title: mmusc primary fibroblasts, LaminB1 DamID, hsapiens array, repl 1

status: Public on Mar 22 2017

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
human_hg19_HACregion_LP160728.txt
channel 1: CMF_345301_S01_aaa_FLIPPED.pair
channel 2: CMF_345301_S01_aab_FLIPPED.pair

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 80 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing:
Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. Subsequently, single channel data was obtained and subjected to quantile-quantile normalisation over all available cell types and replicates.
The score was calculated as the average log2 Dam-LaminB1: Dam ratio of the loess-quantile normalized data of the two replicates.

source_name: Dam-LaminB1 DamID DNA from primary mouse Fibroblast Cells

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: 1-2x10e5 cells were infected with lenti-virus expressing either Dam-LaminB1 or only Dam. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs)), adapters were ligated with T4 ligase ((New England Biolabs)), and the ligation reaction was subsequently digested with DpnII ((New England Biolabs)). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

value: primary fibroblast

source_name: Dam DNA from primary mouse Fibroblast Cells


title: mmusc primary fibroblasts, LaminB1 DamID, hsapiens array, repl 2

type: genomic

description:
human_hg19_HACregion_LP160728.txt
channel 1: CMF_345311_S01_aaa_FLIPPED.pair
channel 2: CMF_345311_S01_aab_FLIPPED.pair

molecule: genomic DNA

organism: Mus musculus

tag: cell type


title: NA12878 Genomic DNA Replicate 1 (IlluminaHumanOmni5Exome)

status: Public on Mar 23 2017

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: 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 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: Cy5, Cy3

organism: Homo sapiens

source_name: Blood, B Lymphocyte

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

tag: gender

value: Female

tag: ethnicity

value: Caucasian

tag: cell line


title: sample 25

type: RNA

city: Nashville

first: Susan

middle: M

last: Majka

state: TN

address: 1161 21st Ave S

country: USA

institute: Vanderbilt University Medical Center

description: Primary human control 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

label: biotin

molecule: total RNA

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: control

tag: tissue

value: Explanted lung tissue

value: mesenchymal progenitor cell (MPC)


title: Control, biological replicate 3

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

description: Gene expression data from liver of wild-type 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: strain

tag: age

tag: genotype

value: wild-type


title: A549_H5N1_8_h_rep2

city: Beijing

first: Bing-hui

last: Xia

address: No.20 Dongda Street, Fengtai District

country: China

institute: Beijing Institute of Biotechnology

description: miRNA expression in lung epithelial cells after 8 hours of A/goose/Jilin/hb/2003 (H5N1) infection, replication 2.

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, US) in hybridization Oven (Agilent Technologies, Santa Clara, CA, US) at 55C, 20rpm for 20 hours according to the manufacturer's instructions, hybridization section. After hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent Technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, US) using the standard setting for 8x15k array slides.

data_processing: Fluorescence intensity was calculated using Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings and analysis performed using GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). Data normalization and transformation were all performed by the Shanghai Biochip Corporation.

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, US) following the manufacturer's instructions, labeling section.

growth_protocol: A549 cells were propagated in Dulbecco's Modified Eagle's Medium (DMEM; Life Technologies, USA) supplemented with 10% fetal bovine serum (FBS; HyClone, USA) at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Ambion, Austin, TX, US) following the manufacturer's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: A549 cells were washed with phosphate-buffered saline (PBS) and subsequently infected with influenza A viruses at a MOI of 5 in a minimal volume of DMEM supplemented 0.5 mg/ml TPCK-treated trypsin (Sigma-Aldrich, USA) and 0.3% bovine serum albumin (Sangon, China) (infection medium). After one hour, cells were overlaid with fresh infection medium and incubated at 37°C for the indicated times.

value: alveolar adenocarcinoma cell line

tag: infection

value: A/goose/Jilin/hb/2003 (H5N1)

tag: time

value: 8 h post-infection


title: A549_H1N1_8_h_rep3

description: miRNA expression in lung epithelial cells after 8 hours of A/Beijing/501/2009 (H1N1) infection, replication 3.


title: A549_mock_24_h_rep2

description: miRNA expression in lung epithelial cells after 24 hours of mock infection, replication 2.

value: mock

value: 24 h post-infection


title: A549_mock_24_h_rep3

description: miRNA expression in lung epithelial cells after 24 hours of mock infection, replication 3.


title: A549_H1N1_24_h_rep1

description: miRNA expression in lung epithelial cells after 24 hours of A/Beijing/501/2009 (H1N1) infection, replication 1.


title: A549_H5N1_8_h_rep1

description: miRNA expression in lung epithelial cells after 8 hours of A/goose/Jilin/hb/2003 (H5N1) infection, replication 1.


title: A549_mock_24_h_rep1

description: miRNA expression in lung epithelial cells after 24 hours of mock infection, replication 1.


title: A549_H1N1_24_h_rep2

description: miRNA expression in lung epithelial cells after 24 hours of A/Beijing/501/2009 (H1N1) infection, replication 2.


title: A549_H5N1_8_h_rep3

description: miRNA expression in lung epithelial cells after 8 hours of A/goose/Jilin/hb/2003 (H5N1) infection, replication 3.


title: A549_H1N1_24_h_rep3

description: miRNA expression in lung epithelial cells after 24 hours of A/Beijing/501/2009 (H1N1) infection, replication 3.


title: A549_H5N1_24_h_rep1

description: miRNA expression in lung epithelial cells after 24 hours of A/goose/Jilin/hb/2003 (H5N1) infection, replication 1.


title: Control, biological replicate 2


title: Control, biological replicate 1


title: A549_H5N1_24_h_rep3

description: miRNA expression in lung epithelial cells after 24 hours of A/goose/Jilin/hb/2003 (H5N1) infection, replication 3.


title: A549_H5N1_24_h_rep2

description: miRNA expression in lung epithelial cells after 24 hours of A/goose/Jilin/hb/2003 (H5N1) infection, replication 2.


title: sample 28

description: Primary human control lung MPC


title: Untreated vs toxin treated midgut 18hr 4

city: Baltimore

first: George

last: Dimopoulos

state: Maryland

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

hyb_protocol: Probes prepared from the RNA of Bin toxin-treated mosquito midgut were co-hybridized with probes prepared from the RNA obtained from untreated mosquito midgut.  The hybridizations were conducted on an Agilent-based microarray platform using custom-designed whole-genome 4 x 44K C. quinquefasciatus microarrays

scan_protocol: The arrays were scanned with an Agilent High Resolution Scanner (Agilent Technologies Inc., Santa Clara, CA, USA).

data_processing: Spot intensity was quantified using Agilent Feature Extraction Software. The linear models for microarray data (limma) package in R program was used to process the gene expression data from microarray. The raw signal intensities of each array were corrected by backgroundCorrect then normalized within array by loess method. Replicate spots in each array were averaged with avereps function. Linear model was generated with lmFit function then the statistical significance of differential expression was analyzed by empirical Bayes moderated t-statistics. Finally, the raw p value was adjusted with Benjamini-Hochberg (BH) method at a significance level of adjusted p<0.05. Self-self hybridization was used to determine the intensity-dependent cutoff value for the significance of differentially expressed genes on these types of microarrays as 0.75 in log2 scale, which corresponds to a 1.68 fold-change in regulation. Gene expression data were described in terms of function by homology to functionally annotated genes in Culex gene databases such as Gene Ontology

organism: Culex quinquefasciatus

source_name: Midgut untreated control at 18 hr

label_protocol: Cy5- and Cy3-labeled probes were synthesized from 200 ng of total RNA of each sample using Low Input Quick Amp Labeling Kit from Agilent Technologies

growth_protocol: Mosquitoes were reared at 27°C with 12-h light/dark cycle.

extract_protocol: Pools of at least 20 midguts were collected from each treatment type. RNA was extracted from dissected tissues using an RNeasy kit (Qiagen) according to standard protocol.

treatment_protocol: The third-instar C. quinquefasciatus larvae were starved for 3 h before feeding with the mixture of BinA and BinB at a 1:1 molar ratio. Four biological replicates of 20 third-instar Culex larvae were treated with an LC90 dose (80 ng/ml) of Bin toxin for 6, 12, or 18 h

tag: developmental stage

value: larvae

tag: treatment

value: 18 hr

value: Midgut

source_name: Midgut 18 hr after toxin treatment

value: toxin


title: mmusc primary fibroblasts, LaminB1 DamID, mmusc array, repl 2

description:
mouse_mm9_wholeGenome_LP160728.txt
channel 1: M2_CMF_366273_S01_aaa_FLIPPED.pair
channel 2: M2_CMF_366273_S01_aab_FLIPPED.pair

value: primary fibroblast


title: Untreated vs toxin treated midgut 18hr 1


title: A549_H1N1_8_h_rep2

description: miRNA expression in lung epithelial cells after 8 hours of A/Beijing/501/2009 (H1N1) infection, replication 2.


title: Untreated vs toxin treated midgut 12hr 4

source_name: Midgut untreated control at 12 hr

value: 12 hr

source_name: Midgut 12 hr after toxin treatment


title: Untreated vs toxin treated midgut 12hr 1


title: Untreated vs toxin treated midgut 6hr 4

source_name: Midgut untreated control at 6 hr

value: 6 hr

source_name: Midgut 6 hr after toxin treatment


title: Untreated vs toxin treated midgut 6hr 2

value: control


title: Untreated vs toxin treated midgut 6hr 1


title: Untreated vs toxin treated midgut 12hr 3


title: Untreated vs toxin treated midgut 12hr 2


title: Untreated vs toxin treated midgut 18hr 2


title: Untreated vs toxin treated midgut 18hr 3


title: A549_H1N1_8_h_rep1

description: miRNA expression in lung epithelial cells after 8 hours of A/Beijing/501/2009 (H1N1) infection, replication 1.


title: Untreated vs toxin treated midgut 6hr 3


title: A549_mock_8_h_rep1

description: miRNA expression in lung epithelial cells after 8 hours of mock infection, replication 1.

source_name: A549, mock, 8 h


title: A549_mock_8_h_rep2

description: miRNA expression in lung epithelial cells after 8 hours of mock infection, replication 2.


title: mmusc primary fibroblasts, LaminB1 DamID, mmusc array, repl 1

description:
mouse_mm9_wholeGenome_LP160728.txt
channel 1: M1_CMF_366155_S01_aaa_FLIPPED.pair
channel 2: M1_CMF_366155_S01_aab_FLIPPED.pair


title: A549_mock_8_h_rep3

description: miRNA expression in lung epithelial cells after 8 hours of mock infection, replication 3.


title: In Vitro HPMCs Treated TGF-β1 and IL-1β Sample 1 vs In Vitro Control HPMCs Sample 1 Replicate 2

city: Madrid

first: Vicente

last: Ruiz-Carpio

address: Nicolás Cabrera, 1

department: Biología Celular e Inmunologia

country: Spain

institute: Centro de Biología Molecular "Severo Ochoa"

hyb_protocol: Whole Human Genome Microarray Kit, 4x44K (Agilent Technologies) was used in hybridations. Controls and samples were incubated in blocking agent and fragmentacion buffer. Labeled RNA was added in incubation buffer and applied to microarray. Excess fluorochrome and unhybridized RNA was eliminated with different stringencies saline buffer. Stabilization solution and dry recomended by Agilent Technologies was employed.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction v9.5 Software.

data_processing: Babelomics free software (babelomics.bioinfo.cipf.es) was used for background subtraction and LOESS/ LOWESS and quantiles normalization.

source_name: Omentum-derived HPMC_Treated

label_protocol: 400-800 ng of total RNA was labeled using Quick Amp Labeling Kit, two-color (Agilent Technologies) following manufacturer's instructions.

growth_protocol: HPMCs were cultured in Earle’s M199 medium (Biological Industries, Kibbutz Beit Haemek, Israel) supplemented with 20% fetal bovine serum (FBS; Thermo Scientific, Cramligton, UK), 50 U/ml penicillin, 50 µg/ml streptomycin (PPA Laboratories GmbH, Pasching, Austria), 2% Biogro-2 (Biological Industries).

extract_protocol: Total RNA extracted using Tri-Reagent following manufacturer's instructions

treatment_protocol: To induce MMT in vitro model, omentum-derived HPMC samples were treated with 0.5 ng/ml human recombinant TGF-β1 and 2 ng/ml IL-1β (R&D Systems, Minneapolis, Minnesota, USA) for 72h.

value: Omentum

source_name: Omentum-derived HPMC_Control


title: In Vitro HPMCs Treated TGF-β1 and IL-1β Sample 1 vs In Vitro Control HPMCs Sample 1 Replicate 1


title: In Vitro HPMCs Treated TGF-β1 and IL-1β Sample 2 vs In Vitro Control HPMCs Sample 2 Replicate 2


title: In Vitro HPMCs Treated TGF-β1 and IL-1β Sample 2 vs In Vitro Control HPMCs Sample 2 Replicate 1


title: Pacific oyster B1_96_8A25_170

city: Qingdao

first: Haigang

last: Qi

state: Shandong

address: 7 Nanhai Rd.

department: Key Laboratory of Experimental Marine Biology

institute: Institute of Oceanology, Chinese Academy of Sciences

hyb_protocol: According to the manufacturer's directions

scan_protocol: Scanning the oyster SNP chip was conducted on the Affymetrix GeneTitan Multi-Channel (MC) Instrument according to the standard operating instructions

data_processing: The raw data stored in the form of CEL files were processed Affymetrix Axiom Analysis Suite software version 1.1.1.66

organism: Magallana gigas

source_name: Pacific oyster B1_96_8A25_170

extract_protocol: DNA were extracted from mantle tissues using the standard phenol-chloroform method

value: mantle


title: Pacific oyster B1_90_8A25_113

source_name: Pacific oyster B1_90_8A25_113

label_protocol: According to the manufacturer's directions


title: Pacific oyster B1_91_8A25_132

source_name: Pacific oyster B1_91_8A25_132


title: Pacific oyster B1_94_8A25_157

source_name: Pacific oyster B1_94_8A25_157


title: Pacific oyster B1_93_8A25_148

source_name: Pacific oyster B1_93_8A25_148


title: Pacific oyster B1_89_8A25_106

source_name: Pacific oyster B1_89_8A25_106


title: Pacific oyster B1_79_8A25_039

source_name: Pacific oyster B1_79_8A25_039


title: Pacific oyster B1_95_8A25_164

source_name: Pacific oyster B1_95_8A25_164


title: Pacific oyster B1_88_8A25_098

source_name: Pacific oyster B1_88_8A25_098


title: Pacific oyster B1_86_8A25_091

source_name: Pacific oyster B1_86_8A25_091


title: Pacific oyster B1_84_8A25_084

source_name: Pacific oyster B1_84_8A25_084


title: Pacific oyster B1_87_8A25_096

source_name: Pacific oyster B1_87_8A25_096


title: Pacific oyster B1_77_8A25_005

source_name: Pacific oyster B1_77_8A25_005


title: Pacific oyster B1_80_8A25_046

source_name: Pacific oyster B1_80_8A25_046


title: Pacific oyster B1_78_8A25_029

source_name: Pacific oyster B1_78_8A25_029


title: Pacific oyster B1_85_8A25_086

source_name: Pacific oyster B1_85_8A25_086


title: Pacific oyster B1_92_8A25_135

source_name: Pacific oyster B1_92_8A25_135


title: Pacific oyster B1_83_8A25_072

source_name: Pacific oyster B1_83_8A25_072


title: Pacific oyster B1_76_8A25_004

source_name: Pacific oyster B1_76_8A25_004


title: Pacific oyster B1_68_LBS_163

source_name: Pacific oyster B1_68_LBS_163


title: Pacific oyster B1_82_8A25_063

source_name: Pacific oyster B1_82_8A25_063


title: Pacific oyster B1_67_LBS_161

source_name: Pacific oyster B1_67_LBS_161


title: Pacific oyster B1_75_8A25_003

source_name: Pacific oyster B1_75_8A25_003


title: Pacific oyster B1_72_LBS_191

source_name: Pacific oyster B1_72_LBS_191


title: Pacific oyster B1_74_8A25_002

source_name: Pacific oyster B1_74_8A25_002


title: Pacific oyster B1_81_8A25_053

source_name: Pacific oyster B1_81_8A25_053


title: Pacific oyster B1_69_LBS_168

source_name: Pacific oyster B1_69_LBS_168


title: Pacific oyster B1_73_8A25_001

source_name: Pacific oyster B1_73_8A25_001


title: Pacific oyster B1_71_LBS_172

source_name: Pacific oyster B1_71_LBS_172


title: Pacific oyster B1_70_LBS_169

source_name: Pacific oyster B1_70_LBS_169


title: Pacific oyster B1_65_LBS_149

source_name: Pacific oyster B1_65_LBS_149


title: Pacific oyster B1_66_LBS_151

source_name: Pacific oyster B1_66_LBS_151


title: Pacific oyster B1_64_LBS_141

source_name: Pacific oyster B1_64_LBS_141


title: Pacific oyster B1_62_LBS_129

source_name: Pacific oyster B1_62_LBS_129


title: Pacific oyster B1_59_LBS_113

source_name: Pacific oyster B1_59_LBS_113


title: Pacific oyster B1_58_LBS_110

source_name: Pacific oyster B1_58_LBS_110


title: Pacific oyster B1_61_LBS_123

source_name: Pacific oyster B1_61_LBS_123


title: Pacific oyster B1_60_LBS_115

source_name: Pacific oyster B1_60_LBS_115


title: Pacific oyster B1_57_LBS_101

source_name: Pacific oyster B1_57_LBS_101


title: Pacific oyster B1_54_LBS_092

source_name: Pacific oyster B1_54_LBS_092


title: Chicken # 873 lung, 3 dpi, rH5N3 P6 infected

city: Winnnipeg

first: John

last: Pasick

state: Manitoba

address: 1015 Arlington Street

department: NCFAD

country: Canada

institute: CFIA

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented and hybridized to Agilent Chicken (V2) Gene Expression Microarray, 4x44K (G2519F-026441) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed then dried immediately as per manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B-C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sept09) to obtain background subtracted and spatially detrended Processed Signal intensities. Data was then uploaded to GeneSpring v12.1 (Agilent) for further analysis.

organism: Gallus gallus

source_name: lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) 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: 100 mg of brain and lung was homogenized in 1 ml of TriPure isolation reagent with 1.0 mm zirconia/silica beads. This was followed by the addition of 0.2 ml chloroform, thorough vortexing and phase separation by centrifugation. The aqueous phase was mixed with an equal volume of 75% ethanol and passed through an RNeasy column (Qiagen). The column was washed once with RW1 and twice with RPE buffer before eluting the RNA in nuclease free water. OD260, OD280 and RNA concentration were determined on a NanoDrop ND-1000 spectrophotometer. RNA concentration and integrity were further assessed using a eukaryotic total RNA nanochip and an Agilent Bioanalyzer 2100.

tag: subject

value: Chicken #873

value: rH5N3 P6

value: 3 days

value: lung


title: Pacific oyster B1_56_LBS_095

source_name: Pacific oyster B1_56_LBS_095


title: Chicken # 873 brain, 3 dpi, rH5N3 P6 infected

source_name: brain

value: brain


title: Chicken # 868 lung, 3 dpi, rH5N3 P6 infected

value: Chicken #868


title: Chicken # 871 brain, 3 dpi, rH5N3 P6 infected

value: Chicken #871


title: Pacific oyster B1_55_LBS_094

source_name: Pacific oyster B1_55_LBS_094


title: Pacific oyster B1_53_LBS_082

source_name: Pacific oyster B1_53_LBS_082


title: Chicken # 871 lung, 3 dpi, rH5N3 P6 infected


title: Pacific oyster B1_63_LBS_134

source_name: Pacific oyster B1_63_LBS_134


title: Pacific oyster B1_52_LBS_078

source_name: Pacific oyster B1_52_LBS_078


title: Pacific oyster B1_49_LBS_055

source_name: Pacific oyster B1_49_LBS_055


title: Pacific oyster B1_50_LBS_058

source_name: Pacific oyster B1_50_LBS_058


title: Pacific oyster B1_45_UN_21_9

source_name: Pacific oyster B1_45_UN_21_9


title: Chicken # 868 brain, 3 dpi, rH5N3 P6 infected


title: Pacific oyster B1_39_RE_Fu

source_name: Pacific oyster B1_39_RE_Fu


title: Pacific oyster B1_44_RE_16A7

source_name: Pacific oyster B1_44_RE_16A7


title: Pacific oyster B1_43_RE_15_12

source_name: Pacific oyster B1_43_RE_15_12


title: Pacific oyster B1_40_RE_25_24

source_name: Pacific oyster B1_40_RE_25_24


title: Chicken # 872 lung, 1 dpi, rH5N3 P6 infected

value: Chicken #872

value: 1 day


title: Pacific oyster B1_48_LBS_052

source_name: Pacific oyster B1_48_LBS_052


title: Pacific oyster B1_46_UN_30_9

source_name: Pacific oyster B1_46_UN_30_9


title: Pacific oyster B1_47_LBS_040

source_name: Pacific oyster B1_47_LBS_040


title: Pacific oyster B1_41_RE_10A5

source_name: Pacific oyster B1_41_RE_10A5


title: Pacific oyster B1_51_LBS_070

source_name: Pacific oyster B1_51_LBS_070


title: Pacific oyster B1_38_RE_20A15

source_name: Pacific oyster B1_38_RE_20A15


title: Chicken # 872 brain, 1 dpi, rH5N3 P6 infected

source_name: brain


title: Chicken # 869 brain, 1 dpi, rH5N3 P6 infected

value: Chicken #869


title: Pacific oyster B1_37_RE_8A25

source_name: Pacific oyster B1_37_RE_8A25


title: Pacific oyster B1_36_RE_24A22

source_name: Pacific oyster B1_36_RE_24A22


title: Chicken # 866 brain, 1 dpi, rH5N3 P6 infected

value: Chicken #866


title: Pacific oyster B1_34_RE_4A6

source_name: Pacific oyster B1_34_RE_4A6


title: Chicken # 866 lung, 1 dpi, rH5N3 P6 infected

source_name: lung


title: Chicken # 869 lung, 1 dpi, rH5N3 P6 infected


title: Pacific oyster B1_31_RE_7_4

source_name: Pacific oyster B1_31_RE_7_4


title: Pacific oyster B1_42_RE_32A17

source_name: Pacific oyster B1_42_RE_32A17


title: Pacific oyster B1_30_RE_14A21

source_name: Pacific oyster B1_30_RE_14A21


title: Pacific oyster B1_33_RE_16A15

source_name: Pacific oyster B1_33_RE_16A15


title: Osaim1 under SA treatment repeat1

city: Hangzhou

first: Xu

last: Lei

state: Zhejiang province

address: 198, Shiqiao Rd.

department: The Institute of Virology and Biotechnology

institute: zhejiang Academy of Agricultural sciences

description:
Gene expression data from root tips of four-day-old rice seedlings
Osaim1_SA-1

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

scan_protocol: GeneChips were scanned using the affymetrix Genechip Scanner 3000.

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

organism: Oryza sativa

source_name: Root tips (~2.5mm) of four-day-old rice seedlings_osaim1_SA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (GeneChip® 3’ IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: The hydroponically cultured mutants and wild-type were grown in a greenhouse with a 12h day (30°C)/12 h night (22°C) photoperiod, approximately 200 μmol m-2 s-1 photon density, and approximately 60% humidity.

extract_protocol: Total RNA was isolated using an RNeasy plant mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: WT and Osaim1 were treated with or without SA (500μM) after sowing.

value: root tips

value: four-day-old seedling


title: Pacific oyster B1_32_RE_14A10

source_name: Pacific oyster B1_32_RE_14A10


title: Osaim1 under SA treatment repeat2

description:
Gene expression data from root tips of four-day-old rice seedlings
Osaim1_SA-2


title: Wildtype under SA treatment repeat2

description:
Gene expression data from root tips of four-day-old rice seedlings
SSBM_SA-2

source_name: Root tips (~2.5mm) of four-day-old rice seedlings_wildtype_SA

value: Wildtype


title: Chicken # 865 lung, 3 dpi, rH5N3 Ori infected

value: Chicken #865

value: rH5N3 Ori


title: Chicken # 863 lung, 3 dpi, rH5N3 Ori infected

value: Chicken #863


title: Wildtype under SA treatment repeat1

description:
Gene expression data from root tips of four-day-old rice seedlings
SSBM_SA-1


title: Chicken # 865 brain, 3 dpi, rH5N3 Ori infected


title: Pacific oyster B1_29_RE_12_13

source_name: Pacific oyster B1_29_RE_12_13

value: mantle


title: Chicken # 857 lung, 3 dpi, rH5N3 Ori infected

value: Chicken #857


title: Osaim1 under control condition repeat1

description:
Gene expression data from root tips of four-day-old rice seedlings
Osaim1-1

source_name: Root tips (~2.5mm) of four-day-old rice seedlings_osaim1_control


title: Pacific oyster B1_28_RE_25_15

source_name: Pacific oyster B1_28_RE_25_15


title: Osaim1 under control condition repeat2

description:
Gene expression data from root tips of four-day-old rice seedlings
Osaim1-2


title: Chicken # 863 brain, 3 dpi, rH5N3 Ori infected

value: 3 days


title: Chicken # 862 lung, 1 dpi, rH5N3 Ori infected

value: Chicken #862

value: lung


title: Chicken # 857 brain, 3 dpi, rH5N3 Ori infected

value: brain


title: Pacific oyster B1_27_RE_30A7

source_name: Pacific oyster B1_27_RE_30A7


title: Chicken # 862 brain, 1 dpi, rH5N3 Ori infected


title: Wildtype under control condition repeat2

description:
Gene expression data from root tips of four-day-old rice seedlings
SSBM-2

source_name: Root tips (~2.5mm) of four-day-old rice seedlings_wildtype_control


title: Pacific oyster B1_25_RE_8A10

source_name: Pacific oyster B1_25_RE_8A10


title: MEF_day10_rep3

city: Tsukuba

first: Yasuyuki

middle: S

last: Kida

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression of MEFs after exposure to small molecular cocktails (chem) replicate 3

hyb_protocol: cDNA synthesis from 140 ng total RNAs and hybridization were performed with SurePrint G3 Mouse GE microarray 8x60K (Agilent).

scan_protocol: Agilent DNA microarray scanner (Agilent) was used to obtain fluorescence intensity of the microarray.

data_processing: Signal intensities were measured by Feature Extraction Software (Agilent), and were intra- and inter-array normalized using the limma package in the R statistical computing environment. Signal intensities for non-unique probe names were averaged.

source_name: Mouse embryonic fibroblasts (MEFs) after treatment (chem) replicate 3

growth_protocol: MEFs were isolated from 12.5 days old embryos of C57BL/6NCrSlc mice. Briefly, the pregnant female mouse was sacrificed by cervical dislocation. The uterus was dissected out and placed into a φ100mm dish containing phosphate buffered saline (PBS; Wako). Each embryo was separated from the uterus. Then, head and visceral tissues were removed from each embryo with forceps and tweezers. The remaining portion of the embryo was transferred into a single well of 12-well plate containing PBS and minced into pieces. The pieces were treated with 1 ml/well 0.05% Trypsin-EDTA (Wako) for 5 min at 37 oC. After trypsinization, 1 ml/well Dulbecco's modified eagle medium (DMEM; Wako) supplemented with 10% fetal bovine serum (FBS; Hyclone), 1% Non-essential amino acid solution (NEAA; Wako) and 1% Penicillin-Streptomycin solution (PS; Wako), was added and the pieces were suspended by pipetting. Cells were collected by centrifugation (1000 rpm, 3 min) and resuspended with DMEM supplemented with 20% FBS, 1% NEAA and 1% PS (defined as P0 MEFs). These P0 MEFs were harvested on T175 flasks and cultured at 37 oC with 5% CO2. The P0 MEFs were grown to confluent, then passed and cryopreserved. The P1 MEFs were used for further neuronal induction.

extract_protocol: Total RNAs extracted from the day10 chemical-treated MEFs and the control MEFs were used for microarray analysis.

treatment_protocol: For modulating cellular fate, small compound cocktails were applied to the cultured samples for 3 days. At first, the combination of 0.25 mM valproic acid (an inhibitor of histone deacetylase; VPA; Wako), 1.5 uM CHIR99021 (an inhibitor of glycogen synthase kinase 3 (GSK3); CHIR; Cayman Chemical Company), 0.5 uM 616452 (an inhibitor of transforming growth factor-beta [TGFb] RI kinase; Merck Millipore), 5 uM Forskolin (an agonist of cyclic adenosine monophosphate; FSK; Wako) and 2.5 uM Tranylcypromine (an inhibitor of lysine-specific demethylase 1; Tranyl; Abcam) was used. These small molecular compounds were previously identified and used for converting mouse somatic cells to pluripotent state. The cocktail was mixed in DMEM supplemented with 20% FBS, 1% NEAA, 1% PS, 50 ng/ml bFGF and a culture supernatant from CHO cells producing leukemia inhibitory factor (LIF). The CHO cells producing LIF were kindly gifted from Prof. Toru Nakano (Osaka University, Japan). The chemical medium was applied to the culture samples for 2 days. Then, another small compound cocktail, which was composed of 0.25 mM VPA, 5 uM FSK, 2.5 uM Tranyl, 2.5 uM dorsomorphin (an inhibitor of bone morphogenic protein (BMP) signaling; DM; Sigma-Aldrich) and 2.5 uM SB431542 (an inhibitor of TGFb/Activin/Nodal signaling; SB; Sigma-Aldrich), was applied for one day. This small molecular cocktail was also mixed in DMEM-based medium same as above. After exposure to small molecular cocktails for 3 days, cells were collected and transferred to poly-L-ornithine (PLO; Sigma-Aldrich) and Laminin (Sigma-Aldrich) coated dishes for neuronal differentiation. Briefly, cells were rinsed with PBS and then dissociated with 0.025% Trypsin-EDTA for 5 min at 37 oC. After stopping trypsin reaction with FBS-containing DMEM, cells were collected by centrifugation at 1000 rpm for 3 min. Cells were suspended into Differentiation Medium consisted of DMEM/F-12 (Life Technologies), 25 ug/ml Insulin (Wako), 50 ug/ml Human Transferrin (Sigma-Aldrich), 30 nM Sodium Selenite (Sigma-Aldrich), 20 nM Progesterone (Sigma-Aldrich), 100 nM Putrescine (Sigma-Aldrich) and 1% PS. For neuronal differentiation, the differentiation medium was further supplemented with 1 uM Retinoic Acid (RA; Sigma-Aldrich), 10 M FSK, 10 ng/ml Brain-derived neurotrophic factor (BDNF; Wako), 10 ng/ml Glial cell-derived neurotrophic factor (GDNF; Wako) and 50 ug/ml Ascorbic Acid (Wako), which was defined as the neuronal differentiation medium (NDM). Culture dishes were previously coated with 20 ug/ml PLO for 1 hour at 37 oC and subsequent 5 ug/ml Laminin for 2 hours at 37 oC. Finally, cells were plated onto coated dishes at a density of 5 x 10^4 cells/cm2. Half of NDM was changed twice a week for maintaining the cultures.

value: embryonic fibroblast


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 8 vs Ex Vivo Control Pool HPMCs Relicate 2

source_name: Pooled HPMCs derived from 4 omentum

value: Omentum

source_name: Effluent-derived HPMC from Patients on Peritoneal Dialysis

value: Peritoneal Membrane

tag: phenotype

value: Non-Epitheliod


title: Wildtype under control condition repeat1

description:
Gene expression data from root tips of four-day-old rice seedlings
SSBM-1


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 8 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Pacific oyster B1_26_RE_16_25

source_name: Pacific oyster B1_26_RE_16_25


title: MEF_day0_rep3

description: Gene expression of MEFs before exposure to small molecular cocktails (ctrl) replicate 3

source_name: Mouse embryonic fibroblasts (MEFs) before treatment (ctrl) replicate 3

label_protocol: cDNA synthesis from 140 ng total RNAs and hybridization were performed with SurePrint G3 Mouse GE microarray 8x60K (Agilent).


title: MEF_day10_rep2

description: Gene expression of MEFs after exposure to small molecular cocktails (chem) replicate 2

source_name: Mouse embryonic fibroblasts (MEFs) after treatment (chem) replicate 2


title: Chicken # 856 lung, 1 dpi, rH5N3 Ori infected

source_name: lung

value: Chicken #856

value: 1 day


title: Pacific oyster B1_24_RE_24A9

source_name: Pacific oyster B1_24_RE_24A9


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 7 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Chicken # 859 brain, 1 dpi, rH5N3 Ori infected

source_name: brain

value: Chicken #859


title: Chicken # 859 lung, 1 dpi, rH5N3 Ori infected


title: MEF_day10_rep1

description: Gene expression of MEFs after exposure to small molecular cocktails (chem) replicate 1

source_name: Mouse embryonic fibroblasts (MEFs) after treatment (chem) replicate 1


title: MEF_day0_rep2

description: Gene expression of MEFs before exposure to small molecular cocktails (ctrl) replicate 2

source_name: Mouse embryonic fibroblasts (MEFs) before treatment (ctrl) replicate 2


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 6 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Pacific oyster B1_35_RE_4A2

source_name: Pacific oyster B1_35_RE_4A2


title: Pacific oyster B1_23_RE_24_A7

source_name: Pacific oyster B1_23_RE_24_A7


title: Pacific oyster B1_22_RE_8_12

source_name: Pacific oyster B1_22_RE_8_12


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 7 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Pacific oyster B1_21_RE_20_17A

source_name: Pacific oyster B1_21_RE_20_17A


title: Chicken # 854 lung, 3 dpi, uninfected control

value: Chicken #854

value: uninfected control


title: Pacific oyster B1_20_RE_21_25

source_name: Pacific oyster B1_20_RE_21_25


title: Chicken # 856 brain, 1 dpi, rH5N3 Ori infected

value: rH5N3 Ori


title: MEF_day0_rep1

description: Gene expression of MEFs before exposure to small molecular cocktails (ctrl) replicate 1

source_name: Mouse embryonic fibroblasts (MEFs) before treatment (ctrl) replicate 1


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 5 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Chicken # 854 brain, 3 dpi, uninfected control


title: Pacific oyster B1_19_RE_30_1

source_name: Pacific oyster B1_19_RE_30_1


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 6 vs Ex Vivo Control Pool HPMCs Relicate 1

source_name: Pooled HPMCs derived from 4 omentum


title: Pacific oyster B1_16_RE_18A25

source_name: Pacific oyster B1_16_RE_18A25


title: Liver_aERKO_high fat diet diet_rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
13406_ERKOalpha_HFD_Rep_3
Gene expression from 2 weeks high fat diet fed ERa KO liver.

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Expression Console Software (AGCC; Version 1.2) using the MAS5 algorithm to generate .CHP files.

source_name: 2 weeks high fat diet fed ERa KO liver

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours.

extract_protocol: RNA was isolated by Trizol and cleaned up with Qiagen RNeasy kits with DNase treatments.

treatment_protocol: High-fat diet or regular diet feeding for 2 weeks.

tag: strain/background

tag: genotype/variation

value: Female

value: adult

value: liver

tag: diet

value: high fat diet:research diet #12492 (60% kcal% fat)


title: Liver_aERKO_high fat diet diet_rep2

description:
13405_ERKOalpha_HFD_Rep_2
Gene expression from 2 weeks high fat diet fed ERa KO liver.

tag: gender


title: Chicken # 849 lung, 3 dpi, uninfected control

value: Chicken #849

value: 3 days


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 5 vs Ex Vivo Control Pool HPMCs Relicate 1

source_name: Effluent-derived HPMC from Patients on Peritoneal Dialysis


title: Liver_aERKO_high fat diet diet_rep1

description:
13404_ERKOalpha_HFD_Rep_1
Gene expression from 2 weeks high fat diet fed ERa KO liver.


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 4 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Liver_aERKO_normal diet_rep3

description:
13409_ERKOalpha_Reg_Rep_3
Gene expression from normal diet fed ERa KO liver.

source_name: Normal diet fed ERa KO liver

value: normal diet:NIH-31diet


title: Chicken # 849 brain, 3 dpi, uninfected control

value: brain


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 3 vs Ex Vivo Control Pool HPMCs Relicate 2

value: Omentum


title: Pacific oyster B1_18_RE_24_22

source_name: Pacific oyster B1_18_RE_24_22

value: mantle


title: Chicken # 853 lung, 1 dpi, uninfected control

source_name: lung

value: Chicken #853

value: lung


title: Chicken # 846 brain, 3 dpi, uninfected control

source_name: brain

value: Chicken #846


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 3 vs Ex Vivo Control Pool HPMCs Relicate 1

value: Peritoneal Membrane

value: Non-Epitheliod


title: Pacific oyster B1_15_RE_18A3

source_name: Pacific oyster B1_15_RE_18A3


title: Pacific oyster B1_17_RE_16A18

source_name: Pacific oyster B1_17_RE_16A18


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 4 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Liver_aERKO_normal diet_rep1

description:
13407_ERKOalpha_Reg_Rep_1
Gene expression from normal diet fed ERa KO liver.


title: Liver_aERKO_normal diet_rep2

description:
13408_ERKOalpha_Reg_Rep_2
Gene expression from normal diet fed ERa KO liver.


title: Chicken # 846 lung, 3 dpi,  uninfected control

value: uninfected control


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 2 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Pacific oyster B1_13_RE_12A2

source_name: Pacific oyster B1_13_RE_12A2


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 2 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Liver_WT_high fat diet diet_rep3

description:
13412_WT_HFD_Rep_3
Gene expression from 2 weeks high fat diet fed wt liver.

source_name: 2 weeks high fat diet fed wt liver


title: Liver_WT_high fat diet diet_rep2

description:
13411_WT_HFD_Rep_2
Gene expression from 2 weeks high fat diet fed wt liver.


title: Chicken # 850 lung, 1 dpi, uninfected control

value: Chicken #850

value: 1 day


title: Chicken # 850 brain, 1 dpi, uninfected control


title: Pacific oyster B1_11_RE_13_21

source_name: Pacific oyster B1_11_RE_13_21


title: Pacific oyster B1_12_RE_16_9

source_name: Pacific oyster B1_12_RE_16_9


title: Pacific oyster B1_10_RE_13_10

source_name: Pacific oyster B1_10_RE_13_10


title: Chicken # 853 brain, 1 dpi, uninfected control


title: Liver_WT_normal diet_rep3

description:
13415_WT_Reg_Rep_3
Gene expression from normal diet fed wt liver.

source_name: Normal diet fed wt liver

value: Female

value: adult


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 1 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Chicken # 847 lung, 1 dpi, uninfected control

value: Chicken #847


title: Liver_WT_high fat diet diet_rep1

description:
13410_WT_HFD_Rep_1
Gene expression from 2 weeks high fat diet fed wt liver.

value: liver

value: high fat diet:research diet #12492 (60% kcal% fat)


title: Liver_WT_normal diet_rep2

description:
13414_WT_Reg_Rep_2
Gene expression from normal diet fed wt liver.

value: normal diet:NIH-31diet


title: Beta_cells_2yo_rep4

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: 7.5 ug of labeled RNA was fragmented and hybridized to Affymetrix Mouse 430 2.0 arrays for 16 hours at 45° C. Arrays were then washed and stained on the Affymetrix Fluidics Station 450,  using the hybridization, wash, and stain kit from Affymetrix.

scan_protocol: Arrays were scanned using the GCS 3000 7G Scanner from Affymetrix.

data_processing: The data were normalized using RMA on Affymetrix Expression Console.

source_name: pancreatic beta cells_2yo

label_protocol: Biotin-labeled aRNA was made using 1 ug input aRNA and the Turbo Labeling Biotin Kit.

extract_protocol: Total RNA was extracted using PicoPure (Arcturus) according to the manufacturer's instructions.

value: 2 years

tag: cell type

value: FACS-purified MIP:GFP beta cells


title: Ex Vivo HPMCs with Non-Epithelioid phenotype Sample 1 vs Ex Vivo Control Pool HPMCs Relicate 2

source_name: Pooled HPMCs derived from 4 omentum

value: Omentum


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 9 vs Ex Vivo Control Pool HPMCs Relicate 1

value: Epithelioid


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 8 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Pacific oyster B1_08_RE_22A22

source_name: Pacific oyster B1_08_RE_22A22

value: mantle


title: Pacific oyster B1_07_RE_22A10

source_name: Pacific oyster B1_07_RE_22A10


title: Chicken # 847 brain, 1 dpi, uninfected control

value: brain


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 8 vs Ex Vivo Control Pool HPMCs Relicate 2

source_name: Effluent-derived HPMC from Patients on Peritoneal Dialysis

value: Peritoneal Membrane

value: Epitheliod


title: Pacific oyster B1_09_RE_21_16

source_name: Pacific oyster B1_09_RE_21_16


title: Beta_cells_2yo_rep3


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 9 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 7 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Liver_WT_normal diet_rep1

description:
13413_WT_Reg_Rep_1
Gene expression from normal diet fed wt liver.


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 6 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 7 vs Ex Vivo Control Pool HPMCs Relicate 2


title: Beta_cells_2yo_rep1


title: Beta_cells_2yo_rep2


title: Pacific oyster B1_05_RE_6A7

source_name: Pacific oyster B1_05_RE_6A7


title: Pacific oyster B1_03_RE_30_22

source_name: Pacific oyster B1_03_RE_30_22


title: Pacific oyster B1_04_RE_18_2A

source_name: Pacific oyster B1_04_RE_18_2A


title: Beta_cells_1yo_rep2

source_name: pancreatic beta cells_1yo

value: 1 year


title: Beta_cells_1yo_rep4


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 6 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 5 vs Ex Vivo Control Pool HPMCs Relicate 2


title: UCN34 -60min c2 M3 - 159 D1_re-analyzed

city: Bad Oeynhausen

first: Imke

last: Grimm

address: Georgstraße 11

department: Institut für Laboratoriums- und Transfusionsmedizin

country: Germany

institute: Herz- und Diabeteszentrum NRW; Universitätsklinikum der Ruhr-Universität Bochum

description: after adhesion

hyb_protocol: The Hybridization was also carried out with the Quick Amp WT Labeling Kit, one-color (Agilent, Santa Clara, USA) according to the manufacturer’s recommendations. To achieve sufficient fluorescent signals, hybridization was extended to 38 h. The slides were washed and hybridization was stabilized with Stabilization & Drying solution (Agilent, Santa Clara, USA).

scan_protocol: After drying, the hybridized microarrays were scanned with the high resolution Agilent microarray scanner G2565CA with a resolution of 5 µm and analyzed with the Feature extraction software (Agilent, Santa Clara, USA).

data_processing: Raw data were quantile-normalized and gene expression data were generated by the Direct Array software (OakLabs, Hennigsdorf, Germany). All log2 values between -1 and 1 were ignored and only statistically significant values (p<0.05) have been taken.

organism: Streptococcus gallolyticus subsp. gallolyticus

source_name: S. gallolyticus UCN34; adhesion to THP-1 macrophages; -60min

label_protocol: The cDNA and cRNA synthesis including Cy3-labeling, and the microarray hybridization was carried out with the Quick Amp WT Labeling Kit, one-color (Agilent, Santa Clara, USA) according to the manufacturer’s recommendations but with following exceptions. Due to mixed RNA (prokaryotic and eukaryotic) more RNA (75 ng) was used for labeling and 900 ng labeled cRNA were used for hybridization.

growth_protocol: THP-1 cells were cultivated in RPMI 1640 medium (RPMI 1640; Thermo Scientific, Waltham, USA) supplemented with 10 % fetal calf serum (FCS, Pan Biotech; Aidenbach, Germany) and 1 ´ antibiotic/antimycotic solution (AB/AM, Pan Biotech) at 37 °C and 5 % CO2. S. gallolyticus subsp. gallolyticus strains (table 1) were grown overnight in brain heart infusion broth (BHI; Thermo Scientific, Waltham, USA) at 37 °C and 220 rpm. Overnight cultures were used by phagocytosis assays.

extract_protocol: Gene expression was analyzed from the two S. gallolyticus subsp. gallolyticus isolates BAA-2069 and UCN 34. RNA from these strains was isolated at three different time points. The first time point was directly after centrifugation (400 × g, 5 min) of the well plates (-60 min). The second RNA extraction was at the timepoint 0 h and the third at the timepoint 5 h. RNA was extracted with the peqGOLD Bacterial RNA Kit (VWR, Radnor, USA). Bacterial cells were resuspended in TE buffer and lysis buffer T and transferred in Lysing Matrix B tubes (MP Biomedicals, Santa Ana, USA). Bacterial cells were disrupted by using Vortex-Genie 2 (scientific industries, New York, USA) for 3 min at full speed. Further RNA extraction was done following the manufacturer’s instructions. RNA was eluted with 30 µl RNase-free water and quantified using the NanoDrop 2000.

treatment_protocol: This phagocytosis assay based on the assays of Boleji et al. and Kaneko et al. (13, 32). For Phagocytosis assay 1.5 ´ 106 THP-1 monocytes per well were disseminated in 12-well plates with 50 ng/ml PMA-supplemented medium to differentiate the monocytes into macrophages within three days. On the third day the medium was changed into PMA-free medium after washing the cells twice with Dulbecco’s phosphate-buffered saline (DPBS) (Thermo Scientific, Waltham, USA). An overnight culture of S. gallolyticus subsp. gallolyticus was serial diluted (103 dilution) in RPMI 1640 supplemented with 10 % FCS without AB/AM and the final bacterial titer of the inoculum was determined by plating assay. After washing macrophages with DPBS thrice, the S. gallolyticus subsp. gallolyticus dilution was added and plates were centrifuged 5 min with 400 ´ g to assure attachment of bacteria to macrophages (adhesion to macrophages; -60 min). Phagocytic uptake of bacteria was ensured for 30 min at 37 °C and 5 % CO2 and macrophages were washed thrice with DPBS. RPMI 1640 including 10 % FCS, 1 ´ AB/AM and 200 µg/ml gentamycin was added for 20 min to kill residual extracellular bacteria. Initially after the step (0 h) and after 5 h cells were prepared for RNA extraction.

value: UCN 34

tag: interaction status

value: adhesion to THP-1 macrophages (-60min)

tag: time point


title: UCN34 5h a2 M3 - 159 D3

description: long time after phagocytosis

source_name: S. gallolyticus UCN34; 5h after phagocytosis by THP-1 macrophages; -60min

value: after maturation of phagosomes (5h)


title: UCN34 5h a2 M1 - 159 B3

description: long time after phagocytosis


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 4 vs Ex Vivo Control Pool HPMCs Relicate 2

tag: tissue


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 5 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Beta_cells_1yo_rep1

tag: strain


title: Beta_cells_young_rep3

source_name: pancreatic beta cells_young

tag: age

value: 3.5-9 weeks


title: Beta_cells_1yo_rep3


title: Pacific oyster B1_02_RE_24A17

source_name: Pacific oyster B1_02_RE_24A17


title: Pacific oyster B1_01_RE_23_25

source_name: Pacific oyster B1_01_RE_23_25


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 4 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Beta_cells_young_rep2


title: UCN34 -60min c2 M1 - 159 B1_re-analyzed

description: after adhesion


title: UCN34 5h a2 M1 - 159 A3

description: long time after phagocytosis


title: Beta_cells_young_rep1


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 3 vs Ex Vivo Control Pool HPMCs Relicate 1


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 3 vs Ex Vivo Control Pool HPMCs Relicate 2


title: UCN34 0h a2 M3 - 159 D2

description: after phagocytosis

source_name: S. gallolyticus UCN34; initial after phagocytosis by THP-1 macrophages; 0h

value: initial after phagocytosis (0h)


title: UCN34 -60min c2 M3 - 159 D1

description: after adhesion


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 2 vs Ex Vivo Control Pool HPMCs Relicate 2


title: RGC replicate 2

city: Taipei

first: Aliaksandr

middle: A

last: Yarmishyn

address: No. 201, Section 2, Shipai Road, Beitou District

country: Taiwan

institute: Taipei Veterans General Hospital

description: RGC-B

hyb_protocol: According to standard Affymetrix protocol.

data_processing: The raw intensity data were background corrected, log2 transformed and quantile normalized using RMA algorithm implemented by Bioconductor affy package.

source_name: RGC cells

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

value: retinal ganglion cells (RGCs) differentiated from iPSCs


title: UCN34 -60min a1 M1 - 159 A1_re-analyzed

description: after adhesion


title: UCN34 -60min c2 M1 - 159 B1

description: after adhesion


title: UCN34 0h a2 M1 - 159 B2

description: after phagocytosis


title: colon tissue_case2

city: Nanjing

first: yankai

last: xia

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

description: The pooled  colon tissue of case

hyb_protocol: Hybridization was performed at 42℃ for 14h with NimbleGen Hybridization System.

scan_protocol: Arrays were washed in wash buffer I and II and III supplied by NimbleGen, and dried in NimbleGen Microarray Dryer. The arrays were scanned using MS200 scanner(NimbleGen) with 2µm resolution.

data_processing: NimbleScan software (NimbleGen) was used to extract fluorescent intensity raw data from the scanned images. The expression data of probes were normalized using quantile normalization and expression data of genes were generated using the Robust Multichip Average (RMA) algorithm.

source_name: human colon tissue, case

label_protocol: Labeling was performed according to CapitalBio standard protocol for NimbleGen system.

growth_protocol: A total of 30 colon samples from 15 Hirschsprung’s disease cases and 15 matched controls were randomly pooled, generating 3 pooled control and 3 pooled case colon samples.

extract_protocol: Total RNA was extracted with Trizol reagent, and then was purified with NucleoSpin® RNA clean-up (MACHEREY-NAGEL, Germany) according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

tag: group

value: case


title: colon tissue_case1

description: The pooled  colon tissue of case


title: RPE replicate 1

description: RPE-A

scan_protocol: According to standard Affymetrix protocol.

source_name: RPE cells

value: retinal pigment epithelium (RPE) cells differentiated from iPSCs


title: UCN34 0h a2 M1 - 159 A2

description: after phagocytosis


title: IRAS

city: São Paulo

first: Leonardo

middle: José Tadeu

last: Araújo

address: Av. Dr. Enéas de Carvalho Aguiar, 155, 2 andar, Bloco 6

country: Brazil

institute: HCFMUSP

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at ICESP-Brazil Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix Scanner 3000 7G®)

data_processing: Raw data were processed with the Expression Console® (Affymetrix) for background correction and normalization.

label: Biotin

source_name: Invasive Macroadenoma (Female)

label_protocol: The RNA was amplified into single-stranded-cDNA, fragmented, biotin-labeled and hybridized to a chip using the Gene Chip® WT Plus Reagent Kit according to the manufacturer’s instructions.

growth_protocol: Tissue specimens of ACTH-oma were obtained during transsphenoidal surgery and subsequently subjected to histological and immunohistochemical studies to confirm ACTH-oma

extract_protocol: Total RNA was extracted from these tissues using an AllPrep DNA/RNA kit®, according to the manufacturer’s instructions.

tag: diagnosis

value: Cushing's disease

value: female

value: corticotrophinoma


title: OV replicate 1

description: OV-A

source_name: optic vesicles

label_protocol: According to standard Affymetrix protocol.

value: optic vesicles (OVs) derived from iPSCs


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 1 vs Ex Vivo Control Pool HPMCs Relicate 1

source_name: Effluent-derived HPMC from Patients on Peritoneal Dialysis

value: Epithelioid

source_name: Pooled HPMCs derived from 4 omentum

value: Omentum


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 1 vs Ex Vivo Control Pool HPMCs Relicate 2

value: Peritoneal Membrane


title: Pacific oyster B1_14_RE_12A25

source_name: Pacific oyster B1_14_RE_12A25

value: mantle


title: colon tissue_case3

description: The pooled  colon tissue of case


title: Ex Vivo Control Pool HPMCs Sample 4 vs Ex Vivo Control Pool HPMCs Sample 2 Rep 2

description: Pool Control.4

source_name: Omentum-derived HPMC


title: DRT


title: OV replicate 2

description: OV-B


title: colon tissue_control2

description: The pooled  colon tissue of control

source_name: human colon tissue, control

value: control


title: colon tissue_control3

description: The pooled  colon tissue of control


title: iPSC replicate 2

description: NTA-B

source_name: iPSC cell line

value: induced pluripotent stem cells (iPSCs)


title: Ex Vivo HPMCs with Epithelioid phenotype Sample 2 vs Ex Vivo Control Pool HPMCs Relicate 1


title: RGC replicate 1

description: RGC-A


title: UCN34 -60min a1 M1 - 159 A1

description: after adhesion

source_name: S. gallolyticus UCN34; adhesion to THP-1 macrophages; -60min

value: UCN 34

value: adhesion to THP-1 macrophages (-60min)


title: iPSC replicate 1

description: NTA-A


title: ARV


title: Ex Vivo Control Pool HPMCs Sample 4 vs Ex Vivo Control Pool HPMCs Sample 2 Rep 1

description: Pool Control.3


title: NA12878 Genomic DNA Replicate 2 (HumanOmni2.5Exome)

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

scan_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 HumanOmni2.5Exome 8v1 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)

source_name: Blood, B Lymphocyte

value: Female

tag: ethnicity

value: Caucasian

tag: cell line


title: ASA

source_name: Macroadenoma (Female)


title: SCM

source_name: Microadenoma (Female)


title: BAA-2069 -60min b1 M2 - 26 A1_re-analyzed

description: after adhesion

source_name: S. gallolyticus BAA-2069; adhesion to THP-1 macrophages; -60min


title: NBF


title: BAA-2069 5h b2 M2 - 26 A3

description: after phagocytosis

source_name: S. gallolyticus BAA-2069; 5h after phagocytosis by THP-1 macrophages; -60min

value: after maturation of phagosomes (5h)


title: BAA-2069 5h b2 M2 - 26 C3

description: after phagocytosis


title: AAR


title: BAA-2069 5h b2 M2 - 26 B3

description: after phagocytosis


title: Ex Vivo Control Pool HPMCs Sample 3 vs Ex Vivo Control Pool HPMCs Sample 2

description: Pool Control.2


title: BAA-2069 -60min c1 26 B1_re-analyzed

description: after adhesion


title: BAA-2069 -60min M3 c1 26 C1

description: after adhesion


title: BAA-2069 -60min M3 c1 26 C1_re-analyzed

description: after adhesion


title: BAA-2069 0h b1 M2 - 26 C2

description: after phagocytosis

source_name: S. gallolyticus BAA-2069; initial after phagocytosis by THP-1 macrophages; 0h

value: initial after phagocytosis (0h)


title: BAA-2069 -60min c1 26 B1

description: after adhesion


title: OSF


title: EFSA


title: EPS


title: Pacific oyster B1_06_RE_20A25

source_name: Pacific oyster B1_06_RE_20A25


title: BAA-2069 0h b1 M2 - 26 B2

description: after phagocytosis


title: BAA-2069 0h b1 M2 - 26 A2

description: after phagocytosis


title: colon tissue_control1

description: The pooled  colon tissue of control


title: NA12878 Genomic DNA Replicate 1 (HumanOmni2.5Exome)

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


title: MMR


title: EFSB


title: BAA-2069 -60min b1 M2 - 26 A1

description: after adhesion


title: ND-75 RNAi rep2

status: Public on Mar 21 2017

city: London

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

country: United Kingdom

institute: King's College London

description: Gene expression data from CNS tissue with knock-down of ND-75 in neurons.

hyb_protocol: 7mg of labelled cDNA was hybridised to Affymetrix Drosophila genome v2 GeneChips

scan_protocol: Genechips were washed, stained (GeneChip® Fluidics Station 450) and scanned (GeneChip Scanner 3000 7G) according to manufacturer’s instructions (Nugen Technologies Inc & Affymetrix)

data_processing: Data was processed using a MAS5.0 algorithm and analysed using the Affymetrix Expression Console and the Affymetrix Transcriptome Analysis Console (Affymetrix Inc.) using gene level differential expression analysis. Means were calculated using Tukey's Bi-weight average algorithm and differential expression between groups was calculated using un-paired one way one way analysis of variance (ANOVA). A statistical cutoff of p<0.05 was used.

organism: Drosophila melanogaster

source_name: CNS tissue from nsybGal4/ND-75 RNAi larvae

label_protocol: 10ng of RNA per genotype was converted into labelled cDNA with the Nugen Ovation V2 protocol (NuGEN Technologies Inc.)

growth_protocol: Larvae were grown on standard fly food at 25 degrees.

extract_protocol: For the microarray analysis the complete CNS from 15 wandering third instar larvae were dissected in PBS and placed into PBS on ice and then transferred into 100ul of lysis buffer from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in triplicate and stored at -80oC.

treatment_protocol: One control and four experimental genotypes were used: Control (nsybGal4/+), Experimental group 1: ND-75 RNAi (nsybGal4>ND-75 RNAi; complex I, RNAi line #33910), Experimental group 2: UQCR-14 RNAi (nsybGal4>UQCR-14 RNAi; complex III, RNAi line #109542), Experimental group 3: COX5B RNAi (nsybGal4>COX5B RNAi; complex IV, RNAi line #105769), Experimental group 4:  ATPsynCf6 RNAi (nsybGal4>ATPsynCf6 RNAi; complex V, RNAi line #107826).

value: nsybGal4/ND-75 RNAi


title: COX5B RNAi rep1

description: Gene expression data from CNS tissue with knock-down of COX5B in neurons.

source_name: CNS tissue from nsybGal4/COX5B RNAi larvae


title: COX5B RNAi rep2


title: UQCR-14 rep1

description: Gene expression data from CNS tissue with knock-down of UQCR-14 in neurons.

source_name: CNS tissue from nsybGal4/UQCR-14 RNAi larvae

value: nsybGal4/UQCR-14 RNAi


title: COX5B RNAi rep3


title: ND-75 RNAi rep1


title: control CNS tissue rep2

description: Gene expression data from control CNS tissue

source_name: CNS tissue from nsybGal4/+ control larvae


title: control CNS tissue rep1


title: UQCR-14 rep2


title: UQCR-14 rep3


title: control CNS tissue rep3


title: ND-75 RNAi rep3


title: H3-FLAG ChIP in clr3∆ cells_series2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (ChIP_107_Sep09 or ChIP_1200_Jun14 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

organism: Schizosaccharomyces pombe

source_name: HU blocked cells_immunoprecipitated DNA

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Cells were grown in minimal media at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with anti-FLAG M2 agarose (Sigma, A2220). Immunoprecipitated DNA was recovered by incubation with protein A or G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Mid-log phase cells grown in minimal media supplemented with 8% glucose were treated with 15mM HU for 4h. Cells were switched to minimal media supplemented with 4% sucrose and 15mM HU for 2h for induction of H3-FLAG expression. Cells were fixed in 1% formaldehyde at 30˚C.

tag: genotype

source_name: HU blocked cells_whole-cell extract DNA

tag: genotpye


title: H3-FLAG ChIP in fft3∆ clr3∆ cells_series2

value: fft3_delta clr3_delta


title: RPE replicate 2

description: RPE-B

source_name: RPE cells

value: retinal pigment epithelium (RPE) cells differentiated from iPSCs


title: TCF3-ZNF384-010

city: Setagaya-ku

first: NOBUTAKA

last: KIYOKAWA

state: Tokyo

department: Pediatric Hematology & Oncology Research

institute: National Research Institute for Child Health & Development

description: Gene expression data from TCF3-ZNF384-positive BCP-ALL

hyb_protocol: Following fragmentation, 5 ug of cDNA were biotinylated and hybridized for 16 hr at 45C on GeneChip Human Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: TCF3-ZNF384-positive BCP-ALL

label_protocol: cDNA were prepared using Ovation Pico WTA System V2 (Nugen) according to the the manufacturer's instructions.

extract_protocol: QIAzole extraction of total RNA using miRNA mini kit (Qiagen) was performed according to the manufacturer's instructions.

value: B-cell precursor ALL (BCP-ALL)


title: H3-FLAG ChIP in wild-type cells_series1

value: wild-type


title: H3-FLAG ChIP in wild-type cells_series2


title: ATPsynCf6 RNAi rep2

description: Gene expression data from CNS tissue with knock-down of ATPsynCf6 in neurons.

source_name: CNS tissue from nsybGal4/ATPsynCf6 RNAi

value: nsybGal4/ATPsynCf6 RNAi


title: H3-FLAG ChIP in fft3∆ cells


title: ATPsynCf6 RNAi rep1


title: ATPsynCf6 RNAi rep3


title: H3-FLAG ChIP in wild-type cells


title: TCF3-ZNF384-009


title: H3-FLAG ChIP in fft3∆ cells_series1


title: TCF3-ZNF384-008


title: TCF3-ZNF384-005


title: TCF3-ZNF384-006


title: TCF3-ZNF384-007


title: TCF3-ZNF384-004


title: TCF3-ZNF384-001


title: TCF3-ZNF384-002


title: TCF3-ZNF384-003


title: TCF3-PBX1-018

description: Gene expression data from TCF3-PBX1-positive BCP-ALL

source_name: TCF3-PBX1-positive BCP-ALL


title: TCF3-PBX1-017


title: TCF3-PBX1-016


title: TCF3-PBX1-015


title: TCF3-PBX1-019


title: TCF3-PBX1-014


title: Ex Vivo Control Pool HPMCs Sample 1 vs Ex Vivo Control Pool HPMCs Sample 2

description: Pool Control.1

source_name: Omentum-derived HPMC

value: Omentum


title: TCF3-PBX1-009


title: TCF3-PBX1-012


title: TCF3-PBX1-010


title: TCF3-PBX1-004


title: TCF3-PBX1-002


title: TCF3-PBX1-013


title: TCF3-PBX1-008


title: TCF3-PBX1-005


title: TCF3-PBX1-011


title: TCF3-PBX1-006


title: TCF3-PBX1-007


title: TCF3-PBX1-001


title: Normal-BCP-003

description: Gene expression data from Non-leukemic BCP

source_name: Non-leukemic B-cell precursor

value: Non-leukemic BCP

value: Normal


title: Normal-BCP-001


title: Normal-BCP-002


title: MLL-AF4-012

description: Gene expression data from MLL-AF4-positive BCP-ALL

source_name: MLL-AF4-positive BCP-ALL


title: TCF3-PBX1-003


title: MLL-AF4-011


title: MLL-AF4-001


title: MLL-AF4-002


title: MLL-AF4-010


title: MLL-AF4-009


title: MLL-AF4-003


title: MLL-AF4-007


title: MLL-AF4-013


title: Hyperdiploid-088

description: Gene expression data from High Hyperdiploid BCP-ALL

source_name: High Hyperdiploid BCP-ALL

value: Hyperdiploid


title: MLL-AF4-008


title: MLL-AF4-004


title: MLL-AF4-005


title: Hyperdiploid-080


title: Hyperdiploid-083


title: Hyperdiploid-085


title: Hyperdiploid-084


title: Hyperdiploid-075


title: Hyperdiploid-086


title: Hyperdiploid-079


title: Hyperdiploid-073


title: Hyperdiploid-077


title: Hyperdiploid-082


title: Hyperdiploid-087


title: Hyperdiploid-076


title: Hyperdiploid-074


title: Hyperdiploid-078


title: Hyperdiploid-089


title: MLL-AF4-006


title: Hyperdiploid-072


title: Hyperdiploid-070


title: Hyperdiploid-071


title: Hyperdiploid-069


title: Hyperdiploid-066


title: Hyperdiploid-067


title: Liver_Liverl _CL diet_Vitamin E_rep3

first: Masuko

last: Kobori

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from the liver after 12 week feeding of CL diet containing 0.02% vitamin E

hyb_protocol: Fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: liver, fed CL diet containing 0.02% vitamin E for 12 weeks

label_protocol: The fragmented biotin-labeled aRNA was synthesized from the total RNA of each mouse using the GeneChip® 3′ IVT Express Kit (Affymetrix Japan KK, Tokyo, Japan).

growth_protocol: Mice were maintained on a 12/12-h light/dark cycle and were given free access to food and water.

extract_protocol: The liver tissues were collected after 2-h fasting and snap-frozen in liquid nitrogen.  Total RNA was isolated from frozen liver samples using a GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich Japan, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: 7-week-old C57BL/6J male mice were fed NC (CRF-1) or CL diet (60% calories from fat, 1.25% cholesterol, and 0.5% sodium cholate), CL diet containing 0.02% astaxanthin, or CL diet containing 0.02% vitamin E for 12 weeks.

value: male

value: liver

value: CL diet containing Vitamin E


title: Liver_Liverl _CL diet_Vitamin E_rep1


title: Hyperdiploid-068


title: Hyperdiploid-064


title: Liver_Liverl _CL diet_Vitamin E_rep2


title: Hyperdiploid-062


title: Liver_Liverl _CL diet_Astaxanthin_rep5

description: Gene expression data from the liver after 12 week feeding of CL diet containing 0.02% astaxanthin

source_name: liver, fed CL diet containing 0.02% astaxanthin for 12 weeks

value: CL diet containing Astaxanthin


title: Liver_Liverl _CL diet_Vitamin E_rep5


title: Hyperdiploid-061


title: Liver_Liverl _CL diet_Astaxanthin_rep1


title: Liver_Liverl _CL diet_Astaxanthin_rep3


title: Liver_Liverl _CL diet_Astaxanthin_rep4


title: Hyperdiploid-058


title: Liver_Liverl _CL diet_Astaxanthin_rep2


title: Hyperdiploid-059


title: Hyperdiploid-056


title: Hyperdiploid-057


title: Liver_Liverl _CL diet_rep5

description: Gene expression data from the liver after 12 week feeding of CL diet

source_name: liver, fed CL diet for 12 weeks

value: CL diet


title: Liver_Liverl _CL diet_rep4


title: Liver_Liverl _CL diet_Vitamin E_rep4


title: Liver_Liverl _CL diet_rep3


title: Hyperdiploid-060


title: Hyperdiploid-055


title: Hyperdiploid-054


title: Hyperdiploid-053


title: Liver_Liverl _CL diet_rep1


title: Liver_normal chow_rep4

description: Gene expression data from the liver after 12 week feeding of normal CRF-1 chow

source_name: liver, fed normal CRF-1 chow for 12 weeks

value: normal chow


title: Hyperdiploid-048


title: Liver_normal chow_rep3


title: Liver_normal chow_rep1


title: Liver_normal chow_rep2


title: Hyperdiploid-043


title: 96h_WLSSD2_4

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description: Gene expression after 96h exposure at the WLSSD-2 site

scan_protocol: Arrays were scanned with scanned with a high-resolution microarray scanner (Agilent, Santa Clara, CA, USA)

data_processing: Raw microarray data were imported into Genespring GX 12.6 (Agilent, Palo Alto, CA, USA), log2 transformed and quantile normalized. Normalized data were then used to identify differentially expressed genes (DEG) using a one-way ANOVA followed by pair-wise Tukey test (p<0.05). The normalized data were not available at the time of submission and therefore not included in these records.

organism: Pimephales promelas

source_name: ovary

label_protocol: One μg total RNA was used for all hybridizations. cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s protocols (Quick Amp Labeling kit and One-color microarray hybridization protocol) and scanned with a high-resolution microarray scanner (Agilent, Santa Clara, CA, USA).

growth_protocol: All fish used in the study were reproductively mature adult fathead minnows (5-6 months old) obtained from the US EPA Mid-Continent Ecology Division (Duluth, MN). All procedures involving animals were reviewed and approved by the Animal Care and Use Committee in accordance with Animal Welfare Act and Interagency Research Animal Committee guidelines.

extract_protocol: Ovary samples from four to six biological replicates per deployment site and time were used for RNA extraction. Total RNA was isolated using RNeasy kits following manufacturer’s protocol (Qiagen, Valencia, CA, USA) and was DNAse treated.  RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Total RNA quantity was determined using a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). RNA was stored at -80oC until analyzed.

treatment_protocol: Briefly, three buoys anchored to the bottom sediment at each site. Three cages of fish, each containing 6 male and 6 female adult fathead minnows (5-6 month old) were attached to a buoy and its anchor, suspending cages at a depth of 1-2 m. After 2, 4, or 8 d of exposure, fish from two cages, each from a separate buoy, were transferred into separate buckets containing surface water collected at the appropriate site, and transported to the laboratory (transit time <60 min) for sampling. Animals were not fed during transit nor in the field. Fish were individually anesthetized and euthanized with MS-222 (Argent, Redmond, WA, USA), weighed, and evaluated for any external lesions. Blood and tissues (liver, gonad) were collected and stored at -80°C until extracted and analyzed.

tag: Sex

value: female

value: ovary

value: 5-6 months


title: 96h_WLSSD2_5

hyb_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s protocols (Quick Amp Labeling kit and One-color microarray hybridization protocol)


title: 96h_WLSSD2_6


title: Hyperdiploid-047


title: 96h_WLSSD2_2


title: 96h_WLSSD2_1


title: Hyperdiploid-051


title: Hyperdiploid-052


title: Hyperdiploid-046


title: Hyperdiploid-045


title: 96h_WLSSD2_3


title: Liver_Liverl _CL diet_rep2


title: Hyperdiploid-049


title: Hyperdiploid-041


title: Hyperdiploid-050


title: Liver_normal chow_rep5


title: Hyperdiploid-081


title: Hyperdiploid-044


title: Hyperdiploid-042


title: 96h_WLSSD1_5

description: Gene expression after 96h exposure at the WLSSD site


title: 96h_WLSSD1_4


title: 96h_WLSSD1_2


title: 96h_WLSSD1_6


title: 96h_WLSSD1_3


title: 96h_SMTP_3

description: Gene expression after 96h exposure at the SMTP site


title: Hyperdiploid-040


title: Hyperdiploid-034


title: 96h_SMTP_2


title: 96h_WLSSD1_1


title: 96h_SMTP_6


title: 96h_FDL_6

description: Gene expression after 96h exposure at the FDL reference site


title: 96h_SMTP_4


title: 96h_SMTP_5


title: 96h_SMTP_1


title: 96h_FDL_5


title: Hyperdiploid-038


title: Hyperdiploid-037


title: Hyperdiploid-035


title: Hyperdiploid-033


title: Hyperdiploid-036


title: Hyperdiploid-039


title: Hyperdiploid-029


title: Hyperdiploid-031


title: Hyperdiploid-065


title: Hyperdiploid-032


title: Hyperdiploid-028


title: Hyperdiploid-090


title: Hyperdiploid-030


title: 96h_FDL_3


title: 96h_FDL_4


title: 48h_WLSSD2_5

description: Gene expression after 48h exposure at the WLSSD-2 site


title: 48h_WLSSD2_6


title: 48h_WLSSD2_3


title: 48h_WLSSD2_2


title: 48h_WLSSD2_4


title: Hyperdiploid-026


title: 48h_WLSSD1_4

description: Gene expression after 48h exposure at the WLSSD site


title: 48h_WLSSD1_6


title: Hyperdiploid-024


title: Hyperdiploid-025


title: 48h_WLSSD1_5


title: Hyperdiploid-022


title: Hyperdiploid-021


title: Hyperdiploid-020


title: 96h_FDL_1


title: Hyperdiploid-019


title: Hyperdiploid-027


title: 48h_WLSSD2_1


title: 48h_WLSSD1_3


title: 96h_FDL_2


title: Hyperdiploid-017


title: Hyperdiploid-023


title: Hyperdiploid-015


title: Hyperdiploid-013


title: Hyperdiploid-016


title: Hyperdiploid-014


title: Hyperdiploid-063


title: Hyperdiploid-018


title: 48h_SMTP_5

description: Gene expression after 48h exposure at the SMTP site


title: 48h_SMTP_4


title: 48h_SMTP_6


title: 48h_SMTP_3


title: 48h_WLSSD1_1


title: Hyperdiploid-012


title: 48h_FDL_6

description: Gene expression after 48h exposure at the FDL reference site


title: 48h_FDL_5


title: 48h_SMTP_2


title: 48h_WLSSD1_2


title: 48h_SMTP_1


title: Hyperdiploid-010


title: Hyperdiploid-009


title: Hyperdiploid-007


title: 48h_FDL_3


title: 48h_FDL_4


title: Hyperdiploid-003


title: Hyperdiploid-004


title: Hyperdiploid-008


title: 48h_FDL_2


title: Hyperdiploid-006


title: Hyperdiploid-005


title: Hyperdiploid-011


title: 8d_WLSSD2_4

description: Gene expression after 8 day exposure at the WLSSD-2 site


title: Hyperdiploid-002


title: 8d_WLSSD2_3


title: ETV6-RUNX1-070

description: Gene expression data from ETV6-RUNX1-positive BCP-ALL

source_name: ETV6-RUNX1-positive BCP-ALL


title: Hyperdiploid-001


title: 8d_WLSSD2_2


title: 8d_WLSSD2_1


title: 8d_WLSSD1_5

description: Gene expression after 8 day exposure at the WLSSD site


title: 48h_FDL_1


title: 8d_WLSSD1_4


title: 8d_WLSSD2_5


title: ETV6-RUNX1-069


title: 8d_WLSSD1_3


title: ETV6-RUNX1-067


title: 8d_WLSSD1_1


title: 8d_SMTP_6

description: Gene expression after 8 day exposure at the SMTP site


title: 8d_WLSSD1_2


title: ETV6-RUNX1-066


title: ETV6-RUNX1-068


title: ETV6-RUNX1-064


title: ETV6-RUNX1-063


title: ETV6-RUNX1-061


title: ETV6-RUNX1-065


title: 8d_SMTP_4


title: ETV6-RUNX1-058


title: ETV6-RUNX1-057


title: 8d_SMTP_5


title: ETV6-RUNX1-060


title: ETV6-RUNX1-059


title: ETV6-RUNX1-062


title: 8d_SMTP_2


title: 8d_SMTP_3


title: 8d_FDL_6

description: Gene expression after 8 day exposure at the FDL reference site


title: 8d_FDL_4


title: 8d_SMTP_1


title: 8d_FDL_3


title: 8d_FDL_2


title: 8d_FDL_5


title: ETV6-RUNX1-050


title: ETV6-RUNX1-052


title: ETV6-RUNX1-056


title: ETV6-RUNX1-055


title: ETV6-RUNX1-048


title: ETV6-RUNX1-054


title: 8d_FDL_1


title: ETV6-RUNX1-049


title: ETV6-RUNX1-045


title: ETV6-RUNX1-041


title: ETV6-RUNX1-043


title: ETV6-RUNX1-053


title: ETV6-RUNX1-039


title: ETV6-RUNX1-044


title: ETV6-RUNX1-046


title: ETV6-RUNX1-042


title: ETV6-RUNX1-047


title: ETV6-RUNX1-038


title: ETV6-RUNX1-035


title: ETV6-RUNX1-037


title: ETV6-RUNX1-040


title: ETV6-RUNX1-036


title: ETV6-RUNX1-028


title: ETV6-RUNX1-032


title: ETV6-RUNX1-030


title: ETV6-RUNX1-031


title: ETV6-RUNX1-034


title: ETV6-RUNX1-020


title: ETV6-RUNX1-023


title: ETV6-RUNX1-027


title: ETV6-RUNX1-022


title: ETV6-RUNX1-011


title: ETV6-RUNX1-025


title: ETV6-RUNX1-013


title: ETV6-RUNX1-033


title: ETV6-RUNX1-016


title: ETV6-RUNX1-026


title: ETV6-RUNX1-017


title: ETV6-RUNX1-015


title: ETV6-RUNX1-024


title: ETV6-RUNX1-018


title: ETV6-RUNX1-014


title: ETV6-RUNX1-012


title: ETV6-RUNX1-010


title: ETV6-RUNX1-019


title: ETV6-RUNX1-007


title: ETV6-RUNX1-008


title: ETV6-RUNX1-029


title: ETV6-RUNX1-004


title: ETV6-RUNX1-021


title: ETV6-RUNX1-005


title: EP300-ZNF384-003

description: Gene expression data from EP300-ZNF384-positive BCP-ALL

source_name: EP300-ZNF384-positive BCP-ALL


title: EP300-ZNF384-002


title: BCR-ABL1-015

description: Gene expression data from BCR-ABL1-positive BCP-ALL

source_name: BCR-ABL1-positive BCP-ALL


title: ETV6-RUNX1-002


title: BCR-ABL1-009


title: CREBBP-ZNF384-002

description: Gene expression data from CREBBP-ZNF384-positive BCP-ALL

source_name: CREBBP-ZNF384-positive BCP-ALL


title: EP300-ZNF384-001


title: BCR-ABL1-012


title: BCR-ABL1-010


title: ETV6-RUNX1-009


title: EP300-ZNF384-004


title: BCR-ABL1-014


title: CREBBP-ZNF384-001


title: BCR-ABL1-017


title: BCR-ABL1-013


title: BCR-ABL1-011


title: BCR-ABL1-006


title: BCR-ABL1-004


title: ETV6-RUNX1-051


title: BCR-ABL1-005


title: BCR-ABL1-008


title: BCR-ABL1-003


title: BCR-ABL1-002


title: BCR-ABL1-001


title: BCR-ABL1-016


title: NA12878 Genomic DNA Replicate 2 (IlluminaHumanOmni2.5)

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

institute: The University of the West Indies

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 HumanOmni2.5-8v1-1 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)

source_name: Blood, B Lymphocyte

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

value: Female

value: Caucasian


title: Porcupine epi-KO #4

city: Montreal

first: Daniel

last: Dufort

state: Quebec

address: 1001 Bould. Decaire Room EM0.3211

department: OBGYN

institute: McGill University

description: RMA expression value derived from Expression Console software; gene-level analysis

hyb_protocol: The Ambion® Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix® GeneChip  WT Terminal Labeling and Controls Reagent kit, is recommended for preparing samples for use with the  Gene 1.0 ST Array and the Gene 2.0 ST Array.

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

data_processing: Raw data were processed with expression console (Affymetrix)and was later analyzed in the Transcriptome analysis console (affymetrics)

source_name: Porcupine epithelium mutant

label_protocol: The Ambion® Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix® GeneChip  WT Terminal Labeling and Controls Reagent kit for preparing samples for use with the  Gene 2.0 ST Array.

growth_protocol: RNA samples were collected from whole uteri after homozogization of 1 uterine horn, trizol extraction and running them through an RNA column

extract_protocol: Qiagen Rneasy kit was used to extract the RNA according to the manufactor's protocol

value: uterus


title: Porcupine epi-KO #2


title: C57BL/6Je/e + NDP-MSH_rep1

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

description: total brain C57BL/6Je/e-6943/3

hyb_protocol: End labeled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol (GeneChip Whole Transcript (WT) Sense Labeling Assay User Manual, Affymetrix, Inc.)

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing:
Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by GeneSpring´s ExonRMA16 algorithm after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

source_name: C57BL/6Je/e + NDP-MSH

label_protocol: Synthesis of biotin labeled cDNA was performed according to the manufacturer´s protocol (WT Plus Reagent Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA. After amplification by in vitro transcription and 2nd cycle synthesis, cDNA was fragmented and biotin labeled by terminal transferase

growth_protocol: Mouse brain, day 14 after MOG-immunization (disease maximum).

extract_protocol: Mice were phenotypically identified as wild-type or mutant (coat color black in wild-type or yellow in C57BL/6Je/e), brain tissue was isolated and snap-frozen in liquid nitrogen, RNA was extracted using the innuPrep RNA kit according to the manufacturer's instructions (Analytik Jena), cDNA was synthesized from 1 μg of total RNA using random hexanucleotide primers and the RevertAid First strand cDNA Synthesis Kit (Thermo Scientific).

treatment_protocol: Intravenous injection of NDP-MSH (5 µg/mouse) at day 8, 10 and 12 after MOG-immunization.

tag: day after immunization

value: d14 (disease maximum)

value: brain

tag: treatment

value: NDP-MSH


title: Floxed Control Female #4

source_name: Floxed control female


title: Porcupine epi-KO #1


title: C57BL/6Je/e + PBS_rep2

description: total brain C57BL/6Je/e-6641/2

source_name: C57BL/6Je/e + PBS

value: PBS


title: BrdU IP in cdc25-22 synchronized fft3∆ cells 120min_series2

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP_1105_Oct12 or ChIP_1200_Jun14 ). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

source_name: cdc25 synchronized cells_BrdU immunoprecipitated DNA

label_protocol: Immunoprecipitated and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (IP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Cdc25-22 cells carrying thymidine kinase expression module Pnmt1-TK and nucleoside transport module Padh1-hENT were grown in minimal media at 26˚C and arrested at the G2/M block by raising temperature to 37˚C for 4h and 15 min.  Cells were released from block by reducing temperature to 26˚C, and cultures were supplemented at this time by 10mM hydroxyurea and 200μΜ 5-bromo-2'-deoxyuridine.

extract_protocol: The DNA was phenol-extracted from fixed cells by bead-beating with glass beads, sheared by sonication to 500-1000bp fragments and immunoprecipitated with anti-BrdU antibody (BD Pharmigen, 555627) immobilized to Dynal anti-mouse magnetic beads (Invitrogen).

treatment_protocol: Cells were collected at time intervals corresponding to maximum septation index and fixed with 0.1% sodium azide.

value: cdc25-22 fft3_delta

source_name: cdc25 synchronized cells_whole-cell extract DNA


title: BCR-ABL1-007

value: B-cell precursor ALL (BCP-ALL)


title: BrdU IP in cdc25-22 synchronized wt cells 120min_series1


title: BrdU IP in cdc25-22 synchronized fft3∆ cells 120min_series1


title: BrdU IP in cdc25-22 synchronized wt cells 120min_series2


title: Floxed Control Female #3


title: Floxed Control Female #2


title: BrdU IP in cdc25-22 synchronized wt cells 50min (HU)

data_processing: Data were extracted using Agilent Feature Extraction Software (ChIP_1200_Jun14 ). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

growth_protocol: Cdc25-22 cells carrying thymidine kinase expression module Pnmt1-TK and nucleoside transport module Padh1-hENT were grown in minimal media at 26˚C and arrested at the G2/M block by raising temperature to 37˚C for 4h and 15 min.  Cells were released from block by reducing temperature to 25˚C in water incubator with rotation of 140 rpm, and cultures were supplemented at this time by 200μΜ 5-bromo-2'-deoxyuridine.

extract_protocol: The DNA was phenol-extracted from fixed cells by bead-beating with glass beads, sheared by sonication to 500-1000bp fragments and immunoprecipitated with anti-BrdU antibody (BD Pharmingen, 555627) immobilized to Dynal anti-mouse magnetic beads (Invitrogen).

value: cdc25-22 cells


title: H3K9me2 ChIP in fft3∆ cells_series3

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP_1105_Oct12 or ChIP_1200_Jun14 protocol). Signal was normalized by combined rank consistency filtering with LOWESS intensity normalization.

source_name: fft3_delta_immunoprecipitated DNA

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. For Fft3-GFP ChIP, cells were incubated at 18˚C for 6h prior to fixation with 3% paraformaldehyde followed by  treatment with 10mM dimethyl adipimidate

tag: antibody

source_name: fft3_delta_whole-cell extract


title: Fft3-GFP ChIP in WT cells

source_name: WT_immunoprecipitated DNA

value: WT

value: GFP

source_name: WT_whole-cell extract


title: H3K9me2 ChIP in WT cells_series3


title: H3K9me2 ChIP in fft3∆ cells_series2

source_name: fft_3delta_whole-cell extract


title: BrdU IP in  cdc25-22synchronized fft3∆ cells 50min (HU)


title: H3K9me2 ChIP in WT cells_series2


title: wild-type + NDP-MSH_rep1

description: total brain wt-6234/1

source_name: wild-type + NDP-MSH

value: wild-type


title: wild-type + NDP-MSH_rep2

description: total brain wt-6234/5


title: wild-type + PBS_rep2

description: total brain wt-6233/2

source_name: wild-type + PBS


title: ETV6-RUNX1-003

source_name: ETV6-RUNX1-positive BCP-ALL


title: NA12878 Genomic DNA Replicate 1 (IlluminaHumanOmni2.5)

tag: gender


title: H3K9me2 ChIP in UV21  cells _series1

source_name: UV21_immunoprecipitated DNA

source_name: UV21_whole-cell extract


title: wild-type + PBS_rep1

description: total brain wt-6233/1


title: H3K9me2 ChIP in WT cells_series1