient NTXc

value: NTXc


title: Surgically removed parathyroid gland from patient NTXe

value: NTXe


title: S4-Th2-24h

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

country: China

institute: Xuzhou Medical University

description: Replicate 4.

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 total volume of 25ul following the manufacturer's instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data was extracted using GeneSpring GX software and quantile normalized using the limma package in the R program.

source_name: Th2, 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75ng total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Naïve CD4+ T cells were isolated from buffy coat from four healthy subjects using the naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany).

extract_protocol: Total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), in the presence of IL-12 (5 ng/ml), IL-2 (10 ng/mL) and anti-IL-4 (5 ug/mL) for Th1 cells, IL-4 (10 ng/ml), IL-2 (10 ng/mL) and anti-IL-12 (5 ug/mL) and anti-IFN-g (5 ug/mL) for Th2 cells. In vitro polarized Th1 and Th2 cells at day 6 were restimulated with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL) in the corresponding polarizing conditions for another 2 days.

tag: subject

tag: disease status

value: healthy

value: whole blood

value: Th2 CD4+ T cells

tag: time

value: 24 hours


title: S3-Th2-8d

description: Replicate 3.

source_name: Th2, 8 days

value: 8 days


title: S4-Th2-3d

description: Replicate 4.

source_name: Th2, 3 days

value: 3 days


title: Surgically removed parathyroid gland from patient NHDc

value: NHDc

value: hemodialysis patients with nodular hyperplasia


title: S3-Th2-6d-technical replicate

description: Replicate 3, technical replicate.

source_name: Th2, 6 days

value: 6 days


title: S4-Th1-6d

description: Replicate 4.

source_name: Th1, 6 days

value: Th1 CD4+ T cells


title: S4-Th2-6h

description: Replicate 4.

source_name: Th2, 6 hours

value: 6 hours


title: S4-Th2-6d-technical replicate

description: Replicate 4, technical replicate.


title: S4-Th2-8d

description: Replicate 4.


title: S4-Th1-24h

description: Replicate 4.

source_name: Th1, 24 hours


title: Surgically removed parathyroid gland from patient NTXb

value: NTXb

value: kidney transplant patients with nodular hyperplasia


title: S3-Th1-6d

description: Replicate 3.


title: S4-Th2-6d

description: Replicate 4.


title: S4-Th1-8d

description: Replicate 4.

source_name: Th1, 8 days


title: S3-Th1-8d

description: Replicate 3.


title: S4-Naive T

description: Replicate 4.

source_name: Naive T cells

value: naive CD4+ T cells


title: S3-Th2-3d

description: Replicate 3.


title: S4-Th1-3d

description: Replicate 4.

source_name: Th1, 3 days


title: E31

source_name: MDA-MB-231 WT

value: MDA-MB-231 WT

value: Hypoxia


title: S3-Th2-6h

description: Replicate 3.


title: S4-Th1-6h

description: Replicate 4.

source_name: Th1, 6 hours


title: S3-Th2-6d

description: Replicate 3.


title: S3-Th1-3d

description: Replicate 3.


title: S3-Th1-24h

description: Replicate 3.


title: S2-Th2-8d

description: Replicate 2.


title: S1-Th2-8d

description: Replicate 1.


title: S3-Naive T

description: Replicate 3.


title: S2-Th1-3d

description: Replicate 2.


title: S2-Th2-24h

description: Replicate 2.


title: S1-Th1-8d

description: Replicate 1.


title: S1-Th2-3d

description: Replicate 1.


title: S2-Th2-3d

description: Replicate 2.


title: S3-Th1-6h

description: Replicate 3.


title: S2-Th2-6h

description: Replicate 2.


title: S2-Th1-6h

description: Replicate 2.


title: S2-Th1-6d

description: Replicate 2.


title: S2-Th2-6d

description: Replicate 2.


title: S1-Th1-6d

description: Replicate 1.


title: S1-Th2-6d-technical replicate

description: Replicate 1, technical replicate.


title: S2-Th1-8d

description: Replicate 2.


title: S2-Th1-24h

description: Replicate 2.


title: S1-Th2-24h

description: Replicate 1.


title: S1-Th2-6d

description: Replicate 1.


title: S1-Th2-6h

description: Replicate 1.


title: S2-Naive T

description: Replicate 2.


title: S1-Th1-3d

description: Replicate 1.


title: P_77_A

hyb_protocol: 1650 ng of Cy3-labelled cRNA from each sample was hybridized to Agilent SurePrint G3 Human Exon 4x180K Microarrays according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x180k array slides.

source_name: Patient 77, allergen challenged

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng total RNA using the Agilent One-Color Microarray-Based Exon Analysis (Low Input Quick Amp Labeling) kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total CD4+ T cells were enriched from PBMCs by MACS negative sorting. Total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: PBMCs from 10 patients with seasonal allergic rhinitis and 10 healthy controls were challenged with diluent and grass pollen extract (ALK-Abelló A/S; 100 μg/mL) for 17 hours.

value: seasonal allergic rhinitis (SAR)

value: CD4+ T cells

tag: treatment

value: allergen


title: HC_33_A

source_name: Healthy control 33, allergen challenged

value: healthy

value: whole blood


title: S1-Naive T

description: Replicate 1.


title: S1-Th1-6h

description: Replicate 1.


title: S1-Th1-24h

description: Replicate 1.

value: 24 hours


title: P_77_D

source_name: Patient 77, diluent challenged

value: diluent


title: HC_33_D

source_name: Healthy control 33, diluent challenged


title: HC_80_A

source_name: Healthy control 80, allergen challenged


title: P_71_A

source_name: Patient 71, allergen challenged


title: mMAC D3

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

description:
iMAC treated with LPS for 24 h
mMAC_donor 3

hyb_protocol: cDNA was hybridized to Affymetrix PrimeView arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using a Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GCS3000 system scanner (Affymetrix, Santa Clara, CA)

data_processing: The data was normalized and transformed using R v3.1 language and Bioconductor package “vsn”. Selecting vsnrma algorithm with all default values for the analysis.

source_name: iMAC treated with LPS for 24 h

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was  subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol

extract_protocol: not provided

value: iMAC


title: S2-Th2-6d-technical replicate

description: Replicate 2, technical replicate.

value: Th2 CD4+ T cells


title: HC_80_D

source_name: Healthy control 80, diluent challenged


title: HC_76_D

source_name: Healthy control 76, diluent challenged


title: P_57_A

source_name: Patient 57, allergen challenged


title: P_71_D

source_name: Patient 71, diluent challenged


title: P_59_A

source_name: Patient 59, allergen challenged


title: mMAC D1

description:
iMAC treated with LPS for 24 h
mMAC_donor 1


title: P_57_D

source_name: Patient 57, diluent challenged


title: P_50_D

source_name: Patient 50, diluent challenged


title: mMAC D2

description:
iMAC treated with LPS for 24 h
mMAC_donor 2


title: P_59_D

source_name: Patient 59, diluent challenged


title: P_50_A

source_name: Patient 50, allergen challenged


title: HC_38_D

source_name: Healthy control 38, diluent challenged


title: HC_38_A

source_name: Healthy control 38, allergen challenged


title: iMAC D3

description:
CD14 cells treated with GM-CSF for 96 h
iMAC_donor 3

source_name: CD14 cells treated with GM-CSF for 96 h


title: Resistant UKRV-Mel-15a-derived melanoma cell clone 18

city: Berlin

first: Frédéric

last: Ebstein

address: Charité Platz 1/Virchowweg 6

department: Institut für Biochemie

institute: Charité Universitätsmedizin Berlin

description:
766
UKRV-Mel-15a-derived clone 18 isolated following exposure to Melan-A/MART-1 (26-35) CTL

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS_v5_450 protocol.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4.0.036 (MAS 5.0) using Affymetrix default analysis settings. Normalization was performed by GCRMA.

source_name: UKRV-Mel-15a-derived clone 18 resistant to cytolysis by Melan-A/MART-1 (26-35) CTL

label_protocol: Total RNA was amplified and labelled using Message AmpII-Biotin enhanced Kit, Ambion.

growth_protocol: The human UKRV-Mel-15a melanoma cell line and the UKRV-Mel-15a-derived clones were cultivated in RPMI supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted from frozen cell pellets using the High Pure RNA Isolation kit according to the manufacturer’s (Roche) protocol.

treatment_protocol: To obtain UKRV-Mel-15a-derived melanoma clones resistant to cytolysis by HLA-A*0201-restricted Melan-A/MART-1 (26-35)-specific CTL, the  UKRV-Mel-15a melanoma cell line was co-cultured for 5 h with a Melan-A/MART-1 (26-35)-specific CTL clone at a ratio of 1:50. Resistant melanoma cells were kept in culture for two weeks, followed by two additional rounds of co-incubation with Melan-A/MART-1 (26-35)-specific CTL. The surviving UKRV-Mel-15a cells were then cloned by limiting dilution at 0,3 cells/well in 96 well plates and the single clones 6, 18 and 30 were expanded for further analysis.

tag: cell line/clone id

value: UKRV-Mel-15a-derived clone 18

value: Metastatic melaoma cell line (isolated from patient after informed consent)

tag: phenotype


title: HC_32_A

source_name: Healthy control 32, allergen challenged


title: Resistant UKRV-Mel-15a-derived melanoma cell clone 30

description:
768
UKRV-Mel-15a-derived clone 30 isolated following exposure to Melan-A/MART-1 (26-35) CTL

source_name: UKRV-Mel-15a-derived clone 30 resistant to cytolysis by Melan-A/MART-1 (26-35) CTL

value: UKRV-Mel-15a-derived clone 30


title: Resistant UKRV-Mel-15a-derived melanoma cell clone 6

description:
763
UKRV-Mel-15a-derived clone 6 isolated following exposure to Melan-A/MART-1 (26-35) CTL

source_name: UKRV-Mel-15a-derived clone 6 resistant to cytolysis by Melan-A/MART-1 (26-35) CTL

value: UKRV-Mel-15a-derived clone 6


title: S3-Th2-24h

description: Replicate 3.

source_name: Th2, 24 hours


title: Parental and sensitive UKRV-Mel-15a melanoma cell line

description:
761
UKRV-Mel-15a cells before exposure to Melan-A/MART-1 (26-35) CTL

source_name: Parental UKRV-Mel-15a melanoma cell line sensitive to cytolysis by Melan-A/MART-1 (26-35) CTL

value: Parental cell line sensitive to cytolysis by Melan-A/MART-1 (26-35) CTL


title: HC_11_A

source_name: Healthy control 11, allergen challenged


title: P_2_A

source_name: Patient 2, allergen challenged


title: HC_32_D

source_name: Healthy control 32, diluent challenged


title: VSMC_LncVSM_2

city: Beijing

first: Lei

last: Yang

address: No.8 Gongtinanlu

department: Medical Research Center

institute: Beijing Chaoyang Hosptial, Capital Mediacal Unversity

description: transfeted with adenovirus lncVSM vector for 24 hours

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BAB) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Adenovirus (Adv)LncVSM 24 hours

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted with Trizol reagents.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Before,the human aorta vascular smooth muscle cells were washed with PBS for three time. The cells were transfected with advenorius vetor could expression full length LncVSM or empty vetor (EV) (1.5X108pfu/ml) with Smooth Muscle Cells (ECM) media conatined 5% FBS. The media were removed and the cells were collected after 24 hours.

value: vascular smooth muscle cells


title: VSMC_LncVSM_3


title: VSMC_LncVSM_4


title: VSMC_Empty_Vector_2

description: transfeted with adenovirus empty vector for 24 hours

source_name: Adenovirus (Adv) empty vector (EC)24 hours


title: VSMC_Empty_Vector_4


title: HC_11_D

source_name: Healthy control 11, diluent challenged


title: iMAC D1

description:
CD14 cells treated with GM-CSF for 96 h
iMAC_donor 1


title: mDC D3

description:
iDC treated with LPS for 24 h
mDC_donor 3

source_name: iDC treated with LPS for 24 h

value: iDC


title: iMAC D2

description:
CD14 cells treated with GM-CSF for 96 h
iMAC_donor 2


title: VSMC_LncVSM_1


title: HC_76_A

source_name: Healthy control 76, allergen challenged


title: VSMC_Empty_Vector_1


title: VSMC_Empty_Vector_3


title: mDC D1

description:
iDC treated with LPS for 24 h
mDC_donor 1


title: P_35_A

source_name: Patient 35, allergen challenged


title: HT29 5x2Gy irradiation replicate 3

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description: HT29 cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Human Gene Expression (v2) 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C  using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned  using Tecan LS Reloaded scanner

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized

source_name: Colorectal cancer HT29 cells cultivated under 3D cell culture conditions, without iradiation

label_protocol: 1µg of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion).  cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Apllied Biosystems).

growth_protocol: Cells were cultured in DMEM (HT29 cell line) or RPMI-1640 (DLD1 cell line) cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2nM glutamine (Gibco), 100 UI/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2. For 3D cell culture conditions, cells were plated in 0.5 mg/ml laminin rich extracellular matrix (GeltrexTM, Gibco) and cell culture medium upon a layer of agarose ir a 24-well cell culture plates.

extract_protocol: Total RNA was isolated from harvested cells using GeneJET RNA Purification Kit (ThermoFisher Scientific) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

treatment_protocol: Cell were treated with single (2 Gy or 10 Gy) or fractionated (5x2 Gy) doses of ionizing radiation

tag: origin

value: Colorectal cancer

value: Control

source_name: Colorectal cancer HT29 cells cultivated under 3D cell culture conditions, irradiated with 5x2 Gy

value: fractionated dose of 5x2Gy


title: mDC D2

description:
iDC treated with LPS for 24 h
mDC_donor 2


title: P_35_D

source_name: Patient 35, diluent challenged

value: seasonal allergic rhinitis (SAR)

value: CD4+ T cells


title: HT29 5x2Gy irradiation replicate 1

description: HT29 cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: iDC D3

description:
CD14 cells treated with IL4/ GM-CSF for 96 h
iDC_donor 3


title: HC_28_D

source_name: Healthy control 28, diluent challenged

value: healthy

value: whole blood


title: HC_28_A

source_name: Healthy control 28, allergen challenged

value: allergen


title: HT29 10Gy irradiation replicate 3

description: HT29 cells were cultivated under 3D cell culture and irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

source_name: Colorectal cancer HT29 cells cultivated under 3D cell culture conditions, irradiated with 10 Gy

value: single dose of 10Gy


title: HT29 10Gy irradiation replicate 1

description: HT29 cells were cultivated under 3D cell culture and irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: HT29 2Gy irradiation replicate 2

description: HT29 cells were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.

source_name: Colorectal cancer HT29 cells cultivated under 3D cell culture conditions, irradiated with 2 Gy

value: single dose of 2Gy


title: HT29 5x2Gy irradiation replicate 2

description: HT29 cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.


title: HC_40_A

source_name: Healthy control 40, allergen challenged


title: HT29 2Gy irradiation replicate 1

description: HT29 cells were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: HT29 2Gy irradiation replicate 3

description: HT29 cells were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.


title: HT29 10Gy irradiation replicate 2

description: HT29 cells were cultivated under 3D cell culture and irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.


title: iDC D1

description:
CD14 cells treated with IL4/ GM-CSF for 96 h
iDC_donor 1


title: iDC D2

description:
CD14 cells treated with IL4/ GM-CSF for 96 h
iDC_donor 2


title: MO D2

description:
peripheral blood isolated CD14+ cells (monocytes)
CD14_monocyte_donor 2


title: MO D1

description:
peripheral blood isolated CD14+ cells (monocytes)
CD14_monocyte_donor 1


title: P_2_D

source_name: Patient 2, diluent challenged

value: diluent


title: Heterozygote 2

city: Jena

first: Abinaya

last: Nathan

address: Beutenberg Str. 11

institute: Leibniz Institute on Aging - FLI

hyb_protocol: cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned.

data_processing:
The data were analysed using Microsoft Excel and the probe IDs were ranked according to up- or downregulation.
Signal intensity (probe IDs where signal intensity < 30 were eliminated)
Programmatic identifier: GeneChip.CallGEBaseCall.1
Algorithm: ExpressionStat 5.0

source_name: Oviduct E2.5

label_protocol: Biotinylated cRNA was preparedl from 1 ug total RNA

growth_protocol: Female mice were mated with wild type males and the oviducts were harvested at embryonic day 2.5 (E2.5)

extract_protocol: The integrity of each RNA sample was first checked with a RNA 6000 Nano chip. 1 μg total RNA per sample was used for the analysis

treatment_protocol: Oviducts were harvested, washed in PBS and RNA was extracted using the RNEasy Mini kit (Qiagen).

tag: genotype

value: Wt1 ko/+

value: oviduct


title: DLD1 5x2Gy irradiation  replicate 3

description: DLD1 cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

source_name: Colorectal cancer DLD1 cells cultivated under 3D cell culture conditions, without iradiation

source_name: Colorectal cancer DLD1 cells cultivated under 3D cell culture conditions, irradiated with 5x2 Gy


title: Heterozygote 3

tag: strain


title: DLD1 5x2Gy irradiation  replicate 2

description: DLD1 cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.


title: HC_40_D

source_name: Healthy control 40, diluent challenged


title: P_3_A

source_name: Patient 3, allergen challenged


title: Heterozygote 1


title: HC_27_D

source_name: Healthy control 27, diluent challenged


title: HC_27_A

source_name: Healthy control 27, allergen challenged


title: P_3_D

source_name: Patient 3, diluent challenged


title: DLD1 10Gy irradiation replicate 3

description: DLD1 cells were cultivated under 3D cell culture and irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

source_name: Colorectal cancer DLD1 cells cultivated under 3D cell culture conditions, irradiated with 10 Gy


title: DLD1 10Gy irradiation replicate 2

description: DLD1 cells were cultivated under 3D cell culture and irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.


title: DLD1 5x2Gy irradiation replicate 1

description: DLD1 cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: s_H3K4_WT_Bcells

type: SRA

city: Copenhagen N

first: Laura

middle: Maarit

last: Pikkupeura

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: Chromatin IP

library_source: genomic

data_processing:
Sequence reads were aligned to the mm9 mouse genome using the standard Illumina Genome Analyzer Pipeline. Only uniquely mapped reads were retained for further anaylsis.
Wig data files were built using SICER by summing sequence read numbers into 200bp non-overlapping windows, with read position shifted 75bp to represent the DNA fragment center. More details as described in Daniel et al., Science, 2010.
Genome_build: mm9
Supplementary_files_format_and_content: wig, bed files

source_name: mouse B cells

growth_protocol: B cells were isolated from spleens of 6- to 14-week old mice by immunomagnetic depletion with α-CD43 beads (Miltenyi Biotech) and stimulated with LPS (25 μg/ml; Sigma), and either α-IgD-dextran (2.5ng/ml; FinaBio) or IL4 (5 ng/ml; Sigma) for 2 days as indicated.

extract_protocol:
2 day stimulated B cells were harvested for chromatin preparation, and ChIP and Illumina sequencing was performed.  Briefly, for histone modification ChIPs, cells were washed and digested with MNase to generate native mononuclesomal chromatin fragments. Chromatin from 10^7 cells was used for each ChIP experiment. DNA was quantified using PicoGreen (Invitrogen) prior to library preparation.
Libraries were prepared by making blut-end DNA with End-It end repair kit (Epicentre #ER81050) according the manufacturer's instructions.  The blunt, phosphorylated ends were treated with Taq DNA polymerase (5U/ul, Invitrogen #18038-042) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~220 bp were band isolated from an agarose gel. The purified DNA quantified using PicoGreen (Invitrogen) and was captured on an Illumina flow cell for cluster generation using Single-Read Cluster Generation Kit v2. Libraries were sequenced on the Genome Analyzer following the SBS Sequencing 36 Cycle Kit v3 protocol.

tag: genotype/variation

tag: antibody


title: P_72_A

source_name: Patient 72, allergen challenged

tag: cell type


title: Wild type 2