title: 5W P1 D10


title: 5W P1 E6

status: Public on Mar 18 2016

type: RNA

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description: H2B-mCherry labeling was induced in Col1a1-tetO-H2B-mCherry mice - 5 weeks after labeling HSCs were isolated. After fluidigm run RT-PCR data was correlated to proliferation history.

data_processing: Ct values calculated and exported using Fluidigm Biomark software. Data normalised by subtraction of the median Ct per cell followed by z-score scaling.

label: EvaGreen

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow HSC

label_protocol: For cDNA synthesis, qScript cDNA supermix (Quanta Bioscience, Carlsbad, CA) was used. Specific target amplification (STA) of genes of interest were performed in multiplex using 96 Delta Gene assays and TATAA preAmp GrandMaster Mix (Tataa Biocenter, Gothenburg, Sweden) using cycling conditions of 95°C for 10 minutes followed by 22 x (96°C for 15 seconds, 60°C for 6 minutes). After STA, samples were treated with Exonuclease I (New England Biolabs, Ipswich, MA) at 37°C for 30 minutes to remove excess primers. Thereafter, inactivation of the enzyme was performed at 80°C for 15 minutes. The cDNA was diluted 5 times with TE low buffer (10mM TrisHCl pH 8.0, 0.1 mM EDTA) prior to qPCR on the BioMark HD (Fluidigm Corporation, San Francisco, CA). All primers were used at 500 nM in the final reaction and EvaGreen Supermix with Low ROX (Bio-Rad, Hercules, CA) was used for detection of the qPCR products. The qPCR was performed using the 96.96 Dynamic Array Integrated Fluidic Circuits (IFC) (Fluidigm Corporation, San Francisco, CA) chip in combination with the BioMark HD with the following thermal cycler program: thermal mix 70°C for 4 minutes followed by 60°C for 30 seconds, hot start 95°C for 60 seconds, PCR cycle 30x (96°C 5 seconds, 60°C for 20 seconds), followed by melting curve analysis.

extract_protocol: Cells were sorted into 96 well plates with 5µl lysis buffer (10mM TrisHCl pH 8.0, 0,1 mM EDTA, 0.1 units/µl SUPERase-In™ (Life Technologies, Carlsbad, CA), 0.5% NP40)  and immediately frozen at -80°C.

treatment_protocol: Single cell suspension of BM cells were FACS sorted to obtain HSC cells

tag: tissue

value: bone marrow

tag: cell type

value: hematopoietic stem cells

tag: genotype

tag: cell subtype


title: 5W P1 E4


title: 5W P1 E7


title: 5W P1 D2


title: 5W P1 E8


title: 5W P1 D3


title: 5W P1 E9


title: 5W P1 D1


title: 5W P1 D4


title: 5W P1 C7


title: 5W P1 F3


title: 5W P1 E11


title: 5W P1 E12


title: 5W P1 C10


title: 5W P1 F1


title: 5W P1 D6


title: 5W P1 C8


title: 5W P1 F2


title: 5W P1 C9


title: 5W P1 F5


title: 5W P1 C11


title: 5W P1 F6


title: 5W P1 C12


title: 5W P1 C1


title: 5W P1F7


title: 5W P1 C2


title: 5W P1 F8


title: 5W P1 F10


title: 5W P1 E10


title: 5W P1 D5


title: 5W P1 C4


title: 5W P1 F11


title: 5W P1 C5


title: 5W P1 C3


title: 5W P1 F4


title: 5W P1 C6


title: 5W P1 F12


title: 5W P1 G2


title: 5W P1 B9


title: 5W P1 G1


title: 5W P1 G3


title: 5W P1 B8


title: 5W P1 B7


title: 5W P1 G5


title: 5W P1 G6


title: 5W P1 B2


title: 5W P1 F9


title: 5W P1 B11


title: 5W P1 B12


title: 5W P1 G8


title: 5W P1 G7


title: 5W P1 G4


title: 5W P1 B4


title: 5W P1 B5


title: 5W P1 B1


title: 5W P1 G10


title: 5W P1 G9


title: 5W P1 G11


title: 5W P1 B6


title: 5W P1 G12


title: 5W P1 H1


title: 5W P1 A7


title: 5W P1 B10


title: 5W P1 H2


title: 5W P1 A12


title: 5W P1 H3


title: 5W P1 H5


title: 5W P1 H4


title: 5W P1 A11


title: 5W P1 B3


title: 5W P1 A10


title: 5W P1 H6


title: 5W P1 H10


title: 5W P1 A5


title: 5W P1 A4


title: 5W P1 H8


title: 5W P1 A3


title: 5W P1 H11


title: 5W P1 A6


title: 2w P2 D7

description: H2B-mCherry labeling was induced in Col1a1-tetO-H2B-mCherry mice - 2 weeks after labeling HSCs were isolated. After fluidigm run RT-PCR data was correlated to proliferation history.


title: 2w P2 E2


title: 2w P2 E3


title: 2w P2 D9


title: 2w P2 D8


title: 2w P2 D10


title: 2w P2 E4


title: 2w P2 D11


title: 2w P2 E5


title: 5W P1 H7


title: UT-SCC-25_Mock irradiated [miRNA]

status: Public on Mar 19 2016

city: Amsterdam

first: Monique

middle: C.

last: de Jong

address: Plesmanlaan 121

department: Dept of Biological Stress Response and Dept. of Radiation Oncology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: hybridized in a TECAN HS4800 Hybridization Station

scan_protocol: The slides were scanned in a DNA Microarray Scanner (Model G250B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11).

data_processing: After subtraction of the mean background signal, arrays were log2 transformed and normalized using the lowess method (using Imagene 6.0 software). Probes with missing data for more than 1 sample were removed. Data from spots for the same reporter were averaged. Annotations were updated (data in matrix norm used for analyses).

organism: Homo sapiens

source_name: HNSCC cell line derived from tongue

label_protocol: Using the Exiqon miRCURY LNA microRNA Array kit (5th generation),  1ug total RNA was labeled with Hy3 and a reference pool of all samples with Hy5.

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 1% L-glutamine, 1% nonessential amino acids, 10% fetal bovine serum and antibiotics. Cells were incubated in humidified air with 5% CO2 at 37°C. Depending on the doubling time, cells were subcultured every 3-14 days to ensure exponential growth. Cells were used for experiments when they were around 60-70% confluent. Preferably low passages (10-20) were used.

extract_protocol: Mock-irradiated cells were harvested for all cell lines, as well as cells at 6 hours after 4 Gy. At the given time points cells were rinsed with ice-cold PBS twice and then collected in RNA-Bee (Campro Scientific). Cells in RNA-Bee were used to extract total RNA. Messenger RNAs were further purified using the Rneasy Mini Kit and the RNase-Free DNase Set from Qiagen. The RNA was isolated and DNAse treated using the spin columns according to the manufacturer’s instructions. The Agilent 2100 bioanalyzer was used to confirm the presence of intact RNA.

treatment_protocol: Cells were irradiated using a 137Cs irradiation unit with a dose rate of  0.662 Gy/min.

tag: cell line

value: Head and neck squamous cell carcinoma (HNSCC) cell line

tag: source subsite

value: tongue

tag: time from (mock) irradiation to harvest of rna

tag: irradiation dose (gy)

tag: radiosensitivity (auc)

tag: radiosensitivity (auc) binary

tag: passage tested

tag: gender

value: M

source_name: Pool of all HNSCC cell line samples


title: 5W P1 A2


title: 2w P2 D12


title: 2w P2 E6


title: 2w P2 E8


title: 2w P2 D2


title: 2w P2 E7


title: 2w P2 D1


title: 2w P2 D4


title: 2w P2 E1


title: 2w P2 D3


title: 2w P2 E9


title: 2w P2 E12


title: 2w P2 E11


title: 2w P2 D6


title: 2w P2 E10


title: 2w P2 F1


title: 2w P2 D5


title: 2w P2 F2


title: 2w P2 F3


title: 2w P2 C7


title: 2w P2 C8


title: 2w P2 C10


title: 2w P2 F4


title: 2w P2 F5


title: 2w P2 C11


title: 2w P2 C12


title: 2w P2 F6


title: 2w P2 C1


title: 2w P2F7


title: 2w P2 F8


title: 2w P2 C5


title: 2w P2 C3


title: 2w P2 C4


title: 2w P2 F10


title: 2w P2 F11


title: 2w P2 F9


title: 2w P2 G3


title: 2w P2 B9


title: 2w P2 C6


title: 2w P2 G1


title: 2w P2 F12


title: 2w P2 G4


title: 2w P2 C2


title: 2w P2 B11


title: 2w P2 G2


title: 2w P2 B7


title: 2w P2 B12


title: 2w P2 B1


title: 2w P2 G5


title: 2w P2 G7


title: 2w P2 B8


title: 2w P2 B2


title: 2w P2 B3


title: 2w P2 G8


title: 2w P2 G9


title: 2w P2 G6


title: 2w P2 G10


title: 2w P2 B5


title: 2w P2 H2


title: 2w P2 A8


title: 2w P2 A10


title: 2w P2 B4


title: 2w P2 H1


title: 2w P2 A7


title: 2w P2 B6


title: 2w P2 H6


title: 2w P2 H5


title: 2w P2 H4


title: 2w P2 G12


title: 2w P2 A11


title: 2w P2 A9


title: 2w P2 A12


title: 2w P2 H8


title: 2w P2 H9


title: 2w P2 A2


title: 2w P2 H10


title: 2w P2 A3


title: 2w P2 A5


title: 2w P2 H11


title: 2w P2 G11


title: 2w P2 H3


title: 2w P2 A6


title: 2w P1 D7


title: 2w P1 E1


title: 2w P1 D8


title: 2w P2 H7


title: 2w P1 D9


title: 2w P2 A4


title: 2w P1 E2


title: 2w P1 E3


title: 2w P1 D10


title: 2w P1 D12


title: 2w P1 E4


title: 2w P1 E5


title: 2w P1 E6


title: 2w P2 B10


title: 2w P1 E7


title: 2w P1 D1


title: 2w P1 E9


title: 2w P1 D2


title: 2w P1 E8


title: 2w P1 D3


title: 2w P1 E10


title: 2w P1 D4


title: 2w P1 D5


title: 2w P1 E11


title: 2w P1 D6


title: 2w P1 E12


title: 2w P1 C7


title: 2w P1 F1


title: 2w P1 F2


title: 2w P1 C9


title: 2w P1 F3


title: 2w P1 F5


title: 2w P1 C10


title: 2w P1 C11


title: 2w P1 F6


title: 2w P1 F4


title: 2w P1 F8


title: 2w P1 C5


title: 2w P1 C2


title: 2w P1 F9


title: 2w P1 D11


title: 2w P1 F11


title: 2w P1 F10


title: 2w P1 C4


title: 2w P1 C3


title: 2w P1 C8


title: 2w P1 C6


title: 2w P1 C12


title: 2w P1 C1


title: 2w P1F7


title: 5W P2 D3


title: 2w P1 B8


title: 2w P1 G2


title: MCF-10a - pMSCV-GNA13_1

city: SIngapore

first: Suhail Ahmed Kabeer

last: Rasheed

address: 8 College Road

department: Programme in Cancer and Stem Cell Biology

country: Singapore

institute: Duke-NUS Medical School

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: MCF-10a expressing pMSCV GNA13

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

extract_protocol: RNA was extracted with QUAGEN RNAeasy mini kit, followed by clean-up and DNase I treatment as per the  protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Breast Epithelial cells


title: MCF-10a - pMSCV-Vector_2

description: Replicate 2

source_name: MCF-10a expressing pMSCV Vector


title: 2w P1 G3


title: 2w P1 F12


title: MCF-10a - pMSCV-GNA13_3

description: Replicate 3


title: 2w P1 B7


title: MCF-10a - pMSCV-Vector_1

description: Replicate 1


title: BMDM_SA_20h_rep1

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

country: USA

institute: University of California, San Francisco

description: saturated fatty acid

hyb_protocol: The labeled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA) according to the manufacturer's technical manual.

scan_protocol: Signal intensities of fluorescent images produced during GeneChip hybridizations were read by an Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).

data_processing: Data were RMA normalized, log2 normalized, and filtered for genes lacking expression above log2 signal intensity in any group. Data were additionally quantile normalized using Limma and median centered across samples. Differentially expressed genes were identified using Significance Analysis of Microarrays using two-class unpaired comparisons with 3% false discovery rate (FDR) and 1.5-fold change cutoffs.

source_name: 20 h SA-treated BMDMs

label_protocol: The NuGEN Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation, and biotin-labeling of ~10 ng input RNA.

growth_protocol: Bone marrow-derived macrophages (BMDMs) were differentiated from wild type C57Bl/6 bone marrow using 10 ng/mL M-CSF (Peprotech) in RPMI 1640 (Gibco) supplemented with 10% FBS (Atlanta Biologicals) and penicillin/streptomycin.  M-CSF was removed after 6 days, and adherent cells were treated 1-3 days later.

extract_protocol: Total RNA was isolated using Trizol according to the manufacturer's instructions and further purified using the Zymo RNA Clean & Concentrator kit.  Purified DNase-treated total RNA was analyzed for quality using chip-based capillary electrophoresis (Bioanalyzer, Agilent, Inc) and quantity and purity was determined with a NanoDrop spectrometer.

treatment_protocol: Replicate wells of BMDMs (n=3-4) were treated for 5 or 20 hours with either 125 μM bovine serum albumin (BSA; vehicle), 1 ng/mL lipopolysaccharide (LPS; Sigma Aldrich L4391), 250 μM oleic acid (OA), or 250 μM stearic acid (SA). OA and SA (Nuchek Prep) were complexed in a 2:1 molar ratio with fatty acid-free, low-endotoxin BSA (Sigma Aldrich A8806).

tag: strain

value: C57/Bl6 wild type

value: Bone marrow-derived macrophages

tag: treatment

value: SA

tag: duration

value: macrophage


title: BMDM_SA_20h_rep2

description: saturated fatty acid


title: MCF-10a - pMSCV-GNA13_2

description: Replicate 2


title: BMDM_SA_5h_rep3

description: saturated fatty acid

source_name: 5 h SA-treated BMDMs

value: 5 h


title: BMDM_SA_5h_rep4

description: saturated fatty acid


title: MCF-10a - pMSCV-Vector_3

description: Replicate 3


title: BMDM_SA_5h_rep1

description: saturated fatty acid


title: BMDM_OA_20h_rep1

description: unsaturated fatty acid

source_name: 20 h OA-treated BMDMs

value: OA


title: BMDM_SA_5h_rep2

description: saturated fatty acid


title: BMDM_OA_20h_rep4

description: unsaturated fatty acid


title: BMDM_OA_5h_rep4

description: unsaturated fatty acid

source_name: 5 h OA-treated BMDMs


title: BMDM_OA_20h_rep2

description: unsaturated fatty acid


title: 2w P1 G1


title: 2w P1 B9


title: BMDM_OA_5h_rep2

description: unsaturated fatty acid


title: BMDM_SA_20h_rep3

description: saturated fatty acid


title: BMDM_OA_20h_rep3

description: unsaturated fatty acid


title: BMDM_SA_20h_rep4

description: saturated fatty acid


title: BMDM_OA_5h_rep1

description: unsaturated fatty acid


title: BMDM_OA_5h_rep3

description: unsaturated fatty acid


title: 2w P1 B10


title: 2w P1 B12


title: 2w P1 G7


title: 2w P1 B1


title: 2w P1 B11


title: 2w P1 B2


title: BMDM_LPS_5h_rep3

description: pro-inflammatory positive control

source_name: 5 h LPS-treated BMDMs

value: LPS


title: BMDM_LPS_5h_rep2

description: pro-inflammatory positive control


title: BMDM_BSA_5h_rep3

description: vehicle control

source_name: 5 h BSA-treated BMDMs

value: BSA


title: BMDM_LPS_5h_rep1

description: pro-inflammatory positive control


title: 2w P1 G8


title: 2w P1 B3


title: 2w P1 G4


title: BMDM_BSA_5h_rep2

description: vehicle control


title: 2w P1 B4


title: 2w P1 G12


title: 2w P1 H1


title: 2w P1 G11


title: 2w P1 B6


title: 2w P1 A7


title: 2w P1 H2


title: BMDM_LPS_5h_rep4

description: pro-inflammatory positive control


title: 2w P1 G10


title: 2w P1 H3


title: BMDM_BSA_5h_rep1

description: vehicle control


title: 2w P1 G9


title: 2w P1 A9


title: 2w P1 A10


title: 2w P1 B5


title: 2w P1 H4


title: 2w P1 A2


title: 2w P1 A12


title: 2w P1 A8


title: 2w P1 A3


title: 2w P1 H7


title: 2w P1 H8


title: Wild-type Replicate 1 vs Brdt KO Replicate 1

city: Tel Aviv

first: Shimi

last: Barda

address: 6 Weizman Street

department: Lis Maternity Hospital

country: Israel

institute: Tel Aviv Sourasky Medical Center

hyb_protocol: The hybridization was performed with canine-specific AMADID Release GE 4x44K microarrays (Agilent), using a Gene Expression Hybridization Kit in a hybridization oven, according to the manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent)

source_name: pooled Wild-type pituitary tissue

label_protocol: Total RNA was amplified and labeled with Cy3 or Cy5 using the Low Input Quick Amp Labeling Kit, Two-Color (Agilent), following the manufacturer's instructions.

growth_protocol: Heterozygous Brdt tm1a (EUCOMM) Wtsi mice (C57BL/6) were purchased from the International Knockout Mouse Consortium, Welcome Trust Sanger Institute, UK. The ‘knockout-first’ allele (tm1a) contains an IRES: lacZ trapping cassette and a floxed promoter-driven neo cassette inserted into the fourth intron of the Brdt gene and disrupting its function. Mice were housed and maintained in plastic cages in the animal facility at Tel Aviv Sourasky Medical Center, in a temperature-controlled room (21-25oC) with a 12-h light/12-h dark cycle.

extract_protocol: RNA extraction was performed using the Trizole reagent according to the manufacturer’s instructions (Sigma, St. Louis, MO). RNA purity and integrity were analyzed by Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).

tag: strain background

tag: genotype/variation

value: wild type

value: male

tag: age

value: 8 weeks

value: pituitary

source_name: pooled Brdt KO pituitary tissue

value: Brdt-/-


title: Wild-type Replicate 2 vs Brdt KO Replicate 2

tag: tissue


title: 8wks WT Bff

city: San Antonio

first: Rong

last: Li

state: TX

address: 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

description:
Brca1f/f 3 animals
WT_Bff 8wks

source_name: CD24+ primary mammary epithelial cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit AMIL1791 for Illumina arrays

extract_protocol: RNA was extracted using QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Mixed

value: Mouse mammary gland

tag: genotype

tag: cell type

value: CD24+ primary mammary epithelial cells


title: 2w P1 H9

value: bone marrow

value: hematopoietic stem cells

tag: cell subtype


title: 8wks DKO

description:
Cobra1 and Brca1 KO 3 animals
DKO 8wks

value: Cobra1 and Brca1 KO


title: 8wks BKO

description:
Brca1 Knockout 3 animals
BKO 8wks

value: Brca1 Knockout


title: 2w P1 H10


title: 2w P1 A4


title: 2w P1 A5


title: 6wks BKO

description:
Brca1 Knockout 3 animals
BKO 6wks

value: 6 weeks


title: 2w P1 A6


title: 2w P1 H11


title: 2w P1 A11


title: 8wks WT Dff

description:
Cobra1f/f Brca1f/f 3 animals
WT_Dff 8wks

value: Cobra1f/f Brca1f/f


title: 8wks CKO

description:
Cobra1 Knockout 3 animals
CKO 8wks

value: Cobra1 Knockout


title: 6wks WT Bff

description:
Brca1f/f 3 animals
WT_Bff 6wks


title: 6wks WT Dff

description:
Cobra1f/f Brca1f/f 3 animals
WT_Dff 6wks


title: 6wks WT Cff

description:
Cobra1f/f 3 animals
WT_Cff 6wks


title: 6wks CKO

description:
Cobra1 Knockout 3 animals
CKO 6wks


title: 35S::JMJ24_rep3

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

hyb_protocol: Performed by Atlas Biolabs, Berlin, Germany.

data_processing: Data were rma normalized using the R/Bioconductor affy package.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown in long day conditions on soil in a greenhouse or on GM plates (1 % (w/v) glucose) at 23 °C day/ 21 °C night cycles for 10-14 d before analysis.

extract_protocol: RNA was extracted from 9 day old seedlings using a hot-phenol RNA extraction protocol and then purified over an Rneasy Plant RNA extraction column (Qiagen) and processed for hybridization of Affymetrix ATH1 GeneChips at Atlas Biolabs, Berlin, Germany.

treatment_protocol: The jmj24 (At1g09060, N521260) mutant was obtained from the European Arabidopsis Stock Centre. 35S::JMJ24 line was generated by Agrobacterium-mediated transformation.


title: 4wks CKO

description:
Cobra1 Knockout 3 animals
CKO 4wks

value: 4 weeks


title: WT_rep1

scan_protocol: Performed by Atlas Biolabs, Berlin, Germany.


title: WT_rep2

label_protocol: Performed by Atlas Biolabs, Berlin, Germany.


title: 4wks WT Dff

description:
Cobra1f/f Brca1f/f 3 animals
WT_Dff 4wks


title: 4wks WT Cff

description:
Cobra1f/f 3 animals
WT_Cff 4wks


title: 6wks DKO

description:
Cobra1 and Brca1 KO 3 animals
DKO 6wks


title: WT_rep3


title: jmj24_rep3


title: 4wks DKO

description:
Cobra1 and Brca1 KO 3 animals
DKO 4wks


title: 35S::JMJ24_rep2


title: jmj24_rep1


title: jmj24_rep2


title: 35S::JMJ24_rep1


title: NRP-V7_3

status: Public on Mar 17 2016

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description:
NRP-V7
SAMPLE 6

data_processing: Raw microarray expression data was transformed (variance-stabilizing transformation) and normalized (quantile method) using the Lumi package from R and Bioconductor (19,20)(http://www.R-project.org).  After quality control there were 11 samples including replicates; 5 for the NRP-V7-reactive cells, 3 for the phenotype+, and 3 for LCMV-reactive cells.  The expression data was further filtered by removing transcripts with a detection p-value cut-off >0.01. Genes with multiple probe-sets were collapsed by choosing the probe-set with the highest average expression across samples

organism: Mus sp.

source_name: splenocytes

label_protocol: The cells were labeled with LIVE/DEAD fixable stain, tetramer, and antibodies to CD44, CD62L, PD-1, and CXCR3.

growth_protocol: Single cell suspensions of splenocytes were prepared from pools of 4-6, 10 to 18 week-old NOD` or NOD mice 9 days after infection with LCMV virus

extract_protocol: They were pooled and RNA was isolated using RNeasy kit

treatment_protocol: Single cell suspensions of splenocytes were infected with LCMV virus

value: NRP-V7 tetramer+ CD8+ T cells


title: NRP-V7_2

description:
NRP-V7
SAMPLE 5


title: LCMV_2

description:
LCMV
SAMPLE 2

value: LCMV antigen specific CD8+ T


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 3.2 pH 7

city: ottawa

first: ALAIN

last: STINTZI

state: ONTARIO

address: 451 SMYTH ROAD

department: BIOCHEMSISTRY, MICROBIOLOGY AND IMMUNOLOGY

country: Canada

institute: UOTTAWA

hyb_protocol: not provided

scan_protocol: The signal intensities of each spot were collected using ScanArray software (PerkinElmer).

data_processing: The spot intensities were normalized via locally weighted linear regression (LOWESS) using MIDAS

organism: Campylobacter jejuni

source_name: US-C. jejuni  NCTC 11168

label_protocol: The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 350 μL of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 10000 X g, followed by washing with sterile ddH2O. Following concentration and resuspension into NaHCO3 pH 9.0, the aminoallyl-labeled cDNA was coupled to either Cy3 (used to label control samples) or Cy5 dye (used to label test samples) by adding 10 μL of Cy3  or Cy5 (GE Healthcare) in dimethyl sulfoxide followed by incubation in the dark for 1 h at room temperature. Next, the fluorescently labeled cDNA was purified using QIAquick PCR purification kit according to the manufacturer’s instructions (Qiagen). Fluorescent Cy3- and Cy5-labeled cDNAs were combined and the fluor-labeled cDNA mix was dried under vacuum with a SpeedVac and resuspended in 15.14 μL of water, to which the following was added: 2.5 μL of salmon sperm DNA (10 mg/mL), 9 μL of 20X SSC, 0.36 μL of 10% SDS, and 9 μL of formamide.

growth_protocol: C. jejuni strains was grown to logarithmic phase in biphasic MH medium (pH 7.4) under microaerophilic conditions. Bacterial cells were exposed to acid stress at pH3 or 4 for 8 min in HCl-adjusted MH broth

extract_protocol: 10 μg of total RNA samples from each control (C. jejuni NCTC11168) and test sample ( C. jejuni ∆Fur) were converted to cDNA using Superscript II (Invitrogen); 10 µg of random hexamers (Amersham Biosciences); a dNTP mixture of 0.5 mM dGTP, dATP and dCTP each; 0.16 mM dTTP; and 0.34 mM aminoallyl-dUTP. Aminoallyl-dUTP was incorporated in the reaction to permit the labeling of the cDNA with the monoreactive fluors indocarbocyanine (Cy3) and indodicarbocyanine (Cy5) (GE Healthcare)

treatment_protocol: Total RNA was extracted using a hot phenol-chloroform method

value: Unstressed

tag: ph

value: pH 7 for 8 min

source_name: US-C.jejuni delta fur

value: delta fur

value: unstressed


title: NRP-V7_5

description:
NRP-V7
SAMPLE 8


title: PhenotypePositive_2

description:
Phenotype Positive
SAMPLE 10

value: CD8+ T Phenotype Positive


title: PhenotypePositive_1

description:
Phenotype Positive
SAMPLE 9


title: NRP-V7_4

description:
NRP-V7
SAMPLE 7


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 3.1 pH 7


title: PhenotypePositive_3

description:
Phenotype Positive
SAMPLE 11


title: 8wks WT Cff

description:
Cobra1f/f 3 animals
WT_Cff 8wks

value: Mixed

value: 8 weeks

value: Mouse mammary gland


title: LCMV_3

description:
LCMV
SAMPLE 3


title: NRP-V7_1

description:
NRP-V7
SAMPLE 4


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 2.3 pH 7


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 2.2 pH 7


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 1.2 pH 7

source_name: AS-C.jejuni delta fur


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 2.1 pH 7


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 1.3 pH 7


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 3.3 pH 7


title: Control unstressed C. jejuni NCTC 11168 VS Test unstressed C. jejuni∆fur_Exp 1.1 pH 7


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 3.2 pH 4

source_name: AS-C. jejuni  NCTC 11168

value: Acid-stressed

value: pH 4 for 8 min


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 3.3 pH 4


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 3.1 pH 4


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 2.2 pH 4


title: JS15_GlutaCandesartan_3

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Rat GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

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

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files.

label: Biotin

organism: Rattus norvegicus

source_name: Rat Primary cerebellar granule cells

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Rat HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: Brains were dissected immediately and the cerebella were collected and placed in ice-cold Hank’s balanced salt solution (HBSS) (Invitrogen, Carlsbad, CA). After removal of the meninges, the cerebella were dispersed into the same buffer containing 0.025% trypsin (Invitrogen) and digested for 15 min at 37ºC. Trypsin digestion was stopped by adding a same volume of Dulbecco’s Modified Eagle medium (DMEM) (Invitrogen), supplemented with 10% FBS (Invitrogen) and 0.1 mg/ml DNase I (Sigma-Aldrich, St. Louis, MO). After gentle trituration, digested tissues were centrifuged at 1000 X rpm for 5 min. The cell pellets were resuspended in the complete Neurobasal culture medium supplemented with 2% B27 (Invitrogen) and 0.5 mM GlutaMax (Invitrogen). After filtration through a 70 mm cell restrainer (BD Falcon, Vernon Hills, IL), cells were plated at a density of 1 X 106 cells/ml onto poly-L-lysine coated plates (Becton Dickinson and Company, Franklin Lakes, NJ) or chamber glass slides (Nalge Nunc International, Naperville, IL). Cultures were incubated in a humidified atmosphere of 5% CO2-95% air at 37ºC. Cytosine arabinofuranoside (Invitrogen) (10 mm) was added to the cultures 24 h after plating to arrest the growth of non-neuronal cells. Cultures 6 to7 days in vitro were used in this study.

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Primary cerebellar granule cells (CGCs) were treated with DMSO, Glutamate, Candesartan or Glutamate +candesartan

value: Glutamate+Candesartan

value: cerebellum

value: Primary cerebellar granule cells


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 1.3 pH 4


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 2.1 pH 4


title: JS14_GlutaCandesartan_2


title: JS13_GlutaCandesartan_1


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 1.1 pH 4


title: JS16_GlutaCandesartan_4


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 1.2 pH 4


title: JS10_100uMGluta_2

value: Glutamate


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 3.3 pH 3

value: pH 3 for 8 min


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 2.3 pH 4


title: JS06_10uMCandy_2

value: Candesartan


title: LCMV_1

description:
LCMV
SAMPLE 1

value: LCMV antigen specific CD8+ T


title: JS08_10uMCandy_4


title: JS11_100uMGluta_3


title: JS09_100uMGluta_1


title: JS07_10uMCandy_3


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 3.2 pH 3


title: JS01_Ctrl_1


title: JS02_Ctrl_2


title: JS05_10uMCandy_1


title: JS12_100uMGluta_4


title: JS03_Ctrl_3


title: NT siRNA Rep2

city: Helsinki

first: Markku

last: Heikinheimo

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

description: replicate 2

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay Guide, Rev. A

data_processing: quantile normalization was performed using Illumina Genome Studio software

source_name: TM4 cell line

label_protocol: lllumina®  TotalPrep RNA Labeling Kit-protocol, revision E (Ambion)

growth_protocol: TM4 cells were cultured in cultured in DMEM/F12+GlutaMAX media supplemented with 10% FBS, 25 mM HEPES, and 100 mg/L penicillin/streptomycin (all from Life Technologies).

extract_protocol: RNA was extracted with Nucleospin RNA/Protein kit (Machrey-Nagel, Dueren, Germany), followed by clean-up with NucleoSpin RNA Clean-up XS kit (Machrey-Nagel, Düren, Germany). RNA quality was assessed via Bioanalyzer (Agilent, Santa Clara, CA). Array hybridization was performed using an Illumina MouseWG-6 v2.0 oligonucleotide BeadChip.

treatment_protocol: TM4 cells passage 13 were transiently transfected in the absence of antibiotics with a pool of 4 siRNAs targeting Gata4 (5’-AGAGAAUAGCUUCGAACCA-3’, 5’-GGAUAUGGGUGUUCCGGGU-3’, 5’-CUGAAUAAAUCUAAGACGC-3’, 5’-GGACAUAAUCACCGCGUAA-3’) or with non-targeting control siRNA (5’-UGGUUUACAUGUCGACUAA-3’; all from Dharmacon, Lafayette, CO) using Lipofectamine® RNAiMAX transfection reagent in Opti-MEM (Life Technologies) at a final concentration of 0.1 µM

tag: cell line

value: Sertoli cell line TM4

tag: passage #

value: control


title: NT siRNA Rep1

description: replicate 1


title: NT siRNA Rep3

description: replicate 3


title: Gata4 siRNA Rep3

description: replicate 3

value: siRNA-mediated Gata4 inhibition


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 3.1 pH 3

value: delta fur


title: Gata4 siRNA Rep2

description: replicate 2


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 2.2 pH 3


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 2.1 pH 3


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 1.3 pH 3


title: JS04_Ctrl_4


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 2.3 pH 3


title: 2 days TNFα rep2

city: Boston

first: Daniel

last: Okin

state: MA

address: 55 Fruit St, BUL148

department: Department of Medicine, Division of Pulmonary and Critical Care

institute: Massachusetts General Hospital

description: replicate 2

data_processing: Data were processed using the GenePattern Illumina pipeline

source_name: Mouse primary hepatocytes_2days_TNFα

growth_protocol: Cells were grown on collagen coated tissue-culture plates and maintained in Williams' E media supplemented with 5% Fetal Calf Serum, 2mM L-glutamine, 10mM HEPES, 200U/mL penicillin, 200µg/mL streptomycin, 8µg/mL gentamycin, 50nM dexamethasone, 1nM insulin

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

treatment_protocol: Cells were treated with 2ng/mL recombinant murine TNFα for either 2 hours or 2 days

value: liver

value: primary hepatocytes

value: male


title: 2 hours TNFα rep2

description: replicate 2

source_name: Mouse primary hepatocytes_2hours_TNFα


title: 2 days TNFα rep1

description: replicate 1


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 1.1 pH 3


title: Control acid-stressed C. jejuni NCTC 11168 VS Test acid-stressed C. jejuni∆fur_Exp 1.2 pH 3


title: 2 hours TNFα rep1

description: replicate 1


title: Cont 0hr

city: Tokorozawa

first: Motoshi

last: Nagao

state: Saitama

address: 4-1 Namiki

department: Department of Rehabilitation for the Movement Functions

country: Japan

institute: Research Institute, National Rehabilitation Center for Persons with Disabilities

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 1.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tools 1.15.0 software, and obtained normalized intensity values.

source_name: Control virus-infected mouse E11.5 NPCs, cultured in the presence of FGF2 and EGF

label_protocol: The cRNA was amplified, labeled using GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

growth_protocol: NPCs derived from E11.5 mouse forebrains were maintained in the presence of FGF2 and EGF. After infection, the virus-infected NPCs were cultured with or  without  FGF2 and EGF.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: developmental stage

value: brain

value: neural precursor cells

tag: infection

value: control retrovirus


title: Unstimulated rep2

description: replicate 2

source_name: Mouse primary hepatocytes_unstimulated


title: Z20 0hr

source_name: Zbtb20 virus-infected mouse E11.5 NPCs, cultured in the presence of FGF2 and EGF

value: Zbtb20 retrovirus


title: Gata4 siRNA Rep1

description: replicate 1


title: Z20 24hr

source_name: Zbtb20 virus-infected mouse E11.5 NPCs, cultured in the absence of FGF2 and EGF


title: Cont 24hr

source_name: Control virus-infected mouse E11.5 NPCs, cultured in the absence of FGF2 and EGF


title: Unstimulated rep1

description: replicate 1


title: CSC-PNA

city: Bangkok

first: Preeyaporn

middle: Plaimee

last: Phiboonchaiyanan

address: 254  Phyathai Rd. Wangmai Patumwan Bangkok

department: Department of Pharmacology and Physiology

country: Thailand

institute: Faculty of Pharmaceutical Sciences, Chulalongkorn University

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

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

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

source_name: PNA-treated CSC-rich

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

growth_protocol: Cancer stem cell-rich (CSC-rich) population was isolated from a non-small cell lung cancer (NSCLC) cell line, NCI-H460, by selectively propagating the cells in a spheroid culture condition. The parental wild type H460 and CSC-rich cells were maintained at 37°C in 5% CO2 under sterile conditions in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco, USA). Fetal bovine serum (10%) was supplemented for parental wild type H460 culture.

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

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

value: cancer stem cell-rich cells derived from non-small cell lung cancer cell line


title: WT-ctr

source_name: WT control

value: non-small cell lung cancer cell line


title: CSC-ctr

source_name: CSC-rich control


title: CSC-SC

source_name: Scramble-treated CSC-rich


title: IL-4 DCs rep2

city: Edegem

first: Heleen

middle: Hugo

last: Van Acker

address: Wilrijkstraat 10

department: Faculty of Medicine and Health Sciences

country: Belgium

institute: University of Antwerp

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000 7G from Affymetrix.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings using the RMA method.

source_name: Mature IL-4 DCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll density gradient centrifugation (Ficoll-Paque PLUS; GE Healthcare, Diegem, Belgium). Positive magnetic cell selection was used for purification of CD14+ monocytes

extract_protocol: Total RNA was extracted from 7-11x106 mature IL-15 DCs and IL-4 DCs, of three independent donors, using RLT lysis buffer (Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions.

treatment_protocol: Monocytes were seeded in Roswell Park Memorial Institute medium (RPMI; Gibco Paisley, UK) supplemented with 2.5 % heat-inactivated human AB serum (Invitrogen, Merelbeke, Belgium) at a final concentration of 1.0-1.2x106 cells/mL. Differentiation was induced with 800 IU/mL granulocyte macrophage colony-stimulating factor and 200 ng/mL IL-15 (Immunotools, Friesoythe, Germany) to obtain immature IL-15 DCs. A TLR-activating maturation cocktail, comprising R848 (3 µg/mL; Alexis Biochemicals, San Diego, USA), tumor necrosis factor-α (2.5 ng/mL), interferon-γ (250 ng/mL; Immunotools) and prostaglandin E2 (1 µg/mL; Pfizer, Puurs, Belgium), was added after 24-48 hours of differentiation for 18-20 hours. Monocytes were cultured with 800 IU/mL GM-CSF (Gentaur; Brussels, Belgium) and 20 ng/mL IL-4 (Gentaur; Brussels, Belgium) in order to generate immature IL-4 DCs.

tag: individual

value: healthy donor 2

value: peripheral blood

value: Mature IL-4 DCs


title: IL-4 DCs rep3

value: healthy donor 3


title: WT-PNA

source_name: PNAs-A15-treated WT


title: WT-SC

source_name: Scramble-treated WT


title: Dox 12h_3

city: Oslo

first: Ian

last: Mills

address: Gaustadalleen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

hyb_protocol: Hybridisation of cRNA onto the Illumina HumanHT-12 v.4 Expression BeadChips (Illumina Inc, California, USA) was carried out as per manufacturer's instructions

scan_protocol: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Here the quality of each array and scan is investigated, and text files with both non-normalized and quantile normalized data exported.

data_processing: Data extraction, quantile normalization and initial quality control of the bead summary raw data were performed using GenomeStudio v2011.1 from Illumina and the Gene Expression module v1.9.0. The data were annotated using the HumanHT-12_V4_0_R2_15002873_B.bgx annotation file from Illumina.

label: Illumina Total Prep 96 RNA Amp Kit

source_name: LNCaP MYC

label_protocol: Labelling was performed with Illumina® TotalPrep™-96 RNA Amplification Kit according to manufacturer's instructions

growth_protocol: LNCaP cells were maintained in RPMI media supplemented with 10% FBS.

extract_protocol: RNA was collected using the Rneasy kit (Qiagen) according to manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Cells were kept in phenol red-free RPMI +10% charcoal-stripped serum (CSS) for 72 h prior to treatment with 2 ug/mL Doxycycline (Dox) or vehicle

value: LNCaP MYC

tag: treament

value: Dox 12h


title: IL-15 DCs rep3

source_name: Mature IL-15 DCs

value: Mature IL-15 DCs


title: Dox 12h_1


title: Dox 5h_3

value: Dox 5h


title: EtOH 12h_3

value: EtOH 12h


title: IL-4 DCs rep1

value: healthy donor 1


title: Dox 12h_2


title: Dox 5h_1


title: IL-15 DCs rep1


title: EtOH 5h_1

value: EtOH 5h


title: EtOH 12h_1


title: EtOH 12h_2


title: Dox 5h_2


title: meristems; fertile plants; arrested

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Microarray meristems arrested fertile plants

hyb_protocol: Hybridization of the Affymetrix ATH1 microarrays and subsequent washing and scanning were performed at the FGCZ or the Biozentrum Basel according to the manufacturer's instructions.

scan_protocol: Scanning were performed at the FGCZ or the Biozentrum Basel according to the manufacturer's instructions.

data_processing: Microarrays were normalized (invariant-set normalization) and preprocessed (PM-only model) using the dChip software version 2010 (Li and Wong, 2001).

source_name: laser-dissected shoot apex (meristematic region)

label_protocol:
RNA extracted from laser-microdissected tissues was amplified using the Arcturus® RiboAmp® Plus kit (Applied Biosystems) according to the manufacturer’s instruction, but with the second in-vitro transcription performed using Affymetrix 3’IVT labeling kit reagents.
For whole tissue samples, RNA labeling for microarray hybridizations was performed using the GeneAtlas 3'IVT Express Kit (Affymetrix)

growth_protocol: Plants of Arabidopsis thaliana accessions Landsberg erecta (L-er) and male sterile 1 (ms1-1, NASC-Code N75, see www.arabidopsis.info) were grown on soil (ED73, Universalerde, Germany) covered with a thin quartz sand layer, in a growth chamber at the Institute of Evolutionary Biology and Environmental Studies under 16 hours light (at 20°C and 5 kLux) and 8 hours dark (at 16°C) and 60% humidity. The positions of individual plants were fully randomized, and regularly changed (at least every 10 days).

extract_protocol:
For laser-microdissected samples, the total RNA was extracted using the PicoPure RNA isolation kit (Life Technologies), including the DNAseI-treatment as recommended in the technical manual. Two to four caps containing tissue sections were pooled on-column.
For whole tissue samples (i.e. inflorescences) and microarray profiling, total RNA was extracted using the Sigma Plant Mini RNA extraction kit as described in the technical manual, and included a DNAseI-treatment (Roche).

treatment_protocol:
Whole inflorescences containing flowers up to approximately floral stage 10 were collected under a dissecting microscope using ultrafine tweezers. Inflorescences from primary and secondary branches were pooled from several plants (between 3-10, for microarray analyses) and immediately frozen in liquid nitrogen.  For laser-assisted microdissection (LAM), inflorescences from at least 20 individual plants were collected on ice and fixed in Ethanol:Acetic Acid 3:1 [v/v] under vacuum (~ 500 mBar) for 2x10 min at 4°C and then left in the fixative overnight at 4°C. The tissue was embedded into Paraplast X-tra Embedding Media (Sigma-Aldrich) using an automated protocol and the Leica ASP200 embedding machine as follows: 1h 70% EtOH, 3x1h 90% EtOH, 3x 1h 100% EtOH, 2x 1h 100% Xylol, 1x 15 min. 100% Xylol, all at room temperature, and then 2x 1h Paraplast X-tra and 1x 3h Paraplast X-tra at 56 °C. Inflorescences were then poured into paraplast blocks and cooled at 4°C until use. Embedded samples were sectioned on a Leica RM2145 microtome to 10 μm thickness and mounted on membrane-slides (Molecular Machines and Industries (MMI), Glattbrugg, Switzerland) using sterile water for mounting. The slides were then dried overnight at 42°C on a heating table and laser-dissected immediately. LAM was performed on an MMI CellCut Plus after dewaxing the tissue sections for 2x 10 minutes in Xylol as described in Wuest et al, Current Biology 2010, (20) 506–512
For the laser-dissected meristem samples from sterile growing plants, fruit-bearing growing plants, fruit-bearing arrested plants, as well as arrested plants that had their fruit removed 48 hours prior to sample collection. For the microarray profiling of whole inflorescences, L-er plants were allowed to arrest and collected at 0, 6, 24 and 48 hours after removal of all but 3-4 fruits closest to the inflorescence. Several inflorescences (including flowers up to approximately Stage 10 of at least three plants were pooled.

value: ms1-1 co-segregant

tag: fertility

value: fertile

tag: growth

value: arrested


title: meristems; sterile plants; growing

department: Institute of Evolutionary Biology and Environmental Studies

description: Microarray growing meristems sterile plants

value: ms1-1 homozygous

value: sterile

value: growing


title: meristems; fertile plants; growing

description: Microarray meristems growing fertile plants


title: g8 inflorescences; fertile plants; fruits removed (48hrs)

description: Microarray arrested whole inflorescences, 48 hours after fruit removal

source_name: whole inflorescences from primary and secondary branches, up to floral stages ~10

value: fertile; fruits removed (48 hrs prior to tissue collection)

value: arrested + fruits removed


title: EtOH 5h_3


title: wheat leaf at PH

city: Nanjing

first: Xiao

last: Wang

address: NO.1 Weigang Road

country: China

institute: Nanjing Agricultural University

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

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

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

organism: Triticum aestivum

source_name: progeny of primed plants with post-anthesis high temperature stress

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Pot experiments (25 cm in diameter and 22 cm in depth) were conducted at the Experimental Station of Nanjing Agricultural University, Nanjing, China

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

treatment_protocol: Seeds of a commercial winter wheat (Triticum aestivum L. cv. Yangmai 16) were used in this study. During the first generation, wheat plants were divided into two groups: one group was not primed (N) while the other was heat-primed (P) at pre-anthesis stages (at a day/night temperature of 32/28˚C for two days at the seven-leaf stage and the nine-leaf stage, respectively) and post-anthesis stage (34/30˚C for seven days started at the 10th day after anthesis, DAA). At maturity, seeds from both groups were harvested. Plants (the progeny) grown from seeds harvested in each group were further divided in two sub-groups from 10 DAA: one was subjected to high temperature stress at a day/night temperature of 34/30˚C, while the other was set at 26/22˚C for six days. During both priming and high-temperature stress, plants under different treatments were moved into separate growth chambers.

tag: cultivar

value: cv. Yangmai 16

value: flag leaf


title: EtOH 5h_2

value: LNCaP MYC


title: g7 inflorescences; fertile plants; fruits removed (24hrs)

description: Microarray arrested whole inflorescences, 24 hours after fruit removal

value: fertile; fruits removed (24 hrs prior to tissue collection)


title: wheat leaf at PC

source_name: progeny of primed plants (P) without post-anthesis high temperature stress


title: g6 inflorescences; fertile plants; fruits removed (6hrs)

description: Microarray arrested whole inflorescences, 6 hours after fruit removal

value: fertile; fruits removed (6 hrs prior to tissue collection)


title: g11 inflorescences; fertile plants; fruits removed (48hrs)


title: meristems; fertile plants; fruits removed

description: Microarray re-activated meristems fertile plants after fruit removal

value: fertile; fruits removed


title: IL-15 DCs rep2

value: healthy donor 2

value: peripheral blood

value: Mature IL-15 DCs


title: wheat leaf at NC

source_name: progeny of non-primed plants (N) without post-anthesis high temperature stress


title: r13 inflorescences; fertile plants; growing

description: Microarray whole inflorescences growing fertile plants

value: ms1-1 co-segregant


title: g5 inflorescences; fertile plants; fruits removed (6hrs)


title: r9 inflorescences; sterile plants; growing

description: Microarray growing whole inflorescences sterile plants


title: g10 inflorescences; fertile plants; fruits removed (24hrs)


title: g3 inflorescences; fertile plants; arrested

description: Microarray whole inflorescences arrested fertile plants

value: fertile


title: r1 inflorescences; fertile plants; arrested

value: arrested


title: wheat leaf at NH

source_name: progeny of non-primed plants with post-anthesis high temperature stress


title: 5DeltaNTPOP1

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

data_processing: The data were normalized by RMA with Partek Genomic Suite 6.6

organism: Caenorhabditis elegans

source_name: 5DeltaNTPOP1 (Wnt underactivation)

treatment_protocol: mRNA obtained by Co-Ip with FLAG tagged PAB-1 expressed in seam cells and VPCs converted to cDNA and amplified using NuGEN pico amplification kit

value: L2-L3 stage

tag: strain

value: deIs10;deIs26, integrated flag::pab-1 and markers

value: VPCs and seam cells

tag: protocol


title: 4DeltaNTPOP1

source_name: 4DeltaNTPOP1 (Wnt underactivation)

value: mRNA obtained by Co-Ip with FLAG tagged PAB-1 expressed in seam cells and VPCs


title: 2N2

value: N2 (control)


title: 3Huis1

source_name: 3Huis1 (Wnt over activation)

value: deIs10;huIs1, integrated flag::pab-1 and markers


title: 4Huis1

source_name: 4Huis1 (Wnt over activation)


title: 4N2


title: 3N2


title: Lats2-CKO, high-cholesterol (Paigen) diet, biological rep2

city: Rehovot

first: Yael

last: Aylon

address: 234 Herzl St.

department: Department of Molecular Cell Biology

institute: Weizmann Institute of Science

description: Gene expression data from Lats2-KO mice liver, fed on high-cholesterol diet for 9 weeks.

hyb_protocol: 5.5ug ss cDNA in 130 ul were hybridized to a Mouse Gene 2.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0002 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Partek Genomics Suite, ver. 6.6, using RMA background correction and quantile normalization.

label_protocol: 250ng Total RNA were used. cDNA samples were generated and labeled using Ambion WT Expression kit

growth_protocol: Eight week old male WT and Lats2-KO mice were fed either normal chow diet (ND) containing no cholesterol (Harlan #2018) or high cholesterol diet (HCD) containing 1.25% cholesterol (Harlan #TD.90221).

extract_protocol: Total RNA was isolated using a NucleoSpin RNA II kit (Macherey-Nagel).

value: liver

tag: Sex

value: male

tag: age

value: 8 week

tag: diet

value: PD


title: wild-type, high-cholesterol (Paigen) diet, biological rep2

description: Gene expression data from WT mice liver, fed on high-cholesterol diet for 9 weeks.

tag: tissue

tag: genotype

value: WT


title: cg-BL-1-LGK-Glc-2 vs. cg-BL-1-LGK-LG-2

city: Seoul

first: Han

middle: Min

last: Woo

address: Hwarangno 14-gil 5, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing: Gene Pix Pro 6.0 (Axon Instruments, CA) was used for background subtraction and GenoWiz 4.0 (Ocimumbiosolutions, India) was used for Loess normalization. The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India).

organism: Corynebacterium glutamicum

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for all)

growth_protocol: CgXII medium with either 2% glucose or 2% levoglucosan

extract_protocol: The Corynebacterium glutamicum was frozen in liquid nitrogen in mortar and grinded using pestle. Total RNA was extracted from the grinded samples by using TRIzol reagent (Invitrogen, USA). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-2000 Spectrophotometer (Thermo Inc., DE, USA).

tag: carbon source


title: Lats2-CKO, normal diet, biological rep3

description: Gene expression data from Lats2-KO mice liver, fed on normal diet for 9 weeks.

value: ND


title: Lats2-CKO, high-cholesterol (Paigen) diet, biological rep1

source_name: Lats2-KO mice liver, fed on high-cholesterol diet for 9 weeks.


title: 2DeltaNTPOP1

source_name: 2DeltaNTPOP1 (Wnt underactivation)

tag: cell type


title: Lats2-CKO, high-cholesterol (Paigen) diet, biological rep3


title: shRAD21-transduced cells, biological rep4

city: Lund

first: Roman

last: Galeev

address: Sölvegatan 17

institute: Lund University

description: Gene expression data from shRAD21-transduced cells

hyb_protocol: 3,0 µg of fragmented and labeled SPIA cDNA was hybridized to Affymetrix Human Genome U133 PM Array Plates. For hybridization, washing and staining an Affymetrix GeneTitan system was used.

scan_protocol: GeneChips were scanned using an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v3.3 (AGCC).

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using the RMA algorithm (Irizarry et al., 2003) in the Affymetrix GeneChip Expression Console v1.3 software.

label_protocol: The NuGEN Ovation PicoSL WTA System V2 Kit Protocol was used for the preparation of SPIA cDNA from 25 ng of total RNA, followed by fragmentation and  terminal biotin-labeling according to the NUGEN Encore Biotin Module manual.

growth_protocol: Human CD34 positive cells were grown in serum-free expansion medium (SFEM) supplemented with SCF, TPO and FLT3L at 100ng/ml

extract_protocol: Total RNA was extracted from cells stabilized in RLT buffer according to the “Purification of total RNA from animal cells using spin technology” protocol of the Qiagen RNeasy Micro Kit.

treatment_protocol: Cells were transduced with lentiviral particles, cultured for 36 hours, and sorted into RLT-buffer from Qiagen for subsequent RNA extraction and analysis.

value: human cord-blood derived CD34+ cells

value: human, normal karyotype

value: Less than 24h old cordblood from uncomplicated births


title: wild-type, high-cholesterol (Paigen) diet, biological rep3

source_name: WT mice liver, fed on high-cholesterol diet for 9 weeks.


title: shRAD21-transduced cells, biological rep5


title: 1Huis1

source_name: 1Huis1 (Wnt over activation)


title: wild-type, high-cholesterol (Paigen) diet, biological rep1


title: wild-type, normal diet, biological rep2

description: Gene expression data from WT mice liver, fed on normal diet for 9 weeks.


title: shSTAG1-transduced cells, biological rep1

description: Gene expression data from shSTAG1-transduced cells


title: shSTAG1-transduced cells, biological rep2


title: cg-BL-1-LGK-Glc-1 vs. cg-BL-1-LGK-LG-1


title: shSTAG1-transduced cells, biological rep3


title: wild-type, normal diet, biological rep3

source_name: WT mice liver, fed on normal diet for 9 weeks.


title: Lats2-CKO, normal diet, biological rep1

source_name: Lats2-KO mice liver, fed on normal diet for 9 weeks.


title: shSTAG1-transduced cells, biological rep5


title: shRAD21-transduced cells, biological rep2


title: shRAD21-transduced cells, biological rep1


title: wild-type, normal diet, biological rep1


title: shSMC3-transduced cells, biological rep5

description: Gene expression data from shSMC3-transduced cells


title: shSTAG2-transduced cells, biological rep4

description: Gene expression data from shSTAG2-transduced cells


title: shRAD21-transduced cells, biological rep3


title: Lats2-CKO, normal diet, biological rep2


title: shSMC3-transduced cells, biological rep1


title: shSTAG2-transduced cells, biological rep2


title: Control (sh-Scrambled)-transduced cells, biological rep3

description: Gene expression data from shScrambled-transduced cells


title: shSMC3-transduced cells, biological rep3


title: shSMC3-transduced cells, biological rep4


title: shSMC3-transduced cells, biological rep2


title: shSTAG1-transduced cells, biological rep4


title: shSTAG2-transduced cells, biological rep5


title: Control (sh-Scrambled)-transduced cells, biological rep4


title: Control (sh-Scrambled)-transduced cells, biological rep1


title: Control (sh-Scrambled)-transduced cells, biological rep2


title: Control (sh-Luciferase)-transduced cells, biological rep4

description: Gene expression data from shLuciferase-transduced cells


title: Control (sh-Luciferase)-transduced cells, biological rep3


title: Control (sh-Luciferase)-transduced cells, biological rep5


title: Control (sh-Luciferase)-transduced cells, biological rep2


title: Control (sh-Scrambled)-transduced cells, biological rep5


title: Non-transduced cells, biological rep3

description: Gene expression data from non-transduced cells

source_name: Non-transduced cells, biological rep3


title: Non-transduced cells, biological rep2

source_name: Non-transduced cells, biological rep2


title: Control (sh-Luciferase)-transduced cells, biological rep1


title: shSTAG2-transduced cells, biological rep3


title: RA_subject_377

status: Public on Mar 16 2016

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

hyb_protocol: Microarray hybridization was performed on GeneChip Human Genome U133 Plus 2.0 Array according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data were normalized using Robust Multi-array Average (RMA) algorithm and log base 2 transformed using R/Bioconductor.

source_name: whole blood

label_protocol: Subject cDNA was amplified through utilization of the NuGEN Ovation Pico WTA System V2 (NuGEN, San Carlos, CA, USA).

extract_protocol: RNA was isolated using the Qiagen Biorobot (Qiagen, Valencia, CA, USA), which followed the protocol from the Qiagen PAXgene MDX kit (cat# 752431), and was modified to collect both total and microRNA

tag: gender

value: F

tag: rheumatoid factor positivity

value: Positive

tag: disease

value: Rheumatoid arthritis

value: whole blood


title: RA_subject_368


title: RA_subject_375

value: Negative


title: RA_subject_370

value: M


title: RA_subject_365


title: RA_subject_366


title: RA_subject_372


title: RA_subject_367


title: RA_subject_373


title: RA_subject_376


title: RA_subject_369


title: RA_subject_364


title: RA_subject_363


title: RA_subject_374


title: RA_subject_362


title: RA_subject_371


title: RA_subject_360


title: RA_subject_361


title: Non-transduced cells, biological rep1

source_name: Non-transduced cells, biological rep1


title: RA_subject_359


title: RA_subject_354


title: RA_subject_357


title: RA_subject_353


title: RA_subject_358


title: RA_subject_351


title: RA_subject_352


title: RA_subject_356


title: RA_subject_350


title: RA_subject_355


title: RA_subject_348


title: RA_subject_349


title: RA_subject_345


title: RA_subject_344


title: RA_subject_347


title: RA_subject_342


title: RA_subject_343


title: RA_subject_336


title: RA_subject_337


title: RA_subject_340


title: RA_subject_331


title: RA_subject_346


title: RA_subject_339


title: RA_subject_335


title: RA_subject_332


title: RA_subject_334


title: RA_subject_338


title: RA_subject_330


title: RA_subject_329


title: RA_subject_322


title: RA_subject_327


title: RA_subject_341


title: RA_subject_324


title: RA_subject_323


title: RA_subject_333


title: RA_subject_325


title: RA_subject_328


title: RA_subject_320


title: RA_subject_317


title: RA_subject_326


title: RA_subject_321


title: shSTAG2-transduced cells, biological rep1


title: RA_subject_313


title: RA_subject_319


title: RA_subject_318


title: RA_subject_316


title: RA_subject_311


title: RA_subject_310


title: RA_subject_312


title: RA_subject_305


title: RA_subject_308


title: RA_subject_306


title: RA_subject_307


title: RA_subject_304


title: RA_subject_298


title: RA_subject_303


title: RA_subject_294


title: RA_subject_309


title: RA_subject_297


title: RA_subject_289


title: RA_subject_301


title: RA_subject_292


title: RA_subject_295


title: RA_subject_299


title: RA_subject_290


title: RA_subject_286


title: RA_subject_302


title: RA_subject_288


title: RA_subject_300


title: RA_subject_291


title: RA_subject_287


title: RA_subject_285


title: RA_subject_314


title: RA_subject_296


title: RA_subject_284


title: RA_subject_293


title: RA_subject_277


title: RA_subject_279


title: RA_subject_280


title: RA_subject_283


title: RA_subject_282


title: RA_subject_275


title: RA_subject_274


title: RA_subject_278


title: RA_subject_276


title: RA_subject_272


title: RA_subject_267


title: RA_subject_270


title: RA_subject_268


title: RA_subject_263


title: RA_subject_260


title: RA_subject_266


title: RA_subject_273


title: RA_subject_261


title: RA_subject_264


title: RA_subject_259


title: RA_subject_258


title: RA_subject_257


title: RA_subject_269


title: RA_subject_262


title: RA_subject_256


title: RA_subject_254


title: RA_subject_253


title: RA_subject_271


title: RA_subject_265


title: RA_subject_255


title: RA_subject_252


title: RA_subject_244


title: RA_subject_251


title: RA_subject_248


title: RA_subject_245


title: RA_subject_239


title: RA_subject_241


title: RA_subject_247


title: RA_subject_243


title: RA_subject_235


title: RA_subject_240


title: RA_subject_233


title: RA_subject_238


title: RA_subject_246


title: RA_subject_237


title: RA_subject_242


title: RA_subject_315


title: RA_subject_236


title: RA_subject_232


title: RA_subject_250


title: RA_subject_234


title: RA_subject_230


title: RA_subject_226


title: RA_subject_224


title: RA_subject_229


title: RA_subject_222


title: RA_subject_228


title: RA_subject_227


title: RA_subject_220


title: RA_subject_217


title: RA_subject_219


title: RA_subject_218


title: RA_subject_221


title: RA_subject_216


title: RA_subject_223


title: RA_subject_225


title: RA_subject_212


title: RA_subject_214


title: RA_subject_211


title: RA_subject_210


title: RA_subject_213


title: RA_subject_209


title: RA_subject_281


title: RA_subject_207


title: RA_subject_205


title: RA_subject_195


title: RA_subject_206


title: RA_subject_208


title: RA_subject_190


title: RA_subject_201


title: RA_subject_203


title: RA_subject_191


title: RA_subject_189


title: RA_subject_194


title: RA_subject_185


title: RA_subject_198


title: RA_subject_196


title: RA_subject_202


title: RA_subject_193


title: RA_subject_188


title: RA_subject_197


title: RA_subject_200


title: RA_subject_187


title: RA_subject_204


title: RA_subject_215


title: RA_subject_199


title: RA_subject_231


title: RA_subject_186


title: RA_subject_183


title: RA_subject_184


title: RA_subject_192


title: RA_subject_180


title: RA_subject_179


title: RA_subject_175


title: RA_subject_174


title: RA_subject_165


title: RA_subject_161


title: RA_subject_182


title: RA_subject_181


title: RA_subject_170


title: RA_subject_176


title: RA_subject_169


title: RA_subject_163


title: RA_subject_177


title: RA_subject_168


title: RA_subject_249


title: RA_subject_178


title: RA_subject_171


title: RA_subject_173


title: RA_subject_172


title: RA_subject_166


title: RA_subject_167


title: RA_subject_158


title: RA_subject_164


title: RA_subject_159


title: RA_subject_160


title: RA_subject_156


title: RA_subject_155


title: RA_subject_162


title: RA_subject_152


title: RA_subject_157


title: RA_subject_154


title: RA_subject_151


title: RA_subject_144


title: RA_subject_147


title: RA_subject_140


title: RA_subject_150


title: RA_subject_149


title: RA_subject_136


title: RA_subject_138


title: RA_subject_142


title: RA_subject_148


title: RA_subject_143


title: RA_subject_133


title: RA_subject_146


title: RA_subject_126


title: RA_subject_135


title: RA_subject_145


title: RA_subject_153


title: RA_subject_128


title: RA_subject_130


title: RA_subject_129


title: RA_subject_127


title: RA_subject_131


title: RA_subject_125


title: RA_subject_137


title: RA_subject_141


title: RA_subject_134


title: RA_subject_132


title: RA_subject_139


title: RA_subject_118


title: RA_subject_108


title: RA_subject_120


title: RA_subject_107


title: RA_subject_113


title: RA_subject_105


title: RA_subject_102


title: RA_subject_115


title: RA_subject_97


title: RA_subject_123


title: RA_subject_124


title: RA_subject_110


title: RA_subject_101


title: RA_subject_121


title: RA_subject_103


title: RA_subject_119


title: RA_subject_116


title: RA_subject_100


title: RA_subject_111


title: RA_subject_96


title: RA_subject_106


title: RA_subject_98


title: RA_subject_114


title: RA_subject_89


title: RA_subject_117


title: RA_subject_122


title: RA_subject_112


title: RA_subject_92


title: RA_subject_88


title: RA_subject_104


title: RA_subject_99


title: RA_subject_93


title: RA_subject_94


title: RA_subject_109


title: RA_subject_86


title: RA_subject_90


title: RA_subject_95


title: RA_subject_91


title: RA_subject_85


title: RA_subject_83


title: RA_subject_84


title: RA_subject_82


title: RA_subject_81


title: RA_subject_87


title: RA_subject_80


title: RA_subject_77


title: RA_subject_79


title: RA_subject_76


title: RA_subject_78


title: RA_subject_72


title: RA_subject_67


title: RA_subject_63


title: RA_subject_71


title: RA_subject_60


title: RA_subject_74


title: RA_subject_65


title: RA_subject_73


title: RA_subject_66


title: RA_subject_59


title: RA_subject_64


title: RA_subject_68


title: RA_subject_70


title: RA_subject_56


title: RA_subject_61


title: RA_subject_69


title: RA_subject_75


title: RA_subject_58


title: RA_subject_54


title: RA_subject_62


title: RA_subject_57


title: RA_subject_55


title: RA_subject_52


title: RA_subject_49


title: RA_subject_48


title: RA_subject_51


title: RA_subject_47


title: RA_subject_50


title: RA_subject_43


title: RA_subject_40


title: RA_subject_44


title: RA_subject_38


title: RA_subject_45


title: RA_subject_41


title: RA_subject_42


title: RA_subject_33


title: RA_subject_37


title: RA_subject_26


title: RA_subject_28


title: RA_subject_34


title: RA_subject_29


title: RA_subject_27


title: RA_subject_35


title: RA_subject_39


title: RA_subject_24


title: RA_subject_32


title: RA_subject_25


title: RA_subject_36


title: RA_subject_31


title: RA_subject_30


title: RA_subject_22


title: RA_subject_46


title: RA_subject_17


title: RA_subject_14


title: RA_subject_5


title: RA_subject_12


title: RA_subject_19


title: RA_subject_20


title: RA_subject_7


title: RA_subject_21


title: RA_subject_8


title: RA_subject_2


title: RA_subject_10


title: RA_subject_9


title: RA_subject_13


title: RA_subject_23


title: RA_subject_18


title: RA_subject_15


title: RA_subject_16


title: RA_subject_1


title: RA_subject_4


title: RA_subject_11


title: RA_subject_6


title: ko 1 infected

city: Erlangen

first: Heike

last: Schmitt

address: Staudtstraße 5

department: Biology

institute: Friedrich Alexander University

description: Gene expression 26 weeks after mCMV infection

hyb_protocol: Following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent 026655 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2505C Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.5.1. (Agilent Technologies Germany). Data extraction using protocol GE1_1105_0ct12

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.6 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in both replicates in at least one conditions were selected by filtering  on data present. Entitie lists were further filtered by selection of genes which do not change their expression in all conditions. This list was subtracted from the entities present in at least one conditions  by means of VENN diagramms. Entities differentially expressed  in mCMV infected Siglec-H ko mice compared to infected Siglec-H wt mice or uninfected controls were obtained by Volcano plot analysis (fold change >=2, p-value <=0.05, Benjamini Hochberg fals discovery fals poitive correction).

source_name: Siglec-H ko 26 weeks after mCMV infection, replicate 1

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 100ng total RNA (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Animals were bred and kept under pathogen-free conditions, with a 12 h day/night interval, in the local animal facility of the Biotechnologisches Entwicklungslabor (BTE). All experiments were performed according to the German law for protection of animals, after approval by the animal welfare committee.

extract_protocol: RNA from 1x107 splenic cells was isolated by using QIAshredder and RNeasy kits (QIAGEN) according to the manufacturer’s instructions, 100ng RNA were used for cDNA synthesis

treatment_protocol: Mice were infected for 26 weeks with 5x105 pfu mCMV or left untreated

value: Siglec-H ko

value: Spleen


title: RA_subject_3


title: wt 1 infected

source_name: Siglec-H wt 26 weeks after mCMV infection, replicate 1

value: Siglec-H wt


title: wt 2 non infected

description: Gene expression of non infected control mice

source_name: Siglec-H wt non infected control, replicate 2


title: ko 2 infected

source_name: Siglec-H ko 26 weeks after mCMV infection, replicate 2


title: wt 2 infected

source_name: Siglec-H wt 26 weeks after mCMV infection, replicate 2


title: ko 1 non infected

source_name: Siglec-H ko non infected control, replicate 1


title: ko 2 non infected

source_name: Siglec-H ko non infected control, replicate 2


title: wt 1 non infected

source_name: Siglec-H wt non infected control, replicate 1


title: Infection with Brucella abortus C24 strain for 24 h-2

first: Myunghwan

last: Jung

address: 1 Gwanak-ro

department: Veterinary Medicine

institute: Seoul National University

description: Leukemic monocyte macrophage cell line

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: RAW 264.7 cells

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: 8.0 x 104 cells/cm2 in 6-well plates with 2 mL of RPMI containing 2 % FBS

extract_protocol: Total RNA was isolated from the cells using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were infected with 10 MOI of Brucella abortus wild and mutant strains for 0, 6, 12, and 24 h.

tag: cell line

tag: culture media

value: RPMI

tag: infection

value: Brucella abortus C24 strain

tag: time point


title: Infection with Brucella abortus wild strain for 24 h-1

description: Leukemic monocyte macrophage cell line

value: Brucella abortus wild strain


title: RA_subject_53


title: Infection with Brucella abortus C30 strain for 12 h-2

description: Leukemic monocyte macrophage cell line

value: Brucella abortus C30 strain


title: Infection with Brucella abortus wild strain for 12 h-2

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C3 strain for 24 h-2

description: Leukemic monocyte macrophage cell line

value: Brucella abortus C3 strain


title: Infection with Brucella abortus C3 strain for 12 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C30 strain for 12 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C3 strain for 24 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C30 strain for 24 h-2

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus wild strain for 12 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C24 strain for 12 h-2

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C24 strain for 24 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus wild strain for 24 h-2

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C3 strain for 12 h-2

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C24 strain for 12 h-1

description: Leukemic monocyte macrophage cell line


title: Myotubes DMD 8036 Primary rep4

city: Londonderry

first: William

middle: John

last: Duddy

address: C-TRIC building, Altnagelvin Hospital Campus

department: Northern Ireland Centre for Stratified Medicine

country: United Kingdom

institute: Ulster University

description: Myotubes DMD 8036 Primary rep4

hyb_protocol: 750ng of the biotin-labeled IVT product (cRNA) was hybridized to HumanHT-12v4_BeadChip for 16 hours, followed by washing, blocking, and streptavidin-Cy3 staining according to the WholeGenome Gene Expression Direct Hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScanSQ System

data_processing: Raw intensity values (Illumina idat files) of 94 samples were passed to the R lumidat library to create an EListRaw class object compatible with further downstream analyses in R/Bioconductor. Two samples were excluded at this stage due to having zero proportion of expressed probes (all other samples had more than 40% of probes expressed). The limma library was then used to carry out neqc normalization – this involves background correction followed by quantile normalization, using negative control probes for background correction and both negative and positive controls for normalization. Probes were excluded if: (1) they had low bead numbers in at least one sample; (2) they were not expressed (expression p-value < 0.01) in at least 16 arrays; (3) they were annotated as ‘no match’ or ‘bad’ quality according to the Bioconductor illuminaHumanv4.db library. This gave a total of 15,342 probes for further analysis.

source_name: Cultured cells

label_protocol: An aliquot of 150 ng of high-quality total RNA from each sample was used for mRNA expression profiling. Reverse Transcription for synthesis of the cDNA strand, followed by a single in vitro transcription (IVT) amplification, that incorporates biotin-labeled nucleotides, were performed with Illumina® TotalPrep™ -96 RNA Amplification Kit (Ambion, Austin, TX).

extract_protocol: Cells were scraped and collected in PBS (100 uL). Cells were centrifuged at 13,000 rpm for 10 minutes, and PBS supernatant removed. Each pellet was dissolved in TRIzol (1 mL). The RNA was subsequently isolated (PureLink RNA Mini Kit, ‘Using TRIzol® Reagent with the PureLink® RNA Mini Kit’ section of the standard protocol) with the RNA eluted in 30 µL H2O.

tag: differentiation state

value: Myotube

tag: clonal state

value: Primary

tag: disease state

value: Duchenne muscular dystrophy


title: Myotubes DMD 8036 Clone rep4

description: Myotubes DMD 8036 Clone rep4

value: Clone


title: Myotubes DMD 8036 Primary rep3

description: Myotubes DMD 8036 Primary rep3


title: Infection with Brucella abortus C30 strain for 24 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C30 strain for 6 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus C30 strain for 6 h-2

description: Leukemic monocyte macrophage cell line


title: Myotubes DMD 8036 Primary rep2

description: Myotubes DMD 8036 Primary rep2


title: Myotubes DMD 8036 Clone rep3

description: Myotubes DMD 8036 Clone rep3


title: Myotubes DMD 8036 Primary rep1

description: Myotubes DMD 8036 Primary rep1


title: Blood_Control_85

type: genomic

city: Utrecht

first: Marco

last: Boks

state: Nederland

address: Heidelberglaan 100, PO box 85500, Huispostnr A01.146

department: Department of Psychiatry

institute: University Medical Center Utrecht

description: Human whole blood DNA methylation sample; SAMPLE 85

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: Intensity read outs, quality control parameters and methylation measures were obtained from the genome studio software. X chromosome, Y chromosome, and non-specific binding probes were removed. Failed probes were excluded based on a detection p-value larger than 0.001 and bead count lower than 5. In addition, probes with SNPs of Minor Allele Frequency(MAF) larger than 5 percent within 10 base pairs of the primer were excluded after constructing ancestry estimates based on their principal components as proposed by Barfield et al (lists of CpG sites available at http://genetics.emory.edu/research/conneely/annotation-r-code.html). DNA methylation analysis was performed in R, using wateRmelon (providing routines to handle Illumina BeadStudio data and normalization), sva(batch effect removal)  and limma (for statistical routines). The data was normalized to remove systematic differences in overall signal distribution due to probe design bias using the Beta MIxture Quantile dilation (BMIQ) normalization as implemented in the watermelon package. After removing batch effects of sentrix array and position with the Combat procedure from the sva package.

molecule: genomic DNA

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood with the Gentra Puregene Kit (Qiagen, Valencia, CA, USA) following manufacturer's protocol. DNA concentration and integrity was assessed using riboGreen and BioAnalyser.

treatment_protocol: Bisulphite conversion was conducted with Zimo kits (ZYMO Research, Orange, CA, USA) using standard procedures.

tag: race

value: Caucasian

value: Female

tag: cortisol stress response area under the curve (auc) with respect to the increase

tag: total score on the childhood trauma questionnaire

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion

tag: monocytes cell proportion

tag: natural killer cell proportion

tag: cd4 t cell proportion

tag: bcell proportion

tag: granulocytes cell proportion

tag: sentrix

tag: position


title: Blood_Control_84

description: Human whole blood DNA methylation sample; SAMPLE 84

tag: gender

tag: age


title: Infection with Brucella abortus C24 strain for 6 h-2

description: Leukemic monocyte macrophage cell line

tag: cell line

tag: culture media

tag: infection

tag: time point


title: Myotubes DMD 8036 Clone rep2

description: Myotubes DMD 8036 Clone rep2

tag: differentiation state

tag: clonal state

tag: disease state


title: Infection with Brucella abortus C3 strain for 6 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus wild strain for 6 h-2

description: Leukemic monocyte macrophage cell line


title: Infection for 0h-1

description: Leukemic monocyte macrophage cell line


title: SNU-886

city: Daejeon

first: Yang

last: Suk-Jin

address: 125 Gwahak-ro, Yuseong-gu

institute: KRIBB (Korea Research Institute of Bioscience and Biotechnology)

hyb_protocol: Labeled cRNA (750ng) was hybridized to HumanHT-12 v3 or v4 chips at 58℃ for 16 hours.

scan_protocol: After hybridizing procedures, chips were scanned using a BeadArray Reader and BeadScan software (Illumina).

data_processing: Data extraction and normalization were elevated by BeadStudio software (Illumina).

source_name: SNU-886 cells

label_protocol: Illumina TotalPrep RNA Amplification kit (Applied Biosystem/Ambion, Austin, TX, USA) was used to generate biotin-UTP labeled cRNA according to manufacturer’s instructions

growth_protocol: ATCC (ATCC, Manassas, VA) and SNU (KCLB, Seoul, Korea) were maintained in Dulbecco’s modified Eagle medium (DMEM; Gibco BRL, Grand Island, NY) or Roswell Park Memorial Institute 1640 medium (RPMI1640; GIBCO BRL). JHH cell lines obtained from JCRB were maintained in William’s E medium (GIBCO BRL). All media was supplemented with heat-inactivated 10% fetal bovine serum (GIBCO BRL) and 1× Antibiotic-Antimycotic (GIBCO BRL). Cells were cultured at 37℃ in a humidified incubator under 5% CO2.

extract_protocol: Total RNA extraction was perforemd using QIAGEN RNeasy mini kit according to manufacturer's instruction. Total RNA integrity was determined with ExperionTM RNA StdSens (BIO-RAD).

treatment_protocol: None.

tag: cell type

value: Human HCC cells


title: PLC/PRF/5

source_name: PLC/PRF/5 cells


title: Myotubes DMD 6594 Primary rep4

description: Myotubes DMD 6594 Primary rep4


title: Infection with Brucella abortus C3 strain for 6 h-2

description: Leukemic monocyte macrophage cell line


title: Myotubes DMD 8036 Clone rep1

description: Myotubes DMD 8036 Clone rep1


title: SNU-423

source_name: SNU-423 cells


title: Myotubes DMD 6594 Primary rep2

description: Myotubes DMD 6594 Primary rep2


title: Infection with Brucella abortus C24 strain for 6 h-1

description: Leukemic monocyte macrophage cell line


title: Infection with Brucella abortus wild strain for 6 h-1

description: Leukemic monocyte macrophage cell line


title: Myotubes DMD 6594 Primary rep1

description: Myotubes DMD 6594 Primary rep1


title: Blood_Control_83

description: Human whole blood DNA methylation sample; SAMPLE 83

tag: race

tag: cortisol stress response area under the curve (auc) with respect to the increase

tag: total score on the childhood trauma questionnaire

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion

tag: monocytes cell proportion


title: Hep3B

source_name: Hep3B cells


title: Infection for 0h-2

description: Leukemic monocyte macrophage cell line


title: Blood_Control_82

description: Human whole blood DNA methylation sample; SAMPLE 82

tag: natural killer cell proportion

tag: cd4 t cell proportion

tag: bcell proportion

tag: granulocytes cell proportion

tag: sentrix

tag: position


title: Myotubes DMD 6594 Primary rep3

description: Myotubes DMD 6594 Primary rep3


title: Myotubes DMD 6594 Clone rep4

description: Myotubes DMD 6594 Clone rep4


title: SNU-739

source_name: SNU-739 cells

tag: cell line


title: SK-HEP-1

source_name: SK-HEP-1 cells


title: Myotubes DMD 6594 Clone rep3

description: Myotubes DMD 6594 Clone rep3

tag: differentiation state


title: JHH-4

source_name: JHH-4 cells


title: HLF

source_name: HLF cells

value: HLF


title: Myotubes DMD 6594 Clone rep2

description: Myotubes DMD 6594 Clone rep2

tag: clonal state


title: JHH-6

source_name: JHH-6 cells


title: Myotubes DMD 6311 Primary repB1

description: Myotubes DMD 6311 Primary repB1

tag: disease state


title: Myotubes DMD 6311 Primary rep3

description: Myotubes DMD 6311 Primary rep3


title: Blood_Control_79

description: Human whole blood DNA methylation sample; SAMPLE 79

tag: gender

tag: age


title: Myotubes DMD 6311 Primary repB2

description: Myotubes DMD 6311 Primary repB2


title: NCI-H292 cells_Control siRNA_rep1

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

institute: Pusan National University

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: NCI-H292 cells were grown in RPMI-1640 medium supplemented with 10% FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin at 37℃ in a 5% CO2/95% air atmosphere.

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

treatment_protocol: NCI-H292 cells were transiently transfected with control siRNA or TFAP2C siRNA using Lipofectamine® RNAi Max (Invitrogen, Carlsbad, CA), according to the manufacturers' instructions.

tag: cell type

value: Non-small cell lung cancer (NSCLC) cell line

tag: genotype/variation

value: EGFR/KRAS-wild type cells

tag: transfected with

value: control siRNA


title: Myotubes DMD 6311 Primary rep4

description: Myotubes DMD 6311 Primary rep4


title: Blood_Control_76

description: Human whole blood DNA methylation sample; SAMPLE 76

tag: race

tag: cortisol stress response area under the curve (auc) with respect to the increase

tag: total score on the childhood trauma questionnaire

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion


title: Huh-1

source_name: Huh-1 cells


title: NCI-H292 cells_TFAP2C siRNA_rep1

source_name: NCI-H292_TFAP2C knockdown

value: TFAP2C siRNA


title: Blood_Control_77

description: Human whole blood DNA methylation sample; SAMPLE 77

tag: monocytes cell proportion

tag: natural killer cell proportion

tag: cd4 t cell proportion

tag: bcell proportion

tag: granulocytes cell proportion


title: Blood_Control_81

description: Human whole blood DNA methylation sample; SAMPLE 81

tag: sentrix

tag: position


title: Blood_Control_78

description: Human whole blood DNA methylation sample; SAMPLE 78

tag: gender


title: Myotubes DMD 6311 Primary rep2

description: Myotubes DMD 6311 Primary rep2

tag: differentiation state

tag: clonal state

tag: disease state


title: Blood_Control_75

description: Human whole blood DNA methylation sample; SAMPLE 75

value: Male

tag: age


title: Myotubes DMD 6594 Clone rep1

description: Myotubes DMD 6594 Clone rep1


title: Myotubes DMD 6311 Primary rep1

description: Myotubes DMD 6311 Primary rep1


title: Blood_Control_74

description: Human whole blood DNA methylation sample; SAMPLE 74

tag: race


title: Myotubes DMD 6311 Clone rep4

description: Myotubes DMD 6311 Clone rep4


title: Myotubes DMD 6311 Clone repB2

description: Myotubes DMD 6311 Clone repB2


title: Myotubes DMD 6311 Clone rep3

description: Myotubes DMD 6311 Clone rep3


title: Myotubes Healthy CHQ Primary repB1

description: Myotubes Healthy CHQ Primary repB1

value: Healthy


title: Myotubes Healthy CHQ Primary repB2

description: Myotubes Healthy CHQ Primary repB2


title: Myotubes DMD 6311 Clone rep1

description: Myotubes DMD 6311 Clone rep1


title: Myotubes DMD 6311 Clone rep2

description: Myotubes DMD 6311 Clone rep2


title: Blood_Control_71

description: Human whole blood DNA methylation sample; SAMPLE 71

tag: cortisol stress response area under the curve (auc) with respect to the increase


title: Myotubes Healthy CHQ Primary rep3

description: Myotubes Healthy CHQ Primary rep3


title: Blood_Control_80

description: Human whole blood DNA methylation sample; SAMPLE 80

tag: total score on the childhood trauma questionnaire


title: Blood_Control_69

description: Human whole blood DNA methylation sample; SAMPLE 69

tag: total score on the life stressor checklist- revised


title: Myotubes DMD 6311 Clone repB1

description: Myotubes DMD 6311 Clone repB1


title: Myotubes Healthy CHQ Primary rep2

description: Myotubes Healthy CHQ Primary rep2


title: Blood_Control_67

description: Human whole blood DNA methylation sample; SAMPLE 67

tag: cd8 t cell proportion


title: Blood_Control_66

description: Human whole blood DNA methylation sample; SAMPLE 66

tag: monocytes cell proportion


title: Blood_Control_73

description: Human whole blood DNA methylation sample; SAMPLE 73

tag: natural killer cell proportion


title: skin-anti-IFNAR1 d28-rep2

city: Gaithersburg

first: Tracy

middle: Anne

last: Delaney

address: One Medimmune Way

department: Research

institute: MedImmune LLC

description: RAG2 KO grafted with B10.D2 splenocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed in R.

source_name: skin, GVH-SSc, anti-IFNAR1, d28

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen Rneasy Fibrous Tissue Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Shaved dorsal scapular skin was snap frozen in liquid nitrogen and stored at -80C

value: female

tag: genotype/variation


title: skin-anti-IFNAR1 d28-rep1

description: RAG2 KO grafted with B10.D2 splenocytes


title: skin-anti-IFNAR1 d28-rep3

description: RAG2 KO grafted with B10.D2 splenocytes


title: Blood_Control_64

description: Human whole blood DNA methylation sample; SAMPLE 64

tag: cd4 t cell proportion

tag: bcell proportion


title: skin-anti-IFNAR1 d28-rep4

description: RAG2 KO grafted with B10.D2 splenocytes


title: Myotubes Healthy CHQ Primary rep1

description: Myotubes Healthy CHQ Primary rep1


title: Blood_Control_62

description: Human whole blood DNA methylation sample; SAMPLE 62

tag: granulocytes cell proportion

tag: sentrix


title: Blood_Control_60

description: Human whole blood DNA methylation sample; SAMPLE 60

tag: gender

tag: position


title: Blood_Control_63

description: Human whole blood DNA methylation sample; SAMPLE 63


title: Myotubes Healthy CHQ Clone repB2

description: Myotubes Healthy CHQ Clone repB2

tag: differentiation state

tag: clonal state


title: skin-isotype d28-rep2

description: RAG2 KO grafted with B10.D2 splenocytes

source_name: skin, GVH-SSc, isotype, d28


title: skin-isotype d28-rep3

description: RAG2 KO grafted with B10.D2 splenocytes


title: Blood_Control_65

description: Human whole blood DNA methylation sample; SAMPLE 65

tag: age


title: Blood_Control_57

description: Human whole blood DNA methylation sample; SAMPLE 57

tag: race


title: Blood_Control_72

description: Human whole blood DNA methylation sample; SAMPLE 72

tag: cortisol stress response area under the curve (auc) with respect to the increase


title: Blood_Control_58

description: Human whole blood DNA methylation sample; SAMPLE 58

tag: total score on the childhood trauma questionnaire


title: skin-control-d28-rep3

description: RAG2 KO grafted with Balb/c splenocytes

source_name: skin, syngeneic graft, d28


title: skin-isotype d28-rep1

description: RAG2 KO grafted with B10.D2 splenocytes


title: Myotubes Healthy CHQ Clone rep4

description: Myotubes Healthy CHQ Clone rep4

tag: disease state


title: Myotubes Healthy CHQ Clone repB1

description: Myotubes Healthy CHQ Clone repB1


title: Blood_Control_59

description: Human whole blood DNA methylation sample; SAMPLE 59

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion


title: skin-control-d28-rep4

description: RAG2 KO grafted with Balb/c splenocytes


title: Myotubes Healthy CHQ Primary rep4

description: Myotubes Healthy CHQ Primary rep4


title: Myotubes Healthy CHQ Clone rep3

description: Myotubes Healthy CHQ Clone rep3


title: Blood_Control_56

description: Human whole blood DNA methylation sample; SAMPLE 56

tag: monocytes cell proportion

tag: natural killer cell proportion


title: skin-anti-IFNAR1 d14-rep4

description: RAG2 KO grafted with B10.D2 splenocytes

source_name: skin, GVH-SSc, anti-IFNAR1, d14

tag: genotype/variation


title: skin-control-d28-rep1

description: RAG2 KO grafted with Balb/c splenocytes


title: Blood_Control_68

description: Human whole blood DNA methylation sample; SAMPLE 68

tag: cd4 t cell proportion

tag: bcell proportion


title: Blood_Control_70

description: Human whole blood DNA methylation sample; SAMPLE 70

tag: granulocytes cell proportion

tag: sentrix


title: skin-isotype d28-rep4

description: RAG2 KO grafted with B10.D2 splenocytes

tag: gender


title: skin-anti-IFNAR1 d14-rep2

description: RAG2 KO grafted with B10.D2 splenocytes


title: Myotubes Healthy CHQ Clone rep2

description: Myotubes Healthy CHQ Clone rep2

source_name: Cultured cells

tag: differentiation state


title: skin-anti-IFNAR1 d14-rep3

description: RAG2 KO grafted with B10.D2 splenocytes


title: Blood_Control_55

description: Human whole blood DNA methylation sample; SAMPLE 55

source_name: Whole blood

tag: position


title: Blood_Control_61

description: Human whole blood DNA methylation sample; SAMPLE 61

tag: age


title: skin-isotype d14-rep4

description: RAG2 KO grafted with B10.D2 splenocytes

source_name: skin, GVH-SSc, isotype, d14


title: Blood_Control_53

description: Human whole blood DNA methylation sample; SAMPLE 53

tag: race


title: skin-anti-IFNAR1 d14-rep1

description: RAG2 KO grafted with B10.D2 splenocytes


title: skin-isotype d14-rep2

description: RAG2 KO grafted with B10.D2 splenocytes


title: Myotubes Healthy CHQ Clone rep1

description: Myotubes Healthy CHQ Clone rep1

tag: clonal state


title: Myotubes Healthy C25 Primary rep4

description: Myotubes Healthy C25 Primary rep4


title: Myotubes Healthy C25 Primary rep3

description: Myotubes Healthy C25 Primary rep3


title: skin-control-d28-rep2

description: RAG2 KO grafted with Balb/c splenocytes