title: Lymphocytes_LowH2AX_24hr_2Gy_rep1

city: Tomsk

first: Aleksei

middle: A

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

hyb_protocol: Labeled cDNA were hybridized to SurePrint G3 Human GE v2, 8x60K microarrays (G4851B) for 22 h at 65°C in a rotating Agilent hybridization oven. The cDNA was not fragmented before hybridization. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%). Images were quantified using Agilent Feature Extraction Software (version v. 10.7.3.1).

data_processing:
Agilent Feature Extraction Software (v. 10.7.3.1) was used for background subtraction and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity by nec and normalizeBetweenArrays functions from limma package

source_name: Lymphocytes, donor with low level of endogenous gH2AX foci and high radiation-induced micronucleus frequency, 24 hr, 2 Gy

label_protocol: cDNA samples was Cy3-labeled using the SureTag DNA labeling kit (Agilent Technologies, Inc., USA), followed by RNAeasy MinElute column purification (Qiagen, USA). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) following the manufacturer's protocol. RNA quality was assessed by RNA integrity number using Agilent 2200 TapeStation (Agilent Technologies).

treatment_protocol: Freshly drawn whole blood samples from healthy individuals were collected in vacuum tubes with sodium heparin and exposed to 2 Gy of 60Co g-rays (0.67 Gy/min). After transportation on ice, 1.5 ml of whole blood was cultured in 6 ml of RPMI 1640 medium with 10% FBS in the presence of 20 μg/ml phytohaemagglutinin. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2 and lymphocytes wereisolated using Ficoll gradient.

tag: individual

value: Person 4

value: Peripheral blood lymphocytes

value: Male

tag: treatment

value: 2 Gy g-rays


title: T4

status: Public on Mar 25 2017

type: RNA

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

description: Gene expression in the left lobe of the thyroid gland of a 33y old male with papillary carconoma

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

molecule: total RNA

organism: Homo sapiens

source_name: Papillary cancer region of the thyroid tumor_ Replicate 4

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: unilateral, single, 32.0 mm papillary carcinoma, classical type in the left thyroid lobe. Pathological stage pT3N0Mx.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Lobectomy of the left lobe of the thyroid gland

tag: Sex

value: male

tag: age

value: 33 years old

tag: status

value: papillary carcinoma

tag: tissue

value: left lobe of the thyroid gland


title: T2

source_name: Papillary cancer region of the thyroid tumor_ Replicate 2


title: N2

source_name: Benign region of the thyroid tumor_Replicate 2


title: N4

source_name: Benign region of the thyroid tumor_Replicate 4


title: Lymphocytes_LowH2AX_24hr_2Gy_rep3

value: Person 6

tag: cell type

tag: gender

tag: group

value: donor with low level of endogenous gH2AX foci and high radiation-induced micronucleus frequency


title: AP3

description: Gene expression in the DDX19B transfected cells from papillary carcinoma with local and lymph node metastasis of a 76y old female

source_name: Stably transfected with PANK2 BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 3

growth_protocol: BCPAP cells protocol described in: Fabien N. Fusco A. Santoro M. Barbier Y. Dubois PM. Paulin C. (1994) Description of a human papillary thyroid-carcinoma cell-line—morphologic study and expression of tumoral markers. Cancer. 73:2206–2212. 8505C cells protocol described in: Ito T, Seyama T, Hayashi Y, Hayashi T, Dohi K, Mizuno T, Iwamoto K, Tsuyama N, Nakamura N, Akiyama M. (1994). Establishment of 2 human thyroid-carcinoma cell-lines (8305c, 8505c) bearing p53 gene-mutations. Int J Oncol. 4(3):583-6.

treatment_protocol: Cells were cultured in Rosswell Park Memorial Institute (RPMI)-1640 supplemented with 10% fetal bovine serum (FBS), penicillin 10,000 IU/mL, streptomycin 10 mg/mL, and 2 mM L-glutamine. Cells were stably transfected using pLX304 lentiviral vector (marker blasticidin, V5 epitope tag) with the ORF clone of PANK2 (pantothenate kinase 2), ORF clone accession number CCSB53315.1. The clone was produced by the shRNA Core Facility of the Albert Einstein College of Medicine (Catalog # HsCD00440361, (https://www.einstein.yu.edu/research/shared-facilities/shrna/resources).

value: female

value: 76 years old

value: thyroid gland


title: 2-y-o day 7 post-wounded

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Mus musculus

source_name: wounded skin

label_protocol: Microarray assay was performed using a service provider (LC Sciences). A strand-labeling reaction was carried out with total RNA (0.5 ug), control oligo-nucleotides, App-Cap3(5’-adenylated and 3’-dideoxy oligo-adaptor) and T4 RNA ligase (Rnl2tr-K227Q, New England BioLabs) in T4 RNA ligase buffer with PEG 8000 and RNase inhibitor (Promega).  The reaction mixture was incubated at 16ºC for 16 hours and stopped by adding equal volume of hybridization buffer.  The adapter sequence contains a tag segment for capturing fluorescent dye during a later dye staining process.

extract_protocol: Direct-zol™ RNA MiniPrep

value: 2 years old

value: back skin

value: days 7 after wounding


title: 2-y-o day 5 post-wounded

value: days 5 after wounding


title: 8-w-o unwounded skin

source_name: unwounded skin

value: 8 weeks old


title: 2-y-o Unwounded skin


title: 2-y-o day 3 post-wounded

tag: time point

value: days 3 after wounding


title: Lymphocytes_LowH2AX_24hr_0Gy_rep3

source_name: Lymphocytes, donor with low level of endogenous gH2AX foci and high radiation-induced micronucleus frequency, 24 hr, 0 Gy

value: Peripheral blood lymphocytes

value: Male

value: control


title: Lymphocytes_HighH2AX_24hr_2Gy_rep2

source_name: Lymphocytes, donor with high level of endogenous gH2AX foci and low radiation-induced micronucleus frequency, 24 hr, 2 Gy

value: Person 2

value: 2 Gy g-rays


title: MCF7_Aconitine_10μM_rep2

status: Public on Mar 26 2017

city: Shanghai

first: chao

last: lv

state: None Selected

address: No. 325, Guohe Rd

department: School of Pharmacy

country: China

institute: Second Military Medical University

description: Gene expression data from human breast cancer cell line MCF7

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: biotin

source_name: Human breast cancer cell line MCF7

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The MCF7 cells were cultured in MEM/EBSS supplemented with 10% fetal bovine serum, 1mmol/L sodium pyruvate, 0.1mmol/L MEM non-essential amino acids, 100 unit/mL penicillin, and 100 mg/mL streptomycin in a incubator containing 5% CO2 at 37℃.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The MCF7 cells were treated by 102 molecules at 10μM or 1μM, DMSO, and 10μM mixture of four compounds (1:1:1:1) for 12h.

value: treatment

tag: perturbagen

value: Aconitine

tag: cell line

value: breast cancer cell line MCF7

tag: duration


title: Lymphocytes_LowH2AX_24hr_0Gy_rep2

value: Person 5

value: donor with low level of endogenous gH2AX foci and high radiation-induced micronucleus frequency


title: Lymphocytes_LowH2AX_24hr_0Gy_rep1

value: Person 4


title: Lymphocytes_HighH2AX_24hr_0Gy_rep2

source_name: Lymphocytes, donor with high level of endogenous gH2AX foci and low radiation-induced micronucleus frequency, 24 hr, 0 Gy


title: Lymphocytes_HighH2AX_24hr_0Gy_rep1

value: Person 1

value: donor with high level of endogenous gH2AX foci and low radiation-induced micronucleus frequency


title: Enchytraeus crypticus_Control dispersant 7days_rep2

status: Public on Mar 24 2017

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: Whole body extracts (20 organisms)

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

tag: exposure

value: soil spiked with the NM300K dispersant agent_tween 20, for 7 days

value: Whole body extracts

tag: stage of development

value: Adult organisms with well developed clitellum


title: Enchytraeus crypticus_Ag NM300K EC50 7days_rep1

value: Ag NM300K EC50 (effect concentration on reproduction) in soil for 7 days


title: Enchytraeus crypticus_Ag NM300K EC20 7days_rep1

value: Ag NM300K EC20 (effect concentration on reproduction) in soil for 7 days


title: Enchytraeus crypticus_Ag NM300K EC50 7days_rep2


title: Enchytraeus crypticus_Ag NM300K EC20 7days_rep3


title: Enchytraeus crypticus_Control dispersant 7days_rep3


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC50 7days_rep3

value: Ag-NPs Non-Coated EC50 (effect concentration on reproduction) in soil for 7 days


title: Lymphocytes_HighH2AX_24hr_2Gy_rep1

value: Peripheral blood lymphocytes

value: Male


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC50 7days_rep2


title: Enchytraeus crypticus_Control dispersant 7days_rep1


title: Enchytraeus crypticus_Ag NM300K EC20 7days_rep2


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC20 7days_rep2

value: Ag-NPs Non-Coated EC20 (effect concentration on reproduction) in soil for 7 days


title: Lymphocytes_HighH2AX_24hr_0Gy_rep3

value: Person 3

value: control


title: Enchytraeus crypticus_Ag NM300K EC50 7days_rep3


title: Lymphocytes_HighH2AX_24hr_2Gy_rep3

value: 2 Gy g-rays


title: Lymphocytes_LowH2AX_24hr_2Gy_rep2

value: Person 5


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC20 7days_rep3

value: Ag-NPs PVP-Coated EC20 (effect concentration on reproduction) in soil for 7 days


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC50 7days_rep2

value: Ag-NPs PVP-Coated EC50 (effect concentration on reproduction) in soil for 7 days


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC50 7days_rep1


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC50 7days_rep1


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC20 7days_rep3


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC50 7days_rep3


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC20 7days_rep1


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC20 7days_rep2


title: Enchytraeus crypticus_AgNO3 EC50 7days_rep2

value: AgNO3 EC50 (effect concentration on reproduction) in soil for 7 days


title: Enchytraeus crypticus_AgNO3 EC20 7days_rep3

value: AgNO3 EC20 (effect concentration on reproduction) in soil for 7 days


title: Enchytraeus crypticus_Control 7days_rep3

value: un-spiked soil for 7 days


title: Enchytraeus crypticus_Ag NM300K EC50 3days_rep2

value: Ag NM300K EC50 (effect concentration on reproduction) in soil for 3 days

value: Whole body extracts


title: Enchytraeus crypticus_AgNO3 EC50 7days_rep1

value: Adult organisms with well developed clitellum


title: Enchytraeus crypticus_AgNO3 EC50 7days_rep3


title: Enchytraeus crypticus_AgNO3 EC20 7days_rep1


title: Enchytraeus crypticus_Ag NM300K EC50 3days_rep1


title: Enchytraeus crypticus_AgNO3 EC20 7days_rep2


title: Enchytraeus crypticus_Ag NM300K EC20 3days_rep1

value: Ag NM300K EC20 (effect concentration on reproduction) in soil for 3 days


title: Enchytraeus crypticus_Control 7days_rep1


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC50 3days_rep2

value: Ag-NPs Non-Coated EC50 (effect concentration on reproduction) in soil for 3 days


title: Enchytraeus crypticus_Control dispersant 3days_rep1

value: soil spiked with the NM300K dispersant agent_tween 20, for 3 days


title: Enchytraeus crypticus_Ag NM300K EC20 3days_rep3


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC20 7days_rep1


title: Enchytraeus crypticus_Ag NM300K EC50 3days_rep3


title: Enchytraeus crypticus_Control dispersant 3days_rep2


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC50 3days_rep3


title: Enchytraeus crypticus_Ag NM300K EC20 3days_rep2


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC20 3days_rep3

value: Ag-NPs Non-Coated EC20 (effect concentration on reproduction) in soil for 3 days


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC20 3days_rep1


title: Enchytraeus crypticus_Control dispersant 3days_rep3


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC20 3days_rep2


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC50 3days_rep2

value: Ag-NPs PVP-Coated EC50 (effect concentration on reproduction) in soil for 3 days


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC50 3days_rep1


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC20 3days_rep2

value: Ag-NPs PVP-Coated EC20 (effect concentration on reproduction) in soil for 3 days


title: Enchytraeus crypticus_Ag-NPs Non-Coated EC50 3days_rep1


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC20 3days_rep3


title: Enchytraeus crypticus_AgNO3 EC50 3days_rep2

value: AgNO3 EC50 (effect concentration on reproduction) in soil for 3 days


title: Enchytraeus crypticus_AgNO3 EC50 3days_rep1


title: Enchytraeus crypticus_AgNO3 EC50 3days_rep3


title: Enchytraeus crypticus_AgNO3 EC20 3days_rep1

value: AgNO3 EC20 (effect concentration on reproduction) in soil for 3 days


title: Enchytraeus crypticus_Control 3days_rep1

value: un-spiked soil for 3 days


title: Enchytraeus crypticus_AgNO3 EC20 3days_rep3


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC20 3days_rep1


title: Enchytraeus crypticus_Control 3days_rep3


title: Enchytraeus crypticus_AgNO3 EC20 3days_rep2


title: Enchytraeus crypticus_Ag-NPs PVP-Coated EC50 3days_rep3


title: Enchytraeus crypticus_Control 7days_rep2


title: Enchytraeus crypticus_Control 3days_rep2


title: NPTr_uninfection_36h_rep2

city: Wuhan

first: Shishuo

last: Zhang

address: Shizishan Street

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

hyb_protocol: The biotin-labeled RNA was hybridized on an Affymetrix GeneChip miRNA 2.0 Array for 16h at 45℃ using the Affymetrix Hybridization Oven 645, following by washing and staining using the Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned using Affymetrix GeneChip Scanner 3000 for collecting signals, and the scanned images were quantified with the Affymetrix GCOS 1.4 software.

data_processing: The raw data were normalized with the Affymetrix miRNA QC tool software and analyzed with the Silicon Genetics GeneSpring 10.

organism: Sus scrofa

label_protocol: The qualified total RNA was labeled with the biotin using an Affymetrix Flash Tag Biotin HSR Kit according to the manufacturer's instructions.

growth_protocol: NPTr cells were cultured in DMEM supplemented with 10% FBS and maintained at 37℃ in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted using an Ambion miRNA isolation kit according to the manufacturer's instructions.

treatment_protocol: NPTr Cells were firstly washed with PBS for three times, then infected with swine H1N1/2009 influenza A virus at a MOI of 0.01. After one hour, the cells were re-suspended in DMEM with 0.5 μg/ml of TPCK-treated trypsin, and collected at 36h post-infection. The cells of uninfected groups as the mock simulated the procedure for virus infection.

value: newborn pig trachea (NPTr) cells

tag: agent


title: NPTr_infection_36h_rep2

value: swine H1N1/2009 influenza A virus


title: NPTr_infection_36h_rep1


title: NPTr_uninfection_36h_rep1


title: NPTr_infection_36h_rep3


title: NPTr_uninfection_36h_rep3


title: 127756, Passage 5, Technical Replicate 2

city: Silver Spring

first: Ian

last: Bellayr

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

description:
miRNA Expression between passages and compared to human cancer cell lines
It should be noted that the microarrays 8F3560_P7_1 and PCBM1641_P5_1 were removed from the set for further analysis as they were determined to be outliers.

hyb_protocol: Assembled slide chambers were placed in the hybridization oven set to 55oC with a rotator speed of 20rpm for 20 hours.  See manuscript for more detailed description

scan_protocol: All images were produced using the DNA microarray scanner with surescan high-resolution technology (Agilent Technologies).  Slides were scanned at 446 nm for the Cy3 dye and a resolution of 2 µm double pass.  See manuscript for more detailed description

data_processing: The spots were annotated through the Agilent Feature Extraction (AFE) 11.0 software.  All methods and analyses used in this study were implemented in JMP Genomics, which included normalization, principle component analysis, clustering, box plots and statistics.  See manuscript for more detailed description.

source_name: MSC Bone Marrow Derived

label_protocol: Individual RNA material was labeled with Cy3.  See manuscript for more detailed description

growth_protocol: MSCs were grown in alpha minimum essential media with 10% FBS, 1% L-gluatmine & 1% penicillin G and streptomycin under humidified atmosphere of 5% CO2 at 37C

extract_protocol: Total RNA was extracted by the Absolutely RNA miRNA Kit from Agilent Technologies

treatment_protocol: MSCs were passaged after reaching 80% confluency as determined by one sole cell biologist

value: Male

tag: age (years)


title: Universal RNA, Technical Replicate 1

description:
miRNA Expression compared to human cancer cell lines
It should be noted that the microarrays 8F3560_P7_1 and PCBM1641_P5_1 were removed from the set for further analysis as they were determined to be outliers.

organism: unidentified

source_name: Universal RNA


title: PCBM1655, Passage 3, Technical Replicate 3

value: Female


title: 127756, Passage 5, Technical Replicate 3


title: PCBM1655, Passage 3, Technical Replicate 2


title: PCBM1655, Passage 3, Technical Replicate 1


title: NT2, Technical Replicate 1

source_name: Embryonal Carcinoma


title: Universal RNA, Technical Replicate 2


title: NT2, Technical Replicate 2


title: PCBM1662, Passage 7, Technical Replicate 2


title: 127756, Passage 3, Technical Replicate 3


title: PCBM1662, Passage 5, Technical Replicate 3


title: PCBM1662, Passage 7, Technical Replicate 3


title: PCBM1662, Passage 3, Technical Replicate 3


title: PCBM1662, Passage 3, Technical Replicate 2


title: PCBM1662, Passage 5, Technical Replicate 1


title: 127756, Passage 5, Technical Replicate 1


title: PCBM1662, Passage 3, Technical Replicate 1


title: 127756, Passage 3, Technical Replicate 2


title: 8F3560, Passage 7, Technical Replicate 3


title: 127756, Passage 3, Technical Replicate 1


title: PCBM1662, Passage 5, Technical Replicate 2


title: PCBM1662, Passage 7, Technical Replicate 1


title: 8F3560, Passage 3, Technical Replicate 1


title: 8F3560, Passage 3, Technical Replicate 2


title: 8F3560, Passage 5, Technical Replicate 2


title: 8F3560, Passage 3, Technical Replicate 3


title: 8F3560, Passage 5, Technical Replicate 3


title: 8F3560, Passage 5, Technical Replicate 1


title: 167696, Passage 3, Technical Replicate 3


title: 167696, Passage 7, Technical Replicate 1


title: 167696, Passage 3, Technical Replicate 2


title: 167696, Passage 7, Technical Replicate 3


title: 167696, Passage 5, Technical Replicate 2


title: 167696, Passage 3, Technical Replicate 1


title: 167696, Passage 5, Technical Replicate 1


title: 167696, Passage 7, Technical Replicate 2


title: 8F3560, Passage 7, Technical Replicate 2


title: 110877, Passage 7, Technical Replicate 2


title: 110877, Passage 7, Technical Replicate 3


title: 110877, Passage 5, Technical Replicate 3


title: 110877, Passage 7, Technical Replicate 1


title: 110877, Passage 5, Technical Replicate 2


title: 110877, Passage 3, Technical Replicate 3


title: 110877, Passage 5, Technical Replicate 1


title: PCBM1632, Passage 7, Technical Replicate 1


title: 110877, Passage 3, Technical Replicate 2


title: 110877, Passage 3, Technical Replicate 1


title: PCBM1632, Passage 5, Technical Replicate 3


title: PCBM1632, Passage 7, Technical Replicate 2


title: PCBM1632, Passage 7, Technical Replicate 3


title: 167696, Passage 5, Technical Replicate 3


title: PCBM1632, Passage 3, Technical Replicate 3


title: PCBM1632, Passage 3, Technical Replicate 2


title: PCBM1641, Passage 7, Technical Replicate 2


title: PCBM1641, Passage 7, Technical Replicate 3


title: PCBM1632, Passage 3, Technical Replicate 1


title: PCBM1632, Passage 5, Technical Replicate 2


title: PCBM1641, Passage 5, Technical Replicate 2


title: PCBM1641, Passage 3, Technical Replicate 1


title: PCBM1641, Passage 3, Technical Replicate 3


title: PCBM1641, Passage 3, Technical Replicate 2


title: PCBM1641, Passage 5, Technical Replicate 3


title: PCBM1641, Passage 7, Technical Replicate 1


title: PCBM1632, Passage 5, Technical Replicate 1


title: E. coli CRP Q strain_acetate_stationary phase_repl2

city: ESPINARDO

first: ANA

last: ÉCIJA

state: MURCIA

address: CAMPUS ESPINARDO

department: BIOQUÍMICA Y BIOLOGÍA MOLECULAR B E INMUNOLOGÍA

country: Spain

institute: UNIVERSIDAD DE MURCIA

description: E. coli Δcrp JW5702-4 background with a K100Q mutant of CRP (CRP Q) inserted into paaH gene locus

hyb_protocol: Following fragmentation and labeling, 1,0 ug of cDNA was hybridized for 16 hr at 45ºC on GeneChip E. coli Genome 2.0 Array using the GeneChip Hybridization Oven 645.  After hybridization, arrays  were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using  GeneChip Scanner 7000 with Autoloader.

data_processing: Data were analyzed with RMA (Robust Multiarray Analysis) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Escherichia coli K-12

source_name: E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 5ug of total RNA (GeneChip Expression Analysis Technical Manual, PN 702232, Affymetrix).

growth_protocol: E. coli Wild type and its mutants were grown in M9 minimal medium with 10mM glucose or 30mM acetate as sole carbon source. Samples for RNA extraction were taken in middle exponential phase (OD600≈0.5) and in stationary phase (OD600≈1.5)

extract_protocol: Total RNA extraction using Vantage™ RNA Purification Kit (Origene, Rockville, MD, USA) was performed according with the manufacter instructions.  Purity and concentration of isolated RNA were assessed in a NanoDrop One spectrophotometer (Thermo Scientific Incorporated, WI, USA). Quality was evaluated by microfluidic capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, USA).

tag: genotyp/variation

value: deltacrp JW5702-4 background with a K100Q mutant of CRP (CRP Q) inserted into paaH gene locus


title: E. coli CRP Q strain_acetate_stationary phase_repl1

source_name: E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1


title: E. coli CRP R strain_acetate_stationary phase_repl2

description: E. coli Δcrp JW5702-4 background with a K100R mutant of CRP (CRP R) inserted into paaH gene locus

source_name: E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2

value: deltacrp JW5702-4 background with a K100R mutant of CRP (CRP R) inserted into paaH gene locus


title: wt CD45RBhigh

city: Rehovot

first: Idit

last: Shachar

address: Herzel Street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: 2ug ss cDNA in 80 ul total volume 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_0007 protocol.

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

data_processing: The analysis was carried out using Partek Genomic Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

source_name: splenic T cells, CD45RBhigh, WT

label_protocol: 200ng Total RNA were used for labeling. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit.

growth_protocol: CD4+CD25-CD45RBhigh/low T cells were FACS sorted from the spleens of 6- to 8-week-old C57bl/6 wt or CCR2-/- mice. Cells were grown at 37 Celsius, 5% CO2 in full RPMI medium containing 10% FCS on plates coated with aCD3/aCD28 antibodies for 48hr.

extract_protocol: Total RNA was isolated by TRI Reagent Kit (Sigma Aldrich, #T9424) according to the manufacturer's instructions.

treatment_protocol: Sorted T cells were activated on aCD3/aCD28 coated plates for 48hr.

tag: strain/background

tag: genotype/variation

value: wild type

value: splenic CD4+CD25-CD45RBhigh T cells


title: wt CD45RBlow 2

source_name: splenic T cells, CD45RBlow, WT

value: splenic CD4+CD25-CD45RBlow T cells


title: E. coli CRP Q strain_acetate_exponential phase_repl2

source_name: E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2


title: wt CD45RBhigh 2


title: CCR2-/- CD45RBlow 2

source_name: splenic T cells, CD45RBlow, CCR2-/-


title: CCR2-/- CD45RBlow


title: CCR2-/- CD45RBhigh

source_name: splenic T cells, CD45RBhigh, CCR2-/-


title: CCR2-/- CD45RBhigh 2


title: E. coli CRP Q strain_acetate_exponential phase_repl1

source_name: E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1


title: wt CD45RBlow


title: E. coli CRP R strain_acetate_stationary phase_repl1

source_name: E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1


title: E. coli CRP R strain_acetate_exponential phase_repl2

source_name: E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2


title: iPS

city: Pamplona

first: Olalla

last: Iglesias-Garcia

address: Pio XII 55

institute: CIMA

description: Gene expression data from iPS cells

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: iPS

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: iPS cells were maintained in serum containing media with feeder cells. Culture media consisted of 15% of serum (Hyclone) and DMEM high glucose (Gibco) supplemented with 1% P/S (Biowhittaker), 1% L-Glu (Gibco), 0.1 mM b-mercaptoehanol (Gibco), 1% non-essential amino acids (Gibco) and LIF Chemicon).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: For cardiac differentiation, iPS cells were culture on suspension during 5 days to allow EBs formation. After 5 days, EBs were plated on gelatin coated dishes and treated with 1% of DMSO and/or 100 ng/ml of NRG-1 protein.

tag: strain

value: female

tag: differentiation stage

value: undifferentiated cells


title: E. coli CRP N strain_acetate_stationary phase_repl1

description: E. coli Δcrp JW5702-4 background with a wild type CRP (CRP N) inserted into paaH gene locus

source_name: E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1

value: deltacrp JW5702-4 background with a wild type CRP (CRP N) inserted into paaH gene locus


title: E. coli CRP N strain_acetate_stationary phase_repl2

source_name: E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2


title: E. coli CRP R strain_acetate_exponential phase_repl1

source_name: E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1


title: NRG1_CMs

description: Gene expression data from iPS cells treated with NRG1

source_name: iPS treated with NRG1

value: iPS-CMs treated with NRG1 at day 7 of differentiation


title: DMSO_NRG1_CMs

description: Gene expression data from iPS cells treated with DMSO and NRG1

source_name: iPS treated with DMSO and NRG1

value: iPS-CMs treated with DMSO+NRG1 at day 7 of differentiation


title: Neonatal_CMs

description: Gene expression data from neonatal cardiomyocytes

source_name: Neonatal cardiomyocyte

value: CMs derived from mice neonatal heart


title: DMSO_CMs

description: Gene expression data from iPS cells treated with DMSO

source_name: iPS treated with DMSO

value: iPS-CMs treated with DMSO at day 7 of differentiation


title: E. coli CRP N strain_acetate_exponential phase_repl2

source_name: E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2


title: E. coli Wild type_acetate_exponential phase_repl2

description: E. coli BW25113 wt

source_name: E. coli wt grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2


title: E. coli Wild type_acetate_stationary phase_repl1

description: E. coli BW25113 wt

source_name: E. coli wt grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1


title: E. coli Wild type_acetate_exponential phase_repl1

description: E. coli BW25113 wt

source_name: E. coli wt grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1


title: E. coli Wild type_acetate_stationary phase_repl2

description: E. coli BW25113 wt

source_name: E. coli wt grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2


title: E. coli CRP Q strain_glucose_stationary phase_repl2

source_name: E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2


title: Adult_CMs

description: Gene expression data from adult cardiomyocytes

source_name: Adult cardiomyocyte

value: CMs derived from mice adult heart


title: E. coli CRP Q strain_glucose_stationary phase_repl1

source_name: E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1


title: E. coli CRP Q strain_glucose_exponential phase_repl2

source_name: E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2


title: NPTr_infection_36h_rep2

hyb_protocol: The biotin-labeled cRNA was hybridized on an Affymetrix  Porcine genome array Array for 16h at 45℃ using the Affymetrix Hybridization Oven 645, following by washing and staining using the Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned using the Affymetrix GeneChip Scanner 3000 for collecting signals, and the scanned images were quantified with the Affymetrix Command Console software 3.1.

data_processing: The raw data were loaded to the Agilent GeneSpring 11.0 and analyzed using the Affymetrix Microarray Analysis Suit 5.0 algorithm.

label_protocol: The qualified total RNA was labeled with the biotin using an Affymetrix GeneChip 3'IVT Express Kit according to the manufacturer's instructions.

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

value: newborn pig trachea (NPTr) cells


title: E. coli CRP R strain_glucose_exponential phase_repl2

source_name: E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2


title: E. coli CRP N strain_acetate_exponential phase_repl1

source_name: E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1


title: E. coli CRP R strain_glucose_stationary phase_repl1

source_name: E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1


title: E. coli CRP R strain_glucose_exponential phase_repl1

source_name: E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1


title: E. coli CRP N strain_glucose_stationary phase_repl2

source_name: E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2


title: NPTr_infection_36h_rep3

value: swine H1N1/2009 influenza A virus


title: NPTr_infection_36h_rep1


title: E. coli CRP N strain_glucose_stationary phase_repl1

source_name: E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1


title: NPTr_uninfection_36h_rep2


title: NPTr_uninfection_36h_rep1


title: NPTr_uninfection_36h_rep3


title: E. coli CRP Q strain_glucose_exponential phase_repl1

source_name: E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1


title: E. coli CRP R strain_glucose_stationary phase_repl2

source_name: E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2


title: E. coli Wild type_glucose_stationary phase_repl1

description: E. coli BW25113 wt

source_name: E. coli wt grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1


title: E. coli Wild type_glucose_stationary phase_repl2

description: E. coli BW25113 wt

source_name: E. coli wt grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2


title: B. subtilis speD midlog Exp.2 rep.3

city: Dallas

first: Anthony

middle: John

last: Michael

address: 6001 Forest Park

department: Pharmacology

institute: UT Southwestern Medical Center, Dallas

description: Expression data from midlog planktonic speD mutant strain

hyb_protocol: Labeled cDNAs were hybridized to Affymetrix antisense Bacillus subtilis microarrays using the suggested Affymetrix protocol

scan_protocol: Affymetrix standard procedure

data_processing: Data was processed with MAS5 using Expression Console software.

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: Midlog cells

label_protocol: 5 microgram of total RNA was labelled according to Affymetrix standard protocol

growth_protocol: Bacterial cultures were grown to midlog phase in MSgg polyamine-free chemically defined medium

extract_protocol: Total RNA was extracted with an Ambion Ribopure kit.

treatment_protocol: No treatment, comparison between parental strain B. subtilis NCIB3610 and an S-adenosylmethionine decarboxylase (speD) mutant

tag: genotype

value: ΔspeD


title: E. coli Wild type_glucose_exponential phase_repl2

description: E. coli BW25113 wt

source_name: E. coli wt grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2


title: E. coli Wild type_glucose_exponential phase_repl1

description: E. coli BW25113 wt

source_name: E. coli wt grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1


title: B. subtilis 3610 midlog Exp.2 rep.2

description: Expression data from midlog planktonic NCIB3610 parental strain

value: Wild Type


title: B. subtilis speD midlog Exp.2 rep.1


title: E. coli CRP N strain_glucose_exponential phase_repl2

source_name: E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2


title: ST486-miR-150-Tot2

city: Poznan

first: Agnieszka

last: Dzikiewicz-Krawczyk

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

description:
mRNA and lncRNA expression analysis_ST486-miR-150_total fraction_2
Cy5 signals in raw data files represent unrelated samples

hyb_protocol: Each Cy-3 sample was mixed with the same amount of a Cy5-labeled sample, which was non-relevant for this study, and hybridized at 65oC overnight on Agilent-050524 SurePrint G3 Custom Human 8x60K Microarrays.

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: ST486 cell line with miR-150 overexpression vector

label_protocol: Cy3 labelled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 3 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies).

growth_protocol: RPMI-1640 medium supplemented with 100U/ml penicillin, 0.1mg/ml  streptomycin, 2mM ultraglutamine and 10% (DG75) or 20% (ST486) Fetal Calf Serum, 37⁰C, 5% CO2

extract_protocol: miRNeasy Micro/Mini Kit (Qiagen)

treatment_protocol: Cells were transduced with lentiviral pCDH-EF1α vector with miR-150 overexpression construct and GFP+ cell were sorted

tag: cell type

value: Burkitt lymphoma cell line

tag: transduced with

value: miR-150 overexpression vector

tag: ip with

value: none (input)

tag: molecule subtype

value: total RNA


title: ST486-miR-150-Tot1

description:
mRNA and lncRNA expression analysis_ST486-miR-150_total fraction_1
Cy5 signals in raw data files represent unrelated samples


title: ST486-miR-150-IP2

description:
mRNA and lncRNA expression analysis_ST486-miR-150_AGO2IP fraction_2
Cy5 signals in raw data files represent unrelated samples

treatment_protocol: Cells were transduced with lentiviral pCDH-EF1α vector with miR-150 overexpression construct, GFP+ cell were sorted and subjected to imunoprecipitation using AGO2 ab (Clone 2E12-1C9)

value: AGO2 ab (Clone 2E12-1C9)

value: AGO2-IP RNA


title: B. subtilis speD midlog Exp.1 rep.3


title: B. subtilis 3610 midlog Exp.2 rep.3


title: B. subtilis speD midlog Exp.1 rep.1


title: B. subtilis speD midlog Exp.1 rep.2


title: B. subtilis 3610 midlog Exp.2 rep.1


title: ST486-miR-150-IP1

description:
mRNA and lncRNA expression analysis_ST486-miR-150_AGO2IP fraction_1
Cy5 signals in raw data files represent unrelated samples


title: B. subtilis 3610 midlog Exp.1 rep.3


title: ST486-EV-IP2

description:
mRNA and lncRNA expression analysis_ST486-EV_AGO2IP fraction_2
Cy5 signals in raw data files represent unrelated samples

source_name: ST486 cell line with empty vector

treatment_protocol: Cells were transduced with empty lentiviral pCDH-EF1α vector, GFP+ cell were sorted and subjected to imunoprecipitation using AGO2 ab (Clone 2E12-1C9)

value: empty vector


title: Brown Adipose Tissue_High fat diet_ID16

city: Takasaki

first: Toshitada

last: Nagai

state: Gunma

address: 37-1 Nakaorui-machi

department: Department of Food and Life-Science

country: Japan

institute: Takasaki University of Health and Welfare

description: A 3-week-old rat was fed high fat diets (H) containing a ratio of carbohydrate:fat (C:F) (35:45 in energy percent). A Rat consumed the diets for 9 weeks and was subjected to DNA microarray analysis.

hyb_protocol: The aRNA was fragmented and hybridized to a GeneChip Rat Genome 230 2.0 Array (Affymetrix) for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin using the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Genechips were submitted to scanning on an Affymetrix GeneChip Scanner 3000 7G. The Affymetrix GeneChip® Command Console Software was used to make CEL files.

data_processing: The CEL files derived from liver, WAT and BAT were quantified using robust multi-array average (RMA), factor analysis for robust microarray summarization (quantile normalization, qFARMS) and GCRMA, respectively, using the statistical language R (2.7.1) (http://www.r-project), and Bioconductor (2.2) (http://www.bioconductor.org/).

organism: Rattus norvegicus

source_name: brown adipose tittue of a rat fed high fat diets

label_protocol: Anti-sense RNA was synthesized from 100 or 200 ng of purified total RNA, and biotinylated aRNA was obtained using a GeneChip 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Rats were acclimated to the laboratory environment for a week with chow diets (MF, Oriental yeast, Tokyo, Japan). Animals were divided into three groups so that the average body weights of each group were equal to each other before being given diets with different C:F energy ratios: low (L) 65:15, moderate (M) 60:20, and high (H) 35:45 fat diet groups. Rats were fed diets ad libitum for a week. Then, the L-group was fed ad libitum and the other groups were fed isoenergetically compared with the L-group for 9 weeks. Diets were removed 17 hours before dissection, and rats were sacrificed to collect liver, white adipose tissue (WAT) and brown adipose tissue (BAT). Because a decreased dietary intake was found in two rats belonging to the M- or H-groups (M_7 and H_11 in identical number), these two rats were omitted from all analyses.

extract_protocol: Total RNA was isolated from each hepatic piece, WAT and BAT by TRIzol reagent (Invitrogen Japan, Tokyo, Japan) and purified using RNeasy mini kits (Qiagen, Tokyo, Japan).

treatment_protocol: Small hepatic pieces were immersed into RNAlater (Qiagen, Tokyo, Japan). WAT and BAT were frozen immediately after extirpation using liquid nitrogen. All samples were stored at -80 or -150ºC until analysis.

value: Wistar


title: ST486-EV-Tot2

description:
mRNA and lncRNA expression analysis_ST486-EV_total fraction_2
Cy5 signals in raw data files represent unrelated samples

treatment_protocol: Cells were transduced with empty lentiviral pCDH-EF1α vector and GFP+ cell were sorted


title: Brown Adipose Tissue_Low fat diet_ID3

description: A 3-week-old rat was fed low fat diets (L) containing a ratio of carbohydrate:fat (C:F) (65:15 in energy percent). A Rat consumed the diets for 9 weeks and was subjected to DNA microarray analysis.

source_name: brown adipose tittue of a rat fed low fat diets


title: Brown Adipose Tissue_High fat diet_ID15


title: Brown Adipose Tissue_High fat diet_ID13


title: E. coli CRP N strain_glucose_exponential phase_repl1

source_name: E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1

value: deltacrp JW5702-4 background with a wild type CRP (CRP N) inserted into paaH gene locus


title: ST486-EV-Tot1

description:
mRNA and lncRNA expression analysis_ST486-EV_total fraction_1
Cy5 signals in raw data files represent unrelated samples


title: Brown Adipose Tissue_Low fat diet_ID4


title: ST486-EV-IP1

description:
mRNA and lncRNA expression analysis_ST486-EV_AGO2IP fraction_1
Cy5 signals in raw data files represent unrelated samples


title: Brown Adipose Tissue_High fat diet_ID12


title: Brown Adipose Tissue_Low fat diet_ID5


title: B. subtilis 3610 midlog Exp.1 rep.2


title: White Adipose Tissue_High fat diet_ID16

source_name: white adipose tittue of a rat fed high fat diets


title: DG75-miR-150-Tot2

description:
mRNA and lncRNA expression analysis_DG75-miR-150_total fraction_2
Cy5 signals in raw data files represent unrelated samples

source_name: DG75 cell line with miR-150 overexpression vector


title: Brown Adipose Tissue_Low fat diet_ID2


title: White Adipose Tissue_High fat diet_ID15


title: B. subtilis 3610 midlog Exp.1 rep.1


title: White Adipose Tissue_Low fat diet_ID5

source_name: white adipose tittue of a rat fed low fat diets


title: DG75-miR-150-Tot1

description:
mRNA and lncRNA expression analysis_DG75-miR-150_total fraction_1
Cy5 signals in raw data files represent unrelated samples


title: White Adipose Tissue_High fat diet_ID13


title: White Adipose Tissue_High fat diet_ID12


title: White Adipose Tissue_Low fat diet_ID2


title: Brown Adipose Tissue_Low fat diet_ID1


title: DG75-miR-150-IP2

description:
mRNA and lncRNA expression analysis_DG75-miR-150_AGO2IP fraction_2
Cy5 signals in raw data files represent unrelated samples


title: White Adipose Tissue_Low fat diet_ID1

source_name: white adipose tissue of a rat fed low fat diets


title: White Adipose Tissue_Low fat diet_ID4


title: DG75-EV-Tot2

description:
mRNA and lncRNA expression analysis_DG75-EV_total fraction_2
Cy5 signals in raw data files represent unrelated samples

source_name: DG75 cell line with empty vector


title: Liver_High fat diet_ID13

source_name: liver of a rat fed high fat diets


title: DG75-miR-150-IP1

description:
mRNA and lncRNA expression analysis_DG75-miR-150_AGO2IP fraction_1
Cy5 signals in raw data files represent unrelated samples


title: Liver_High fat diet_ID12


title: Liver_High fat diet_ID16


title: Liver_Moderate fat diet_ID10

description: A 3-week-old rat was fed moderate fat diets (M) containing a ratio of carbohydrate:fat (C:F) (60:20 in energy percent). A Rat consumed the diets for 9 weeks and was subjected to DNA microarray analysis.

source_name: liver of a rat fed moderate fat diets


title: Sample5_CS_ATRA_1

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: all-trans-retinoic acid (0.1ug/ml) in control solvent

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: Psoriasiform keratinocyte cultures were established by incubating epidermal keratinocyte progenitors from stratum basale (Zen-Bio, Research Triangle Park, NC) with CnT-PCT media supplemented with cytokines IL-17A/IL-22/TNFα (100ng/ml;100ng/ml;10ng/ml).

extract_protocol: Total RNA was extracted with NucleoSpin II kit (Machery Nagel, Bethlehem, PA)

treatment_protocol: Test materials were added and the incubation in the presence of cytokines (IL-17A/IL-22/TNFα; 100ng/ml;100ng/ml;10ng/ml) was pursued for 24h.

value: Dermal keratinocytes

tag: treatment

value: ATRA


title: White Adipose Tissue_Low fat diet_ID3


title: Sample3_CS_SE_1

source_name: bakusylan (10ug/ml) in control solvent

value: SE


title: Liver_High fat diet_ID15


title: DG75-EV-IP2

description:
mRNA and lncRNA expression analysis_DG75-EV_AGO2IP fraction_2
Cy5 signals in raw data files represent unrelated samples

tag: cell line


title: Sample4_CS_SE_2


title: Liver_Low fat diet_ID5

source_name: liver of a rat fed low fat diets


title: Sample6_CS_ATRA_2


title: Sample2_CS_2

source_name: control solvent (3% dimethyl isosorbide; 40% glycerin; 57% butylene glycol)

value: control


title: Liver_Moderate fat diet_ID9


title: Sample1_CS_1


title: Liver_Moderate fat diet_ID8


title: Liver_Low fat diet_ID4


title: Liver_Low fat diet_ID3


title: B. subtilis speD midlog Exp.2 rep.2

description: Expression data from midlog planktonic speD mutant strain

source_name: Midlog cells


title: Liver_Low fat diet_ID1


title: xeno26_control

city: Padova

first: Luca

last: Trentin

address: Via Giustiniani, 3

department: Department of Women's and Children's Health

country: Italy

institute: University of Padova

description: Gene expression data from  leukemia samples treated with DMSO ex vivo for 6h

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: leukemia cell isolated from BM of NOD/SCID  mice with full-blown leukemia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 100ng of Total RNA using the Affymetrix 3' IVT Plus Kit

growth_protocol: xenograft leukemia blasts were cultured in alpha-MEM without stroma

extract_protocol: RNA was extracted using Trizol.

treatment_protocol: Givinostat (ITF2357, 0.2uM) dissolved in DMSO, or only DMSO as vehicle, in 24-well plates for  6h.

value: DMSO

tag: tissue

value: B-cell precursor acute lymphoblastic leukemia

tag: xenograft host

value: bone marrow of NOD/SCID  mice


title: xeno31_control


title: xeno17_treatment

description: Gene expression data from  leukemia samplestreated with ITF2357 0.2uM for 6h


title: Liver_Low fat diet_ID2


title: xeno17_control


title: xeno22_control


title: xeno22_treatment


title: DG75-EV-Tot1

description:
mRNA and lncRNA expression analysis_DG75-EV_total fraction_1
Cy5 signals in raw data files represent unrelated samples


title: S2 cells, incubated with apoptotic cell fragments, biological rep3

status: Public on Mar 23 2017

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

hyb_protocol: Following fragmentation, 6.5 µg cRNA was hybridized for 16 hr at 45°C on Affymetrix GeneChip Drosophila Genome 2.0 Array. GeneChip was washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Drosophila melanogaster

source_name: Drosophila S2 cells, stimulated with apoptotic cell fragments

label_protocol: Biotinylated cRNA was obtained from 150 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: S2 cell lines were maintained at 25 °C in Schneider's Drosophila medium containing 10% (v/v) heat-inactivated fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific K.K.), then purified with an RNeasy Micro kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Semi-confluent S2 cells maintained in Schneider's Drosophila medium with 1% heat-inactivated FBS were supplemented with the apoptotic cell fragments, at a responder/effector ratio of 1 : 25.  The mixtures, together with phagocyte cultures with no fragments added as a negative control, were incubated at 25 °C for 1h, and cells were detached from culture containers by the treatment with 0.25% (w/v) trypsin and 0.02% (w/v) EDTA.

value: Schneider 2 (S2) cells, a macrophage-like cell line

value: with apoptotic cell fragments

tag: time


title: xeno1L_control


title: xeno1L_treatment


title: xeno31_treatment


title: S2 cells, incubated with apoptotic cell fragments, biological rep1


title: C57BL-mice_liver_CFDdiet-12wks_rep3

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description: Gene expression in the livers of C57BL/6J mice fed a CFD diet for 12 weeks

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: C57BL-mice, liver, CFDdiet-12wks, replicate 3

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

extract_protocol: Total RNA was extracted from liver tissue using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male C57BL/6J were housed in sterilized cages in a temperature-controlled room (24°C) with a 12-h light/dark cycle, and given ad libitum access to water and NIH-41 irradiated pelleted diet. At 8 weeks of age, mice allocated randomly to control and experimental groups. Mice in the CFD diet experimental group were maintained on a diet low in methionine (0.17% w/w) and lacking choline and folic acid (diet no. 519541, choline- and folate-deficient, iron-supplemented, and l-amino acid-defined diet; Dyets, Bethlehem, PA, USA) for 12 weeks. Mice in the control group received the same diet supplemented with 0.4% methionine, 0.3% choline bitartrate, and 2 mg/kg folic acid. Experimental and control mice were euthanized by exsanguination following deep isoflurane anesthesia 12 weeks after diet initiation. The liver was snap-frozen immediately in liquid nitrogen and stored at −80 °C for subsequent analyses.

value: liver

tag: gender

value: Male

tag: age

value: 20 weeks


title: C57BL-mice_liver_control_rep1

description: Gene expression in the livers of C57BL/6J mice fed a control diet

source_name: C57BL-mice, liver, control, replicate 1


title: S2 cells, incubated with apoptotic cell fragments, biological rep2


title: C57BL-mice_liver_control_rep3

source_name: C57BL-mice, liver, control, replicate 3


title: C57BL-mice_liver_CFDdiet-12wks_rep2

source_name: C57BL-mice, liver, CFDdiet-12wks, replicate 2


title: C3H_BZT+INFgamma

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

institute: SRC Bioclinicum

description: mRNA expression data from primary astrocytes exposed to interferon-gamma and benztropine

hyb_protocol: The samples were hybridized on Affymetrix microarray GeneChip Mouse Gene 2.0 ST for 16 h at 48°C.

scan_protocol: Arrays were washed to remove nonspecifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix) and then scanned on Gene-Chip Scanner 3000 7G system (Affymetrix).

data_processing: CEL-files were jointly preprocessed in Affymetrix Expression Console (build 1.4.1.46) using RMA-sketch method

label_protocol: cDNA synthesis and labelling were carried out according to the Ambion WT Expression Kit (Life Technologies, Darmstadt, Germany) using 500 ng total RNA as starting material

growth_protocol: The cells were maintained in Advanced DMEM, 10% FBS, 1xGlutaMAX,1xSodium Piruvate,1xMEM NEAA, Gentamicin 40 mkg/ml (Gibco)

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

treatment_protocol: Cells were treated with IFNγ at a concentration of 250 IU/mL or with benztropine at a concentration of 2.0 μM in culture medium for 48 h before analysis.

value: primary astrocytes

tag: agent

value: interferon-gamma and benztropine


title: C3H_BZT

description: mRNA expression data from primary astrocytes exposed to benztropine

value: benztropine


title: C57BL-mice_liver_CFDdiet-12wks_rep1

source_name: C57BL-mice, liver, CFDdiet-12wks, replicate 1


title: C57BL-mice_liver_control_rep2

source_name: C57BL-mice, liver, control, replicate 2


title: C3H_control

description: mRNA expression data from primary astrocytes


title: 164337

type: genomic

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridized with the hybridization kit according the Agilent protocol

scan_protocol: We used a Surescan provided by Agilent and controled by SureScan Software

data_processing: the data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method - CGH v2 proposed by Agilent

molecule: genomic DNA

source_name: RCC

label_protocol: DNA was labeled with the sureTag labeling kit accirding the agilent protocol

extract_protocol: DNA was extracted from fresh, frozen or formol fixed-paraffin embedded fragments using Qiamp DNA mini kit.

value: ALK rearrangement

source_name: Female DNA control provided in SureTag Labeling Kit

tag: sample type

value: commercial DNA from cell lines


title: NA12878 Genomic DNA Replicate 2 (Agilent023642)

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

department: Life Sciences

country: Trinidad and Tobago

institute: The University of the West Indies

description: Test sample (ch1) = NA12878, Control sample (ch2) = NA10851

hyb_protocol: Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.genomics.agilent.com/en/SurePrint-CGH-CNV-Microarrays/Human-Genome-CGH-Microarrays/?cid=AG-PT-110&tabId=AG-PR-1079&navAction=pop

data_processing:
Raw data in the form of Feature Extraction (FE) files from the hybridization of NA12878 and NA10851 genomic DNA to the Agilent SurePrint G3 Human High Resolution Microarray 1x1M (Design ID 023642) were obtained from Agilent-recommended service providers. The FE files were processed to obtain CNV calls by using both Agilent Genomic Workbench 7.0.4.0 (Agilent Technologies, Santa Clara CA 95051, U.S.A.) and Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.) software packages. CNV calls were obtained by generating Interval Based Reports using Agilent Genomic Workbench with default settings according to the manufacturer's user guide, and by using the FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
Processed data are interval based reports generated using the ADM-2 algorithm in the Agilent Genomic Workbench software package. Header information lists the specific parameters used for the analysis. Columns include Chr (chromosome of CNV), Cytoband (cytoband of CNV), Start (start coordinate of CNV), Stop (stop coordinate of CNV), #Probes (number of probes in CNV interval), Amplification (Base2 log ratio indicating an amplification in the genome of NA12878 compared to that of NA10851), Deletion (Base2 log ratio indicating a deletion in the genome of NA12878 compared to that of NA10851), pval (p value), Gene Names (names of any genes overalpping with the CNV interval)
There are no intermediate processed files containing values for every probe. The only output generated were the final CNV calls from these software packages.

source_name: Blood, B Lymphocyte

extract_protocol: Genomic DNA was extracted from GM12878 and GM10851 cell lines by Coriell Cell Repositories

value: female

tag: ethnicity

value: Caucasian

value: male


title: NA12878 Genomic DNA Replicate 1 (Agilent022060)

scan_protocol: Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.genomics.agilent.com/en/SurePrint-CGH-CNV-Microarrays/Human-Genome-CGH-Microarrays/?cid=AG-PT-110&tabId=AG-PR-1079&navAction=pop

data_processing:
Raw data in the form of Feature Extraction (FE) files from the hybridization of NA12878 and NA10851 genomic DNA to the Agilent SurePrint G3 Human CGH Microarray 4x180K (Design ID 022060) were obtained from Agilent-recommended service providers. The FE files were processed to obtain CNV calls by using both Agilent Genomic Workbench 7.0.4.0 (Agilent Technologies, Santa Clara CA 95051, U.S.A.) and Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.) software packages. CNV calls were obtained by generating Interval Based Reports using Agilent Genomic Workbench with default settings according to the manufacturer's user guide, and by using the FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
Processed data are interval based reports generated using the ADM-2 algorithm in the Agilent Genomic Workbench software package. Header information lists the specific parameters used for the analysis. Columns include Chr (chromosome of CNV), Cytoband (cytoband of CNV), Start (start coordinate of CNV), Stop (stop coordinate of CNV), #Probes (number of probes in CNV interval), Amplification (Base2 log ratio indicating an amplification in the genome of NA12878 compared to that of NA10851), Deletion (Base2 log ratio indicating a deletion in the genome of NA12878 compared to that of NA10851), pval (p value), Gene Names (names of any genes overalpping with the CNV interval)
There are no intermediate processed files containing values for every probe. The only output generated were the final CNV calls from these software packages.


title: NA12878 Genomic DNA Replicate 1 (Agilent023642)

label_protocol: Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.genomics.agilent.com/en/SurePrint-CGH-CNV-Microarrays/Human-Genome-CGH-Microarrays/?cid=AG-PT-110&tabId=AG-PR-1079&navAction=pop


title: NA12878 Genomic DNA Replicate 1 (AffymetrixCytoScanHD)

hyb_protocol: Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.affymetrix.com/estore/browse/products.jsp?productId=prod520004#1_3

data_processing:
Raw data in the form of .cel files from the hybridization of NA12878 to the Affymetrix CytoScan HD array were obtained from Affymetrix (Santa Clara, CA 95051, U.S.A.). The .cel files were analyzed to generate CNV calls using both the ChAS software (Affymetrix Inc. Santa Clara, CA 95051, U.S.A.) with default settings against a reference composed of a female and male HapMap sample (NA10847 and NA10851 respectively), and Nexus Copy Number 7.5 (BioDiscovery, Hawthorne CA 90250, U.S.A.) using the SNP-FASST2 Segmentation Algorithm.
Processed data are output text files from the ChAS software showing CNV calls. Columns include CN State (number of copies of genomic region), Type (Copy number Gain or Loss), Chromosome (chromosome containing the CNV), Cytoband Start (cytoband containing start of CNV), Size (size of CNV in kbp), Marker Count (number of probes in CNV), Gene Count (number of genes in CNV), Microarray Nomenclature (array, cytoband, start-end coordinates of CNV, copy number), Genes (names of genes overlapping CNV)
The .cychp files are not available.

extract_protocol: Genomic DNA was extracted from GM12878 by Coriell Cell Repositories

value: Female


title: NA12878 Genomic DNA Replicate 2 (AffymetrixCytoScanHD)

scan_protocol: Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.affymetrix.com/estore/browse/products.jsp?productId=prod520004#1_3


title: NA12878 Genomic DNA Replicate 2 (Agilent022060)


title: Control tBRD-2 RNAi replicate 3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: Undriven tbrd-2RNAi control males carried one copy of tbrd-2RNAi (III chromosome).

hyb_protocol: According to manufacturers instructions without modifications.

data_processing: Data processing was done in R. CEL files were parsed using the affy package, intensities were background corrected and normalized using the rma function with default settings.

source_name: D. melanogaster testes

label_protocol: Biotinylated cRNA was prepared according to the appropriate Affymetrix protocol without further amplification.

growth_protocol: Drosophila melanogaster strains were maintained on standard medium at 30°C

extract_protocol: Total RNA was extracted from control testes and tbrd-2 knockdown testes by using TRIzol® (Invitrogen). RNA quality was validated using the Agilent Bioanalyser 2100 with the RNA 6000 Nano kit. Gene expression analysis was carried out using Affymetrix Drosophila Genome 2.0 arrays. For each array, independent RNA from whole testes pooled from 30 animals was used.

treatment_protocol: Testes from 0-2 day old control and tbrd-2 knockdown flies were dissected in PBS

value: adult testis


title: Control tBRD-2 RNAi replicate 2

scan_protocol: According to manufacturers instructions without modifications.


title: Control tBRD-2 RNAi replicate 1


title: C3H_INFgamma

description: mRNA expression data from primary astrocytes exposed to interferon-gamma

tag: strain

value: interferon-gamma


title: S2 cells, incubated with medium alone, biological rep1

source_name: Drosophila S2 cells, unstimulated

value: without apoptotic cell fragments


title: Control Bam replicate 1

description: bam-Gal4 control males carried two copies of bam-Gal4 (on chromosomes X and III).

value: bam/y;+/+;bam/Sb


title: S2 cells, incubated with medium alone, biological rep2

value: Schneider 2 (S2) cells, a macrophage-like cell line


title: Control Bam replicate 3


title: tBRD2 RNAi replicate 1

description: tbrd-2 knockdown males analyzed here carried two copies of bam-Gal4 (on chromosomes X and III) and one copy of tbrd-2RNAi (on the third chromosome).


title: tBRD2 RNAi replicate 2


title: Control Bam replicate 2


title: tBRD2 RNAi replicate 3

description: tbrd-2 knockdown males analyzed here carried two copies of bam-Gal4 (on chromosomes X and III) and one copy of tbrd-2RNAi (on the third chromosome). i


title: S2 cells, incubated with medium alone, biological rep3


title: AN18_Period3

city: Boston

first: Vladislav

last: Malkov

state: MA

address: 33 Avenue Loius Pasteur

department: Human Genetics and Pharmacogenomics

institute: Merck Sharp & Dohme Corp

hyb_protocol: The amplified cDNAs were hybridized to Affymetrix gene expression chips (Human Rosetta Custom Affymetrix 2.0, Affymetrix, Santa Clara, CA) using standard Affymetrix protocols.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 7G. The images were analyzed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Expression values were extracted using the Robust Multichip Average method (Irizarry RA et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003;4:249-64) as implemented in the Affymetrix Power Tools software (available at: http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx).

label: Biotin

source_name: Whole-genome gene expression profiles of nasal scrapes

label_protocol: Samples were amplified and labeled using the Ovation WB protocol (NuGEN Technologies, San Carlos, CA), according to the manufacturer’s instructions. In brief, 50 ng of total RNA was amplified using the Ribo-SPIA technology (NuGEN Technologies). After quantification, 4.4 ug cDNA was fragmented and labeled with biotin using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).

extract_protocol: Total RNA was extracted and purified from the clinical nasal scrapes specimens using the SV96 Total RNA Isolation System (Promega) according to a custom automated protocol. The extracted RNA was quantified using RiboGreen RNA Quantitation Reagent (Invitrogen) and its quality was assessed using Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA) in an Agilent 2100 Bioanalyzer (Agilent).

tag: subject

tag: period

value: nasal scrape specimen


title: AN16_Period1


title: AN18_Period0


title: AN16_Period0


title: AN16_Period2


title: AN18_Period2


title: AN16_Period3


title: AN17_Period1


title: AN17_Period3


title: AN19_Period0


title: AN14_Period0


title: AN15_Period0


title: AN18_Period1


title: AN14_Period2


title: AN17_Period2


title: AN14_Period3


title: AN15_Period2


title: AN10_Period3


title: AN19_Period3


title: AN9_Period0


title: AN15_Period3


title: AN13_Period3 (failed QC)

description: failed QC, no CEL file submitted


title: AN13_Period1


title: AN10_Period2


title: Liver_Moderate fat diet_ID6

description: A 3-week-old rat was fed moderate fat diets (M) containing a ratio of carbohydrate:fat (C:F) (60:20 in energy percent). A Rat consumed the diets for 9 weeks and was subjected to DNA microarray analysis.

source_name: liver of a rat fed moderate fat diets

value: Wistar


title: AN10_Period1


title: AN17_Period0


title: AN19_Period2


title: AN13_Period2


title: AN19_Period1


title: AN10_Period0


title: AN15_Period1


title: AN14_Period1


title: AN13_Period0


title: xeno26_treatment

value: B-cell precursor acute lymphoblastic leukemia

value: bone marrow of NOD/SCID  mice


title: AN9_Period3


title: AN7_Period0


title: DG75-EV-IP1

description:
mRNA and lncRNA expression analysis_DG75-EV_AGO2IP fraction_1
Cy5 signals in raw data files represent unrelated samples

source_name: DG75 cell line with empty vector

tag: cell type

value: Burkitt lymphoma cell line

value: empty vector

value: AGO2 ab (Clone 2E12-1C9)

value: AGO2-IP RNA


title: AN9_Period1


title: AN8_Period2


title: AN12_Period2


title: AN7_Period3


title: AN7_Period1


title: AN9_Period2


title: AN8_Period3


title: AN8_Period1


title: AN8_Period0


title: AN12_Period3


title: AN3_Period1


title: AN3_Period2


title: AN4_Period2


title: AN6_Period2


title: AN6_Period0


title: AN11_Period0


title: AN4_Period1


title: AN11_Period3


title: AN11_Period2


title: AN12_Period0


title: AN6_Period1


title: AN11_Period1


title: AN12_Period1


title: AN4_Period3


title: NA12878 Genomic DNA Replicate 2 (Agilent021365)

data_processing:
Raw data in the form of Feature Extraction (FE) files from the hybridization of NA12878 and NA10851 genomic DNA to the Agilent SurePrint G3 Human CNV Microarray 2x400K (Design ID 021365) were obtained from Agilent-recommended service providers. The FE files were processed to obtain CNV calls by using both Agilent Genomic Workbench 7.0.4.0 (Agilent Technologies, Santa Clara CA 95051, U.S.A.) and Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.) software packages. CNV calls were obtained by generating Interval Based Reports using Agilent Genomic Workbench with default settings according to the manufacturer's user guide, and by using the FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
Processed data are interval based reports generated using the ADM-2 algorithm in the Agilent Genomic Workbench software package. Header information lists the specific parameters used for the analysis. Columns include Chr (chromosome of CNV), Cytoband (cytoband of CNV), Start (start coordinate of CNV), Stop (stop coordinate of CNV), #Probes (number of probes in CNV interval), Amplification (Base2 log ratio indicating an amplification in the genome of NA12878 compared to that of NA10851), Deletion (Base2 log ratio indicating a deletion in the genome of NA12878 compared to that of NA10851), pval (p value), Gene Names (names of any genes overalpping with the CNV interval)
There are no intermediate processed files containing values for every probe. The only output generated were the final CNV calls from these software packages.

value: female


title: NA12878 Genomic DNA Replicate 1 (Agilent021365)

value: Caucasian


title: NA12878 Genomic DNA Replicate 2 (Agilent021850)

data_processing:
Raw data in the form of Feature Extraction (FE) files from the hybridization of NA12878 and NA10851 genomic DNA to the Agilent SurePrint G3 Human CGH Microarray 2x400K (Design ID 021850) were obtained from Agilent-recommended service providers. The FE files were processed to obtain CNV calls by using both Agilent Genomic Workbench 7.0.4.0 (Agilent Technologies, Santa Clara CA 95051, U.S.A.) and Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.) software packages. CNV calls were obtained by generating Interval Based Reports using Agilent Genomic Workbench with default settings according to the manufacturer's user guide, and by using the FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
Processed data are interval based reports generated using the ADM-2 algorithm in the Agilent Genomic Workbench software package. Header information lists the specific parameters used for the analysis. Columns include Chr (chromosome of CNV), Cytoband (cytoband of CNV), Start (start coordinate of CNV), Stop (stop coordinate of CNV), #Probes (number of probes in CNV interval), Amplification (Base2 log ratio indicating an amplification in the genome of NA12878 compared to that of NA10851), Deletion (Base2 log ratio indicating a deletion in the genome of NA12878 compared to that of NA10851), pval (p value), Gene Names (names of any genes overalpping with the CNV interval)
There are no intermediate processed files containing values for every probe. The only output generated were the final CNV calls from these software packages.

value: male


title: NA12878 Genomic DNA Replicate 1 (Agilent021850)


title: AN4_Period0


title: AN5_Period0


title: AN1_Period0


title: AN2_Period2


title: AN5_Period1


title: AN1_Period2


title: AN2_Period0


title: AN1_Period3


title: AN7_Period2


title: AN5_Period2


title: AN2_Period1


title: AN5_Period3


title: blastocysts_day6+2_rep3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description:
aRNA
Biological replicate 3 of 3

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Microarray statistical analyses were done in the BioConductor version 3.2 and R version 3.2.4 environments. To identify genes that were differentially expressed, we applied the empirical Bayes on normalized data(background correction, quantile), moderated t-statistics implemented in the BioConductor package LIMMA (version 3.28.5) (Ritchie et al, 2015). P values were adjusted for multiple testing using the Benjamini and Hochberg method.

organism: Bos taurus

source_name: Blastocyst

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Cow ovaries were collected at a local slaughterhouse and transported within 3h to the laboratory, PBS at 30ºC. Immature oocytes were aspirated from antral follicles (2-7 mm in diameter) and Cumulus Oocyte Complexes (COCs) with more than three compact layers of cumulus cells were selected, pooled and rinsed in fresh medium before maturation. The COCs were cultured for 24 h at 39°C under a humidified atmosphere of 5% CO2 in air. At the end of the maturation period, the oocytes were fertilised in vitro in TALP medium supplemented with 1 μg heparin/mL and PHE . Sperm was added in a concentration of 1e6 spermatozoa/mL and the day of in vitro insemination was referred to as day 0. Frozen semen from a single bull was used in all the in vitro experiments. 18 hours after insemination, COCs were removed from the fertilisation medium and presumptive zygotes were denuded from cumulus cells by vortexing, and randomly assigned to micro-drops. In vitro development up to the blastocyst stage was achieved using the co-culture technique on VERO cells.

extract_protocol:
Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: After in vitro fertilization, bovine zygotes were cultured in batch of 25 embryos in 50 µl drops, at 39°C with 5% O2, 5% CO2 and 90% N2 until blastocoel formed at day 6 (condition “6”) or day 8 (condition “8”). Two days after day 6, early formed blastocysts were also collected, not as “day 8 forming ones” but as “cultured 2 more days” (condition “6+2”).

tag: production

value: in-vitro

tag: collected

value: Day 6+2 post-fertilization


title: blastocysts_day6+2_rep1

description:
aRNA
Biological replicate 1 of 3


title: AN1_Period1


title: blastocysts_day8_rep3

description:
aRNA
Biological replicate 3 of 3

value: Day 8 post-fertilization


title: blastocysts_day6+2_rep2

description:
aRNA
Biological replicate 2 of 3


title: Blastocysts_day6_rep3

description:
aRNA
Biological replicate 3 of 3

value: Day 6 post-fertilization


title: blastocysts_day8_rep2

description:
aRNA
Biological replicate 2 of 3


title: miR-331-3p B

city: Nedlands

first: Peter

last: Leedman

address: 6 Verdun Street

country: Australia

institute: Harry Perkins Institute of Medical Research

description: Androgen Sensitive cell line

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

source_name: Supraclavicular Lymph Node

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

growth_protocol: RPMI supplemented with 10% FBS

extract_protocol: Modified Trizol protocol

treatment_protocol: Transient transfection for 24 hours with 30nM miRNA with Lipofectamine 2000

value: LNCaP

tag: transfection


title: miR-331-3p A

description: Androgen Sensitive cell line


title: miR-331-3p C

description: Androgen Sensitive cell line


title: miR-NC C

description: Androgen Sensitive cell line

value: miR-NC


title: blastocysts_day8_rep1

description:
aRNA
Biological replicate 1 of 3


title: Blastocysts_day6_rep2

description:
aRNA
Biological replicate 2 of 3


title: Blastocysts_day6_rep1

description:
aRNA
Biological replicate 1 of 3


title: NA12878 Genomic DNA Replicate 2 (IlluminaHumanOmni5)

description: Genomic DNA extracted from GM12878 cell lines. Genomic DNA obtained from Coriell

hyb_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

data_processing:
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Infinium HumanOmni5-4v1 array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package  (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary material of the manuscript.
Processed data are final reports exported from GenomeStudio in the required format for downstream analysis in Nexus Copy Number. Columns include Sample Name (blank field - sample is NA12878), Sample ID (corresponding array barcode and sub-field on which sample was hybridized), SNP Name (equivalent to ID REF - unique identifier for each probe on the array), Chr (chromosome containing probe), Position (chromosomal coordinate of probe), Log R Ratio (the base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the cluster)), B Allele Freq (B allele theta value of this SNP for the sample, relative to the cluster positions),  GC Score (value between 0 and 1 indicating reliability of genotype call), SNP (Nucleotide substitution for the SNP on the Illumina top strand)

label: Cy5, Cy3

extract_protocol: Genomic DNA was extracted from GM12878 cell lines by Coriell Cell Repositories

value: Female


title: miR-NC A

description: Androgen Sensitive cell line


title: NA12878 Genomic DNA Replicate 1 (IlluminaHumanOmni5)

scan_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html


title: miR-NC B

description: Androgen Sensitive cell line


title: sample 38

city: Nashville

first: Susan

middle: M

last: Majka

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University Medical Center

description: Primary human IPF lung MPC

hyb_protocol: per UCCC core-Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affy 1.0st chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Bioconductor v 3.2, oligo package for reading data, followed by rma normalization

source_name: Explanted lung tissue

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

growth_protocol: Lung MPC were cultured according to published protocols

extract_protocol: Qiagen RNA Isolation Kit

treatment_protocol: The MPC were harvested when 75% confluent under normal culture conditions.

tag: disease state

value: idiopathic pulmonary fibrosis (IPF)

value: Explanted lung tissue

value: mesenchymal progenitor cell (MPC)


title: NA12878 Genomic DNA Replicate 2 (Agilent021529)

data_processing:
Raw data in the form of Feature Extraction (FE) files from the hybridization of NA12878 and NA10851 genomic DNA to the Agilent SurePrint G3 Human CGH Microarray 1x1M (Design ID 021529)  were obtained from Agilent-recommended service providers. The FE files were processed to obtain CNV calls by using both Agilent Genomic Workbench 7.0.4.0 (Agilent Technologies, Santa Clara CA 95051, U.S.A.) and Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.) software packages. CNV calls were obtained by generating Interval Based Reports using Agilent Genomic Workbench with default settings according to the manufacturer's user guide, and by using the FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
Processed data are interval based reports generated using the ADM-2 algorithm in the Agilent Genomic Workbench software package. Header information lists the specific parameters used for the analysis. Columns include Chr (chromosome of CNV), Cytoband (cytoband of CNV), Start (start coordinate of CNV), Stop (stop coordinate of CNV), #Probes (number of probes in CNV interval), Amplification (Base2 log ratio indicating an amplification in the genome of NA12878 compared to that of NA10851), Deletion (Base2 log ratio indicating a deletion in the genome of NA12878 compared to that of NA10851), pval (p value), Gene Names (names of any genes overalpping with the CNV interval)
There are no intermediate processed files containing values for every probe. The only output generated were the final CNV calls from these software packages.

tag: cell line


title: sample 39

description: Primary human IPF lung MPC

tag: tissue


title: NA12878 Genomic DNA Replicate 2 (IlluminaHumanOmni5Exome)

data_processing:
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Infinium HumanOmni5Exome v1 array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package  (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary material of the manuscript.
Processed data are final reports exported from GenomeStudio in the required format for downstream analysis in Nexus Copy Number. Columns include Sample Name (blank field - sample is NA12878), Sample ID (corresponding array barcode and sub-field on which sample was hybridized), SNP Name (equivalent to ID REF - unique identifier for each probe on the array), Chr (chromosome containing probe), Position (chromosomal coordinate of probe), Log R Ratio (the base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the cluster)), B Allele Freq (B allele theta value of this SNP for the sample, relative to the cluster positions),  GC Score (value between 0 and 1 indicating reliability of genotype call), SNP (Nucleotide substitution for the SNP on the Illumina top strand)

label_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html


title: sample 27

description: Primary human IPF lung MPC


title: Piz6, biological replicate2

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

description: Gene expression data from liver of transgenic PiZ mouse

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: liver

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: Animal procedures were performed in accordance to regulations of the Italian Ministry of Health. PiZ transgenic mice were maintained on a C57/BL6 background.

extract_protocol: Total RNAs from either Piz and wild-type livers were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

value: liver

tag: genotype

value: PiZ


title: sample 55

description: Primary human control lung MPC

value: control


title: NA12878 Genomic DNA Replicate 1 (Agilent021529)


title: Piz6, biological replicate1


title: sample 54

description: Primary human control lung MPC


title: sample 34

description: Primary human control lung MPC


title: sample 23

description: Primary human IPF lung MPC


title: Piz6, biological replicate3